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authorPicca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>2017-08-18 14:48:52 +0200
committerPicca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>2017-08-18 14:48:52 +0200
commitf7bdc2acff3c13a6d632c28c4569690ab106eed7 (patch)
tree9d67cdb7152ee4e711379e03fe0546c7c3b97303 /silx
Import Upstream version 0.5.0+dfsg
Diffstat (limited to 'silx')
-rw-r--r--silx/__init__.py43
-rw-r--r--silx/__main__.py66
-rw-r--r--silx/app/__init__.py29
-rw-r--r--silx/app/setup.py40
-rw-r--r--silx/app/test/__init__.py41
-rw-r--r--silx/app/test/test_view.py135
-rw-r--r--silx/app/view.py326
-rw-r--r--silx/gui/__init__.py29
-rw-r--r--silx/gui/_glutils/Context.py63
-rw-r--r--silx/gui/_glutils/FramebufferTexture.py164
-rw-r--r--silx/gui/_glutils/Program.py202
-rw-r--r--silx/gui/_glutils/Texture.py308
-rw-r--r--silx/gui/_glutils/VertexBuffer.py266
-rw-r--r--silx/gui/_glutils/__init__.py41
-rw-r--r--silx/gui/_glutils/font.py152
-rw-r--r--silx/gui/_glutils/gl.py165
-rw-r--r--silx/gui/_glutils/utils.py70
-rw-r--r--silx/gui/_utils.py102
-rw-r--r--silx/gui/console.py214
-rw-r--r--silx/gui/data/ArrayTableModel.py610
-rw-r--r--silx/gui/data/ArrayTableWidget.py490
-rw-r--r--silx/gui/data/DataViewer.py464
-rw-r--r--silx/gui/data/DataViewerFrame.py186
-rw-r--r--silx/gui/data/DataViewerSelector.py153
-rw-r--r--silx/gui/data/DataViews.py988
-rw-r--r--silx/gui/data/Hdf5TableView.py414
-rw-r--r--silx/gui/data/NXdataWidgets.py523
-rw-r--r--silx/gui/data/NumpyAxesSelector.py468
-rw-r--r--silx/gui/data/RecordTableView.py405
-rw-r--r--silx/gui/data/TextFormatter.py222
-rw-r--r--silx/gui/data/__init__.py35
-rw-r--r--silx/gui/data/setup.py41
-rw-r--r--silx/gui/data/test/__init__.py45
-rw-r--r--silx/gui/data/test/test_arraywidget.py320
-rw-r--r--silx/gui/data/test/test_dataviewer.py281
-rw-r--r--silx/gui/data/test/test_numpyaxesselector.py152
-rw-r--r--silx/gui/data/test/test_textformatter.py94
-rw-r--r--silx/gui/fit/BackgroundWidget.py530
-rw-r--r--silx/gui/fit/FitConfig.py540
-rw-r--r--silx/gui/fit/FitWidget.py727
-rw-r--r--silx/gui/fit/FitWidgets.py559
-rw-r--r--silx/gui/fit/Parameters.py882
-rw-r--r--silx/gui/fit/__init__.py28
-rw-r--r--silx/gui/fit/setup.py43
-rw-r--r--silx/gui/fit/test/__init__.py43
-rw-r--r--silx/gui/fit/test/testBackgroundWidget.py83
-rw-r--r--silx/gui/fit/test/testFitConfig.py95
-rw-r--r--silx/gui/fit/test/testFitWidget.py135
-rw-r--r--silx/gui/hdf5/Hdf5HeaderView.py192
-rw-r--r--silx/gui/hdf5/Hdf5Item.py421
-rw-r--r--silx/gui/hdf5/Hdf5LoadingItem.py68
-rw-r--r--silx/gui/hdf5/Hdf5Node.py210
-rw-r--r--silx/gui/hdf5/Hdf5TreeModel.py581
-rw-r--r--silx/gui/hdf5/Hdf5TreeView.py204
-rw-r--r--silx/gui/hdf5/NexusSortFilterProxyModel.py152
-rw-r--r--silx/gui/hdf5/__init__.py44
-rw-r--r--silx/gui/hdf5/_utils.py247
-rw-r--r--silx/gui/hdf5/setup.py41
-rw-r--r--silx/gui/hdf5/test/__init__.py39
-rw-r--r--silx/gui/hdf5/test/_mock.py130
-rw-r--r--silx/gui/hdf5/test/test_hdf5.py480
-rw-r--r--silx/gui/icons.py360
-rw-r--r--silx/gui/plot/AlphaSlider.py300
-rw-r--r--silx/gui/plot/ColorBar.py790
-rw-r--r--silx/gui/plot/ColormapDialog.py506
-rw-r--r--silx/gui/plot/Colors.py359
-rw-r--r--silx/gui/plot/CurvesROIWidget.py975
-rw-r--r--silx/gui/plot/ImageView.py860
-rw-r--r--silx/gui/plot/Interaction.py300
-rw-r--r--silx/gui/plot/LegendSelector.py1087
-rw-r--r--silx/gui/plot/MPLColormap.py1062
-rw-r--r--silx/gui/plot/MaskToolsWidget.py615
-rw-r--r--silx/gui/plot/Plot.py2925
-rw-r--r--silx/gui/plot/PlotActions.py1386
-rw-r--r--silx/gui/plot/PlotEvents.py166
-rw-r--r--silx/gui/plot/PlotInteraction.py1493
-rw-r--r--silx/gui/plot/PlotToolButtons.py280
-rw-r--r--silx/gui/plot/PlotTools.py313
-rw-r--r--silx/gui/plot/PlotWidget.py267
-rw-r--r--silx/gui/plot/PlotWindow.py766
-rw-r--r--silx/gui/plot/Profile.py741
-rw-r--r--silx/gui/plot/ProfileMainWindow.py99
-rw-r--r--silx/gui/plot/ScatterMaskToolsWidget.py529
-rw-r--r--silx/gui/plot/StackView.py1033
-rw-r--r--silx/gui/plot/_BaseMaskToolsWidget.py1138
-rw-r--r--silx/gui/plot/__init__.py71
-rw-r--r--silx/gui/plot/_utils/__init__.py104
-rw-r--r--silx/gui/plot/_utils/panzoom.py156
-rw-r--r--silx/gui/plot/_utils/setup.py42
-rw-r--r--silx/gui/plot/_utils/test/__init__.py41
-rw-r--r--silx/gui/plot/_utils/test/test_ticklayout.py78
-rw-r--r--silx/gui/plot/_utils/ticklayout.py224
-rw-r--r--silx/gui/plot/backends/BackendBase.py474
-rw-r--r--silx/gui/plot/backends/BackendMatplotlib.py821
-rw-r--r--silx/gui/plot/backends/BackendOpenGL.py1631
-rw-r--r--silx/gui/plot/backends/ModestImage.py174
-rw-r--r--silx/gui/plot/backends/__init__.py29
-rw-r--r--silx/gui/plot/backends/_matplotlib.py64
-rw-r--r--silx/gui/plot/backends/glutils/GLPlotCurve.py1317
-rw-r--r--silx/gui/plot/backends/glutils/GLPlotFrame.py1039
-rw-r--r--silx/gui/plot/backends/glutils/GLPlotImage.py707
-rw-r--r--silx/gui/plot/backends/glutils/GLSupport.py192
-rw-r--r--silx/gui/plot/backends/glutils/GLText.py222
-rw-r--r--silx/gui/plot/backends/glutils/GLTexture.py239
-rw-r--r--silx/gui/plot/backends/glutils/PlotImageFile.py149
-rw-r--r--silx/gui/plot/backends/glutils/__init__.py44
-rw-r--r--silx/gui/plot/items/__init__.py43
-rw-r--r--silx/gui/plot/items/core.py839
-rw-r--r--silx/gui/plot/items/curve.py192
-rw-r--r--silx/gui/plot/items/histogram.py288
-rw-r--r--silx/gui/plot/items/image.py385
-rw-r--r--silx/gui/plot/items/marker.py241
-rw-r--r--silx/gui/plot/items/scatter.py169
-rw-r--r--silx/gui/plot/items/shape.py121
-rw-r--r--silx/gui/plot/setup.py47
-rw-r--r--silx/gui/plot/test/__init__.py71
-rw-r--r--silx/gui/plot/test/testAlphaSlider.py221
-rw-r--r--silx/gui/plot/test/testColorBar.py240
-rw-r--r--silx/gui/plot/test/testColormapDialog.py68
-rw-r--r--silx/gui/plot/test/testColors.py94
-rw-r--r--silx/gui/plot/test/testCurvesROIWidget.py153
-rw-r--r--silx/gui/plot/test/testInteraction.py89
-rw-r--r--silx/gui/plot/test/testLegendSelector.py143
-rw-r--r--silx/gui/plot/test/testMaskToolsWidget.py295
-rw-r--r--silx/gui/plot/test/testPlot.py633
-rw-r--r--silx/gui/plot/test/testPlotInteraction.py167
-rw-r--r--silx/gui/plot/test/testPlotTools.py203
-rw-r--r--silx/gui/plot/test/testPlotWidget.py967
-rw-r--r--silx/gui/plot/test/testPlotWindow.py138
-rw-r--r--silx/gui/plot/test/testProfile.py183
-rw-r--r--silx/gui/plot/test/testScatterMaskToolsWidget.py313
-rw-r--r--silx/gui/plot/test/testStackView.py209
-rw-r--r--silx/gui/plot3d/Plot3DActions.py362
-rw-r--r--silx/gui/plot3d/Plot3DToolBar.py119
-rw-r--r--silx/gui/plot3d/Plot3DWidget.py341
-rw-r--r--silx/gui/plot3d/Plot3DWindow.py94
-rw-r--r--silx/gui/plot3d/SFViewParamTree.py1467
-rw-r--r--silx/gui/plot3d/ScalarFieldView.py1385
-rw-r--r--silx/gui/plot3d/ViewpointToolBar.py114
-rw-r--r--silx/gui/plot3d/__init__.py45
-rw-r--r--silx/gui/plot3d/scene/__init__.py34
-rw-r--r--silx/gui/plot3d/scene/axes.py224
-rw-r--r--silx/gui/plot3d/scene/camera.py350
-rw-r--r--silx/gui/plot3d/scene/core.py334
-rw-r--r--silx/gui/plot3d/scene/cutplane.py374
-rw-r--r--silx/gui/plot3d/scene/event.py225
-rw-r--r--silx/gui/plot3d/scene/function.py471
-rw-r--r--silx/gui/plot3d/scene/interaction.py652
-rw-r--r--silx/gui/plot3d/scene/primitives.py1764
-rw-r--r--silx/gui/plot3d/scene/setup.py41
-rw-r--r--silx/gui/plot3d/scene/test/__init__.py43
-rw-r--r--silx/gui/plot3d/scene/test/test_transform.py91
-rw-r--r--silx/gui/plot3d/scene/test/test_utils.py275
-rw-r--r--silx/gui/plot3d/scene/text.py534
-rw-r--r--silx/gui/plot3d/scene/transform.py968
-rw-r--r--silx/gui/plot3d/scene/utils.py516
-rw-r--r--silx/gui/plot3d/scene/viewport.py492
-rw-r--r--silx/gui/plot3d/scene/window.py420
-rw-r--r--silx/gui/plot3d/setup.py44
-rw-r--r--silx/gui/plot3d/test/__init__.py62
-rw-r--r--silx/gui/plot3d/utils/__init__.py28
-rw-r--r--silx/gui/plot3d/utils/mng.py121
-rw-r--r--silx/gui/qt/__init__.py61
-rw-r--r--silx/gui/qt/_macosx.py68
-rw-r--r--silx/gui/qt/_pyside_dynamic.py158
-rw-r--r--silx/gui/qt/_pyside_missing.py274
-rw-r--r--silx/gui/qt/_qt.py229
-rw-r--r--silx/gui/qt/_utils.py44
-rw-r--r--silx/gui/setup.py51
-rw-r--r--silx/gui/test/__init__.py108
-rw-r--r--silx/gui/test/test_console.py91
-rw-r--r--silx/gui/test/test_icons.py116
-rw-r--r--silx/gui/test/test_qt.py144
-rw-r--r--silx/gui/test/test_utils.py77
-rw-r--r--silx/gui/test/utils.py428
-rw-r--r--silx/gui/widgets/FrameBrowser.py307
-rw-r--r--silx/gui/widgets/HierarchicalTableView.py172
-rw-r--r--silx/gui/widgets/MedianFilterDialog.py74
-rw-r--r--silx/gui/widgets/PeriodicTable.py825
-rw-r--r--silx/gui/widgets/TableWidget.py488
-rw-r--r--silx/gui/widgets/ThreadPoolPushButton.py233
-rw-r--r--silx/gui/widgets/WaitingPushButton.py243
-rw-r--r--silx/gui/widgets/__init__.py27
-rw-r--r--silx/gui/widgets/setup.py41
-rw-r--r--silx/gui/widgets/test/__init__.py45
-rw-r--r--silx/gui/widgets/test/test_hierarchicaltableview.py117
-rw-r--r--silx/gui/widgets/test/test_periodictable.py163
-rw-r--r--silx/gui/widgets/test/test_tablewidget.py61
-rw-r--r--silx/gui/widgets/test/test_threadpoolpushbutton.py129
-rw-r--r--silx/image/__init__.py27
-rw-r--r--silx/image/bilinear.c20006
-rw-r--r--silx/image/bilinear.pyx335
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-rw-r--r--silx/image/test/__init__.py42
-rw-r--r--silx/image/test/test_bilinear.py142
-rw-r--r--silx/image/test/test_medianfilter.py76
-rw-r--r--silx/image/test/test_shapes.py334
-rw-r--r--silx/io/__init__.py45
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611 files changed, 395651 insertions, 0 deletions
diff --git a/silx/__init__.py b/silx/__init__.py
new file mode 100644
index 0000000..cfb306b
--- /dev/null
+++ b/silx/__init__.py
@@ -0,0 +1,43 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+from __future__ import absolute_import, print_function, division
+
+__authors__ = ["Jérôme Kieffer"]
+__license__ = "MIT"
+__date__ = "23/05/2016"
+
+import os as _os
+import logging as _logging
+
+_logging.basicConfig() # Make sure logging is initialised
+
+project = _os.path.basename(_os.path.dirname(_os.path.abspath(__file__)))
+
+try:
+ from ._version import __date__ as date # noqa
+ from ._version import version, version_info, hexversion, strictversion # noqa
+except ImportError:
+ raise RuntimeError("Do NOT use %s from its sources: build it and use the built version" % project)
diff --git a/silx/__main__.py b/silx/__main__.py
new file mode 100644
index 0000000..4c05ef3
--- /dev/null
+++ b/silx/__main__.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2004-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module describe silx applications which are available through
+the silx launcher.
+
+Your environment should provide a command `silx`. You can reach help with
+`silx --help`, and check the version with `silx --version`.
+"""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "18/04/2017"
+
+
+import logging
+logging.basicConfig()
+
+import sys
+from silx.utils.launcher import Launcher
+import silx._version
+
+
+def main():
+ """Main function of the launcher
+
+ This function is referenced in the setup.py file.
+ Thisfor it is executed by a launcher script generated by setuptools.
+
+ :rtype: int
+ :returns: The execution status
+ """
+ launcher = Launcher(prog="silx", version=silx._version.version)
+ launcher.add_command("view",
+ module_name="silx.app.view",
+ description="Browse a data file with a GUI")
+ status = launcher.execute(sys.argv)
+ return status
+
+
+if __name__ == "__main__":
+ # executed when using python -m PROJECT_NAME
+ status = main()
+ sys.exit(status)
diff --git a/silx/app/__init__.py b/silx/app/__init__.py
new file mode 100644
index 0000000..9cbb8bb
--- /dev/null
+++ b/silx/app/__init__.py
@@ -0,0 +1,29 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Application provided by the launcher"""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "30/03/2017"
diff --git a/silx/app/setup.py b/silx/app/setup.py
new file mode 100644
index 0000000..bf6f3af
--- /dev/null
+++ b/silx/app/setup.py
@@ -0,0 +1,40 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ############################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "30/03/2017"
+
+from numpy.distutils.misc_util import Configuration
+
+
+def configuration(parent_package='', top_path=None):
+ config = Configuration('app', parent_package, top_path)
+ config.add_subpackage('test')
+ return config
+
+
+if __name__ == "__main__":
+ from numpy.distutils.core import setup
+ setup(configuration=configuration)
diff --git a/silx/app/test/__init__.py b/silx/app/test/__init__.py
new file mode 100644
index 0000000..54241dc
--- /dev/null
+++ b/silx/app/test/__init__.py
@@ -0,0 +1,41 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "30/03/2017"
+
+
+import logging
+import os
+import sys
+import unittest
+
+
+_logger = logging.getLogger(__name__)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ return test_suite
diff --git a/silx/app/test/test_view.py b/silx/app/test/test_view.py
new file mode 100644
index 0000000..774bc01
--- /dev/null
+++ b/silx/app/test/test_view.py
@@ -0,0 +1,135 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Module testing silx.app.view"""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "12/04/2017"
+
+
+import unittest
+from silx.gui.test.utils import TestCaseQt
+from .. import view
+import sys
+
+
+class QApplicationMock(object):
+
+ def __init__(self, args):
+ pass
+
+ def exec_(self):
+ return 0
+
+ def deleteLater(self):
+ pass
+
+
+class ViewerMock(object):
+
+ def __init__(self):
+ super(ViewerMock, self).__init__()
+ self.__class__._instance = self
+ self.appendFileCalls = []
+
+ def appendFile(self, filename):
+ self.appendFileCalls.append(filename)
+
+ def resize(self, size):
+ pass
+
+ def show(self):
+ pass
+
+
+class TestLauncher(unittest.TestCase):
+ """Test command line parsing"""
+
+ @classmethod
+ def setUpClass(cls):
+ super(TestLauncher, cls).setUpClass()
+ cls._Viewer = view.Viewer
+ view.Viewer = ViewerMock
+ cls._QApplication = view.qt.QApplication
+ view.qt.QApplication = QApplicationMock
+
+ @classmethod
+ def tearDownClass(cls):
+ view.Viewer = cls._Viewer
+ view.qt.QApplication = cls._QApplication
+ cls._Viewer = None
+ super(TestLauncher, cls).tearDownClass()
+
+ def testHelp(self):
+ try:
+ result = view.main(["view", "--help"])
+ self.assertNotEqual(result, 0)
+ except SystemExit as e:
+ result = e.args[0]
+ self.assertEqual(result, 0)
+
+ def testWrongOption(self):
+ try:
+ result = view.main(["view", "--foo"])
+ self.assertNotEqual(result, 0)
+ except SystemExit as e:
+ result = e.args[0]
+ self.assertNotEqual(result, 0)
+
+ def testWrongFile(self):
+ try:
+ result = view.main(["view", "__file.not.found__"])
+ self.assertNotEqual(result, 0)
+ except SystemExit as e:
+ result = e.args[0]
+ self.assertNotEqual(result, 0)
+
+ def testFile(self):
+ # sys.executable is an existing readable file
+ result = view.main(["view", sys.executable])
+ self.assertEqual(result, 0)
+ viewer = ViewerMock._instance
+ self.assertEqual(viewer.appendFileCalls, [sys.executable])
+ ViewerMock._instance = None
+
+
+class TestViewer(TestCaseQt):
+ """Test for Viewer class"""
+
+ def testConstruct(self):
+ widget = view.Viewer()
+ self.qWaitForWindowExposed(widget)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ loader = unittest.defaultTestLoader.loadTestsFromTestCase
+ test_suite.addTest(loader(TestViewer))
+ test_suite.addTest(loader(TestLauncher))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/app/view.py b/silx/app/view.py
new file mode 100644
index 0000000..8fdabde
--- /dev/null
+++ b/silx/app/view.py
@@ -0,0 +1,326 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ############################################################################*/
+"""Browse a data file with a GUI"""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "12/04/2017"
+
+import sys
+import os
+import argparse
+import logging
+import collections
+
+
+logging.basicConfig()
+_logger = logging.getLogger(__name__)
+"""Module logger"""
+
+try:
+ # it should be loaded before h5py
+ import hdf5plugin # noqa
+except ImportError:
+ hdf5plugin = None
+
+try:
+ import h5py
+ import silx.gui.hdf5
+except ImportError:
+ h5py = None
+
+try:
+ import fabio
+except ImportError:
+ fabio = None
+
+from silx.gui import qt
+from silx.gui.data.DataViewerFrame import DataViewerFrame
+
+
+class Viewer(qt.QMainWindow):
+ """
+ This window allows to browse a data file like images or HDF5 and it's
+ content.
+ """
+
+ def __init__(self):
+ """
+ :param files_: List of HDF5 or Spec files (pathes or
+ :class:`silx.io.spech5.SpecH5` or :class:`h5py.File`
+ instances)
+ """
+ qt.QMainWindow.__init__(self)
+ self.setWindowTitle("Silx viewer")
+
+ self.__asyncload = False
+ self.__dialogState = None
+ self.__treeview = silx.gui.hdf5.Hdf5TreeView(self)
+ """Silx HDF5 TreeView"""
+
+ self.__dataViewer = DataViewerFrame(self)
+ vSpliter = qt.QSplitter(qt.Qt.Vertical)
+ vSpliter.addWidget(self.__dataViewer)
+ vSpliter.setSizes([10, 0])
+
+ spliter = qt.QSplitter(self)
+ spliter.addWidget(self.__treeview)
+ spliter.addWidget(vSpliter)
+ spliter.setStretchFactor(1, 1)
+
+ main_panel = qt.QWidget(self)
+ layout = qt.QVBoxLayout()
+ layout.addWidget(spliter)
+ layout.setStretchFactor(spliter, 1)
+ main_panel.setLayout(layout)
+
+ self.setCentralWidget(main_panel)
+
+ self.__treeview.selectionModel().selectionChanged.connect(self.displayData)
+
+ self.__treeview.addContextMenuCallback(self.customContextMenu)
+ # lambda function will never be called cause we store it as weakref
+ self.__treeview.addContextMenuCallback(lambda event: None)
+ # you have to store it first
+ self.__store_lambda = lambda event: self.closeAndSyncCustomContextMenu(event)
+ self.__treeview.addContextMenuCallback(self.__store_lambda)
+
+ self.createActions()
+ self.createMenus()
+
+ def createActions(self):
+ action = qt.QAction("E&xit", self)
+ action.setShortcuts(qt.QKeySequence.Quit)
+ action.setStatusTip("Exit the application")
+ action.triggered.connect(self.close)
+ self._exitAction = action
+
+ action = qt.QAction("&Open", self)
+ action.setStatusTip("Open a file")
+ action.triggered.connect(self.open)
+ self._openAction = action
+
+ action = qt.QAction("&About", self)
+ action.setStatusTip("Show the application's About box")
+ action.triggered.connect(self.about)
+ self._aboutAction = action
+
+ def createMenus(self):
+ fileMenu = self.menuBar().addMenu("&File")
+ fileMenu.addAction(self._openAction)
+ fileMenu.addSeparator()
+ fileMenu.addAction(self._exitAction)
+ helpMenu = self.menuBar().addMenu("&Help")
+ helpMenu.addAction(self._aboutAction)
+
+ def open(self):
+ dialog = self.createFileDialog()
+ if self.__dialogState is None:
+ currentDirectory = os.getcwd()
+ dialog.setDirectory(currentDirectory)
+ else:
+ dialog.restoreState(self.__dialogState)
+
+ result = dialog.exec_()
+ if not result:
+ return
+
+ self.__dialogState = dialog.saveState()
+
+ filenames = dialog.selectedFiles()
+ for filename in filenames:
+ self.appendFile(filename)
+
+ def createFileDialog(self):
+ dialog = qt.QFileDialog(self)
+ dialog.setWindowTitle("Open")
+ dialog.setModal(True)
+
+ extensions = collections.OrderedDict()
+ # expect h5py
+ extensions["HDF5 files"] = "*.h5"
+ # no dependancy
+ extensions["Spec files"] = "*.dat *.spec *.mca"
+ # expect fabio
+ extensions["EDF files"] = "*.edf"
+ extensions["TIFF image files"] = "*.tif *.tiff"
+ extensions["NumPy binary files"] = "*.npy"
+ extensions["CBF files"] = "*.cbf"
+ extensions["MarCCD image files"] = "*.mccd"
+
+ filters = []
+ filters.append("All supported files (%s)" % " ".join(extensions.values()))
+ for name, extension in extensions.items():
+ filters.append("%s (%s)" % (name, extension))
+ filters.append("All files (*)")
+
+ dialog.setNameFilters(filters)
+ dialog.setFileMode(qt.QFileDialog.ExistingFiles)
+ return dialog
+
+ def about(self):
+ import silx._version
+ message = """<p align="center"><b>Silx viewer</b>
+ <br />
+ <br />{silx_version}
+ <br />
+ <br /><a href="{project_url}">Upstream project on GitHub</a>
+ </p>
+ <p align="left">
+ <dl>
+ <dt><b>Silx version</b></dt><dd>{silx_version}</dd>
+ <dt><b>Qt version</b></dt><dd>{qt_version}</dd>
+ <dt><b>Qt binding</b></dt><dd>{qt_binding}</dd>
+ <dt><b>Python version</b></dt><dd>{python_version}</dd>
+ <dt><b>Optional libraries</b></dt><dd>{optional_lib}</dd>
+ </dl>
+ </p>
+ <p>
+ Copyright (C) <a href="{esrf_url}">European Synchrotron Radiation Facility</a>
+ </p>
+ """
+ def format_optional_lib(name, isAvailable):
+ if isAvailable:
+ template = '<b>%s</b> is <font color="green">installed</font>'
+ else:
+ template = '<b>%s</b> is <font color="red">not installed</font>'
+ return template % name
+
+ optional_lib = []
+ optional_lib.append(format_optional_lib("FabIO", fabio is not None))
+ optional_lib.append(format_optional_lib("H5py", h5py is not None))
+ optional_lib.append(format_optional_lib("hdf5plugin", hdf5plugin is not None))
+
+ info = dict(
+ esrf_url="http://www.esrf.eu",
+ project_url="https://github.com/silx-kit/silx",
+ silx_version=silx._version.version,
+ qt_binding=qt.BINDING,
+ qt_version=qt.qVersion(),
+ python_version=sys.version.replace("\n", "<br />"),
+ optional_lib="<br />".join(optional_lib)
+ )
+ qt.QMessageBox.about(self, "About Menu", message.format(**info))
+
+ def appendFile(self, filename):
+ self.__treeview.findHdf5TreeModel().appendFile(filename)
+
+ def displayData(self):
+ """Called to update the dataviewer with the selected data.
+ """
+ selected = list(self.__treeview.selectedH5Nodes())
+ if len(selected) == 1:
+ # Update the viewer for a single selection
+ data = selected[0]
+ self.__dataViewer.setData(data)
+
+ def useAsyncLoad(self, useAsync):
+ self.__asyncload = useAsync
+
+ def customContextMenu(self, event):
+ """Called to populate the context menu
+
+ :param silx.gui.hdf5.Hdf5ContextMenuEvent event: Event
+ containing expected information to populate the context menu
+ """
+ selectedObjects = event.source().selectedH5Nodes()
+ menu = event.menu()
+
+ hasDataset = False
+ for obj in selectedObjects:
+ if obj.ntype is h5py.Dataset:
+ hasDataset = True
+ break
+
+ if len(menu.children()):
+ menu.addSeparator()
+
+ if hasDataset:
+ action = qt.QAction("Do something on the datasets", event.source())
+ menu.addAction(action)
+
+ def closeAndSyncCustomContextMenu(self, event):
+ """Called to populate the context menu
+
+ :param silx.gui.hdf5.Hdf5ContextMenuEvent event: Event
+ containing expected information to populate the context menu
+ """
+ selectedObjects = event.source().selectedH5Nodes()
+ menu = event.menu()
+
+ if len(menu.children()):
+ menu.addSeparator()
+
+ for obj in selectedObjects:
+ if obj.ntype is h5py.File:
+ action = qt.QAction("Remove %s" % obj.local_filename, event.source())
+ action.triggered.connect(lambda: self.__treeview.findHdf5TreeModel().removeH5pyObject(obj.h5py_object))
+ menu.addAction(action)
+ action = qt.QAction("Synchronize %s" % obj.local_filename, event.source())
+ action.triggered.connect(lambda: self.__treeview.findHdf5TreeModel().synchronizeH5pyObject(obj.h5py_object))
+ menu.addAction(action)
+
+
+def main(argv):
+ """
+ Main function to launch the viewer as an application
+
+ :param argv: Command line arguments
+ :returns: exit status
+ """
+ parser = argparse.ArgumentParser(description=__doc__)
+ parser.add_argument(
+ 'files',
+ type=argparse.FileType('rb'),
+ nargs=argparse.ZERO_OR_MORE,
+ help='Data file to show (h5 file, edf files, spec files)')
+
+ options = parser.parse_args(argv[1:])
+
+ if h5py is None:
+ message = "Module 'h5py' is not installed but is mandatory."\
+ + " You can install it using \"pip install h5py\"."
+ _logger.error(message)
+ return -1
+
+ if hdf5plugin is None:
+ message = "Module 'hdf5plugin' is not installed. It supports some hdf5"\
+ + " compressions. You can install it using \"pip install hdf5plugin\"."
+ _logger.warning(message)
+
+ app = qt.QApplication([])
+ sys.excepthook = qt.exceptionHandler
+ window = Viewer()
+ window.resize(qt.QSize(640, 480))
+
+ for f in options.files:
+ filename = f.name
+ f.close()
+ window.appendFile(filename)
+
+ window.show()
+ result = app.exec_()
+ # remove ending warnings relative to QTimer
+ app.deleteLater()
+ return result
diff --git a/silx/gui/__init__.py b/silx/gui/__init__.py
new file mode 100644
index 0000000..6baf238
--- /dev/null
+++ b/silx/gui/__init__.py
@@ -0,0 +1,29 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Set of Qt widgets"""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "23/05/2016"
diff --git a/silx/gui/_glutils/Context.py b/silx/gui/_glutils/Context.py
new file mode 100644
index 0000000..7600992
--- /dev/null
+++ b/silx/gui/_glutils/Context.py
@@ -0,0 +1,63 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Abstraction of OpenGL context.
+
+It defines a way to get current OpenGL context to support multiple
+OpenGL contexts.
+"""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "25/07/2016"
+
+
+# context #####################################################################
+
+
+def _defaultGLContextGetter():
+ return None
+
+_glContextGetter = _defaultGLContextGetter
+
+
+def getGLContext():
+ """Returns platform dependent object of current OpenGL context.
+
+ This is useful to associate OpenGL resources with the context they are
+ created in.
+
+ :return: Platform specific OpenGL context
+ :rtype: None by default or a platform dependent object"""
+ return _glContextGetter()
+
+
+def setGLContextGetter(getter=_defaultGLContextGetter):
+ """Set a platform dependent function to retrieve the current OpenGL context
+
+ :param getter: Platform dependent GL context getter
+ :type getter: Function with no args returning the current OpenGL context
+ """
+ global _glContextGetter
+ _glContextGetter = getter
diff --git a/silx/gui/_glutils/FramebufferTexture.py b/silx/gui/_glutils/FramebufferTexture.py
new file mode 100644
index 0000000..b01eb41
--- /dev/null
+++ b/silx/gui/_glutils/FramebufferTexture.py
@@ -0,0 +1,164 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Association of a texture and a framebuffer object for off-screen rendering.
+"""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "25/07/2016"
+
+
+import logging
+
+from . import gl
+from .Texture import Texture
+
+
+_logger = logging.getLogger(__name__)
+
+
+class FramebufferTexture(object):
+ """Framebuffer with a texture.
+
+ Aimed at off-screen rendering to texture.
+
+ :param internalFormat: OpenGL texture internal format
+ :param shape: Shape (height, width) of the framebuffer and texture
+ :type shape: 2-tuple of int
+ :param stencilFormat: Stencil renderbuffer format
+ :param depthFormat: Depth renderbuffer format
+ :param kwargs: Extra arguments for :class:`Texture` constructor
+ """
+
+ _PACKED_FORMAT = gl.GL_DEPTH24_STENCIL8, gl.GL_DEPTH_STENCIL
+
+ def __init__(self,
+ internalFormat,
+ shape,
+ stencilFormat=gl.GL_DEPTH24_STENCIL8,
+ depthFormat=gl.GL_DEPTH24_STENCIL8,
+ **kwargs):
+
+ self._texture = Texture(internalFormat, shape=shape, **kwargs)
+
+ self._previousFramebuffer = 0 # Used by with statement
+
+ self._name = gl.glGenFramebuffers(1)
+ gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self._name)
+
+ # Attachments
+ gl.glFramebufferTexture2D(gl.GL_FRAMEBUFFER,
+ gl.GL_COLOR_ATTACHMENT0,
+ gl.GL_TEXTURE_2D,
+ self._texture.name,
+ 0)
+
+ height, width = self._texture.shape
+
+ if stencilFormat is not None:
+ self._stencilId = gl.glGenRenderbuffers(1)
+ gl.glBindRenderbuffer(gl.GL_RENDERBUFFER, self._stencilId)
+ gl.glRenderbufferStorage(gl.GL_RENDERBUFFER,
+ stencilFormat,
+ width, height)
+ gl.glFramebufferRenderbuffer(gl.GL_FRAMEBUFFER,
+ gl.GL_STENCIL_ATTACHMENT,
+ gl.GL_RENDERBUFFER,
+ self._stencilId)
+ else:
+ self._stencilId = None
+
+ if depthFormat is not None:
+ if self._stencilId and depthFormat in self._PACKED_FORMAT:
+ self._depthId = self._stencilId
+ else:
+ self._depthId = gl.glGenRenderbuffers(1)
+ gl.glBindRenderbuffer(gl.GL_RENDERBUFFER, self._depthId)
+ gl.glRenderbufferStorage(gl.GL_RENDERBUFFER,
+ depthFormat,
+ width, height)
+ gl.glFramebufferRenderbuffer(gl.GL_FRAMEBUFFER,
+ gl.GL_DEPTH_ATTACHMENT,
+ gl.GL_RENDERBUFFER,
+ self._depthId)
+ else:
+ self._depthId = None
+
+ assert gl.glCheckFramebufferStatus(gl.GL_FRAMEBUFFER) == \
+ gl.GL_FRAMEBUFFER_COMPLETE
+ gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, 0)
+
+ @property
+ def shape(self):
+ """Shape of the framebuffer (height, width)"""
+ return self._texture.shape
+
+ @property
+ def texture(self):
+ """The texture this framebuffer is rendering to.
+
+ The life-cycle of the texture is managed by this object"""
+ return self._texture
+
+ @property
+ def name(self):
+ """OpenGL name of the framebuffer"""
+ if self._name is not None:
+ return self._name
+ else:
+ raise RuntimeError("No OpenGL framebuffer resource, \
+ discard has already been called")
+
+ def bind(self):
+ """Bind this framebuffer for rendering"""
+ gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.name)
+
+ # with statement
+
+ def __enter__(self):
+ self._previousFramebuffer = gl.glGetInteger(gl.GL_FRAMEBUFFER_BINDING)
+ self.bind()
+
+ def __exit__(self, exctype, excvalue, traceback):
+ gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self._previousFramebuffer)
+
+ def discard(self):
+ """Delete associated OpenGL resources including texture"""
+ if self._name is not None:
+ gl.glDeleteFramebuffers(self._name)
+ self._name = None
+
+ if self._stencilId is not None:
+ gl.glDeleteRenderbuffers(self._stencilId)
+ if self._stencilId == self._depthId:
+ self._depthId = None
+ self._stencilId = None
+ if self._depthId is not None:
+ gl.glDeleteRenderbuffers(self._depthId)
+ self._depthId = None
+
+ self._texture.discard() # Also discard the texture
+ else:
+ _logger.warning("Discard has already been called")
diff --git a/silx/gui/_glutils/Program.py b/silx/gui/_glutils/Program.py
new file mode 100644
index 0000000..48c12f5
--- /dev/null
+++ b/silx/gui/_glutils/Program.py
@@ -0,0 +1,202 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides a class to handle shader program compilation."""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "25/07/2016"
+
+
+import logging
+
+import numpy
+
+from . import gl
+from .Context import getGLContext
+
+_logger = logging.getLogger(__name__)
+
+
+class Program(object):
+ """Wrap OpenGL shader program.
+
+ The program is compiled lazily (i.e., at first program :meth:`use`).
+ When the program is compiled, it stores attributes and uniforms locations.
+ So, attributes and uniforms must be used after :meth:`use`.
+
+ This object supports multiple OpenGL contexts.
+
+ :param str vertexShader: The source of the vertex shader.
+ :param str fragmentShader: The source of the fragment shader.
+ :param str attrib0:
+ Attribute's name to bind to position 0 (default: 'position').
+ On certain platform, this attribute MUST be active and with an
+ array attached to it in order for the rendering to occur....
+ """
+
+ def __init__(self, vertexShader, fragmentShader,
+ attrib0='position'):
+ self._vertexShader = vertexShader
+ self._fragmentShader = fragmentShader
+ self._attrib0 = attrib0
+ self._programs = {}
+
+ @staticmethod
+ def _compileGL(vertexShader, fragmentShader, attrib0):
+ program = gl.glCreateProgram()
+
+ gl.glBindAttribLocation(program, 0, attrib0.encode('ascii'))
+
+ vertex = gl.glCreateShader(gl.GL_VERTEX_SHADER)
+ gl.glShaderSource(vertex, vertexShader)
+ gl.glCompileShader(vertex)
+ if gl.glGetShaderiv(vertex, gl.GL_COMPILE_STATUS) != gl.GL_TRUE:
+ raise RuntimeError(gl.glGetShaderInfoLog(vertex))
+ gl.glAttachShader(program, vertex)
+ gl.glDeleteShader(vertex)
+
+ fragment = gl.glCreateShader(gl.GL_FRAGMENT_SHADER)
+ gl.glShaderSource(fragment, fragmentShader)
+ gl.glCompileShader(fragment)
+ if gl.glGetShaderiv(fragment,
+ gl.GL_COMPILE_STATUS) != gl.GL_TRUE:
+ raise RuntimeError(gl.glGetShaderInfoLog(fragment))
+ gl.glAttachShader(program, fragment)
+ gl.glDeleteShader(fragment)
+
+ gl.glLinkProgram(program)
+ if gl.glGetProgramiv(program, gl.GL_LINK_STATUS) != gl.GL_TRUE:
+ raise RuntimeError(gl.glGetProgramInfoLog(program))
+
+ attributes = {}
+ for index in range(gl.glGetProgramiv(program,
+ gl.GL_ACTIVE_ATTRIBUTES)):
+ name = gl.glGetActiveAttrib(program, index)[0]
+ namestr = name.decode('ascii')
+ attributes[namestr] = gl.glGetAttribLocation(program, name)
+
+ uniforms = {}
+ for index in range(gl.glGetProgramiv(program, gl.GL_ACTIVE_UNIFORMS)):
+ name = gl.glGetActiveUniform(program, index)[0]
+ namestr = name.decode('ascii')
+ uniforms[namestr] = gl.glGetUniformLocation(program, name)
+
+ return program, attributes, uniforms
+
+ def _getProgramInfo(self):
+ glcontext = getGLContext()
+ if glcontext not in self._programs:
+ raise RuntimeError(
+ "Program was not compiled for current OpenGL context.")
+ return self._programs[glcontext]
+
+ @property
+ def attributes(self):
+ """Vertex attributes names and locations as a dict of {str: int}.
+
+ WARNING:
+ Read-only usage.
+ To use only with a valid OpenGL context and after :meth:`use`
+ has been called for this context.
+ """
+ return self._getProgramInfo()[1]
+
+ @property
+ def uniforms(self):
+ """Program uniforms names and locations as a dict of {str: int}.
+
+ WARNING:
+ Read-only usage.
+ To use only with a valid OpenGL context and after :meth:`use`
+ has been called for this context.
+ """
+ return self._getProgramInfo()[2]
+
+ @property
+ def program(self):
+ """OpenGL id of the program.
+
+ WARNING:
+ To use only with a valid OpenGL context and after :meth:`use`
+ has been called for this context.
+ """
+ return self._getProgramInfo()[0]
+
+ # def discard(self):
+ # pass # Not implemented yet
+
+ def use(self):
+ """Make use of the program, compiling it if necessary"""
+ glcontext = getGLContext()
+
+ if glcontext not in self._programs:
+ self._programs[glcontext] = self._compileGL(
+ self._vertexShader,
+ self._fragmentShader,
+ self._attrib0)
+
+ if _logger.getEffectiveLevel() <= logging.DEBUG:
+ gl.glValidateProgram(self.program)
+ if gl.glGetProgramiv(
+ self.program, gl.GL_VALIDATE_STATUS) != gl.GL_TRUE:
+ _logger.debug('Cannot validate program: %s',
+ gl.glGetProgramInfoLog(self.program))
+
+ gl.glUseProgram(self.program)
+
+ def setUniformMatrix(self, name, value, transpose=True, safe=False):
+ """Wrap glUniformMatrix[2|3|4]fv
+
+ :param str name: The name of the uniform.
+ :param value: The 2D matrix (or the array of matrices, 3D).
+ Matrices are 2x2, 3x3 or 4x4.
+ :type value: numpy.ndarray with 2 or 3 dimensions of float32
+ :param bool transpose: Whether to transpose (True, default) or not.
+ :param bool safe: False: raise an error if no uniform with this name;
+ True: silently ignores it.
+
+ :raises KeyError: if no uniform corresponds to name.
+ """
+ assert value.dtype == numpy.float32
+
+ shape = value.shape
+ assert len(shape) in (2, 3)
+ assert shape[-1] in (2, 3, 4)
+ assert shape[-1] == shape[-2] # As in OpenGL|ES 2.0
+
+ location = self.uniforms.get(name)
+ if location is not None:
+ count = 1 if len(shape) == 2 else shape[0]
+ transpose = gl.GL_TRUE if transpose else gl.GL_FALSE
+
+ if shape[-1] == 2:
+ gl.glUniformMatrix2fv(location, count, transpose, value)
+ elif shape[-1] == 3:
+ gl.glUniformMatrix3fv(location, count, transpose, value)
+ elif shape[-1] == 4:
+ gl.glUniformMatrix4fv(location, count, transpose, value)
+
+ elif not safe:
+ raise KeyError('No uniform: %s' % name)
diff --git a/silx/gui/_glutils/Texture.py b/silx/gui/_glutils/Texture.py
new file mode 100644
index 0000000..9f09a86
--- /dev/null
+++ b/silx/gui/_glutils/Texture.py
@@ -0,0 +1,308 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides a class wrapping OpenGL 2D and 3D texture."""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "04/10/2016"
+
+
+import collections
+from ctypes import c_void_p
+import logging
+
+import numpy
+
+from . import gl, utils
+
+
+_logger = logging.getLogger(__name__)
+
+
+class Texture(object):
+ """Base class to wrap OpenGL 2D and 3D texture
+
+ :param internalFormat: OpenGL texture internal format
+ :param data: The data to copy to the texture or None for an empty texture
+ :type data: numpy.ndarray or None
+ :param format_: Input data format if different from internalFormat
+ :param shape: If data is None, shape of the texture
+ :type shape: 2 or 3-tuple of int (height, width) or (depth, height, width)
+ :param int texUnit: The texture unit to use
+ :param minFilter: OpenGL texture minimization filter (default: GL_NEAREST)
+ :param magFilter: OpenGL texture magnification filter (default: GL_LINEAR)
+ :param wrap: Texture wrap mode for dimensions: (t, s) or (r, t, s)
+ If a single value is provided, it used for all dimensions.
+ :type wrap: OpenGL wrap mode or 2 or 3-tuple of wrap mode
+ """
+
+ def __init__(self, internalFormat, data=None, format_=None,
+ shape=None, texUnit=0,
+ minFilter=None, magFilter=None, wrap=None):
+
+ self._internalFormat = internalFormat
+ if format_ is None:
+ format_ = self.internalFormat
+
+ if data is None:
+ assert shape is not None
+ else:
+ assert shape is None
+ data = numpy.array(data, copy=False, order='C')
+ if format_ != gl.GL_RED:
+ shape = data.shape[:-1] # Last dimension is channels
+ else:
+ shape = data.shape
+
+ assert len(shape) in (2, 3)
+ self._shape = tuple(shape)
+ self._ndim = len(shape)
+
+ self.texUnit = texUnit
+
+ self._name = gl.glGenTextures(1)
+ self.bind(self.texUnit)
+
+ self._minFilter = None
+ self.minFilter = minFilter if minFilter is not None else gl.GL_NEAREST
+
+ self._magFilter = None
+ self.magFilter = magFilter if magFilter is not None else gl.GL_LINEAR
+
+ if wrap is not None:
+ if not isinstance(wrap, collections.Iterable):
+ wrap = [wrap] * self.ndim
+
+ assert len(wrap) == self.ndim
+
+ gl.glTexParameter(self.target,
+ gl.GL_TEXTURE_WRAP_S,
+ wrap[-1])
+ gl.glTexParameter(self.target,
+ gl.GL_TEXTURE_WRAP_T,
+ wrap[-2])
+ if self.ndim == 3:
+ gl.glTexParameter(self.target,
+ gl.GL_TEXTURE_WRAP_R,
+ wrap[0])
+
+ gl.glPixelStorei(gl.GL_UNPACK_ALIGNMENT, 1)
+
+ # This are the defaults, useless to set if not modified
+ # gl.glPixelStorei(gl.GL_UNPACK_ROW_LENGTH, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_PIXELS, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_ROWS, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_IMAGE_HEIGHT, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_IMAGES, 0)
+
+ if data is None:
+ data = c_void_p(0)
+ type_ = gl.GL_UNSIGNED_BYTE
+ else:
+ type_ = utils.numpyToGLType(data.dtype)
+
+ if self.ndim == 2:
+ _logger.debug(
+ 'Creating 2D texture shape: (%d, %d),'
+ ' internal format: %s, format: %s, type: %s',
+ self.shape[0], self.shape[1],
+ str(self.internalFormat), str(format_), str(type_))
+
+ gl.glTexImage2D(
+ gl.GL_TEXTURE_2D,
+ 0,
+ self.internalFormat,
+ self.shape[1],
+ self.shape[0],
+ 0,
+ format_,
+ type_,
+ data)
+ else:
+ _logger.debug(
+ 'Creating 3D texture shape: (%d, %d, %d),'
+ ' internal format: %s, format: %s, type: %s',
+ self.shape[0], self.shape[1], self.shape[2],
+ str(self.internalFormat), str(format_), str(type_))
+
+ gl.glTexImage3D(
+ gl.GL_TEXTURE_3D,
+ 0,
+ self.internalFormat,
+ self.shape[2],
+ self.shape[1],
+ self.shape[0],
+ 0,
+ format_,
+ type_,
+ data)
+
+ gl.glBindTexture(self.target, 0)
+
+ @property
+ def target(self):
+ """OpenGL target type of this texture"""
+ return gl.GL_TEXTURE_2D if self.ndim == 2 else gl.GL_TEXTURE_3D
+
+ @property
+ def ndim(self):
+ """The number of dimensions: 2 or 3"""
+ return self._ndim
+
+ @property
+ def internalFormat(self):
+ """Texture internal format"""
+ return self._internalFormat
+
+ @property
+ def shape(self):
+ """Shape of the texture: (height, width) or (depth, height, width)"""
+ return self._shape
+
+ @property
+ def name(self):
+ """OpenGL texture name"""
+ if self._name is not None:
+ return self._name
+ else:
+ raise RuntimeError(
+ "No OpenGL texture resource, discard has already been called")
+
+ @property
+ def minFilter(self):
+ """Minifying function parameter (GL_TEXTURE_MIN_FILTER)"""
+ return self._minFilter
+
+ @minFilter.setter
+ def minFilter(self, minFilter):
+ if minFilter != self.minFilter:
+ self._minFilter = minFilter
+ self.bind()
+ gl.glTexParameter(self.target,
+ gl.GL_TEXTURE_MIN_FILTER,
+ self.minFilter)
+
+ @property
+ def magFilter(self):
+ """Magnification function parameter (GL_TEXTURE_MAG_FILTER)"""
+ return self._magFilter
+
+ @magFilter.setter
+ def magFilter(self, magFilter):
+ if magFilter != self.magFilter:
+ self._magFilter = magFilter
+ self.bind()
+ gl.glTexParameter(self.target,
+ gl.GL_TEXTURE_MAG_FILTER,
+ self.magFilter)
+
+ def discard(self):
+ """Delete associated OpenGL texture"""
+ if self._name is not None:
+ gl.glDeleteTextures(self._name)
+ self._name = None
+ else:
+ _logger.warning("Discard as already been called")
+
+ def bind(self, texUnit=None):
+ """Bind the texture to a texture unit.
+
+ :param int texUnit: The texture unit to use
+ """
+ if texUnit is None:
+ texUnit = self.texUnit
+ gl.glActiveTexture(gl.GL_TEXTURE0 + texUnit)
+ gl.glBindTexture(self.target, self.name)
+
+ # with statement
+
+ def __enter__(self):
+ self.bind()
+
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ gl.glActiveTexture(gl.GL_TEXTURE0 + self.texUnit)
+ gl.glBindTexture(self.target, 0)
+
+ def update(self,
+ format_,
+ data,
+ offset=(0, 0, 0),
+ texUnit=None):
+ """Update the content of the texture.
+
+ Texture is not resized, so data must fit into texture with the
+ given offset.
+
+ :param format_: The OpenGL format of the data
+ :param data: The data to use to update the texture
+ :param offset: The offset in the texture where to copy the data
+ :type offset: 2 or 3-tuple of int
+ :param int texUnit:
+ The texture unit to use (default: the one provided at init)
+ """
+ data = numpy.array(data, copy=False, order='C')
+
+ assert data.ndim == self.ndim
+ assert len(offset) >= self.ndim
+ for i in range(self.ndim):
+ assert offset[i] + data.shape[i] <= self.shape[i]
+
+ gl.glPixelStorei(gl.GL_UNPACK_ALIGNMENT, 1)
+
+ # This are the defaults, useless to set if not modified
+ # gl.glPixelStorei(gl.GL_UNPACK_ROW_LENGTH, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_PIXELS, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_ROWS, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_IMAGE_HEIGHT, 0)
+ # gl.glPixelStorei(gl.GL_UNPACK_SKIP_IMAGES, 0)
+
+ self.bind(texUnit)
+
+ type_ = utils.numpyToGLType(data.dtype)
+
+ if self.ndim == 2:
+ gl.glTexSubImage2D(gl.GL_TEXTURE_2D,
+ 0,
+ offset[1],
+ offset[0],
+ data.shape[1],
+ data.shape[0],
+ format_,
+ type_,
+ data)
+ gl.glBindTexture(gl.GL_TEXTURE_2D, 0)
+ else:
+ gl.glTexSubImage3D(gl.GL_TEXTURE_3D,
+ 0,
+ offset[2],
+ offset[1],
+ offset[0],
+ data.shape[2],
+ data.shape[1],
+ data.shape[0],
+ format_,
+ type_,
+ data)
+ gl.glBindTexture(gl.GL_TEXTURE_3D, 0)
diff --git a/silx/gui/_glutils/VertexBuffer.py b/silx/gui/_glutils/VertexBuffer.py
new file mode 100644
index 0000000..689b543
--- /dev/null
+++ b/silx/gui/_glutils/VertexBuffer.py
@@ -0,0 +1,266 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides a class managing an OpenGL vertex buffer."""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "10/01/2017"
+
+
+import logging
+from ctypes import c_void_p
+import numpy
+
+from . import gl
+from .utils import numpyToGLType, sizeofGLType
+
+
+_logger = logging.getLogger(__name__)
+
+
+class VertexBuffer(object):
+ """Object handling an OpenGL vertex buffer object
+
+ :param data: Data used to fill the vertex buffer
+ :type data: numpy.ndarray or None
+ :param int size: Size in bytes of the buffer or None for data size
+ :param usage: OpenGL vertex buffer expected usage pattern:
+ GL_STREAM_DRAW, GL_STATIC_DRAW (default) or GL_DYNAMIC_DRAW
+ :param target: Target buffer:
+ GL_ARRAY_BUFFER (default) or GL_ELEMENT_ARRAY_BUFFER
+ """
+ # OpenGL|ES 2.0 subset:
+ _USAGES = gl.GL_STREAM_DRAW, gl.GL_STATIC_DRAW, gl.GL_DYNAMIC_DRAW
+ _TARGETS = gl.GL_ARRAY_BUFFER, gl.GL_ELEMENT_ARRAY_BUFFER
+
+ def __init__(self,
+ data=None,
+ size=None,
+ usage=None,
+ target=None):
+ if usage is None:
+ usage = gl.GL_STATIC_DRAW
+ assert usage in self._USAGES
+
+ if target is None:
+ target = gl.GL_ARRAY_BUFFER
+ assert target in self._TARGETS
+
+ self._target = target
+ self._usage = usage
+
+ self._name = gl.glGenBuffers(1)
+ self.bind()
+
+ if data is None:
+ assert size is not None
+ self._size = size
+ gl.glBufferData(self._target,
+ self._size,
+ c_void_p(0),
+ self._usage)
+ else:
+ data = numpy.array(data, copy=False, order='C')
+ if size is not None:
+ assert size <= data.nbytes
+
+ self._size = size or data.nbytes
+ gl.glBufferData(self._target,
+ self._size,
+ data,
+ self._usage)
+
+ gl.glBindBuffer(self._target, 0)
+
+ @property
+ def target(self):
+ """The target buffer of the vertex buffer"""
+ return self._target
+
+ @property
+ def usage(self):
+ """The expected usage of the vertex buffer"""
+ return self._usage
+
+ @property
+ def name(self):
+ """OpenGL Vertex Buffer object name (int)"""
+ if self._name is not None:
+ return self._name
+ else:
+ raise RuntimeError("No OpenGL buffer resource, \
+ discard has already been called")
+
+ @property
+ def size(self):
+ """Size in bytes of the Vertex Buffer Object (int)"""
+ if self._size is not None:
+ return self._size
+ else:
+ raise RuntimeError("No OpenGL buffer resource, \
+ discard has already been called")
+
+ def bind(self):
+ """Bind the vertex buffer"""
+ gl.glBindBuffer(self._target, self.name)
+
+ def update(self, data, offset=0, size=None):
+ """Update vertex buffer content.
+
+ :param numpy.ndarray data: The data to put in the vertex buffer
+ :param int offset: Offset in bytes in the buffer where to put the data
+ :param int size: If provided, size of data to copy
+ """
+ data = numpy.array(data, copy=False, order='C')
+ if size is None:
+ size = data.nbytes
+ assert offset + size <= self.size
+ with self:
+ gl.glBufferSubData(self._target, offset, size, data)
+
+ def discard(self):
+ """Delete the vertex buffer"""
+ if self._name is not None:
+ gl.glDeleteBuffers(self._name)
+ self._name = None
+ self._size = None
+ else:
+ _logger.warning("Discard has already been called")
+
+ # with statement
+
+ def __enter__(self):
+ self.bind()
+
+ def __exit__(self, exctype, excvalue, traceback):
+ gl.glBindBuffer(self._target, 0)
+
+
+class VertexBufferAttrib(object):
+ """Describes data stored in a vertex buffer
+
+ Convenient class to store info for glVertexAttribPointer calls
+
+ :param VertexBuffer vbo: The vertex buffer storing the data
+ :param int type_: The OpenGL type of the data
+ :param int size: The number of data elements stored in the VBO
+ :param int dimension: The number of `type_` element(s) in [1, 4]
+ :param int offset: Start offset of data in the vertex buffer
+ :param int stride: Data stride in the vertex buffer
+ """
+
+ _GL_TYPES = gl.GL_UNSIGNED_BYTE, gl.GL_FLOAT, gl.GL_INT
+
+ def __init__(self,
+ vbo,
+ type_,
+ size,
+ dimension=1,
+ offset=0,
+ stride=0,
+ normalisation=False):
+ self.vbo = vbo
+ assert type_ in self._GL_TYPES
+ self.type_ = type_
+ self.size = size
+ assert 1 <= dimension <= 4
+ self.dimension = dimension
+ self.offset = offset
+ self.stride = stride
+ self.normalisation = bool(normalisation)
+
+ @property
+ def itemsize(self):
+ """Size in bytes of a vertex buffer element (int)"""
+ return self.dimension * sizeofGLType(self.type_)
+
+ itemSize = itemsize # Backward compatibility
+
+ def setVertexAttrib(self, attribute):
+ """Call glVertexAttribPointer with objects information"""
+ normalisation = gl.GL_TRUE if self.normalisation else gl.GL_FALSE
+ with self.vbo:
+ gl.glVertexAttribPointer(attribute,
+ self.dimension,
+ self.type_,
+ normalisation,
+ self.stride,
+ c_void_p(self.offset))
+
+ def copy(self):
+ return VertexBufferAttrib(self.vbo,
+ self.type_,
+ self.size,
+ self.dimension,
+ self.offset,
+ self.stride,
+ self.normalisation)
+
+
+def vertexBuffer(arrays, prefix=None, suffix=None, usage=None):
+ """Create a single vertex buffer from multiple 1D or 2D numpy arrays.
+
+ It is possible to reserve memory before and after each array in the VBO
+
+ :param arrays: Arrays of data to store
+ :type arrays: Iterable of numpy.ndarray
+ :param prefix: If given, number of elements to reserve before each array
+ :type prefix: Iterable of int or None
+ :param suffix: If given, number of elements to reserve after each array
+ :type suffix: Iterable of int or None
+ :param int usage: vertex buffer expected usage or None for default
+ :returns: List of VertexBufferAttrib objects sharing the same vertex buffer
+ """
+ info = []
+ vbosize = 0
+
+ if prefix is None:
+ prefix = (0,) * len(arrays)
+ if suffix is None:
+ suffix = (0,) * len(arrays)
+
+ for data, pre, post in zip(arrays, prefix, suffix):
+ data = numpy.array(data, copy=False, order='C')
+ shape = data.shape
+ assert len(shape) <= 2
+ type_ = numpyToGLType(data.dtype)
+ size = shape[0] + pre + post
+ dimension = 1 if len(shape) == 1 else shape[1]
+ sizeinbytes = size * dimension * sizeofGLType(type_)
+ sizeinbytes = 4 * ((sizeinbytes + 3) >> 2) # 4 bytes alignment
+ copyoffset = vbosize + pre * dimension * sizeofGLType(type_)
+ info.append((data, type_, size, dimension,
+ vbosize, sizeinbytes, copyoffset))
+ vbosize += sizeinbytes
+
+ vbo = VertexBuffer(size=vbosize, usage=usage)
+
+ result = []
+ for data, type_, size, dimension, offset, sizeinbytes, copyoffset in info:
+ copysize = data.shape[0] * dimension * sizeofGLType(type_)
+ vbo.update(data, offset=copyoffset, size=copysize)
+ result.append(
+ VertexBufferAttrib(vbo, type_, size, dimension, offset, 0))
+ return result
diff --git a/silx/gui/_glutils/__init__.py b/silx/gui/_glutils/__init__.py
new file mode 100644
index 0000000..e86a58f
--- /dev/null
+++ b/silx/gui/_glutils/__init__.py
@@ -0,0 +1,41 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This package provides utility functions to handle OpenGL resources.
+
+The :mod:`gl` module provides a wrapper to OpenGL based on PyOpenGL.
+"""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "25/07/2016"
+
+
+# OpenGL convenient functions
+from .Context import getGLContext, setGLContextGetter # noqa
+from .FramebufferTexture import FramebufferTexture # noqa
+from .Program import Program # noqa
+from .Texture import Texture # noqa
+from .VertexBuffer import VertexBuffer, VertexBufferAttrib, vertexBuffer # noqa
+from .utils import sizeofGLType, isSupportedGLType, numpyToGLType # noqa
diff --git a/silx/gui/_glutils/font.py b/silx/gui/_glutils/font.py
new file mode 100644
index 0000000..566ae49
--- /dev/null
+++ b/silx/gui/_glutils/font.py
@@ -0,0 +1,152 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Text rasterisation feature leveraging Qt font and text layout support."""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "13/10/2016"
+
+
+import logging
+import sys
+import numpy
+from .. import qt
+from .._utils import convertQImageToArray
+
+
+_logger = logging.getLogger(__name__)
+
+
+def getDefaultFontFamily():
+ """Returns the default font family of the application"""
+ return qt.QApplication.instance().font().family()
+
+
+# Font weights
+ULTRA_LIGHT = 0
+"""Lightest characters: Minimum font weight"""
+
+LIGHT = 25
+"""Light characters"""
+
+NORMAL = 50
+"""Normal characters"""
+
+SEMI_BOLD = 63
+"""Between normal and bold characters"""
+
+BOLD = 74
+"""Thicker characters"""
+
+BLACK = 87
+"""Really thick characters"""
+
+ULTRA_BLACK = 99
+"""Thickest characters: Maximum font weight"""
+
+
+def rasterText(text, font,
+ size=-1,
+ weight=-1,
+ italic=False,
+ devicePixelRatio=1.0):
+ """Raster text using Qt.
+
+ It supports multiple lines.
+
+ :param str text: The text to raster
+ :param font: Font name or QFont to use
+ :type font: str or :class:`QFont`
+ :param int size:
+ Font size in points
+ Used only if font is given as name.
+ :param int weight:
+ Font weight in [0, 99], see QFont.Weight.
+ Used only if font is given as name.
+ :param bool italic:
+ True for italic font (default: False).
+ Used only if font is given as name.
+ :param float devicePixelRatio:
+ The current ratio between device and device-independent pixel
+ (default: 1.0)
+ :return: Corresponding image in gray scale and baseline offset from top
+ :rtype: (HxW numpy.ndarray of uint8, int)
+ """
+ if not text:
+ _logger.info("Trying to raster empty text, replaced by white space")
+ text = ' ' # Replace empty text by white space to produce an image
+
+ if not isinstance(font, qt.QFont):
+ font = qt.QFont(font, size, weight, italic)
+
+ metrics = qt.QFontMetrics(font)
+ size = metrics.size(qt.Qt.TextExpandTabs, text)
+ bounds = metrics.boundingRect(
+ qt.QRect(0, 0, size.width(), size.height()),
+ qt.Qt.TextExpandTabs,
+ text)
+
+ if (devicePixelRatio != 1.0 and
+ not hasattr(qt.QImage, 'setDevicePixelRatio')): # Qt 4
+ _logger.error('devicePixelRatio not supported')
+ devicePixelRatio = 1.0
+
+ # Add extra border and handle devicePixelRatio
+ width = bounds.width() * devicePixelRatio + 2
+ # align line size to 32 bits to ease conversion to numpy array
+ width = 4 * ((width + 3) // 4)
+ image = qt.QImage(width,
+ bounds.height() * devicePixelRatio,
+ qt.QImage.Format_RGB888)
+ if (devicePixelRatio != 1.0 and
+ hasattr(image, 'setDevicePixelRatio')): # Qt 5
+ image.setDevicePixelRatio(devicePixelRatio)
+
+ # TODO if Qt5 use Format_Grayscale8 instead
+ image.fill(0)
+
+ # Raster text
+ painter = qt.QPainter()
+ painter.begin(image)
+ painter.setPen(qt.Qt.white)
+ painter.setFont(font)
+ painter.drawText(bounds, qt.Qt.TextExpandTabs, text)
+ painter.end()
+
+ array = convertQImageToArray(image)
+
+ # RGB to R
+ array = numpy.ascontiguousarray(array[:, :, 0])
+
+ # Remove leading and trailing empty columns but one on each side
+ column_cumsum = numpy.cumsum(numpy.sum(array, axis=0))
+ array = array[:, column_cumsum.argmin():column_cumsum.argmax() + 2]
+
+ # Remove leading and trailing empty rows but one on each side
+ row_cumsum = numpy.cumsum(numpy.sum(array, axis=1))
+ min_row = row_cumsum.argmin()
+ array = array[min_row:row_cumsum.argmax() + 2, :]
+
+ return array, metrics.ascent() - min_row
diff --git a/silx/gui/_glutils/gl.py b/silx/gui/_glutils/gl.py
new file mode 100644
index 0000000..4b9a7bb
--- /dev/null
+++ b/silx/gui/_glutils/gl.py
@@ -0,0 +1,165 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module loads PyOpenGL and provides a namespace for OpenGL."""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "25/07/2016"
+
+
+from contextlib import contextmanager as _contextmanager
+from ctypes import c_uint
+import logging
+
+_logger = logging.getLogger(__name__)
+
+import OpenGL
+# Set the following to true for debugging
+if _logger.getEffectiveLevel() <= logging.DEBUG:
+ _logger.debug('Enabling PyOpenGL debug flags')
+ OpenGL.ERROR_LOGGING = True
+ OpenGL.ERROR_CHECKING = True
+ OpenGL.ERROR_ON_COPY = True
+else:
+ OpenGL.ERROR_LOGGING = False
+ OpenGL.ERROR_CHECKING = False
+ OpenGL.ERROR_ON_COPY = False
+
+import OpenGL.GL as _GL
+from OpenGL.GL import * # noqa
+
+# Extentions core in OpenGL 3
+from OpenGL.GL.ARB import framebuffer_object as _FBO
+from OpenGL.GL.ARB.framebuffer_object import * # noqa
+from OpenGL.GL.ARB.texture_rg import GL_R32F, GL_R16F # noqa
+from OpenGL.GL.ARB.texture_rg import GL_R16, GL_R8 # noqa
+
+# PyOpenGL 3.0.1 does not define it
+try:
+ GLchar
+except NameError:
+ from ctypes import c_char
+ GLchar = c_char
+
+
+def testGL():
+ """Test if required OpenGL version and extensions are available.
+
+ This MUST be run with an active OpenGL context.
+ """
+ version = glGetString(GL_VERSION).split()[0] # get version number
+ major, minor = int(version[0]), int(version[2])
+ if major < 2 or (major == 2 and minor < 1):
+ raise RuntimeError(
+ "Requires at least OpenGL version 2.1, running with %s" % version)
+
+ from OpenGL.GL.ARB.framebuffer_object import glInitFramebufferObjectARB
+ from OpenGL.GL.ARB.texture_rg import glInitTextureRgARB
+
+ if not glInitFramebufferObjectARB():
+ raise RuntimeError(
+ "OpenGL GL_ARB_framebuffer_object extension required !")
+
+ if not glInitTextureRgARB():
+ raise RuntimeError("OpenGL GL_ARB_texture_rg extension required !")
+
+
+# Additional setup
+if hasattr(glget, 'addGLGetConstant'):
+ glget.addGLGetConstant(GL_FRAMEBUFFER_BINDING, (1,))
+
+
+@_contextmanager
+def enabled(capacity, enable=True):
+ """Context manager enabling an OpenGL capacity.
+
+ This is not checking the current state of the capacity.
+
+ :param capacity: The OpenGL capacity enum to enable/disable
+ :param bool enable:
+ True (default) to enable during context, False to disable
+ """
+ if enable:
+ glEnable(capacity)
+ yield
+ glDisable(capacity)
+ else:
+ glDisable(capacity)
+ yield
+ glEnable(capacity)
+
+
+def disabled(capacity, disable=True):
+ """Context manager disabling an OpenGL capacity.
+
+ This is not checking the current state of the capacity.
+
+ :param capacity: The OpenGL capacity enum to disable/enable
+ :param bool disable:
+ True (default) to disable during context, False to enable
+ """
+ return enabled(capacity, not disable)
+
+
+# Additional OpenGL wrapping
+
+def glGetActiveAttrib(program, index):
+ """Wrap PyOpenGL glGetActiveAttrib"""
+ bufsize = glGetProgramiv(program, GL_ACTIVE_ATTRIBUTE_MAX_LENGTH)
+ length = GLsizei()
+ size = GLint()
+ type_ = GLenum()
+ name = (GLchar * bufsize)()
+
+ _GL.glGetActiveAttrib(program, index, bufsize, length, size, type_, name)
+ return name.value, size.value, type_.value
+
+
+def glDeleteRenderbuffers(buffers):
+ if not hasattr(buffers, '__len__'): # Support single int argument
+ buffers = [buffers]
+ length = len(buffers)
+ _FBO.glDeleteRenderbuffers(length, (c_uint * length)(*buffers))
+
+
+def glDeleteFramebuffers(buffers):
+ if not hasattr(buffers, '__len__'): # Support single int argument
+ buffers = [buffers]
+ length = len(buffers)
+ _FBO.glDeleteFramebuffers(length, (c_uint * length)(*buffers))
+
+
+def glDeleteBuffers(buffers):
+ if not hasattr(buffers, '__len__'): # Support single int argument
+ buffers = [buffers]
+ length = len(buffers)
+ _GL.glDeleteBuffers(length, (c_uint * length)(*buffers))
+
+
+def glDeleteTextures(textures):
+ if not hasattr(textures, '__len__'): # Support single int argument
+ textures = [textures]
+ length = len(textures)
+ _GL.glDeleteTextures((c_uint * length)(*textures))
diff --git a/silx/gui/_glutils/utils.py b/silx/gui/_glutils/utils.py
new file mode 100644
index 0000000..73af338
--- /dev/null
+++ b/silx/gui/_glutils/utils.py
@@ -0,0 +1,70 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2014-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides conversion functions between OpenGL and numpy types.
+"""
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "10/01/2017"
+
+from . import gl
+import numpy
+
+
+_GL_TYPE_SIZES = {
+ gl.GL_FLOAT: 4,
+ gl.GL_BYTE: 1,
+ gl.GL_SHORT: 2,
+ gl.GL_INT: 4,
+ gl.GL_UNSIGNED_BYTE: 1,
+ gl.GL_UNSIGNED_SHORT: 2,
+ gl.GL_UNSIGNED_INT: 4,
+}
+
+
+def sizeofGLType(type_):
+ """Returns the size in bytes of an element of type `type_`"""
+ return _GL_TYPE_SIZES[type_]
+
+
+_TYPE_CONVERTER = {
+ numpy.dtype(numpy.float32): gl.GL_FLOAT,
+ numpy.dtype(numpy.int8): gl.GL_BYTE,
+ numpy.dtype(numpy.int16): gl.GL_SHORT,
+ numpy.dtype(numpy.int32): gl.GL_INT,
+ numpy.dtype(numpy.uint8): gl.GL_UNSIGNED_BYTE,
+ numpy.dtype(numpy.uint16): gl.GL_UNSIGNED_SHORT,
+ numpy.dtype(numpy.uint32): gl.GL_UNSIGNED_INT,
+}
+
+
+def isSupportedGLType(type_):
+ """Test if a numpy type or dtype can be converted to a GL type."""
+ return numpy.dtype(type_) in _TYPE_CONVERTER
+
+
+def numpyToGLType(type_):
+ """Returns the GL type corresponding the provided numpy type or dtype."""
+ return _TYPE_CONVERTER[numpy.dtype(type_)]
diff --git a/silx/gui/_utils.py b/silx/gui/_utils.py
new file mode 100644
index 0000000..e29141f
--- /dev/null
+++ b/silx/gui/_utils.py
@@ -0,0 +1,102 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides convenient functions to use with Qt objects.
+
+It provides conversion between numpy and QImage.
+"""
+
+from __future__ import division
+
+
+__authors__ = ["T. Vincent"]
+__license__ = "MIT"
+__date__ = "16/01/2017"
+
+
+import sys
+import numpy
+
+from . import qt
+
+
+def convertArrayToQImage(image):
+ """Convert an array-like RGB888 image to a QImage.
+
+ The created QImage is using a copy of the array data.
+
+ Limitation: Only supports RGB888 format.
+
+ :param image: Array-like image data
+ :type image: numpy.ndarray of uint8 of dimension HxWx3
+ :return: Corresponding Qt image
+ :rtype: QImage
+ """
+ # Possible extension: add a format argument to support more formats
+
+ image = numpy.array(image, copy=False, order='C', dtype=numpy.uint8)
+
+ height, width, depth = image.shape
+ assert depth == 3
+
+ qimage = qt.QImage(
+ image.data,
+ width,
+ height,
+ image.strides[0], # bytesPerLine
+ qt.QImage.Format_RGB888)
+
+ return qimage.copy() # Making a copy of the image and its data
+
+
+def convertQImageToArray(image):
+ """Convert a RGB888 QImage to a numpy array.
+
+ Limitation: Only supports RGB888 format.
+ If QImage is not RGB888 it gets converted to this format.
+
+ :param QImage: The QImage to convert.
+ :return: The image array
+ :rtype: numpy.ndarray of uint8 of shape HxWx3
+ """
+ # Possible extension: avoid conversion to support more formats
+
+ if image.format() != qt.QImage.Format_RGB888:
+ # Convert to RGB888 if needed
+ image = image.convertToFormat(qt.QImage.Format_RGB888)
+
+ ptr = image.bits()
+ if qt.BINDING != 'PySide':
+ ptr.setsize(image.byteCount())
+ if qt.BINDING == 'PyQt4' and sys.version_info[0] == 2:
+ ptr = ptr.asstring()
+ elif sys.version_info[0] == 3: # PySide with Python3
+ ptr = ptr.tobytes()
+
+ array = numpy.fromstring(ptr, dtype=numpy.uint8)
+
+ # Lines are 32 bits aligned: remove padding bytes
+ array = array.reshape(image.height(), -1)[:, :image.width() * 3]
+ array.shape = image.height(), image.width(), 3
+ return array
diff --git a/silx/gui/console.py b/silx/gui/console.py
new file mode 100644
index 0000000..13760b4
--- /dev/null
+++ b/silx/gui/console.py
@@ -0,0 +1,214 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module provides an IPython console widget.
+
+You can push variables - any python object - to the
+console's interactive namespace. This provides users with an advanced way
+of interacting with your program. For instance, if your program has a
+:class:`PlotWidget` or a :class:`PlotWindow`, you can push a reference to
+these widgets to allow your users to add curves, save data to files… by using
+the widgets' methods from the console.
+
+.. note::
+
+ This module has a dependency on
+ `IPython <https://pypi.python.org/pypi/ipython>`_ and
+ `qtconsole <https://pypi.python.org/pypi/qtconsole>`_ (or *ipython.qt* for
+ older versions of *IPython*). An ``ImportError`` will be raised if it is
+ imported while the dependencies are not satisfied.
+
+Basic usage example::
+
+ from silx.gui import qt
+ from silx.gui.console import IPythonWidget
+
+ app = qt.QApplication([])
+
+ hello_button = qt.QPushButton("Hello World!", None)
+ hello_button.show()
+
+ console = IPythonWidget()
+ console.show()
+ console.pushVariables({"the_button": hello_button})
+
+ app.exec_()
+
+This program will display a console widget and a push button in two separate
+windows. You will be able to interact with the button from the console,
+for example change its text::
+
+ >>> the_button.setText("Spam spam")
+
+An IPython interactive console is a powerful tool that enables you to work
+with data and plot it.
+See `this tutorial <https://plot.ly/python/ipython-notebook-tutorial/>`_
+for more information on some of the rich features of IPython.
+"""
+__authors__ = ["Tim Rae", "V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "24/05/2016"
+
+import logging
+
+from . import qt
+
+_logger = logging.getLogger(__name__)
+
+try:
+ import IPython
+except ImportError as e:
+ raise ImportError("Failed to import IPython, required by " + __name__)
+
+# This widget cannot be used inside an interactive IPython shell.
+# It would raise MultipleInstanceError("Multiple incompatible subclass
+# instances of InProcessInteractiveShell are being created").
+try:
+ __IPYTHON__
+except NameError:
+ pass # Not in IPython
+else:
+ msg = "Module " + __name__ + " cannot be used within an IPython shell"
+ raise ImportError(msg)
+
+# qtconsole is a separate module in recent versions of IPython/Jupyter
+# http://blog.jupyter.org/2015/04/15/the-big-split/
+if IPython.__version__.startswith("2"):
+ qtconsole = None
+else:
+ try:
+ import qtconsole
+ except ImportError:
+ qtconsole = None
+
+if qtconsole is not None:
+ try:
+ from qtconsole.rich_ipython_widget import RichJupyterWidget as \
+ RichIPythonWidget
+ except ImportError:
+ try:
+ from qtconsole.rich_ipython_widget import RichIPythonWidget
+ except ImportError as e:
+ qtconsole = None
+ else:
+ from qtconsole.inprocess import QtInProcessKernelManager
+ else:
+ from qtconsole.inprocess import QtInProcessKernelManager
+
+
+if qtconsole is None:
+ # Import the console machinery from ipython
+
+ # The `has_binding` test of IPython does not find the Qt bindings
+ # in case silx is used in a frozen binary
+ import IPython.external.qt_loaders
+
+ def has_binding(*var, **kw):
+ return True
+
+ IPython.external.qt_loaders.has_binding = has_binding
+
+ from IPython.qt.console.rich_ipython_widget import RichIPythonWidget
+ from IPython.qt.inprocess import QtInProcessKernelManager
+
+
+class IPythonWidget(RichIPythonWidget):
+ """Live IPython console widget.
+
+ :param custom_banner: Custom welcome message to be printed at the top of
+ the console.
+ """
+
+ def __init__(self, parent=None, custom_banner=None, *args, **kwargs):
+ if parent is not None:
+ kwargs["parent"] = parent
+ super(IPythonWidget, self).__init__(*args, **kwargs)
+ if custom_banner is not None:
+ self.banner = custom_banner
+ self.setWindowTitle(self.banner)
+ self.kernel_manager = kernel_manager = QtInProcessKernelManager()
+ kernel_manager.start_kernel()
+ self.kernel_client = kernel_client = self._kernel_manager.client()
+ kernel_client.start_channels()
+
+ def stop():
+ kernel_client.stop_channels()
+ kernel_manager.shutdown_kernel()
+ self.exit_requested.connect(stop)
+
+ def sizeHint(self):
+ """Return a reasonable default size for usage in :class:`PlotWindow`"""
+ return qt.QSize(500, 300)
+
+ def pushVariables(self, variable_dict):
+ """ Given a dictionary containing name / value pairs, push those
+ variables to the IPython console widget.
+
+ :param variable_dict: Dictionary of variables to be pushed to the
+ console's interactive namespace (```{variable_name: object, …}```)
+ """
+ self.kernel_manager.kernel.shell.push(variable_dict)
+
+
+class IPythonDockWidget(qt.QDockWidget):
+ """Dock Widget including a :class:`IPythonWidget` inside
+ a vertical layout.
+
+ :param available_vars: Dictionary of variables to be pushed to the
+ console's interactive namespace: ``{"variable_name": object, …}``
+ :param custom_banner: Custom welcome message to be printed at the top of
+ the console
+ :param title: Dock widget title
+ :param parent: Parent :class:`qt.QMainWindow` containing this
+ :class:`qt.QDockWidget`
+ """
+ def __init__(self, parent=None, available_vars=None, custom_banner=None,
+ title="Console"):
+ super(IPythonDockWidget, self).__init__(title, parent)
+
+ self.ipyconsole = IPythonWidget(custom_banner=custom_banner)
+
+ self.layout().setContentsMargins(0, 0, 0, 0)
+ self.setWidget(self.ipyconsole)
+
+ if available_vars is not None:
+ self.ipyconsole.pushVariables(available_vars)
+
+ def showEvent(self, event):
+ """Make sure this widget is raised when it is shown
+ (when it is first created as a tab in PlotWindow or when it is shown
+ again after hiding).
+ """
+ self.raise_()
+
+
+def main():
+ """Run a Qt app with an IPython console"""
+ app = qt.QApplication([])
+ widget = IPythonDockWidget()
+ widget.show()
+ app.exec_()
+
+if __name__ == '__main__':
+ main()
diff --git a/silx/gui/data/ArrayTableModel.py b/silx/gui/data/ArrayTableModel.py
new file mode 100644
index 0000000..87a2fc1
--- /dev/null
+++ b/silx/gui/data/ArrayTableModel.py
@@ -0,0 +1,610 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""
+This module defines a data model for displaying and editing arrays of any
+number of dimensions in a table view.
+"""
+from __future__ import division
+import numpy
+import logging
+from silx.gui import qt
+from silx.gui.data.TextFormatter import TextFormatter
+
+__authors__ = ["V.A. Sole"]
+__license__ = "MIT"
+__date__ = "24/01/2017"
+
+
+_logger = logging.getLogger(__name__)
+
+
+def _is_array(data):
+ """Return True if object implements all necessary attributes to be used
+ as a numpy array.
+
+ :param object data: Array-like object (numpy array, h5py dataset...)
+ :return: boolean
+ """
+ # add more required attribute if necessary
+ for attr in ("shape", "dtype"):
+ if not hasattr(data, attr):
+ return False
+ return True
+
+
+class ArrayTableModel(qt.QAbstractTableModel):
+ """This data model provides access to 2D slices in a N-dimensional
+ array.
+
+ A slice for a 3-D array is characterized by a perspective (the number of
+ the axis orthogonal to the slice) and an index at which the slice
+ intersects the orthogonal axis.
+
+ In the n-D case, only slices parallel to the last two axes are handled. A
+ slice is therefore characterized by a list of indices locating the
+ slice on all the :math:`n - 2` orthogonal axes.
+
+ :param parent: Parent QObject
+ :param data: Numpy array, or object implementing a similar interface
+ (e.g. h5py dataset)
+ :param str fmt: Format string for representing numerical values.
+ Default is ``"%g"``.
+ :param sequence[int] perspective: See documentation
+ of :meth:`setPerspective`.
+ """
+ def __init__(self, parent=None, data=None, perspective=None):
+ qt.QAbstractTableModel.__init__(self, parent)
+
+ self._array = None
+ """n-dimensional numpy array"""
+
+ self._bgcolors = None
+ """(n+1)-dimensional numpy array containing RGB(A) color data
+ for the background color
+ """
+
+ self._fgcolors = None
+ """(n+1)-dimensional numpy array containing RGB(A) color data
+ for the foreground color
+ """
+
+ self._formatter = None
+ """Formatter for text representation of data"""
+
+ formatter = TextFormatter(self)
+ formatter.setUseQuoteForText(False)
+ self.setFormatter(formatter)
+
+ self._index = None
+ """This attribute stores the slice index, as a list of indices
+ where the frame intersects orthogonal axis."""
+
+ self._perspective = None
+ """Sequence of dimensions orthogonal to the frame to be viewed.
+ For an array with ``n`` dimensions, this is a sequence of ``n-2``
+ integers. the first dimension is numbered ``0``.
+ By default, the data frames use the last two dimensions as their axes
+ and therefore the perspective is a sequence of the first ``n-2``
+ dimensions.
+ For example, for a 5-D array, the default perspective is ``(0, 1, 2)``
+ and the default frames axes are ``(3, 4)``."""
+
+ # set _data and _perspective
+ self.setArrayData(data, perspective=perspective)
+
+ def _getRowDim(self):
+ """The row axis is the first axis parallel to the frames
+ (lowest dimension number)
+
+ Return None for 0-D (scalar) or 1-D arrays
+ """
+ n_dimensions = len(self._array.shape)
+ if n_dimensions < 2:
+ # scalar or 1D array: no row index
+ return None
+ # take all dimensions and remove the orthogonal ones
+ frame_axes = set(range(0, n_dimensions)) - set(self._perspective)
+ # sanity check
+ assert len(frame_axes) == 2
+ return min(frame_axes)
+
+ def _getColumnDim(self):
+ """The column axis is the second (highest dimension) axis parallel
+ to the frames
+
+ Return None for 0-D (scalar)
+ """
+ n_dimensions = len(self._array.shape)
+ if n_dimensions < 1:
+ # scalar: no column index
+ return None
+ frame_axes = set(range(0, n_dimensions)) - set(self._perspective)
+ # sanity check
+ assert (len(frame_axes) == 2) if n_dimensions > 1 else (len(frame_axes) == 1)
+ return max(frame_axes)
+
+ def _getIndexTuple(self, table_row, table_col):
+ """Return the n-dimensional index of a value in the original array,
+ based on its row and column indices in the table view
+
+ :param table_row: Row index (0-based) of a table cell
+ :param table_col: Column index (0-based) of a table cell
+ :return: Tuple of indices of the element in the numpy array
+ """
+ row_dim = self._getRowDim()
+ col_dim = self._getColumnDim()
+
+ # get indices on all orthogonal axes
+ selection = list(self._index)
+ # insert indices on parallel axes
+ if row_dim is not None:
+ selection.insert(row_dim, table_row)
+ if col_dim is not None:
+ selection.insert(col_dim, table_col)
+ return tuple(selection)
+
+ # Methods to be implemented to subclass QAbstractTableModel
+ def rowCount(self, parent_idx=None):
+ """QAbstractTableModel method
+ Return number of rows to be displayed in table"""
+ row_dim = self._getRowDim()
+ if row_dim is None:
+ # 0-D and 1-D arrays
+ return 1
+ return self._array.shape[row_dim]
+
+ def columnCount(self, parent_idx=None):
+ """QAbstractTableModel method
+ Return number of columns to be displayed in table"""
+ col_dim = self._getColumnDim()
+ if col_dim is None:
+ # 0-D array
+ return 1
+ return self._array.shape[col_dim]
+
+ def data(self, index, role=qt.Qt.DisplayRole):
+ """QAbstractTableModel method to access data values
+ in the format ready to be displayed"""
+ if index.isValid():
+ selection = self._getIndexTuple(index.row(),
+ index.column())
+ if role == qt.Qt.DisplayRole:
+ return self._formatter.toString(self._array[selection])
+
+ if role == qt.Qt.BackgroundRole and self._bgcolors is not None:
+ r, g, b = self._bgcolors[selection][0:3]
+ if self._bgcolors.shape[-1] == 3:
+ return qt.QColor(r, g, b)
+ if self._bgcolors.shape[-1] == 4:
+ a = self._bgcolors[selection][3]
+ return qt.QColor(r, g, b, a)
+
+ if role == qt.Qt.ForegroundRole:
+ if self._fgcolors is not None:
+ r, g, b = self._fgcolors[selection][0:3]
+ if self._fgcolors.shape[-1] == 3:
+ return qt.QColor(r, g, b)
+ if self._fgcolors.shape[-1] == 4:
+ a = self._fgcolors[selection][3]
+ return qt.QColor(r, g, b, a)
+
+ # no fg color given, use black or white
+ # based on luminosity threshold
+ elif self._bgcolors is not None:
+ r, g, b = self._bgcolors[selection][0:3]
+ lum = 0.21 * r + 0.72 * g + 0.07 * b
+ if lum < 128:
+ return qt.QColor(qt.Qt.white)
+ else:
+ return qt.QColor(qt.Qt.black)
+
+ def headerData(self, section, orientation, role=qt.Qt.DisplayRole):
+ """QAbstractTableModel method
+ Return the 0-based row or column index, for display in the
+ horizontal and vertical headers"""
+ if role == qt.Qt.DisplayRole:
+ if orientation == qt.Qt.Vertical:
+ return "%d" % section
+ if orientation == qt.Qt.Horizontal:
+ return "%d" % section
+ return None
+
+ def flags(self, index):
+ """QAbstractTableModel method to inform the view whether data
+ is editable or not."""
+ if not self._editable:
+ return qt.QAbstractTableModel.flags(self, index)
+ return qt.QAbstractTableModel.flags(self, index) | qt.Qt.ItemIsEditable
+
+ def setData(self, index, value, role=None):
+ """QAbstractTableModel method to handle editing data.
+ Cast the new value into the same format as the array before editing
+ the array value."""
+ if index.isValid() and role == qt.Qt.EditRole:
+ try:
+ # cast value to same type as array
+ v = numpy.asscalar(
+ numpy.array(value, dtype=self._array.dtype))
+ except ValueError:
+ return False
+
+ selection = self._getIndexTuple(index.row(),
+ index.column())
+ self._array[selection] = v
+ self.dataChanged.emit(index, index)
+ return True
+ else:
+ return False
+
+ # Public methods
+ def setArrayData(self, data, copy=True,
+ perspective=None, editable=False):
+ """Set the data array and the viewing perspective.
+
+ You can set ``copy=False`` if you need more performances, when dealing
+ with a large numpy array. In this case, a simple reference to the data
+ is used to access the data, rather than a copy of the array.
+
+ .. warning::
+
+ Any change to the data model will affect your original data
+ array, when using a reference rather than a copy..
+
+ :param data: n-dimensional numpy array, or any object that can be
+ converted to a numpy array using ``numpy.array(data)`` (e.g.
+ a nested sequence).
+ :param bool copy: If *True* (default), a copy of the array is stored
+ and the original array is not modified if the table is edited.
+ If *False*, then the behavior depends on the data type:
+ if possible (if the original array is a proper numpy array)
+ a reference to the original array is used.
+ :param perspective: See documentation of :meth:`setPerspective`.
+ If None, the default perspective is the list of the first ``n-2``
+ dimensions, to view frames parallel to the last two axes.
+ :param bool editable: Flag to enable editing data. Default *False*.
+ """
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+ else:
+ self.reset()
+
+ if data is None:
+ # empty array
+ self._array = numpy.array([])
+ elif copy:
+ # copy requested (default)
+ self._array = numpy.array(data, copy=True)
+ elif not _is_array(data):
+ raise TypeError("data is not a proper array. Try setting" +
+ " copy=True to convert it into a numpy array" +
+ " (this will cause the data to be copied!)")
+ # # copy not requested, but necessary
+ # _logger.warning(
+ # "data is not an array-like object. " +
+ # "Data must be copied.")
+ # self._array = numpy.array(data, copy=True)
+ else:
+ # Copy explicitly disabled & data implements required attributes.
+ # We can use a reference.
+ self._array = data
+
+ # reset colors to None if new data shape is inconsistent
+ valid_color_shapes = (self._array.shape + (3,),
+ self._array.shape + (4,))
+ if self._bgcolors is not None:
+ if self._bgcolors.shape not in valid_color_shapes:
+ self._bgcolors = None
+ if self._fgcolors is not None:
+ if self._fgcolors.shape not in valid_color_shapes:
+ self._fgcolors = None
+
+ self.setEditable(editable)
+
+ self._index = [0 for _i in range((len(self._array.shape) - 2))]
+ self._perspective = tuple(perspective) if perspective is not None else\
+ tuple(range(0, len(self._array.shape) - 2))
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+
+ def setArrayColors(self, bgcolors=None, fgcolors=None):
+ """Set the colors for all table cells by passing an array
+ of RGB or RGBA values (integers between 0 and 255).
+
+ The shape of the colors array must be consistent with the data shape.
+
+ If the data array is n-dimensional, the colors array must be
+ (n+1)-dimensional, with the first n-dimensions identical to the data
+ array dimensions, and the last dimension length-3 (RGB) or
+ length-4 (RGBA).
+
+ :param bgcolors: RGB or RGBA colors array, defining the background color
+ for each cell in the table.
+ :param fgcolors: RGB or RGBA colors array, defining the foreground color
+ (text color) for each cell in the table.
+ """
+ # array must be RGB or RGBA
+ valid_shapes = (self._array.shape + (3,), self._array.shape + (4,))
+ errmsg = "Inconsistent shape for color array, should be %s or %s" % valid_shapes
+
+ if bgcolors is not None:
+ if not _is_array(bgcolors):
+ bgcolors = numpy.array(bgcolors)
+ assert bgcolors.shape in valid_shapes, errmsg
+
+ self._bgcolors = bgcolors
+
+ if fgcolors is not None:
+ if not _is_array(fgcolors):
+ fgcolors = numpy.array(fgcolors)
+ assert fgcolors.shape in valid_shapes, errmsg
+
+ self._fgcolors = fgcolors
+
+ def setEditable(self, editable):
+ """Set flags to make the data editable.
+
+ .. warning::
+
+ If the data is a reference to a h5py dataset open in read-only
+ mode, setting *editable=True* will fail and print a warning.
+
+ .. warning::
+
+ Making the data editable means that the underlying data structure
+ in this data model will be modified.
+ If the data is a reference to a public object (open with
+ ``copy=False``), this could have side effects. If it is a
+ reference to an HDF5 dataset, this means the file will be
+ modified.
+
+ :param bool editable: Flag to enable editing data.
+ :return: True if setting desired flag succeeded, False if it failed.
+ """
+ self._editable = editable
+ if hasattr(self._array, "file"):
+ if hasattr(self._array.file, "mode"):
+ if editable and self._array.file.mode == "r":
+ _logger.warning(
+ "Data is a HDF5 dataset open in read-only " +
+ "mode. Editing must be disabled.")
+ self._editable = False
+ return False
+ return True
+
+ def getData(self, copy=True):
+ """Return a copy of the data array, or a reference to it
+ if *copy=False* is passed as parameter.
+
+ In case the shape was modified, to convert 0-D or 1-D data
+ into 2-D data, the original shape is restored in the returned data.
+
+ :param bool copy: If *True* (default), return a copy of the data. If
+ *False*, return a reference.
+ :return: numpy array of data, or reference to original data object
+ if *copy=False*
+ """
+ data = self._array if not copy else numpy.array(self._array, copy=True)
+ return data
+
+ def setFrameIndex(self, index):
+ """Set the active slice index.
+
+ This method is only relevant to arrays with at least 3 dimensions.
+
+ :param index: Index of the active slice in the array.
+ In the general n-D case, this is a sequence of :math:`n - 2`
+ indices where the slice intersects the respective orthogonal axes.
+ :raise IndexError: If any index in the index sequence is out of bound
+ on its respective axis.
+ """
+ shape = self._array.shape
+ if len(shape) < 3:
+ # index is ignored
+ return
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+ else:
+ self.reset()
+
+ if len(shape) == 3:
+ len_ = shape[self._perspective[0]]
+ # accept integers as index in the case of 3-D arrays
+ if not hasattr(index, "__len__"):
+ self._index = [index]
+ else:
+ self._index = index
+ if not 0 <= self._index[0] < len_:
+ raise ValueError("Index must be a positive integer " +
+ "lower than %d" % len_)
+ else:
+ # general n-D case
+ for i_, idx in enumerate(index):
+ if not 0 <= idx < shape[self._perspective[i_]]:
+ raise IndexError("Invalid index %d " % idx +
+ "not in range 0-%d" % (shape[i_] - 1))
+ self._index = index
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+
+ def setFormatter(self, formatter):
+ """Set the formatter object to be used to display data from the model
+
+ :param TextFormatter formatter: Formatter to use
+ """
+ if formatter is self._formatter:
+ return
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+
+ if self._formatter is not None:
+ self._formatter.formatChanged.disconnect(self.__formatChanged)
+
+ self._formatter = formatter
+ if self._formatter is not None:
+ self._formatter.formatChanged.connect(self.__formatChanged)
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+ else:
+ self.reset()
+
+ def getFormatter(self):
+ """Returns the text formatter used.
+
+ :rtype: TextFormatter
+ """
+ return self._formatter
+
+ def __formatChanged(self):
+ """Called when the format changed.
+ """
+ self.reset()
+
+ def setPerspective(self, perspective):
+ """Set the perspective by defining a sequence listing all axes
+ orthogonal to the frame or 2-D slice to be visualized.
+
+ Alternatively, you can use :meth:`setFrameAxes` for the complementary
+ approach of specifying the two axes parallel to the frame.
+
+ In the 1-D or 2-D case, this parameter is irrelevant.
+
+ In the 3-D case, if the unit vectors describing
+ your axes are :math:`\vec{x}, \vec{y}, \vec{z}`, a perspective of 0
+ means you slices are parallel to :math:`\vec{y}\vec{z}`, 1 means they
+ are parallel to :math:`\vec{x}\vec{z}` and 2 means they
+ are parallel to :math:`\vec{x}\vec{y}`.
+
+ In the n-D case, this parameter is a sequence of :math:`n-2` axes
+ numbers.
+ For instance if you want to display 2-D frames whose axes are the
+ second and third dimensions of a 5-D array, set the perspective to
+ ``(0, 3, 4)``.
+
+ :param perspective: Sequence of dimensions/axes orthogonal to the
+ frames.
+ :raise: IndexError if any value in perspective is higher than the
+ number of dimensions minus one (first dimension is 0), or
+ if the number of values is different from the number of dimensions
+ minus two.
+ """
+ n_dimensions = len(self._array.shape)
+ if n_dimensions < 3:
+ _logger.warning(
+ "perspective is not relevant for 1D and 2D arrays")
+ return
+
+ if not hasattr(perspective, "__len__"):
+ # we can tolerate an integer for 3-D array
+ if n_dimensions == 3:
+ perspective = [perspective]
+ else:
+ raise ValueError("perspective must be a sequence of integers")
+
+ # ensure unicity of dimensions in perspective
+ perspective = tuple(set(perspective))
+
+ if len(perspective) != n_dimensions - 2 or\
+ min(perspective) < 0 or max(perspective) >= n_dimensions:
+ raise IndexError(
+ "Invalid perspective " + str(perspective) +
+ " for %d-D array " % n_dimensions +
+ "with shape " + str(self._array.shape))
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+ else:
+ self.reset()
+
+ self._perspective = perspective
+
+ # reset index
+ self._index = [0 for _i in range(n_dimensions - 2)]
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+
+ def setFrameAxes(self, row_axis, col_axis):
+ """Set the perspective by specifying the two axes parallel to the frame
+ to be visualised.
+
+ The complementary approach of defining the orthogonal axes can be used
+ with :meth:`setPerspective`.
+
+ :param int row_axis: Index (0-based) of the first dimension used as a frame
+ axis
+ :param int col_axis: Index (0-based) of the 2nd dimension used as a frame
+ axis
+ :raise: IndexError if axes are invalid
+ """
+ if row_axis > col_axis:
+ _logger.warning("The dimension of the row axis must be lower " +
+ "than the dimension of the column axis. Swapping.")
+ row_axis, col_axis = min(row_axis, col_axis), max(row_axis, col_axis)
+
+ n_dimensions = len(self._array.shape)
+ if n_dimensions < 3:
+ _logger.warning(
+ "Frame axes cannot be changed for 1D and 2D arrays")
+ return
+
+ perspective = tuple(set(range(0, n_dimensions)) - {row_axis, col_axis})
+
+ if len(perspective) != n_dimensions - 2 or\
+ min(perspective) < 0 or max(perspective) >= n_dimensions:
+ raise IndexError(
+ "Invalid perspective " + str(perspective) +
+ " for %d-D array " % n_dimensions +
+ "with shape " + str(self._array.shape))
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+ else:
+ self.reset()
+
+ self._perspective = perspective
+ # reset index
+ self._index = [0 for _i in range(n_dimensions - 2)]
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+
+
+if __name__ == "__main__":
+ app = qt.QApplication([])
+ w = qt.QTableView()
+ d = numpy.random.normal(0, 1, (5, 1000, 1000))
+ for i in range(5):
+ d[i, :, :] += i * 10
+ m = ArrayTableModel(data=d)
+ w.setModel(m)
+ m.setFrameIndex(3)
+ # m.setArrayData(numpy.ones((100,)))
+ w.show()
+ app.exec_()
diff --git a/silx/gui/data/ArrayTableWidget.py b/silx/gui/data/ArrayTableWidget.py
new file mode 100644
index 0000000..ba3fa11
--- /dev/null
+++ b/silx/gui/data/ArrayTableWidget.py
@@ -0,0 +1,490 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines a widget designed to display data arrays with any
+number of dimensions as 2D frames (images, slices) in a table view.
+The dimensions not displayed in the table can be browsed using improved
+sliders.
+
+The widget uses a TableView that relies on a custom abstract item
+model: :class:`silx.gui.data.ArrayTableModel`.
+"""
+from __future__ import division
+import sys
+
+from silx.gui import qt
+from silx.gui.widgets.TableWidget import TableView
+from .ArrayTableModel import ArrayTableModel
+from silx.gui.widgets.FrameBrowser import HorizontalSliderWithBrowser
+
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "24/01/2017"
+
+
+class AxesSelector(qt.QWidget):
+ """Widget with two combo-boxes to select two dimensions among
+ all possible dimensions of an n-dimensional array.
+
+ The first combobox contains values from :math:`0` to :math:`n-2`.
+
+ The choices in the 2nd CB depend on the value selected in the first one.
+ If the value selected in the first CB is :math:`m`, the second one lets you
+ select values from :math:`m+1` to :math:`n-1`.
+
+ The two axes can be used to select the row axis and the column axis t
+ display a slice of the array data in a table view.
+ """
+ sigDimensionsChanged = qt.Signal(int, int)
+ """Signal emitted whenever one of the comboboxes is changed.
+ The signal carries the two selected dimensions."""
+
+ def __init__(self, parent=None, n=None):
+ qt.QWidget.__init__(self, parent)
+ self.layout = qt.QHBoxLayout(self)
+ self.layout.setContentsMargins(0, 2, 0, 2)
+ self.layout.setSpacing(10)
+
+ self.rowsCB = qt.QComboBox(self)
+ self.columnsCB = qt.QComboBox(self)
+
+ self.layout.addWidget(qt.QLabel("Rows dimension", self))
+ self.layout.addWidget(self.rowsCB)
+ self.layout.addWidget(qt.QLabel(" ", self))
+ self.layout.addWidget(qt.QLabel("Columns dimension", self))
+ self.layout.addWidget(self.columnsCB)
+ self.layout.addStretch(1)
+
+ self._slotsAreConnected = False
+ if n is not None:
+ self.setNDimensions(n)
+
+ def setNDimensions(self, n):
+ """Initialize combo-boxes depending on number of dimensions of array.
+ Initially, the rows dimension is the second-to-last one, and the
+ columns dimension is the last one.
+
+ Link the CBs together. MAke them emit a signal when their value is
+ changed.
+
+ :param int n: Number of dimensions of array
+ """
+ # remember the number of dimensions and the rows dimension
+ self.n = n
+ self._rowsDim = n - 2
+
+ # ensure slots are disconnected before (re)initializing widget
+ if self._slotsAreConnected:
+ self.rowsCB.currentIndexChanged.disconnect(self._rowDimChanged)
+ self.columnsCB.currentIndexChanged.disconnect(self._colDimChanged)
+
+ self._clear()
+ self.rowsCB.addItems([str(i) for i in range(n - 1)])
+ self.rowsCB.setCurrentIndex(n - 2)
+ if n >= 1:
+ self.columnsCB.addItem(str(n - 1))
+ self.columnsCB.setCurrentIndex(0)
+
+ # reconnect slots
+ self.rowsCB.currentIndexChanged.connect(self._rowDimChanged)
+ self.columnsCB.currentIndexChanged.connect(self._colDimChanged)
+ self._slotsAreConnected = True
+
+ # emit new dimensions
+ if n > 2:
+ self.sigDimensionsChanged.emit(n - 2, n - 1)
+
+ def setDimensions(self, row_dim, col_dim):
+ """Set the rows and columns dimensions.
+
+ The rows dimension must be lower than the columns dimension.
+
+ :param int row_dim: Rows dimension
+ :param int col_dim: Columns dimension
+ """
+ if row_dim >= col_dim:
+ raise IndexError("Row dimension must be lower than column dimension")
+ if not (0 <= row_dim < self.n - 1):
+ raise IndexError("Row dimension must be between 0 and %d" % (self.n - 2))
+ if not (row_dim < col_dim <= self.n - 1):
+ raise IndexError("Col dimension must be between %d and %d" % (row_dim + 1, self.n - 1))
+
+ # set the rows dimension; this triggers an update of columnsCB
+ self.rowsCB.setCurrentIndex(row_dim)
+ # columnsCB first item is "row_dim + 1". So index of "col_dim" is
+ # col_dim - (row_dim + 1)
+ self.columnsCB.setCurrentIndex(col_dim - row_dim - 1)
+
+ def getDimensions(self):
+ """Return a 2-tuple of the rows dimension and the columns dimension.
+
+ :return: 2-tuple of axes numbers (row_dimension, col_dimension)
+ """
+ return self._getRowDim(), self._getColDim()
+
+ def _clear(self):
+ """Empty the combo-boxes"""
+ self.rowsCB.clear()
+ self.columnsCB.clear()
+
+ def _getRowDim(self):
+ """Get rows dimension, selected in :attr:`rowsCB`
+ """
+ # rows combobox contains elements "0", ..."n-2",
+ # so the selected dim is always equal to the index
+ return self.rowsCB.currentIndex()
+
+ def _getColDim(self):
+ """Get columns dimension, selected in :attr:`columnsCB`"""
+ # columns combobox contains elements "row_dim+1", "row_dim+2", ..., "n-1"
+ # so the selected dim is equal to row_dim + 1 + index
+ return self._rowsDim + 1 + self.columnsCB.currentIndex()
+
+ def _rowDimChanged(self):
+ """Update columns combobox when the rows dimension is changed.
+
+ Emit :attr:`sigDimensionsChanged`"""
+ old_col_dim = self._getColDim()
+ new_row_dim = self._getRowDim()
+
+ # clear cols CB
+ self.columnsCB.currentIndexChanged.disconnect(self._colDimChanged)
+ self.columnsCB.clear()
+ # refill cols CB
+ for i in range(new_row_dim + 1, self.n):
+ self.columnsCB.addItem(str(i))
+
+ # keep previous col dimension if possible
+ new_col_cb_idx = old_col_dim - (new_row_dim + 1)
+ if new_col_cb_idx < 0:
+ # if row_dim is now greater than the previous col_dim,
+ # we select a new col_dim = row_dim + 1 (first element in cols CB)
+ new_col_cb_idx = 0
+ self.columnsCB.setCurrentIndex(new_col_cb_idx)
+
+ # reconnect slot
+ self.columnsCB.currentIndexChanged.connect(self._colDimChanged)
+
+ self._rowsDim = new_row_dim
+
+ self.sigDimensionsChanged.emit(self._getRowDim(), self._getColDim())
+
+ def _colDimChanged(self):
+ """Emit :attr:`sigDimensionsChanged`"""
+ self.sigDimensionsChanged.emit(self._getRowDim(), self._getColDim())
+
+
+def _get_shape(array_like):
+ """Return shape of an array like object.
+
+ In case the object is a nested sequence (list of lists, tuples...),
+ the size of each dimension is assumed to be uniform, and is deduced from
+ the length of the first sequence.
+
+ :param array_like: Array like object: numpy array, hdf5 dataset,
+ multi-dimensional sequence
+ :return: Shape of array, as a tuple of integers
+ """
+ if hasattr(array_like, "shape"):
+ return array_like.shape
+
+ shape = []
+ subsequence = array_like
+ while hasattr(subsequence, "__len__"):
+ shape.append(len(subsequence))
+ subsequence = subsequence[0]
+
+ return tuple(shape)
+
+
+class ArrayTableWidget(qt.QWidget):
+ """This widget is designed to display data of 2D frames (images, slices)
+ in a table view. The widget can load any n-dimensional array, and display
+ any 2-D frame/slice in the array.
+
+ The index of the dimensions orthogonal to the displayed frame can be set
+ interactively using a browser widget (sliders, buttons and text entries).
+
+ To set the data, use :meth:`setArrayData`.
+ To select the perspective, use :meth:`setPerspective` or
+ use :meth:`setFrameAxes`.
+ To select the frame, use :meth:`setFrameIndex`.
+ """
+ def __init__(self, parent=None):
+ """
+
+ :param parent: parent QWidget
+ :param labels: list of labels for each dimension of the array
+ """
+ qt.QWidget.__init__(self, parent)
+ self.mainLayout = qt.QVBoxLayout(self)
+ self.mainLayout.setContentsMargins(0, 0, 0, 0)
+ self.mainLayout.setSpacing(0)
+
+ self.browserContainer = qt.QWidget(self)
+ self.browserLayout = qt.QGridLayout(self.browserContainer)
+ self.browserLayout.setContentsMargins(0, 0, 0, 0)
+ self.browserLayout.setSpacing(0)
+
+ self._dimensionLabelsText = []
+ """List of text labels sorted in the increasing order of the dimension
+ they apply to."""
+ self._browserLabels = []
+ """List of QLabel widgets."""
+ self._browserWidgets = []
+ """List of HorizontalSliderWithBrowser widgets."""
+
+ self.axesSelector = AxesSelector(self)
+
+ self.view = TableView(self)
+
+ self.mainLayout.addWidget(self.browserContainer)
+ self.mainLayout.addWidget(self.axesSelector)
+ self.mainLayout.addWidget(self.view)
+
+ self.model = ArrayTableModel(self)
+ self.view.setModel(self.model)
+
+ def setArrayData(self, data, labels=None, copy=True, editable=False):
+ """Set the data array. Update frame browsers and labels.
+
+ :param data: Numpy array or similar object (e.g. nested sequence,
+ h5py dataset...)
+ :param labels: list of labels for each dimension of the array, or
+ boolean ``True`` to use default labels ("dimension 0",
+ "dimension 1", ...). `None` to disable labels (default).
+ :param bool copy: If *True*, store a copy of *data* in the model. If
+ *False*, store a reference to *data* if possible (only possible if
+ *data* is a proper numpy array or an object that implements the
+ same methods).
+ :param bool editable: Flag to enable editing data. Default is *False*
+ """
+ self._data_shape = _get_shape(data)
+
+ n_widgets = len(self._browserWidgets)
+ n_dimensions = len(self._data_shape)
+
+ # Reset text of labels
+ self._dimensionLabelsText = []
+ for i in range(n_dimensions):
+ if labels in [True, 1]:
+ label_text = "Dimension %d" % i
+ elif labels is None or i >= len(labels):
+ label_text = ""
+ else:
+ label_text = labels[i]
+ self._dimensionLabelsText.append(label_text)
+
+ # not enough widgets, create new ones (we need n_dim - 2)
+ for i in range(n_widgets, n_dimensions - 2):
+ browser = HorizontalSliderWithBrowser(self.browserContainer)
+ self.browserLayout.addWidget(browser, i, 1)
+ self._browserWidgets.append(browser)
+ browser.valueChanged.connect(self._browserSlot)
+ browser.setEnabled(False)
+ browser.hide()
+
+ label = qt.QLabel(self.browserContainer)
+ self._browserLabels.append(label)
+ self.browserLayout.addWidget(label, i, 0)
+ label.hide()
+
+ n_widgets = len(self._browserWidgets)
+ for i in range(n_widgets):
+ label = self._browserLabels[i]
+ browser = self._browserWidgets[i]
+
+ if (i + 2) < n_dimensions:
+ label.setText(self._dimensionLabelsText[i])
+ browser.setRange(0, self._data_shape[i] - 1)
+ browser.setEnabled(True)
+ browser.show()
+ if labels is not None:
+ label.show()
+ else:
+ label.hide()
+ else:
+ browser.setEnabled(False)
+ browser.hide()
+ label.hide()
+
+ # set model
+ self.model.setArrayData(data, copy=copy, editable=editable)
+ # some linux distributions need this call
+ self.view.setModel(self.model)
+ if editable:
+ self.view.enableCut()
+ self.view.enablePaste()
+
+ # initialize & connect axesSelector
+ self.axesSelector.setNDimensions(n_dimensions)
+ self.axesSelector.sigDimensionsChanged.connect(self.setFrameAxes)
+
+ def setArrayColors(self, bgcolors=None, fgcolors=None):
+ """Set the colors for all table cells by passing an array
+ of RGB or RGBA values (integers between 0 and 255).
+
+ The shape of the colors array must be consistent with the data shape.
+
+ If the data array is n-dimensional, the colors array must be
+ (n+1)-dimensional, with the first n-dimensions identical to the data
+ array dimensions, and the last dimension length-3 (RGB) or
+ length-4 (RGBA).
+
+ :param bgcolors: RGB or RGBA colors array, defining the background color
+ for each cell in the table.
+ :param fgcolors: RGB or RGBA colors array, defining the foreground color
+ (text color) for each cell in the table.
+ """
+ self.model.setArrayColors(bgcolors, fgcolors)
+
+ def displayAxesSelector(self, isVisible):
+ """Allow to display or hide the axes selector.
+
+ :param bool isVisible: True to display the axes selector.
+ """
+ self.axesSelector.setVisible(isVisible)
+
+ def setFrameIndex(self, index):
+ """Set the active slice/image index in the n-dimensional array.
+
+ A frame is a 2D array extracted from an array. This frame is
+ necessarily parallel to 2 axes, and orthogonal to all other axes.
+
+ The index of a frame is a sequence of indices along the orthogonal
+ axes, where the frame intersects the respective axis. The indices
+ are listed in the same order as the corresponding dimensions of the
+ data array.
+
+ For example, it the data array has 5 dimensions, and we are
+ considering frames whose parallel axes are the 2nd and 4th dimensions
+ of the array, the frame index will be a sequence of length 3
+ corresponding to the indices where the frame intersects the 1st, 3rd
+ and 5th axes.
+
+ :param index: Sequence of indices defining the active data slice in
+ a n-dimensional array. The sequence length is :math:`n-2`
+ :raise: IndexError if any index in the index sequence is out of bound
+ on its respective axis.
+ """
+ self.model.setFrameIndex(index)
+
+ def _resetBrowsers(self, perspective):
+ """Adjust limits for browsers based on the perspective and the
+ size of the corresponding dimensions. Reset the index to 0.
+ Update the dimension in the labels.
+
+ :param perspective: Sequence of axes/dimensions numbers (0-based)
+ defining the axes orthogonal to the frame.
+ """
+ # for 3D arrays we can accept an int rather than a 1-tuple
+ if not hasattr(perspective, "__len__"):
+ perspective = [perspective]
+
+ # perspective must be sorted
+ perspective = sorted(perspective)
+
+ n_dimensions = len(self._data_shape)
+ for i in range(n_dimensions - 2):
+ browser = self._browserWidgets[i]
+ label = self._browserLabels[i]
+ browser.setRange(0, self._data_shape[perspective[i]] - 1)
+ browser.setValue(0)
+ label.setText(self._dimensionLabelsText[perspective[i]])
+
+ def setPerspective(self, perspective):
+ """Set the *perspective* by specifying which axes are orthogonal
+ to the frame.
+
+ For the opposite approach (defining parallel axes), use
+ :meth:`setFrameAxes` instead.
+
+ :param perspective: Sequence of unique axes numbers (0-based) defining
+ the orthogonal axes. For a n-dimensional array, the sequence
+ length is :math:`n-2`. The order is of the sequence is not taken
+ into account (the dimensions are displayed in increasing order
+ in the widget).
+ """
+ self.model.setPerspective(perspective)
+ self._resetBrowsers(perspective)
+
+ def setFrameAxes(self, row_axis, col_axis):
+ """Set the *perspective* by specifying which axes are parallel
+ to the frame.
+
+ For the opposite approach (defining orthogonal axes), use
+ :meth:`setPerspective` instead.
+
+ :param int row_axis: Index (0-based) of the first dimension used as a frame
+ axis
+ :param int col_axis: Index (0-based) of the 2nd dimension used as a frame
+ axis
+ """
+ self.model.setFrameAxes(row_axis, col_axis)
+ n_dimensions = len(self._data_shape)
+ perspective = tuple(set(range(0, n_dimensions)) - {row_axis, col_axis})
+ self._resetBrowsers(perspective)
+
+ def _browserSlot(self, value):
+ index = []
+ for browser in self._browserWidgets:
+ if browser.isEnabled():
+ index.append(browser.value())
+ self.setFrameIndex(index)
+ self.view.reset()
+
+ def getData(self, copy=True):
+ """Return a copy of the data array, or a reference to it if
+ *copy=False* is passed as parameter.
+
+ :param bool copy: If *True* (default), return a copy of the data. If
+ *False*, return a reference.
+ :return: Numpy array of data, or reference to original data object
+ if *copy=False*
+ """
+ return self.model.getData(copy=copy)
+
+
+def main():
+ import numpy
+ a = qt.QApplication([])
+ d = numpy.random.normal(0, 1, (4, 5, 1000, 1000))
+ for j in range(4):
+ for i in range(5):
+ d[j, i, :, :] += i + 10 * j
+ w = ArrayTableWidget()
+ if "2" in sys.argv:
+ print("sending a single image")
+ w.setArrayData(d[0, 0])
+ elif "3" in sys.argv:
+ print("sending 5 images")
+ w.setArrayData(d[0])
+ else:
+ print("sending 4 * 5 images ")
+ w.setArrayData(d, labels=True)
+ w.show()
+ a.exec_()
+
+if __name__ == "__main__":
+ main()
diff --git a/silx/gui/data/DataViewer.py b/silx/gui/data/DataViewer.py
new file mode 100644
index 0000000..3a3ac64
--- /dev/null
+++ b/silx/gui/data/DataViewer.py
@@ -0,0 +1,464 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines a widget designed to display data using to most adapted
+view from available ones from silx.
+"""
+from __future__ import division
+
+from silx.gui.data import DataViews
+from silx.gui.data.DataViews import _normalizeData
+import logging
+from silx.gui import qt
+from silx.gui.data.NumpyAxesSelector import NumpyAxesSelector
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "26/04/2017"
+
+
+_logger = logging.getLogger(__name__)
+
+
+class DataViewer(qt.QFrame):
+ """Widget to display any kind of data
+
+ .. image:: img/DataViewer.png
+
+ The method :meth:`setData` allows to set any data to the widget. Mostly
+ `numpy.array` and `h5py.Dataset` are supported with adapted views. Other
+ data types are displayed using a text viewer.
+
+ A default view is automatically selected when a data is set. The method
+ :meth:`setDisplayMode` allows to change the view. To have a graphical tool
+ to select the view, prefer using the widget :class:`DataViewerFrame`.
+
+ The dimension of the input data and the expected dimension of the selected
+ view can differ. For example you can display an image (2D) from 4D
+ data. In this case a :class:`NumpyAxesSelector` is displayed to allow the
+ user to select the axis mapping and the slicing of other axes.
+
+ .. code-block:: python
+
+ import numpy
+ data = numpy.random.rand(500,500)
+ viewer = DataViewer()
+ viewer.setData(data)
+ viewer.setVisible(True)
+ """
+
+ EMPTY_MODE = 0
+ PLOT1D_MODE = 10
+ PLOT2D_MODE = 20
+ PLOT3D_MODE = 30
+ RAW_MODE = 40
+ RAW_ARRAY_MODE = 41
+ RAW_RECORD_MODE = 42
+ RAW_SCALAR_MODE = 43
+ STACK_MODE = 50
+ HDF5_MODE = 60
+
+ displayedViewChanged = qt.Signal(object)
+ """Emitted when the displayed view changes"""
+
+ dataChanged = qt.Signal()
+ """Emitted when the data changes"""
+
+ currentAvailableViewsChanged = qt.Signal()
+ """Emitted when the current available views (which support the current
+ data) change"""
+
+ def __init__(self, parent=None):
+ """Constructor
+
+ :param QWidget parent: The parent of the widget
+ """
+ super(DataViewer, self).__init__(parent)
+
+ self.__stack = qt.QStackedWidget(self)
+ self.__numpySelection = NumpyAxesSelector(self)
+ self.__numpySelection.selectedAxisChanged.connect(self.__numpyAxisChanged)
+ self.__numpySelection.selectionChanged.connect(self.__numpySelectionChanged)
+ self.__numpySelection.customAxisChanged.connect(self.__numpyCustomAxisChanged)
+
+ self.setLayout(qt.QVBoxLayout(self))
+ self.layout().addWidget(self.__stack, 1)
+
+ group = qt.QGroupBox(self)
+ group.setLayout(qt.QVBoxLayout())
+ group.layout().addWidget(self.__numpySelection)
+ group.setTitle("Axis selection")
+ self.__axisSelection = group
+
+ self.layout().addWidget(self.__axisSelection)
+
+ self.__currentAvailableViews = []
+ self.__currentView = None
+ self.__data = None
+ self.__useAxisSelection = False
+ self.__userSelectedView = None
+
+ self.__views = []
+ self.__index = {}
+ """store stack index for each views"""
+
+ self._initializeViews()
+
+ def _initializeViews(self):
+ """Inisialize the available views"""
+ views = self.createDefaultViews(self.__stack)
+ self.__views = list(views)
+ self.setDisplayMode(self.EMPTY_MODE)
+
+ def createDefaultViews(self, parent=None):
+ """Create and returns available views which can be displayed by default
+ by the data viewer. It is called internally by the widget. It can be
+ overwriten to provide a different set of viewers.
+
+ :param QWidget parent: QWidget parent of the views
+ :rtype: list[silx.gui.data.DataViews.DataView]
+ """
+ viewClasses = [
+ DataViews._EmptyView,
+ DataViews._Hdf5View,
+ DataViews._NXdataView,
+ DataViews._Plot1dView,
+ DataViews._Plot2dView,
+ DataViews._Plot3dView,
+ DataViews._RawView,
+ DataViews._StackView,
+ ]
+ views = []
+ for viewClass in viewClasses:
+ try:
+ view = viewClass(parent)
+ views.append(view)
+ except Exception:
+ _logger.warning("%s instantiation failed. View is ignored" % viewClass.__name__)
+ _logger.debug("Backtrace", exc_info=True)
+
+ return views
+
+ def clear(self):
+ """Clear the widget"""
+ self.setData(None)
+
+ def normalizeData(self, data):
+ """Returns a normalized data if the embed a numpy or a dataset.
+ Else returns the data."""
+ return _normalizeData(data)
+
+ def __getStackIndex(self, view):
+ """Get the stack index containing the view.
+
+ :param silx.gui.data.DataViews.DataView view: The view
+ """
+ if view not in self.__index:
+ widget = view.getWidget()
+ index = self.__stack.addWidget(widget)
+ self.__index[view] = index
+ else:
+ index = self.__index[view]
+ return index
+
+ def __clearCurrentView(self):
+ """Clear the current selected view"""
+ view = self.__currentView
+ if view is not None:
+ view.clear()
+
+ def __numpyCustomAxisChanged(self, name, value):
+ view = self.__currentView
+ if view is not None:
+ view.setCustomAxisValue(name, value)
+
+ def __updateNumpySelectionAxis(self):
+ """
+ Update the numpy-selector according to the needed axis names
+ """
+ previous = self.__numpySelection.blockSignals(True)
+ self.__numpySelection.clear()
+ info = DataViews.DataInfo(self.__data)
+ axisNames = self.__currentView.axesNames(self.__data, info)
+ if info.isArray and self.__data is not None and len(axisNames) > 0:
+ self.__useAxisSelection = True
+ self.__numpySelection.setAxisNames(axisNames)
+ self.__numpySelection.setCustomAxis(self.__currentView.customAxisNames())
+ data = self.normalizeData(self.__data)
+ self.__numpySelection.setData(data)
+ if hasattr(data, "shape"):
+ isVisible = not (len(axisNames) == 1 and len(data.shape) == 1)
+ else:
+ isVisible = True
+ self.__axisSelection.setVisible(isVisible)
+ else:
+ self.__useAxisSelection = False
+ self.__axisSelection.setVisible(False)
+ self.__numpySelection.blockSignals(previous)
+
+ def __updateDataInView(self):
+ """
+ Update the views using the current data
+ """
+ if self.__useAxisSelection:
+ self.__displayedData = self.__numpySelection.selectedData()
+ else:
+ self.__displayedData = self.__data
+
+ qt.QTimer.singleShot(10, self.__setDataInView)
+
+ def __setDataInView(self):
+ self.__currentView.setData(self.__displayedData)
+
+ def setDisplayedView(self, view):
+ """Set the displayed view.
+
+ Change the displayed view according to the view itself.
+
+ :param silx.gui.data.DataViews.DataView view: The DataView to use to display the data
+ """
+ self.__userSelectedView = view
+ self._setDisplayedView(view)
+
+ def _setDisplayedView(self, view):
+ """Internal set of the displayed view.
+
+ Change the displayed view according to the view itself.
+
+ :param silx.gui.data.DataViews.DataView view: The DataView to use to display the data
+ """
+ if self.__currentView is view:
+ return
+ self.__clearCurrentView()
+ self.__currentView = view
+ self.__updateNumpySelectionAxis()
+ self.__updateDataInView()
+ stackIndex = self.__getStackIndex(self.__currentView)
+ if self.__currentView is not None:
+ self.__currentView.select()
+ self.__stack.setCurrentIndex(stackIndex)
+ self.displayedViewChanged.emit(view)
+
+ def getViewFromModeId(self, modeId):
+ """Returns the first available view which have the requested modeId.
+
+ :param int modeId: Requested mode id
+ :rtype: silx.gui.data.DataViews.DataView
+ """
+ for view in self.__views:
+ if view.modeId() == modeId:
+ return view
+ return view
+
+ def setDisplayMode(self, modeId):
+ """Set the displayed view using display mode.
+
+ Change the displayed view according to the requested mode.
+
+ :param int modeId: Display mode, one of
+
+ - `EMPTY_MODE`: display nothing
+ - `PLOT1D_MODE`: display the data as a curve
+ - `PLOT2D_MODE`: display the data as an image
+ - `PLOT3D_MODE`: display the data as an isosurface
+ - `RAW_MODE`: display the data as a table
+ - `STACK_MODE`: display the data as a stack of images
+ - `HDF5_MODE`: display the data as a table
+ """
+ try:
+ view = self.getViewFromModeId(modeId)
+ except KeyError:
+ raise ValueError("Display mode %s is unknown" % modeId)
+ self._setDisplayedView(view)
+
+ def displayedView(self):
+ """Returns the current displayed view.
+
+ :rtype: silx.gui.data.DataViews.DataView
+ """
+ return self.__currentView
+
+ def addView(self, view):
+ """Allow to add a view to the dataview.
+
+ If the current data support this view, it will be displayed.
+
+ :param DataView view: A dataview
+ """
+ self.__views.append(view)
+ # TODO It can be skipped if the view do not support the data
+ self.__updateAvailableViews()
+
+ def removeView(self, view):
+ """Allow to remove a view which was available from the dataview.
+
+ If the view was displayed, the widget will be updated.
+
+ :param DataView view: A dataview
+ """
+ self.__views.remove(view)
+ self.__stack.removeWidget(view.getWidget())
+ # invalidate the full index. It will be updated as expected
+ self.__index = {}
+
+ if self.__userSelectedView is view:
+ self.__userSelectedView = None
+
+ if view is self.__currentView:
+ self.__updateView()
+ else:
+ # TODO It can be skipped if the view is not part of the
+ # available views
+ self.__updateAvailableViews()
+
+ def __updateAvailableViews(self):
+ """
+ Update available views from the current data.
+ """
+ data = self.__data
+ # sort available views according to priority
+ info = DataViews.DataInfo(data)
+ priorities = [v.getDataPriority(data, info) for v in self.__views]
+ views = zip(priorities, self.__views)
+ views = filter(lambda t: t[0] > DataViews.DataView.UNSUPPORTED, views)
+ views = sorted(views, reverse=True)
+
+ # store available views
+ if len(views) == 0:
+ self.__setCurrentAvailableViews([])
+ available = []
+ else:
+ available = [v[1] for v in views]
+ self.__setCurrentAvailableViews(available)
+
+ def __updateView(self):
+ """Display the data using the widget which fit the best"""
+ data = self.__data
+
+ # update available views for this data
+ self.__updateAvailableViews()
+ available = self.__currentAvailableViews
+
+ # display the view with the most priority (the default view)
+ view = self.getDefaultViewFromAvailableViews(data, available)
+ self.__clearCurrentView()
+ try:
+ self._setDisplayedView(view)
+ except Exception as e:
+ # in case there is a problem to read the data, try to use a safe
+ # view
+ view = self.getSafeViewFromAvailableViews(data, available)
+ self._setDisplayedView(view)
+ raise e
+
+ def getSafeViewFromAvailableViews(self, data, available):
+ """Returns a view which is sure to display something without failing
+ on rendering.
+
+ :param object data: data which will be displayed
+ :param list[view] available: List of available views, from highest
+ priority to lowest.
+ :rtype: DataView
+ """
+ hdf5View = self.getViewFromModeId(DataViewer.HDF5_MODE)
+ if hdf5View in available:
+ return hdf5View
+ return self.getViewFromModeId(DataViewer.EMPTY_MODE)
+
+ def getDefaultViewFromAvailableViews(self, data, available):
+ """Returns the default view which will be used according to available
+ views.
+
+ :param object data: data which will be displayed
+ :param list[view] available: List of available views, from highest
+ priority to lowest.
+ :rtype: DataView
+ """
+ if len(available) > 0:
+ # returns the view with the highest priority
+ if self.__userSelectedView in available:
+ return self.__userSelectedView
+ self.__userSelectedView = None
+ view = available[0]
+ else:
+ # else returns the empty view
+ view = self.getViewFromModeId(DataViewer.EMPTY_MODE)
+ return view
+
+ def __setCurrentAvailableViews(self, availableViews):
+ """Set the current available viewa
+
+ :param List[DataView] availableViews: Current available viewa
+ """
+ self.__currentAvailableViews = availableViews
+ self.currentAvailableViewsChanged.emit()
+
+ def currentAvailableViews(self):
+ """Returns the list of available views for the current data
+
+ :rtype: List[DataView]
+ """
+ return self.__currentAvailableViews
+
+ def availableViews(self):
+ """Returns the list of registered views
+
+ :rtype: List[DataView]
+ """
+ return self.__views
+
+ def setData(self, data):
+ """Set the data to view.
+
+ It mostly can be a h5py.Dataset or a numpy.ndarray. Other kind of
+ objects will be displayed as text rendering.
+
+ :param numpy.ndarray data: The data.
+ """
+ self.__data = data
+ self.__displayedData = None
+ self.__updateView()
+ self.__updateNumpySelectionAxis()
+ self.__updateDataInView()
+ self.dataChanged.emit()
+
+ def __numpyAxisChanged(self):
+ """
+ Called when axis selection of the numpy-selector changed
+ """
+ self.__clearCurrentView()
+
+ def __numpySelectionChanged(self):
+ """
+ Called when data selection of the numpy-selector changed
+ """
+ self.__updateDataInView()
+
+ def data(self):
+ """Returns the data"""
+ return self.__data
+
+ def displayMode(self):
+ """Returns the current display mode"""
+ return self.__currentView.modeId()
diff --git a/silx/gui/data/DataViewerFrame.py b/silx/gui/data/DataViewerFrame.py
new file mode 100644
index 0000000..b48fa7b
--- /dev/null
+++ b/silx/gui/data/DataViewerFrame.py
@@ -0,0 +1,186 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module contains a DataViewer with a view selector.
+"""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "10/04/2017"
+
+from silx.gui import qt
+from .DataViewer import DataViewer
+from .DataViewerSelector import DataViewerSelector
+
+
+class DataViewerFrame(qt.QWidget):
+ """
+ A :class:`DataViewer` with a view selector.
+
+ .. image:: img/DataViewerFrame.png
+
+ This widget provides the same API as :class:`DataViewer`. Therefore, for more
+ documentation, take a look at the documentation of the class
+ :class:`DataViewer`.
+
+ .. code-block:: python
+
+ import numpy
+ data = numpy.random.rand(500,500)
+ viewer = DataViewerFrame()
+ viewer.setData(data)
+ viewer.setVisible(True)
+
+ """
+
+ displayedViewChanged = qt.Signal(object)
+ """Emitted when the displayed view changes"""
+
+ dataChanged = qt.Signal()
+ """Emitted when the data changes"""
+
+ def __init__(self, parent=None):
+ """
+ Constructor
+
+ :param qt.QWidget parent:
+ """
+ super(DataViewerFrame, self).__init__(parent)
+
+ class _DataViewer(DataViewer):
+ """Overwrite methods to avoid to create views while the instance
+ is not created. `initializeViews` have to be called manually."""
+
+ def _initializeViews(self):
+ pass
+
+ def initializeViews(self):
+ """Avoid to create views while the instance is not created."""
+ super(_DataViewer, self)._initializeViews()
+
+ self.__dataViewer = _DataViewer(self)
+ # initialize views when `self.__dataViewer` is set
+ self.__dataViewer.initializeViews()
+ self.__dataViewer.setFrameShape(qt.QFrame.StyledPanel)
+ self.__dataViewer.setFrameShadow(qt.QFrame.Sunken)
+ self.__dataViewerSelector = DataViewerSelector(self, self.__dataViewer)
+ self.__dataViewerSelector.setFlat(True)
+
+ layout = qt.QVBoxLayout(self)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.setSpacing(0)
+ layout.addWidget(self.__dataViewer, 1)
+ layout.addWidget(self.__dataViewerSelector)
+ self.setLayout(layout)
+
+ self.__dataViewer.dataChanged.connect(self.__dataChanged)
+ self.__dataViewer.displayedViewChanged.connect(self.__displayedViewChanged)
+
+ def __dataChanged(self):
+ """Called when the data is changed"""
+ self.dataChanged.emit()
+
+ def __displayedViewChanged(self, view):
+ """Called when the displayed view changes"""
+ self.displayedViewChanged.emit(view)
+
+ def availableViews(self):
+ """Returns the list of registered views
+
+ :rtype: List[DataView]
+ """
+ return self.__dataViewer.availableViews()
+
+ def currentAvailableViews(self):
+ """Returns the list of available views for the current data
+
+ :rtype: List[DataView]
+ """
+ return self.__dataViewer.currentAvailableViews()
+
+ def createDefaultViews(self, parent=None):
+ """Create and returns available views which can be displayed by default
+ by the data viewer. It is called internally by the widget. It can be
+ overwriten to provide a different set of viewers.
+
+ :param QWidget parent: QWidget parent of the views
+ :rtype: list[silx.gui.data.DataViews.DataView]
+ """
+ return self.__dataViewer.createDefaultViews(parent)
+
+ def addView(self, view):
+ """Allow to add a view to the dataview.
+
+ If the current data support this view, it will be displayed.
+
+ :param DataView view: A dataview
+ """
+ return self.__dataViewer.addView(view)
+
+ def removeView(self, view):
+ """Allow to remove a view which was available from the dataview.
+
+ If the view was displayed, the widget will be updated.
+
+ :param DataView view: A dataview
+ """
+ return self.__dataViewer.removeView(view)
+
+ def setData(self, data):
+ """Set the data to view.
+
+ It mostly can be a h5py.Dataset or a numpy.ndarray. Other kind of
+ objects will be displayed as text rendering.
+
+ :param numpy.ndarray data: The data.
+ """
+ self.__dataViewer.setData(data)
+
+ def data(self):
+ """Returns the data"""
+ return self.__dataViewer.data()
+
+ def setDisplayedView(self, view):
+ self.__dataViewer.setDisplayedView(view)
+
+ def displayedView(self):
+ return self.__dataViewer.displayedView()
+
+ def displayMode(self):
+ return self.__dataViewer.displayMode()
+
+ def setDisplayMode(self, modeId):
+ """Set the displayed view using display mode.
+
+ Change the displayed view according to the requested mode.
+
+ :param int modeId: Display mode, one of
+
+ - `EMPTY_MODE`: display nothing
+ - `PLOT1D_MODE`: display the data as a curve
+ - `PLOT2D_MODE`: display the data as an image
+ - `TEXT_MODE`: display the data as a text
+ - `ARRAY_MODE`: display the data as a table
+ """
+ return self.__dataViewer.setDisplayMode(modeId)
diff --git a/silx/gui/data/DataViewerSelector.py b/silx/gui/data/DataViewerSelector.py
new file mode 100644
index 0000000..32cc636
--- /dev/null
+++ b/silx/gui/data/DataViewerSelector.py
@@ -0,0 +1,153 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines a widget to be able to select the available view
+of the DataViewer.
+"""
+from __future__ import division
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "26/01/2017"
+
+import weakref
+import functools
+from silx.gui import qt
+from silx.gui.data.DataViewer import DataViewer
+import silx.utils.weakref
+
+
+class DataViewerSelector(qt.QWidget):
+ """Widget to be able to select a custom view from the DataViewer"""
+
+ def __init__(self, parent=None, dataViewer=None):
+ """Constructor
+
+ :param QWidget parent: The parent of the widget
+ :param DataViewer dataViewer: The connected `DataViewer`
+ """
+ super(DataViewerSelector, self).__init__(parent)
+
+ self.__group = None
+ self.__buttons = {}
+ self.__buttonDummy = None
+ self.__dataViewer = None
+
+ if dataViewer is not None:
+ self.setDataViewer(dataViewer)
+
+ def __updateButtons(self):
+ if self.__group is not None:
+ self.__group.deleteLater()
+ self.__buttons = {}
+ self.__buttonDummy = None
+
+ self.__group = qt.QButtonGroup(self)
+ self.setLayout(qt.QHBoxLayout())
+ self.layout().setContentsMargins(0, 0, 0, 0)
+ if self.__dataViewer is None:
+ return
+
+ iconSize = qt.QSize(16, 16)
+
+ for view in self.__dataViewer.availableViews():
+ label = view.label()
+ icon = view.icon()
+ button = qt.QPushButton(label)
+ button.setIcon(icon)
+ button.setIconSize(iconSize)
+ button.setCheckable(True)
+ # the weak objects are needed to be able to destroy the widget safely
+ weakView = weakref.ref(view)
+ weakMethod = silx.utils.weakref.WeakMethodProxy(self.__setDisplayedView)
+ callback = functools.partial(weakMethod, weakView)
+ button.clicked.connect(callback)
+ self.layout().addWidget(button)
+ self.__group.addButton(button)
+ self.__buttons[view] = button
+
+ button = qt.QPushButton("Dummy")
+ button.setCheckable(True)
+ button.setVisible(False)
+ self.layout().addWidget(button)
+ self.__group.addButton(button)
+ self.__buttonDummy = button
+
+ self.layout().addStretch(1)
+
+ self.__updateButtonsVisibility()
+ self.__displayedViewChanged(self.__dataViewer.displayedView())
+
+ def setDataViewer(self, dataViewer):
+ """Define the dataviewer connected to this status bar
+
+ :param DataViewer dataViewer: The connected `DataViewer`
+ """
+ if self.__dataViewer is dataViewer:
+ return
+ if self.__dataViewer is not None:
+ self.__dataViewer.dataChanged.disconnect(self.__updateButtonsVisibility)
+ self.__dataViewer.displayedViewChanged.disconnect(self.__displayedViewChanged)
+ self.__dataViewer = dataViewer
+ if self.__dataViewer is not None:
+ self.__dataViewer.dataChanged.connect(self.__updateButtonsVisibility)
+ self.__dataViewer.displayedViewChanged.connect(self.__displayedViewChanged)
+ self.__updateButtons()
+
+ def setFlat(self, isFlat):
+ """Set the flat state of all the buttons.
+
+ :param bool isFlat: True to display the buttons flatten.
+ """
+ for b in self.__buttons.values():
+ b.setFlat(isFlat)
+ self.__buttonDummy.setFlat(isFlat)
+
+ def __displayedViewChanged(self, view):
+ """Called on displayed view changeS"""
+ selectedButton = self.__buttons.get(view, self.__buttonDummy)
+ selectedButton.setChecked(True)
+
+ def __setDisplayedView(self, refView, clickEvent=None):
+ """Display a data using the requested view
+
+ :param DataView view: Requested view
+ :param clickEvent: Event sent by the clicked event
+ """
+ if self.__dataViewer is None:
+ return
+ view = refView()
+ if view is None:
+ return
+ self.__dataViewer.setDisplayedView(view)
+
+ def __updateButtonsVisibility(self):
+ """Called on data changed"""
+ if self.__dataViewer is None:
+ for b in self.__buttons.values():
+ b.setVisible(False)
+ else:
+ availableViews = set(self.__dataViewer.currentAvailableViews())
+ for view, button in self.__buttons.items():
+ button.setVisible(view in availableViews)
diff --git a/silx/gui/data/DataViews.py b/silx/gui/data/DataViews.py
new file mode 100644
index 0000000..d8d605a
--- /dev/null
+++ b/silx/gui/data/DataViews.py
@@ -0,0 +1,988 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines a views used by :class:`silx.gui.data.DataViewer`.
+"""
+
+import logging
+import numbers
+import numpy
+
+import silx.io
+from silx.gui import qt, icons
+from silx.gui.data.TextFormatter import TextFormatter
+from silx.io import nxdata
+from silx.gui.hdf5 import H5Node
+from silx.io.nxdata import NXdata
+
+__authors__ = ["V. Valls", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "07/04/2017"
+
+_logger = logging.getLogger(__name__)
+
+
+# DataViewer modes
+EMPTY_MODE = 0
+PLOT1D_MODE = 10
+PLOT2D_MODE = 20
+PLOT3D_MODE = 30
+RAW_MODE = 40
+RAW_ARRAY_MODE = 41
+RAW_RECORD_MODE = 42
+RAW_SCALAR_MODE = 43
+STACK_MODE = 50
+HDF5_MODE = 60
+
+
+def _normalizeData(data):
+ """Returns a normalized data.
+
+ If the data embed a numpy data or a dataset it is returned.
+ Else returns the input data."""
+ if isinstance(data, H5Node):
+ return data.h5py_object
+ return data
+
+
+def _normalizeComplex(data):
+ """Returns a normalized complex data.
+
+ If the data is a numpy data with complex, returns the
+ absolute value.
+ Else returns the input data."""
+ if hasattr(data, "dtype"):
+ isComplex = numpy.issubdtype(data.dtype, numpy.complex)
+ else:
+ isComplex = isinstance(data, numbers.Complex)
+ if isComplex:
+ data = numpy.absolute(data)
+ return data
+
+
+class DataInfo(object):
+ """Store extracted information from a data"""
+
+ def __init__(self, data):
+ data = self.normalizeData(data)
+ self.isArray = False
+ self.interpretation = None
+ self.isNumeric = False
+ self.isComplex = False
+ self.isRecord = False
+ self.isNXdata = False
+ self.shape = tuple()
+ self.dim = 0
+
+ if data is None:
+ return
+
+ if silx.io.is_group(data) and nxdata.is_valid_nxdata(data):
+ self.isNXdata = True
+ nxd = nxdata.NXdata(data)
+
+ if isinstance(data, numpy.ndarray):
+ self.isArray = True
+ elif silx.io.is_dataset(data) and data.shape != tuple():
+ self.isArray = True
+ else:
+ self.isArray = False
+
+ if silx.io.is_dataset(data):
+ self.interpretation = data.attrs.get("interpretation", None)
+ elif self.isNXdata:
+ self.interpretation = nxd.interpretation
+ else:
+ self.interpretation = None
+
+ if hasattr(data, "dtype"):
+ self.isNumeric = numpy.issubdtype(data.dtype, numpy.number)
+ self.isRecord = data.dtype.fields is not None
+ self.isComplex = numpy.issubdtype(data.dtype, numpy.complex)
+ elif self.isNXdata:
+ self.isNumeric = numpy.issubdtype(nxd.signal.dtype,
+ numpy.number)
+ self.isComplex = numpy.issubdtype(nxd.signal.dtype, numpy.complex)
+ else:
+ self.isNumeric = isinstance(data, numbers.Number)
+ self.isComplex = isinstance(data, numbers.Complex)
+ self.isRecord = False
+
+ if hasattr(data, "shape"):
+ self.shape = data.shape
+ elif self.isNXdata:
+ self.shape = nxd.signal.shape
+ else:
+ self.shape = tuple()
+ self.dim = len(self.shape)
+
+ def normalizeData(self, data):
+ """Returns a normalized data if the embed a numpy or a dataset.
+ Else returns the data."""
+ return _normalizeData(data)
+
+
+class DataView(object):
+ """Holder for the data view."""
+
+ UNSUPPORTED = -1
+ """Priority returned when the requested data can't be displayed by the
+ view."""
+
+ def __init__(self, parent, modeId=None, icon=None, label=None):
+ """Constructor
+
+ :param qt.QWidget parent: Parent of the hold widget
+ """
+ self.__parent = parent
+ self.__widget = None
+ self.__modeId = modeId
+ if label is None:
+ label = self.__class__.__name__
+ self.__label = label
+ if icon is None:
+ icon = qt.QIcon()
+ self.__icon = icon
+
+ def icon(self):
+ """Returns the default icon"""
+ return self.__icon
+
+ def label(self):
+ """Returns the default label"""
+ return self.__label
+
+ def modeId(self):
+ """Returns the mode id"""
+ return self.__modeId
+
+ def normalizeData(self, data):
+ """Returns a normalized data if the embed a numpy or a dataset.
+ Else returns the data."""
+ return _normalizeData(data)
+
+ def customAxisNames(self):
+ """Returns names of axes which can be custom by the user and provided
+ to the view."""
+ return []
+
+ def setCustomAxisValue(self, name, value):
+ """
+ Set the value of a custom axis
+
+ :param str name: Name of the custom axis
+ :param int value: Value of the custom axis
+ """
+ pass
+
+ def isWidgetInitialized(self):
+ """Returns true if the widget is already initialized.
+ """
+ return self.__widget is not None
+
+ def select(self):
+ """Called when the view is selected to display the data.
+ """
+ return
+
+ def getWidget(self):
+ """Returns the widget hold in the view and displaying the data.
+
+ :returns: qt.QWidget
+ """
+ if self.__widget is None:
+ self.__widget = self.createWidget(self.__parent)
+ return self.__widget
+
+ def createWidget(self, parent):
+ """Create the the widget displaying the data
+
+ :param qt.QWidget parent: Parent of the widget
+ :returns: qt.QWidget
+ """
+ raise NotImplementedError()
+
+ def clear(self):
+ """Clear the data from the view"""
+ return None
+
+ def setData(self, data):
+ """Set the data displayed by the view
+
+ :param data: Data to display
+ :type data: numpy.ndarray or h5py.Dataset
+ """
+ return None
+
+ def axesNames(self, data, info):
+ """Returns names of the expected axes of the view, according to the
+ input data.
+
+ :param data: Data to display
+ :type data: numpy.ndarray or h5py.Dataset
+ :param DataInfo info: Pre-computed information on the data
+ :rtype: list[str]
+ """
+ return []
+
+ def getDataPriority(self, data, info):
+ """
+ Returns the priority of using this view according to a data.
+
+ - `UNSUPPORTED` means this view can't display this data
+ - `1` means this view can display the data
+ - `100` means this view should be used for this data
+ - `1000` max value used by the views provided by silx
+ - ...
+
+ :param object data: The data to check
+ :param DataInfo info: Pre-computed information on the data
+ :rtype: int
+ """
+ return DataView.UNSUPPORTED
+
+ def __lt__(self, other):
+ return str(self) < str(other)
+
+
+class CompositeDataView(DataView):
+ """Data view which can display a data using different view according to
+ the kind of the data."""
+
+ def __init__(self, parent, modeId=None, icon=None, label=None):
+ """Constructor
+
+ :param qt.QWidget parent: Parent of the hold widget
+ """
+ super(CompositeDataView, self).__init__(parent, modeId, icon, label)
+ self.__views = {}
+ self.__currentView = None
+
+ def addView(self, dataView):
+ """Add a new dataview to the available list."""
+ self.__views[dataView] = None
+
+ def getBestView(self, data, info):
+ """Returns the best view according to priorities."""
+ info = DataInfo(data)
+ views = [(v.getDataPriority(data, info), v) for v in self.__views.keys()]
+ views = filter(lambda t: t[0] > DataView.UNSUPPORTED, views)
+ views = sorted(views, reverse=True)
+
+ if len(views) == 0:
+ return None
+ elif views[0][0] == DataView.UNSUPPORTED:
+ return None
+ else:
+ return views[0][1]
+
+ def customAxisNames(self):
+ if self.__currentView is None:
+ return
+ return self.__currentView.customAxisNames()
+
+ def setCustomAxisValue(self, name, value):
+ if self.__currentView is None:
+ return
+ self.__currentView.setCustomAxisValue(name, value)
+
+ def __updateDisplayedView(self):
+ widget = self.getWidget()
+ if self.__currentView is None:
+ return
+
+ # load the widget if it is not yet done
+ index = self.__views[self.__currentView]
+ if index is None:
+ w = self.__currentView.getWidget()
+ index = widget.addWidget(w)
+ self.__views[self.__currentView] = index
+ if widget.currentIndex() != index:
+ widget.setCurrentIndex(index)
+ self.__currentView.select()
+
+ def select(self):
+ self.__updateDisplayedView()
+ if self.__currentView is not None:
+ self.__currentView.select()
+
+ def createWidget(self, parent):
+ return qt.QStackedWidget()
+
+ def clear(self):
+ for v in self.__views.keys():
+ v.clear()
+
+ def setData(self, data):
+ if self.__currentView is None:
+ return
+ self.__updateDisplayedView()
+ self.__currentView.setData(data)
+
+ def axesNames(self, data, info):
+ view = self.getBestView(data, info)
+ self.__currentView = view
+ return view.axesNames(data, info)
+
+ def getDataPriority(self, data, info):
+ view = self.getBestView(data, info)
+ self.__currentView = view
+ if view is None:
+ return DataView.UNSUPPORTED
+ else:
+ return view.getDataPriority(data, info)
+
+
+class _EmptyView(DataView):
+ """Dummy view to display nothing"""
+
+ def __init__(self, parent):
+ DataView.__init__(self, parent, modeId=EMPTY_MODE)
+
+ def axesNames(self, data, info):
+ return []
+
+ def createWidget(self, parent):
+ return qt.QLabel(parent)
+
+ def getDataPriority(self, data, info):
+ return DataView.UNSUPPORTED
+
+
+class _Plot1dView(DataView):
+ """View displaying data using a 1d plot"""
+
+ def __init__(self, parent):
+ super(_Plot1dView, self).__init__(
+ parent=parent,
+ modeId=PLOT1D_MODE,
+ label="Curve",
+ icon=icons.getQIcon("view-1d"))
+ self.__resetZoomNextTime = True
+
+ def createWidget(self, parent):
+ from silx.gui import plot
+ return plot.Plot1D(parent=parent)
+
+ def clear(self):
+ self.getWidget().clear()
+ self.__resetZoomNextTime = True
+
+ def normalizeData(self, data):
+ data = DataView.normalizeData(self, data)
+ data = _normalizeComplex(data)
+ return data
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ self.getWidget().addCurve(legend="data",
+ x=range(len(data)),
+ y=data,
+ resetzoom=self.__resetZoomNextTime)
+ self.__resetZoomNextTime = True
+
+ def axesNames(self, data, info):
+ return ["y"]
+
+ def getDataPriority(self, data, info):
+ if data is None or not info.isArray or not info.isNumeric:
+ return DataView.UNSUPPORTED
+ if info.dim < 1:
+ return DataView.UNSUPPORTED
+ if info.interpretation == "spectrum":
+ return 1000
+ if info.dim == 2 and info.shape[0] == 1:
+ return 210
+ if info.dim == 1:
+ return 100
+ else:
+ return 10
+
+
+class _Plot2dView(DataView):
+ """View displaying data using a 2d plot"""
+
+ def __init__(self, parent):
+ super(_Plot2dView, self).__init__(
+ parent=parent,
+ modeId=PLOT2D_MODE,
+ label="Image",
+ icon=icons.getQIcon("view-2d"))
+ self.__resetZoomNextTime = True
+
+ def createWidget(self, parent):
+ from silx.gui import plot
+ widget = plot.Plot2D(parent=parent)
+ widget.setKeepDataAspectRatio(True)
+ widget.setGraphXLabel('X')
+ widget.setGraphYLabel('Y')
+ return widget
+
+ def clear(self):
+ self.getWidget().clear()
+ self.__resetZoomNextTime = True
+
+ def normalizeData(self, data):
+ data = DataView.normalizeData(self, data)
+ data = _normalizeComplex(data)
+ return data
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ self.getWidget().addImage(legend="data",
+ data=data,
+ resetzoom=self.__resetZoomNextTime)
+ self.__resetZoomNextTime = False
+
+ def axesNames(self, data, info):
+ return ["y", "x"]
+
+ def getDataPriority(self, data, info):
+ if data is None or not info.isArray or not info.isNumeric:
+ return DataView.UNSUPPORTED
+ if info.dim < 2:
+ return DataView.UNSUPPORTED
+ if info.interpretation == "image":
+ return 1000
+ if info.dim == 2:
+ return 200
+ else:
+ return 190
+
+
+class _Plot3dView(DataView):
+ """View displaying data using a 3d plot"""
+
+ def __init__(self, parent):
+ super(_Plot3dView, self).__init__(
+ parent=parent,
+ modeId=PLOT3D_MODE,
+ label="Cube",
+ icon=icons.getQIcon("view-3d"))
+ try:
+ import silx.gui.plot3d #noqa
+ except ImportError:
+ _logger.warning("Plot3dView is not available")
+ _logger.debug("Backtrace", exc_info=True)
+ raise
+ self.__resetZoomNextTime = True
+
+ def createWidget(self, parent):
+ from silx.gui.plot3d import ScalarFieldView
+ from silx.gui.plot3d import SFViewParamTree
+
+ plot = ScalarFieldView.ScalarFieldView(parent)
+ plot.setAxesLabels(*reversed(self.axesNames(None, None)))
+ plot.addIsosurface(
+ lambda data: numpy.mean(data) + numpy.std(data), '#FF0000FF')
+
+ # Create a parameter tree for the scalar field view
+ options = SFViewParamTree.TreeView(plot)
+ options.setSfView(plot)
+
+ # Add the parameter tree to the main window in a dock widget
+ dock = qt.QDockWidget()
+ dock.setWidget(options)
+ plot.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
+
+ return plot
+
+ def clear(self):
+ self.getWidget().setData(None)
+ self.__resetZoomNextTime = True
+
+ def normalizeData(self, data):
+ data = DataView.normalizeData(self, data)
+ data = _normalizeComplex(data)
+ return data
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ plot = self.getWidget()
+ plot.setData(data)
+ self.__resetZoomNextTime = False
+
+ def axesNames(self, data, info):
+ return ["z", "y", "x"]
+
+ def getDataPriority(self, data, info):
+ if data is None or not info.isArray or not info.isNumeric:
+ return DataView.UNSUPPORTED
+ if info.dim < 3:
+ return DataView.UNSUPPORTED
+ if min(data.shape) < 2:
+ return DataView.UNSUPPORTED
+ if info.dim == 3:
+ return 100
+ else:
+ return 10
+
+
+class _ArrayView(DataView):
+ """View displaying data using a 2d table"""
+
+ def __init__(self, parent):
+ DataView.__init__(self, parent, modeId=RAW_ARRAY_MODE)
+
+ def createWidget(self, parent):
+ from silx.gui.data.ArrayTableWidget import ArrayTableWidget
+ widget = ArrayTableWidget(parent)
+ widget.displayAxesSelector(False)
+ return widget
+
+ def clear(self):
+ self.getWidget().setArrayData(numpy.array([[]]))
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ self.getWidget().setArrayData(data)
+
+ def axesNames(self, data, info):
+ return ["col", "row"]
+
+ def getDataPriority(self, data, info):
+ if data is None or not info.isArray or info.isRecord:
+ return DataView.UNSUPPORTED
+ if info.dim < 2:
+ return DataView.UNSUPPORTED
+ if info.interpretation in ["scalar", "scaler"]:
+ return 1000
+ return 500
+
+
+class _StackView(DataView):
+ """View displaying data using a stack of images"""
+
+ def __init__(self, parent):
+ super(_StackView, self).__init__(
+ parent=parent,
+ modeId=STACK_MODE,
+ label="Image stack",
+ icon=icons.getQIcon("view-2d-stack"))
+ self.__resetZoomNextTime = True
+
+ def customAxisNames(self):
+ return ["depth"]
+
+ def setCustomAxisValue(self, name, value):
+ if name == "depth":
+ self.getWidget().setFrameNumber(value)
+ else:
+ raise Exception("Unsupported axis")
+
+ def createWidget(self, parent):
+ from silx.gui import plot
+ widget = plot.StackView(parent=parent)
+ widget.setKeepDataAspectRatio(True)
+ widget.setLabels(self.axesNames(None, None))
+ # hide default option panel
+ widget.setOptionVisible(False)
+ return widget
+
+ def clear(self):
+ self.getWidget().clear()
+ self.__resetZoomNextTime = True
+
+ def normalizeData(self, data):
+ data = DataView.normalizeData(self, data)
+ data = _normalizeComplex(data)
+ return data
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ self.getWidget().setStack(stack=data, reset=self.__resetZoomNextTime)
+ self.__resetZoomNextTime = False
+
+ def axesNames(self, data, info):
+ return ["depth", "y", "x"]
+
+ def getDataPriority(self, data, info):
+ if data is None or not info.isArray or not info.isNumeric:
+ return DataView.UNSUPPORTED
+ if info.dim < 3:
+ return DataView.UNSUPPORTED
+ if info.interpretation == "image":
+ return 500
+ return 90
+
+
+class _ScalarView(DataView):
+ """View displaying data using text"""
+
+ def __init__(self, parent):
+ DataView.__init__(self, parent, modeId=RAW_SCALAR_MODE)
+
+ def createWidget(self, parent):
+ widget = qt.QTextEdit(parent)
+ widget.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
+ widget.setAlignment(qt.Qt.AlignLeft | qt.Qt.AlignTop)
+ self.__formatter = TextFormatter(parent)
+ return widget
+
+ def clear(self):
+ self.getWidget().setText("")
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ if silx.io.is_dataset(data):
+ data = data[()]
+ text = self.__formatter.toString(data)
+ self.getWidget().setText(text)
+
+ def axesNames(self, data, info):
+ return []
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if data is None:
+ return DataView.UNSUPPORTED
+ if silx.io.is_group(data):
+ return DataView.UNSUPPORTED
+ return 2
+
+
+class _RecordView(DataView):
+ """View displaying data using text"""
+
+ def __init__(self, parent):
+ DataView.__init__(self, parent, modeId=RAW_RECORD_MODE)
+
+ def createWidget(self, parent):
+ from .RecordTableView import RecordTableView
+ widget = RecordTableView(parent)
+ widget.setWordWrap(False)
+ return widget
+
+ def clear(self):
+ self.getWidget().setArrayData(None)
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ widget = self.getWidget()
+ widget.setArrayData(data)
+ widget.resizeRowsToContents()
+ widget.resizeColumnsToContents()
+
+ def axesNames(self, data, info):
+ return ["data"]
+
+ def getDataPriority(self, data, info):
+ if info.isRecord:
+ return 40
+ if data is None or not info.isArray:
+ return DataView.UNSUPPORTED
+ if info.dim == 1:
+ if info.interpretation in ["scalar", "scaler"]:
+ return 1000
+ if info.shape[0] == 1:
+ return 510
+ return 500
+ elif info.isRecord:
+ return 40
+ return DataView.UNSUPPORTED
+
+
+class _Hdf5View(DataView):
+ """View displaying data using text"""
+
+ def __init__(self, parent):
+ super(_Hdf5View, self).__init__(
+ parent=parent,
+ modeId=HDF5_MODE,
+ label="HDF5",
+ icon=icons.getQIcon("view-hdf5"))
+
+ def createWidget(self, parent):
+ from .Hdf5TableView import Hdf5TableView
+ widget = Hdf5TableView(parent)
+ return widget
+
+ def clear(self):
+ widget = self.getWidget()
+ widget.setData(None)
+
+ def setData(self, data):
+ widget = self.getWidget()
+ widget.setData(data)
+
+ def axesNames(self, data, info):
+ return []
+
+ def getDataPriority(self, data, info):
+ widget = self.getWidget()
+ if widget.isSupportedData(data):
+ return 1
+ else:
+ return DataView.UNSUPPORTED
+
+
+class _RawView(CompositeDataView):
+ """View displaying data as raw data.
+
+ This implementation use a 2d-array view, or a record array view, or a
+ raw text output.
+ """
+
+ def __init__(self, parent):
+ super(_RawView, self).__init__(
+ parent=parent,
+ modeId=RAW_MODE,
+ label="Raw",
+ icon=icons.getQIcon("view-raw"))
+ self.addView(_ScalarView(parent))
+ self.addView(_ArrayView(parent))
+ self.addView(_RecordView(parent))
+
+
+class _NXdataScalarView(DataView):
+ """DataView using a table view for displaying NXdata scalars:
+ 0-D signal or n-D signal with *@interpretation=scalar*"""
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def createWidget(self, parent):
+ from silx.gui.data.ArrayTableWidget import ArrayTableWidget
+ widget = ArrayTableWidget(parent)
+ # widget.displayAxesSelector(False)
+ return widget
+
+ def axesNames(self, data, info):
+ return ["col", "row"]
+
+ def clear(self):
+ self.getWidget().setArrayData(numpy.array([[]]),
+ labels=True)
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ signal = NXdata(data).signal
+ self.getWidget().setArrayData(signal,
+ labels=True)
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if info.isNXdata:
+ nxd = NXdata(data)
+ if nxd.signal_is_0d or nxd.interpretation in ["scalar", "scaler"]:
+ return 100
+ return DataView.UNSUPPORTED
+
+
+class _NXdataCurveView(DataView):
+ """DataView using a Plot1D for displaying NXdata curves:
+ 1-D signal or n-D signal with *@interpretation=spectrum*.
+
+ It also handles basic scatter plots:
+ a 1-D signal with one axis whose values are not monotonically increasing.
+ """
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def createWidget(self, parent):
+ from silx.gui.data.NXdataWidgets import ArrayCurvePlot
+ widget = ArrayCurvePlot(parent)
+ return widget
+
+ def axesNames(self, data, info):
+ # disabled (used by default axis selector widget in Hdf5Viewer)
+ return []
+
+ def clear(self):
+ self.getWidget().clear()
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ nxd = NXdata(data)
+ signal_name = data.attrs["signal"]
+ group_name = data.name
+ if nxd.axes_names[-1] is not None:
+ x_errors = nxd.get_axis_errors(nxd.axes_names[-1])
+ else:
+ x_errors = None
+
+ self.getWidget().setCurveData(nxd.signal, nxd.axes[-1],
+ yerror=nxd.errors, xerror=x_errors,
+ ylabel=signal_name, xlabel=nxd.axes_names[-1],
+ title="NXdata group " + group_name)
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if info.isNXdata:
+ nxd = NXdata(data)
+ if nxd.is_x_y_value_scatter or nxd.is_unsupported_scatter:
+ return DataView.UNSUPPORTED
+ if nxd.signal_is_1d and \
+ not nxd.interpretation in ["scalar", "scaler"]:
+ return 100
+ if nxd.interpretation == "spectrum":
+ return 100
+ return DataView.UNSUPPORTED
+
+
+class _NXdataXYVScatterView(DataView):
+ """DataView using a Plot1D for displaying NXdata 3D scatters as
+ a scatter of coloured points (1-D signal with 2 axes)"""
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def createWidget(self, parent):
+ from silx.gui.data.NXdataWidgets import ArrayCurvePlot
+ widget = ArrayCurvePlot(parent)
+ return widget
+
+ def axesNames(self, data, info):
+ # disabled (used by default axis selector widget in Hdf5Viewer)
+ return []
+
+ def clear(self):
+ self.getWidget().clear()
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ nxd = NXdata(data)
+ signal_name = data.attrs["signal"]
+ # signal_errors = nx.errors # not supported
+ group_name = data.name
+ x_axis, y_axis = nxd.axes[-2:]
+
+ x_label, y_label = nxd.axes_names[-2:]
+ if x_label is not None:
+ x_errors = nxd.get_axis_errors(x_label)
+ else:
+ x_errors = None
+
+ if y_label is not None:
+ y_errors = nxd.get_axis_errors(y_label)
+ else:
+ y_errors = None
+
+ self.getWidget().setCurveData(y_axis, x_axis, values=nxd.signal,
+ yerror=y_errors, xerror=x_errors,
+ ylabel=signal_name, xlabel=x_label,
+ title="NXdata group " + group_name)
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if info.isNXdata:
+ if NXdata(data).is_x_y_value_scatter:
+ return 100
+ return DataView.UNSUPPORTED
+
+
+class _NXdataImageView(DataView):
+ """DataView using a Plot2D for displaying NXdata images:
+ 2-D signal or n-D signals with *@interpretation=spectrum*."""
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def createWidget(self, parent):
+ from silx.gui.data.NXdataWidgets import ArrayImagePlot
+ widget = ArrayImagePlot(parent)
+ return widget
+
+ def axesNames(self, data, info):
+ return []
+
+ def clear(self):
+ self.getWidget().clear()
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ nxd = NXdata(data)
+ signal_name = data.attrs["signal"]
+ group_name = data.name
+ y_axis, x_axis = nxd.axes[-2:]
+ y_label, x_label = nxd.axes_names[-2:]
+
+ self.getWidget().setImageData(
+ nxd.signal, x_axis=x_axis, y_axis=y_axis,
+ signal_name=signal_name, xlabel=x_label, ylabel=y_label,
+ title="NXdata group %s: %s" % (group_name, signal_name))
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if info.isNXdata:
+ nxd = NXdata(data)
+ if nxd.signal_is_2d:
+ if nxd.interpretation not in ["scalar", "spectrum", "scaler"]:
+ return 100
+ if nxd.interpretation == "image":
+ return 100
+ return DataView.UNSUPPORTED
+
+
+class _NXdataStackView(DataView):
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def createWidget(self, parent):
+ from silx.gui.data.NXdataWidgets import ArrayStackPlot
+ widget = ArrayStackPlot(parent)
+ return widget
+
+ def axesNames(self, data, info):
+ return []
+
+ def clear(self):
+ self.getWidget().clear()
+
+ def setData(self, data):
+ data = self.normalizeData(data)
+ nxd = NXdata(data)
+ signal_name = data.attrs["signal"]
+ group_name = data.name
+ z_axis, y_axis, x_axis = nxd.axes[-3:]
+ z_label, y_label, x_label = nxd.axes_names[-3:]
+
+ self.getWidget().setStackData(
+ nxd.signal, x_axis=x_axis, y_axis=y_axis, z_axis=z_axis,
+ signal_name=signal_name,
+ xlabel=x_label, ylabel=y_label, zlabel=z_label,
+ title="NXdata group %s: %s" % (group_name, signal_name))
+
+ def getDataPriority(self, data, info):
+ data = self.normalizeData(data)
+ if info.isNXdata:
+ nxd = NXdata(data)
+ if nxd.signal_ndim >= 3:
+ if nxd.interpretation not in ["scalar", "scaler",
+ "spectrum", "image"]:
+ return 100
+ return DataView.UNSUPPORTED
+
+
+class _NXdataView(CompositeDataView):
+ """Composite view displaying NXdata groups using the most adequate
+ widget depending on the dimensionality."""
+ def __init__(self, parent):
+ super(_NXdataView, self).__init__(
+ parent=parent,
+ label="NXdata",
+ icon=icons.getQIcon("view-nexus"))
+
+ self.addView(_NXdataScalarView(parent))
+ self.addView(_NXdataCurveView(parent))
+ self.addView(_NXdataXYVScatterView(parent))
+ self.addView(_NXdataImageView(parent))
+ self.addView(_NXdataStackView(parent))
diff --git a/silx/gui/data/Hdf5TableView.py b/silx/gui/data/Hdf5TableView.py
new file mode 100644
index 0000000..5d79907
--- /dev/null
+++ b/silx/gui/data/Hdf5TableView.py
@@ -0,0 +1,414 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""
+This module define model and widget to display 1D slices from numpy
+array using compound data types or hdf5 databases.
+"""
+from __future__ import division
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "07/04/2017"
+
+import functools
+import os.path
+import logging
+from silx.gui import qt
+import silx.io
+from .TextFormatter import TextFormatter
+import silx.gui.hdf5
+from silx.gui.widgets import HierarchicalTableView
+
+_logger = logging.getLogger(__name__)
+
+
+class _CellData(object):
+ """Store a table item
+ """
+ def __init__(self, value=None, isHeader=False, span=None):
+ """
+ Constructor
+
+ :param str value: Label of this property
+ :param bool isHeader: True if the cell is an header
+ :param tuple span: Tuple of row, column span
+ """
+ self.__value = value
+ self.__isHeader = isHeader
+ self.__span = span
+
+ def isHeader(self):
+ """Returns true if the property is a sub-header title.
+
+ :rtype: bool
+ """
+ return self.__isHeader
+
+ def value(self):
+ """Returns the value of the item.
+ """
+ return self.__value
+
+ def span(self):
+ """Returns the span size of the cell.
+
+ :rtype: tuple
+ """
+ return self.__span
+
+
+class _TableData(object):
+ """Modelize a table with header, row and column span.
+
+ It is mostly defined as a row based table.
+ """
+
+ def __init__(self, columnCount):
+ """Constructor.
+
+ :param int columnCount: Define the number of column of the table
+ """
+ self.__colCount = columnCount
+ self.__data = []
+
+ def rowCount(self):
+ """Returns the number of rows.
+
+ :rtype: int
+ """
+ return len(self.__data)
+
+ def columnCount(self):
+ """Returns the number of columns.
+
+ :rtype: int
+ """
+ return self.__colCount
+
+ def clear(self):
+ """Remove all the cells of the table"""
+ self.__data = []
+
+ def cellAt(self, row, column):
+ """Returns the cell at the row column location. Else None if there is
+ nothing.
+
+ :rtype: _CellData
+ """
+ if row < 0:
+ return None
+ if column < 0:
+ return None
+ if row >= len(self.__data):
+ return None
+ cells = self.__data[row]
+ if column >= len(cells):
+ return None
+ return cells[column]
+
+ def addHeaderRow(self, headerLabel):
+ """Append the table with header on the full row.
+
+ :param str headerLabel: label of the header.
+ """
+ item = _CellData(value=headerLabel, isHeader=True, span=(1, self.__colCount))
+ self.__data.append([item])
+
+ def addHeaderValueRow(self, headerLabel, value):
+ """Append the table with a row using the first column as an header and
+ other cells as a single cell for the value.
+
+ :param str headerLabel: label of the header.
+ :param object value: value to store.
+ """
+ header = _CellData(value=headerLabel, isHeader=True)
+ value = _CellData(value=value, span=(1, self.__colCount))
+ self.__data.append([header, value])
+
+ def addRow(self, *args):
+ """Append the table with a row using arguments for each cells
+
+ :param list[object] args: List of cell values for the row
+ """
+ row = []
+ for value in args:
+ if not isinstance(value, _CellData):
+ value = _CellData(value=value)
+ row.append(value)
+ self.__data.append(row)
+
+
+class Hdf5TableModel(HierarchicalTableView.HierarchicalTableModel):
+ """This data model provides access to HDF5 node content (File, Group,
+ Dataset). Main info, like name, file, attributes... are displayed
+ """
+
+ def __init__(self, parent=None, data=None):
+ """
+ Constructor
+
+ :param qt.QObject parent: Parent object
+ :param object data: An h5py-like object (file, group or dataset)
+ """
+ super(Hdf5TableModel, self).__init__(parent)
+
+ self.__obj = None
+ self.__data = _TableData(columnCount=4)
+ self.__formatter = None
+ formatter = TextFormatter(self)
+ self.setFormatter(formatter)
+ self.setObject(data)
+
+ def rowCount(self, parent_idx=None):
+ """Returns number of rows to be displayed in table"""
+ return self.__data.rowCount()
+
+ def columnCount(self, parent_idx=None):
+ """Returns number of columns to be displayed in table"""
+ return self.__data.columnCount()
+
+ def data(self, index, role=qt.Qt.DisplayRole):
+ """QAbstractTableModel method to access data values
+ in the format ready to be displayed"""
+ if not index.isValid():
+ return None
+
+ cell = self.__data.cellAt(index.row(), index.column())
+ if cell is None:
+ return None
+
+ if role == self.SpanRole:
+ return cell.span()
+ elif role == self.IsHeaderRole:
+ return cell.isHeader()
+ elif role == qt.Qt.DisplayRole:
+ value = cell.value()
+ if callable(value):
+ value = value(self.__obj)
+ return str(value)
+ return None
+
+ def flags(self, index):
+ """QAbstractTableModel method to inform the view whether data
+ is editable or not.
+ """
+ return qt.QAbstractTableModel.flags(self, index)
+
+ def isSupportedObject(self, h5pyObject):
+ """
+ Returns true if the provided object can be modelized using this model.
+ """
+ isSupported = False
+ isSupported = isSupported or silx.io.is_group(h5pyObject)
+ isSupported = isSupported or silx.io.is_dataset(h5pyObject)
+ isSupported = isSupported or isinstance(h5pyObject, silx.gui.hdf5.H5Node)
+ return isSupported
+
+ def setObject(self, h5pyObject):
+ """Set the h5py-like object exposed by the model
+
+ :param h5pyObject: A h5py-like object. It can be a `h5py.Dataset`,
+ a `h5py.File`, a `h5py.Group`. It also can be a,
+ `silx.gui.hdf5.H5Node` which is needed to display some local path
+ information.
+ """
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+
+ if h5pyObject is None or self.isSupportedObject(h5pyObject):
+ self.__obj = h5pyObject
+ else:
+ _logger.warning("Object class %s unsupported. Object ignored.", type(h5pyObject))
+ self.__initProperties()
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+ else:
+ self.reset()
+
+ def __initProperties(self):
+ """Initialize the list of available properties according to the defined
+ h5py-like object."""
+ self.__data.clear()
+ if self.__obj is None:
+ return
+
+ obj = self.__obj
+
+ hdf5obj = obj
+ if isinstance(obj, silx.gui.hdf5.H5Node):
+ hdf5obj = obj.h5py_object
+
+ if silx.io.is_file(hdf5obj):
+ objectType = "File"
+ elif silx.io.is_group(hdf5obj):
+ objectType = "Group"
+ elif silx.io.is_dataset(hdf5obj):
+ objectType = "Dataset"
+ else:
+ objectType = obj.__class__.__name__
+ self.__data.addHeaderRow(headerLabel="HDF5 %s" % objectType)
+ self.__data.addHeaderRow(headerLabel="Path info")
+
+ self.__data.addHeaderValueRow("basename", lambda x: os.path.basename(x.name))
+ self.__data.addHeaderValueRow("name", lambda x: x.name)
+ if silx.io.is_file(obj):
+ self.__data.addHeaderValueRow("filename", lambda x: x.filename)
+
+ if isinstance(obj, silx.gui.hdf5.H5Node):
+ # helpful informations if the object come from an HDF5 tree
+ self.__data.addHeaderValueRow("local_basename", lambda x: x.local_basename)
+ self.__data.addHeaderValueRow("local_name", lambda x: x.local_name)
+ self.__data.addHeaderValueRow("local_filename", lambda x: x.local_file.filename)
+
+ if hasattr(obj, "dtype"):
+ self.__data.addHeaderRow(headerLabel="Data info")
+ self.__data.addHeaderValueRow("dtype", lambda x: x.dtype)
+ if hasattr(obj, "shape"):
+ self.__data.addHeaderValueRow("shape", lambda x: x.shape)
+ if hasattr(obj, "size"):
+ self.__data.addHeaderValueRow("size", lambda x: x.size)
+ if hasattr(obj, "chunks") and obj.chunks is not None:
+ self.__data.addHeaderValueRow("chunks", lambda x: x.chunks)
+
+ # relative to compression
+ # h5py expose compression, compression_opts but are not initialized
+ # for external plugins, then we use id
+ # h5py also expose fletcher32 and shuffle attributes, but it is also
+ # part of the filters
+ if hasattr(obj, "shape") and hasattr(obj, "id"):
+ dcpl = obj.id.get_create_plist()
+ if dcpl.get_nfilters() > 0:
+ self.__data.addHeaderRow(headerLabel="Compression info")
+ pos = _CellData(value="Position", isHeader=True)
+ hdf5id = _CellData(value="HDF5 ID", isHeader=True)
+ name = _CellData(value="Name", isHeader=True)
+ options = _CellData(value="Options", isHeader=True)
+ self.__data.addRow(pos, hdf5id, name, options)
+ for index in range(dcpl.get_nfilters()):
+ callback = lambda index, dataIndex, x: self.__get_filter_info(x, index)[dataIndex]
+ pos = _CellData(value=functools.partial(callback, index, 0))
+ hdf5id = _CellData(value=functools.partial(callback, index, 1))
+ name = _CellData(value=functools.partial(callback, index, 2))
+ options = _CellData(value=functools.partial(callback, index, 3))
+ self.__data.addRow(pos, hdf5id, name, options)
+
+ if hasattr(obj, "attrs"):
+ if len(obj.attrs) > 0:
+ self.__data.addHeaderRow(headerLabel="Attributes")
+ for key in sorted(obj.attrs.keys()):
+ callback = lambda key, x: self.__formatter.toString(x.attrs[key])
+ self.__data.addHeaderValueRow(headerLabel=key, value=functools.partial(callback, key))
+
+ def __get_filter_info(self, dataset, filterIndex):
+ """Get a tuple of readable info from dataset filters
+
+ :param h5py.Dataset dataset: A h5py dataset
+ :param int filterId:
+ """
+ try:
+ dcpl = dataset.id.get_create_plist()
+ info = dcpl.get_filter(filterIndex)
+ filterId, _flags, cdValues, name = info
+ name = self.__formatter.toString(name)
+ options = " ".join([self.__formatter.toString(i) for i in cdValues])
+ return (filterIndex, filterId, name, options)
+ except Exception:
+ _logger.debug("Backtrace", exc_info=True)
+ return [filterIndex, None, None, None]
+
+ def object(self):
+ """Returns the internal object modelized.
+
+ :rtype: An h5py-like object
+ """
+ return self.__obj
+
+ def setFormatter(self, formatter):
+ """Set the formatter object to be used to display data from the model
+
+ :param TextFormatter formatter: Formatter to use
+ """
+ if formatter is self.__formatter:
+ return
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+
+ if self.__formatter is not None:
+ self.__formatter.formatChanged.disconnect(self.__formatChanged)
+
+ self.__formatter = formatter
+ if self.__formatter is not None:
+ self.__formatter.formatChanged.connect(self.__formatChanged)
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+ else:
+ self.reset()
+
+ def getFormatter(self):
+ """Returns the text formatter used.
+
+ :rtype: TextFormatter
+ """
+ return self.__formatter
+
+ def __formatChanged(self):
+ """Called when the format changed.
+ """
+ self.reset()
+
+
+class Hdf5TableView(HierarchicalTableView.HierarchicalTableView):
+ """A widget to display metadata about a HDF5 node using a table."""
+
+ def __init__(self, parent=None):
+ super(Hdf5TableView, self).__init__(parent)
+ self.setModel(Hdf5TableModel(self))
+
+ def isSupportedData(self, data):
+ """
+ Returns true if the provided object can be modelized using this model.
+ """
+ return self.model().isSupportedObject(data)
+
+ def setData(self, data):
+ """Set the h5py-like object exposed by the model
+
+ :param h5pyObject: A h5py-like object. It can be a `h5py.Dataset`,
+ a `h5py.File`, a `h5py.Group`. It also can be a,
+ `silx.gui.hdf5.H5Node` which is needed to display some local path
+ information.
+ """
+ self.model().setObject(data)
+ header = self.horizontalHeader()
+ if qt.qVersion() < "5.0":
+ setResizeMode = header.setResizeMode
+ else:
+ setResizeMode = header.setSectionResizeMode
+ setResizeMode(0, qt.QHeaderView.Fixed)
+ setResizeMode(1, qt.QHeaderView.Stretch)
+ header.setStretchLastSection(True)
diff --git a/silx/gui/data/NXdataWidgets.py b/silx/gui/data/NXdataWidgets.py
new file mode 100644
index 0000000..343c7f9
--- /dev/null
+++ b/silx/gui/data/NXdataWidgets.py
@@ -0,0 +1,523 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines widgets used by _NXdataView.
+"""
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "20/03/2017"
+
+import numpy
+
+from silx.gui import qt
+from silx.gui.data.NumpyAxesSelector import NumpyAxesSelector
+from silx.gui.plot import Plot1D, Plot2D, StackView
+
+from silx.math.calibration import ArrayCalibration, NoCalibration, LinearCalibration
+
+
+class ArrayCurvePlot(qt.QWidget):
+ """
+ Widget for plotting a curve from a multi-dimensional signal array
+ and a 1D axis array.
+
+ The signal array can have an arbitrary number of dimensions, the only
+ limitation being that the last dimension must have the same length as
+ the axis array.
+
+ The widget provides sliders to select indices on the first (n - 1)
+ dimensions of the signal array, and buttons to add/replace selected
+ curves to the plot.
+
+ This widget also handles simple 2D or 3D scatter plots (third dimension
+ displayed as colour of points).
+ """
+ def __init__(self, parent=None):
+ """
+
+ :param parent: Parent QWidget
+ """
+ super(ArrayCurvePlot, self).__init__(parent)
+
+ self.__signal = None
+ self.__signal_name = None
+ self.__signal_errors = None
+ self.__axis = None
+ self.__axis_name = None
+ self.__axis_errors = None
+ self.__values = None
+
+ self.__first_curve_added = False
+
+ self._plot = Plot1D(self)
+ self._plot.setDefaultColormap( # for scatters
+ {"name": "viridis",
+ "vmin": 0., "vmax": 1., # ignored (autoscale) but mandatory
+ "normalization": "linear",
+ "autoscale": True})
+
+ self.selectorDock = qt.QDockWidget("Data selector", self._plot)
+ # not closable
+ self.selectorDock.setFeatures(qt.QDockWidget.DockWidgetMovable |
+ qt.QDockWidget.DockWidgetFloatable)
+ self._selector = NumpyAxesSelector(self.selectorDock)
+ self._selector.setNamedAxesSelectorVisibility(False)
+ self.__selector_is_connected = False
+ self.selectorDock.setWidget(self._selector)
+ self._plot.addTabbedDockWidget(self.selectorDock)
+
+ layout = qt.QGridLayout()
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.addWidget(self._plot, 0, 0)
+
+ self.setLayout(layout)
+
+ def setCurveData(self, y, x=None, values=None,
+ yerror=None, xerror=None,
+ ylabel=None, xlabel=None, title=None):
+ """
+
+ :param y: dataset to be represented by the y (vertical) axis.
+ For a scatter, this must be a 1D array and x and values must be
+ 1-D arrays of the same size.
+ In other cases, it can be a n-D array whose last dimension must
+ have the same length as x (and values must be None)
+ :param x: 1-D dataset used as the curve's x values. If provided,
+ its lengths must be equal to the length of the last dimension of
+ ``y`` (and equal to the length of ``value``, for a scatter plot).
+ :param values: Values, to be provided for a x-y-value scatter plot.
+ This will be used to compute the color map and assign colors
+ to the points.
+ :param yerror: 1-D dataset of errors for y, or None
+ :param xerror: 1-D dataset of errors for x, or None
+ :param ylabel: Label for Y axis
+ :param xlabel: Label for X axis
+ :param title: Graph title
+ """
+ self.__signal = y
+ self.__signal_name = ylabel
+ self.__signal_errors = yerror
+ self.__axis = x
+ self.__axis_name = xlabel
+ self.__axis_errors = xerror
+ self.__values = values
+
+ if self.__selector_is_connected:
+ self._selector.selectionChanged.disconnect(self._updateCurve)
+ self.__selector_is_connected = False
+ self._selector.setData(y)
+ self._selector.setAxisNames([ylabel or "Y"])
+
+ if len(y.shape) < 2:
+ self.selectorDock.hide()
+ else:
+ self.selectorDock.show()
+
+ self._plot.setGraphTitle(title or "")
+ self._plot.setGraphXLabel(self.__axis_name or "X")
+ self._plot.setGraphYLabel(self.__signal_name or "Y")
+ self._updateCurve()
+
+ if not self.__selector_is_connected:
+ self._selector.selectionChanged.connect(self._updateCurve)
+ self.__selector_is_connected = True
+
+ def _updateCurve(self):
+ y = self._selector.selectedData()
+ x = self.__axis
+ if x is None:
+ x = numpy.arange(len(y))
+ elif numpy.isscalar(x) or len(x) == 1:
+ # constant axis
+ x = x * numpy.ones_like(y)
+ elif len(x) == 2 and len(y) != 2:
+ # linear calibration a + b * x
+ x = x[0] + x[1] * numpy.arange(len(y))
+ legend = self.__signal_name + "["
+ for sl in self._selector.selection():
+ if sl == slice(None):
+ legend += ":, "
+ else:
+ legend += str(sl) + ", "
+ legend = legend[:-2] + "]"
+ if self.__signal_errors is not None:
+ y_errors = self.__signal_errors[self._selector.selection()]
+ else:
+ y_errors = None
+
+ self._plot.remove(kind=("curve", "scatter"))
+
+ # values: x-y-v scatter
+ if self.__values is not None:
+ self._plot.addScatter(x, y, self.__values,
+ legend=legend,
+ xerror=self.__axis_errors,
+ yerror=y_errors)
+
+ # x monotonically increasing: curve
+ elif numpy.all(numpy.diff(x) > 0):
+ self._plot.addCurve(x, y, legend=legend,
+ xerror=self.__axis_errors,
+ yerror=y_errors)
+
+ # scatter
+ else:
+ self._plot.addScatter(x, y, value=numpy.ones_like(y),
+ legend=legend,
+ xerror=self.__axis_errors,
+ yerror=y_errors)
+ self._plot.resetZoom()
+ self._plot.setGraphXLabel(self.__axis_name)
+ self._plot.setGraphYLabel(self.__signal_name)
+
+ def clear(self):
+ self._plot.clear()
+
+
+class ArrayImagePlot(qt.QWidget):
+ """
+ Widget for plotting an image from a multi-dimensional signal array
+ and two 1D axes array.
+
+ The signal array can have an arbitrary number of dimensions, the only
+ limitation being that the last two dimensions must have the same length as
+ the axes arrays.
+
+ Sliders are provided to select indices on the first (n - 2) dimensions of
+ the signal array, and the plot is updated to show the image corresponding
+ to the selection.
+
+ If one or both of the axes does not have regularly spaced values, the
+ the image is plotted as a coloured scatter plot.
+ """
+ def __init__(self, parent=None):
+ """
+
+ :param parent: Parent QWidget
+ """
+ super(ArrayImagePlot, self).__init__(parent)
+
+ self.__signal = None
+ self.__signal_name = None
+ self.__x_axis = None
+ self.__x_axis_name = None
+ self.__y_axis = None
+ self.__y_axis_name = None
+
+ self._plot = Plot2D(self)
+ self._plot.setDefaultColormap(
+ {"name": "viridis",
+ "vmin": 0., "vmax": 1., # ignored (autoscale) but mandatory
+ "normalization": "linear",
+ "autoscale": True})
+
+ self.selectorDock = qt.QDockWidget("Data selector", self._plot)
+ # not closable
+ self.selectorDock.setFeatures(qt.QDockWidget.DockWidgetMovable |
+ qt.QDockWidget.DockWidgetFloatable)
+ self._legend = qt.QLabel(self)
+ self._selector = NumpyAxesSelector(self.selectorDock)
+ self._selector.setNamedAxesSelectorVisibility(False)
+ self.__selector_is_connected = False
+
+ layout = qt.QVBoxLayout()
+ layout.addWidget(self._plot)
+ layout.addWidget(self._legend)
+ self.selectorDock.setWidget(self._selector)
+ self._plot.addTabbedDockWidget(self.selectorDock)
+
+ self.setLayout(layout)
+
+ def setImageData(self, signal,
+ x_axis=None, y_axis=None,
+ signal_name=None,
+ xlabel=None, ylabel=None,
+ title=None):
+ """
+
+ :param signal: n-D dataset, whose last 2 dimensions are used as the
+ image's values.
+ :param x_axis: 1-D dataset used as the image's x coordinates. If
+ provided, its lengths must be equal to the length of the last
+ dimension of ``signal``.
+ :param y_axis: 1-D dataset used as the image's y. If provided,
+ its lengths must be equal to the length of the 2nd to last
+ dimension of ``signal``.
+ :param signal_name: Label used in the legend
+ :param xlabel: Label for X axis
+ :param ylabel: Label for Y axis
+ :param title: Graph title
+ """
+ if self.__selector_is_connected:
+ self._selector.selectionChanged.disconnect(self._updateImage)
+ self.__selector_is_connected = False
+
+ self.__signal = signal
+ self.__signal_name = signal_name or ""
+ self.__x_axis = x_axis
+ self.__x_axis_name = xlabel
+ self.__y_axis = y_axis
+ self.__y_axis_name = ylabel
+
+ self._selector.setData(signal)
+ self._selector.setAxisNames([ylabel or "Y", xlabel or "X"])
+
+ if len(signal.shape) < 3:
+ self.selectorDock.hide()
+ else:
+ self.selectorDock.show()
+
+ self._plot.setGraphTitle(title or "")
+ self._plot.setGraphXLabel(self.__x_axis_name or "X")
+ self._plot.setGraphYLabel(self.__y_axis_name or "Y")
+
+ self._updateImage()
+
+ if not self.__selector_is_connected:
+ self._selector.selectionChanged.connect(self._updateImage)
+ self.__selector_is_connected = True
+
+ def _updateImage(self):
+ legend = self.__signal_name + "["
+ for sl in self._selector.selection():
+ if sl == slice(None):
+ legend += ":, "
+ else:
+ legend += str(sl) + ", "
+ legend = legend[:-2] + "]"
+ self._legend.setText("Displayed data: " + legend)
+
+ img = self._selector.selectedData()
+ x_axis = self.__x_axis
+ y_axis = self.__y_axis
+
+ if x_axis is None and y_axis is None:
+ xcalib = NoCalibration()
+ ycalib = NoCalibration()
+ else:
+ if x_axis is None:
+ # no calibration
+ x_axis = numpy.arange(img.shape[-1])
+ elif numpy.isscalar(x_axis) or len(x_axis) == 1:
+ # constant axis
+ x_axis = x_axis * numpy.ones((img.shape[-1], ))
+ elif len(x_axis) == 2:
+ # linear calibration
+ x_axis = x_axis[0] * numpy.arange(img.shape[-1]) + x_axis[1]
+
+ if y_axis is None:
+ y_axis = numpy.arange(img.shape[-2])
+ elif numpy.isscalar(y_axis) or len(y_axis) == 1:
+ y_axis = y_axis * numpy.ones((img.shape[-2], ))
+ elif len(y_axis) == 2:
+ y_axis = y_axis[0] * numpy.arange(img.shape[-2]) + y_axis[1]
+
+ xcalib = ArrayCalibration(x_axis)
+ ycalib = ArrayCalibration(y_axis)
+
+ self._plot.remove(kind=("scatter", "image"))
+ if xcalib.is_affine() and ycalib.is_affine():
+ # regular image
+ xorigin, xscale = xcalib(0), xcalib.get_slope()
+ yorigin, yscale = ycalib(0), ycalib.get_slope()
+ origin = (xorigin, yorigin)
+ scale = (xscale, yscale)
+
+ self._plot.addImage(img, legend=legend,
+ origin=origin, scale=scale)
+ else:
+ scatterx, scattery = numpy.meshgrid(x_axis, y_axis)
+ self._plot.addScatter(numpy.ravel(scatterx),
+ numpy.ravel(scattery),
+ numpy.ravel(img),
+ legend=legend)
+ self._plot.setGraphXLabel(self.__x_axis_name)
+ self._plot.setGraphYLabel(self.__y_axis_name)
+ self._plot.resetZoom()
+
+ def clear(self):
+ self._plot.clear()
+
+
+class ArrayStackPlot(qt.QWidget):
+ """
+ Widget for plotting a n-D array (n >= 3) as a stack of images.
+ Three axis arrays can be provided to calibrate the axes.
+
+ The signal array can have an arbitrary number of dimensions, the only
+ limitation being that the last 3 dimensions must have the same length as
+ the axes arrays.
+
+ Sliders are provided to select indices on the first (n - 3) dimensions of
+ the signal array, and the plot is updated to load the stack corresponding
+ to the selection.
+ """
+ def __init__(self, parent=None):
+ """
+
+ :param parent: Parent QWidget
+ """
+ super(ArrayStackPlot, self).__init__(parent)
+
+ self.__signal = None
+ self.__signal_name = None
+ # the Z, Y, X axes apply to the last three dimensions of the signal
+ # (in that order)
+ self.__z_axis = None
+ self.__z_axis_name = None
+ self.__y_axis = None
+ self.__y_axis_name = None
+ self.__x_axis = None
+ self.__x_axis_name = None
+
+ self._stack_view = StackView(self)
+ self._hline = qt.QFrame(self)
+ self._hline.setFrameStyle(qt.QFrame.HLine)
+ self._hline.setFrameShadow(qt.QFrame.Sunken)
+ self._legend = qt.QLabel(self)
+ self._selector = NumpyAxesSelector(self)
+ self._selector.setNamedAxesSelectorVisibility(False)
+ self.__selector_is_connected = False
+
+ layout = qt.QVBoxLayout()
+ layout.addWidget(self._stack_view)
+ layout.addWidget(self._hline)
+ layout.addWidget(self._legend)
+ layout.addWidget(self._selector)
+
+ self.setLayout(layout)
+
+ def setStackData(self, signal,
+ x_axis=None, y_axis=None, z_axis=None,
+ signal_name=None,
+ xlabel=None, ylabel=None, zlabel=None,
+ title=None):
+ """
+
+ :param signal: n-D dataset, whose last 3 dimensions are used as the
+ 3D stack values.
+ :param x_axis: 1-D dataset used as the image's x coordinates. If
+ provided, its lengths must be equal to the length of the last
+ dimension of ``signal``.
+ :param y_axis: 1-D dataset used as the image's y. If provided,
+ its lengths must be equal to the length of the 2nd to last
+ dimension of ``signal``.
+ :param z_axis: 1-D dataset used as the image's z. If provided,
+ its lengths must be equal to the length of the 3rd to last
+ dimension of ``signal``.
+ :param signal_name: Label used in the legend
+ :param xlabel: Label for X axis
+ :param ylabel: Label for Y axis
+ :param zlabel: Label for Z axis
+ :param title: Graph title
+ """
+ if self.__selector_is_connected:
+ self._selector.selectionChanged.disconnect(self._updateStack)
+ self.__selector_is_connected = False
+
+ self.__signal = signal
+ self.__signal_name = signal_name or ""
+ self.__x_axis = x_axis
+ self.__x_axis_name = xlabel
+ self.__y_axis = y_axis
+ self.__y_axis_name = ylabel
+ self.__z_axis = z_axis
+ self.__z_axis_name = zlabel
+
+ self._selector.setData(signal)
+ self._selector.setAxisNames([ylabel or "Y", xlabel or "X", zlabel or "Z"])
+
+ self._stack_view.setGraphTitle(title or "")
+ # by default, the z axis is the image position (dimension not plotted)
+ self._stack_view.setGraphXLabel(self.__x_axis_name or "X")
+ self._stack_view.setGraphYLabel(self.__y_axis_name or "Y")
+
+ self._updateStack()
+
+ ndims = len(signal.shape)
+ self._stack_view.setFirstStackDimension(ndims - 3)
+
+ # the legend label shows the selection slice producing the volume
+ # (only interesting for ndim > 3)
+ if ndims > 3:
+ self._selector.setVisible(True)
+ self._legend.setVisible(True)
+ self._hline.setVisible(True)
+ else:
+ self._selector.setVisible(False)
+ self._legend.setVisible(False)
+ self._hline.setVisible(False)
+
+ if not self.__selector_is_connected:
+ self._selector.selectionChanged.connect(self._updateStack)
+ self.__selector_is_connected = True
+
+ @staticmethod
+ def _get_origin_scale(axis):
+ """Assuming axis is a regularly spaced 1D array,
+ return a tuple (origin, scale) where:
+ - origin = axis[0]
+ - scale = (axis[n-1] - axis[0]) / (n -1)
+ :param axis: 1D numpy array
+ :return: Tuple (axis[0], (axis[-1] - axis[0]) / (len(axis) - 1))
+ """
+ return axis[0], (axis[-1] - axis[0]) / (len(axis) - 1)
+
+ def _updateStack(self):
+ """Update displayed stack according to the current axes selector
+ data."""
+ stk = self._selector.selectedData()
+ x_axis = self.__x_axis
+ y_axis = self.__y_axis
+ z_axis = self.__z_axis
+
+ calibrations = []
+ for axis in [z_axis, y_axis, x_axis]:
+
+ if axis is None:
+ calibrations.append(NoCalibration())
+ elif len(axis) == 2:
+ calibrations.append(
+ LinearCalibration(y_intercept=axis[0],
+ slope=axis[1]))
+ else:
+ calibrations.append(ArrayCalibration(axis))
+
+ legend = self.__signal_name + "["
+ for sl in self._selector.selection():
+ if sl == slice(None):
+ legend += ":, "
+ else:
+ legend += str(sl) + ", "
+ legend = legend[:-2] + "]"
+ self._legend.setText("Displayed data: " + legend)
+
+ self._stack_view.setStack(stk, calibrations=calibrations)
+ self._stack_view.setLabels(
+ labels=[self.__z_axis_name,
+ self.__y_axis_name,
+ self.__x_axis_name])
+
+ def clear(self):
+ self._stack_view.clear()
diff --git a/silx/gui/data/NumpyAxesSelector.py b/silx/gui/data/NumpyAxesSelector.py
new file mode 100644
index 0000000..f4641da
--- /dev/null
+++ b/silx/gui/data/NumpyAxesSelector.py
@@ -0,0 +1,468 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This module defines a widget able to convert a numpy array from n-dimensions
+to a numpy array with less dimensions.
+"""
+from __future__ import division
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "16/01/2017"
+
+import numpy
+import functools
+from silx.gui.widgets.FrameBrowser import HorizontalSliderWithBrowser
+from silx.gui import qt
+import silx.utils.weakref
+
+
+class _Axis(qt.QWidget):
+ """Widget displaying an axis.
+
+ It allows to display and scroll in the axis, and provide a widget to
+ map the axis with a named axis (the one from the view).
+ """
+
+ valueChanged = qt.Signal(int)
+ """Emitted when the location on the axis change."""
+
+ axisNameChanged = qt.Signal(object)
+ """Emitted when the user change the name of the axis."""
+
+ def __init__(self, parent=None):
+ """Constructor
+
+ :param parent: Parent of the widget
+ """
+ super(_Axis, self).__init__(parent)
+ self.__axisNumber = None
+ self.__customAxisNames = set([])
+ self.__label = qt.QLabel(self)
+ self.__axes = qt.QComboBox(self)
+ self.__axes.currentIndexChanged[int].connect(self.__axisMappingChanged)
+ self.__slider = HorizontalSliderWithBrowser(self)
+ self.__slider.valueChanged[int].connect(self.__sliderValueChanged)
+ layout = qt.QHBoxLayout(self)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.addWidget(self.__label)
+ layout.addWidget(self.__axes)
+ layout.addWidget(self.__slider, 10000)
+ layout.addStretch(1)
+ self.setLayout(layout)
+
+ def slider(self):
+ """Returns the slider used to display axes location.
+
+ :rtype: HorizontalSliderWithBrowser
+ """
+ return self.__slider
+
+ def setAxis(self, number, position, size):
+ """Set axis information.
+
+ :param int number: The number of the axis (from the original numpy
+ array)
+ :param int position: The current position in the axis (for a slicing)
+ :param int size: The size of this axis (0..n)
+ """
+ self.__label.setText("Dimension %s" % number)
+ self.__axisNumber = number
+ self.__slider.setMaximum(size - 1)
+
+ def axisNumber(self):
+ """Returns the axis number.
+
+ :rtype: int
+ """
+ return self.__axisNumber
+
+ def setAxisName(self, axisName):
+ """Set the current used axis name.
+
+ If this name is not available an exception is raised. An empty string
+ means that no name is selected.
+
+ :param str axisName: The new name of the axis
+ :raise ValueError: When the name is not available
+ """
+ if axisName == "" and self.__axes.count() == 0:
+ self.__axes.setCurrentIndex(-1)
+ self.__updateSliderVisibility()
+ for index in range(self.__axes.count()):
+ name = self.__axes.itemData(index)
+ if name == axisName:
+ self.__axes.setCurrentIndex(index)
+ self.__updateSliderVisibility()
+ return
+ raise ValueError("Axis name '%s' not found", axisName)
+
+ def axisName(self):
+ """Returns the selected axis name.
+
+ If no names are selected, an empty string is retruned.
+
+ :rtype: str
+ """
+ index = self.__axes.currentIndex()
+ if index == -1:
+ return ""
+ return self.__axes.itemData(index)
+
+ def setAxisNames(self, axesNames):
+ """Set the available list of names for the axis.
+
+ :param list[str] axesNames: List of available names
+ """
+ self.__axes.clear()
+ previous = self.__axes.blockSignals(True)
+ self.__axes.addItem(" ", "")
+ for axis in axesNames:
+ self.__axes.addItem(axis, axis)
+ self.__axes.blockSignals(previous)
+ self.__updateSliderVisibility()
+
+ def setCustomAxis(self, axesNames):
+ """Set the available list of named axis which can be set to a value.
+
+ :param list[str] axesNames: List of customable axis names
+ """
+ self.__customAxisNames = set(axesNames)
+ self.__updateSliderVisibility()
+
+ def __axisMappingChanged(self, index):
+ """Called when the selected name change.
+
+ :param int index: Selected index
+ """
+ self.__updateSliderVisibility()
+ name = self.axisName()
+ self.axisNameChanged.emit(name)
+
+ def __updateSliderVisibility(self):
+ """Update the visibility of the slider according to axis names and
+ customable axis names."""
+ name = self.axisName()
+ isVisible = name == "" or name in self.__customAxisNames
+ self.__slider.setVisible(isVisible)
+
+ def value(self):
+ """Returns the current selected position in the axis.
+
+ :rtype: int
+ """
+ return self.__slider.value()
+
+ def __sliderValueChanged(self, value):
+ """Called when the selected position in the axis change.
+
+ :param int value: Position of the axis
+ """
+ self.valueChanged.emit(value)
+
+ def setNamedAxisSelectorVisibility(self, visible):
+ """Hide or show the named axis combobox.
+ If both the selector and the slider are hidden,
+ hide the entire widget.
+
+ :param visible: boolean
+ """
+ self.__axes.setVisible(visible)
+ name = self.axisName()
+
+ if not visible and name != "":
+ self.setVisible(False)
+ else:
+ self.setVisible(True)
+
+
+class NumpyAxesSelector(qt.QWidget):
+ """Widget to select a view from a numpy array.
+
+ .. image:: img/NumpyAxesSelector.png
+
+ The widget is set with an input data using :meth:`setData`, and a requested
+ output dimension using :meth:`setAxisNames`.
+
+ Widgets are provided to selected expected input axis, and a slice on the
+ non-selected axis.
+
+ The final selected array can be reached using the getter
+ :meth:`selectedData`, and the event `selectionChanged`.
+
+ If the input data is a HDF5 Dataset, the selected output data will be a
+ new numpy array.
+ """
+
+ dataChanged = qt.Signal()
+ """Emitted when the input data change"""
+
+ selectedAxisChanged = qt.Signal()
+ """Emitted when the selected axis change"""
+
+ selectionChanged = qt.Signal()
+ """Emitted when the selected data change"""
+
+ customAxisChanged = qt.Signal(str, int)
+ """Emitted when a custom axis change"""
+
+ def __init__(self, parent=None):
+ """Constructor
+
+ :param parent: Parent of the widget
+ """
+ super(NumpyAxesSelector, self).__init__(parent)
+
+ self.__data = None
+ self.__selectedData = None
+ self.__selection = tuple()
+ self.__axis = []
+ self.__axisNames = []
+ self.__customAxisNames = set([])
+ self.__namedAxesVisibility = True
+ layout = qt.QVBoxLayout(self)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.setSizeConstraint(qt.QLayout.SetMinAndMaxSize)
+ self.setLayout(layout)
+
+ def clear(self):
+ """Clear the widget."""
+ self.setData(None)
+
+ def setAxisNames(self, axesNames):
+ """Set the axis names of the output selected data.
+
+ Axis names are defined from slower to faster axis.
+
+ The size of the list will constrain the dimension of the resulting
+ array.
+
+ :param list[str] axesNames: List of string identifying axis names
+ """
+ self.__axisNames = list(axesNames)
+ delta = len(self.__axis) - len(self.__axisNames)
+ if delta < 0:
+ delta = 0
+ for index, axis in enumerate(self.__axis):
+ previous = axis.blockSignals(True)
+ axis.setAxisNames(self.__axisNames)
+ if index >= delta and index - delta < len(self.__axisNames):
+ axis.setAxisName(self.__axisNames[index - delta])
+ else:
+ axis.setAxisName("")
+ axis.blockSignals(previous)
+ self.__updateSelectedData()
+
+ def setCustomAxis(self, axesNames):
+ """Set the available list of named axis which can be set to a value.
+
+ :param list[str] axesNames: List of customable axis names
+ """
+ self.__customAxisNames = set(axesNames)
+ for axis in self.__axis:
+ axis.setCustomAxis(self.__customAxisNames)
+
+ def setData(self, data):
+ """Set the input data unsed by the widget.
+
+ :param numpy.ndarray data: The input data
+ """
+ if self.__data is not None:
+ # clean up
+ for widget in self.__axis:
+ self.layout().removeWidget(widget)
+ widget.deleteLater()
+ self.__axis = []
+
+ self.__data = data
+
+ if data is not None:
+ # create expected axes
+ dimensionNumber = len(data.shape)
+ delta = dimensionNumber - len(self.__axisNames)
+ for index in range(dimensionNumber):
+ axis = _Axis(self)
+ axis.setAxis(index, 0, data.shape[index])
+ axis.setAxisNames(self.__axisNames)
+ axis.setCustomAxis(self.__customAxisNames)
+ if index >= delta and index - delta < len(self.__axisNames):
+ axis.setAxisName(self.__axisNames[index - delta])
+ # this weak method was expected to be able to delete sub widget
+ callback = functools.partial(silx.utils.weakref.WeakMethodProxy(self.__axisValueChanged), axis)
+ axis.valueChanged.connect(callback)
+ # this weak method was expected to be able to delete sub widget
+ callback = functools.partial(silx.utils.weakref.WeakMethodProxy(self.__axisNameChanged), axis)
+ axis.axisNameChanged.connect(callback)
+ axis.setNamedAxisSelectorVisibility(self.__namedAxesVisibility)
+ self.layout().addWidget(axis)
+ self.__axis.append(axis)
+ self.__normalizeAxisGeometry()
+
+ self.dataChanged.emit()
+ self.__updateSelectedData()
+
+ def __normalizeAxisGeometry(self):
+ """Update axes geometry to align all axes components together."""
+ if len(self.__axis) <= 0:
+ return
+ lineEditWidth = max([a.slider().lineEdit().minimumSize().width() for a in self.__axis])
+ limitWidth = max([a.slider().limitWidget().minimumSizeHint().width() for a in self.__axis])
+ for a in self.__axis:
+ a.slider().lineEdit().setFixedWidth(lineEditWidth)
+ a.slider().limitWidget().setFixedWidth(limitWidth)
+
+ def __axisValueChanged(self, axis, value):
+ name = axis.axisName()
+ if name in self.__customAxisNames:
+ self.customAxisChanged.emit(name, value)
+ else:
+ self.__updateSelectedData()
+
+ def __axisNameChanged(self, axis, name):
+ """Called when an axis name change.
+
+ :param _Axis axis: The changed axis
+ :param str name: The new name of the axis
+ """
+ names = [x.axisName() for x in self.__axis]
+ missingName = set(self.__axisNames) - set(names) - set("")
+ if len(missingName) == 0:
+ missingName = None
+ elif len(missingName) == 1:
+ missingName = list(missingName)[0]
+ else:
+ raise Exception("Unexpected state")
+
+ axisChanged = True
+
+ if axis.axisName() == "":
+ # set the removed label to another widget if it is possible
+ availableWidget = None
+ for widget in self.__axis:
+ if widget is axis:
+ continue
+ if widget.axisName() == "":
+ availableWidget = widget
+ break
+ if availableWidget is None:
+ # If there is no other solution we set the name at the same place
+ axisChanged = False
+ availableWidget = axis
+ previous = availableWidget.blockSignals(True)
+ availableWidget.setAxisName(missingName)
+ availableWidget.blockSignals(previous)
+ else:
+ # there is a duplicated name somewhere
+ # we swap it with the missing name or with nothing
+ dupWidget = None
+ for widget in self.__axis:
+ if widget is axis:
+ continue
+ if widget.axisName() == axis.axisName():
+ dupWidget = widget
+ break
+ if missingName is None:
+ missingName = ""
+ previous = dupWidget.blockSignals(True)
+ dupWidget.setAxisName(missingName)
+ dupWidget.blockSignals(previous)
+
+ if self.__data is None:
+ return
+ if axisChanged:
+ self.selectedAxisChanged.emit()
+ self.__updateSelectedData()
+
+ def __updateSelectedData(self):
+ """Update the selected data according to the state of the widget.
+
+ It fires a `selectionChanged` event.
+ """
+ if self.__data is None:
+ if self.__selectedData is not None:
+ self.__selectedData = None
+ self.__selection = tuple()
+ self.selectionChanged.emit()
+ return
+
+ selection = []
+ axisNames = []
+ for slider in self.__axis:
+ name = slider.axisName()
+ if name == "":
+ selection.append(slider.value())
+ else:
+ selection.append(slice(None))
+ axisNames.append(name)
+
+ self.__selection = tuple(selection)
+ # get a view with few fixed dimensions
+ # with a h5py dataset, it create a copy
+ # TODO we can reuse the same memory in case of a copy
+ view = self.__data[self.__selection]
+
+ # order axis as expected
+ source = []
+ destination = []
+ order = []
+ for index, name in enumerate(self.__axisNames):
+ destination.append(index)
+ source.append(axisNames.index(name))
+ for _, s in sorted(zip(destination, source)):
+ order.append(s)
+ view = numpy.transpose(view, order)
+
+ self.__selectedData = view
+ self.selectionChanged.emit()
+
+ def data(self):
+ """Returns the input data.
+
+ :rtype: numpy.ndarray
+ """
+ return self.__data
+
+ def selectedData(self):
+ """Returns the output data.
+
+ :rtype: numpy.ndarray
+ """
+ return self.__selectedData
+
+ def selection(self):
+ """Returns the selection tuple used to slice the data.
+
+ :rtype: tuple
+ """
+ return self.__selection
+
+ def setNamedAxesSelectorVisibility(self, visible):
+ """Show or hide the combo-boxes allowing to map the plot axes
+ to the data dimension.
+
+ :param visible: Boolean
+ """
+ self.__namedAxesVisibility = visible
+ for axis in self.__axis:
+ axis.setNamedAxisSelectorVisibility(visible)
diff --git a/silx/gui/data/RecordTableView.py b/silx/gui/data/RecordTableView.py
new file mode 100644
index 0000000..ce6a178
--- /dev/null
+++ b/silx/gui/data/RecordTableView.py
@@ -0,0 +1,405 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""
+This module define model and widget to display 1D slices from numpy
+array using compound data types or hdf5 databases.
+"""
+from __future__ import division
+
+import itertools
+import numpy
+from silx.gui import qt
+import silx.io
+from .TextFormatter import TextFormatter
+from silx.gui.widgets.TableWidget import CopySelectedCellsAction
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "27/01/2017"
+
+
+class _MultiLineItem(qt.QItemDelegate):
+ """Draw a multiline text without hiding anything.
+
+ The paint method display a cell without any wrap. And an editor is
+ available to scroll into the selected cell.
+ """
+
+ def __init__(self, parent=None):
+ """
+ Constructor
+
+ :param qt.QWidget parent: Parent of the widget
+ """
+ qt.QItemDelegate.__init__(self, parent)
+ self.__textOptions = qt.QTextOption()
+ self.__textOptions.setFlags(qt.QTextOption.IncludeTrailingSpaces |
+ qt.QTextOption.ShowTabsAndSpaces)
+ self.__textOptions.setWrapMode(qt.QTextOption.NoWrap)
+ self.__textOptions.setAlignment(qt.Qt.AlignTop | qt.Qt.AlignLeft)
+
+ def paint(self, painter, option, index):
+ """
+ Write multiline text without using any wrap or any alignment according
+ to the cell size.
+
+ :param qt.QPainter painter: Painter context used to displayed the cell
+ :param qt.QStyleOptionViewItem option: Control how the editor is shown
+ :param qt.QIndex index: Index of the data to display
+ """
+ painter.save()
+
+ # set colors
+ painter.setPen(qt.QPen(qt.Qt.NoPen))
+ if option.state & qt.QStyle.State_Selected:
+ brush = option.palette.highlight()
+ painter.setBrush(brush)
+ else:
+ brush = index.data(qt.Qt.BackgroundRole)
+ if brush is None:
+ # default background color for a cell
+ brush = qt.Qt.white
+ painter.setBrush(brush)
+ painter.drawRect(option.rect)
+
+ if index.isValid():
+ if option.state & qt.QStyle.State_Selected:
+ brush = option.palette.highlightedText()
+ else:
+ brush = index.data(qt.Qt.ForegroundRole)
+ if brush is None:
+ brush = option.palette.text()
+ painter.setPen(qt.QPen(brush.color()))
+ text = index.data(qt.Qt.DisplayRole)
+ painter.drawText(qt.QRectF(option.rect), text, self.__textOptions)
+
+ painter.restore()
+
+ def createEditor(self, parent, option, index):
+ """
+ Returns the widget used to edit the item specified by index for editing.
+
+ We use it not to edit the content but to show the content with a
+ convenient scroll bar.
+
+ :param qt.QWidget parent: Parent of the widget
+ :param qt.QStyleOptionViewItem option: Control how the editor is shown
+ :param qt.QIndex index: Index of the data to display
+ """
+ if not index.isValid():
+ return super(_MultiLineItem, self).createEditor(parent, option, index)
+
+ editor = qt.QTextEdit(parent)
+ editor.setReadOnly(True)
+ return editor
+
+ def setEditorData(self, editor, index):
+ """
+ Read data from the model and feed the editor.
+
+ :param qt.QWidget editor: Editor widget
+ :param qt.QIndex index: Index of the data to display
+ """
+ text = index.model().data(index, qt.Qt.EditRole)
+ editor.setText(text)
+
+ def updateEditorGeometry(self, editor, option, index):
+ """
+ Update the geometry of the editor according to the changes of the view.
+
+ :param qt.QWidget editor: Editor widget
+ :param qt.QStyleOptionViewItem option: Control how the editor is shown
+ :param qt.QIndex index: Index of the data to display
+ """
+ editor.setGeometry(option.rect)
+
+
+class RecordTableModel(qt.QAbstractTableModel):
+ """This data model provides access to 1D slices from numpy array using
+ compound data types or hdf5 databases.
+
+ Each entries are displayed in a single row, and each columns contain a
+ specific field of the compound type.
+
+ It also allows to display 1D arrays of simple data types.
+ array.
+
+ :param qt.QObject parent: Parent object
+ :param numpy.ndarray data: A numpy array or a h5py dataset
+ """
+ def __init__(self, parent=None, data=None):
+ qt.QAbstractTableModel.__init__(self, parent)
+
+ self.__data = None
+ self.__is_array = False
+ self.__fields = None
+ self.__formatter = None
+ self.__editFormatter = None
+ self.setFormatter(TextFormatter(self))
+
+ # set _data
+ self.setArrayData(data)
+
+ # Methods to be implemented to subclass QAbstractTableModel
+ def rowCount(self, parent_idx=None):
+ """Returns number of rows to be displayed in table"""
+ if self.__data is None:
+ return 0
+ elif not self.__is_array:
+ return 1
+ else:
+ return len(self.__data)
+
+ def columnCount(self, parent_idx=None):
+ """Returns number of columns to be displayed in table"""
+ if self.__fields is None:
+ return 1
+ else:
+ return len(self.__fields)
+
+ def data(self, index, role=qt.Qt.DisplayRole):
+ """QAbstractTableModel method to access data values
+ in the format ready to be displayed"""
+ if not index.isValid():
+ return None
+
+ if self.__data is None:
+ return None
+
+ if self.__is_array:
+ if index.row() >= len(self.__data):
+ return None
+ data = self.__data[index.row()]
+ else:
+ if index.row() > 0:
+ return None
+ data = self.__data
+
+ if self.__fields is not None:
+ if index.column() >= len(self.__fields):
+ return None
+ key = self.__fields[index.column()][1]
+ data = data[key[0]]
+ if len(key) > 1:
+ data = data[key[1]]
+
+ if role == qt.Qt.DisplayRole:
+ return self.__formatter.toString(data)
+ elif role == qt.Qt.EditRole:
+ return self.__editFormatter.toString(data)
+ return None
+
+ def headerData(self, section, orientation, role=qt.Qt.DisplayRole):
+ """Returns the 0-based row or column index, for display in the
+ horizontal and vertical headers"""
+ if section == -1:
+ # PyQt4 send -1 when there is columns but no rows
+ return None
+
+ if role == qt.Qt.DisplayRole:
+ if orientation == qt.Qt.Vertical:
+ if not self.__is_array:
+ return "Scalar"
+ else:
+ return str(section)
+ if orientation == qt.Qt.Horizontal:
+ if self.__fields is None:
+ if section == 0:
+ return "Data"
+ else:
+ return None
+ else:
+ if section < len(self.__fields):
+ return self.__fields[section][0]
+ else:
+ return None
+ return None
+
+ def flags(self, index):
+ """QAbstractTableModel method to inform the view whether data
+ is editable or not.
+ """
+ return qt.QAbstractTableModel.flags(self, index)
+
+ def setArrayData(self, data):
+ """Set the data array and the viewing perspective.
+
+ You can set ``copy=False`` if you need more performances, when dealing
+ with a large numpy array. In this case, a simple reference to the data
+ is used to access the data, rather than a copy of the array.
+
+ .. warning::
+
+ Any change to the data model will affect your original data
+ array, when using a reference rather than a copy..
+
+ :param data: 1D numpy array, or any object that can be
+ converted to a numpy array using ``numpy.array(data)`` (e.g.
+ a nested sequence).
+ """
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+
+ self.__data = data
+ if isinstance(data, numpy.ndarray):
+ self.__is_array = True
+ elif silx.io.is_dataset(data) and data.shape != tuple():
+ self.__is_array = True
+ else:
+ self.__is_array = False
+
+
+ self.__fields = []
+ if data is not None:
+ if data.dtype.fields is not None:
+ for name, (dtype, _index) in data.dtype.fields.items():
+ if dtype.shape != tuple():
+ keys = itertools.product(*[range(x) for x in dtype.shape])
+ for key in keys:
+ label = "%s%s" % (name, list(key))
+ array_key = (name, key)
+ self.__fields.append((label, array_key))
+ else:
+ self.__fields.append((name, (name,)))
+ else:
+ self.__fields = None
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+ else:
+ self.reset()
+
+ def arrayData(self):
+ """Returns the internal data.
+
+ :rtype: numpy.ndarray of h5py.Dataset
+ """
+ return self.__data
+
+ def setFormatter(self, formatter):
+ """Set the formatter object to be used to display data from the model
+
+ :param TextFormatter formatter: Formatter to use
+ """
+ if formatter is self.__formatter:
+ return
+
+ if qt.qVersion() > "4.6":
+ self.beginResetModel()
+
+ if self.__formatter is not None:
+ self.__formatter.formatChanged.disconnect(self.__formatChanged)
+
+ self.__formatter = formatter
+ self.__editFormatter = TextFormatter(formatter)
+ self.__editFormatter.setUseQuoteForText(False)
+
+ if self.__formatter is not None:
+ self.__formatter.formatChanged.connect(self.__formatChanged)
+
+ if qt.qVersion() > "4.6":
+ self.endResetModel()
+ else:
+ self.reset()
+
+ def getFormatter(self):
+ """Returns the text formatter used.
+
+ :rtype: TextFormatter
+ """
+ return self.__formatter
+
+ def __formatChanged(self):
+ """Called when the format changed.
+ """
+ self.__editFormatter = TextFormatter(self, self.getFormatter())
+ self.__editFormatter.setUseQuoteForText(False)
+ self.reset()
+
+
+class _ShowEditorProxyModel(qt.QIdentityProxyModel):
+ """
+ Allow to custom the flag edit of the model
+ """
+
+ def __init__(self, parent=None):
+ """
+ Constructor
+
+ :param qt.QObject arent: parent object
+ """
+ super(_ShowEditorProxyModel, self).__init__(parent)
+ self.__forceEditable = False
+
+ def flags(self, index):
+ flag = qt.QIdentityProxyModel.flags(self, index)
+ if self.__forceEditable:
+ flag = flag | qt.Qt.ItemIsEditable
+ return flag
+
+ def forceCellEditor(self, show):
+ """
+ Enable the editable flag to allow to display cell editor.
+ """
+ if self.__forceEditable == show:
+ return
+ self.beginResetModel()
+ self.__forceEditable = show
+ self.endResetModel()
+
+
+class RecordTableView(qt.QTableView):
+ """TableView using DatabaseTableModel as default model.
+ """
+ def __init__(self, parent=None):
+ """
+ Constructor
+
+ :param qt.QWidget parent: parent QWidget
+ """
+ qt.QTableView.__init__(self, parent)
+
+ model = _ShowEditorProxyModel(self)
+ model.setSourceModel(RecordTableModel())
+ self.setModel(model)
+ self.__multilineView = _MultiLineItem(self)
+ self.setEditTriggers(qt.QAbstractItemView.AllEditTriggers)
+ self._copyAction = CopySelectedCellsAction(self)
+ self.addAction(self._copyAction)
+
+ def copy(self):
+ self._copyAction.trigger()
+
+ def setArrayData(self, data):
+ self.model().sourceModel().setArrayData(data)
+ if data is not None:
+ if issubclass(data.dtype.type, (numpy.string_, numpy.unicode_)):
+ # TODO it would be nice to also fix fields
+ # but using it only for string array is already very useful
+ self.setItemDelegateForColumn(0, self.__multilineView)
+ self.model().forceCellEditor(True)
+ else:
+ self.setItemDelegateForColumn(0, None)
+ self.model().forceCellEditor(False)
diff --git a/silx/gui/data/TextFormatter.py b/silx/gui/data/TextFormatter.py
new file mode 100644
index 0000000..f074de5
--- /dev/null
+++ b/silx/gui/data/TextFormatter.py
@@ -0,0 +1,222 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This package provides a class sharred by widget from the
+data module to format data as text in the same way."""
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "26/04/2017"
+
+import numpy
+import numbers
+import binascii
+from silx.third_party import six
+from silx.gui import qt
+
+
+class TextFormatter(qt.QObject):
+ """Formatter to convert data to string.
+
+ The method :meth:`toString` returns a formatted string from an input data
+ using parameters set to this object.
+
+ It support most python and numpy data, expecting dictionary. Unsupported
+ data are displayed using the string representation of the object (`str`).
+
+ It provides a set of parameters to custom the formatting of integer and
+ float values (:meth:`setIntegerFormat`, :meth:`setFloatFormat`).
+
+ It also allows to custom the use of quotes to display text data
+ (:meth:`setUseQuoteForText`), and custom unit used to display imaginary
+ numbers (:meth:`setImaginaryUnit`).
+
+ The object emit an event `formatChanged` every time a parametter is
+ changed.
+ """
+
+ formatChanged = qt.Signal()
+ """Emitted when properties of the formatter change."""
+
+ def __init__(self, parent=None, formatter=None):
+ """
+ Constructor
+
+ :param qt.QObject parent: Owner of the object
+ :param TextFormatter formatter: Instantiate this object from the
+ formatter
+ """
+ qt.QObject.__init__(self, parent)
+ if formatter is not None:
+ self.__integerFormat = formatter.integerFormat()
+ self.__floatFormat = formatter.floatFormat()
+ self.__useQuoteForText = formatter.useQuoteForText()
+ self.__imaginaryUnit = formatter.imaginaryUnit()
+ else:
+ self.__integerFormat = "%d"
+ self.__floatFormat = "%g"
+ self.__useQuoteForText = True
+ self.__imaginaryUnit = u"j"
+
+ def integerFormat(self):
+ """Returns the format string controlling how the integer data
+ are formated by this object.
+
+ This is the C-style format string used by python when formatting
+ strings with the modulus operator.
+
+ :rtype: str
+ """
+ return self.__integerFormat
+
+ def setIntegerFormat(self, value):
+ """Set format string controlling how the integer data are
+ formated by this object.
+
+ :param str value: Format string (e.g. "%d", "%i", "%08i").
+ This is the C-style format string used by python when formatting
+ strings with the modulus operator.
+ """
+ if self.__integerFormat == value:
+ return
+ self.__integerFormat = value
+ self.formatChanged.emit()
+
+ def floatFormat(self):
+ """Returns the format string controlling how the floating-point data
+ are formated by this object.
+
+ This is the C-style format string used by python when formatting
+ strings with the modulus operator.
+
+ :rtype: str
+ """
+ return self.__floatFormat
+
+ def setFloatFormat(self, value):
+ """Set format string controlling how the floating-point data are
+ formated by this object.
+
+ :param str value: Format string (e.g. "%.3f", "%d", "%-10.2f",
+ "%10.3e").
+ This is the C-style format string used by python when formatting
+ strings with the modulus operator.
+ """
+ if self.__floatFormat == value:
+ return
+ self.__floatFormat = value
+ self.formatChanged.emit()
+
+ def useQuoteForText(self):
+ """Returns true if the string data are formatted using double quotes.
+
+ Else, no quotes are used.
+ """
+ return self.__integerFormat
+
+ def setUseQuoteForText(self, useQuote):
+ """Set the use of quotes to delimit string data.
+
+ :param bool useQuote: True to use quotes.
+ """
+ if self.__useQuoteForText == useQuote:
+ return
+ self.__useQuoteForText = useQuote
+ self.formatChanged.emit()
+
+ def imaginaryUnit(self):
+ """Returns the unit display for imaginary numbers.
+
+ :rtype: str
+ """
+ return self.__imaginaryUnit
+
+ def setImaginaryUnit(self, imaginaryUnit):
+ """Set the unit display for imaginary numbers.
+
+ :param str imaginaryUnit: Unit displayed after imaginary numbers
+ """
+ if self.__imaginaryUnit == imaginaryUnit:
+ return
+ self.__imaginaryUnit = imaginaryUnit
+ self.formatChanged.emit()
+
+ def toString(self, data):
+ """Format a data into a string using formatter options
+
+ :param object data: Data to render
+ :rtype: str
+ """
+ if isinstance(data, tuple):
+ text = [self.toString(d) for d in data]
+ return "(" + " ".join(text) + ")"
+ elif isinstance(data, (list, numpy.ndarray)):
+ text = [self.toString(d) for d in data]
+ return "[" + " ".join(text) + "]"
+ elif isinstance(data, numpy.void):
+ dtype = data.dtype
+ if data.dtype.fields is not None:
+ text = [self.toString(data[f]) for f in dtype.fields]
+ return "(" + " ".join(text) + ")"
+ return "0x" + binascii.hexlify(data).decode("ascii")
+ elif isinstance(data, (numpy.string_, numpy.object_, bytes)):
+ # This have to be done before checking python string inheritance
+ try:
+ text = "%s" % data.decode("utf-8")
+ if self.__useQuoteForText:
+ text = "\"%s\"" % text.replace("\"", "\\\"")
+ return text
+ except UnicodeDecodeError:
+ pass
+ return "0x" + binascii.hexlify(data).decode("ascii")
+ elif isinstance(data, six.string_types):
+ text = "%s" % data
+ if self.__useQuoteForText:
+ text = "\"%s\"" % text.replace("\"", "\\\"")
+ return text
+ elif isinstance(data, (numpy.integer, numbers.Integral)):
+ return self.__integerFormat % data
+ elif isinstance(data, (numbers.Real, numpy.floating)):
+ # It have to be done before complex checking
+ return self.__floatFormat % data
+ elif isinstance(data, (numpy.complex_, numbers.Complex)):
+ text = ""
+ if data.real != 0:
+ text += self.__floatFormat % data.real
+ if data.real != 0 and data.imag != 0:
+ if data.imag < 0:
+ template = self.__floatFormat + " - " + self.__floatFormat + self.__imaginaryUnit
+ params = (data.real, -data.imag)
+ else:
+ template = self.__floatFormat + " + " + self.__floatFormat + self.__imaginaryUnit
+ params = (data.real, data.imag)
+ else:
+ if data.imag != 0:
+ template = self.__floatFormat + self.__imaginaryUnit
+ params = (data.imag)
+ else:
+ template = self.__floatFormat
+ params = (data.real)
+ return template % params
+ return str(data)
diff --git a/silx/gui/data/__init__.py b/silx/gui/data/__init__.py
new file mode 100644
index 0000000..560062d
--- /dev/null
+++ b/silx/gui/data/__init__.py
@@ -0,0 +1,35 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""This package provides a set of Qt widgets for displaying data arrays using
+table views and plot widgets.
+
+.. note::
+
+ Widgets in this package may rely on additional dependencies that are
+ not mandatory for *silx*.
+ :class:`DataViewer.DataViewer` relies on :mod:`silx.gui.plot` which
+ depends on *matplotlib*. It also optionally depends on *PyOpenGL* for 3D
+ visualization.
+"""
diff --git a/silx/gui/data/setup.py b/silx/gui/data/setup.py
new file mode 100644
index 0000000..23ccbdd
--- /dev/null
+++ b/silx/gui/data/setup.py
@@ -0,0 +1,41 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "16/01/2017"
+
+
+from numpy.distutils.misc_util import Configuration
+
+
+def configuration(parent_package='', top_path=None):
+ config = Configuration('data', parent_package, top_path)
+ config.add_subpackage('test')
+ return config
+
+
+if __name__ == "__main__":
+ from numpy.distutils.core import setup
+ setup(configuration=configuration)
diff --git a/silx/gui/data/test/__init__.py b/silx/gui/data/test/__init__.py
new file mode 100644
index 0000000..08c044b
--- /dev/null
+++ b/silx/gui/data/test/__init__.py
@@ -0,0 +1,45 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+import unittest
+
+from . import test_arraywidget
+from . import test_numpyaxesselector
+from . import test_dataviewer
+from . import test_textformatter
+
+__authors__ = ["V. Valls", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "24/01/2017"
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTests(
+ [test_arraywidget.suite(),
+ test_numpyaxesselector.suite(),
+ test_dataviewer.suite(),
+ test_textformatter.suite(),
+ ])
+ return test_suite
diff --git a/silx/gui/data/test/test_arraywidget.py b/silx/gui/data/test/test_arraywidget.py
new file mode 100644
index 0000000..bbd7ee5
--- /dev/null
+++ b/silx/gui/data/test/test_arraywidget.py
@@ -0,0 +1,320 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "05/12/2016"
+
+import os
+import tempfile
+import unittest
+
+import numpy
+
+from silx.gui import qt
+from silx.gui.data import ArrayTableWidget
+from silx.gui.test.utils import TestCaseQt
+
+try:
+ import h5py
+except ImportError:
+ h5py = None
+
+
+class TestArrayWidget(TestCaseQt):
+ """Basic test for ArrayTableWidget with a numpy array"""
+ def setUp(self):
+ super(TestArrayWidget, self).setUp()
+ self.aw = ArrayTableWidget.ArrayTableWidget()
+
+ def tearDown(self):
+ del self.aw
+ super(TestArrayWidget, self).tearDown()
+
+ def testShow(self):
+ """test for errors"""
+ self.aw.show()
+ self.qWaitForWindowExposed(self.aw)
+
+ def testSetData0D(self):
+ a = 1
+ self.aw.setArrayData(a)
+ b = self.aw.getData(copy=True)
+
+ self.assertTrue(numpy.array_equal(a, b))
+
+ # scalar/0D data has no frame index
+ self.assertEqual(len(self.aw.model._index), 0)
+ # and no perspective
+ self.assertEqual(len(self.aw.model._perspective), 0)
+
+ def testSetData1D(self):
+ a = [1, 2]
+ self.aw.setArrayData(a)
+ b = self.aw.getData(copy=True)
+
+ self.assertTrue(numpy.array_equal(a, b))
+
+ # 1D data has no frame index
+ self.assertEqual(len(self.aw.model._index), 0)
+ # and no perspective
+ self.assertEqual(len(self.aw.model._perspective), 0)
+
+ def testSetData4D(self):
+ a = numpy.reshape(numpy.linspace(0.213, 1.234, 1250),
+ (5, 5, 5, 10))
+ self.aw.setArrayData(a)
+
+ # default perspective (0, 1)
+ self.assertEqual(list(self.aw.model._perspective),
+ [0, 1])
+ self.aw.setPerspective((1, 3))
+ self.assertEqual(list(self.aw.model._perspective),
+ [1, 3])
+
+ b = self.aw.getData(copy=True)
+ self.assertTrue(numpy.array_equal(a, b))
+
+ # 4D data has a 2-tuple as frame index
+ self.assertEqual(len(self.aw.model._index), 2)
+ # default index is (0, 0)
+ self.assertEqual(list(self.aw.model._index),
+ [0, 0])
+ self.aw.setFrameIndex((3, 1))
+
+ self.assertEqual(list(self.aw.model._index),
+ [3, 1])
+
+ def testColors(self):
+ a = numpy.arange(256, dtype=numpy.uint8)
+ self.aw.setArrayData(a)
+
+ bgcolor = numpy.empty(a.shape + (3,), dtype=numpy.uint8)
+ # Black & white palette
+ bgcolor[..., 0] = a
+ bgcolor[..., 1] = a
+ bgcolor[..., 2] = a
+
+ fgcolor = numpy.bitwise_xor(bgcolor, 255)
+
+ self.aw.setArrayColors(bgcolor, fgcolor)
+
+ # test colors are as expected in model
+ for i in range(256):
+ # all RGB channels for BG equal to data value
+ self.assertEqual(
+ self.aw.model.data(self.aw.model.index(0, i),
+ role=qt.Qt.BackgroundRole),
+ qt.QColor(i, i, i),
+ "Unexpected background color"
+ )
+
+ # all RGB channels for FG equal to XOR(data value, 255)
+ self.assertEqual(
+ self.aw.model.data(self.aw.model.index(0, i),
+ role=qt.Qt.ForegroundRole),
+ qt.QColor(i ^ 255, i ^ 255, i ^ 255),
+ "Unexpected text color"
+ )
+
+ # test colors are reset to None when a new data array is loaded
+ # with different shape
+ self.aw.setArrayData(numpy.arange(300))
+
+ for i in range(300):
+ # all RGB channels for BG equal to data value
+ self.assertIsNone(
+ self.aw.model.data(self.aw.model.index(0, i),
+ role=qt.Qt.BackgroundRole))
+
+ def testDefaultFlagNotEditable(self):
+ """editable should be False by default, in setArrayData"""
+ self.aw.setArrayData([[0]])
+ idx = self.aw.model.createIndex(0, 0)
+ # model is editable
+ self.assertFalse(
+ self.aw.model.flags(idx) & qt.Qt.ItemIsEditable)
+
+ def testFlagEditable(self):
+ self.aw.setArrayData([[0]], editable=True)
+ idx = self.aw.model.createIndex(0, 0)
+ # model is editable
+ self.assertTrue(
+ self.aw.model.flags(idx) & qt.Qt.ItemIsEditable)
+
+ def testFlagNotEditable(self):
+ self.aw.setArrayData([[0]], editable=False)
+ idx = self.aw.model.createIndex(0, 0)
+ # model is editable
+ self.assertFalse(
+ self.aw.model.flags(idx) & qt.Qt.ItemIsEditable)
+
+ def testReferenceReturned(self):
+ """when setting the data with copy=False and
+ retrieving it with getData(copy=False), we should recover
+ the same original object.
+ """
+ # n-D (n >=2)
+ a0 = numpy.reshape(numpy.linspace(0.213, 1.234, 1000),
+ (10, 10, 10))
+ self.aw.setArrayData(a0, copy=False)
+ a1 = self.aw.getData(copy=False)
+
+ self.assertIs(a0, a1)
+
+ # 1D
+ b0 = numpy.linspace(0.213, 1.234, 1000)
+ self.aw.setArrayData(b0, copy=False)
+ b1 = self.aw.getData(copy=False)
+ self.assertIs(b0, b1)
+
+
+@unittest.skipIf(h5py is None, "Could not import h5py")
+class TestH5pyArrayWidget(TestCaseQt):
+ """Basic test for ArrayTableWidget with a dataset.
+
+ Test flags, for dataset open in read-only or read-write modes"""
+ def setUp(self):
+ super(TestH5pyArrayWidget, self).setUp()
+ self.aw = ArrayTableWidget.ArrayTableWidget()
+ self.data = numpy.reshape(numpy.linspace(0.213, 1.234, 1000),
+ (10, 10, 10))
+ # create an h5py file with a dataset
+ self.tempdir = tempfile.mkdtemp()
+ self.h5_fname = os.path.join(self.tempdir, "array.h5")
+ h5f = h5py.File(self.h5_fname)
+ h5f["my_array"] = self.data
+ h5f["my_scalar"] = 3.14
+ h5f["my_1D_array"] = numpy.array(numpy.arange(1000))
+ h5f.close()
+
+ def tearDown(self):
+ del self.aw
+ os.unlink(self.h5_fname)
+ os.rmdir(self.tempdir)
+ super(TestH5pyArrayWidget, self).tearDown()
+
+ def testShow(self):
+ self.aw.show()
+ self.qWaitForWindowExposed(self.aw)
+
+ def testReadOnly(self):
+ """Open H5 dataset in read-only mode, ensure the model is not editable."""
+ h5f = h5py.File(self.h5_fname, "r")
+ a = h5f["my_array"]
+ # ArrayTableModel relies on following condition
+ self.assertTrue(a.file.mode == "r")
+
+ self.aw.setArrayData(a, copy=False, editable=True)
+
+ self.assertIsInstance(a, h5py.Dataset) # simple sanity check
+ # internal representation must be a reference to original data (copy=False)
+ self.assertIsInstance(self.aw.model._array, h5py.Dataset)
+ self.assertTrue(self.aw.model._array.file.mode == "r")
+
+ b = self.aw.getData()
+ self.assertTrue(numpy.array_equal(self.data, b))
+
+ # model must have detected read-only dataset and disabled editing
+ self.assertFalse(self.aw.model._editable)
+ idx = self.aw.model.createIndex(0, 0)
+ self.assertFalse(
+ self.aw.model.flags(idx) & qt.Qt.ItemIsEditable)
+
+ # force editing read-only datasets raises IOError
+ self.assertRaises(IOError, self.aw.model.setData,
+ idx, 123.4, role=qt.Qt.EditRole)
+ h5f.close()
+
+ def testReadWrite(self):
+ h5f = h5py.File(self.h5_fname, "r+")
+ a = h5f["my_array"]
+ self.assertTrue(a.file.mode == "r+")
+
+ self.aw.setArrayData(a, copy=False, editable=True)
+ b = self.aw.getData(copy=False)
+ self.assertTrue(numpy.array_equal(self.data, b))
+
+ idx = self.aw.model.createIndex(0, 0)
+ # model is editable
+ self.assertTrue(
+ self.aw.model.flags(idx) & qt.Qt.ItemIsEditable)
+ h5f.close()
+
+ def testSetData0D(self):
+ h5f = h5py.File(self.h5_fname, "r+")
+ a = h5f["my_scalar"]
+ self.aw.setArrayData(a)
+ b = self.aw.getData(copy=True)
+
+ self.assertTrue(numpy.array_equal(a, b))
+
+ h5f.close()
+
+ def testSetData1D(self):
+ h5f = h5py.File(self.h5_fname, "r+")
+ a = h5f["my_1D_array"]
+ self.aw.setArrayData(a)
+ b = self.aw.getData(copy=True)
+
+ self.assertTrue(numpy.array_equal(a, b))
+
+ h5f.close()
+
+ def testReferenceReturned(self):
+ """when setting the data with copy=False and
+ retrieving it with getData(copy=False), we should recover
+ the same original object.
+
+ This only works for array with at least 2D. For 1D and 0D
+ arrays, a view is created at some point, which in the case
+ of an hdf5 dataset creates a copy."""
+ h5f = h5py.File(self.h5_fname, "r+")
+
+ # n-D
+ a0 = h5f["my_array"]
+ self.aw.setArrayData(a0, copy=False)
+ a1 = self.aw.getData(copy=False)
+ self.assertIs(a0, a1)
+
+ # 1D
+ b0 = h5f["my_1D_array"]
+ self.aw.setArrayData(b0, copy=False)
+ b1 = self.aw.getData(copy=False)
+ self.assertIs(b0, b1)
+
+ h5f.close()
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestArrayWidget))
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestH5pyArrayWidget))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/data/test/test_dataviewer.py b/silx/gui/data/test/test_dataviewer.py
new file mode 100644
index 0000000..5a0de0b
--- /dev/null
+++ b/silx/gui/data/test/test_dataviewer.py
@@ -0,0 +1,281 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "10/04/2017"
+
+import os
+import tempfile
+import unittest
+from contextlib import contextmanager
+
+import numpy
+from ..DataViewer import DataViewer
+from ..DataViews import DataView
+from .. import DataViews
+
+from silx.gui import qt
+
+from silx.gui.data.DataViewerFrame import DataViewerFrame
+from silx.gui.test.utils import SignalListener
+from silx.gui.test.utils import TestCaseQt
+
+from silx.gui.hdf5.test import _mock
+
+try:
+ import h5py
+except ImportError:
+ h5py = None
+
+
+class _DataViewMock(DataView):
+ """Dummy view to display nothing"""
+
+ def __init__(self, parent):
+ DataView.__init__(self, parent)
+
+ def axesNames(self, data, info):
+ return []
+
+ def createWidget(self, parent):
+ return qt.QLabel(parent)
+
+ def getDataPriority(self, data, info):
+ return 0
+
+
+class AbstractDataViewerTests(TestCaseQt):
+
+ def create_widget(self):
+ raise NotImplementedError()
+
+ @contextmanager
+ def h5_temporary_file(self):
+ # create tmp file
+ fd, tmp_name = tempfile.mkstemp(suffix=".h5")
+ os.close(fd)
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ # create h5 data
+ h5file = h5py.File(tmp_name, "w")
+ h5file["data"] = data
+ yield h5file
+ # clean up
+ h5file.close()
+ os.unlink(tmp_name)
+
+ def test_text_data(self):
+ data_list = ["aaa", int, 8, self]
+ widget = self.create_widget()
+ for data in data_list:
+ widget.setData(data)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayMode())
+
+ def test_plot_1d_data(self):
+ data = numpy.arange(3 ** 1)
+ data.shape = [3] * 1
+ widget = self.create_widget()
+ widget.setData(data)
+ availableModes = set([v.modeId() for v in widget.currentAvailableViews()])
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayMode())
+ self.assertIn(DataViewer.PLOT1D_MODE, availableModes)
+
+ def test_plot_2d_data(self):
+ data = numpy.arange(3 ** 2)
+ data.shape = [3] * 2
+ widget = self.create_widget()
+ widget.setData(data)
+ availableModes = set([v.modeId() for v in widget.currentAvailableViews()])
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayMode())
+ self.assertIn(DataViewer.PLOT2D_MODE, availableModes)
+
+ def test_plot_3d_data(self):
+ data = numpy.arange(3 ** 3)
+ data.shape = [3] * 3
+ widget = self.create_widget()
+ widget.setData(data)
+ availableModes = set([v.modeId() for v in widget.currentAvailableViews()])
+ try:
+ import silx.gui.plot3d # noqa
+ self.assertIn(DataViewer.PLOT3D_MODE, availableModes)
+ except ImportError:
+ self.assertIn(DataViewer.STACK_MODE, availableModes)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayMode())
+
+ def test_array_1d_data(self):
+ data = numpy.array(["aaa"] * (3 ** 1))
+ data.shape = [3] * 1
+ widget = self.create_widget()
+ widget.setData(data)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayedView().modeId())
+
+ def test_array_2d_data(self):
+ data = numpy.array(["aaa"] * (3 ** 2))
+ data.shape = [3] * 2
+ widget = self.create_widget()
+ widget.setData(data)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayedView().modeId())
+
+ def test_array_4d_data(self):
+ data = numpy.array(["aaa"] * (3 ** 4))
+ data.shape = [3] * 4
+ widget = self.create_widget()
+ widget.setData(data)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayedView().modeId())
+
+ def test_record_4d_data(self):
+ data = numpy.zeros(3 ** 4, dtype='3int8, float32, (2,3)float64')
+ data.shape = [3] * 4
+ widget = self.create_widget()
+ widget.setData(data)
+ self.assertEqual(DataViewer.RAW_MODE, widget.displayedView().modeId())
+
+ def test_3d_h5_dataset(self):
+ if h5py is None:
+ self.skipTest("h5py library is not available")
+ with self.h5_temporary_file() as h5file:
+ dataset = h5file["data"]
+ widget = self.create_widget()
+ widget.setData(dataset)
+
+ def test_data_event(self):
+ listener = SignalListener()
+ widget = self.create_widget()
+ widget.dataChanged.connect(listener)
+ widget.setData(10)
+ widget.setData(None)
+ self.assertEquals(listener.callCount(), 2)
+
+ def test_display_mode_event(self):
+ listener = SignalListener()
+ widget = self.create_widget()
+ widget.displayedViewChanged.connect(listener)
+ widget.setData(10)
+ widget.setData(None)
+ modes = [v.modeId() for v in listener.arguments(argumentIndex=0)]
+ self.assertEquals(modes, [DataViewer.RAW_MODE, DataViewer.EMPTY_MODE])
+ listener.clear()
+
+ def test_change_display_mode(self):
+ data = numpy.arange(10 ** 4)
+ data.shape = [10] * 4
+ widget = self.create_widget()
+ widget.setData(data)
+ widget.setDisplayMode(DataViewer.PLOT1D_MODE)
+ self.assertEquals(widget.displayedView().modeId(), DataViewer.PLOT1D_MODE)
+ widget.setDisplayMode(DataViewer.PLOT2D_MODE)
+ self.assertEquals(widget.displayedView().modeId(), DataViewer.PLOT2D_MODE)
+ widget.setDisplayMode(DataViewer.RAW_MODE)
+ self.assertEquals(widget.displayedView().modeId(), DataViewer.RAW_MODE)
+ widget.setDisplayMode(DataViewer.EMPTY_MODE)
+ self.assertEquals(widget.displayedView().modeId(), DataViewer.EMPTY_MODE)
+
+ def test_create_default_views(self):
+ widget = self.create_widget()
+ views = widget.createDefaultViews()
+ self.assertTrue(len(views) > 0)
+
+ def test_add_view(self):
+ widget = self.create_widget()
+ view = _DataViewMock(widget)
+ widget.addView(view)
+ self.assertTrue(view in widget.availableViews())
+ self.assertTrue(view in widget.currentAvailableViews())
+
+ def test_remove_view(self):
+ widget = self.create_widget()
+ widget.setData("foobar")
+ view = widget.currentAvailableViews()[0]
+ widget.removeView(view)
+ self.assertTrue(view not in widget.availableViews())
+ self.assertTrue(view not in widget.currentAvailableViews())
+
+class TestDataViewer(AbstractDataViewerTests):
+ def create_widget(self):
+ return DataViewer()
+
+
+class TestDataViewerFrame(AbstractDataViewerTests):
+ def create_widget(self):
+ return DataViewerFrame()
+
+
+class TestDataView(TestCaseQt):
+
+ def createComplexData(self):
+ line = [1, 2j, 3+3j, 4]
+ image = [line, line, line, line]
+ cube = [image, image, image, image]
+ data = numpy.array(cube,
+ dtype=numpy.complex)
+ return data
+
+ def createDataViewWithData(self, dataViewClass, data):
+ viewer = dataViewClass(None)
+ widget = viewer.getWidget()
+ viewer.setData(data)
+ return widget
+
+ def testCurveWithComplex(self):
+ data = self.createComplexData()
+ dataViewClass = DataViews._Plot1dView
+ widget = self.createDataViewWithData(dataViewClass, data[0, 0])
+ self.qWaitForWindowExposed(widget)
+
+ def testImageWithComplex(self):
+ data = self.createComplexData()
+ dataViewClass = DataViews._Plot2dView
+ widget = self.createDataViewWithData(dataViewClass, data[0])
+ self.qWaitForWindowExposed(widget)
+
+ def testCubeWithComplex(self):
+ self.skipTest("OpenGL widget not yet tested")
+ try:
+ import silx.gui.plot3d # noqa
+ except ImportError:
+ self.skipTest("OpenGL not available")
+ data = self.createComplexData()
+ dataViewClass = DataViews._Plot3dView
+ widget = self.createDataViewWithData(dataViewClass, data)
+ self.qWaitForWindowExposed(widget)
+
+ def testImageStackWithComplex(self):
+ data = self.createComplexData()
+ dataViewClass = DataViews._StackView
+ widget = self.createDataViewWithData(dataViewClass, data)
+ self.qWaitForWindowExposed(widget)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ loadTestsFromTestCase = unittest.defaultTestLoader.loadTestsFromTestCase
+ test_suite.addTest(loadTestsFromTestCase(TestDataViewer))
+ test_suite.addTest(loadTestsFromTestCase(TestDataViewerFrame))
+ test_suite.addTest(loadTestsFromTestCase(TestDataView))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/data/test/test_numpyaxesselector.py b/silx/gui/data/test/test_numpyaxesselector.py
new file mode 100644
index 0000000..cc15f83
--- /dev/null
+++ b/silx/gui/data/test/test_numpyaxesselector.py
@@ -0,0 +1,152 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "15/12/2016"
+
+import os
+import tempfile
+import unittest
+from contextlib import contextmanager
+
+import numpy
+
+from silx.gui.data.NumpyAxesSelector import NumpyAxesSelector
+from silx.gui.test.utils import SignalListener
+from silx.gui.test.utils import TestCaseQt
+
+try:
+ import h5py
+except ImportError:
+ h5py = None
+
+
+class TestNumpyAxesSelector(TestCaseQt):
+
+ def test_creation(self):
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ widget = NumpyAxesSelector()
+ widget.setVisible(True)
+
+ def test_none(self):
+ data = numpy.arange(3 * 3 * 3)
+ widget = NumpyAxesSelector()
+ widget.setData(data)
+ widget.setData(None)
+ result = widget.selectedData()
+ self.assertIsNone(result)
+
+ def test_output_samedim(self):
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ expectedResult = data
+
+ widget = NumpyAxesSelector()
+ widget.setAxisNames(["x", "y", "z"])
+ widget.setData(data)
+ result = widget.selectedData()
+ self.assertTrue(numpy.array_equal(result, expectedResult))
+
+ def test_output_lessdim(self):
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ expectedResult = data[0]
+
+ widget = NumpyAxesSelector()
+ widget.setAxisNames(["y", "x"])
+ widget.setData(data)
+ result = widget.selectedData()
+ self.assertTrue(numpy.array_equal(result, expectedResult))
+
+ def test_output_1dim(self):
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ expectedResult = data[0, 0, 0]
+
+ widget = NumpyAxesSelector()
+ widget.setData(data)
+ result = widget.selectedData()
+ self.assertTrue(numpy.array_equal(result, expectedResult))
+
+ @contextmanager
+ def h5_temporary_file(self):
+ # create tmp file
+ fd, tmp_name = tempfile.mkstemp(suffix=".h5")
+ os.close(fd)
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ # create h5 data
+ h5file = h5py.File(tmp_name, "w")
+ h5file["data"] = data
+ yield h5file
+ # clean up
+ h5file.close()
+ os.unlink(tmp_name)
+
+ def test_h5py_dataset(self):
+ if h5py is None:
+ self.skipTest("h5py library is not available")
+ with self.h5_temporary_file() as h5file:
+ dataset = h5file["data"]
+ expectedResult = dataset[0]
+
+ widget = NumpyAxesSelector()
+ widget.setData(dataset)
+ widget.setAxisNames(["y", "x"])
+ result = widget.selectedData()
+ self.assertTrue(numpy.array_equal(result, expectedResult))
+
+ def test_data_event(self):
+ data = numpy.arange(3 * 3 * 3)
+ widget = NumpyAxesSelector()
+ listener = SignalListener()
+ widget.dataChanged.connect(listener)
+ widget.setData(data)
+ widget.setData(None)
+ self.assertEqual(listener.callCount(), 2)
+
+ def test_selected_data_event(self):
+ data = numpy.arange(3 * 3 * 3)
+ data.shape = 3, 3, 3
+ widget = NumpyAxesSelector()
+ listener = SignalListener()
+ widget.selectionChanged.connect(listener)
+ widget.setData(data)
+ widget.setAxisNames(["x"])
+ widget.setData(None)
+ self.assertEqual(listener.callCount(), 3)
+ listener.clear()
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestNumpyAxesSelector))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/data/test/test_textformatter.py b/silx/gui/data/test/test_textformatter.py
new file mode 100644
index 0000000..f21e033
--- /dev/null
+++ b/silx/gui/data/test/test_textformatter.py
@@ -0,0 +1,94 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "24/01/2017"
+
+import unittest
+
+from silx.gui.test.utils import TestCaseQt
+from silx.gui.test.utils import SignalListener
+from ..TextFormatter import TextFormatter
+
+
+class TestTextFormatter(TestCaseQt):
+
+ def test_copy(self):
+ formatter = TextFormatter()
+ copy = TextFormatter(formatter=formatter)
+ self.assertIsNot(formatter, copy)
+ copy.setFloatFormat("%.3f")
+ self.assertEquals(formatter.integerFormat(), copy.integerFormat())
+ self.assertNotEquals(formatter.floatFormat(), copy.floatFormat())
+ self.assertEquals(formatter.useQuoteForText(), copy.useQuoteForText())
+ self.assertEquals(formatter.imaginaryUnit(), copy.imaginaryUnit())
+
+ def test_event(self):
+ listener = SignalListener()
+ formatter = TextFormatter()
+ formatter.formatChanged.connect(listener)
+ formatter.setFloatFormat("%.3f")
+ formatter.setIntegerFormat("%03i")
+ formatter.setUseQuoteForText(False)
+ formatter.setImaginaryUnit("z")
+ self.assertEquals(listener.callCount(), 4)
+
+ def test_int(self):
+ formatter = TextFormatter()
+ formatter.setIntegerFormat("%05i")
+ result = formatter.toString(512)
+ self.assertEquals(result, "00512")
+
+ def test_float(self):
+ formatter = TextFormatter()
+ formatter.setFloatFormat("%.3f")
+ result = formatter.toString(1.3)
+ self.assertEquals(result, "1.300")
+
+ def test_complex(self):
+ formatter = TextFormatter()
+ formatter.setFloatFormat("%.1f")
+ formatter.setImaginaryUnit("i")
+ result = formatter.toString(1.0 + 5j)
+ result = result.replace(" ", "")
+ self.assertEquals(result, "1.0+5.0i")
+
+ def test_string(self):
+ formatter = TextFormatter()
+ formatter.setIntegerFormat("%.1f")
+ formatter.setImaginaryUnit("z")
+ result = formatter.toString("toto")
+ self.assertEquals(result, '"toto"')
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestTextFormatter))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/fit/BackgroundWidget.py b/silx/gui/fit/BackgroundWidget.py
new file mode 100644
index 0000000..577a8c7
--- /dev/null
+++ b/silx/gui/fit/BackgroundWidget.py
@@ -0,0 +1,530 @@
+# coding: utf-8
+#/*##########################################################################
+# Copyright (C) 2004-2017 V.A. Sole, European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF by the Software group.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# #########################################################################*/
+"""This module provides a background configuration widget
+:class:`BackgroundWidget` and a corresponding dialog window
+:class:`BackgroundDialog`."""
+import sys
+import numpy
+from silx.gui import qt
+from silx.gui.plot import PlotWidget
+from silx.math.fit import filters
+
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "24/01/2017"
+
+
+class HorizontalSpacer(qt.QWidget):
+ def __init__(self, *args):
+ qt.QWidget.__init__(self, *args)
+ self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Expanding,
+ qt.QSizePolicy.Fixed))
+
+
+class BackgroundParamWidget(qt.QWidget):
+ """Background configuration composite widget.
+
+ Strip and snip filters parameters can be adjusted using input widgets.
+
+ Updating the widgets causes :attr:`sigBackgroundParamWidgetSignal` to
+ be emitted.
+ """
+ sigBackgroundParamWidgetSignal = qt.pyqtSignal(object)
+
+ def __init__(self, parent=None):
+ qt.QWidget.__init__(self, parent)
+
+ self.mainLayout = qt.QGridLayout(self)
+ self.mainLayout.setColumnStretch(1, 1)
+
+ # Algorithm choice ---------------------------------------------------
+ self.algorithmComboLabel = qt.QLabel(self)
+ self.algorithmComboLabel.setText("Background algorithm")
+ self.algorithmCombo = qt.QComboBox(self)
+ self.algorithmCombo.addItem("Strip")
+ self.algorithmCombo.addItem("Snip")
+ self.algorithmCombo.activated[int].connect(
+ self._algorithmComboActivated)
+
+ # Strip parameters ---------------------------------------------------
+ self.stripWidthLabel = qt.QLabel(self)
+ self.stripWidthLabel.setText("Strip Width")
+
+ self.stripWidthSpin = qt.QSpinBox(self)
+ self.stripWidthSpin.setMaximum(100)
+ self.stripWidthSpin.setMinimum(1)
+ self.stripWidthSpin.valueChanged[int].connect(self._emitSignal)
+
+ self.stripIterLabel = qt.QLabel(self)
+ self.stripIterLabel.setText("Strip Iterations")
+ self.stripIterValue = qt.QLineEdit(self)
+ validator = qt.QIntValidator(self.stripIterValue)
+ self.stripIterValue._v = validator
+ self.stripIterValue.setText("0")
+ self.stripIterValue.editingFinished[()].connect(self._emitSignal)
+ self.stripIterValue.setToolTip(
+ "Number of iterations for strip algorithm.\n" +
+ "If greater than 999, an 2nd pass of strip filter is " +
+ "applied to remove artifacts created by first pass.")
+
+ # Snip parameters ----------------------------------------------------
+ self.snipWidthLabel = qt.QLabel(self)
+ self.snipWidthLabel.setText("Snip Width")
+
+ self.snipWidthSpin = qt.QSpinBox(self)
+ self.snipWidthSpin.setMaximum(300)
+ self.snipWidthSpin.setMinimum(0)
+ self.snipWidthSpin.valueChanged[int].connect(self._emitSignal)
+
+
+ # Smoothing parameters -----------------------------------------------
+ self.smoothingFlagCheck = qt.QCheckBox(self)
+ self.smoothingFlagCheck.setText("Smoothing Width (Savitsky-Golay)")
+ self.smoothingFlagCheck.toggled.connect(self._smoothingToggled)
+
+ self.smoothingSpin = qt.QSpinBox(self)
+ self.smoothingSpin.setMinimum(3)
+ #self.smoothingSpin.setMaximum(40)
+ self.smoothingSpin.setSingleStep(2)
+ self.smoothingSpin.valueChanged[int].connect(self._emitSignal)
+
+ # Anchors ------------------------------------------------------------
+
+ self.anchorsGroup = qt.QWidget(self)
+ anchorsLayout = qt.QHBoxLayout(self.anchorsGroup)
+ anchorsLayout.setSpacing(2)
+ anchorsLayout.setContentsMargins(0, 0, 0, 0)
+
+ self.anchorsFlagCheck = qt.QCheckBox(self.anchorsGroup)
+ self.anchorsFlagCheck.setText("Use anchors")
+ self.anchorsFlagCheck.setToolTip(
+ "Define X coordinates of points that must remain fixed")
+ self.anchorsFlagCheck.stateChanged[int].connect(
+ self._anchorsToggled)
+ anchorsLayout.addWidget(self.anchorsFlagCheck)
+
+ maxnchannel = 16384 * 4 # Fixme ?
+ self.anchorsList = []
+ num_anchors = 4
+ for i in range(num_anchors):
+ anchorSpin = qt.QSpinBox(self.anchorsGroup)
+ anchorSpin.setMinimum(0)
+ anchorSpin.setMaximum(maxnchannel)
+ anchorSpin.valueChanged[int].connect(self._emitSignal)
+ anchorsLayout.addWidget(anchorSpin)
+ self.anchorsList.append(anchorSpin)
+
+ # Layout ------------------------------------------------------------
+ self.mainLayout.addWidget(self.algorithmComboLabel, 0, 0)
+ self.mainLayout.addWidget(self.algorithmCombo, 0, 2)
+ self.mainLayout.addWidget(self.stripWidthLabel, 1, 0)
+ self.mainLayout.addWidget(self.stripWidthSpin, 1, 2)
+ self.mainLayout.addWidget(self.stripIterLabel, 2, 0)
+ self.mainLayout.addWidget(self.stripIterValue, 2, 2)
+ self.mainLayout.addWidget(self.snipWidthLabel, 3, 0)
+ self.mainLayout.addWidget(self.snipWidthSpin, 3, 2)
+ self.mainLayout.addWidget(self.smoothingFlagCheck, 4, 0)
+ self.mainLayout.addWidget(self.smoothingSpin, 4, 2)
+ self.mainLayout.addWidget(self.anchorsGroup, 5, 0, 1, 4)
+
+ # Initialize interface -----------------------------------------------
+ self._setAlgorithm("strip")
+ self.smoothingFlagCheck.setChecked(False)
+ self._smoothingToggled(is_checked=False)
+ self.anchorsFlagCheck.setChecked(False)
+ self._anchorsToggled(is_checked=False)
+
+ def _algorithmComboActivated(self, algorithm_index):
+ self._setAlgorithm("strip" if algorithm_index == 0 else "snip")
+
+ def _setAlgorithm(self, algorithm):
+ """Enable/disable snip and snip input widgets, depending on the
+ chosen algorithm.
+ :param algorithm: "snip" or "strip"
+ """
+ if algorithm not in ["strip", "snip"]:
+ raise ValueError(
+ "Unknown background filter algorithm %s" % algorithm)
+
+ self.algorithm = algorithm
+ self.stripWidthSpin.setEnabled(algorithm == "strip")
+ self.stripIterValue.setEnabled(algorithm == "strip")
+ self.snipWidthSpin.setEnabled(algorithm == "snip")
+
+ def _smoothingToggled(self, is_checked):
+ """Enable/disable smoothing input widgets, emit dictionary"""
+ self.smoothingSpin.setEnabled(is_checked)
+ self._emitSignal()
+
+ def _anchorsToggled(self, is_checked):
+ """Enable/disable all spin widgets defining anchor X coordinates,
+ emit signal.
+ """
+ for anchor_spin in self.anchorsList:
+ anchor_spin.setEnabled(is_checked)
+ self._emitSignal()
+
+ def setParameters(self, ddict):
+ """Set values for all input widgets.
+
+ :param dict ddict: Input dictionary, must have the same
+ keys as the dictionary output by :meth:`getParameters`
+ """
+ if "algorithm" in ddict:
+ self._setAlgorithm(ddict["algorithm"])
+
+ if "SnipWidth" in ddict:
+ self.snipWidthSpin.setValue(int(ddict["SnipWidth"]))
+
+ if "StripWidth" in ddict:
+ self.stripWidthSpin.setValue(int(ddict["StripWidth"]))
+
+ if "StripIterations" in ddict:
+ self.stripIterValue.setText("%d" % int(ddict["StripIterations"]))
+
+ if "SmoothingFlag" in ddict:
+ self.smoothingFlagCheck.setChecked(bool(ddict["SmoothingFlag"]))
+
+ if "SmoothingWidth" in ddict:
+ self.smoothingSpin.setValue(int(ddict["SmoothingWidth"]))
+
+ if "AnchorsFlag" in ddict:
+ self.anchorsFlagCheck.setChecked(bool(ddict["AnchorsFlag"]))
+
+ if "AnchorsList" in ddict:
+ anchorslist = ddict["AnchorsList"]
+ if anchorslist in [None, 'None']:
+ anchorslist = []
+ for spin in self.anchorsList:
+ spin.setValue(0)
+
+ i = 0
+ for value in anchorslist:
+ self.anchorsList[i].setValue(int(value))
+ i += 1
+
+ def getParameters(self):
+ """Return dictionary of parameters defined in the GUI
+
+ The returned dictionary contains following values:
+
+ - *algorithm*: *"strip"* or *"snip"*
+ - *StripWidth*: width of strip iterator
+ - *StripIterations*: number of iterations
+ - *StripThreshold*: curvature parameter (currently fixed to 1.0)
+ - *SnipWidth*: width of snip algorithm
+ - *SmoothingFlag*: flag to enable/disable smoothing
+ - *SmoothingWidth*: width of Savitsky-Golay smoothing filter
+ - *AnchorsFlag*: flag to enable/disable anchors
+ - *AnchorsList*: list of anchors (X coordinates of fixed values)
+ """
+ stripitertext = self.stripIterValue.text()
+ stripiter = int(stripitertext) if len(stripitertext) else 0
+
+ return {"algorithm": self.algorithm,
+ "StripThreshold": 1.0,
+ "SnipWidth": self.snipWidthSpin.value(),
+ "StripIterations": stripiter,
+ "StripWidth": self.stripWidthSpin.value(),
+ "SmoothingFlag": self.smoothingFlagCheck.isChecked(),
+ "SmoothingWidth": self.smoothingSpin.value(),
+ "AnchorsFlag": self.anchorsFlagCheck.isChecked(),
+ "AnchorsList": [spin.value() for spin in self.anchorsList]}
+
+ def _emitSignal(self, dummy=None):
+ self.sigBackgroundParamWidgetSignal.emit(
+ {'event': 'ParametersChanged',
+ 'parameters': self.getParameters()})
+
+
+class BackgroundWidget(qt.QWidget):
+ """Background configuration widget, with a :class:`PlotWindow`.
+
+ Strip and snip filters parameters can be adjusted using input widgets,
+ and the computed backgrounds are plotted next to the original data to
+ show the result."""
+ def __init__(self, parent=None):
+ qt.QWidget.__init__(self, parent)
+ self.setWindowTitle("Strip and SNIP Configuration Window")
+ self.mainLayout = qt.QVBoxLayout(self)
+ self.mainLayout.setContentsMargins(0, 0, 0, 0)
+ self.mainLayout.setSpacing(2)
+ self.parametersWidget = BackgroundParamWidget(self)
+ self.graphWidget = PlotWidget(parent=self)
+ self.mainLayout.addWidget(self.parametersWidget)
+ self.mainLayout.addWidget(self.graphWidget)
+ self._x = None
+ self._y = None
+ self.parametersWidget.sigBackgroundParamWidgetSignal.connect(self._slot)
+
+ def getParameters(self):
+ """Return dictionary of parameters defined in the GUI
+
+ The returned dictionary contains following values:
+
+ - *algorithm*: *"strip"* or *"snip"*
+ - *StripWidth*: width of strip iterator
+ - *StripIterations*: number of iterations
+ - *StripThreshold*: strip curvature (currently fixed to 1.0)
+ - *SnipWidth*: width of snip algorithm
+ - *SmoothingFlag*: flag to enable/disable smoothing
+ - *SmoothingWidth*: width of Savitsky-Golay smoothing filter
+ - *AnchorsFlag*: flag to enable/disable anchors
+ - *AnchorsList*: list of anchors (X coordinates of fixed values)
+ """
+ return self.parametersWidget.getParameters()
+
+ def setParameters(self, ddict):
+ """Set values for all input widgets.
+
+ :param dict ddict: Input dictionary, must have the same
+ keys as the dictionary output by :meth:`getParameters`
+ """
+ return self.parametersWidget.setParameters(ddict)
+
+ def setData(self, x, y, xmin=None, xmax=None):
+ """Set data for the original curve, and _update strip and snip
+ curves accordingly.
+
+ :param x: Array or sequence of curve abscissa values
+ :param y: Array or sequence of curve ordinate values
+ :param xmin: Min value to be displayed on the X axis
+ :param xmax: Max value to be displayed on the X axis
+ """
+ self._x = x
+ self._y = y
+ self._xmin = xmin
+ self._xmax = xmax
+ self._update(resetzoom=True)
+
+ def _slot(self, ddict):
+ self._update()
+
+ def _update(self, resetzoom=False):
+ """Compute strip and snip backgrounds, update the curves
+ """
+ if self._y is None:
+ return
+
+ pars = self.getParameters()
+
+ # smoothed data
+ y = numpy.ravel(numpy.array(self._y)).astype(numpy.float)
+ if pars["SmoothingFlag"]:
+ ysmooth = filters.savitsky_golay(y, pars['SmoothingWidth'])
+ f = [0.25, 0.5, 0.25]
+ ysmooth[1:-1] = numpy.convolve(ysmooth, f, mode=0)
+ ysmooth[0] = 0.5 * (ysmooth[0] + ysmooth[1])
+ ysmooth[-1] = 0.5 * (ysmooth[-1] + ysmooth[-2])
+ else:
+ ysmooth = y
+
+
+ # loop for anchors
+ x = self._x
+ niter = pars['StripIterations']
+ anchors_indices = []
+ if pars['AnchorsFlag'] and pars['AnchorsList'] is not None:
+ ravelled = x
+ for channel in pars['AnchorsList']:
+ if channel <= ravelled[0]:
+ continue
+ index = numpy.nonzero(ravelled >= channel)[0]
+ if len(index):
+ index = min(index)
+ if index > 0:
+ anchors_indices.append(index)
+
+ stripBackground = filters.strip(ysmooth,
+ w=pars['StripWidth'],
+ niterations=niter,
+ factor=pars['StripThreshold'],
+ anchors=anchors_indices)
+
+ if niter >= 1000:
+ # final smoothing
+ stripBackground = filters.strip(stripBackground,
+ w=1,
+ niterations=50*pars['StripWidth'],
+ factor=pars['StripThreshold'],
+ anchors=anchors_indices)
+
+ if len(anchors_indices) == 0:
+ anchors_indices = [0, len(ysmooth)-1]
+ anchors_indices.sort()
+ snipBackground = 0.0 * ysmooth
+ lastAnchor = 0
+ for anchor in anchors_indices:
+ if (anchor > lastAnchor) and (anchor < len(ysmooth)):
+ snipBackground[lastAnchor:anchor] =\
+ filters.snip1d(ysmooth[lastAnchor:anchor],
+ pars['SnipWidth'])
+ lastAnchor = anchor
+ if lastAnchor < len(ysmooth):
+ snipBackground[lastAnchor:] =\
+ filters.snip1d(ysmooth[lastAnchor:],
+ pars['SnipWidth'])
+
+ self.graphWidget.addCurve(x, y,
+ legend='Input Data',
+ replace=True,
+ resetzoom=resetzoom)
+ self.graphWidget.addCurve(x, stripBackground,
+ legend='Strip Background',
+ resetzoom=False)
+ self.graphWidget.addCurve(x, snipBackground,
+ legend='SNIP Background',
+ resetzoom=False)
+ if self._xmin is not None and self._xmax is not None:
+ self.graphWidget.setGraphXLimits(xmin=self._xmin, xmax=self._xmax)
+
+
+class BackgroundDialog(qt.QDialog):
+ """QDialog window featuring a :class:`BackgroundWidget`"""
+ def __init__(self, parent=None):
+ qt.QDialog.__init__(self, parent)
+ self.setWindowTitle("Strip and Snip Configuration Window")
+ self.mainLayout = qt.QVBoxLayout(self)
+ self.mainLayout.setContentsMargins(0, 0, 0, 0)
+ self.mainLayout.setSpacing(2)
+ self.parametersWidget = BackgroundWidget(self)
+ self.mainLayout.addWidget(self.parametersWidget)
+ hbox = qt.QWidget(self)
+ hboxLayout = qt.QHBoxLayout(hbox)
+ hboxLayout.setContentsMargins(0, 0, 0, 0)
+ hboxLayout.setSpacing(2)
+ self.okButton = qt.QPushButton(hbox)
+ self.okButton.setText("OK")
+ self.okButton.setAutoDefault(False)
+ self.dismissButton = qt.QPushButton(hbox)
+ self.dismissButton.setText("Cancel")
+ self.dismissButton.setAutoDefault(False)
+ hboxLayout.addWidget(HorizontalSpacer(hbox))
+ hboxLayout.addWidget(self.okButton)
+ hboxLayout.addWidget(self.dismissButton)
+ self.mainLayout.addWidget(hbox)
+ self.dismissButton.clicked.connect(self.reject)
+ self.okButton.clicked.connect(self.accept)
+
+ self.output = {}
+ """Configuration dictionary containing following fields:
+
+ - *SmoothingFlag*
+ - *SmoothingWidth*
+ - *StripWidth*
+ - *StripIterations*
+ - *StripThreshold*
+ - *SnipWidth*
+ - *AnchorsFlag*
+ - *AnchorsList*
+ """
+
+ # self.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(self.updateOutput)
+
+ # def updateOutput(self, ddict):
+ # self.output = ddict
+
+ def accept(self):
+ """Update :attr:`output`, then call :meth:`QDialog.accept`
+ """
+ self.output = self.getParameters()
+ super(BackgroundDialog, self).accept()
+
+ def sizeHint(self):
+ return qt.QSize(int(1.5*qt.QDialog.sizeHint(self).width()),
+ qt.QDialog.sizeHint(self).height())
+
+ def setData(self, x, y, xmin=None, xmax=None):
+ """See :meth:`BackgroundWidget.setData`"""
+ return self.parametersWidget.setData(x, y, xmin, xmax)
+
+ def getParameters(self):
+ """See :meth:`BackgroundWidget.getParameters`"""
+ return self.parametersWidget.getParameters()
+
+ def setParameters(self, ddict):
+ """See :meth:`BackgroundWidget.setParameters`"""
+ return self.parametersWidget.setParameters(ddict)
+
+ def setDefault(self, ddict):
+ """Alias for :meth:`setParameters`"""
+ return self.setParameters(ddict)
+
+
+def getBgDialog(parent=None, default=None, modal=True):
+ """Instantiate and return a bg configuration dialog, adapted
+ for configuring standard background theories from
+ :mod:`silx.math.fit.bgtheories`.
+
+ :return: Instance of :class:`BackgroundDialog`
+ """
+ bgd = BackgroundDialog(parent=parent)
+ # apply default to newly added pages
+ bgd.setParameters(default)
+
+ return bgd
+
+
+def main():
+ # synthetic data
+ from silx.math.fit.functions import sum_gauss
+
+ x = numpy.arange(5000)
+ # (height1, center1, fwhm1, ...) 5 peaks
+ params1 = (50, 500, 100,
+ 20, 2000, 200,
+ 50, 2250, 100,
+ 40, 3000, 75,
+ 23, 4000, 150)
+ y0 = sum_gauss(x, *params1)
+
+ # random values between [-1;1]
+ noise = 2 * numpy.random.random(5000) - 1
+ # make it +- 5%
+ noise *= 0.05
+
+ # 2 gaussians with very large fwhm, as background signal
+ actual_bg = sum_gauss(x, 15, 3500, 3000, 5, 1000, 1500)
+
+ # Add 5% random noise to gaussians and add background
+ y = y0 + numpy.average(y0) * noise + actual_bg
+
+ # Open widget
+ a = qt.QApplication(sys.argv)
+ a.lastWindowClosed.connect(a.quit)
+
+ def mySlot(ddict):
+ print(ddict)
+
+ w = BackgroundDialog()
+ w.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(mySlot)
+ w.setData(x, y)
+ w.exec_()
+ #a.exec_()
+
+if __name__ == "__main__":
+ main()
diff --git a/silx/gui/fit/FitConfig.py b/silx/gui/fit/FitConfig.py
new file mode 100644
index 0000000..70b6fbe
--- /dev/null
+++ b/silx/gui/fit/FitConfig.py
@@ -0,0 +1,540 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2004-2016 V.A. Sole, European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF by the Software group.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ######################################################################### */
+"""This module defines widgets used to build a fit configuration dialog.
+The resulting dialog widget outputs a dictionary of configuration parameters.
+"""
+from silx.gui import qt
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "30/11/2016"
+
+
+class TabsDialog(qt.QDialog):
+ """Dialog widget containing a QTabWidget :attr:`tabWidget`
+ and a buttons:
+
+ # - buttonHelp
+ - buttonDefaults
+ - buttonOk
+ - buttonCancel
+
+ This dialog defines a __len__ returning the number of tabs,
+ and an __iter__ method yielding the tab widgets.
+ """
+ def __init__(self, parent=None):
+ qt.QDialog.__init__(self, parent)
+ self.tabWidget = qt.QTabWidget(self)
+
+ layout = qt.QVBoxLayout(self)
+ layout.addWidget(self.tabWidget)
+
+ layout2 = qt.QHBoxLayout(None)
+
+ # self.buttonHelp = qt.QPushButton(self)
+ # self.buttonHelp.setText("Help")
+ # layout2.addWidget(self.buttonHelp)
+
+ self.buttonDefault = qt.QPushButton(self)
+ self.buttonDefault.setText("Default")
+ layout2.addWidget(self.buttonDefault)
+
+ spacer = qt.QSpacerItem(20, 20,
+ qt.QSizePolicy.Expanding,
+ qt.QSizePolicy.Minimum)
+ layout2.addItem(spacer)
+
+ self.buttonOk = qt.QPushButton(self)
+ self.buttonOk.setText("OK")
+ layout2.addWidget(self.buttonOk)
+
+ self.buttonCancel = qt.QPushButton(self)
+ self.buttonCancel.setText("Cancel")
+ layout2.addWidget(self.buttonCancel)
+
+ layout.addLayout(layout2)
+
+ self.buttonOk.clicked.connect(self.accept)
+ self.buttonCancel.clicked.connect(self.reject)
+
+ def __len__(self):
+ """Return number of tabs"""
+ return self.tabWidget.count()
+
+ def __iter__(self):
+ """Return the next tab widget in :attr:`tabWidget` every
+ time this method is called.
+
+ :return: Tab widget
+ :rtype: QWidget
+ """
+ for widget_index in range(len(self)):
+ yield self.tabWidget.widget(widget_index)
+
+ def addTab(self, page, label):
+ """Add a new tab
+
+ :param page: Content of new page. Must be a widget with
+ a get() method returning a dictionary.
+ :param str label: Tab label
+ """
+ self.tabWidget.addTab(page, label)
+
+ def getTabLabels(self):
+ """
+ Return a list of all tab labels in :attr:`tabWidget`
+ """
+ return [self.tabWidget.tabText(i) for i in range(len(self))]
+
+
+class TabsDialogData(TabsDialog):
+ """This dialog adds a data attribute to :class:`TabsDialog`.
+
+ Data input in widgets, such as text entries or checkboxes, is stored in an
+ attribute :attr:`output` when the user clicks the OK button.
+
+ A default dictionary can be supplied when this dialog is initialized, to
+ be used as default data for :attr:`output`.
+ """
+ def __init__(self, parent=None, modal=True, default=None):
+ """
+
+ :param parent: Parent :class:`QWidget`
+ :param modal: If `True`, dialog is modal, meaning this dialog remains
+ in front of it's parent window and disables it until the user is
+ done interacting with the dialog
+ :param default: Default dictionary, used to initialize and reset
+ :attr:`output`.
+ """
+ TabsDialog.__init__(self, parent)
+ self.setModal(modal)
+ self.setWindowTitle("Fit configuration")
+
+ self.output = {}
+
+ self.default = {} if default is None else default
+
+ self.buttonDefault.clicked.connect(self.setDefault)
+ # self.keyPressEvent(qt.Qt.Key_Enter).
+
+ def keyPressEvent(self, event):
+ """Redefining this method to ignore Enter key
+ (for some reason it activates buttonDefault callback which
+ resets all widgets)
+ """
+ if event.key() in [qt.Qt.Key_Enter, qt.Qt.Key_Return]:
+ return
+ TabsDialog.keyPressEvent(self, event)
+
+ def accept(self):
+ """When *OK* is clicked, update :attr:`output` with data from
+ various widgets
+ """
+ self.output.update(self.default)
+
+ # loop over all tab widgets (uses TabsDialog.__iter__)
+ for tabWidget in self:
+ self.output.update(tabWidget.get())
+
+ # avoid pathological None cases
+ for key in self.output.keys():
+ if self.output[key] is None:
+ if key in self.default:
+ self.output[key] = self.default[key]
+ super(TabsDialogData, self).accept()
+
+ def reject(self):
+ """When the *Cancel* button is clicked, reinitialize :attr:`output`
+ and quit
+ """
+ self.setDefault()
+ super(TabsDialogData, self).reject()
+
+ def setDefault(self, newdefault=None):
+ """Reinitialize :attr:`output` with :attr:`default` or with
+ new dictionary ``newdefault`` if provided.
+ Call :meth:`setDefault` for each tab widget, if available.
+ """
+ self.output = {}
+ if newdefault is None:
+ newdefault = self.default
+ else:
+ self.default = newdefault
+ self.output.update(newdefault)
+
+ for tabWidget in self:
+ if hasattr(tabWidget, "setDefault"):
+ tabWidget.setDefault(self.output)
+
+
+class ConstraintsPage(qt.QGroupBox):
+ """Checkable QGroupBox widget filled with QCheckBox widgets,
+ to configure the fit estimation for standard fit theories.
+ """
+ def __init__(self, parent=None, title="Set constraints"):
+ super(ConstraintsPage, self).__init__(parent)
+ self.setTitle(title)
+ self.setToolTip("Disable 'Set constraints' to remove all " +
+ "constraints on all fit parameters")
+ self.setCheckable(True)
+
+ layout = qt.QVBoxLayout(self)
+ self.setLayout(layout)
+
+ self.positiveHeightCB = qt.QCheckBox("Force positive height/area", self)
+ self.positiveHeightCB.setToolTip("Fit must find positive peaks")
+ layout.addWidget(self.positiveHeightCB)
+
+ self.positionInIntervalCB = qt.QCheckBox("Force position in interval", self)
+ self.positionInIntervalCB.setToolTip(
+ "Fit must position peak within X limits")
+ layout.addWidget(self.positionInIntervalCB)
+
+ self.positiveFwhmCB = qt.QCheckBox("Force positive FWHM", self)
+ self.positiveFwhmCB.setToolTip("Fit must find a positive FWHM")
+ layout.addWidget(self.positiveFwhmCB)
+
+ self.sameFwhmCB = qt.QCheckBox("Force same FWHM for all peaks", self)
+ self.sameFwhmCB.setToolTip("Fit must find same FWHM for all peaks")
+ layout.addWidget(self.sameFwhmCB)
+
+ self.quotedEtaCB = qt.QCheckBox("Force Eta between 0 and 1", self)
+ self.quotedEtaCB.setToolTip(
+ "Fit must find Eta between 0 and 1 for pseudo-Voigt function")
+ layout.addWidget(self.quotedEtaCB)
+
+ layout.addStretch()
+
+ self.setDefault()
+
+ def setDefault(self, default_dict=None):
+ """Set default state for all widgets.
+
+ :param default_dict: If a default config dictionary is provided as
+ a parameter, its values are used as default state."""
+ if default_dict is None:
+ default_dict = {}
+ # this one uses reverse logic: if checked, NoConstraintsFlag must be False
+ self.setChecked(
+ not default_dict.get('NoConstraintsFlag', False))
+ self.positiveHeightCB.setChecked(
+ default_dict.get('PositiveHeightAreaFlag', True))
+ self.positionInIntervalCB.setChecked(
+ default_dict.get('QuotedPositionFlag', False))
+ self.positiveFwhmCB.setChecked(
+ default_dict.get('PositiveFwhmFlag', True))
+ self.sameFwhmCB.setChecked(
+ default_dict.get('SameFwhmFlag', False))
+ self.quotedEtaCB.setChecked(
+ default_dict.get('QuotedEtaFlag', False))
+
+ def get(self):
+ """Return a dictionary of constraint flags, to be processed by the
+ :meth:`configure` method of the selected fit theory."""
+ ddict = {
+ 'NoConstraintsFlag': not self.isChecked(),
+ 'PositiveHeightAreaFlag': self.positiveHeightCB.isChecked(),
+ 'QuotedPositionFlag': self.positionInIntervalCB.isChecked(),
+ 'PositiveFwhmFlag': self.positiveFwhmCB.isChecked(),
+ 'SameFwhmFlag': self.sameFwhmCB.isChecked(),
+ 'QuotedEtaFlag': self.quotedEtaCB.isChecked(),
+ }
+ return ddict
+
+
+class SearchPage(qt.QWidget):
+ def __init__(self, parent=None):
+ super(SearchPage, self).__init__(parent)
+ layout = qt.QVBoxLayout(self)
+
+ self.manualFwhmGB = qt.QGroupBox("Define FWHM manually", self)
+ self.manualFwhmGB.setCheckable(True)
+ self.manualFwhmGB.setToolTip(
+ "If disabled, the FWHM parameter used for peak search is " +
+ "estimated based on the highest peak in the data")
+ layout.addWidget(self.manualFwhmGB)
+ # ------------ GroupBox fwhm--------------------------
+ layout2 = qt.QHBoxLayout(self.manualFwhmGB)
+ self.manualFwhmGB.setLayout(layout2)
+
+ label = qt.QLabel("Fwhm Points", self.manualFwhmGB)
+ layout2.addWidget(label)
+
+ self.fwhmPointsSpin = qt.QSpinBox(self.manualFwhmGB)
+ self.fwhmPointsSpin.setRange(0, 999999)
+ self.fwhmPointsSpin.setToolTip("Typical peak fwhm (number of data points)")
+ layout2.addWidget(self.fwhmPointsSpin)
+ # ----------------------------------------------------
+
+ self.manualScalingGB = qt.QGroupBox("Define scaling manually", self)
+ self.manualScalingGB.setCheckable(True)
+ self.manualScalingGB.setToolTip(
+ "If disabled, the Y scaling used for peak search is " +
+ "estimated automatically")
+ layout.addWidget(self.manualScalingGB)
+ # ------------ GroupBox scaling-----------------------
+ layout3 = qt.QHBoxLayout(self.manualScalingGB)
+ self.manualScalingGB.setLayout(layout3)
+
+ label = qt.QLabel("Y Scaling", self.manualScalingGB)
+ layout3.addWidget(label)
+
+ self.yScalingEntry = qt.QLineEdit(self.manualScalingGB)
+ self.yScalingEntry.setToolTip(
+ "Data values will be multiplied by this value prior to peak" +
+ " search")
+ self.yScalingEntry.setValidator(qt.QDoubleValidator())
+ layout3.addWidget(self.yScalingEntry)
+ # ----------------------------------------------------
+
+ # ------------------- grid layout --------------------
+ containerWidget = qt.QWidget(self)
+ layout4 = qt.QHBoxLayout(containerWidget)
+ containerWidget.setLayout(layout4)
+
+ label = qt.QLabel("Sensitivity", containerWidget)
+ layout4.addWidget(label)
+
+ self.sensitivityEntry = qt.QLineEdit(containerWidget)
+ self.sensitivityEntry.setToolTip(
+ "Peak search sensitivity threshold, expressed as a multiple " +
+ "of the standard deviation of the noise.\nMinimum value is 1 " +
+ "(to be detected, peak must be higher than the estimated noise)")
+ sensivalidator = qt.QDoubleValidator()
+ sensivalidator.setBottom(1.0)
+ self.sensitivityEntry.setValidator(sensivalidator)
+ layout4.addWidget(self.sensitivityEntry)
+ # ----------------------------------------------------
+ layout.addWidget(containerWidget)
+
+ self.forcePeakPresenceCB = qt.QCheckBox("Force peak presence", self)
+ self.forcePeakPresenceCB.setToolTip(
+ "If peak search algorithm is unsuccessful, place one peak " +
+ "at the maximum of the curve")
+ layout.addWidget(self.forcePeakPresenceCB)
+
+ layout.addStretch()
+
+ self.setDefault()
+
+ def setDefault(self, default_dict=None):
+ """Set default values for all widgets.
+
+ :param default_dict: If a default config dictionary is provided as
+ a parameter, its values are used as default values."""
+ if default_dict is None:
+ default_dict = {}
+ self.manualFwhmGB.setChecked(
+ not default_dict.get('AutoFwhm', True))
+ self.fwhmPointsSpin.setValue(
+ default_dict.get('FwhmPoints', 8))
+ self.sensitivityEntry.setText(
+ str(default_dict.get('Sensitivity', 1.0)))
+ self.manualScalingGB.setChecked(
+ not default_dict.get('AutoScaling', False))
+ self.yScalingEntry.setText(
+ str(default_dict.get('Yscaling', 1.0)))
+ self.forcePeakPresenceCB.setChecked(
+ default_dict.get('ForcePeakPresence', False))
+
+ def get(self):
+ """Return a dictionary of peak search parameters, to be processed by
+ the :meth:`configure` method of the selected fit theory."""
+ ddict = {
+ 'AutoFwhm': not self.manualFwhmGB.isChecked(),
+ 'FwhmPoints': self.fwhmPointsSpin.value(),
+ 'Sensitivity': safe_float(self.sensitivityEntry.text()),
+ 'AutoScaling': not self.manualScalingGB.isChecked(),
+ 'Yscaling': safe_float(self.yScalingEntry.text()),
+ 'ForcePeakPresence': self.forcePeakPresenceCB.isChecked()
+ }
+ return ddict
+
+
+class BackgroundPage(qt.QGroupBox):
+ """Background subtraction configuration, specific to fittheories
+ estimation functions."""
+ def __init__(self, parent=None,
+ title="Subtract strip background prior to estimation"):
+ super(BackgroundPage, self).__init__(parent)
+ self.setTitle(title)
+ self.setCheckable(True)
+ self.setToolTip(
+ "The strip algorithm strips away peaks to compute the " +
+ "background signal.\nAt each iteration, a sample is compared " +
+ "to the average of the two samples at a given distance in both" +
+ " directions,\n and if its value is higher than the average,"
+ "it is replaced by the average.")
+
+ layout = qt.QGridLayout(self)
+ self.setLayout(layout)
+
+ for i, label_text in enumerate(
+ ["Strip width (in samples)",
+ "Number of iterations",
+ "Strip threshold factor"]):
+ label = qt.QLabel(label_text)
+ layout.addWidget(label, i, 0)
+
+ self.stripWidthSpin = qt.QSpinBox(self)
+ self.stripWidthSpin.setToolTip(
+ "Width, in number of samples, of the strip operator")
+ self.stripWidthSpin.setRange(1, 999999)
+
+ layout.addWidget(self.stripWidthSpin, 0, 1)
+
+ self.numIterationsSpin = qt.QSpinBox(self)
+ self.numIterationsSpin.setToolTip(
+ "Number of iterations of the strip algorithm")
+ self.numIterationsSpin.setRange(1, 999999)
+ layout.addWidget(self.numIterationsSpin, 1, 1)
+
+ self.thresholdFactorEntry = qt.QLineEdit(self)
+ self.thresholdFactorEntry.setToolTip(
+ "Factor used by the strip algorithm to decide whether a sample" +
+ "value should be stripped.\nThe value must be higher than the " +
+ "average of the 2 samples at +- w times this factor.\n")
+ self.thresholdFactorEntry.setValidator(qt.QDoubleValidator())
+ layout.addWidget(self.thresholdFactorEntry, 2, 1)
+
+ self.smoothStripGB = qt.QGroupBox("Apply smoothing prior to strip", self)
+ self.smoothStripGB.setCheckable(True)
+ self.smoothStripGB.setToolTip(
+ "Apply a smoothing before subtracting strip background" +
+ " in fit and estimate processes")
+ smoothlayout = qt.QHBoxLayout(self.smoothStripGB)
+ label = qt.QLabel("Smoothing width (Savitsky-Golay)")
+ smoothlayout.addWidget(label)
+ self.smoothingWidthSpin = qt.QSpinBox(self)
+ self.smoothingWidthSpin.setToolTip(
+ "Width parameter for Savitsky-Golay smoothing (number of samples, must be odd)")
+ self.smoothingWidthSpin.setRange(3, 101)
+ self.smoothingWidthSpin.setSingleStep(2)
+ smoothlayout.addWidget(self.smoothingWidthSpin)
+
+ layout.addWidget(self.smoothStripGB, 3, 0, 1, 2)
+
+ layout.setRowStretch(4, 1)
+
+ self.setDefault()
+
+ def setDefault(self, default_dict=None):
+ """Set default values for all widgets.
+
+ :param default_dict: If a default config dictionary is provided as
+ a parameter, its values are used as default values."""
+ if default_dict is None:
+ default_dict = {}
+
+ self.setChecked(
+ default_dict.get('StripBackgroundFlag', True))
+
+ self.stripWidthSpin.setValue(
+ default_dict.get('StripWidth', 2))
+ self.numIterationsSpin.setValue(
+ default_dict.get('StripIterations', 5000))
+ self.thresholdFactorEntry.setText(
+ str(default_dict.get('StripThreshold', 1.0)))
+ self.smoothStripGB.setChecked(
+ default_dict.get('SmoothingFlag', False))
+ self.smoothingWidthSpin.setValue(
+ default_dict.get('SmoothingWidth', 3))
+
+ def get(self):
+ """Return a dictionary of background subtraction parameters, to be
+ processed by the :meth:`configure` method of the selected fit theory.
+ """
+ ddict = {
+ 'StripBackgroundFlag': self.isChecked(),
+ 'StripWidth': self.stripWidthSpin.value(),
+ 'StripIterations': self.numIterationsSpin.value(),
+ 'StripThreshold': safe_float(self.thresholdFactorEntry.text()),
+ 'SmoothingFlag': self.smoothStripGB.isChecked(),
+ 'SmoothingWidth': self.smoothingWidthSpin.value()
+ }
+ return ddict
+
+
+def safe_float(string_, default=1.0):
+ """Convert a string into a float.
+ If the conversion fails, return the default value.
+ """
+ try:
+ ret = float(string_)
+ except ValueError:
+ return default
+ else:
+ return ret
+
+
+def safe_int(string_, default=1):
+ """Convert a string into a integer.
+ If the conversion fails, return the default value.
+ """
+ try:
+ ret = int(float(string_))
+ except ValueError:
+ return default
+ else:
+ return ret
+
+
+def getFitConfigDialog(parent=None, default=None, modal=True):
+ """Instantiate and return a fit configuration dialog, adapted
+ for configuring standard fit theories from
+ :mod:`silx.math.fit.fittheories`.
+
+ :return: Instance of :class:`TabsDialogData` with 3 tabs:
+ :class:`ConstraintsPage`, :class:`SearchPage` and
+ :class:`BackgroundPage`
+ """
+ tdd = TabsDialogData(parent=parent, default=default)
+ tdd.addTab(ConstraintsPage(), label="Constraints")
+ tdd.addTab(SearchPage(), label="Peak search")
+ tdd.addTab(BackgroundPage(), label="Background")
+ # apply default to newly added pages
+ tdd.setDefault()
+
+ return tdd
+
+
+def main():
+ a = qt.QApplication([])
+
+ mw = qt.QMainWindow()
+ mw.show()
+
+ tdd = getFitConfigDialog(mw, default={"a": 1})
+ tdd.show()
+ tdd.exec_()
+ print("TabsDialogData result: ", tdd.result())
+ print("TabsDialogData output: ", tdd.output)
+
+ a.exec_()
+
+if __name__ == "__main__":
+ main()
diff --git a/silx/gui/fit/FitWidget.py b/silx/gui/fit/FitWidget.py
new file mode 100644
index 0000000..a5c3cfd
--- /dev/null
+++ b/silx/gui/fit/FitWidget.py
@@ -0,0 +1,727 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF by the Software group.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ######################################################################### */
+"""This module provides a widget designed to configure and run a fitting
+process with constraints on parameters.
+
+The main class is :class:`FitWidget`. It relies on
+:mod:`silx.math.fit.fitmanager`, which relies on :func:`silx.math.fit.leastsq`.
+
+The user can choose between functions before running the fit. These function can
+be user defined, or by default are loaded from
+:mod:`silx.math.fit.fittheories`.
+"""
+
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "15/02/2017"
+
+import logging
+import sys
+import traceback
+import warnings
+
+from silx.math.fit import fittheories
+from silx.math.fit import fitmanager, functions
+from silx.gui import qt
+from .FitWidgets import (FitActionsButtons, FitStatusLines,
+ FitConfigWidget, ParametersTab)
+from .FitConfig import getFitConfigDialog
+from .BackgroundWidget import getBgDialog, BackgroundDialog
+
+QTVERSION = qt.qVersion()
+DEBUG = 0
+_logger = logging.getLogger(__name__)
+
+
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "30/11/2016"
+
+
+class FitWidget(qt.QWidget):
+ """This widget can be used to configure, run and display results of a
+ fitting process.
+
+ The standard steps for using this widget is to initialize it, then load
+ the data to be fitted.
+
+ Optionally, you can also load user defined fit theories. If you skip this
+ step, a series of default fit functions will be presented (gaussian-like
+ functions), and you can later load your custom fit theories from an
+ external file using the GUI.
+
+ A fit theory is a fit function and its associated features:
+
+ - estimation function,
+ - list of parameter names
+ - numerical derivative algorithm
+ - configuration widget
+
+ Once the widget is up and running, the user may select a fit theory and a
+ background theory, change configuration parameters specific to the theory
+ run the estimation, set constraints on parameters and run the actual fit.
+
+ The results are displayed in a table.
+ """
+ sigFitWidgetSignal = qt.Signal(object)
+ """This signal is emitted by the estimation and fit methods.
+ It carries a dictionary with two items:
+
+ - *event*: one of the following strings
+
+ - *EstimateStarted*,
+ - *FitStarted*
+ - *EstimateFinished*,
+ - *FitFinished*
+ - *EstimateFailed*
+ - *FitFailed*
+
+ - *data*: None, or fit/estimate results (see documentation for
+ :attr:`silx.math.fit.fitmanager.FitManager.fit_results`)
+ """
+
+ def __init__(self, parent=None, title=None, fitmngr=None,
+ enableconfig=True, enablestatus=True, enablebuttons=True):
+ """
+
+ :param parent: Parent widget
+ :param title: Window title
+ :param fitmngr: User defined instance of
+ :class:`silx.math.fit.fitmanager.FitManager`, or ``None``
+ :param enableconfig: If ``True``, activate widgets to modify the fit
+ configuration (select between several fit functions or background
+ functions, apply global constraints, peak search parameters…)
+ :param enablestatus: If ``True``, add a fit status widget, to display
+ a message when fit estimation is available and when fit results
+ are available, as well as a measure of the fit error.
+ :param enablebuttons: If ``True``, add buttons to run estimation and
+ fitting.
+ """
+ if title is None:
+ title = "FitWidget"
+ qt.QWidget.__init__(self, parent)
+
+ self.setWindowTitle(title)
+ layout = qt.QVBoxLayout(self)
+
+ self.fitmanager = self._setFitManager(fitmngr)
+ """Instance of :class:`FitManager`.
+ This is the underlying data model of this FitWidget.
+
+ If no custom theories are defined, the default ones from
+ :mod:`silx.math.fit.fittheories` are imported.
+ """
+
+ # reference fitmanager.configure method for direct access
+ self.configure = self.fitmanager.configure
+ self.fitconfig = self.fitmanager.fitconfig
+
+ self.configdialogs = {}
+ """This dictionary defines the fit configuration widgets
+ associated with the fit theories in :attr:`fitmanager.theories`
+
+ Keys must correspond to existing theory names, i.e. existing keys
+ in :attr:`fitmanager.theories`.
+
+ Values must be instances of QDialog widgets with an additional
+ *output* attribute, a dictionary storing configuration parameters
+ interpreted by the corresponding fit theory.
+
+ The dialog can also define a *setDefault* method to initialize the
+ widget values with values in a dictionary passed as a parameter.
+ This will be executed first.
+
+ In case the widget does not actually inherit :class:`QDialog`, it
+ must at least implement the following methods (executed in this
+ particular order):
+
+ - :meth:`show`: should cause the widget to become visible to the
+ user)
+ - :meth:`exec_`: should run while the user is interacting with the
+ widget, interrupting the rest of the program. It should
+ typically end (*return*) when the user clicks an *OK*
+ or a *Cancel* button.
+ - :meth:`result`: must return ``True`` if the new configuration in
+ attribute :attr:`output` is to be accepted (user clicked *OK*),
+ or return ``False`` if :attr:`output` is to be rejected (user
+ clicked *Cancel*)
+
+ To associate a custom configuration widget with a fit theory, use
+ :meth:`associateConfigDialog`. E.g.::
+
+ fw = FitWidget()
+ my_config_widget = MyGaussianConfigWidget(parent=fw)
+ fw.associateConfigDialog(theory_name="Gaussians",
+ config_widget=my_config_widget)
+ """
+
+ self.bgconfigdialogs = {}
+ """Same as :attr:`configdialogs`, except that the widget is associated
+ with a background theory in :attr:`fitmanager.bgtheories`"""
+
+ self._associateDefaultConfigDialogs()
+
+ self.guiConfig = None
+ """Configuration widget at the top of FitWidget, to select
+ fit function, background function, and open an advanced
+ configuration dialog."""
+
+ self.guiParameters = ParametersTab(self)
+ """Table widget for display of fit parameters and constraints"""
+
+ if enableconfig:
+ self.guiConfig = FitConfigWidget(self)
+ """Function selector and configuration widget"""
+
+ self.guiConfig.FunConfigureButton.clicked.connect(
+ self.__funConfigureGuiSlot)
+ self.guiConfig.BgConfigureButton.clicked.connect(
+ self.__bgConfigureGuiSlot)
+
+ self.guiConfig.WeightCheckBox.setChecked(
+ self.fitconfig.get("WeightFlag", False))
+ self.guiConfig.WeightCheckBox.stateChanged[int].connect(self.weightEvent)
+
+ self.guiConfig.BkgComBox.activated[str].connect(self.bkgEvent)
+ self.guiConfig.FunComBox.activated[str].connect(self.funEvent)
+ self._populateFunctions()
+
+ layout.addWidget(self.guiConfig)
+
+ layout.addWidget(self.guiParameters)
+
+ if enablestatus:
+ self.guistatus = FitStatusLines(self)
+ """Status bar"""
+ layout.addWidget(self.guistatus)
+
+ if enablebuttons:
+ self.guibuttons = FitActionsButtons(self)
+ """Widget with estimate, start fit and dismiss buttons"""
+ self.guibuttons.EstimateButton.clicked.connect(self.estimate)
+ self.guibuttons.StartFitButton.clicked.connect(self.startFit)
+ self.guibuttons.DismissButton.clicked.connect(self.dismiss)
+ layout.addWidget(self.guibuttons)
+
+ def _setFitManager(self, fitinstance):
+ """Initialize a :class:`FitManager` instance, to be assigned to
+ :attr:`fitmanager`, or use a custom FitManager instance.
+
+ :param fitinstance: Existing instance of FitManager, possibly
+ customized by the user, or None to load a default instance."""
+ if isinstance(fitinstance, fitmanager.FitManager):
+ # customized
+ fitmngr = fitinstance
+ else:
+ # initialize default instance
+ fitmngr = fitmanager.FitManager()
+
+ # initialize the default fitting functions in case
+ # none is present
+ if not len(fitmngr.theories):
+ fitmngr.loadtheories(fittheories)
+
+ return fitmngr
+
+ def _associateDefaultConfigDialogs(self):
+ """Fill :attr:`bgconfigdialogs` and :attr:`configdialogs` by calling
+ :meth:`associateConfigDialog` with default config dialog widgets.
+ """
+ # associate silx.gui.fit.FitConfig with all theories
+ # Users can later associate their own custom dialogs to
+ # replace the default.
+ configdialog = getFitConfigDialog(parent=self,
+ default=self.fitconfig)
+ for theory in self.fitmanager.theories:
+ self.associateConfigDialog(theory, configdialog)
+ for bgtheory in self.fitmanager.bgtheories:
+ self.associateConfigDialog(bgtheory, configdialog,
+ theory_is_background=True)
+
+ # associate silx.gui.fit.BackgroundWidget with Strip and Snip
+ bgdialog = getBgDialog(parent=self,
+ default=self.fitconfig)
+ for bgtheory in ["Strip", "Snip"]:
+ if bgtheory in self.fitmanager.bgtheories:
+ self.associateConfigDialog(bgtheory, bgdialog,
+ theory_is_background=True)
+
+ def _populateFunctions(self):
+ """Fill combo-boxes with fit theories and background theories
+ loaded by :attr:`fitmanager`.
+ Run :meth:`fitmanager.configure` to ensure the custom configuration
+ of the selected theory has been loaded into :attr:`fitconfig`"""
+ for theory_name in self.fitmanager.bgtheories:
+ self.guiConfig.BkgComBox.addItem(theory_name)
+ self.guiConfig.BkgComBox.setItemData(
+ self.guiConfig.BkgComBox.findText(theory_name),
+ self.fitmanager.bgtheories[theory_name].description,
+ qt.Qt.ToolTipRole)
+
+ for theory_name in self.fitmanager.theories:
+ self.guiConfig.FunComBox.addItem(theory_name)
+ self.guiConfig.FunComBox.setItemData(
+ self.guiConfig.FunComBox.findText(theory_name),
+ self.fitmanager.theories[theory_name].description,
+ qt.Qt.ToolTipRole)
+
+ # - activate selected fit theory (if any)
+ # - activate selected bg theory (if any)
+ configuration = self.fitmanager.configure()
+ if self.fitmanager.selectedtheory is None:
+ # take the first one by default
+ self.guiConfig.FunComBox.setCurrentIndex(1)
+ self.funEvent(list(self.fitmanager.theories.keys())[0])
+ else:
+ idx = list(self.fitmanager.theories).index(self.fitmanager.selectedtheory)
+ self.guiConfig.FunComBox.setCurrentIndex(idx + 1)
+ self.funEvent(self.fitmanager.selectedtheory)
+
+ if self.fitmanager.selectedbg is None:
+ self.guiConfig.BkgComBox.setCurrentIndex(1)
+ self.bkgEvent(list(self.fitmanager.bgtheories.keys())[0])
+ else:
+ idx = list(self.fitmanager.bgtheories).index(self.fitmanager.selectedbg)
+ self.guiConfig.BkgComBox.setCurrentIndex(idx + 1)
+ self.bkgEvent(self.fitmanager.selectedbg)
+
+ configuration.update(self.configure())
+
+ def setdata(self, x, y, sigmay=None, xmin=None, xmax=None):
+ warnings.warn("Method renamed to setData",
+ DeprecationWarning)
+ self.setData(x, y, sigmay, xmin, xmax)
+
+ def setData(self, x, y, sigmay=None, xmin=None, xmax=None):
+ """Set data to be fitted.
+
+ :param x: Abscissa data. If ``None``, :attr:`xdata`` is set to
+ ``numpy.array([0.0, 1.0, 2.0, ..., len(y)-1])``
+ :type x: Sequence or numpy array or None
+ :param y: The dependant data ``y = f(x)``. ``y`` must have the same
+ shape as ``x`` if ``x`` is not ``None``.
+ :type y: Sequence or numpy array or None
+ :param sigmay: The uncertainties in the ``ydata`` array. These are
+ used as weights in the least-squares problem.
+ If ``None``, the uncertainties are assumed to be 1.
+ :type sigmay: Sequence or numpy array or None
+ :param xmin: Lower value of x values to use for fitting
+ :param xmax: Upper value of x values to use for fitting
+ """
+ self.fitmanager.setdata(x=x, y=y, sigmay=sigmay,
+ xmin=xmin, xmax=xmax)
+ for config_dialog in self.bgconfigdialogs.values():
+ if isinstance(config_dialog, BackgroundDialog):
+ config_dialog.setData(x, y, xmin=xmin, xmax=xmax)
+
+ def associateConfigDialog(self, theory_name, config_widget,
+ theory_is_background=False):
+ """Associate an instance of custom configuration dialog widget to
+ a fit theory or to a background theory.
+
+ This adds or modifies an item in the correspondence table
+ :attr:`configdialogs` or :attr:`bgconfigdialogs`.
+
+ :param str theory_name: Name of fit theory. This must be a key of dict
+ :attr:`fitmanager.theories`
+ :param config_widget: Custom configuration widget. See documentation
+ for :attr:`configdialogs`
+ :param bool theory_is_background: If flag is *True*, add dialog to
+ :attr:`bgconfigdialogs` rather than :attr:`configdialogs`
+ (default).
+ :raise: KeyError if parameter ``theory_name`` does not match an
+ existing fit theory or background theory in :attr:`fitmanager`.
+ :raise: AttributeError if the widget does not implement the mandatory
+ methods (*show*, *exec_*, *result*, *setDefault*) or the mandatory
+ attribute (*output*).
+ """
+ theories = self.fitmanager.bgtheories if theory_is_background else\
+ self.fitmanager.theories
+
+ if theory_name not in theories:
+ raise KeyError("%s does not match an existing fitmanager theory")
+
+ if config_widget is not None:
+ for mandatory_attr in ["show", "exec_", "result", "output"]:
+ if not hasattr(config_widget, mandatory_attr):
+ raise AttributeError(
+ "Custom configuration widget must define " +
+ "attribute or method " + mandatory_attr)
+
+ if theory_is_background:
+ self.bgconfigdialogs[theory_name] = config_widget
+ else:
+ self.configdialogs[theory_name] = config_widget
+
+ def _emitSignal(self, ddict):
+ """Emit pyqtSignal after estimation completed
+ (``ddict = {'event': 'EstimateFinished', 'data': fit_results}``)
+ and after fit completed
+ (``ddict = {'event': 'FitFinished', 'data': fit_results}``)"""
+ self.sigFitWidgetSignal.emit(ddict)
+
+ def __funConfigureGuiSlot(self):
+ """Open an advanced configuration dialog widget"""
+ self.__configureGui(dialog_type="function")
+
+ def __bgConfigureGuiSlot(self):
+ """Open an advanced configuration dialog widget"""
+ self.__configureGui(dialog_type="background")
+
+ def __configureGui(self, newconfiguration=None, dialog_type="function"):
+ """Open an advanced configuration dialog widget to get a configuration
+ dictionary, or use a supplied configuration dictionary. Call
+ :meth:`configure` with this dictionary as a parameter. Update the gui
+ accordingly. Reinitialize the fit results in the table and in
+ :attr:`fitmanager`.
+
+ :param newconfiguration: User supplied configuration dictionary. If ``None``,
+ open a dialog widget that returns a dictionary."""
+ configuration = self.configure()
+ # get new dictionary
+ if newconfiguration is None:
+ newconfiguration = self.configureDialog(configuration, dialog_type)
+ # update configuration
+ configuration.update(self.configure(**newconfiguration))
+ # set fit function theory
+ try:
+ i = 1 + \
+ list(self.fitmanager.theories.keys()).index(
+ self.fitmanager.selectedtheory)
+ self.guiConfig.FunComBox.setCurrentIndex(i)
+ self.funEvent(self.fitmanager.selectedtheory)
+ except ValueError:
+ _logger.error("Function not in list %s",
+ self.fitmanager.selectedtheory)
+ self.funEvent(list(self.fitmanager.theories.keys())[0])
+ # current background
+ try:
+ i = 1 + \
+ list(self.fitmanager.bgtheories.keys()).index(
+ self.fitmanager.selectedbg)
+ self.guiConfig.BkgComBox.setCurrentIndex(i)
+ self.bkgEvent(self.fitmanager.selectedbg)
+ except ValueError:
+ _logger.error("Background not in list %s",
+ self.fitmanager.selectedbg)
+ self.bkgEvent(list(self.fitmanager.bgtheories.keys())[0])
+
+ # update the Gui
+ self.__initialParameters()
+
+ def configureDialog(self, oldconfiguration, dialog_type="function"):
+ """Display a dialog, allowing the user to define fit configuration
+ parameters.
+
+ By default, a common dialog is used for all fit theories. But if the
+ defined a custom dialog using :meth:`associateConfigDialog`, it is
+ used instead.
+
+ :param dict oldconfiguration: Dictionary containing previous configuration
+ :param str dialog_type: "function" or "background"
+ :return: User defined parameters in a dictionary
+ """
+ newconfiguration = {}
+ newconfiguration.update(oldconfiguration)
+
+ if dialog_type == "function":
+ theory = self.fitmanager.selectedtheory
+ configdialog = self.configdialogs[theory]
+ elif dialog_type == "background":
+ theory = self.fitmanager.selectedbg
+ configdialog = self.bgconfigdialogs[theory]
+
+ # this should only happen if a user specifically associates None
+ # with a theory, to have no configuration option
+ if configdialog is None:
+ return {}
+
+ # update state of configdialog before showing it
+ if hasattr(configdialog, "setDefault"):
+ configdialog.setDefault(newconfiguration)
+ configdialog.show()
+ configdialog.exec_()
+ if configdialog.result():
+ newconfiguration.update(configdialog.output)
+
+ return newconfiguration
+
+ def estimate(self):
+ """Run parameter estimation function then emit
+ :attr:`sigFitWidgetSignal` with a dictionary containing a status
+ message and a list of fit parameters estimations
+ in the format defined in
+ :attr:`silx.math.fit.fitmanager.FitManager.fit_results`
+
+ The emitted dictionary has an *"event"* key that can have
+ following values:
+
+ - *'EstimateStarted'*
+ - *'EstimateFailed'*
+ - *'EstimateFinished'*
+ """
+ try:
+ theory_name = self.fitmanager.selectedtheory
+ estimation_function = self.fitmanager.theories[theory_name].estimate
+ if estimation_function is not None:
+ ddict = {'event': 'EstimateStarted',
+ 'data': None}
+ self._emitSignal(ddict)
+ self.fitmanager.estimate(callback=self.fitStatus)
+ else:
+ msg = qt.QMessageBox(self)
+ msg.setIcon(qt.QMessageBox.Information)
+ text = "Function does not define a way to estimate\n"
+ text += "the initial parameters. Please, fill them\n"
+ text += "yourself in the table and press Start Fit\n"
+ msg.setText(text)
+ msg.setWindowTitle('FitWidget Message')
+ msg.exec_()
+ return
+ except: # noqa (we want to catch and report all errors)
+ msg = qt.QMessageBox(self)
+ msg.setIcon(qt.QMessageBox.Critical)
+ msg.setText("Error on estimate: %s" % traceback.format_exc())
+ msg.exec_()
+ ddict = {
+ 'event': 'EstimateFailed',
+ 'data': None}
+ self._emitSignal(ddict)
+ return
+
+ self.guiParameters.fillFromFit(
+ self.fitmanager.fit_results, view='Fit')
+ self.guiParameters.removeAllViews(keep='Fit')
+ ddict = {
+ 'event': 'EstimateFinished',
+ 'data': self.fitmanager.fit_results}
+ self._emitSignal(ddict)
+
+ def startfit(self):
+ warnings.warn("Method renamed to startFit",
+ DeprecationWarning)
+ self.startFit()
+
+ def startFit(self):
+ """Run fit, then emit :attr:`sigFitWidgetSignal` with a dictionary
+ containing a status message and a list of fit
+ parameters results in the format defined in
+ :attr:`silx.math.fit.fitmanager.FitManager.fit_results`
+
+ The emitted dictionary has an *"event"* key that can have
+ following values:
+
+ - *'FitStarted'*
+ - *'FitFailed'*
+ - *'FitFinished'*
+ """
+ self.fitmanager.fit_results = self.guiParameters.getFitResults()
+ try:
+ ddict = {'event': 'FitStarted',
+ 'data': None}
+ self._emitSignal(ddict)
+ self.fitmanager.runfit(callback=self.fitStatus)
+ except: # noqa (we want to catch and report all errors)
+ msg = qt.QMessageBox(self)
+ msg.setIcon(qt.QMessageBox.Critical)
+ msg.setText("Error on Fit: %s" % traceback.format_exc())
+ msg.exec_()
+ ddict = {
+ 'event': 'FitFailed',
+ 'data': None
+ }
+ self._emitSignal(ddict)
+ return
+
+ self.guiParameters.fillFromFit(
+ self.fitmanager.fit_results, view='Fit')
+ self.guiParameters.removeAllViews(keep='Fit')
+ ddict = {
+ 'event': 'FitFinished',
+ 'data': self.fitmanager.fit_results
+ }
+ self._emitSignal(ddict)
+ return
+
+ def bkgEvent(self, bgtheory):
+ """Select background theory, then reinitialize parameters"""
+ bgtheory = str(bgtheory)
+ if bgtheory in self.fitmanager.bgtheories:
+ self.fitmanager.setbackground(bgtheory)
+ else:
+ functionsfile = qt.QFileDialog.getOpenFileName(
+ self, "Select python module with your function(s)", "",
+ "Python Files (*.py);;All Files (*)")
+
+ if len(functionsfile):
+ try:
+ self.fitmanager.loadbgtheories(functionsfile)
+ except ImportError:
+ qt.QMessageBox.critical(self, "ERROR",
+ "Function not imported")
+ return
+ else:
+ # empty the ComboBox
+ while self.guiConfig.BkgComBox.count() > 1:
+ self.guiConfig.BkgComBox.removeItem(1)
+ # and fill it again
+ for key in self.fitmanager.bgtheories:
+ self.guiConfig.BkgComBox.addItem(str(key))
+
+ i = 1 + \
+ list(self.fitmanager.bgtheories.keys()).index(
+ self.fitmanager.selectedbg)
+ self.guiConfig.BkgComBox.setCurrentIndex(i)
+ self.__initialParameters()
+
+ def funEvent(self, theoryname):
+ """Select a fit theory to be used for fitting. If this theory exists
+ in :attr:`fitmanager`, use it. Then, reinitialize table.
+
+ :param theoryname: Name of the fit theory to use for fitting. If this theory
+ exists in :attr:`fitmanager`, use it. Else, open a file dialog to open
+ a custom fit function definition file with
+ :meth:`fitmanager.loadtheories`.
+ """
+ theoryname = str(theoryname)
+ if theoryname in self.fitmanager.theories:
+ self.fitmanager.settheory(theoryname)
+ else:
+ # open a load file dialog
+ functionsfile = qt.QFileDialog.getOpenFileName(
+ self, "Select python module with your function(s)", "",
+ "Python Files (*.py);;All Files (*)")
+
+ if len(functionsfile):
+ try:
+ self.fitmanager.loadtheories(functionsfile)
+ except ImportError:
+ qt.QMessageBox.critical(self, "ERROR",
+ "Function not imported")
+ return
+ else:
+ # empty the ComboBox
+ while self.guiConfig.FunComBox.count() > 1:
+ self.guiConfig.FunComBox.removeItem(1)
+ # and fill it again
+ for key in self.fitmanager.theories:
+ self.guiConfig.FunComBox.addItem(str(key))
+
+ i = 1 + \
+ list(self.fitmanager.theories.keys()).index(
+ self.fitmanager.selectedtheory)
+ self.guiConfig.FunComBox.setCurrentIndex(i)
+ self.__initialParameters()
+
+ def weightEvent(self, flag):
+ """This is called when WeightCheckBox is clicked, to configure the
+ *WeightFlag* field in :attr:`fitmanager.fitconfig` and set weights
+ in the least-square problem."""
+ self.configure(WeightFlag=flag)
+ if flag:
+ self.fitmanager.enableweight()
+ else:
+ # set weights back to 1
+ self.fitmanager.disableweight()
+
+ def __initialParameters(self):
+ """Fill the fit parameters names with names of the parameters of
+ the selected background theory and the selected fit theory.
+ Initialize :attr:`fitmanager.fit_results` with these names, and
+ initialize the table with them. This creates a view called "Fit"
+ in :attr:`guiParameters`"""
+ self.fitmanager.parameter_names = []
+ self.fitmanager.fit_results = []
+ for pname in self.fitmanager.bgtheories[self.fitmanager.selectedbg].parameters:
+ self.fitmanager.parameter_names.append(pname)
+ self.fitmanager.fit_results.append({'name': pname,
+ 'estimation': 0,
+ 'group': 0,
+ 'code': 'FREE',
+ 'cons1': 0,
+ 'cons2': 0,
+ 'fitresult': 0.0,
+ 'sigma': 0.0,
+ 'xmin': None,
+ 'xmax': None})
+ if self.fitmanager.selectedtheory is not None:
+ theory = self.fitmanager.selectedtheory
+ for pname in self.fitmanager.theories[theory].parameters:
+ self.fitmanager.parameter_names.append(pname + "1")
+ self.fitmanager.fit_results.append({'name': pname + "1",
+ 'estimation': 0,
+ 'group': 1,
+ 'code': 'FREE',
+ 'cons1': 0,
+ 'cons2': 0,
+ 'fitresult': 0.0,
+ 'sigma': 0.0,
+ 'xmin': None,
+ 'xmax': None})
+
+ self.guiParameters.fillFromFit(
+ self.fitmanager.fit_results, view='Fit')
+
+ def fitStatus(self, data):
+ """Set *status* and *chisq* in status bar"""
+ if 'chisq' in data:
+ if data['chisq'] is None:
+ self.guistatus.ChisqLine.setText(" ")
+ else:
+ chisq = data['chisq']
+ self.guistatus.ChisqLine.setText("%6.2f" % chisq)
+
+ if 'status' in data:
+ status = data['status']
+ self.guistatus.StatusLine.setText(str(status))
+
+ def dismiss(self):
+ """Close FitWidget"""
+ self.close()
+
+
+if __name__ == "__main__":
+ import numpy
+
+ x = numpy.arange(1500).astype(numpy.float)
+ constant_bg = 3.14
+
+ p = [1000, 100., 30.0,
+ 500, 300., 25.,
+ 1700, 500., 35.,
+ 750, 700., 30.0,
+ 1234, 900., 29.5,
+ 302, 1100., 30.5,
+ 75, 1300., 21.]
+ y = functions.sum_gauss(x, *p) + constant_bg
+
+ a = qt.QApplication(sys.argv)
+ w = FitWidget()
+ w.setData(x=x, y=y)
+ w.show()
+ a.exec_()
diff --git a/silx/gui/fit/FitWidgets.py b/silx/gui/fit/FitWidgets.py
new file mode 100644
index 0000000..408666b
--- /dev/null
+++ b/silx/gui/fit/FitWidgets.py
@@ -0,0 +1,559 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2004-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ######################################################################### */
+"""Collection of widgets used to build
+:class:`silx.gui.fit.FitWidget.FitWidget`"""
+
+from collections import OrderedDict
+
+from silx.gui import qt
+from silx.gui.fit.Parameters import Parameters
+
+QTVERSION = qt.qVersion()
+
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "13/10/2016"
+
+
+class FitActionsButtons(qt.QWidget):
+ """Widget with 3 ``QPushButton``:
+
+ The buttons can be accessed as public attributes::
+
+ - ``EstimateButton``
+ - ``StartFitButton``
+ - ``DismissButton``
+
+ You will typically need to access these attributes to connect the buttons
+ to actions. For instance, if you have 3 functions ``estimate``,
+ ``runfit`` and ``dismiss``, you can connect them like this::
+
+ >>> fit_actions_buttons = FitActionsButtons()
+ >>> fit_actions_buttons.EstimateButton.clicked.connect(estimate)
+ >>> fit_actions_buttons.StartFitButton.clicked.connect(runfit)
+ >>> fit_actions_buttons.DismissButton.clicked.connect(dismiss)
+
+ """
+
+ def __init__(self, parent=None):
+ qt.QWidget.__init__(self, parent)
+
+ self.resize(234, 53)
+
+ grid_layout = qt.QGridLayout(self)
+ grid_layout.setContentsMargins(11, 11, 11, 11)
+ grid_layout.setSpacing(6)
+ layout = qt.QHBoxLayout(None)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.setSpacing(6)
+
+ self.EstimateButton = qt.QPushButton(self)
+ self.EstimateButton.setText("Estimate")
+ layout.addWidget(self.EstimateButton)
+ spacer = qt.QSpacerItem(20, 20,
+ qt.QSizePolicy.Expanding,
+ qt.QSizePolicy.Minimum)
+ layout.addItem(spacer)
+
+ self.StartFitButton = qt.QPushButton(self)
+ self.StartFitButton.setText("Start Fit")
+ layout.addWidget(self.StartFitButton)
+ spacer_2 = qt.QSpacerItem(20, 20,
+ qt.QSizePolicy.Expanding,
+ qt.QSizePolicy.Minimum)
+ layout.addItem(spacer_2)
+
+ self.DismissButton = qt.QPushButton(self)
+ self.DismissButton.setText("Dismiss")
+ layout.addWidget(self.DismissButton)
+
+ grid_layout.addLayout(layout, 0, 0)
+
+
+class FitStatusLines(qt.QWidget):
+ """Widget with 2 greyed out write-only ``QLineEdit``.
+
+ These text widgets can be accessed as public attributes::
+
+ - ``StatusLine``
+ - ``ChisqLine``
+
+ You will typically need to access these widgets to update the displayed
+ text::
+
+ >>> fit_status_lines = FitStatusLines()
+ >>> fit_status_lines.StatusLine.setText("Ready")
+ >>> fit_status_lines.ChisqLine.setText("%6.2f" % 0.01)
+
+ """
+
+ def __init__(self, parent=None):
+ qt.QWidget.__init__(self, parent)
+
+ self.resize(535, 47)
+
+ layout = qt.QHBoxLayout(self)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.setSpacing(6)
+
+ self.StatusLabel = qt.QLabel(self)
+ self.StatusLabel.setText("Status:")
+ layout.addWidget(self.StatusLabel)
+
+ self.StatusLine = qt.QLineEdit(self)
+ self.StatusLine.setText("Ready")
+ self.StatusLine.setReadOnly(1)
+ layout.addWidget(self.StatusLine)
+
+ self.ChisqLabel = qt.QLabel(self)
+ self.ChisqLabel.setText("Reduced chisq:")
+ layout.addWidget(self.ChisqLabel)
+
+ self.ChisqLine = qt.QLineEdit(self)
+ self.ChisqLine.setMaximumSize(qt.QSize(16000, 32767))
+ self.ChisqLine.setText("")
+ self.ChisqLine.setReadOnly(1)
+ layout.addWidget(self.ChisqLine)
+
+
+class FitConfigWidget(qt.QWidget):
+ """Widget whose purpose is to select a fit theory and a background
+ theory, load a new fit theory definition file and provide
+ a "Configure" button to open an advanced configuration dialog.
+
+ This is used in :class:`silx.gui.fit.FitWidget.FitWidget`, to offer
+ an interface to quickly modify the main parameters prior to running a fit:
+
+ - select a fitting function through :attr:`FunComBox`
+ - select a background function through :attr:`BkgComBox`
+ - open a dialog for modifying advanced parameters through
+ :attr:`FunConfigureButton`
+ """
+ def __init__(self, parent=None):
+ qt.QWidget.__init__(self, parent)
+
+ self.setWindowTitle("FitConfigGUI")
+
+ layout = qt.QGridLayout(self)
+ layout.setContentsMargins(0, 0, 0, 0)
+ layout.setSpacing(6)
+
+ self.FunLabel = qt.QLabel(self)
+ self.FunLabel.setText("Function")
+ layout.addWidget(self.FunLabel, 0, 0)
+
+ self.FunComBox = qt.QComboBox(self)
+ self.FunComBox.addItem("Add Function(s)")
+ self.FunComBox.setItemData(self.FunComBox.findText("Add Function(s)"),
+ "Load fit theories from a file",
+ qt.Qt.ToolTipRole)
+ layout.addWidget(self.FunComBox, 0, 1)
+
+ self.BkgLabel = qt.QLabel(self)
+ self.BkgLabel.setText("Background")
+ layout.addWidget(self.BkgLabel, 1, 0)
+
+ self.BkgComBox = qt.QComboBox(self)
+ self.BkgComBox.addItem("Add Background(s)")
+ self.BkgComBox.setItemData(self.BkgComBox.findText("Add Background(s)"),
+ "Load background theories from a file",
+ qt.Qt.ToolTipRole)
+ layout.addWidget(self.BkgComBox, 1, 1)
+
+ self.FunConfigureButton = qt.QPushButton(self)
+ self.FunConfigureButton.setText("Configure")
+ self.FunConfigureButton.setToolTip(
+ "Open a configuration dialog for the selected function")
+ layout.addWidget(self.FunConfigureButton, 0, 2)
+
+ self.BgConfigureButton = qt.QPushButton(self)
+ self.BgConfigureButton.setText("Configure")
+ self.BgConfigureButton.setToolTip(
+ "Open a configuration dialog for the selected background")
+ layout.addWidget(self.BgConfigureButton, 1, 2)
+
+ self.WeightCheckBox = qt.QCheckBox(self)
+ self.WeightCheckBox.setText("Weighted fit")
+ self.WeightCheckBox.setToolTip(
+ "Enable usage of weights in the least-square problem.\n Use" +
+ " the uncertainties (sigma) if provided, else use sqrt(y).")
+
+ layout.addWidget(self.WeightCheckBox, 0, 3, 2, 1)
+
+ layout.setColumnStretch(4, 1)
+
+
+class ParametersTab(qt.QTabWidget):
+ """This widget provides tabs to display and modify fit parameters. Each
+ tab contains a table with fit data such as parameter names, estimated
+ values, fit constraints, and final fit results.
+
+ The usual way to initialize the table is to fill it with the fit
+ parameters from a :class:`silx.math.fit.fitmanager.FitManager` object, after
+ the estimation process or after the final fit.
+
+ In the following example we use a :class:`ParametersTab` to display the
+ results of two separate fits::
+
+ from silx.math.fit import fittheories
+ from silx.math.fit import fitmanager
+ from silx.math.fit import functions
+ from silx.gui import qt
+ import numpy
+
+ a = qt.QApplication([])
+
+ # Create synthetic data
+ x = numpy.arange(1000)
+ y1 = functions.sum_gauss(x, 100, 400, 100)
+
+ fit = fitmanager.FitManager(x=x, y=y1)
+
+ fitfuns = fittheories.FitTheories()
+ fit.addtheory(theory="Gaussian",
+ function=functions.sum_gauss,
+ parameters=("height", "peak center", "fwhm"),
+ estimate=fitfuns.estimate_height_position_fwhm)
+ fit.settheory('Gaussian')
+ fit.configure(PositiveFwhmFlag=True,
+ PositiveHeightAreaFlag=True,
+ AutoFwhm=True,)
+
+ # Fit
+ fit.estimate()
+ fit.runfit()
+
+ # Show first fit result in a tab in our widget
+ w = ParametersTab()
+ w.show()
+ w.fillFromFit(fit.fit_results, view='Gaussians')
+
+ # new synthetic data
+ y2 = functions.sum_splitgauss(x,
+ 100, 400, 100, 40,
+ 10, 600, 50, 500,
+ 80, 850, 10, 50)
+ fit.setData(x=x, y=y2)
+
+ # Define new theory
+ fit.addtheory(theory="Asymetric gaussian",
+ function=functions.sum_splitgauss,
+ parameters=("height", "peak center", "left fwhm", "right fwhm"),
+ estimate=fitfuns.estimate_splitgauss)
+ fit.settheory('Asymetric gaussian')
+
+ # Fit
+ fit.estimate()
+ fit.runfit()
+
+ # Show first fit result in another tab in our widget
+ w.fillFromFit(fit.fit_results, view='Asymetric gaussians')
+ a.exec_()
+
+ """
+
+ def __init__(self, parent=None, name="FitParameters"):
+ """
+
+ :param parent: Parent widget
+ :param name: Widget title
+ """
+ qt.QTabWidget.__init__(self, parent)
+ self.setWindowTitle(name)
+ self.setContentsMargins(0, 0, 0, 0)
+
+ self.views = OrderedDict()
+ """Dictionary of views. Keys are view names,
+ items are :class:`Parameters` widgets"""
+
+ self.latest_view = None
+ """Name of latest view"""
+
+ # the widgets/tables themselves
+ self.tables = {}
+ """Dictionary of :class:`silx.gui.fit.parameters.Parameters` objects.
+ These objects store fit results
+ """
+
+ self.setContentsMargins(10, 10, 10, 10)
+
+ def setView(self, view=None, fitresults=None):
+ """Add or update a table. Fill it with data from a fit
+
+ :param view: Tab name to be added or updated. If ``None``, use the
+ latest view.
+ :param fitresults: Fit data to be added to the table
+ :raise: KeyError if no view name specified and no latest view
+ available.
+ """
+ if view is None:
+ if self.latest_view is not None:
+ view = self.latest_view
+ else:
+ raise KeyError(
+ "No view available. You must specify a view" +
+ " name the first time you call this method."
+ )
+
+ if view in self.tables.keys():
+ table = self.tables[view]
+ else:
+ # create the parameters instance
+ self.tables[view] = Parameters(self)
+ table = self.tables[view]
+ self.views[view] = table
+ self.addTab(table, str(view))
+
+ if fitresults is not None:
+ table.fillFromFit(fitresults)
+
+ self.setCurrentWidget(self.views[view])
+ self.latest_view = view
+
+ def renameView(self, oldname=None, newname=None):
+ """Rename a view (tab)
+
+ :param oldname: Name of the view to be renamed
+ :param newname: New name of the view"""
+ error = 1
+ if newname is not None:
+ if newname not in self.views.keys():
+ if oldname in self.views.keys():
+ parameterlist = self.tables[oldname].getFitResults()
+ self.setView(view=newname, fitresults=parameterlist)
+ self.removeView(oldname)
+ error = 0
+ return error
+
+ def fillFromFit(self, fitparameterslist, view=None):
+ """Update a view with data from a fit (alias for :meth:`setView`)
+
+ :param view: Tab name to be added or updated (default: latest view)
+ :param fitparameterslist: Fit data to be added to the table
+ """
+ self.setView(view=view, fitresults=fitparameterslist)
+
+ def getFitResults(self, name=None):
+ """Call :meth:`getFitResults` for the
+ :class:`silx.gui.fit.parameters.Parameters` corresponding to the
+ latest table or to the named table (if ``name`` is not
+ ``None``). This return a list of dictionaries in the format used by
+ :class:`silx.math.fit.fitmanager.FitManager` to store fit parameter
+ results.
+
+ :param name: View name.
+ """
+ if name is None:
+ name = self.latest_view
+ return self.tables[name].getFitResults()
+
+ def removeView(self, name):
+ """Remove a view by name.
+
+ :param name: View name.
+ """
+ if name in self.views:
+ index = self.indexOf(self.tables[name])
+ self.removeTab(index)
+ index = self.indexOf(self.views[name])
+ self.removeTab(index)
+ del self.tables[name]
+ del self.views[name]
+
+ def removeAllViews(self, keep=None):
+ """Remove all views, except the one specified (argument
+ ``keep``)
+
+ :param keep: Name of the view to be kept."""
+ for view in self.tables:
+ if view != keep:
+ self.removeView(view)
+
+ def getHtmlText(self, name=None):
+ """Return the table data as HTML
+
+ :param name: View name."""
+ if name is None:
+ name = self.latest_view
+ table = self.tables[name]
+ lemon = ("#%x%x%x" % (255, 250, 205)).upper()
+ hcolor = ("#%x%x%x" % (230, 240, 249)).upper()
+ text = ""
+ text += "<nobr>"
+ text += "<table>"
+ text += "<tr>"
+ ncols = table.columnCount()
+ for l in range(ncols):
+ text += ('<td align="left" bgcolor="%s"><b>' % hcolor)
+ if QTVERSION < '4.0.0':
+ text += (str(table.horizontalHeader().label(l)))
+ else:
+ text += (str(table.horizontalHeaderItem(l).text()))
+ text += "</b></td>"
+ text += "</tr>"
+ nrows = table.rowCount()
+ for r in range(nrows):
+ text += "<tr>"
+ item = table.item(r, 0)
+ newtext = ""
+ if item is not None:
+ newtext = str(item.text())
+ if len(newtext):
+ color = "white"
+ b = "<b>"
+ else:
+ b = ""
+ color = lemon
+ try:
+ # MyQTable item has color defined
+ cc = table.item(r, 0).color
+ cc = ("#%x%x%x" % (cc.red(), cc.green(), cc.blue())).upper()
+ color = cc
+ except:
+ pass
+ for c in range(ncols):
+ item = table.item(r, c)
+ newtext = ""
+ if item is not None:
+ newtext = str(item.text())
+ if len(newtext):
+ finalcolor = color
+ else:
+ finalcolor = "white"
+ if c < 2:
+ text += ('<td align="left" bgcolor="%s">%s' %
+ (finalcolor, b))
+ else:
+ text += ('<td align="right" bgcolor="%s">%s' %
+ (finalcolor, b))
+ text += newtext
+ if len(b):
+ text += "</td>"
+ else:
+ text += "</b></td>"
+ item = table.item(r, 0)
+ newtext = ""
+ if item is not None:
+ newtext = str(item.text())
+ if len(newtext):
+ text += "</b>"
+ text += "</tr>"
+ text += "\n"
+ text += "</table>"
+ text += "</nobr>"
+ return text
+
+ def getText(self, name=None):
+ """Return the table data as CSV formatted text, using tabulation
+ characters as separators.
+
+ :param name: View name."""
+ if name is None:
+ name = self.latest_view
+ table = self.tables[name]
+ text = ""
+ ncols = table.columnCount()
+ for l in range(ncols):
+ text += (str(table.horizontalHeaderItem(l).text())) + "\t"
+ text += "\n"
+ nrows = table.rowCount()
+ for r in range(nrows):
+ for c in range(ncols):
+ newtext = ""
+ if c != 4:
+ item = table.item(r, c)
+ if item is not None:
+ newtext = str(item.text())
+ else:
+ item = table.cellWidget(r, c)
+ if item is not None:
+ newtext = str(item.currentText())
+ text += newtext + "\t"
+ text += "\n"
+ text += "\n"
+ return text
+
+
+def test():
+ from silx.math.fit import fittheories
+ from silx.math.fit import fitmanager
+ from silx.math.fit import functions
+ from silx.gui.plot.PlotWindow import PlotWindow
+ import numpy
+
+ a = qt.QApplication([])
+
+ x = numpy.arange(1000)
+ y1 = functions.sum_gauss(x, 100, 400, 100)
+
+ fit = fitmanager.FitManager(x=x, y=y1)
+
+ fitfuns = fittheories.FitTheories()
+ fit.addtheory(name="Gaussian",
+ function=functions.sum_gauss,
+ parameters=("height", "peak center", "fwhm"),
+ estimate=fitfuns.estimate_height_position_fwhm)
+ fit.settheory('Gaussian')
+ fit.configure(PositiveFwhmFlag=True,
+ PositiveHeightAreaFlag=True,
+ AutoFwhm=True,)
+
+ # Fit
+ fit.estimate()
+ fit.runfit()
+
+ w = ParametersTab()
+ w.show()
+ w.fillFromFit(fit.fit_results, view='Gaussians')
+
+ y2 = functions.sum_splitgauss(x,
+ 100, 400, 100, 40,
+ 10, 600, 50, 500,
+ 80, 850, 10, 50)
+ fit.setdata(x=x, y=y2)
+
+ # Define new theory
+ fit.addtheory(name="Asymetric gaussian",
+ function=functions.sum_splitgauss,
+ parameters=("height", "peak center", "left fwhm", "right fwhm"),
+ estimate=fitfuns.estimate_splitgauss)
+ fit.settheory('Asymetric gaussian')
+
+ # Fit
+ fit.estimate()
+ fit.runfit()
+
+ w.fillFromFit(fit.fit_results, view='Asymetric gaussians')
+
+ # Plot
+ pw = PlotWindow(control=True)
+ pw.addCurve(x, y1, "Gaussians")
+ pw.addCurve(x, y2, "Asymetric gaussians")
+ pw.show()
+
+ a.exec_()
+
+
+if __name__ == "__main__":
+ test()
diff --git a/silx/gui/fit/Parameters.py b/silx/gui/fit/Parameters.py
new file mode 100644
index 0000000..62e3278
--- /dev/null
+++ b/silx/gui/fit/Parameters.py
@@ -0,0 +1,882 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2004-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ######################################################################### */
+"""This module defines a table widget that is specialized in displaying fit
+parameter results and associated constraints."""
+__authors__ = ["V.A. Sole", "P. Knobel"]
+__license__ = "MIT"
+__date__ = "25/11/2016"
+
+import sys
+from collections import OrderedDict
+
+from silx.gui import qt
+from silx.gui.widgets.TableWidget import TableWidget
+
+
+def float_else_zero(sstring):
+ """Return converted string to float. If conversion fail, return zero.
+
+ :param sstring: String to be converted
+ :return: ``float(sstrinq)`` if ``sstring`` can be converted to float
+ (e.g. ``"3.14"``), else ``0``
+ """
+ try:
+ return float(sstring)
+ except ValueError:
+ return 0
+
+
+class QComboTableItem(qt.QComboBox):
+ """:class:`qt.QComboBox` augmented with a ``sigCellChanged`` signal
+ to emit a tuple of ``(row, column)`` coordinates when the value is
+ changed.
+
+ This signal can be used to locate the modified combo box in a table.
+
+ :param row: Row number of the table cell containing this widget
+ :param col: Column number of the table cell containing this widget"""
+ sigCellChanged = qt.Signal(int, int)
+ """Signal emitted when this ``QComboBox`` is activated.
+ A ``(row, column)`` tuple is passed."""
+
+ def __init__(self, parent=None, row=None, col=None):
+ self._row = row
+ self._col = col
+ qt.QComboBox.__init__(self, parent)
+ self.activated[int].connect(self._cellChanged)
+
+ def _cellChanged(self, idx): # noqa
+ self.sigCellChanged.emit(self._row, self._col)
+
+
+class QCheckBoxItem(qt.QCheckBox):
+ """:class:`qt.QCheckBox` augmented with a ``sigCellChanged`` signal
+ to emit a tuple of ``(row, column)`` coordinates when the check box has
+ been clicked on.
+
+ This signal can be used to locate the modified check box in a table.
+
+ :param row: Row number of the table cell containing this widget
+ :param col: Column number of the table cell containing this widget"""
+ sigCellChanged = qt.Signal(int, int)
+ """Signal emitted when this ``QCheckBox`` is clicked.
+ A ``(row, column)`` tuple is passed."""
+
+ def __init__(self, parent=None, row=None, col=None):
+ self._row = row
+ self._col = col
+ qt.QCheckBox.__init__(self, parent)
+ self.clicked.connect(self._cellChanged)
+
+ def _cellChanged(self):
+ self.sigCellChanged.emit(self._row, self._col)
+
+
+class Parameters(TableWidget):
+ """:class:`TableWidget` customized to display fit results
+ and to interact with :class:`FitManager` objects.
+
+ Data and references to cell widgets are kept in a dictionary
+ attribute :attr:`parameters`.
+
+ :param parent: Parent widget
+ :param labels: Column headers. If ``None``, default headers will be used.
+ :type labels: List of strings or None
+ :param paramlist: List of fit parameters to be displayed for each fitted
+ peak.
+ :type paramlist: list[str] or None
+ """
+ def __init__(self, parent=None, paramlist=None):
+ TableWidget.__init__(self, parent)
+ self.setContentsMargins(0, 0, 0, 0)
+
+ labels = ['Parameter', 'Estimation', 'Fit Value', 'Sigma',
+ 'Constraints', 'Min/Parame', 'Max/Factor/Delta']
+ tooltips = ["Fit parameter name",
+ "Estimated value for fit parameter. You can edit this column.",
+ "Actual value for parameter, after fit",
+ "Uncertainty (same unit as the parameter)",
+ "Constraint to be applied to the parameter for fit",
+ "First parameter for constraint (name of another param or min value)",
+ "Second parameter for constraint (max value, or factor/delta)"]
+
+ self.columnKeys = ['name', 'estimation', 'fitresult',
+ 'sigma', 'code', 'val1', 'val2']
+ """This list assigns shorter keys to refer to columns than the
+ displayed labels."""
+
+ self.__configuring = False
+
+ # column headers and associated tooltips
+ self.setColumnCount(len(labels))
+
+ for i, label in enumerate(labels):
+ item = self.horizontalHeaderItem(i)
+ if item is None:
+ item = qt.QTableWidgetItem(label,
+ qt.QTableWidgetItem.Type)
+ self.setHorizontalHeaderItem(i, item)
+
+ item.setText(label)
+ if tooltips is not None:
+ item.setToolTip(tooltips[i])
+
+ # resize columns
+ for col_key in ["name", "estimation", "sigma", "val1", "val2"]:
+ col_idx = self.columnIndexByField(col_key)
+ self.resizeColumnToContents(col_idx)
+
+ # Initialize the table with one line per supplied parameter
+ paramlist = paramlist if paramlist is not None else []
+ self.parameters = OrderedDict()
+ """This attribute stores all the data in an ordered dictionary.
+ New data can be added using :meth:`newParameterLine`.
+ Existing data can be modified using :meth:`configureLine`
+
+ Keys of the dictionary are:
+
+ - 'name': parameter name
+ - 'line': line index for the parameter in the table
+ - 'estimation'
+ - 'fitresult'
+ - 'sigma'
+ - 'code': constraint code (one of the elements of
+ :attr:`code_options`)
+ - 'val1': first parameter related to constraint, formatted
+ as a string, as typed in the table
+ - 'val2': second parameter related to constraint, formatted
+ as a string, as typed in the table
+ - 'cons1': scalar representation of 'val1'
+ (e.g. when val1 is the name of a fit parameter, cons1
+ will be the line index of this parameter)
+ - 'cons2': scalar representation of 'val2'
+ - 'vmin': equal to 'val1' when 'code' is "QUOTED"
+ - 'vmax': equal to 'val2' when 'code' is "QUOTED"
+ - 'relatedto': name of related parameter when this parameter
+ is constrained to another parameter (same as 'val1')
+ - 'factor': same as 'val2' when 'code' is 'FACTOR'
+ - 'delta': same as 'val2' when 'code' is 'DELTA'
+ - 'sum': same as 'val2' when 'code' is 'SUM'
+ - 'group': group index for the parameter
+ - 'xmin': data range minimum
+ - 'xmax': data range maximum
+ """
+ for line, param in enumerate(paramlist):
+ self.newParameterLine(param, line)
+
+ self.code_options = ["FREE", "POSITIVE", "QUOTED", "FIXED",
+ "FACTOR", "DELTA", "SUM", "IGNORE", "ADD"]
+ """Possible values in the combo boxes in the 'Constraints' column.
+ """
+
+ # connect signal
+ self.cellChanged[int, int].connect(self.onCellChanged)
+
+ def newParameterLine(self, param, line):
+ """Add a line to the :class:`QTableWidget`.
+
+ Each line represents one of the fit parameters for one of
+ the fitted peaks.
+
+ :param param: Name of the fit parameter
+ :type param: str
+ :param line: 0-based line index
+ :type line: int
+ """
+ # get current number of lines
+ nlines = self.rowCount()
+ self.__configuring = True
+ if line >= nlines:
+ self.setRowCount(line + 1)
+
+ # default configuration for fit parameters
+ self.parameters[param] = OrderedDict((('line', line),
+ ('estimation', '0'),
+ ('fitresult', ''),
+ ('sigma', ''),
+ ('code', 'FREE'),
+ ('val1', ''),
+ ('val2', ''),
+ ('cons1', 0),
+ ('cons2', 0),
+ ('vmin', '0'),
+ ('vmax', '1'),
+ ('relatedto', ''),
+ ('factor', '1.0'),
+ ('delta', '0.0'),
+ ('sum', '0.0'),
+ ('group', ''),
+ ('name', param),
+ ('xmin', None),
+ ('xmax', None)))
+ self.setReadWrite(param, 'estimation')
+ self.setReadOnly(param, ['name', 'fitresult', 'sigma', 'val1', 'val2'])
+
+ # Constraint codes
+ a = []
+ for option in self.code_options:
+ a.append(option)
+
+ code_column_index = self.columnIndexByField('code')
+ cellWidget = self.cellWidget(line, code_column_index)
+ if cellWidget is None:
+ cellWidget = QComboTableItem(self, row=line,
+ col=code_column_index)
+ cellWidget.addItems(a)
+ self.setCellWidget(line, code_column_index, cellWidget)
+ cellWidget.sigCellChanged[int, int].connect(self.onCellChanged)
+ self.parameters[param]['code_item'] = cellWidget
+ self.parameters[param]['relatedto_item'] = None
+ self.__configuring = False
+
+ def columnIndexByField(self, field):
+ """
+
+ :param field: Field name (column key)
+ :return: Index of the column with this field name
+ """
+ return self.columnKeys.index(field)
+
+ def fillFromFit(self, fitresults):
+ """Fill table with values from a list of dictionaries
+ (see :attr:`silx.math.fit.fitmanager.FitManager.fit_results`)
+
+ :param fitresults: List of parameters as recorded
+ in the ``paramlist`` attribute of a :class:`FitManager` object
+ :type fitresults: list[dict]
+ """
+ self.setRowCount(len(fitresults))
+
+ # Reinitialize and fill self.parameters
+ self.parameters = OrderedDict()
+ for (line, param) in enumerate(fitresults):
+ self.newParameterLine(param['name'], line)
+
+ for param in fitresults:
+ name = param['name']
+ code = str(param['code'])
+ if code not in self.code_options:
+ # convert code from int to descriptive string
+ code = self.code_options[int(code)]
+ val1 = param['cons1']
+ val2 = param['cons2']
+ estimation = param['estimation']
+ group = param['group']
+ sigma = param['sigma']
+ fitresult = param['fitresult']
+
+ xmin = param.get('xmin')
+ xmax = param.get('xmax')
+
+ self.configureLine(name=name,
+ code=code,
+ val1=val1, val2=val2,
+ estimation=estimation,
+ fitresult=fitresult,
+ sigma=sigma,
+ group=group,
+ xmin=xmin, xmax=xmax)
+
+ def getConfiguration(self):
+ """Return ``FitManager.paramlist`` dictionary
+ encapsulated in another dictionary"""
+ return {'parameters': self.getFitResults()}
+
+ def setConfiguration(self, ddict):
+ """Fill table with values from a ``FitManager.paramlist`` dictionary
+ encapsulated in another dictionary"""
+ self.fillFromFit(ddict['parameters'])
+
+ def getFitResults(self):
+ """Return fit parameters as a list of dictionaries in the format used
+ by :class:`FitManager` (attribute ``paramlist``).
+ """
+ fitparameterslist = []
+ for param in self.parameters:
+ fitparam = {}
+ name = param
+ estimation, [code, cons1, cons2] = self.getEstimationConstraints(name)
+ buf = str(self.parameters[param]['fitresult'])
+ xmin = self.parameters[param]['xmin']
+ xmax = self.parameters[param]['xmax']
+ if len(buf):
+ fitresult = float(buf)
+ else:
+ fitresult = 0.0
+ buf = str(self.parameters[param]['sigma'])
+ if len(buf):
+ sigma = float(buf)
+ else:
+ sigma = 0.0
+ buf = str(self.parameters[param]['group'])
+ if len(buf):
+ group = float(buf)
+ else:
+ group = 0
+ fitparam['name'] = name
+ fitparam['estimation'] = estimation
+ fitparam['fitresult'] = fitresult
+ fitparam['sigma'] = sigma
+ fitparam['group'] = group
+ fitparam['code'] = code
+ fitparam['cons1'] = cons1
+ fitparam['cons2'] = cons2
+ fitparam['xmin'] = xmin
+ fitparam['xmax'] = xmax
+ fitparameterslist.append(fitparam)
+ return fitparameterslist
+
+ def onCellChanged(self, row, col):
+ """Slot called when ``cellChanged`` signal is emitted.
+ Checks the validity of the new text in the cell, then calls
+ :meth:`configureLine` to update the internal ``self.parameters``
+ dictionary.
+
+ :param row: Row number of the changed cell (0-based index)
+ :param col: Column number of the changed cell (0-based index)
+ """
+ if (col != self.columnIndexByField("code")) and (col != -1):
+ if row != self.currentRow():
+ return
+ if col != self.currentColumn():
+ return
+ if self.__configuring:
+ return
+ param = list(self.parameters)[row]
+ field = self.columnKeys[col]
+ oldvalue = self.parameters[param][field]
+ if col != 4:
+ item = self.item(row, col)
+ if item is not None:
+ newvalue = item.text()
+ else:
+ newvalue = ''
+ else:
+ # this is the combobox
+ widget = self.cellWidget(row, col)
+ newvalue = widget.currentText()
+ if self.validate(param, field, oldvalue, newvalue):
+ paramdict = {"name": param, field: newvalue}
+ self.configureLine(**paramdict)
+ else:
+ if field == 'code':
+ # New code not valid, try restoring the old one
+ index = self.code_options.index(oldvalue)
+ self.__configuring = True
+ try:
+ self.parameters[param]['code_item'].setCurrentIndex(index)
+ finally:
+ self.__configuring = False
+ else:
+ paramdict = {"name": param, field: oldvalue}
+ self.configureLine(**paramdict)
+
+ def validate(self, param, field, oldvalue, newvalue):
+ """Check validity of ``newvalue`` when a cell's value is modified.
+
+ :param param: Fit parameter name
+ :param field: Column name
+ :param oldvalue: Cell value before change attempt
+ :param newvalue: New value to be validated
+ :return: True if new cell value is valid, else False
+ """
+ if field == 'code':
+ return self.setCodeValue(param, oldvalue, newvalue)
+ # FIXME: validate() shouldn't have side effects. Move this bit to configureLine()?
+ if field == 'val1' and str(self.parameters[param]['code']) in ['DELTA', 'FACTOR', 'SUM']:
+ _, candidates = self.getRelatedCandidates(param)
+ # We expect val1 to be a fit parameter name
+ if str(newvalue) in candidates:
+ return True
+ else:
+ return False
+ # except for code, val1 and name (which is read-only and does not need
+ # validation), all fields must always be convertible to float
+ else:
+ try:
+ float(str(newvalue))
+ except ValueError:
+ return False
+ return True
+
+ def setCodeValue(self, param, oldvalue, newvalue):
+ """Update 'code' and 'relatedto' fields when code cell is
+ changed.
+
+ :param param: Fit parameter name
+ :param oldvalue: Cell value before change attempt
+ :param newvalue: New value to be validated
+ :return: ``True`` if code was successfully updated
+ """
+
+ if str(newvalue) in ['FREE', 'POSITIVE', 'QUOTED', 'FIXED']:
+ self.configureLine(name=param,
+ code=newvalue)
+ if str(oldvalue) == 'IGNORE':
+ self.freeRestOfGroup(param)
+ return True
+ elif str(newvalue) in ['FACTOR', 'DELTA', 'SUM']:
+ # I should check here that some parameter is set
+ best, candidates = self.getRelatedCandidates(param)
+ if len(candidates) == 0:
+ return False
+ self.configureLine(name=param,
+ code=newvalue,
+ relatedto=best)
+ if str(oldvalue) == 'IGNORE':
+ self.freeRestOfGroup(param)
+ return True
+
+ elif str(newvalue) == 'IGNORE':
+ # I should check if the group can be ignored
+ # for the time being I just fix all of them to ignore
+ group = int(float(str(self.parameters[param]['group'])))
+ candidates = []
+ for param in self.parameters.keys():
+ if group == int(float(str(self.parameters[param]['group']))):
+ candidates.append(param)
+ # print candidates
+ # I should check here if there is any relation to them
+ for param in candidates:
+ self.configureLine(name=param,
+ code=newvalue)
+ return True
+ elif str(newvalue) == 'ADD':
+ group = int(float(str(self.parameters[param]['group'])))
+ if group == 0:
+ # One cannot add a background group
+ return False
+ i = 0
+ for param in self.parameters:
+ if i <= int(float(str(self.parameters[param]['group']))):
+ i += 1
+ if (group == 0) and (i == 1): # FIXME: why +1?
+ i += 1
+ self.addGroup(i, group)
+ return False
+ elif str(newvalue) == 'SHOW':
+ print(self.getEstimationConstraints(param))
+ return False
+
+ def addGroup(self, newg, gtype):
+ """Add a fit parameter group with the same fit parameters as an
+ existing group.
+
+ This function is called when the user selects "ADD" in the
+ "constraints" combobox.
+
+ :param int newg: New group number
+ :param int gtype: Group number whose parameters we want to copy
+
+ """
+ newparam = []
+ # loop through parameters until we encounter group number `gtype`
+ for param in list(self.parameters):
+ paramgroup = int(float(str(self.parameters[param]['group'])))
+ # copy parameter names in group number `gtype`
+ if paramgroup == gtype:
+ # but replace `gtype` with `newg`
+ newparam.append(param.rstrip("0123456789") + "%d" % newg)
+
+ xmin = self.parameters[param]['xmin']
+ xmax = self.parameters[param]['xmax']
+
+ # Add new parameters (one table line per parameter) and configureLine each
+ # one by updating xmin and xmax to the same values as group `gtype`
+ line = len(list(self.parameters))
+ for param in newparam:
+ self.newParameterLine(param, line)
+ line += 1
+ for param in newparam:
+ self.configureLine(name=param, group=newg, xmin=xmin, xmax=xmax)
+
+ def freeRestOfGroup(self, workparam):
+ """Set ``code`` to ``"FREE"`` for all fit parameters belonging to
+ the same group as ``workparam``. This is done when the entire group
+ of parameters was previously ignored and one of them has his code
+ set to something different than ``"IGNORE"``.
+
+ :param workparam: Fit parameter name
+ """
+ if workparam in self.parameters.keys():
+ group = int(float(str(self.parameters[workparam]['group'])))
+ for param in self.parameters:
+ if param != workparam and\
+ group == int(float(str(self.parameters[param]['group']))):
+ self.configureLine(name=param,
+ code='FREE',
+ cons1=0,
+ cons2=0,
+ val1='',
+ val2='')
+
+ def getRelatedCandidates(self, workparam):
+ """If fit parameter ``workparam`` has a constraint that involves other
+ fit parameters, find possible candidates and try to guess which one
+ is the most likely.
+
+ :param workparam: Fit parameter name
+ :return: (best_candidate, possible_candidates) tuple
+ :rtype: (str, list[str])
+ """
+ candidates = []
+ for param_name in self.parameters:
+ if param_name != workparam:
+ # ignore parameters that are fixed by a constraint
+ if str(self.parameters[param_name]['code']) not in\
+ ['IGNORE', 'FACTOR', 'DELTA', 'SUM']:
+ candidates.append(param_name)
+ # take the previous one (before code cell changed) if possible
+ if str(self.parameters[workparam]['relatedto']) in candidates:
+ best = str(self.parameters[workparam]['relatedto'])
+ return best, candidates
+ # take the first with same base name (after removing numbers)
+ for param_name in candidates:
+ basename = param_name.rstrip("0123456789")
+ try:
+ pos = workparam.index(basename)
+ if pos == 0:
+ best = param_name
+ return best, candidates
+ except ValueError:
+ pass
+ # take the first
+ return candidates[0], candidates
+
+ def setReadOnly(self, parameter, fields):
+ """Make table cells read-only by setting it's flags and omitting
+ flag ``qt.Qt.ItemIsEditable``
+
+ :param parameter: Fit parameter names identifying the rows
+ :type parameter: str or list[str]
+ :param fields: Field names identifying the columns
+ :type fields: str or list[str]
+ """
+ editflags = qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled
+ self.setField(parameter, fields, editflags)
+
+ def setReadWrite(self, parameter, fields):
+ """Make table cells read-write by setting it's flags including
+ flag ``qt.Qt.ItemIsEditable``
+
+ :param parameter: Fit parameter names identifying the rows
+ :type parameter: str or list[str]
+ :param fields: Field names identifying the columns
+ :type fields: str or list[str]
+ """
+ editflags = qt.Qt.ItemIsSelectable |\
+ qt.Qt.ItemIsEnabled |\
+ qt.Qt.ItemIsEditable
+ self.setField(parameter, fields, editflags)
+
+ def setField(self, parameter, fields, edit_flags):
+ """Set text and flags in a table cell.
+
+ :param parameter: Fit parameter names identifying the rows
+ :type parameter: str or list[str]
+ :param fields: Field names identifying the columns
+ :type fields: str or list[str]
+ :param edit_flags: Flag combination, e.g::
+
+ qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled |
+ qt.Qt.ItemIsEditable
+ """
+ if isinstance(parameter, list) or \
+ isinstance(parameter, tuple):
+ paramlist = parameter
+ else:
+ paramlist = [parameter]
+ if isinstance(fields, list) or \
+ isinstance(fields, tuple):
+ fieldlist = fields
+ else:
+ fieldlist = [fields]
+
+ # Set _configuring flag to ignore cellChanged signals in
+ # self.onCellChanged
+ _oldvalue = self.__configuring
+ self.__configuring = True
+
+ # 2D loop through parameter list and field list
+ # to update their cells
+ for param in paramlist:
+ row = list(self.parameters.keys()).index(param)
+ for field in fieldlist:
+ col = self.columnIndexByField(field)
+ if field != 'code':
+ key = field + "_item"
+ item = self.item(row, col)
+ if item is None:
+ item = qt.QTableWidgetItem()
+ item.setText(self.parameters[param][field])
+ self.setItem(row, col, item)
+ else:
+ item.setText(self.parameters[param][field])
+ self.parameters[param][key] = item
+ item.setFlags(edit_flags)
+
+ # Restore previous _configuring flag
+ self.__configuring = _oldvalue
+
+ def configureLine(self, name, code=None, val1=None, val2=None,
+ sigma=None, estimation=None, fitresult=None,
+ group=None, xmin=None, xmax=None, relatedto=None,
+ cons1=None, cons2=None):
+ """This function updates values in a line of the table
+
+ :param name: Name of the parameter (serves as unique identifier for
+ a line).
+ :param code: Constraint code *FREE, FIXED, POSITIVE, DELTA, FACTOR,
+ SUM, QUOTED, IGNORE*
+ :param val1: Constraint 1 (can be the index or name of another
+ parameter for code *DELTA, FACTOR, SUM*, or a min value
+ for code *QUOTED*)
+ :param val2: Constraint 2
+ :param sigma: Standard deviation for a fit parameter
+ :param estimation: Estimated initial value for a fit parameter (used
+ as input to iterative fit)
+ :param fitresult: Final result of fit
+ :param group: Group number of a fit parameter (peak number when doing
+ multi-peak fitting, as each peak corresponds to a group
+ of several consecutive parameters)
+ :param xmin:
+ :param xmax:
+ :param relatedto: Index or name of another fit parameter
+ to which this parameter is related to (constraints)
+ :param cons1: similar meaning to ``val1``, but is always a number
+ :param cons2: similar meaning to ``val2``, but is always a number
+ :return:
+ """
+ paramlist = list(self.parameters.keys())
+
+ if name not in self.parameters:
+ raise KeyError("'%s' is not in the parameter list" % name)
+
+ # update code first, if specified
+ if code is not None:
+ code = str(code)
+ self.parameters[name]['code'] = code
+ # update combobox
+ index = self.parameters[name]['code_item'].findText(code)
+ self.parameters[name]['code_item'].setCurrentIndex(index)
+ else:
+ # set code to previous value, used later for setting val1 val2
+ code = self.parameters[name]['code']
+
+ # val1 and sigma have special formats
+ if val1 is not None:
+ fmt = None if self.parameters[name]['code'] in\
+ ['DELTA', 'FACTOR', 'SUM'] else "%8g"
+ self._updateField(name, "val1", val1, fmat=fmt)
+
+ if sigma is not None:
+ self._updateField(name, "sigma", sigma, fmat="%6.3g")
+
+ # other fields are formatted as "%8g"
+ keys_params = (("val2", val2), ("estimation", estimation),
+ ("fitresult", fitresult))
+ for key, value in keys_params:
+ if value is not None:
+ self._updateField(name, key, value, fmat="%8g")
+
+ # the rest of the parameters are treated as strings and don't need
+ # validation
+ keys_params = (("group", group), ("xmin", xmin),
+ ("xmax", xmax), ("relatedto", relatedto),
+ ("cons1", cons1), ("cons2", cons2))
+ for key, value in keys_params:
+ if value is not None:
+ self.parameters[name][key] = str(value)
+
+ # val1 and val2 have different meanings depending on the code
+ if code == 'QUOTED':
+ if val1 is not None:
+ self.parameters[name]['vmin'] = self.parameters[name]['val1']
+ else:
+ self.parameters[name]['val1'] = self.parameters[name]['vmin']
+ if val2 is not None:
+ self.parameters[name]['vmax'] = self.parameters[name]['val2']
+ else:
+ self.parameters[name]['val2'] = self.parameters[name]['vmax']
+
+ # cons1 and cons2 are scalar representations of val1 and val2
+ self.parameters[name]['cons1'] =\
+ float_else_zero(self.parameters[name]['val1'])
+ self.parameters[name]['cons2'] =\
+ float_else_zero(self.parameters[name]['val2'])
+
+ # cons1, cons2 = min(val1, val2), max(val1, val2)
+ if self.parameters[name]['cons1'] > self.parameters[name]['cons2']:
+ self.parameters[name]['cons1'], self.parameters[name]['cons2'] =\
+ self.parameters[name]['cons2'], self.parameters[name]['cons1']
+
+ elif code in ['DELTA', 'SUM', 'FACTOR']:
+ # For these codes, val1 is the fit parameter name on which the
+ # constraint depends
+ if val1 is not None and val1 in paramlist:
+ self.parameters[name]['relatedto'] = self.parameters[name]["val1"]
+
+ elif val1 is not None:
+ # val1 could be the index of the fit parameter
+ try:
+ self.parameters[name]['relatedto'] = paramlist[int(val1)]
+ except ValueError:
+ self.parameters[name]['relatedto'] = self.parameters[name]["val1"]
+
+ elif relatedto is not None:
+ # code changed, val1 not specified but relatedto specified:
+ # set val1 to relatedto (pre-fill best guess)
+ self.parameters[name]["val1"] = relatedto
+
+ # update fields "delta", "sum" or "factor"
+ key = code.lower()
+ self.parameters[name][key] = self.parameters[name]["val2"]
+
+ # FIXME: val1 is sometimes specified as an index rather than a param name
+ self.parameters[name]['val1'] = self.parameters[name]['relatedto']
+
+ # cons1 is the index of the fit parameter in the ordered dictionary
+ if self.parameters[name]['val1'] in paramlist:
+ self.parameters[name]['cons1'] =\
+ paramlist.index(self.parameters[name]['val1'])
+
+ # cons2 is the constraint value (factor, delta or sum)
+ try:
+ self.parameters[name]['cons2'] =\
+ float(str(self.parameters[name]['val2']))
+ except ValueError:
+ self.parameters[name]['cons2'] = 1.0 if code == "FACTOR" else 0.0
+
+ elif code in ['FREE', 'POSITIVE', 'IGNORE', 'FIXED']:
+ self.parameters[name]['val1'] = ""
+ self.parameters[name]['val2'] = ""
+ self.parameters[name]['cons1'] = 0
+ self.parameters[name]['cons2'] = 0
+
+ self._updateCellRWFlags(name, code)
+
+ def _updateField(self, name, field, value, fmat=None):
+ """Update field in ``self.parameters`` dictionary, if the new value
+ is valid.
+
+ :param name: Fit parameter name
+ :param field: Field name
+ :param value: New value to assign
+ :type value: String
+ :param fmat: Format string (e.g. "%8g") to be applied if value represents
+ a scalar. If ``None``, format is not modified. If ``value`` is an
+ empty string, ``fmat`` is ignored.
+ """
+ if value is not None:
+ oldvalue = self.parameters[name][field]
+ if fmat is not None:
+ newvalue = fmat % float(value) if value != "" else ""
+ else:
+ newvalue = value
+ self.parameters[name][field] = newvalue if\
+ self.validate(name, field, oldvalue, newvalue) else\
+ oldvalue
+
+ def _updateCellRWFlags(self, name, code=None):
+ """Set read-only or read-write flags in a row,
+ depending on the constraint code
+
+ :param name: Fit parameter name identifying the row
+ :param code: Constraint code, in `'FREE', 'POSITIVE', 'IGNORE',`
+ `'FIXED', 'FACTOR', 'DELTA', 'SUM', 'ADD'`
+ :return:
+ """
+ if code in ['FREE', 'POSITIVE', 'IGNORE', 'FIXED']:
+ self.setReadWrite(name, 'estimation')
+ self.setReadOnly(name, ['fitresult', 'sigma', 'val1', 'val2'])
+ else:
+ self.setReadWrite(name, ['estimation', 'val1', 'val2'])
+ self.setReadOnly(name, ['fitresult', 'sigma'])
+
+ def getEstimationConstraints(self, param):
+ """
+ Return tuple ``(estimation, constraints)`` where ``estimation`` is the
+ value in the ``estimate`` field and ``constraints`` are the relevant
+ constraints according to the active code
+ """
+ estimation = None
+ constraints = None
+ if param in self.parameters.keys():
+ buf = str(self.parameters[param]['estimation'])
+ if len(buf):
+ estimation = float(buf)
+ else:
+ estimation = 0
+ if str(self.parameters[param]['code']) in self.code_options:
+ code = self.code_options.index(
+ str(self.parameters[param]['code']))
+ else:
+ code = str(self.parameters[param]['code'])
+ cons1 = self.parameters[param]['cons1']
+ cons2 = self.parameters[param]['cons2']
+ constraints = [code, cons1, cons2]
+ return estimation, constraints
+
+
+def main(args):
+ from silx.math.fit import fittheories
+ from silx.math.fit import fitmanager
+ try:
+ from PyMca5 import PyMcaDataDir
+ except ImportError:
+ raise ImportError("This demo requires PyMca data. Install PyMca5.")
+ import numpy
+ import os
+ app = qt.QApplication(args)
+ tab = Parameters(paramlist=['Height', 'Position', 'FWHM'])
+ tab.showGrid()
+ tab.configureLine(name='Height', estimation='1234', group=0)
+ tab.configureLine(name='Position', code='FIXED', group=1)
+ tab.configureLine(name='FWHM', group=1)
+
+ y = numpy.loadtxt(os.path.join(PyMcaDataDir.PYMCA_DATA_DIR,
+ "XRFSpectrum.mca")) # FIXME
+
+ x = numpy.arange(len(y)) * 0.0502883 - 0.492773
+ fit = fitmanager.FitManager()
+ fit.setdata(x=x, y=y, xmin=20, xmax=150)
+
+ fit.loadtheories(fittheories)
+
+ fit.settheory('ahypermet')
+ fit.configure(Yscaling=1.,
+ PositiveFwhmFlag=True,
+ PositiveHeightAreaFlag=True,
+ FwhmPoints=16,
+ QuotedPositionFlag=1,
+ HypermetTails=1)
+ fit.setbackground('Linear')
+ fit.estimate()
+ fit.runfit()
+ tab.fillFromFit(fit.fit_results)
+ tab.show()
+ app.exec_()
+
+if __name__ == "__main__":
+ main(sys.argv)
diff --git a/silx/gui/fit/__init__.py b/silx/gui/fit/__init__.py
new file mode 100644
index 0000000..e4fd3ab
--- /dev/null
+++ b/silx/gui/fit/__init__.py
@@ -0,0 +1,28 @@
+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ############################################################################*/
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "07/07/2016"
+
+from .FitWidget import FitWidget
diff --git a/silx/gui/fit/setup.py b/silx/gui/fit/setup.py
new file mode 100644
index 0000000..6672363
--- /dev/null
+++ b/silx/gui/fit/setup.py
@@ -0,0 +1,43 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "21/07/2016"
+
+
+from numpy.distutils.misc_util import Configuration
+
+
+def configuration(parent_package='', top_path=None):
+ config = Configuration('fit', parent_package, top_path)
+ config.add_subpackage('test')
+
+ return config
+
+
+if __name__ == "__main__":
+ from numpy.distutils.core import setup
+
+ setup(configuration=configuration)
diff --git a/silx/gui/fit/test/__init__.py b/silx/gui/fit/test/__init__.py
new file mode 100644
index 0000000..2236d64
--- /dev/null
+++ b/silx/gui/fit/test/__init__.py
@@ -0,0 +1,43 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+import unittest
+
+from .testFitWidget import suite as testFitWidgetSuite
+from .testFitConfig import suite as testFitConfigSuite
+from .testBackgroundWidget import suite as testBackgroundWidgetSuite
+
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "21/07/2016"
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTests(
+ [testFitWidgetSuite(),
+ testFitConfigSuite(),
+ testBackgroundWidgetSuite()])
+ return test_suite
diff --git a/silx/gui/fit/test/testBackgroundWidget.py b/silx/gui/fit/test/testBackgroundWidget.py
new file mode 100644
index 0000000..2e366e4
--- /dev/null
+++ b/silx/gui/fit/test/testBackgroundWidget.py
@@ -0,0 +1,83 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+import unittest
+
+from ...test.utils import TestCaseQt
+
+from .. import BackgroundWidget
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "05/12/2016"
+
+
+class TestBackgroundWidget(TestCaseQt):
+ def setUp(self):
+ super(TestBackgroundWidget, self).setUp()
+ self.bgdialog = BackgroundWidget.BackgroundDialog()
+ self.bgdialog.setData(list([0, 1, 2, 3]),
+ list([0, 1, 4, 8]))
+ self.qWaitForWindowExposed(self.bgdialog)
+
+ def tearDown(self):
+ del self.bgdialog
+ super(TestBackgroundWidget, self).tearDown()
+
+ def testShow(self):
+ self.bgdialog.show()
+ self.bgdialog.hide()
+
+ def testAccept(self):
+ self.bgdialog.accept()
+ self.assertTrue(self.bgdialog.result())
+
+ def testReject(self):
+ self.bgdialog.reject()
+ self.assertFalse(self.bgdialog.result())
+
+ def testDefaultOutput(self):
+ self.bgdialog.accept()
+ output = self.bgdialog.output
+
+ for key in ["algorithm", "StripThreshold", "SnipWidth",
+ "StripIterations", "StripWidth", "SmoothingFlag",
+ "SmoothingWidth", "AnchorsFlag", "AnchorsList"]:
+ self.assertIn(key, output)
+
+ self.assertFalse(output["AnchorsFlag"])
+ self.assertEqual(output["StripWidth"], 1)
+ self.assertEqual(output["SmoothingFlag"], False)
+ self.assertEqual(output["SmoothingWidth"], 3)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestBackgroundWidget))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/fit/test/testFitConfig.py b/silx/gui/fit/test/testFitConfig.py
new file mode 100644
index 0000000..eea35cc
--- /dev/null
+++ b/silx/gui/fit/test/testFitConfig.py
@@ -0,0 +1,95 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Basic tests for :class:`FitConfig`"""
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "05/12/2016"
+
+import unittest
+
+from ...test.utils import TestCaseQt
+from .. import FitConfig
+
+
+class TestFitConfig(TestCaseQt):
+ """Basic test for FitWidget"""
+
+ def setUp(self):
+ super(TestFitConfig, self).setUp()
+ self.fit_config = FitConfig.getFitConfigDialog(modal=False)
+ self.qWaitForWindowExposed(self.fit_config)
+
+ def tearDown(self):
+ del self.fit_config
+ super(TestFitConfig, self).tearDown()
+
+ def testShow(self):
+ self.fit_config.show()
+ self.fit_config.hide()
+
+ def testAccept(self):
+ self.fit_config.accept()
+ self.assertTrue(self.fit_config.result())
+
+ def testReject(self):
+ self.fit_config.reject()
+ self.assertFalse(self.fit_config.result())
+
+ def testDefaultOutput(self):
+ self.fit_config.accept()
+ output = self.fit_config.output
+
+ for key in ["AutoFwhm",
+ "PositiveHeightAreaFlag",
+ "QuotedPositionFlag",
+ "PositiveFwhmFlag",
+ "SameFwhmFlag",
+ "QuotedEtaFlag",
+ "NoConstraintsFlag",
+ "FwhmPoints",
+ "Sensitivity",
+ "Yscaling",
+ "ForcePeakPresence",
+ "StripBackgroundFlag",
+ "StripWidth",
+ "StripIterations",
+ "StripThreshold",
+ "SmoothingFlag"]:
+ self.assertIn(key, output)
+
+ self.assertTrue(output["AutoFwhm"])
+ self.assertEqual(output["StripWidth"], 2)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestFitConfig))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/fit/test/testFitWidget.py b/silx/gui/fit/test/testFitWidget.py
new file mode 100644
index 0000000..d542fd0
--- /dev/null
+++ b/silx/gui/fit/test/testFitWidget.py
@@ -0,0 +1,135 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Basic tests for :class:`FitWidget`"""
+
+import unittest
+
+from ...test.utils import TestCaseQt
+
+from ... import qt
+from .. import FitWidget
+
+from ....math.fit.fittheory import FitTheory
+from ....math.fit.fitmanager import FitManager
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "05/12/2016"
+
+
+class TestFitWidget(TestCaseQt):
+ """Basic test for FitWidget"""
+
+ def setUp(self):
+ super(TestFitWidget, self).setUp()
+ self.fit_widget = FitWidget()
+ self.fit_widget.show()
+ self.qWaitForWindowExposed(self.fit_widget)
+
+ def tearDown(self):
+ self.fit_widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+ self.fit_widget.close()
+ del self.fit_widget
+ super(TestFitWidget, self).tearDown()
+
+ def testShow(self):
+ pass
+
+ def testInteract(self):
+ self.mouseClick(self.fit_widget, qt.Qt.LeftButton)
+ self.keyClick(self.fit_widget, qt.Qt.Key_Enter)
+ self.qapp.processEvents()
+
+ def testCustomConfigWidget(self):
+ class CustomConfigWidget(qt.QDialog):
+ def __init__(self):
+ qt.QDialog.__init__(self)
+ self.setModal(True)
+ self.ok = qt.QPushButton("ok", self)
+ self.ok.clicked.connect(self.accept)
+ cancel = qt.QPushButton("cancel", self)
+ cancel.clicked.connect(self.reject)
+ layout = qt.QVBoxLayout(self)
+ layout.addWidget(self.ok)
+ layout.addWidget(cancel)
+ self.output = {"hello": "world"}
+
+ def fitfun(x, a, b):
+ return a * x + b
+
+ x = list(range(0, 100))
+ y = [fitfun(x_, 2, 3) for x_ in x]
+
+ def conf(**kw):
+ return {"spam": "eggs",
+ "hello": "world!"}
+
+ theory = FitTheory(
+ function=fitfun,
+ parameters=["a", "b"],
+ configure=conf)
+
+ fitmngr = FitManager()
+ fitmngr.setdata(x, y)
+ fitmngr.addtheory("foo", theory)
+ fitmngr.addtheory("bar", theory)
+ fitmngr.addbgtheory("spam", theory)
+
+ fw = FitWidget(fitmngr=fitmngr)
+ fw.associateConfigDialog("spam", CustomConfigWidget(),
+ theory_is_background=True)
+ fw.associateConfigDialog("foo", CustomConfigWidget())
+ fw.show()
+ self.qWaitForWindowExposed(fw)
+
+ fw.bgconfigdialogs["spam"].accept()
+ self.assertTrue(fw.bgconfigdialogs["spam"].result())
+
+ self.assertEqual(fw.bgconfigdialogs["spam"].output,
+ {"hello": "world"})
+
+ fw.bgconfigdialogs["spam"].reject()
+ self.assertFalse(fw.bgconfigdialogs["spam"].result())
+
+ fw.configdialogs["foo"].accept()
+ self.assertTrue(fw.configdialogs["foo"].result())
+
+ # todo: figure out how to click fw.configdialog.ok to close dialog
+ # open dialog
+ # self.mouseClick(fw.guiConfig.FunConfigureButton, qt.Qt.LeftButton)
+ # clove dialog
+ # self.mouseClick(fw.configdialogs["foo"].ok, qt.Qt.LeftButton)
+ # self.qapp.processEvents()
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestFitWidget))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')
diff --git a/silx/gui/hdf5/Hdf5HeaderView.py b/silx/gui/hdf5/Hdf5HeaderView.py
new file mode 100644
index 0000000..5912230
--- /dev/null
+++ b/silx/gui/hdf5/Hdf5HeaderView.py
@@ -0,0 +1,192 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "08/11/2016"
+
+
+from .. import qt
+
+QTVERSION = qt.qVersion()
+
+
+class Hdf5HeaderView(qt.QHeaderView):
+ """
+ Default HDF5 header
+
+ Manage auto-resize and context menu to display/hide columns
+ """
+
+ def __init__(self, orientation, parent=None):
+ """
+ Constructor
+
+ :param orientation qt.Qt.Orientation: Orientation of the header
+ :param parent qt.QWidget: Parent of the widget
+ """
+ super(Hdf5HeaderView, self).__init__(orientation, parent)
+ self.setContextMenuPolicy(qt.Qt.CustomContextMenu)
+ self.customContextMenuRequested.connect(self.__createContextMenu)
+
+ # default initialization done by QTreeView for it's own header
+ if QTVERSION < "5.0":
+ self.setClickable(True)
+ self.setMovable(True)
+ else:
+ self.setSectionsClickable(True)
+ self.setSectionsMovable(True)
+ self.setDefaultAlignment(qt.Qt.AlignLeft | qt.Qt.AlignVCenter)
+ self.setStretchLastSection(True)
+
+ self.__auto_resize = True
+ self.__hide_columns_popup = True
+
+ def setModel(self, model):
+ """Override model to configure view when a model is expected
+
+ `qt.QHeaderView.setResizeMode` expect already existing columns
+ to work.
+
+ :param model qt.QAbstractItemModel: A model
+ """
+ super(Hdf5HeaderView, self).setModel(model)
+ self.__updateAutoResize()
+
+ def __updateAutoResize(self):
+ """Update the view according to the state of the auto-resize"""
+ if QTVERSION < "5.0":
+ setResizeMode = self.setResizeMode
+ else:
+ setResizeMode = self.setSectionResizeMode
+
+ if self.__auto_resize:
+ setResizeMode(0, qt.QHeaderView.ResizeToContents)
+ setResizeMode(1, qt.QHeaderView.ResizeToContents)
+ setResizeMode(2, qt.QHeaderView.ResizeToContents)
+ setResizeMode(3, qt.QHeaderView.Interactive)
+ setResizeMode(4, qt.QHeaderView.Interactive)
+ setResizeMode(5, qt.QHeaderView.ResizeToContents)
+ else:
+ setResizeMode(0, qt.QHeaderView.Interactive)
+ setResizeMode(1, qt.QHeaderView.Interactive)
+ setResizeMode(2, qt.QHeaderView.Interactive)
+ setResizeMode(3, qt.QHeaderView.Interactive)
+ setResizeMode(4, qt.QHeaderView.Interactive)
+ setResizeMode(5, qt.QHeaderView.Interactive)
+
+ def setAutoResizeColumns(self, autoResize):
+ """Enable/disable auto-resize. When auto-resized, the header take care
+ of the content of the column to set fixed size of some of them, or to
+ auto fix the size according to the content.
+
+ :param autoResize bool: Enable/disable auto-resize
+ """
+ if self.__auto_resize == autoResize:
+ return
+ self.__auto_resize = autoResize
+ self.__updateAutoResize()
+
+ def hasAutoResizeColumns(self):
+ """Is auto-resize enabled.
+
+ :rtype: bool
+ """
+ return self.__auto_resize
+
+ autoResizeColumns = qt.Property(bool, hasAutoResizeColumns, setAutoResizeColumns)
+ """Property to enable/disable auto-resize."""
+
+ def setEnableHideColumnsPopup(self, enablePopup):
+ """Enable/disable a popup to allow to hide/show each column of the
+ model.
+
+ :param bool enablePopup: Enable/disable popup to hide/show columns
+ """
+ self.__hide_columns_popup = enablePopup
+
+ def hasHideColumnsPopup(self):
+ """Is popup to hide/show columns is enabled.
+
+ :rtype: bool
+ """
+ return self.__hide_columns_popup
+
+ enableHideColumnsPopup = qt.Property(bool, hasHideColumnsPopup, setAutoResizeColumns)
+ """Property to enable/disable popup allowing to hide/show columns."""
+
+ def __genHideSectionEvent(self, column):
+ """Generate a callback which change the column visibility according to
+ the event parameter
+
+ :param int column: logical id of the column
+ :rtype: callable
+ """
+ return lambda checked: self.setSectionHidden(column, not checked)
+
+ def __createContextMenu(self, pos):
+ """Callback to create and display a context menu
+
+ :param pos qt.QPoint: Requested position for the context menu
+ """
+ if not self.__hide_columns_popup:
+ return
+
+ model = self.model()
+ if model.columnCount() > 1:
+ menu = qt.QMenu(self)
+ menu.setTitle("Display/hide columns")
+
+ action = qt.QAction("Display/hide column", self)
+ action.setEnabled(False)
+ menu.addAction(action)
+
+ for column in range(model.columnCount()):
+ if column == 0:
+ # skip the main column
+ continue
+ text = model.headerData(column, qt.Qt.Horizontal, qt.Qt.DisplayRole)
+ action = qt.QAction("%s displayed" % text, self)
+ action.setCheckable(True)
+ action.setChecked(not self.isSectionHidden(column))
+ action.toggled.connect(self.__genHideSectionEvent(column))
+ menu.addAction(action)
+
+ menu.popup(self.viewport().mapToGlobal(pos))
+
+ def setSections(self, logicalIndexes):
+ """
+ Defines order of visible sections by logical indexes.
+
+ Use `Hdf5TreeModel.NAME_COLUMN` to set the list.
+
+ :param list logicalIndexes: List of logical indexes to display
+ """
+ for pos, column_id in enumerate(logicalIndexes):
+ current_pos = self.visualIndex(column_id)
+ self.moveSection(current_pos, pos)
+ self.setSectionHidden(column_id, False)
+ for column_id in set(range(self.model().columnCount())) - set(logicalIndexes):
+ self.setSectionHidden(column_id, True)
diff --git a/silx/gui/hdf5/Hdf5Item.py b/silx/gui/hdf5/Hdf5Item.py
new file mode 100644
index 0000000..40793a4
--- /dev/null
+++ b/silx/gui/hdf5/Hdf5Item.py
@@ -0,0 +1,421 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "20/01/2017"
+
+
+import numpy
+import logging
+import collections
+from .. import qt
+from .. import icons
+from . import _utils
+from .Hdf5Node import Hdf5Node
+import silx.io.utils
+from silx.gui.data.TextFormatter import TextFormatter
+
+_logger = logging.getLogger(__name__)
+
+try:
+ import h5py
+except ImportError as e:
+ _logger.error("Module %s requires h5py", __name__)
+ raise e
+
+_formatter = TextFormatter()
+
+
+class Hdf5Item(Hdf5Node):
+ """Subclass of :class:`qt.QStandardItem` to represent an HDF5-like
+ item (dataset, file, group or link) as an element of a HDF5-like
+ tree structure.
+ """
+
+ def __init__(self, text, obj, parent, key=None, h5pyClass=None, isBroken=False, populateAll=False):
+ """
+ :param str text: text displayed
+ :param object obj: Pointer to h5py data. See the `obj` attribute.
+ """
+ self.__obj = obj
+ self.__key = key
+ self.__h5pyClass = h5pyClass
+ self.__isBroken = isBroken
+ self.__error = None
+ self.__text = text
+ Hdf5Node.__init__(self, parent, populateAll=populateAll)
+
+ @property
+ def obj(self):
+ if self.__key:
+ self.__initH5pyObject()
+ return self.__obj
+
+ @property
+ def basename(self):
+ return self.__text
+
+ @property
+ def h5pyClass(self):
+ """Returns the class of the stored object.
+
+ When the object is in lazy loading, this method should be able to
+ return the type of the futrue loaded object. It allows to delay the
+ real load of the object.
+
+ :rtype: h5py.File or h5py.Dataset or h5py.Group
+ """
+ if self.__h5pyClass is None:
+ self.__h5pyClass = silx.io.utils.get_h5py_class(self.obj)
+ return self.__h5pyClass
+
+ def isGroupObj(self):
+ """Returns true if the stored HDF5 object is a group (contains sub
+ groups or datasets).
+
+ :rtype: bool
+ """
+ return issubclass(self.h5pyClass, h5py.Group)
+
+ def isBrokenObj(self):
+ """Returns true if the stored HDF5 object is broken.
+
+ The stored object is then an h5py link (external or not) which point
+ to nowhere (tbhe external file is not here, the expected dataset is
+ still not on the file...)
+
+ :rtype: bool
+ """
+ return self.__isBroken
+
+ def _expectedChildCount(self):
+ if self.isGroupObj():
+ return len(self.obj)
+ return 0
+
+ def __initH5pyObject(self):
+ """Lazy load of the HDF5 node. It is reached from the parent node
+ with the key of the node."""
+ parent_obj = self.parent.obj
+
+ try:
+ obj = parent_obj.get(self.__key)
+ except Exception as e:
+ _logger.debug("Internal h5py error", exc_info=True)
+ try:
+ self.__obj = parent_obj.get(self.__key, getlink=True)
+ except Exception:
+ self.__obj = None
+ self.__error = e.args[0]
+ self.__isBroken = True
+ else:
+ if obj is None:
+ # that's a broken link
+ self.__obj = parent_obj.get(self.__key, getlink=True)
+
+ # TODO monkey-patch file (ask that in h5py for consistency)
+ if not hasattr(self.__obj, "name"):
+ parent_name = parent_obj.name
+ if parent_name == "/":
+ self.__obj.name = "/" + self.__key
+ else:
+ self.__obj.name = parent_name + "/" + self.__key
+ # TODO monkey-patch file (ask that in h5py for consistency)
+ if not hasattr(self.__obj, "file"):
+ self.__obj.file = parent_obj.file
+
+ if isinstance(self.__obj, h5py.ExternalLink):
+ message = "External link broken. Path %s::%s does not exist" % (self.__obj.filename, self.__obj.path)
+ elif isinstance(self.__obj, h5py.SoftLink):
+ message = "Soft link broken. Path %s does not exist" % (self.__obj.path)
+ else:
+ name = self.obj.__class__.__name__.split(".")[-1].capitalize()
+ message = "%s broken" % (name)
+ self.__error = message
+ self.__isBroken = True
+ else:
+ self.__obj = obj
+
+ self.__key = None
+
+ def _populateChild(self, populateAll=False):
+ if self.isGroupObj():
+ for name in self.obj:
+ try:
+ class_ = self.obj.get(name, getclass=True)
+ has_error = False
+ except Exception as e:
+ _logger.error("Internal h5py error", exc_info=True)
+ try:
+ class_ = self.obj.get(name, getclass=True, getlink=True)
+ except Exception as e:
+ class_ = h5py.HardLink
+ has_error = True
+ item = Hdf5Item(text=name, obj=None, parent=self, key=name, h5pyClass=class_, isBroken=has_error)
+ self.appendChild(item)
+
+ def hasChildren(self):
+ """Retuens true of this node have chrild.
+
+ :rtype: bool
+ """
+ if not self.isGroupObj():
+ return False
+ return Hdf5Node.hasChildren(self)
+
+ def _getDefaultIcon(self):
+ """Returns the icon displayed by the main column.
+
+ :rtype: qt.QIcon
+ """
+ style = qt.QApplication.style()
+ if self.__isBroken:
+ icon = style.standardIcon(qt.QStyle.SP_MessageBoxCritical)
+ return icon
+ class_ = self.h5pyClass
+ if issubclass(class_, h5py.File):
+ return style.standardIcon(qt.QStyle.SP_FileIcon)
+ elif issubclass(class_, h5py.Group):
+ return style.standardIcon(qt.QStyle.SP_DirIcon)
+ elif issubclass(class_, h5py.SoftLink):
+ return style.standardIcon(qt.QStyle.SP_DirLinkIcon)
+ elif issubclass(class_, h5py.ExternalLink):
+ return style.standardIcon(qt.QStyle.SP_FileLinkIcon)
+ elif issubclass(class_, h5py.Dataset):
+ if len(self.obj.shape) < 4:
+ name = "item-%ddim" % len(self.obj.shape)
+ else:
+ name = "item-ndim"
+ if str(self.obj.dtype) == "object":
+ name = "item-object"
+ icon = icons.getQIcon(name)
+ return icon
+ return None
+
+ def _humanReadableShape(self, dataset):
+ if dataset.shape == tuple():
+ return "scalar"
+ shape = [str(i) for i in dataset.shape]
+ text = u" \u00D7 ".join(shape)
+ return text
+
+ def _humanReadableValue(self, dataset):
+ if dataset.shape == tuple():
+ numpy_object = dataset[()]
+ text = _formatter.toString(numpy_object)
+ else:
+ if dataset.size < 5 and dataset.compression is None:
+ numpy_object = dataset[0:5]
+ text = _formatter.toString(numpy_object)
+ else:
+ dimension = len(dataset.shape)
+ if dataset.compression is not None:
+ text = "Compressed %dD data" % dimension
+ else:
+ text = "%dD data" % dimension
+ return text
+
+ def _humanReadableDType(self, dtype, full=False):
+ if dtype.type == numpy.string_:
+ text = "string"
+ elif dtype.type == numpy.unicode_:
+ text = "string"
+ elif dtype.type == numpy.object_:
+ text = "object"
+ elif dtype.type == numpy.bool_:
+ text = "bool"
+ elif dtype.type == numpy.void:
+ if dtype.fields is None:
+ text = "raw"
+ else:
+ if not full:
+ text = "compound"
+ else:
+ compound = [d[0] for d in dtype.fields.values()]
+ compound = [self._humanReadableDType(d) for d in compound]
+ text = "compound(%s)" % ", ".join(compound)
+ else:
+ text = str(dtype)
+ return text
+
+ def _humanReadableType(self, dataset, full=False):
+ return self._humanReadableDType(dataset.dtype, full)
+
+ def _setTooltipAttributes(self, attributeDict):
+ """
+ Add key/value attributes that will be displayed in the item tooltip
+
+ :param Dict[str,str] attributeDict: Key/value attributes
+ """
+ if issubclass(self.h5pyClass, h5py.Dataset):
+ attributeDict["Title"] = "HDF5 Dataset"
+ attributeDict["Name"] = self.basename
+ attributeDict["Path"] = self.obj.name
+ attributeDict["Shape"] = self._humanReadableShape(self.obj)
+ attributeDict["Value"] = self._humanReadableValue(self.obj)
+ attributeDict["Data type"] = self._humanReadableType(self.obj, full=True)
+ elif issubclass(self.h5pyClass, h5py.Group):
+ attributeDict["Title"] = "HDF5 Group"
+ attributeDict["Name"] = self.basename
+ attributeDict["Path"] = self.obj.name
+ elif issubclass(self.h5pyClass, h5py.File):
+ attributeDict["Title"] = "HDF5 File"
+ attributeDict["Name"] = self.basename
+ attributeDict["Path"] = "/"
+ elif isinstance(self.obj, h5py.ExternalLink):
+ attributeDict["Title"] = "HDF5 External Link"
+ attributeDict["Name"] = self.basename
+ attributeDict["Path"] = self.obj.name
+ attributeDict["Linked path"] = self.obj.path
+ attributeDict["Linked file"] = self.obj.filename
+ elif isinstance(self.obj, h5py.SoftLink):
+ attributeDict["Title"] = "HDF5 Soft Link"
+ attributeDict["Name"] = self.basename
+ attributeDict["Path"] = self.obj.name
+ attributeDict["Linked path"] = self.obj.path
+ else:
+ pass
+
+ def _getDefaultTooltip(self):
+ """Returns the default tooltip
+
+ :rtype: str
+ """
+ if self.__error is not None:
+ self.obj # lazy loading of the object
+ return self.__error
+
+ attrs = collections.OrderedDict()
+ self._setTooltipAttributes(attrs)
+
+ title = attrs.pop("Title", None)
+ if len(attrs) > 0:
+ tooltip = _utils.htmlFromDict(attrs, title=title)
+ else:
+ tooltip = ""
+
+ return tooltip
+
+ def dataName(self, role):
+ """Data for the name column"""
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ return self.__text
+ if role == qt.Qt.DecorationRole:
+ return self._getDefaultIcon()
+ if role == qt.Qt.ToolTipRole:
+ return self._getDefaultTooltip()
+ return None
+
+ def dataType(self, role):
+ """Data for the type column"""
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ if self.__error is not None:
+ return ""
+ class_ = self.h5pyClass
+ if issubclass(class_, h5py.Dataset):
+ text = self._humanReadableType(self.obj)
+ else:
+ text = ""
+ return text
+
+ return None
+
+ def dataShape(self, role):
+ """Data for the shape column"""
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ if self.__error is not None:
+ return ""
+ class_ = self.h5pyClass
+ if not issubclass(class_, h5py.Dataset):
+ return ""
+ return self._humanReadableShape(self.obj)
+ return None
+
+ def dataValue(self, role):
+ """Data for the value column"""
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ if self.__error is not None:
+ return ""
+ if not issubclass(self.h5pyClass, h5py.Dataset):
+ return ""
+ return self._humanReadableValue(self.obj)
+ return None
+
+ def dataDescription(self, role):
+ """Data for the description column"""
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ if self.__isBroken:
+ self.obj # lazy loading of the object
+ return self.__error
+ if "desc" in self.obj.attrs:
+ text = self.obj.attrs["desc"]
+ else:
+ return ""
+ return text
+ if role == qt.Qt.ToolTipRole:
+ if self.__error is not None:
+ self.obj # lazy loading of the object
+ self.__initH5pyObject()
+ return self.__error
+ if "desc" in self.obj.attrs:
+ text = self.obj.attrs["desc"]
+ else:
+ return ""
+ return "Description: %s" % text
+ return None
+
+ def dataNode(self, role):
+ """Data for the node column"""
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ class_ = self.h5pyClass
+ text = class_.__name__.split(".")[-1]
+ return text
+ if role == qt.Qt.ToolTipRole:
+ class_ = self.h5pyClass
+ return "Class name: %s" % self.__class__
+ return None
diff --git a/silx/gui/hdf5/Hdf5LoadingItem.py b/silx/gui/hdf5/Hdf5LoadingItem.py
new file mode 100644
index 0000000..4467366
--- /dev/null
+++ b/silx/gui/hdf5/Hdf5LoadingItem.py
@@ -0,0 +1,68 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "23/09/2016"
+
+
+from .. import qt
+from .Hdf5Node import Hdf5Node
+
+
+class Hdf5LoadingItem(Hdf5Node):
+ """Item displayed when an Hdf5Node is loading.
+
+ At the end of the loading this item is replaced by the loaded one.
+ """
+
+ def __init__(self, text, parent, animatedIcon):
+ """Constructor"""
+ Hdf5Node.__init__(self, parent)
+ self.__text = text
+ self.__animatedIcon = animatedIcon
+ self.__animatedIcon.register(self)
+
+ @property
+ def obj(self):
+ return None
+
+ def dataName(self, role):
+ if role == qt.Qt.DecorationRole:
+ return self.__animatedIcon.currentIcon()
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ return self.__text
+ return None
+
+ def dataDescription(self, role):
+ if role == qt.Qt.DecorationRole:
+ return None
+ if role == qt.Qt.TextAlignmentRole:
+ return qt.Qt.AlignTop | qt.Qt.AlignLeft
+ if role == qt.Qt.DisplayRole:
+ return "Loading..."
+ return None
diff --git a/silx/gui/hdf5/Hdf5Node.py b/silx/gui/hdf5/Hdf5Node.py
new file mode 100644
index 0000000..31bb097
--- /dev/null
+++ b/silx/gui/hdf5/Hdf5Node.py
@@ -0,0 +1,210 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "23/09/2016"
+
+
+class Hdf5Node(object):
+ """Abstract tree node
+
+ It provides link to the childs and to the parents, and a link to an
+ external object.
+ """
+ def __init__(self, parent=None, populateAll=False):
+ """
+ Constructor
+
+ :param Hdf5Node parent: Parent of the node, if exists, else None
+ :param bool populateAll: If true, populate all the tree node. Else
+ everything is lazy loaded.
+ """
+ self.__child = None
+ self.__parent = parent
+ if populateAll:
+ self.__child = []
+ self._populateChild(populateAll=True)
+
+ @property
+ def parent(self):
+ """Parent of the node, or None if the node is a root
+
+ :rtype: Hdf5Node
+ """
+ return self.__parent
+
+ def setParent(self, parent):
+ """Redefine the parent of the node.
+
+ It does not set the node as the children of the new parent.
+
+ :param Hdf5Node parent: The new parent
+ """
+ self.__parent = parent
+
+ def appendChild(self, child):
+ """Append a child to the node.
+
+ It does not update the parent of the child.
+
+ :param Hdf5Node child: Child to append to the node.
+ """
+ self.__initChild()
+ self.__child.append(child)
+
+ def removeChildAtIndex(self, index):
+ """Remove a child at an index of the children list.
+
+ The child is removed and returned.
+
+ :param int index: Index in the child list.
+ :rtype: Hdf5Node
+ :raises: IndexError if list is empty or index is out of range.
+ """
+ self.__initChild()
+ return self.__child.pop(index)
+
+ def insertChild(self, index, child):
+ """
+ Insert a child at a specific index of the child list.
+
+ It does not update the parent of the child.
+
+ :param int index: Index in the child list.
+ :param Hdf5Node child: Child to insert in the child list.
+ """
+ self.__initChild()
+ self.__child.insert(index, child)
+
+ def indexOfChild(self, child):
+ """
+ Returns the index of the child in the child list of this node.
+
+ :param Hdf5Node child: Child to find
+ :raises: ValueError if the value is not present.
+ """
+ self.__initChild()
+ return self.__child.index(child)
+
+ def hasChildren(self):
+ """Returns true if the node contains children.
+
+ :rtype: bool
+ """
+ return self.childCount() > 0
+
+ def childCount(self):
+ """Returns the number of child in this node.
+
+ :rtype: int
+ """
+ if self.__child is not None:
+ return len(self.__child)
+ return self._expectedChildCount()
+
+ def child(self, index):
+ """Return the child at an expected index.
+
+ :param int index: Index of the child in the child list of the node
+ :rtype: Hdf5Node
+ """
+ self.__initChild()
+ return self.__child[index]
+
+ def __initChild(self):
+ """Init the child of the node in case the list was lazy loaded."""
+ if self.__child is None:
+ self.__child = []
+ self._populateChild()
+
+ def _expectedChildCount(self):
+ """Returns the expected count of children
+
+ :rtype: int
+ """
+ return 0
+
+ def _populateChild(self, populateAll=False):
+ """Recurse through an HDF5 structure to append groups an datasets
+ into the tree model.
+
+ Overwrite it to implement the initialisation of child of the node.
+ """
+ pass
+
+ def dataName(self, role):
+ """Data for the name column
+
+ Overwrite it to implement the content of the 'name' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
+
+ def dataType(self, role):
+ """Data for the type column
+
+ Overwrite it to implement the content of the 'type' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
+
+ def dataShape(self, role):
+ """Data for the shape column
+
+ Overwrite it to implement the content of the 'shape' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
+
+ def dataValue(self, role):
+ """Data for the value column
+
+ Overwrite it to implement the content of the 'value' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
+
+ def dataDescription(self, role):
+ """Data for the description column
+
+ Overwrite it to implement the content of the 'description' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
+
+ def dataNode(self, role):
+ """Data for the node column
+
+ Overwrite it to implement the content of the 'node' column.
+
+ :rtype: qt.QVariant
+ """
+ return None
diff --git a/silx/gui/hdf5/Hdf5TreeModel.py b/silx/gui/hdf5/Hdf5TreeModel.py
new file mode 100644
index 0000000..fb5de06
--- /dev/null
+++ b/silx/gui/hdf5/Hdf5TreeModel.py
@@ -0,0 +1,581 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "19/12/2016"
+
+
+import os
+import logging
+from .. import qt
+from .. import icons
+from .Hdf5Node import Hdf5Node
+from .Hdf5Item import Hdf5Item
+from .Hdf5LoadingItem import Hdf5LoadingItem
+from . import _utils
+from ... import io as silx_io
+
+_logger = logging.getLogger(__name__)
+
+"""Helpers to take care of None objects as signal parameters.
+PySide crash if a signal with a None parameter is emitted between threads.
+"""
+if qt.BINDING == 'PySide':
+ class _NoneWraper(object):
+ pass
+ _NoneWraperInstance = _NoneWraper()
+
+ def _wrapNone(x):
+ """Wrap x if it is a None value, else returns x"""
+ if x is None:
+ return _NoneWraperInstance
+ else:
+ return x
+
+ def _unwrapNone(x):
+ """Unwrap x as a None if a None was stored by `wrapNone`, else returns
+ x"""
+ if x is _NoneWraperInstance:
+ return None
+ else:
+ return x
+else:
+ # Allow to fix None event params to avoid PySide crashes
+ def _wrapNone(x):
+ return x
+
+ def _unwrapNone(x):
+ return x
+
+
+class LoadingItemRunnable(qt.QRunnable):
+ """Runner to process item loading from a file"""
+
+ class __Signals(qt.QObject):
+ """Signal holder"""
+ itemReady = qt.Signal(object, object, object)
+ runnerFinished = qt.Signal(object)
+
+ def __init__(self, filename, item):
+ """Constructor
+
+ :param LoadingItemWorker worker: Object holding data and signals
+ """
+ super(LoadingItemRunnable, self).__init__()
+ self.filename = filename
+ self.oldItem = item
+ self.signals = self.__Signals()
+
+ def setFile(self, filename, item):
+ self.filenames.append((filename, item))
+
+ @property
+ def itemReady(self):
+ return self.signals.itemReady
+
+ @property
+ def runnerFinished(self):
+ return self.signals.runnerFinished
+
+ def __loadItemTree(self, oldItem, h5obj):
+ """Create an item tree used by the GUI from an h5py object.
+
+ :param Hdf5Node oldItem: The current item displayed the GUI
+ :param h5py.File h5obj: The h5py object to display in the GUI
+ :rtpye: Hdf5Node
+ """
+ if silx_io.is_file(h5obj):
+ text = os.path.basename(h5obj.filename)
+ else:
+ filename = os.path.basename(h5obj.file.filename)
+ path = h5obj.name
+ text = "%s::%s" % (filename, path)
+ item = Hdf5Item(text=text, obj=h5obj, parent=oldItem.parent, populateAll=True)
+ return item
+
+ @qt.Slot()
+ def run(self):
+ """Process the file loading. The worker is used as holder
+ of the data and the signal. The result is sent as a signal.
+ """
+ try:
+ h5file = silx_io.open(self.filename)
+ newItem = self.__loadItemTree(self.oldItem, h5file)
+ error = None
+ except IOError as e:
+ # Should be logged
+ error = e
+ newItem = None
+
+ # Take care of None value in case of PySide
+ newItem = _wrapNone(newItem)
+ error = _wrapNone(error)
+ self.itemReady.emit(self.oldItem, newItem, error)
+ self.runnerFinished.emit(self)
+
+ def autoDelete(self):
+ return True
+
+
+class Hdf5TreeModel(qt.QAbstractItemModel):
+ """Tree model storing a list of :class:`h5py.File` like objects.
+
+ The main column display the :class:`h5py.File` list and there hierarchy.
+ Other columns display information on node hierarchy.
+ """
+
+ H5PY_ITEM_ROLE = qt.Qt.UserRole
+ """Role to reach h5py item from an item index"""
+
+ H5PY_OBJECT_ROLE = qt.Qt.UserRole + 1
+ """Role to reach h5py object from an item index"""
+
+ USER_ROLE = qt.Qt.UserRole + 2
+ """Start of range of available user role for derivative models"""
+
+ NAME_COLUMN = 0
+ """Column id containing HDF5 node names"""
+
+ TYPE_COLUMN = 1
+ """Column id containing HDF5 dataset types"""
+
+ SHAPE_COLUMN = 2
+ """Column id containing HDF5 dataset shapes"""
+
+ VALUE_COLUMN = 3
+ """Column id containing HDF5 dataset values"""
+
+ DESCRIPTION_COLUMN = 4
+ """Column id containing HDF5 node description/title/message"""
+
+ NODE_COLUMN = 5
+ """Column id containing HDF5 node type"""
+
+ COLUMN_IDS = [
+ NAME_COLUMN,
+ TYPE_COLUMN,
+ SHAPE_COLUMN,
+ VALUE_COLUMN,
+ DESCRIPTION_COLUMN,
+ NODE_COLUMN,
+ ]
+ """List of logical columns available"""
+
+ def __init__(self, parent=None):
+ super(Hdf5TreeModel, self).__init__(parent)
+
+ self.treeView = parent
+ self.header_labels = [None] * 6
+ self.header_labels[self.NAME_COLUMN] = 'Name'
+ self.header_labels[self.TYPE_COLUMN] = 'Type'
+ self.header_labels[self.SHAPE_COLUMN] = 'Shape'
+ self.header_labels[self.VALUE_COLUMN] = 'Value'
+ self.header_labels[self.DESCRIPTION_COLUMN] = 'Description'
+ self.header_labels[self.NODE_COLUMN] = 'Node'
+
+ # Create items
+ self.__root = Hdf5Node()
+ self.__fileDropEnabled = True
+ self.__fileMoveEnabled = True
+
+ self.__animatedIcon = icons.getWaitIcon()
+ self.__animatedIcon.iconChanged.connect(self.__updateLoadingItems)
+ self.__runnerSet = set([])
+
+ # store used icons to avoid to avoid the cache to release it
+ self.__icons = []
+ self.__icons.append(icons.getQIcon("item-0dim"))
+ self.__icons.append(icons.getQIcon("item-1dim"))
+ self.__icons.append(icons.getQIcon("item-2dim"))
+ self.__icons.append(icons.getQIcon("item-3dim"))
+ self.__icons.append(icons.getQIcon("item-ndim"))
+ self.__icons.append(icons.getQIcon("item-object"))
+
+ def __updateLoadingItems(self, icon):
+ for i in range(self.__root.childCount()):
+ item = self.__root.child(i)
+ if isinstance(item, Hdf5LoadingItem):
+ index1 = self.index(i, 0, qt.QModelIndex())
+ index2 = self.index(i, self.columnCount() - 1, qt.QModelIndex())
+ self.dataChanged.emit(index1, index2)
+
+ def __itemReady(self, oldItem, newItem, error):
+ """Called at the end of a concurent file loading, when the loading
+ item is ready. AN error is defined if an exception occured when
+ loading the newItem .
+
+ :param Hdf5Node oldItem: current displayed item
+ :param Hdf5Node newItem: item loaded, or None if error is defined
+ :param Exception error: An exception, or None if newItem is defined
+ """
+ # Take care of None value in case of PySide
+ newItem = _unwrapNone(newItem)
+ error = _unwrapNone(error)
+ row = self.__root.indexOfChild(oldItem)
+ rootIndex = qt.QModelIndex()
+ self.beginRemoveRows(rootIndex, row, row)
+ self.__root.removeChildAtIndex(row)
+ self.endRemoveRows()
+ if newItem is not None:
+ self.beginInsertRows(rootIndex, row, row)
+ self.__root.insertChild(row, newItem)
+ self.endInsertRows()
+ # FIXME the error must be displayed
+
+ def isFileDropEnabled(self):
+ return self.__fileDropEnabled
+
+ def setFileDropEnabled(self, enabled):
+ self.__fileDropEnabled = enabled
+
+ fileDropEnabled = qt.Property(bool, isFileDropEnabled, setFileDropEnabled)
+ """Property to enable/disable file dropping in the model."""
+
+ def isFileMoveEnabled(self):
+ return self.__fileMoveEnabled
+
+ def setFileMoveEnabled(self, enabled):
+ self.__fileMoveEnabled = enabled
+
+ fileMoveEnabled = qt.Property(bool, isFileMoveEnabled, setFileMoveEnabled)
+ """Property to enable/disable drag-and-drop of files to
+ change the ordering in the model."""
+
+ def supportedDropActions(self):
+ if self.__fileMoveEnabled or self.__fileDropEnabled:
+ return qt.Qt.CopyAction | qt.Qt.MoveAction
+ else:
+ return 0
+
+ def mimeTypes(self):
+ if self.__fileMoveEnabled:
+ return [_utils.Hdf5NodeMimeData.MIME_TYPE]
+ else:
+ return []
+
+ def mimeData(self, indexes):
+ """
+ Returns an object that contains serialized items of data corresponding
+ to the list of indexes specified.
+
+ :param list(qt.QModelIndex) indexes: List of indexes
+ :rtype: qt.QMimeData
+ """
+ if not self.__fileMoveEnabled or len(indexes) == 0:
+ return None