Import Upstream version 0.5.0+dfsg

5 files changed, 571 insertions, 0 deletions

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