New upstream version 0.7.0+dfsg

7 files changed, 227 insertions, 77 deletions

diff --git a/silx/gui/plot/actions/PlotAction.py b/silx/gui/plot/actions/PlotAction.py
index 6eb9ba3..2983775 100644
--- a/silx/gui/plot/actions/PlotAction.py
+++ b/silx/gui/plot/actions/PlotAction.py
@@ -32,10 +32,9 @@ from __future__ import division
 
 __authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
 __license__ = "MIT"
-__date__ = "20/04/2017"
+__date__ = "03/01/2018"
 
 
-from collections import OrderedDict
 import weakref
 from silx.gui import icons
 from silx.gui import qt
diff --git a/silx/gui/plot/actions/__init__.py b/silx/gui/plot/actions/__init__.py
index 73829cd..930c728 100644
--- a/silx/gui/plot/actions/__init__.py
+++ b/silx/gui/plot/actions/__init__.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2017 European Synchrotron Radiation Facility
+# Copyright (c) 2017-2018 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
@@ -22,10 +22,14 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
-"""This package provides a set of QActions to use with :class:`PlotWidget`
+"""This package provides a set of QAction to use with
+:class:`~silx.gui.plot.PlotWidget`
 
-It also contains the :class:'.PlotAction' (Base class for QAction that operates
-on a PlotWidget)
+Those actions are useful to add menu items or toolbar items
+that interact with a :class:`~silx.gui.plot.PlotWidget`.
+
+It provides a base class used to define new plot actions:
+:class:`~silx.gui.plot.actions.PlotAction`.
 """
 
 __authors__ = ["H. Payno"]
diff --git a/silx/gui/plot/actions/control.py b/silx/gui/plot/actions/control.py
index 23e710e..ac6dc2f 100644
--- a/silx/gui/plot/actions/control.py
+++ b/silx/gui/plot/actions/control.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2018 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
@@ -50,11 +50,10 @@ from __future__ import division
 
 __authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
 __license__ = "MIT"
-__date__ = "27/06/2017"
+__date__ = "15/02/2018"
 
 from . import PlotAction
 import logging
-import numpy
 from silx.gui.plot import items
 from silx.gui.plot.ColormapDialog import ColormapDialog
 from silx.gui.plot._utils import applyZoomToPlot as _applyZoomToPlot
@@ -327,67 +326,112 @@ class ColormapAction(PlotAction):
             plot, icon='colormap', text='Colormap',
             tooltip="Change colormap",
             triggered=self._actionTriggered,
-            checkable=False, parent=parent)
+            checkable=True, parent=parent)
+        self.plot.sigActiveImageChanged.connect(self._updateColormap)
+
+    def setColorDialog(self, colorDialog):
+        """Set a specific color dialog instead of using the default dialog."""
+        assert(colorDialog is not None)
+        assert(self._dialog is None)
+        self._dialog = colorDialog
+        self._dialog.visibleChanged.connect(self._dialogVisibleChanged)
+        self.setChecked(self._dialog.isVisible())
+
+    @staticmethod
+    def _createDialog(parent):
+        """Create the dialog if not already existing
+
+        :parent QWidget parent: Parent of the new colormap
+        :rtype: ColormapDialog
+        """
+        dialog = ColormapDialog(parent=parent)
+        dialog.setModal(False)
+        return dialog
 
     def _actionTriggered(self, checked=False):
         """Create a cmap dialog and update active image and default cmap."""
-        # Create the dialog if not already existing
         if self._dialog is None:
-            self._dialog = ColormapDialog()
+            self._dialog = self._createDialog(self.plot)
+            self._dialog.visibleChanged.connect(self._dialogVisibleChanged)
+
+        # Run the dialog listening to colormap change
+        if checked is True:
+            self._dialog.show()
+            self._updateColormap()
+        else:
+            self._dialog.hide()
+
+    def _dialogVisibleChanged(self, isVisible):
+        self.setChecked(isVisible)
 
+    def _updateColormap(self):
+        if self._dialog is None:
+            return
         image = self.plot.getActiveImage()
-        if not isinstance(image, items.ColormapMixIn):
-            # No active image or active image is RGBA,
-            # set dialog from default info
-            colormap = self.plot.getDefaultColormap()
 
-            self._dialog.setHistogram()  # Reset histogram and range if any
+        if isinstance(image, items.ImageComplexData):
+            # Specific init for complex images
+            colormap = image.getColormap()
 
-        else:
+            mode = image.getVisualizationMode()
+            if mode in (items.ImageComplexData.Mode.AMPLITUDE_PHASE,
+                        items.ImageComplexData.Mode.LOG10_AMPLITUDE_PHASE):
+                data = image.getData(
+                    copy=False, mode=items.ImageComplexData.Mode.PHASE)
+            else:
+                data = image.getData(copy=False)
+
+            # Set histogram and range if any
+            self._dialog.setData(data)
+
+        elif isinstance(image, items.ColormapMixIn):
             # Set dialog from active image
             colormap = image.getColormap()
-
             data = image.getData(copy=False)
+            # Set histogram and range if any
+            self._dialog.setData(data)
 
-            goodData = data[numpy.isfinite(data)]
-            if goodData.size > 0:
-                dataMin = goodData.min()
-                dataMax = goodData.max()
-            else:
-                qt.QMessageBox.warning(
-                    None, "No Data",
-                    "Image data does not contain any real value")
-                dataMin, dataMax = 1., 10.
-
-            self._dialog.setHistogram()  # Reset histogram if any
-            self._dialog.setDataRange(dataMin, dataMax)
-            # The histogram should be done in a worker thread
-            # hist, bin_edges = numpy.histogram(goodData, bins=256)
-            # self._dialog.setHistogram(hist, bin_edges)
-
-        self._dialog.setColormap(name=colormap.getName(),
-                                 normalization=colormap.getNormalization(),
-                                 autoscale=colormap.isAutoscale(),
-                                 vmin=colormap.getVMin(),
-                                 vmax=colormap.getVMax(),
-                                 colors=colormap.getColormapLUT())
+        else:
+            # No active image or active image is RGBA,
+            # set dialog from default info
+            colormap = self.plot.getDefaultColormap()
+            # Reset histogram and range if any
+            self._dialog.setData(None)
 
-        # Run the dialog listening to colormap change
-        self._dialog.sigColormapChanged.connect(self._colormapChanged)
-        result = self._dialog.exec_()
-        self._dialog.sigColormapChanged.disconnect(self._colormapChanged)
+        self._dialog.setColormap(colormap)
 
-        if not result:  # Restore the previous colormap
-            self._colormapChanged(colormap)
 
-    def _colormapChanged(self, colormap):
-        # Update default colormap
-        self.plot.setDefaultColormap(colormap)
+class ColorBarAction(PlotAction):
+    """QAction opening the ColorBarWidget of the specified plot.
+
+    :param plot: :class:`.PlotWidget` instance on which to operate
+    :param parent: See :class:`QAction`
+    """
+    def __init__(self, plot, parent=None):
+        self._dialog = None  # To store an instance of ColormapDialog
+        super(ColorBarAction, self).__init__(
+            plot, icon='colorbar', text='Colorbar',
+            tooltip="Show/Hide the colorbar",
+            triggered=self._actionTriggered,
+            checkable=True, parent=parent)
+        colorBarWidget = self.plot.getColorBarWidget()
+        old = self.blockSignals(True)
+        self.setChecked(colorBarWidget.isVisibleTo(self.plot))
+        self.blockSignals(old)
+        colorBarWidget.sigVisibleChanged.connect(self._widgetVisibleChanged)
+
+    def _widgetVisibleChanged(self, isVisible):
+        """Callback when the colorbar `visible` property change."""
+        if self.isChecked() == isVisible:
+            return
+        self.setChecked(isVisible)
 
-        # Update active image colormap
-        activeImage = self.plot.getActiveImage()
-        if isinstance(activeImage, items.ColormapMixIn):
-            activeImage.setColormap(colormap)
+    def _actionTriggered(self, checked=False):
+        """Create a cmap dialog and update active image and default cmap."""
+        colorBarWidget = self.plot.getColorBarWidget()
+        if not colorBarWidget.isHidden() == checked:
+            return
+        self.plot.getColorBarWidget().setVisible(checked)
 
 
 class KeepAspectRatioAction(PlotAction):
diff --git a/silx/gui/plot/actions/fit.py b/silx/gui/plot/actions/fit.py
index d7256ab..5ca649c 100644
--- a/silx/gui/plot/actions/fit.py
+++ b/silx/gui/plot/actions/fit.py
@@ -36,7 +36,7 @@ from __future__ import division
 
 __authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
 __license__ = "MIT"
-__date__ = "28/06/2017"
+__date__ = "03/01/2018"
 
 from . import PlotAction
 import logging
@@ -111,7 +111,7 @@ class FitAction(PlotAction):
 
         if histo is None and curve is None:
             # ambiguous case, we need to ask which plot item to fit
-            isd = ItemsSelectionDialog(plot=self.plot)
+            isd = ItemsSelectionDialog(parent=self.plot, plot=self.plot)
             isd.setWindowTitle("Select item to be fitted")
             isd.setItemsSelectionMode(qt.QTableWidget.SingleSelection)
             isd.setAvailableKinds(["curve", "histogram"])
diff --git a/silx/gui/plot/actions/histogram.py b/silx/gui/plot/actions/histogram.py
index a4a91e9..40ef873 100644
--- a/silx/gui/plot/actions/histogram.py
+++ b/silx/gui/plot/actions/histogram.py
@@ -39,6 +39,7 @@ __license__ = "MIT"
 
 from . import PlotAction
 from silx.math.histogram import Histogramnd
+from silx.math.combo import min_max
 import numpy
 import logging
 from silx.gui import qt
@@ -107,8 +108,7 @@ class PixelIntensitiesHistoAction(PlotAction):
                          image[:, :, 1] * 0.587 +
                          image[:, :, 2] * 0.114)
 
-            xmin = numpy.nanmin(image)
-            xmax = numpy.nanmax(image)
+            xmin, xmax = min_max(image, min_positive=False, finite=True)
             nbins = min(1024, int(numpy.sqrt(image.size)))
             data_range = xmin, xmax
 
diff --git a/silx/gui/plot/actions/io.py b/silx/gui/plot/actions/io.py
index 50410e3..d6d5909 100644
--- a/silx/gui/plot/actions/io.py
+++ b/silx/gui/plot/actions/io.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2018 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
@@ -37,10 +37,11 @@ from __future__ import division
 
 __authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
 __license__ = "MIT"
-__date__ = "27/06/2017"
+__date__ = "02/02/2018"
 
 from . import PlotAction
 from silx.io.utils import save1D, savespec
+from silx.io.nxdata import save_NXdata
 import logging
 import sys
 from collections import OrderedDict
@@ -59,6 +60,10 @@ else:
 _logger = logging.getLogger(__name__)
 
 
+_NEXUS_HDF5_EXT = [".nx5", ".nxs",  ".hdf", ".hdf5", ".cxi", ".h5"]
+_NEXUS_HDF5_EXT_STR = ' '.join(['*' + ext for ext in _NEXUS_HDF5_EXT])
+
+
 class SaveAction(PlotAction):
     """QAction for saving Plot content.
 
@@ -89,12 +94,15 @@ class SaveAction(PlotAction):
         ('Curve as OMNIC CSV (*.csv)',
          {'fmt': '%.7E', 'delimiter': ',', 'header': False}),
         ('Curve as SpecFile (*.dat)',
-         {'fmt': '%.7g', 'delimiter': '', 'header': False})
+         {'fmt': '%.10g', 'delimiter': '', 'header': False})
     ))
 
     CURVE_FILTER_NPY = 'Curve as NumPy binary file (*.npy)'
 
-    CURVE_FILTERS = list(CURVE_FILTERS_TXT.keys()) + [CURVE_FILTER_NPY]
+    CURVE_FILTER_NXDATA = 'Curve as NXdata (%s)' % _NEXUS_HDF5_EXT_STR
+
+    CURVE_FILTERS = list(CURVE_FILTERS_TXT.keys()) + [CURVE_FILTER_NPY,
+                                                      CURVE_FILTER_NXDATA]
 
     ALL_CURVES_FILTERS = ("All curves as SpecFile (*.dat)", )
 
@@ -107,6 +115,7 @@ class SaveAction(PlotAction):
     IMAGE_FILTER_CSV_TAB = 'Image data as tab-separated CSV (*.csv)'
     IMAGE_FILTER_RGB_PNG = 'Image as PNG (*.png)'
     IMAGE_FILTER_RGB_TIFF = 'Image as TIFF (*.tif)'
+    IMAGE_FILTER_NXDATA = 'Image as NXdata (%s)' % _NEXUS_HDF5_EXT_STR
     IMAGE_FILTERS = (IMAGE_FILTER_EDF,
                      IMAGE_FILTER_TIFF,
                      IMAGE_FILTER_NUMPY,
@@ -115,7 +124,11 @@ class SaveAction(PlotAction):
                      IMAGE_FILTER_CSV_SEMICOLON,
                      IMAGE_FILTER_CSV_TAB,
                      IMAGE_FILTER_RGB_PNG,
-                     IMAGE_FILTER_RGB_TIFF)
+                     IMAGE_FILTER_RGB_TIFF,
+                     IMAGE_FILTER_NXDATA)
+
+    SCATTER_FILTER_NXDATA = 'Scatter as NXdata (%s)' % _NEXUS_HDF5_EXT_STR
+    SCATTER_FILTERS = (SCATTER_FILTER_NXDATA, )
 
     def __init__(self, plot, parent=None):
         super(SaveAction, self).__init__(
@@ -183,7 +196,7 @@ class SaveAction(PlotAction):
             csvdelim = filter_['delimiter']
             autoheader = filter_['header']
         else:
-            # .npy
+            # .npy or nxdata
             fmt, csvdelim, autoheader = ("", "", False)
 
         # If curve has no associated label, get the default from the plot
@@ -194,6 +207,19 @@ class SaveAction(PlotAction):
         if ylabel is None:
             ylabel = self.plot.getYAxis().getLabel()
 
+        if nameFilter == self.CURVE_FILTER_NXDATA:
+            return save_NXdata(
+                filename,
+                signal=curve.getYData(copy=False),
+                axes=[curve.getXData(copy=False)],
+                signal_name="y",
+                axes_names=["x"],
+                signal_long_name=ylabel,
+                axes_long_names=[xlabel],
+                signal_errors=curve.getYErrorData(copy=False),
+                axes_errors=[curve.getXErrorData(copy=True)],
+                title=self.plot.getGraphTitle())
+
         try:
             save1D(filename,
                    curve.getXData(copy=False),
@@ -226,11 +252,13 @@ class SaveAction(PlotAction):
         curve = curves[0]
         scanno = 1
         try:
+            xlabel = curve.getXLabel() or self.plot.getGraphXLabel()
+            ylabel = curve.getYLabel() or self.plot.getGraphYLabel(curve.getYAxis())
             specfile = savespec(filename,
                                 curve.getXData(copy=False),
                                 curve.getYData(copy=False),
-                                curve.getXLabel(),
-                                curve.getYLabel(),
+                                xlabel,
+                                ylabel,
                                 fmt="%.7g", scan_number=1, mode="w",
                                 write_file_header=True,
                                 close_file=False)
@@ -241,12 +269,14 @@ class SaveAction(PlotAction):
         for curve in curves[1:]:
             try:
                 scanno += 1
+                xlabel = curve.getXLabel() or self.plot.getGraphXLabel()
+                ylabel = curve.getYLabel() or self.plot.getGraphYLabel(curve.getYAxis())
                 specfile = savespec(specfile,
                                     curve.getXData(copy=False),
                                     curve.getYData(copy=False),
-                                    curve.getXLabel(),
-                                    curve.getYLabel(),
-                                    fmt="%.7g", scan_number=scanno, mode="w",
+                                    xlabel,
+                                    ylabel,
+                                    fmt="%.7g", scan_number=scanno,
                                     write_file_header=False,
                                     close_file=False)
             except IOError:
@@ -294,6 +324,24 @@ class SaveAction(PlotAction):
                 return False
             return True
 
+        elif nameFilter == self.IMAGE_FILTER_NXDATA:
+            xorigin, yorigin = image.getOrigin()
+            xscale, yscale = image.getScale()
+            xaxis = xorigin + xscale * numpy.arange(data.shape[1])
+            yaxis = yorigin + yscale * numpy.arange(data.shape[0])
+            xlabel = image.getXLabel() or self.plot.getGraphXLabel()
+            ylabel = image.getYLabel() or self.plot.getGraphYLabel()
+            interpretation = "image" if len(data.shape) == 2 else "rgba-image"
+
+            return save_NXdata(filename,
+                               signal=data,
+                               axes=[yaxis, xaxis],
+                               signal_name="image",
+                               axes_names=["y", "x"],
+                               axes_long_names=[ylabel, xlabel],
+                               title=self.plot.getGraphTitle(),
+                               interpretation=interpretation)
+
         elif nameFilter in (self.IMAGE_FILTER_ASCII,
                             self.IMAGE_FILTER_CSV_COMMA,
                             self.IMAGE_FILTER_CSV_SEMICOLON,
@@ -343,6 +391,45 @@ class SaveAction(PlotAction):
 
         return False
 
+    def _saveScatter(self, filename, nameFilter):
+        """Save an image from the plot.
+
+        :param str filename: The name of the file to write
+        :param str nameFilter: The selected name filter
+        :return: False if format is not supported or save failed,
+                 True otherwise.
+        """
+        if nameFilter not in self.SCATTER_FILTERS:
+            return False
+
+        if nameFilter == self.SCATTER_FILTER_NXDATA:
+            scatter = self.plot.getScatter()
+            # TODO: we could get all scatters on this plot and concatenate their (x, y, values)
+            x = scatter.getXData(copy=False)
+            y = scatter.getYData(copy=False)
+            z = scatter.getValueData(copy=False)
+
+            xerror = scatter.getXErrorData(copy=False)
+            if isinstance(xerror, float):
+                xerror = xerror * numpy.ones(x.shape, dtype=numpy.float32)
+
+            yerror = scatter.getYErrorData(copy=False)
+            if isinstance(yerror, float):
+                yerror = yerror * numpy.ones(x.shape, dtype=numpy.float32)
+
+            xlabel = self.plot.getGraphXLabel()
+            ylabel = self.plot.getGraphYLabel()
+
+            return save_NXdata(
+                filename,
+                signal=z,
+                axes=[x, y],
+                signal_name="values",
+                axes_names=["x", "y"],
+                axes_long_names=[xlabel, ylabel],
+                axes_errors=[xerror, yerror],
+                title=self.plot.getGraphTitle())
+
     def _actionTriggered(self, checked=False):
         """Handle save action."""
         # Set-up filters
@@ -359,6 +446,11 @@ class SaveAction(PlotAction):
         if len(self.plot.getAllCurves()) > 1:
             filters.extend(self.ALL_CURVES_FILTERS)
 
+        # Add scatter filters if there is a scatter
+        # todo: CSV
+        if self.plot.getScatter() is not None:
+            filters.extend(self.SCATTER_FILTERS)
+
         filters.extend(self.SNAPSHOT_FILTERS)
 
         # Create and run File dialog
@@ -378,10 +470,19 @@ class SaveAction(PlotAction):
         dialog.close()
 
         # Forces the filename extension to match the chosen filter
-        extension = nameFilter.split()[-1][2:-1]
-        if (len(filename) <= len(extension) or
-                filename[-len(extension):].lower() != extension.lower()):
-            filename += extension
+        if "NXdata" in nameFilter:
+            has_allowed_ext = False
+            for ext in _NEXUS_HDF5_EXT:
+                if (len(filename) > len(ext) and
+                        filename[-len(ext):].lower() == ext.lower()):
+                    has_allowed_ext = True
+            if not has_allowed_ext:
+                filename += ".h5"
+        else:
+            default_extension = nameFilter.split()[-1][2:-1]
+            if (len(filename) <= len(default_extension) or
+                    filename[-len(default_extension):].lower() != default_extension.lower()):
+                filename += default_extension
 
         # Handle save
         if nameFilter in self.SNAPSHOT_FILTERS:
@@ -392,6 +493,8 @@ class SaveAction(PlotAction):
             return self._saveCurves(filename, nameFilter)
         elif nameFilter in self.IMAGE_FILTERS:
             return self._saveImage(filename, nameFilter)
+        elif nameFilter in self.SCATTER_FILTERS:
+            return self._saveScatter(filename, nameFilter)
         else:
             _logger.warning('Unsupported file filter: %s', nameFilter)
             return False
diff --git a/silx/gui/plot/actions/medfilt.py b/silx/gui/plot/actions/medfilt.py
index 3305d1b..4284a8b 100644
--- a/silx/gui/plot/actions/medfilt.py
+++ b/silx/gui/plot/actions/medfilt.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2018 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
@@ -39,7 +39,7 @@ from __future__ import division
 __authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
 __license__ = "MIT"
 
-__date__ = "24/05/2017"
+__date__ = "03/01/2018"
 
 from . import PlotAction
 from silx.gui.widgets.MedianFilterDialog import MedianFilterDialog
@@ -67,7 +67,7 @@ class MedianFilterAction(PlotAction):
         self._originalImage = None
         self._legend = None
         self._filteredImage = None
-        self._popup = MedianFilterDialog(parent=None)
+        self._popup = MedianFilterDialog(parent=plot)
         self._popup.sigFilterOptChanged.connect(self._updateFilter)
         self.plot.sigActiveImageChanged.connect(self._updateActiveImage)
         self._updateActiveImage()
@@ -101,7 +101,7 @@ class MedianFilterAction(PlotAction):
         self.plot.sigActiveImageChanged.connect(self._updateActiveImage)
 
     def _computeFilteredImage(self, kernelWidth, conditional):
-        raise NotImplemented('MedianFilterAction is a an abstract class')
+        raise NotImplementedError('MedianFilterAction is a an abstract class')
 
     def getFilteredImage(self):
         """