New upstream version 0.11.0+dfsg

13 files changed, 115 insertions, 88 deletions

diff --git a/doc/source/ext/snapshotqt_directive.py b/doc/source/ext/snapshotqt_directive.py
index 53508df..81305e0 100644
--- a/doc/source/ext/snapshotqt_directive.py
+++ b/doc/source/ext/snapshotqt_directive.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2004-2018 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2019 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
@@ -39,41 +39,14 @@ __date__ = "07/12/2018"
 
 import os
 import logging
-import subprocess
 import sys
-import distutils
-import shutil
 from docutils.parsers.rst.directives.images import Image
 from docutils.parsers.rst import directives
-from docutils.parsers.rst import Directive
-from docutils.nodes import fully_normalize_name
-from docutils import nodes
 
 # from docutils.par
 # note: conf.py is patching the PATH so this will be the 'current' qt version
 
-
-def _distutils_dir_name(dname="lib"):
-    """
-    Returns the name of a distutils build directory
-    """
-    platform = distutils.util.get_platform()
-    architecture = "%s.%s-%i.%i" % (dname, platform,
-                                    sys.version_info[0], sys.version_info[1])
-    return architecture
-
 home = os.path.abspath(os.path.join(__file__, "..", "..", "..", '..'))
-home = os.path.abspath(home)
-LIBPATH = os.path.join(home, 'build', _distutils_dir_name('lib'))
-
-if not os.path.exists(LIBPATH):
-    raise RuntimeError("%s is not on the path. Fix your PYTHONPATH and restart sphinx." % project)
-
-sys.path.append(LIBPATH)
-env = os.environ.copy()
-env.update(
-    {"PYTHONPATH": LIBPATH + os.pathsep + os.environ.get("PYTHONPATH", ""),
-     "PATH": os.environ.get("PATH", "")})
 
 
 if not os.environ.get('DIRECTIVE_SNAPSHOT_QT') == 'True':
diff --git a/doc/source/install.rst b/doc/source/install.rst
index 7941a7b..3862e4c 100644
--- a/doc/source/install.rst
+++ b/doc/source/install.rst
@@ -110,7 +110,7 @@ Linux
 
 Packages are available for a few distributions:
 
-- Debian 8: see `Installing a Debian package`_.
+- Debian 9: see `Installing a Debian package`_.
 - `CentOS 7 RPM packages <http://pubrepo.maxiv.lu.se/rpm/el7/x86_64/>`_ provided by the Max IV institute at Lund, Sweden.
 - `Fedora 23 rpm packages <http://pubrepo.maxiv.lu.se/rpm/fc23/x86_64/>`_ provided by the Max IV institute at Lund, Sweden.
 - `Arch Linux (AUR) package <https://aur.archlinux.org/packages/python-silx>`_ provided by Leonid Bloch.
@@ -125,7 +125,7 @@ You can also follow one of those installation procedures:
 Installing a Debian package
 +++++++++++++++++++++++++++
 
-Debian 8 (Jessie) packages are available on http://www.silx.org/pub/debian/ for amd64 computers.
+Debian 9 (Stretch) packages are available on http://www.silx.org/pub/debian/ for amd64 computers.
 To install it, you need to download this file :
 
 .. code-block:: bash 
diff --git a/doc/source/modules/gui/icons.rst b/doc/source/modules/gui/icons.rst
index 659bc4c..dbd58b4 100644
--- a/doc/source/modules/gui/icons.rst
+++ b/doc/source/modules/gui/icons.rst
@@ -75,6 +75,8 @@ Available icons
      - compare-align-stretch
    * - |compare-keypoints|
      - compare-keypoints
+   * - |compare-mode-a-minus-b|
+     - compare-mode-a-minus-b
    * - |compare-mode-a|
      - compare-mode-a
    * - |compare-mode-b|
@@ -121,6 +123,8 @@ Available icons
      - draw-rubber
    * - |edit-copy|
      - edit-copy
+   * - |eye|
+     - eye
    * - |first|
      - first
    * - |folder|
@@ -251,6 +255,8 @@ Available icons
      - plot-ylog
    * - |plot-yup|
      - plot-yup
+   * - |pointing-hand|
+     - pointing-hand
    * - |previous|
      - previous
    * - |profile-clear|
@@ -370,6 +376,7 @@ Available icons
 .. |compare-align-origin| image:: ../../../../silx/resources/gui/icons/compare-align-origin.png
 .. |compare-align-stretch| image:: ../../../../silx/resources/gui/icons/compare-align-stretch.png
 .. |compare-keypoints| image:: ../../../../silx/resources/gui/icons/compare-keypoints.png
+.. |compare-mode-a-minus-b| image:: ../../../../silx/resources/gui/icons/compare-mode-a-minus-b.png
 .. |compare-mode-a| image:: ../../../../silx/resources/gui/icons/compare-mode-a.png
 .. |compare-mode-b| image:: ../../../../silx/resources/gui/icons/compare-mode-b.png
 .. |compare-mode-hline| image:: ../../../../silx/resources/gui/icons/compare-mode-hline.png
@@ -393,6 +400,7 @@ Available icons
 .. |draw-pencil| image:: ../../../../silx/resources/gui/icons/draw-pencil.png
 .. |draw-rubber| image:: ../../../../silx/resources/gui/icons/draw-rubber.png
 .. |edit-copy| image:: ../../../../silx/resources/gui/icons/edit-copy.png
+.. |eye| image:: ../../../../silx/resources/gui/icons/eye.png
 .. |first| image:: ../../../../silx/resources/gui/icons/first.png
 .. |folder| image:: ../../../../silx/resources/gui/icons/folder.png
 .. |image-mask| image:: ../../../../silx/resources/gui/icons/image-mask.png
@@ -458,6 +466,7 @@ Available icons
 .. |plot-ydown| image:: ../../../../silx/resources/gui/icons/plot-ydown.png
 .. |plot-ylog| image:: ../../../../silx/resources/gui/icons/plot-ylog.png
 .. |plot-yup| image:: ../../../../silx/resources/gui/icons/plot-yup.png
+.. |pointing-hand| image:: ../../../../silx/resources/gui/icons/pointing-hand.png
 .. |previous| image:: ../../../../silx/resources/gui/icons/previous.png
 .. |profile-clear| image:: ../../../../silx/resources/gui/icons/profile-clear.png
 .. |profile1D| image:: ../../../../silx/resources/gui/icons/profile1D.png
diff --git a/doc/source/modules/gui/plot/index.rst b/doc/source/modules/gui/plot/index.rst
index 6f06830..01cb29b 100644
--- a/doc/source/modules/gui/plot/index.rst
+++ b/doc/source/modules/gui/plot/index.rst
@@ -61,6 +61,13 @@ Additionnal plot tool widgets:
    statswidget.rst
    stats/index.rst
 
+Utilities
+
+.. toctree::
+   :maxdepth: 2
+
+   utils.rst
+
 Internals
 ---------
 
diff --git a/doc/source/modules/gui/plot/statswidget.rst b/doc/source/modules/gui/plot/statswidget.rst
index 6cd8ecf..1574abc 100644
--- a/doc/source/modules/gui/plot/statswidget.rst
+++ b/doc/source/modules/gui/plot/statswidget.rst
@@ -32,18 +32,18 @@
    :members:
 
 
-:class:`BasicGridStatsWidget` class
+:class:`BasicLineStatsWidget` class
 -----------------------------------
 
-.. autoclass:: BasicGridStatsWidget
+.. autoclass:: BasicLineStatsWidget
    :show-inheritance:
    :members:
 
 
-:class:`BasicLineStatsWidget` class
+:class:`BasicGridStatsWidget` class
 -----------------------------------
 
-.. autoclass:: BasicLineStatsWidget
+.. autoclass:: BasicGridStatsWidget
    :show-inheritance:
    :members:
 
diff --git a/doc/source/modules/gui/plot/utils.rst b/doc/source/modules/gui/plot/utils.rst
new file mode 100644
index 0000000..e930208
--- /dev/null
+++ b/doc/source/modules/gui/plot/utils.rst
@@ -0,0 +1,12 @@
+.. currentmodule:: silx.gui.plot.utils
+
+
+:mod:`axis`: utilities for plots
+================================
+
+SyncAxes
+--------
+
+.. autoclass:: silx.gui.plot.utils.axis.SyncAxes
+   :members:
+
diff --git a/doc/source/modules/gui/plot3d/glutils.rst b/doc/source/modules/gui/plot3d/glutils.rst
index 2c36e83..21781d9 100644
--- a/doc/source/modules/gui/plot3d/glutils.rst
+++ b/doc/source/modules/gui/plot3d/glutils.rst
@@ -13,13 +13,17 @@
 Utility functions
 -----------------
 
-.. currentmodule:: silx.gui._glutils
+.. currentmodule:: silx.gui._glutils.Context
 
 For OpenGL context management:
 
-.. autofunction:: getGLContext
+.. autofunction:: getCurrent
+
+.. autofunction:: setCurrent
 
-.. autofunction:: setGLContextGetter
+.. autofunction:: current
+
+.. currentmodule:: silx.gui._glutils
 
 For type checking and conversion:
 
diff --git a/doc/source/modules/opencl/convolution.rst b/doc/source/modules/opencl/convolution.rst
new file mode 100644
index 0000000..225d016
--- /dev/null
+++ b/doc/source/modules/opencl/convolution.rst
@@ -0,0 +1,10 @@
+
+.. currentmodule:: silx.opencl
+
+:mod:`convolution`: Convolution
+-------------------------------
+
+.. automodule:: silx.opencl.convolution
+    :members: Convolution, gaussian_kernel
+    :show-inheritance:
+    :undoc-members:
diff --git a/doc/source/modules/opencl/index.rst b/doc/source/modules/opencl/index.rst
index 20a3a01..ef8b9e6 100644
--- a/doc/source/modules/opencl/index.rst
+++ b/doc/source/modules/opencl/index.rst
@@ -11,6 +11,9 @@
    sift/index.rst
    fbp.rst
    sinofilter.rst
+   processing.rst
+   convolution.rst
+   statistics.rst
    medfilt.rst
    codec_cbf.rst
 
diff --git a/doc/source/modules/opencl/processing.rst b/doc/source/modules/opencl/processing.rst
new file mode 100644
index 0000000..a246cc6
--- /dev/null
+++ b/doc/source/modules/opencl/processing.rst
@@ -0,0 +1,10 @@
+
+.. currentmodule:: silx.opencl
+
+:mod:`processing`: Processing
+-------------------------------
+
+.. automodule:: silx.opencl.processing
+    :members: OpenclProcessing, KernelContainer
+    :show-inheritance:
+    :undoc-members:
diff --git a/doc/source/modules/opencl/statistics.rst b/doc/source/modules/opencl/statistics.rst
new file mode 100644
index 0000000..0db7566
--- /dev/null
+++ b/doc/source/modules/opencl/statistics.rst
@@ -0,0 +1,10 @@
+
+.. currentmodule:: silx.opencl
+
+:mod:`statistics`: Statistics
+-------------------------------
+
+.. automodule:: silx.opencl.statistics
+    :members: Statistics
+    :show-inheritance:
+    :undoc-members:
diff --git a/doc/source/sample_code/img/plot3dUpdateScatterFromThread.png b/doc/source/sample_code/img/plot3dUpdateScatterFromThread.png
new file mode 100644
index 0000000..acd1c58
--- /dev/null
+++ b/doc/source/sample_code/img/plot3dUpdateScatterFromThread.png
diff --git a/doc/source/sample_code/index.rst b/doc/source/sample_code/index.rst
index a5cbf11..409391f 100644
--- a/doc/source/sample_code/index.rst
+++ b/doc/source/sample_code/index.rst
@@ -25,8 +25,7 @@ All sample codes can be downloaded as a zip file: |sample_code_archive|.
      - Description
    * - :download:`icons.py <../../../examples/icons.py>`
      - .. image:: img/icons.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Display icons and animated icons provided by silx.
 
 :mod:`silx.gui.data` and :mod:`silx.gui.hdf5`
@@ -41,18 +40,15 @@ All sample codes can be downloaded as a zip file: |sample_code_archive|.
      - Description
    * - :download:`customHdf5TreeModel.py <../../../examples/customHdf5TreeModel.py>`
      - .. image:: img/customHdf5TreeModel.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Qt Hdf5 widget examples
    * - :download:`customDataView.py <../../../examples/customDataView.py>`
      - .. image:: img/customDataView.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Qt data view example
    * - :download:`hdf5widget.py <../../../examples/hdf5widget.py>`
      - .. image:: img/hdf5widget.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Qt Hdf5 widget examples
 
        .. note:: This module has a dependency on the `h5py <http://www.h5py.org/>`_
@@ -71,8 +67,7 @@ All sample codes can be downloaded as a zip file: |sample_code_archive|.
      - Description
    * - :download:`fileDialog.py <../../../examples/fileDialog.py>`
      - .. image:: img/fileDialog.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Example for the use of the ImageFileDialog.
 
 :mod:`silx.gui.widgets`
@@ -87,14 +82,13 @@ All sample codes can be downloaded as a zip file: |sample_code_archive|.
      - Description
    * - :download:`periodicTable.py <../../../examples/periodicTable.py>`
      - .. image:: img/periodicTable.png
-         :height: 150px
+         :width: 150px
          :align: center
      - This script is a simple example of how to use the periodic table widgets,
        select elements and connect signals.
    * - :download:`simplewidget.py <../../../examples/simplewidget.py>`
      - .. image:: img/simplewidget.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script shows a gallery of simple widgets provided by silx.
 
        It shows the following widgets:
@@ -117,8 +111,7 @@ Widgets
      - Description
    * - :download:`imageview.py <../../../examples/imageview.py>`
      - .. image:: img/imageview.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - Example to show the use of :mod:`~silx.gui.plot.ImageView` widget.
 
        It can be used to open an EDF or TIFF file from the shell command line.
@@ -134,14 +127,12 @@ Widgets
        ``./bootstrap.py python examples/imageview.py <file to open>``
    * - :download:`stackView.py <../../../examples/stackView.py>`
      - .. image:: img/stackView.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script is a simple example to illustrate how to use the
        :mod:`~silx.gui.plot.StackView` widget.
    * - :download:`colormapDialog.py <../../../examples/colormapDialog.py>`
      - .. image:: img/colormapDialog.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script shows the features of a :mod:`~silx.gui.dialog.ColormapDialog`.
 
 :class:`silx.gui.plot.actions.PlotAction`
@@ -158,16 +149,14 @@ Sample code that adds buttons to the toolbar of a silx plot widget.
      - Description
    * - :download:`plotClearAction.py <../../../examples/plotClearAction.py>`
      - .. image:: img/plotClearAction.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script shows how to create a minimalistic
        :class:`~silx.gui.plot.actions.PlotAction` that clear the plot.
 
        This illustrates how to add more buttons in a plot widget toolbar.
    * - :download:`shiftPlotAction.py <../../../examples/shiftPlotAction.py>`
      - .. image:: img/shiftPlotAction.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script is a simple (trivial) example of how to create a :class:`~silx.gui.plot.PlotWindow`,
        create a custom :class:`~silx.gui.plot.actions.PlotAction` and add it to the toolbar.
 
@@ -176,8 +165,7 @@ Sample code that adds buttons to the toolbar of a silx plot widget.
    * - :download:`fftPlotAction.py <../../../examples/fftPlotAction.py>`,
        :download:`fft.png <../../../examples/fft.png>`
      - .. image:: img/fftPlotAction.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script is a simple example of how to create a :class:`~silx.gui.plot.PlotWindow`
        with a custom :class:`~silx.gui.plot.actions.PlotAction` added to the toolbar.
 
@@ -206,8 +194,7 @@ Sample code that adds specific tools or functions to plot widgets.
      - Description
    * - :download:`plotWidget.py <../../../examples/plotWidget.py>`
      - .. image:: img/plotWidget.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script shows how to create a custom window around a PlotWidget.
 
        It subclasses :class:`QMainWindow`, uses a :class:`~silx.gui.plot.PlotWidget`
@@ -220,8 +207,7 @@ Sample code that adds specific tools or functions to plot widgets.
        - :class:`silx.gui.plot.ColorBar.ColorBarWidget`
    * - :download:`plotContextMenu.py <../../../examples/plotContextMenu.py>`
      - .. image:: img/plotContextMenu.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates the addition of a context menu to a
        :class:`~silx.gui.plot.PlotWidget`.
 
@@ -237,20 +223,17 @@ Sample code that adds specific tools or functions to plot widgets.
        For more information on context menus, see Qt documentation.
    * - :download:`plotItemsSelector.py <../../../examples/plotItemsSelector.py>`
      - .. image:: img/plotItemsSelector.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This example illustrates how to use a :class:`ItemsSelectionDialog` widget
        associated with a :class:`~silx.gui.plot.PlotWidget`
    * - :download:`plotLimits.py <../../../examples/plotLimits.py>`
      - .. image:: img/plotLimits.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script is an example to illustrate how to use axis synchronization
        tool.
    * - :download:`plotUpdateCurveFromThread.py <../../../examples/plotUpdateCurveFromThread.py>`
      - .. image:: img/plotUpdateCurveFromThread.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates the update of a :mod:`silx.gui.plot` widget from a thread.
 
        The problem is that plot and GUI methods should be called from the main thread.
@@ -263,8 +246,7 @@ Sample code that adds specific tools or functions to plot widgets.
        of a plot.
    * - :download:`plotUpdateImageFromThread.py <../../../examples/plotUpdateImageFromThread.py>`
      - .. image:: img/plotUpdateImageFromThread.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates the update of a :mod:`silx.gui.plot` widget from a thread.
 
        The problem is that plot and GUI methods should be called from the main thread.
@@ -277,8 +259,7 @@ Sample code that adds specific tools or functions to plot widgets.
        of a plot.
    * - :download:`plotInteractiveImageROI.py <../../../examples/plotInteractiveImageROI.py>`
      - .. image:: img/plotInteractiveImageROI.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates image ROI selection in a :class:`~silx.gui.plot.PlotWidget`
 
        It uses :class:`~silx.gui.plot.tools.roi.RegionOfInterestManager` and
@@ -286,8 +267,7 @@ Sample code that adds specific tools or functions to plot widgets.
        interactive selection and to display the list of selected ROIs.
    * - :download:`printPreview.py <../../../examples/printPreview.py>`
      - .. image:: img/printPreview.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates how to add a print preview tool button to any plot
        widget inheriting :class:`~silx.gui.plot.PlotWidget`.
 
@@ -298,14 +278,12 @@ Sample code that adds specific tools or functions to plot widgets.
        which allows them to send their content to the same print preview page.
    * - :download:`scatterMask.py <../../../examples/scatterMask.py>`
      - .. image:: img/scatterMask.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This example demonstrates how to use ScatterMaskToolsWidget
        and NamedScatterAlphaSlider with a PlotWidget.
    * - :download:`syncaxis.py <../../../examples/syncaxis.py>`
      - .. image:: img/syncaxis.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script is an example to illustrate how to use axis synchronization
        tool.
 
@@ -323,8 +301,7 @@ Sample code that adds specific tools or functions to plot widgets.
      - Description
    * - :download:`plot3dContextMenu.py <../../../examples/plot3dContextMenu.py>`
      - .. image:: img/plot3dContextMenu.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script adds a context menu to a :class:`silx.gui.plot3d.ScalarFieldView`.
 
        This is done by adding a custom context menu to the :class:`Plot3DWidget`:
@@ -335,8 +312,7 @@ Sample code that adds specific tools or functions to plot widgets.
        For more information on context menus, see Qt documentation.
    * - :download:`viewer3DVolume.py <../../../examples/viewer3DVolume.py>`
      - .. image:: img/viewer3DVolume.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script illustrates the use of :class:`silx.gui.plot3d.ScalarFieldView`.
 
        It loads a 3D scalar data set from a file and displays iso-surfaces and
@@ -344,8 +320,7 @@ Sample code that adds specific tools or functions to plot widgets.
        It can also be started without providing a file.
    * - :download:`plot3dSceneWindow.py <../../../examples/plot3dSceneWindow.py>`
      - .. image:: img/plot3dSceneWindow.png
-         :height: 150px
-         :align: center
+         :width: 150px
      - This script displays the different items of :class:`~silx.gui.plot3d.SceneWindow`.
 
        It shows the different visualizations of :class:`~silx.gui.plot3d.SceneWindow`
@@ -359,6 +334,20 @@ Sample code that adds specific tools or functions to plot widgets.
        - 3D scatter plot
        - 3D scalar field with iso-surface and cutting plane.
        - A clipping plane.
+   * - :download:`plot3dUpdateScatterFromThread.py <../../../examples/plot3dUpdateScatterFromThread.py>`
+     - .. image:: img/plot3dUpdateScatterFromThread.png
+         :width: 150px
+     - This script illustrates the update of a
+       :class:`~silx.gui.plot3d.SceneWindow.SceneWindow` widget from a thread.
+
+       The problem is that GUI methods should be called from the main thread.
+       To safely update the scene from another thread, one need to execute the update
+       asynchronously in the main thread.
+       In this example, this is achieved with
+       :func:`~silx.gui.utils.concurrent.submitToQtMainThread`.
+
+       In this example a thread calls submitToQtMainThread to append data to a 3D scatter.
+
 
 :mod:`silx.io` sample code
 ++++++++++++++++++++++++++