New upstream version 0.8.0+dfsg

19 files changed, 241 insertions, 85 deletions

diff --git a/doc/source/modules/gui/plot/colormap.rst b/doc/source/modules/gui/plot/colormap.rst
deleted file mode 100644
index a492605..0000000
--- a/doc/source/modules/gui/plot/colormap.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-
-.. currentmodule:: silx.gui.plot.Colormap
-
-:mod:`Colormap`: Colormap API
-=============================
-
-.. automodule:: silx.gui.plot.Colormap
-
-.. currentmodule:: silx.gui.plot.Colormap
-
-:class:`Colormap` class
------------------------
-
-.. autoclass:: Colormap
-   :show-inheritance:
-   :members:
diff --git a/doc/source/modules/gui/plot/dev.rst b/doc/source/modules/gui/plot/dev.rst
index b793b01..d7d4581 100644
--- a/doc/source/modules/gui/plot/dev.rst
+++ b/doc/source/modules/gui/plot/dev.rst
@@ -20,7 +20,6 @@ The different events emitted by :class:`Plot` and by the interaction modes are c
 
 The :class:`PlotWindow` uses additional widgets:
 
-- :mod:`.ColormapDialog` to change colormap settings.
 - :mod:`.CurvesROIWidget` to create regions of interest for curves
 - :mod:`.LegendSelector` to display a list of curves legends which provides some control on the curves (e.g., select, delete).
 - :mod:`.MaskToolsWidget` to provide tools to draw a mask on an image.
@@ -39,7 +38,6 @@ The :class:`PlotWindow` uses additional widgets:
 
 The widgets also use the following miscellaneous modules:
 
-- :mod:`.Colors` to convert colors from name to RGB(A)
 - :mod:`._utils`: utility functions
 
 The :mod:`backends` package provide the implementation of the rendering used by the :class:`Plot`.
@@ -88,22 +86,6 @@ The following modules are the modules used internally by the plot package.
 .. automodule:: silx.gui.plot.backends.BackendMatplotlib
    :members:
 
-:mod:`ColormapDialog`
-+++++++++++++++++++++
-
-.. currentmodule:: silx.gui.plot.ColormapDialog
-
-.. automodule:: silx.gui.plot.ColormapDialog
-   :members:
-
-:mod:`Colors`
-+++++++++++++
-
-.. currentmodule:: silx.gui.plot.Colors
-
-.. automodule:: silx.gui.plot.Colors
-   :members: rgba
-
 :mod:`CurvesROIWidget`
 ++++++++++++++++++++++
 
diff --git a/doc/source/modules/gui/plot/getting_started.rst b/doc/source/modules/gui/plot/getting_started.rst
index bfea8f2..412cc11 100644
--- a/doc/source/modules/gui/plot/getting_started.rst
+++ b/doc/source/modules/gui/plot/getting_started.rst
@@ -20,7 +20,9 @@ For a complete description of the API, see :mod:`silx.gui.plot`.
 Use :mod:`silx.gui.plot` from (I)Python console
 -----------------------------------------------
 
-The simplest way is to import the :mod:`silx.sx` module:
+We recommend to use (I)Python 3.x and PyQt5.
+
+From a Python or IPython interpreter, the simplest way is to import the :mod:`silx.sx` module:
 
 >>> from silx import sx
 
@@ -28,19 +30,27 @@ The :mod:`silx.sx` module initialises Qt and provides access to :mod:`silx.gui.p
 
 .. note:: The :mod:`silx.sx` module does NOT initialise Qt and does NOT expose silx widget in a notebook.
 
+An alternative to run :mod:`silx.gui` widgets from `IPython <http://ipython.org/>`_,
+is to set IPython to use Qt(5), e.g., with the `--gui` option::
+
+  ipython --gui=qt5
+
+
 Compatibility with IPython
 ++++++++++++++++++++++++++
 
-To run :mod:`silx.gui` widgets from `IPython <http://ipython.org/>`_,
-IPython must be set to use Qt (and in case of using PyQt4 and Python 2.7,
-PyQt must be set to use API version 2, see note below for explanation).
-
-As *silx* is configuring the Qt binding and `matplotlib <http://matplotlib.org/>`_, the safest way to use *silx* from IPython is to import :mod:`silx.gui.plot` first and then run either `%gui <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-gui>`_ qt  or `%pylab <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-pylab>`_ qt::
+silx widgets require Qt to be initialized.
+If Qt is not yet loaded, silx tries to load PyQt5 first before trying other supported bindings.
 
-  In [1]: from silx.gui.plot import *
-  In [2]: %pylab qt
+With versions of IPython lower than 3.0 (e.g., on Debian 8), there is an incompatibility between
+the way silx loads Qt and the way IPython is doing it through the ``--gui`` option,
+`%gui <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-gui>`_ or
+`%pylab <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-pylab>`_ magics.
+In this case, IPython magics that initialize Qt might not work after importing modules from silx.gui.
 
-Alternatively, when using Python 2.7 and PyQt4, you can start IPython with the ``QT_API`` environment variable set to ``pyqt``.
+When using Python2.7 and PyQt4, there is another incompatibility to deal with as
+silx requires PyQt4 API version 2 (See note below for explanation).
+In this case, start IPython with the ``QT_API`` environment variable set to ``pyqt``.
 
 On Linux and MacOS X, run from the command line::
 
@@ -289,7 +299,7 @@ A ``colormap`` is described with a :class:`.Colormap` class as follows:
 
 .. code-block:: python
 
-   from silx.gui.plot.Colormap import Colormap
+   from silx.gui.colors import Colormap
 
    colormap = Colormap(name='gray',             # Name of the colormap
                        normalization='linear',  # Either 'linear' or 'log'
@@ -317,7 +327,7 @@ It is possible to change the default colormap of the plot widget by :meth:`.Plot
 
 .. code-block:: python
 
-   from silx.gui.plot.Colormap import Colormap
+   from silx.gui.colors import Colormap
 
    colormap = Colormap(name='viridis',
                        normalization='linear',
diff --git a/doc/source/modules/gui/plot/img/ScatterView.png b/doc/source/modules/gui/plot/img/ScatterView.png
new file mode 100644
index 0000000..a8116b9
--- /dev/null
+++ b/doc/source/modules/gui/plot/img/ScatterView.png
diff --git a/doc/source/modules/gui/plot/img/netArea.png b/doc/source/modules/gui/plot/img/netArea.png
new file mode 100644
index 0000000..f987d1f
--- /dev/null
+++ b/doc/source/modules/gui/plot/img/netArea.png
diff --git a/doc/source/modules/gui/plot/img/netCounts.png b/doc/source/modules/gui/plot/img/netCounts.png
index f987d1f..9f7d2a0 100644
--- a/doc/source/modules/gui/plot/img/netCounts.png
+++ b/doc/source/modules/gui/plot/img/netCounts.png
diff --git a/doc/source/modules/gui/plot/img/rawArea.png b/doc/source/modules/gui/plot/img/rawArea.png
new file mode 100644
index 0000000..fa36b8e
--- /dev/null
+++ b/doc/source/modules/gui/plot/img/rawArea.png
diff --git a/doc/source/modules/gui/plot/img/rawCounts.png b/doc/source/modules/gui/plot/img/rawCounts.png
index fa36b8e..6382438 100644
--- a/doc/source/modules/gui/plot/img/rawCounts.png
+++ b/doc/source/modules/gui/plot/img/rawCounts.png
diff --git a/doc/source/modules/gui/plot/img/statsWidget.png b/doc/source/modules/gui/plot/img/statsWidget.png
new file mode 100644
index 0000000..7e18ec4
--- /dev/null
+++ b/doc/source/modules/gui/plot/img/statsWidget.png
diff --git a/doc/source/modules/gui/plot/index.rst b/doc/source/modules/gui/plot/index.rst
index ab1c7df..5cda6d8 100644
--- a/doc/source/modules/gui/plot/index.rst
+++ b/doc/source/modules/gui/plot/index.rst
@@ -25,22 +25,40 @@ See :ref:`plot-gallery` gallery.
 Public modules
 --------------
 
+Main plot widgets:
+
 .. toctree::
    :maxdepth: 2
 
    plotwidget.rst
    plotwindow.rst
+   compleximageview.rst
    imageview.rst
    stackview.rst
-   compleximageview.rst
-   colormap.rst
+   scatterview.rst
+
+Classes describing plot content:
+
+- :class:`~silx.gui.colors.Colormap`
+
+.. toctree::
+   :maxdepth: 2
+
    items.rst
+
+Additionnal plot tool widgets:
+
+.. toctree::
+   :maxdepth: 2
+
    actions/index.rst
    plottoolbuttons.rst
-   plottools.rst
+   tools.rst
    profile.rst
    roi.rst
    printpreviewtoolbutton.rst
+   statswidget.rst
+   stats/index.rst
 
 Internals
 ---------
diff --git a/doc/source/modules/gui/plot/items.rst b/doc/source/modules/gui/plot/items.rst
index 3cdcf17..eb3ca1a 100644
--- a/doc/source/modules/gui/plot/items.rst
+++ b/doc/source/modules/gui/plot/items.rst
@@ -108,3 +108,10 @@ Axis
 
 .. autoclass:: Axis
    :members:
+
+
+:mod:`~silx.gui.plot.items.roi`: Regions of Interest
+----------------------------------------------------
+
+.. automodule:: silx.gui.plot.items.roi
+   :members:
diff --git a/doc/source/modules/gui/plot/plottools.rst b/doc/source/modules/gui/plot/plottools.rst
deleted file mode 100644
index 4cf8f88..0000000
--- a/doc/source/modules/gui/plot/plottools.rst
+++ /dev/null
@@ -1,36 +0,0 @@
-:mod:`PlotTools`: Tool widgets for PlotWidget
-=============================================
-
-.. currentmodule:: silx.gui.plot.PlotTools
-
-.. automodule:: silx.gui.plot.PlotTools
-
-:class:`PositionInfo` class
----------------------------
-
-.. autoclass:: PositionInfo
-   :show-inheritance:
-   :members:
-
-:class:`LimitsToolBar` class
-----------------------------
-
-.. autoclass:: LimitsToolBar
-   :show-inheritance:
-   :members:
-
-
-.. currentmodule:: silx.gui.plot
-
-:mod:`ColorBar`: ColorBar Widget
-================================
-
-.. currentmodule:: silx.gui.plot.ColorBar
-
-.. automodule:: silx.gui.plot.ColorBar
-
-:class:`ColorBarWidget` class
------------------------------
-
-.. autoclass:: ColorBarWidget
-   :members:
diff --git a/doc/source/modules/gui/plot/plotwidget.rst b/doc/source/modules/gui/plot/plotwidget.rst
index d045f92..4ce69f7 100644
--- a/doc/source/modules/gui/plot/plotwidget.rst
+++ b/doc/source/modules/gui/plot/plotwidget.rst
@@ -148,7 +148,6 @@ Misc.
 
 .. automethod:: PlotWidget.getWidgetHandle
 .. automethod:: PlotWidget.saveGraph
-.. automethod:: PlotWidget.setDefaultBackend
 
 Signals
 .......
diff --git a/doc/source/modules/gui/plot/scatterview.rst b/doc/source/modules/gui/plot/scatterview.rst
new file mode 100644
index 0000000..6a0cf93
--- /dev/null
+++ b/doc/source/modules/gui/plot/scatterview.rst
@@ -0,0 +1,20 @@
+
+.. currentmodule:: silx.gui.plot
+
+:mod:`ScatterView`: Plot 2D scatter data
+========================================
+
+.. automodule:: silx.gui.plot.ScatterView
+
+.. currentmodule:: silx.gui.plot.ScatterView
+
+.. image:: img/ScatterView.png
+   :height: 400px
+   :align: center
+
+:class:`ScatterView` class
+--------------------------
+
+.. autoclass:: ScatterView
+   :show-inheritance:
+   :members:
\ No newline at end of file
diff --git a/doc/source/modules/gui/plot/stats/index.rst b/doc/source/modules/gui/plot/stats/index.rst
new file mode 100644
index 0000000..ccfb3f9
--- /dev/null
+++ b/doc/source/modules/gui/plot/stats/index.rst
@@ -0,0 +1,18 @@
+.. currentmodule:: silx.gui.plot.stats
+
+:mod:`stats`: Stats for PlotWidget
+=================================================
+
+.. automodule:: silx.gui.plot.stats
+
+stats API
+---------
+
+Actions are divided into the following sub-modules:
+
+
+.. toctree::
+   :maxdepth: 1
+
+   stats.rst
+   statshandler.rst
\ No newline at end of file
diff --git a/doc/source/modules/gui/plot/stats/stats.rst b/doc/source/modules/gui/plot/stats/stats.rst
new file mode 100644
index 0000000..717f6eb
--- /dev/null
+++ b/doc/source/modules/gui/plot/stats/stats.rst
@@ -0,0 +1,6 @@
+:mod:`silx.gui.plot.stats.stats`
+````````````````````````````````
+.. currentmodule:: silx.gui.plot.stats.stats
+
+.. automodule:: silx.gui.plot.stats.stats
+    :members:
diff --git a/doc/source/modules/gui/plot/stats/statshandler.rst b/doc/source/modules/gui/plot/stats/statshandler.rst
new file mode 100644
index 0000000..01d56f3
--- /dev/null
+++ b/doc/source/modules/gui/plot/stats/statshandler.rst
@@ -0,0 +1,7 @@
+:mod:`silx.gui.plot.stats.statshandler`
+```````````````````````````````````````
+
+.. currentmodule:: silx.gui.plot.stats.statshandler
+
+.. automodule:: silx.gui.plot.stats.statshandler
+    :members:
diff --git a/doc/source/modules/gui/plot/statswidget.rst b/doc/source/modules/gui/plot/statswidget.rst
new file mode 100644
index 0000000..f534921
--- /dev/null
+++ b/doc/source/modules/gui/plot/statswidget.rst
@@ -0,0 +1,33 @@
+
+.. currentmodule:: silx.gui.plot
+
+:mod:`StatsWidget`: Display a set of statictics for plot items
+==============================================================
+
+.. automodule:: silx.gui.plot.StatsWidget
+
+.. currentmodule:: silx.gui.plot.StatsWidget
+
+:class:`StatsWidget` class
+--------------------------
+
+.. autoclass:: StatsWidget
+   :show-inheritance:
+   :members:
+
+
+:class:`BasicStatsWidget` class
+-------------------------------
+
+.. autoclass:: BasicStatsWidget
+   :show-inheritance:
+   :members:
+
+
+:class:`StatsTable` class
+-------------------------
+
+.. autoclass:: StatsTable
+   :show-inheritance:
+   :members:
+
diff --git a/doc/source/modules/gui/plot/tools.rst b/doc/source/modules/gui/plot/tools.rst
new file mode 100644
index 0000000..766c8f1
--- /dev/null
+++ b/doc/source/modules/gui/plot/tools.rst
@@ -0,0 +1,108 @@
+:mod:`~silx.gui.plot.tools`: Tool widgets for PlotWidget
+========================================================
+
+.. currentmodule:: silx.gui.plot.tools
+
+.. automodule:: silx.gui.plot.tools
+
+:class:`PositionInfo` class
+---------------------------
+
+.. autoclass:: PositionInfo
+   :show-inheritance:
+   :members:
+
+:class:`LimitsToolBar` class
+----------------------------
+
+.. autoclass:: LimitsToolBar
+   :show-inheritance:
+   :members:
+
+:class:`InteractiveModeToolBar` class
+-------------------------------------
+
+.. autoclass:: InteractiveModeToolBar
+   :show-inheritance:
+   :members:
+
+:class:`OutputToolBar` class
+----------------------------
+
+.. autoclass:: OutputToolBar
+   :show-inheritance:
+   :members:
+
+:class:`ImageToolBar` class
+----------------------------
+
+.. autoclass:: ImageToolBar
+   :show-inheritance:
+   :members:
+
+:class:`CurveToolBar` class
+----------------------------
+
+.. autoclass:: CurveToolBar
+   :show-inheritance:
+   :members:
+
+:class:`ScatterToolBar` class
+-----------------------------
+
+.. autoclass:: ScatterToolBar
+   :show-inheritance:
+   :members:
+
+:mod:`~silx.gui.plot.tools.roi`: Region of interest
+---------------------------------------------------
+
+.. automodule:: silx.gui.plot.tools.roi
+
+.. currentmodule:: silx.gui.plot.tools.roi
+
+:class:`RegionOfInterestManager` class
+++++++++++++++++++++++++++++++++++++++
+
+.. autoclass:: RegionOfInterestManager
+   :members:
+
+:class:`InteractiveRegionOfInterestManager` class
++++++++++++++++++++++++++++++++++++++++++++++++++
+
+.. autoclass:: InteractiveRegionOfInterestManager
+   :members:
+
+:class:`RegionOfInterestTableWidget` class
+++++++++++++++++++++++++++++++++++++++++++
+
+.. autoclass:: RegionOfInterestTableWidget
+   :members:
+
+:mod:`~silx.gui.plot.tools.profile`: Profile Tools
+--------------------------------------------------
+
+.. automodule:: silx.gui.plot.tools.profile
+
+.. currentmodule:: silx.gui.plot.tools.profile
+
+:class:`ScatterProfileToolBar`
+++++++++++++++++++++++++++++++
+
+.. autoclass:: ScatterProfileToolBar
+   :members: sigProfileChanged, getProfilePoints, getProfileValues, getProfileTitle, getPlotWidget, isDefaultProfileWindowEnabled, setDefaultProfileWindowEnabled, getDefaultProfileWindow, getColor, setColor, clearProfile, getNPoints, setNPoints
+
+.. currentmodule:: silx.gui.plot
+
+:mod:`ColorBar`: ColorBar Widget
+================================
+
+.. currentmodule:: silx.gui.plot.ColorBar
+
+.. automodule:: silx.gui.plot.ColorBar
+
+:class:`ColorBarWidget` class
+-----------------------------
+
+.. autoclass:: ColorBarWidget
+   :members: