New upstream version 0.8.0+dfsg

39 files changed, 439 insertions, 139 deletions

diff --git a/doc/source/modules/gui/colors.rst b/doc/source/modules/gui/colors.rst
new file mode 100644
index 0000000..3cba7c6
--- /dev/null
+++ b/doc/source/modules/gui/colors.rst
@@ -0,0 +1,9 @@
+.. currentmodule:: silx.gui
+
+:mod:`colors`: Colors and colormap
+----------------------------------
+
+.. currentmodule:: silx.gui.colors
+
+.. automodule:: silx.gui.colors
+   :members:
diff --git a/doc/source/modules/gui/dialog/colormapdialog.rst b/doc/source/modules/gui/dialog/colormapdialog.rst
new file mode 100644
index 0000000..0904431
--- /dev/null
+++ b/doc/source/modules/gui/dialog/colormapdialog.rst
@@ -0,0 +1,12 @@
+
+.. currentmodule:: silx.gui.dialog
+
+:mod:`ColormapDialog`
+=====================
+
+.. automodule:: silx.gui.dialog.ColormapDialog
+
+.. currentmodule:: silx.gui.dialog.ColormapDialog
+
+.. autoclass:: ColormapDialog
+    :members:
diff --git a/doc/source/modules/gui/dialog/groupdialog.rst b/doc/source/modules/gui/dialog/groupdialog.rst
new file mode 100644
index 0000000..85e85ad
--- /dev/null
+++ b/doc/source/modules/gui/dialog/groupdialog.rst
@@ -0,0 +1,8 @@
+
+.. currentmodule:: silx.gui.dialog
+
+:mod:`GroupDialog`
+======================
+
+.. automodule:: silx.gui.dialog.GroupDialog
+
diff --git a/doc/source/modules/gui/dialog/img/abstractdatafiledialog.png b/doc/source/modules/gui/dialog/img/abstractdatafiledialog.png
new file mode 100644
index 0000000..7e4eeeb
--- /dev/null
+++ b/doc/source/modules/gui/dialog/img/abstractdatafiledialog.png
diff --git a/doc/source/modules/gui/dialog/img/groupdialog.png b/doc/source/modules/gui/dialog/img/groupdialog.png
new file mode 100644
index 0000000..ee8c469
--- /dev/null
+++ b/doc/source/modules/gui/dialog/img/groupdialog.png
diff --git a/doc/source/modules/gui/dialog/index.rst b/doc/source/modules/gui/dialog/index.rst
index a13ad31..7e2f687 100644
--- a/doc/source/modules/gui/dialog/index.rst
+++ b/doc/source/modules/gui/dialog/index.rst
@@ -17,10 +17,14 @@ Snapshot of the widgets:
    :height: 150px
    :align: middle
 
-======================== ==========================
-|imgImageFileDialog|        |imgDataFileDialog|
-:class:`ImageFileDialog`  :class:`DataFileDialog`
-======================== ==========================
+.. |imgGroupDialog| image:: ./img/datafiledialog.png
+   :height: 150px
+   :align: middle
+
+======================== ========================== ==========================
+|imgImageFileDialog|      |imgDataFileDialog|       |imgGroupDialog|
+:class:`ImageFileDialog`  :class:`DataFileDialog`   :class:`GroupDialog`
+======================== ========================== ==========================
 
 Public modules:
 
@@ -30,4 +34,6 @@ Public modules:
    imagefiledialog.rst
    datafiledialog.rst
    abstractdatafiledialog.rst
+   groupdialog.rst
+   colormapdialog.rst
 
diff --git a/doc/source/modules/gui/gallery.rst b/doc/source/modules/gui/gallery.rst
index 40d8648..c71a87a 100644
--- a/doc/source/modules/gui/gallery.rst
+++ b/doc/source/modules/gui/gallery.rst
@@ -75,13 +75,20 @@ Widgets gallery
    * - .. image:: dialog/img/datafiledialog.png
          :height: 150px
          :align: center
-     - :class:`DataFileDialog` is a dialog that allow users to select
-       any datasets or groups from an HDF5-like file.
+     - :class:`DataFileDialog` is a dialog that allows users to select
+       any datasets or groups from any HDF5-like file. It features a file
+       browser that can also browse the content of HDF5 file as if they were
+       directories.
    * - .. image:: dialog/img/imagefiledialog_h5.png
          :height: 150px
          :align: center
-     - :class:`ImageFileDialog` is a dialog that allow users to select
-       an image from an HDF5-like file.
+     - :class:`ImageFileDialog` is a dialog that allows users to select
+       an image from any HDF5-like file.
+   * - .. image:: dialog/img/groupdialog.png
+         :height: 150px
+         :align: center
+     - :class:`GroupDialog` is a dialog that allows users to select
+       a group from one or several specified HDF5-like files.
 
 
 :mod:`silx.gui.fit` Widgets
@@ -179,7 +186,10 @@ Plotting widgets:
        2D dataset of complex data.
        It allows to switch between viewing amplitude, phase, real, imaginary,
        colored phase with amplitude or log10(amplitude) as brightness.
-
+   * - .. image:: plot/img/ScatterView.png
+          :height: 150px
+          :align: center
+     - :class:`ScatterView` is a widget dedicated to visualize a scatter plot.
 
 Additional widgets:
 
@@ -204,6 +214,10 @@ Additional widgets:
           :align: center
      - :class:`.ColorBar.ColorBarWidget` display colormap gradient and can be linked with a plot
        to display the colormap
+   * - .. image:: plot/img/statsWidget.png
+          :height: 150px
+          :align: center
+     - :class:`.statsWidget.StatsWidget` display statistics on plot's items (curve, images...)
 
 .. _plot3d-gallery:
 
diff --git a/doc/source/modules/gui/hdf5/getting_started.rst b/doc/source/modules/gui/hdf5/getting_started.rst
index e843cac..1a81a0a 100644
--- a/doc/source/modules/gui/hdf5/getting_started.rst
+++ b/doc/source/modules/gui/hdf5/getting_started.rst
@@ -4,10 +4,9 @@ Getting started with HDF5 widgets
 =================================
 
 Silx provides an implementation of a tree model and a tree view for HDF5 files.
-The aim of this tree is to provide a convenient read-only widget for a big
-amount of data and supporting file formats often used in synchrotrons.
+The aim of this tree is to provide a convenient read-only widget supporting file formats often used in synchrotrons for big amounts of data.
 
-This page provides some source code to show how to use this widget.
+This page displays some source code to explain how to use this widget.
 
 Commented source code
 ---------------------
@@ -34,15 +33,15 @@ HDF5 widgets are all exposed by the package `silx.gui.hdf5`.
 Custom your tree view
 +++++++++++++++++++++
 
-The tree view can be customized to be sorted by default.
+The tree view can be customised to be sorted by default.
 
 .. testcode::
 
    # Sort content of files by time or name
    treeview.setSortingEnabled(True)
 
-The model can be customized to support mouse interaction.
-A convenient method :meth:`Hdf5TreeView.findHdf5TreeModel` returns the main
+The model can be customised to support mouse interaction.
+A convenient method, i.e., :meth:`Hdf5TreeView.findHdf5TreeModel`, returns the main
 HDF5 model used through proxy models.
 
 .. testcode::
@@ -55,8 +54,7 @@ HDF5 model used through proxy models.
    # Allow the user to reorder files with drag-and-drop
    model.setFileMoveEnabled(True)
 
-The tree view is also provided with a custom header which help to choose
-visible columns.
+The tree view is also provided with a custom header that helps to choose visible columns.
 
 .. testcode::
 
@@ -72,18 +70,18 @@ visible columns.
 Add a file by name
 ++++++++++++++++++
 
-The model can be used to add HDF5. It is internally using
+The model can be used to add an HDF5 file. It is internally using
 :func:`silx.io.open`.
 
 .. code-block:: python
 
    model.insertFile("test.h5")
 
-Add a file with h5py
-++++++++++++++++++++
+Add a file using h5py
++++++++++++++++++++++
 
-The model internally uses :mod:`h5py` object API. We can use h5py file, group
-and dataset as it is.
+The model internally uses the :mod:`h5py` object API.
+We can use directly h5py Files, Groups and Datasets.
 
 .. code-block:: python
 
@@ -97,10 +95,10 @@ and dataset as it is.
    model.insertH5pyObject(h5["group1"])
    model.insertH5pyObject(h5["group1/dataset50"])
 
-Add a file with silx
-++++++++++++++++++++
+Add a file using silx
++++++++++++++++++++++
 
-Silx also provides an input API. It supports HDF5 files through :mod:`h5py`.
+Silx also provides an input API and supports HDF5 files through :mod:`h5py`.
 
 .. code-block:: python
 
@@ -119,7 +117,7 @@ Custom context menu
 The :class:`Hdf5TreeView` provides a callback API to populate the context menu.
 The callback receives a :class:`Hdf5ContextMenuEvent` every time the user
 requests the context menu. The event contains :class:`H5Node` objects which wrap
-h5py objects with extra information.
+h5py objects adding extra information.
 
 .. testcode::
 
@@ -147,27 +145,27 @@ The :class:`Hdf5TreeView` widget provides default Qt signals inherited from
 
 - `activated`:
       This signal is emitted when the item specified by index is
-      activated by the user. How to activate items depends on the platform;
+      activated by the user. How to activate items depends on the platform,
       e.g., by single- or double-clicking the item, or by pressing the
-      Return or Enter key when the item is current.
+      Return or Enter key when the item is the current one.
 - `clicked`:
-      This signal is emitted when a mouse button is clicked. The item the mouse
-      was clicked on is specified by index. The signal is only emitted when the
-      index is valid.
+      This signal is emitted when a mouse button is clicked. The item selected by
+      mouse click is specified by index. The signal is only emitted when the
+      index is a valid one.
 - `doubleClicked`:
-      This signal is emitted when a mouse button is double-clicked. The item
-      the mouse was double-clicked on is specified by index. The signal is
-      only emitted when the index is valid.
+      This signal is emitted when a mouse button is double-clicked.
+      The selected item is specified by index.
+      The signal is only emitted when the index is a valid one.
 - `entered`:
       This signal is emitted when the mouse cursor enters the item specified by
       index. Mouse tracking needs to be enabled for this feature to work.
 - `pressed`:
-      This signal is emitted when a mouse button is pressed. The item the mouse
-      was pressed on is specified by index. The signal is only emitted when the
-      index is valid.
+      This signal is emitted when a mouse button is pressed.
+      The selected item is specified by index.
+      The signal is only emitted when the index is a valid one.
 
 The method :meth:`Hdf5TreeView.selectedH5Nodes` returns an iterator of :class:`H5Node`
-objects which wrap h5py objects with extra information.
+objects which wrap h5py objects adding extra information.
 
 .. testcode::
 
@@ -204,7 +202,7 @@ Example
    examples_hdf5widget.rst
 
 The :doc:`examples_hdf5widget` sample code provides an example of properties of
-the view, the model and the header.
+the view, model and header.
 
 .. image:: img/Hdf5Example.png
    :height: 200px
@@ -214,13 +212,12 @@ the view, the model and the header.
 
 Source code: :doc:`examples_hdf5widget`.
 
-After installing `silx` and downloading the script, you can start it from the
-command prompt:
+After installing `silx` and downloading the script, you can run it from the
+command line prompt:
 
 .. code-block:: bash
 
    python hdf5widget.py <files>
 
 This example loads files added to the command line, or files dropped from the
-file system. It also provides a GUI to display test files created
-programmatically.
+file system. It also provides a GUI to display dummy test files.
diff --git a/doc/source/modules/gui/hdf5/hdf5headerview.rst b/doc/source/modules/gui/hdf5/hdf5headerview.rst
new file mode 100644
index 0000000..b3b3a98
--- /dev/null
+++ b/doc/source/modules/gui/hdf5/hdf5headerview.rst
@@ -0,0 +1,9 @@
+
+.. currentmodule:: silx.gui.hdf5
+
+:class:`Hdf5HeaderView` class
+-----------------------------
+
+.. autoclass:: Hdf5HeaderView
+   :show-inheritance:
+   :members:
diff --git a/doc/source/modules/gui/hdf5/index.rst b/doc/source/modules/gui/hdf5/index.rst
index cd2c4eb..9ae416f 100644
--- a/doc/source/modules/gui/hdf5/index.rst
+++ b/doc/source/modules/gui/hdf5/index.rst
@@ -43,4 +43,5 @@ Public modules
    hdf5treemodel.rst
    hdf5contextmenuevent.rst
    h5node.rst
+   hdf5headerview.rst
    nexussortfilterproxymodel.rst
diff --git a/doc/source/modules/gui/icons.rst b/doc/source/modules/gui/icons.rst
index 48fe95c..3105006 100644
--- a/doc/source/modules/gui/icons.rst
+++ b/doc/source/modules/gui/icons.rst
@@ -29,6 +29,20 @@ Available icons
      - 3d-plane-pan
    * - |3d-plane|
      - 3d-plane
+   * - |add-shape-arc|
+     - add-shape-arc
+   * - |add-shape-diagonal|
+     - add-shape-diagonal
+   * - |add-shape-horizontal|
+     - add-shape-horizontal
+   * - |add-shape-point|
+     - add-shape-point
+   * - |add-shape-polygon|
+     - add-shape-polygon
+   * - |add-shape-rectangle|
+     - add-shape-rectangle
+   * - |add-shape-vertical|
+     - add-shape-vertical
    * - |arrow-keys|
      - arrow-keys
    * - |axis|
@@ -117,6 +131,8 @@ Available icons
      - item-object
    * - |last|
      - last
+   * - |layer-nx|
+     - layer-nx
    * - |math-amplitude|
      - math-amplitude
    * - |math-average|
@@ -163,6 +179,14 @@ Available icons
      - next
    * - |normal|
      - normal
+   * - |nxdata-axis-add|
+     - nxdata-axis-add
+   * - |nxdata-axis-remove|
+     - nxdata-axis-remove
+   * - |nxdata-create|
+     - nxdata-create
+   * - |nxdata-remove|
+     - nxdata-remove
    * - |pan|
      - pan
    * - |pixel-intensities|
@@ -179,6 +203,8 @@ Available icons
      - plot-roi-reset
    * - |plot-roi|
      - plot-roi
+   * - |plot-symbols|
+     - plot-symbols
    * - |plot-toggle-points|
      - plot-toggle-points
    * - |plot-widget|
@@ -243,6 +269,18 @@ Available icons
      - sliders-on
    * - |spec|
      - spec
+   * - |stats-active-items|
+     - stats-active-items
+   * - |stats-visible-data|
+     - stats-visible-data
+   * - |stats-whole-data|
+     - stats-whole-data
+   * - |stats-whole-items|
+     - stats-whole-items
+   * - |tree-collapse-all|
+     - tree-collapse-all
+   * - |tree-expand-all|
+     - tree-expand-all
    * - |view-1d|
      - view-1d
    * - |view-2d-stack|
@@ -283,6 +321,13 @@ Available icons
 .. |3d-plane-normal-z| image:: ../../../../silx/resources/gui/icons/3d-plane-normal-z.png
 .. |3d-plane-pan| image:: ../../../../silx/resources/gui/icons/3d-plane-pan.png
 .. |3d-plane| image:: ../../../../silx/resources/gui/icons/3d-plane.png
+.. |add-shape-arc| image:: ../../../../silx/resources/gui/icons/add-shape-arc.png
+.. |add-shape-diagonal| image:: ../../../../silx/resources/gui/icons/add-shape-diagonal.png
+.. |add-shape-horizontal| image:: ../../../../silx/resources/gui/icons/add-shape-horizontal.png
+.. |add-shape-point| image:: ../../../../silx/resources/gui/icons/add-shape-point.png
+.. |add-shape-polygon| image:: ../../../../silx/resources/gui/icons/add-shape-polygon.png
+.. |add-shape-rectangle| image:: ../../../../silx/resources/gui/icons/add-shape-rectangle.png
+.. |add-shape-vertical| image:: ../../../../silx/resources/gui/icons/add-shape-vertical.png
 .. |arrow-keys| image:: ../../../../silx/resources/gui/icons/arrow-keys.png
 .. |axis| image:: ../../../../silx/resources/gui/icons/axis.png
 .. |camera| image:: ../../../../silx/resources/gui/icons/camera.png
@@ -327,6 +372,7 @@ Available icons
 .. |item-none| image:: ../../../../silx/resources/gui/icons/item-none.png
 .. |item-object| image:: ../../../../silx/resources/gui/icons/item-object.png
 .. |last| image:: ../../../../silx/resources/gui/icons/last.png
+.. |layer-nx| image:: ../../../../silx/resources/gui/icons/layer-nx.png
 .. |math-amplitude| image:: ../../../../silx/resources/gui/icons/math-amplitude.png
 .. |math-average| image:: ../../../../silx/resources/gui/icons/math-average.png
 .. |math-derive| image:: ../../../../silx/resources/gui/icons/math-derive.png
@@ -350,6 +396,10 @@ Available icons
 .. |median-filter| image:: ../../../../silx/resources/gui/icons/median-filter.png
 .. |next| image:: ../../../../silx/resources/gui/icons/next.png
 .. |normal| image:: ../../../../silx/resources/gui/icons/normal.png
+.. |nxdata-axis-add| image:: ../../../../silx/resources/gui/icons/nxdata-axis-add.png
+.. |nxdata-axis-remove| image:: ../../../../silx/resources/gui/icons/nxdata-axis-remove.png
+.. |nxdata-create| image:: ../../../../silx/resources/gui/icons/nxdata-create.png
+.. |nxdata-remove| image:: ../../../../silx/resources/gui/icons/nxdata-remove.png
 .. |pan| image:: ../../../../silx/resources/gui/icons/pan.png
 .. |pixel-intensities| image:: ../../../../silx/resources/gui/icons/pixel-intensities.png
 .. |plot-grid| image:: ../../../../silx/resources/gui/icons/plot-grid.png
@@ -358,6 +408,7 @@ Available icons
 .. |plot-roi-between| image:: ../../../../silx/resources/gui/icons/plot-roi-between.png
 .. |plot-roi-reset| image:: ../../../../silx/resources/gui/icons/plot-roi-reset.png
 .. |plot-roi| image:: ../../../../silx/resources/gui/icons/plot-roi.png
+.. |plot-symbols| image:: ../../../../silx/resources/gui/icons/plot-symbols.png
 .. |plot-toggle-points| image:: ../../../../silx/resources/gui/icons/plot-toggle-points.png
 .. |plot-widget| image:: ../../../../silx/resources/gui/icons/plot-widget.png
 .. |plot-window-image| image:: ../../../../silx/resources/gui/icons/plot-window-image.png
@@ -390,6 +441,12 @@ Available icons
 .. |sliders-off| image:: ../../../../silx/resources/gui/icons/sliders-off.png
 .. |sliders-on| image:: ../../../../silx/resources/gui/icons/sliders-on.png
 .. |spec| image:: ../../../../silx/resources/gui/icons/spec.png
+.. |stats-active-items| image:: ../../../../silx/resources/gui/icons/stats-active-items.png
+.. |stats-visible-data| image:: ../../../../silx/resources/gui/icons/stats-visible-data.png
+.. |stats-whole-data| image:: ../../../../silx/resources/gui/icons/stats-whole-data.png
+.. |stats-whole-items| image:: ../../../../silx/resources/gui/icons/stats-whole-items.png
+.. |tree-collapse-all| image:: ../../../../silx/resources/gui/icons/tree-collapse-all.png
+.. |tree-expand-all| image:: ../../../../silx/resources/gui/icons/tree-expand-all.png
 .. |view-1d| image:: ../../../../silx/resources/gui/icons/view-1d.png
 .. |view-2d-stack| image:: ../../../../silx/resources/gui/icons/view-2d-stack.png
 .. |view-2d| image:: ../../../../silx/resources/gui/icons/view-2d.png
diff --git a/doc/source/modules/gui/index.rst b/doc/source/modules/gui/index.rst
index 1f7ee4a..0afc49a 100644
--- a/doc/source/modules/gui/index.rst
+++ b/doc/source/modules/gui/index.rst
@@ -16,9 +16,11 @@ The ``silx.gui`` package provides a set of PyQt widgets.
    dialog/index.rst
    hdf5/index.rst
    icons.rst
+   colors.rst
    plot/index.rst
    plot3d/index.rst
    qt.rst
+   utils.rst
    widgets/index.rst
 
 
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:
diff --git a/doc/source/modules/gui/utils.rst b/doc/source/modules/gui/utils.rst
new file mode 100644
index 0000000..be0f0ae
--- /dev/null
+++ b/doc/source/modules/gui/utils.rst
@@ -0,0 +1,12 @@
+.. currentmodule:: silx.gui.utils
+
+:mod:`~silx.gui.utils`: Qt helpers
+==================================
+
+.. automodule:: silx.gui.utils
+
+:mod:`~silx.gui.utils.concurrent`
+---------------------------------
+
+.. automodule:: silx.gui.utils.concurrent
+   :members:
diff --git a/doc/source/modules/image/index.rst b/doc/source/modules/image/index.rst
index 89c5642..477cc9f 100644
--- a/doc/source/modules/image/index.rst
+++ b/doc/source/modules/image/index.rst
@@ -6,9 +6,10 @@
 
 .. toctree::
    :maxdepth: 1
-   
+
    bilinear.rst
    medianfilter.rst
+   marchingsquares.rst
    shapes.rst
    sift.rst
    backprojection.rst
diff --git a/doc/source/modules/image/marchingsquares.rst b/doc/source/modules/image/marchingsquares.rst
new file mode 100644
index 0000000..b44f66d
--- /dev/null
+++ b/doc/source/modules/image/marchingsquares.rst
@@ -0,0 +1,11 @@
+
+.. currentmodule:: silx.image
+
+:mod:`marchingsquares`: Marching squares
+----------------------------------------
+
+.. automodule:: silx.image.marchingsquares
+    :members:
+
+.. autoclass:: silx.image.marchingsquares.MarchingSquaresMergeImpl
+    :members:
diff --git a/doc/source/modules/io/nxdata.rst b/doc/source/modules/io/nxdata.rst
index 7940270..1ec66fb 100644
--- a/doc/source/modules/io/nxdata.rst
+++ b/doc/source/modules/io/nxdata.rst
@@ -1,8 +1,2 @@
 
-.. currentmodule:: silx.io
-
-:mod:`nxdata`: NXdata group parsing
-------------------------------------
-
 .. automodule:: silx.io.nxdata
-    :members:
diff --git a/doc/source/modules/math/colormap.rst b/doc/source/modules/math/colormap.rst
new file mode 100644
index 0000000..f184b66
--- /dev/null
+++ b/doc/source/modules/math/colormap.rst
@@ -0,0 +1,6 @@
+:mod:`~silx.math.colormap`: Apply colormap to array
+---------------------------------------------------
+
+.. automodule:: silx.math.colormap
+
+.. autofunction:: cmap
diff --git a/doc/source/modules/math/combo.rst b/doc/source/modules/math/combo.rst
index 4d1b5c6..511aacf 100644
--- a/doc/source/modules/math/combo.rst
+++ b/doc/source/modules/math/combo.rst
@@ -1,7 +1,5 @@
-.. currentmodule:: silx.math
-
-:mod:`silx.math.combo`: Statistics combo functions
---------------------------------------------------
+:mod:`~silx.math.combo`: Statistics combo functions
+---------------------------------------------------
 
 .. automodule:: silx.math.combo
 
diff --git a/doc/source/modules/math/index.rst b/doc/source/modules/math/index.rst
index ece49dd..fbecc02 100644
--- a/doc/source/modules/math/index.rst
+++ b/doc/source/modules/math/index.rst
@@ -11,3 +11,4 @@
    histogram.rst
    medianfilter.rst
    combo.rst
+   colormap.rst
diff --git a/doc/source/modules/sx.rst b/doc/source/modules/sx.rst
index d5e0288..f08dd98 100644
--- a/doc/source/modules/sx.rst
+++ b/doc/source/modules/sx.rst
@@ -13,6 +13,7 @@ The following functions plot curves and images with silx widgets:
 
 - :func:`plot` for curves
 - :func:`imshow` for images
+- :func:`scatter` for scatter plot
 
 The :func:`ginput` function handles user selection on those widgets.
 
@@ -29,6 +30,11 @@ The :func:`ginput` function handles user selection on those widgets.
 
 .. autofunction:: imshow
 
+:func:`scatter`
++++++++++++++++
+
+.. autofunction:: scatter
+
 
 :func:`ginput`
 ++++++++++++++