Silx

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* Graphical user interface:

* Plot:

* Add support of foreground color
* Fix plot background colors
* Add tool to mask ellipse
* StatsWidget:

* Add support for plot3D widgets
* Add a PyMca like widget

* `Colormap`: Phase colormap is now editable
* `ImageView`: Add ColorBarWidget
* `PrintPreview`:

* Add API to define 'comment' and 'title'
* Fix resizing in PyQt5

* Selection: Allow style definition
* `ColormapDialog`: display 'values' plot in log if colormap uses log
* Synchronize ColorBar with plot background colors
* `CurvesROIWidget`: ROI is now an object.

* Plot3D:

* `SceneWidget`: add ColormapMesh item
* Add compatibility with the StatsWidget to display statistic on 3D volumes.
* Add `ScalarFieldView.get|setOuterScale`
* Fix label update in param tree
* Add `ColormapMesh` item to the `SceneWidget`

* HDF5 tree:

* Allow URI drop
* Robustness of hdf5 tree with corrupted files

* `silx.gui.widgets`:

* Add URL selection table

* Input/output:

* Support compressed Fabio extensions
* Add a function to create external dataset for .vol file

* `silx view`:

* Support 2D view for 3D NXData
* Add a NXdata for complex images
* Add a 3d scalar field view to the NXdata views zoo
* Improve shortcuts, view loading
* Improve silx view loading, shortcuts and sliders ergonomy
* Support default attribute pointing to an NXdata at any group level

* `silx convert`

* Allow to use a filter id for compression

* Math:

* fft: multibackend fft

* OpenCL:

* Compute statistics on a numpy.ndarray
* Backprojection:

* Add sinogram filters (SinoFilter)
* Input and/or output can be device arrays.

* Miscellaneous:

* End of PySide support (use PyQt5)
* Last version supporting numpy 1.8.0. Next version will drop support for numpy < 1.12
* Python 2.7 support will be dropped before end 2019. From version 0.11, a deprecation warning will be issued.
* Remove some old deprecated methods/arguments
* Set Cython language_level to 3

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* Graphical user interface:

* `silx.gui.widgets`:

* Adds `RangeSlider` widget, a slider with 2 thumbs
* Adds `CurveLegendsWidget` widget to display PlotWidget curve legends
(as an alternative to `LegendSelector` widget)
* Adds `FlowLayout` QWidget layout

* Plot:

* Adds `CompareImages` widget providing tools to compare 2 images
* `ScatterView`: Adds alpha channel support
* `MaskToolsWidget`: Adds load/save masks from/to HDF5 files

* `PlotWidget`:

* Adds `getItems` method, `sigItemAdded` and `sigItemAboutToBeRemoved` signals
* Adds more options for active curve highlighting (see `get|setActiveCurveStyle` method)
* Deprecates `get|setActiveCurveColor` methods
* Adds `get|setActiveCurveSelectionMode` methods to change the behavior of active curve selection
* Adds configurable line style and width to line markers
* Fixes texture cache size in OpenGL backend

* Plot3D:

* Adds `SceneWidget.pickItems` method to retrieve the item and data at a given mouse position
* Adds `PositionInfoWidget` widget to display data value at a given mouse position

* `silx.gui.utils`:

* Adds `image` module for QImage/numpy array conversion functions
* Adds `testutils` helper module for writing Qt tests
(previously available internally as `silx.gui.test.utils`)

* Adds `silx.gui.qt.inspect` module to inspect Qt objects

* Math:

* Updates median filter with support for Not-a-Number and a 'constant' padding mode

* `silx view`:

* Fixes file synchronization
* Adds a refresh button to synchronize file content

* Dependencies:

* Deprecates support of PySide Qt4 binding
(We intend to drop official support of PySide in silx 0.10.0)
* Deprecates support of PyQt4
* Adds `h5py` and `fabio` as strong dependencies

* Miscellaneous:

* Adds `silx.examples` package to ship the example with the library

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* Graphical user interface:

* Plot:

* Adds support of x-axis date/time ticks for time series display (see `silx.gui.plot.items.XAxis.setTickMode`)
* Adds support of interactive authoring of regions of interest (see `silx.gui.plot.items.roi` and `silx.gui.plot.tools.roi`)
* Adds `StatsWidget` widget for displaying statistics on data displayed in a `PlotWidget`
* Adds `ScatterView` widget for displaying scatter plot with tools such as line profile and mask
* Overcomes the limitation to float32 precision with the OpenGL backend
* Splits plot toolbar is several reusable thematic toolbars

* Plot3D: Adds `SceneWidget` items to display many cubes, cylinders or hexagonal prisms at once
* Adds `silx.gui.utils` package with `submitToQtMainThread` for asynchronous execution of Qt-related functions
* Adds Qt signals to `Hdf5TreeView` to manage HDF5 file life-cycle
* Adds `GroupDialog` dialog to select a group in a HDF5 file
* Improves colormap computation with a Cython/OpenMP implementation

* Main API changes:

* `Colormap` is now part of `silx.gui.colors`
* `ColormapDialog` is now part of `silx.gui.dialogs`
* `MaskToolsWidget.getSelectionMask` method now returns `None` if no image is selected
* Clean-up `FrameBrowser` API

* Image

* Adds an optimized marching squares algorithm to compute many iso contours from the same image

* Input/output:

* Improves handling of empty Spec scans
* Add an API to `NXdata` parser to get messages about malformed input data

* `silx.sx`

* Allows to use `silx.sx` in script as in Python interpreter
* `sx.imshow` supports custom y-axis orientation using argument `origin=upper|lower`
* Adds `sx.enable_gui()` to enable silx widgets in IPython notebooks

* `silx convert`

* Improves conversion from EDF file series to HDF5

* `silx view`

* Adds user preferences to restore colormap, plot backend, y-axis of plot image,...
* Adds `--fresh` option to clean up user preferences at startup
* Adds a widget to create custom viewable `NXdata` by combining different datasets
* Supports `CTRL+C` shortcut in the terminal to close the application
* Adds buttons to collapse/expand tree items
* NXdata view now uses the `ScatterView` widget for scatters

* Miscellaneous

* Drops official support of Debian 7
* Drops versions of IPython console widget before the `qtconsole` package
* Fixes EDF file size written by `EdfFile` module with Python 3

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* Input/output:

* Priovides `silx.io.url.DataUrl` to parse supported links identifying
group or dataset from files.
* `silx.io.open` now supports h5pyd and silx custom URLs.
* `silx.io.get_data` is provided to allow to reach a numpy array from silx.

* OpenCL:

* Provides an API to share memory between OpenCL tasks within the same device.
* Provides CBF compression and decompression.
* Simple processing on images (normalization, histogram).
* Sift upgrade using memory sharing.

* `silx.sx`:

* Added `contour3d` function for displaying 3D isosurfaces.
* Added `points3d` function for displaying 2D/3D scatter plots.
* Added `ginput` function for interactive input of points on 1D/2D plots.

* Graphic user interface:

* Provides a file dialog to pick a dataset or a group from HDF5 files.
* Provides a file dialog to pick an image from HDF5 files or multiframes formats.
* The colormap dialog can now be used as non-modal.
* `PlotWidget` can save the displayed data as a new `NXentry` of a HDF5 file.
* `PlotWidget` exports displayed data as spec files using more digits.
* Added new OpenGL-based 3D visualization widgets:

* Supports 3D scalar field view 2D/3D scatter plots and images.
* Provides an object oriented API similar to that of the 1D/2D plot.
* Features a tree of parameters to edit visualized item's properties
(e.g., transforms, colormap...)
* Provides interactive panning of cut and clip planes.

* Updates of `ScalarFieldView` widget:

* Added support for a 3x3 transform matrix (to support non orthogonal axes)
* Added support of an alternative interaction when `ctrl` is pressed
(e.g., rotate by default and pan when ctrl/command key is pressed).
* Added 2 sliders to control light direction in associated parameter tree view.

* `silx view`:

* Uses a single colormap to show any datasets.
* The colormap dialog can stay opened while browsing the data.
* The application is associated with some file types to be used to load files
on Debian.
* Provides a square amplitude display mode to visualize complex images.
* Browsing an `NXentry` can display a default `NXdata`.
* Added explanation when an `NXdata` is not displayable.
* `NXdata` visualization can now show multiple curves (see `auxiliary_signals`).
* Supports older `NXdata` specification.

* `silx convert`:

* Added handling of file series as a single multiframe
* Default behavior changes to avoid to add an extra group at the root,
unless explicitly requested (see `--add-root-group`).
* Writer uses now utf-8 text as default (NeXus specification).
* EDF files containing MCA data are now interpreted as spectrum.

* Miscellaneous:

* Added `silx.utils.testutils` to share useful unittest functions with other
projects.
* Python 2 on Mac OS X is no longer tested.
* Experimental support to PySide2.
* If fabio is used, a version >= 0.6 is mandatory.

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* OpenCl. Tomography. Implement a filtered back projection.
* Add a *PrintPreview* widget and a *PrintPreviewToolButton* for *PlotWidget*.
* Plot:

* Add a context menu on right click.
* Add a *ComplexImageView* widget.
* Merged abstract *Plot* class with *PlotWidget* class.
* Make colormap an object with signals (*sigChanged*)
* Add a colorbar widget *silx.gui.plot.ColorBar*.
* Make axis an object, allow axis synchronization between plots,
allow adding constraints on axes limits.
* Refactor plot actions, new sub-package *silx.gui.plot.actions*.
* Add signals on *PlotWidget* items notifying updates.
* Mask. Support loading of TIFF images.

* Plot3d:

* Rework toolbar and interaction to use only the left mouse button.
* Support any colormap.

* Hdf5TreeView:

* Add an API to select a single tree node item (*setSelectedH5Node*)
* Better support and display of types.
* New column for displaying the kind of links.
* Broken nodes are now selectable.

* StackView. Add a *setTitleCallback* method.
* Median filter. Add new modes (*reflect, mirror, shrink*) in addition to *nearest*.

* IO:

* Rename module *spectoh5* to *convert*. Add support for conversion of *fabio* formats.
* Support NPZ format.
* Support opening an URI (*silx.io.open(filename::path)*).
* *Group* methods *.keys*, *.value* and *.items* now return lists in Python 2
and iterators in Python 3.

* Image. Add tomography utils: *phantomgenerator* to produce Shepp-Logan phantom, function to compute center of rotation (*calc_center_corr*, *calc_center_centroid*) and rescale the intensity of an image (*rescale_intensity*).

* Commands:

* *silx view*:

* Add command line option *--use-opengl-plot*.
* Add command line option *--debug*, to print dataset reading errors.
* Support opening URI (*silx view filename::path*).

* *silx convert*. New command line application to convert supported data files to HDF5.

* Enable usage of *silx.resources* for other projects.
* The *silx* license is now fully MIT.

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* Adds OpenGL backend to 1D and 2D graphics
* Adds Object Oriented plot API with Curve, Histogram, Image, ImageRgba and Scatter items.
* Implements generic launcher (``silx view``)
* NXdataViewer. Module providing NeXus NXdata support
* Math/OpenCL. Implementation of median filter.
* Plot. Implementation of ColorBar widget.
* Plot. Visualization of complex data type.
* Plot. Implementation of Scatter Plot Item supporting colormaps and masks.
* Plot. StackView now supports axes calibration.
* I/O. Supports SPEC files not having F or S as first line character.
* I/O. Correctly exposes UB matrix when found in file.
* ROIs. Simplification of API: setRois, getRois, calculateRois.
* ROIs. Correction of calculation bug when the X-axis values were not ordered.
* Sift. Moves package from ``silx.image`` to ``silx.opencl``.