Silx

------------------

Python 2.7 is no longer officially supported (even if tests pass and most of the library should work).

* silx view application:

* Added: keep the same axes selection when changing dataset except for the stack view (PR 2701, 2780)
* Added a Description column in the browsing tree to display NeXus title or name (PR 2804)
* Added support of URL as filename (PR 2750)
* Behavior changed: no longer lock HDF5 files by default, can be changed with `--hdf5-file-locking` option (PR 2861)

* `silx.gui`:

* `silx.gui.plot`:

* Added scatter plot regular and irregular grid visualization mode (PR 2810, 2815, 2820, 2824, 2831)
* Added `baseline` argument to `PlotWidget` `addCurve` and `addHistogram` methods (PR 2715)
* Added right axis support to `PlotWidget` marker items (PR 2744)
* Added `BoundingRect` `PlotWidget` item (PR 2823)
* Added more markers to `PlotWidget` items using symbols (PR 2792)
* Improved and fixed `PlotWidget` and backends rendering and picking to guarantee rendering order of items (PR 2602, 2694, 2726, 2728, 2730, 2731, 2732, 2734, 2746, 2800, 2822, 2829, 2851, 2853)
* Improved `RegionOfInterest`: Added `sigItemChanged` signal, renamed `get|setLabel` to `get|setName` (PR 2684, 2729, 2794, 2803, 2860)
* Improved `StackView`: Allow to save dataset to HDF5 (PR 2813)

* `silx.gui.plot3d`:

* Added colormapped isosurface display to `ComplexField3D` (PR 2675)

* Miscellaneous:

* Added `cividis` colormap (PR 2763)
* Added `silx.gui.widgets.ColormapNameComboBox` widget (PR 2814)
* Added `silx.gui.widgets.LegendIconWidget` widget (PR 2783)
* Added `silx.gui.utils.blockSignals` context manager (PR 2697, 2702)
* Added `silx.gui.utils.qtutils.getQEventName` function (PR 2725)
* Added `silx.gui.colors.asQColor` function (PR 2753)
* Minor fixes (PR 2662, 2667, 2674, 2719, 2724, 2747, 2757, 2760, 2766, 2789, 2798, 2799, 2805, 2811, 2832, 2834, 2839, 2849, 2852, 2857, 2864, 2867)

* `silx.opencl`:

* Added `silx.opencl.sparse.CSR` with support of different data types (PR 2671)
* Improved support of different platforms like PoCL (PR 2669, 2698, 2806)
* Moved non-OpenCL related utilities to `silx.opencl.utils` module (PR 2782)
* Fixed `silx.opencl.sinofilter.SinoFilter` to avoid importing scikit-cuda (PR 2721)
* Fixed kernel garbage collection (PR 2708)
* Fixed `silx.opencl.convolution.Convolution` (PR 2781)

* `silx.math`/`silx.image`:

* Added trilinear interpolator: `silx.math.interpolate.interp3d` (PR 2678)
* Added `silx.image.utils.gaussian_kernel` function (PR 2782)
* Improved `silx.image.shapes.Polygon` argument check (PR 2761)
* Fixed and improved `silx.math.fft` with FFTW backend (PR 2751)
* Fixed support of not finite data in fit manager (PR 2868)

* `silx.io`:

* Added `asarray=True` argument to `silx.io.dictdump.h5todict` function (PR 2692, 2767)
* Improved `silx.io.utils.DataUrl` (PR 2790)
* Increased max number of motors in `specfile` (PR 2817)
* Fixed data conversion when reading images with `fabio` (PR 2735)

* Build, documentation and tests:

* Added `Cython` as a build dependency (PR 2795, 2807, 2808)
* Added Debian 10 packaging (PR 2670, 2672, 2666, 2686, 2706)
* Improved documentation (PR 2673, 2680, 2679, 2772, 2759, 2779, 2801, 2802, 2833, 2857, 2869)
* Improved testing tools (PR 2704, 2796, 2818)
* Improved `bootstrap.py` script (PR 2727, 2733)

------------------

* Graphical user interface:

* Plot:

* Add sample code on how to update a plot3d widget from a thread
* ScatterPlot: add the possibility to plot as a surface using Delaunay triangulation
* ScatterView: add a tool button to change scatter visualization mode (ex. Solid)
* (OpenGL backend) Fix memory leak when creating/deleting widgets in a loop


* Plot3D:

* Add an action to toggle plot3d's `PositionInfoWidget` picking.
* Add a 3D complex field visualization: Complex3DField (also available from silx view)
* Add a PositionInfoWidget and a tool button to toggle the picking mode to SceneWindow
* Add the possibility to render the scene with linear fog.

* `silx.gui.widgets`:

* Fix ImageFileDialog selection for a cube with shape like `1,y,x`.

* Miscellaneous:

* Requires numpy version >= 1.12
* HDF5 creator script
* Support of Python 3.4 is dropped. Please upgrade to at least Python 3.5.
* This is the last version to officially support Python 2.7.
* The source code is Python 3.8 ready.
* Improve PySide2 support. PyQt4 and PySide are deprecated.

------------------

* 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

-----------------

* 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

-----------------

* 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

-----------------

* 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.