Silx

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Main new features are the `silx.io.h5py_utils` module which provides `h5py` concurrency helpers and image mask support by `silx.gui.plot.PlotWidget`'s tools.

* `silx view`:

* Fixed zoom reseting when scrolling a NXdata 3D stack (PR 3351)
* Fixed support of very large 1D datasets in "Raw" table view (PR 3418)

* `silx.io`:

* Added `h5py_utils` helper module for concurrent HDF5 reading and writing without SWMR (PR 3368, 3426)
* Enhanced `dictdump` module functions regarding overwriting existing files (PR 3376)

* `silx.gui`:

* Added scale to visible or selected area buttons options to `silx.gui.dialog.ColormapDialog` (PR 3365)
* Fixed and enhanced`silx.gui.utils.glutils.isOpenGLAvailable` (PR 3356, 3385)
* Fixed `silx.gui.widgets.FlowLayout` (PR 3389)
* Enhanced `silx.gui.data.ArrayTableWidget`: Added support of array clipping if data is too large (PR 3419)

* `silx.gui.plot`:

* Added mask support to Image items and use it in plot tools (histogram, profile, colormap) (PR 3369, 3381)
* Added `ImageStack` methods to configure automatic reset zoom (PR 3373)
* Added some statistic indicators in `PixelIntensitiesHistoAction` action (PR 3391)
* Enhanced `silx.gui.plot.ImageView` integration of ROI profiles in side plots (PR 3380)
* Enhanced `PositionInfo`: snapping to histogram (PR 3405) and information labels layout (PR 3399)
* Fixed `LegendSelector` blinking when updated (PR 3346)
* Fixed profile tool issue when closing profile window after attaced PlotWidget (PR 3375)
* Fixed histogram action (PR 3396)
* Fixed support of histogram plot items in `stats` module (PR 3398, 3407)
* Fixed `ColorBar` when deleting attached PlotWidget (PR 3403)

* `silx.gui.plot.PlotWidget`:

* Added `getValueData` method to image items (PR 3378)
* Added `discardItem` method (PR 3400)
* Added unified `selection()` handler compatible with active item management (PR 3401)
* Fixed `addCurve` documentation (PR 3371)
* Fixed complex image first displayed mode (PR 3364)
* Fixed curve and scatter items support of complex data input (PR 3384)
* Fixed histogram picking (PR 3405)
* Fixed rendering (PR 3416)

* `silx.gui.plot3d`:

* Added `HeightMapData` and `HeightMapRGBA` items (PR 3386, 3397)
* Fixed support for RGB colored points in internal scene graph (PR 3374)
* Fixed `ImageRgba` alpha channel display (PR 3414)

* `silx.image`:

* Added mask support to `bilinear` interpolator (PR 3286)

* `silx.opencl`:

* Added print statics of OpenCL kernel execution time (PR 3395)

* Miscellaneous:

* Removed debian 9 packaging (PR 3383)
* Enhanced test functions: `silx.test.run_tests` (PR 3331), `silx.utils.testutils.TestLogging` (PR 3393)
* Continuous integration: Added github actions and removed travis-ci (PR 3353, 3359), fixed (PR 3361, 3366)
* Updated documentation (PR 3383, 3387, 3409, 3416, 3427)
* Fixed debian packaging (PR 3362)
* Fixed `silx test` application on Windows (PR 3411)

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

This is a bug-fix version of silx.

* silx.gui.plot: Fixed `PlotWidget` OpenGL backend memory leak (PR 3445)
* silx.gui.utils.glutils: Fixed `isOpenGLAvailable` (PR 3356)

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

This is the first version of `silx` supporting `h5py` >= v3.0.

This is the last version of `silx` officially supporting Python 3.5.

* `silx.gui`:

* Added support for HDF5 external data (virtual and raw) (PR 3222)
* Added lazy update handling of OpenGL textures (PR 3205)
* Deprecated `silx.gui.plot.matplotlib` module (use `silx.gui.utils.matplotlib` instead) (PR 3158)
* Improved memory allocation by using already defined `fontMetrics` instread of creating a new one (PR 3239)
* Make `TextFormatter` compatible with `h5py`>=3 (PR 3253)
* Fixed `matplotlib` 3.3.0rc1 deprecation warnings (PR 3145)

* `silx.gui.colors.Colormap`:

* Added `Colormap.get|setNaNColor` to change color used for NaN, fix different NaN displays for matplotlib/openGL backends (PR 3143)
* Refactored PlotWidget OpenGL backend to enable extensions (PR 3147)
* Fixed use of `QThreadPool.tryTake` to be Qt5.7 compliant (PR 3250)

* `silx.gui.plot`:

* Added the feature to compute statistics inside a specific region of interest (PR 3056)
* Added an action to switch on/off OpenGL rendering on a plot (PR 3261)
* Added test for ROI interaction mode (PR 3283)
* Added saving of error bars when saving a plot (PR 3199)
* Added `ImageStack.clear` (PR 3167)
* Improved image profile tool to support `PlotWidget` item extension (PR 3150)
* Improved `Stackview`: replaced `setColormap` `autoscale` argument by `scaleColormapRangeToStack` method (PR 3279)
* Updated `3 stddev` autoscale algorithm, clamp it with the minmax data in order to improve the contrast (PR 3284)
* Updated ROI module: splitted into 3 modules base/common/arc_roi (PR 3283)
* Fixed `ColormapDialog` custom range input (PR 3153)
* Fixed issue when changing ROI mode while a ROI is being created (PR 3186)
* Fixed `RegionOfInterest` refresh when highlighted (PR 3197)
* Fixed arc roi shape: make sure start and end points are part of the shape (PR 3257)
* Fixed issue in `Colormap` `3 stdev` autoscale mode and avoided warnings (PR 3295)

* Major improvements of `PlotWidget`:

* Added `get|setAxesMargins` methods to control margin ratios around plot area (PR 3196)
* Added `PlotWidget.[get|set]Backend` enabling switching backend (PR 3255)
* Added multi interaction mode for ROIs (can be switched with a single click on an handle, or the context menu) (PR 3260)
* Added polar interaction mode for arc ROI (PR 3260)
* Added `PlotWidget.sigDefaultContextMenu` to allow to feed the default context menu (PR 3260)
* Added context menu to the selected ROI to remove it (PR 3260)
* Added pan interaction to ROI authoring (`select-draw`) interaction mode (PR 3291)
* Added support of right axis label with OpenGL backend (PR 3293)
* Added item visible bounds feature to PlotWidget items (PR 3223)
* Added a `DataItem` base class for items having a "data extent" in the plot (PR 3212)
* Added support for float16 texture in OpenGL backend (PR 3194)
* Improved support of high-DPI screen in OpenGL backend (PR 3203)
* Updated: Use points rather than pixels for marker size and line width with OpenGL backend (PR 3203)
* Updated: Expose `PlotWidget` colors as Qt properties (PR 3269)
* Fixed time serie axis for range < 2.5 microseconds (PR 3195)
* Fixed initial size of OpenGL backend (PR 3209)
* Fixed `PlotWidget` image items displayed below the grid by default (PR 3235)
* Fixed OpenGL backend image display with sqrt colormap normalization (PR 3248)
* Fixed support of shapes with multiple polygons in the OpenGL backend (PR 3259)
* Fixes duplicated callback on ROIs (there was one for each ROI managed created on the plot) (PR 3260)
* Fixed RegionOfInterest `contains` methods (PR 3336)

* `silx.gui.colors.plot3d`:

* Improved scene rendering (PR 3149)
* Fixed handling of transparency of cut plane (PR 3204)

* `silx.image`:

* Fixed slow `image.tomography.get_next_power()` (PR 3168)

* `silx.io`:

* Added support for HDF5 link preservation in `dictdump` (PR 3224)
* Added support for numpy arrays of `numbers` (PR 3251)
* Make `h5todict` resilient to issues in the HDF5 file (PR 3162)

* `silx.math`:

* Improved colormap performances for small datasets (PR 3282)

* `silx.opencl`:

* Added textures availability check (PR 3273)
* Added a warning when there is an issue in the Ocl destruction (PR 3280)
* Fixed Sift test on modern GPU (PR 3262)

* Miscellaneous:

* Added HDF5 strings: handle `h5py` 2.x and 3.x (PR 3240)
* Fixed `cython` 3 compatibility and deprecation warning (PR 3164, 3189)

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

Minor release:

* silx view application: Prevent collapsing browsing panel, Added `-f` command line option (PR 3176)

* `silx.gui`:

* `silx.gui.data`: Fixed `DataViews.titleForSelection` method (PR 3171).
* `silx.gui.plot.items`: Added `DATA_BOUNDS` visualization parameter for `Scatter` item histogram bounds (PR 3180)
* `silx.gui.plot.PlotWidget`: Fixed support of curves with infinite data (PR 3175)
* `silx.gui.utils.glutils`: Fixed `isOpenGLAvailable` function (PR 3184)

* Documentation:

* Update silx view command line options documentation (PR 3173)
* Update version number and changelog (PR 3190)

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

Bug fix release:

* `silx.gui.plot.dialog`: Fixed `ColormapDialog` custom range input (PR 3155)
* Build: Fixed cython 3 compatibility (PR 3163).
* Documentation: Update version number and changelog (PR 3156)

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

This version drops the support of Python 2.7 and Python <= 3.4.

* silx view application:

* Added support of compound data (PR 2948)
* Added `Close All` menu (PR 2963)
* Added default title to plots (PR 2979, 2999)
* Added a button to enable/disable file content sorting (PR 3132)
* Added support of a `SILX_style` HDF5 attribute to provide axes and colormap scale (PR 3092)
* Improved `HDF5TableView` information table to make text selectable and ease copy (PR 2903)
* Fixes (PR 2881, 2902, 3083)

* `silx.gui`:

* `silx.gui.colors.Colormap`:

* Added mean+/-3std autoscale mode (PR 2877, 2900)
* Added sqrt, arcsinh and gamma correction colormap normalizations (PR 3010, 3054, 3057, 3066, 3070, 3133)
* Limit number of threads used for computing the colormap (PR 3073)
* Reordered colormaps (PR 3137)

* `silx.gui.dialog.ColormapDialog`: Improved widget (PR 2874, 2915, 2924, 2954, 3136)
* `silx.gui.plot`:

* Major rework/extension of the regions of interest (ROI) (PR 3007, 3008, 3018, 3020, 3022, 3026, 3029, 3044, 3045, 3055, 3059, 3074, 3076, 3078, 3079, 3081, 3131)
* Major rework/extension of the profile tools (PR 2933, 2980, 2988, 3004, 3011, 3037, 3048, 3058, 3084, 3088, 3095, 3097)
* Added `silx.gui.plot.ImageStack` widget (PR 2480)
* Added support of scatter in `PixelIntensitiesHistoAction` (PR 3089, 3107)
* Added auto update of `FitAction` fitted data and range (PR 2960, 2961, 2969, 2981)
* Improved mask tools (PR 2986)
* Fixed `PlotWindow` (PR 2965) and `MaskToolsWidget` (PR 3125)

* `silx.gui.plot.PlotWidget`:

* Changed behaviour of `PlotWidget.addItem` and `PlotWidget.removeItem` to handle object items (previous behavior deprecated, not removed) and added `PlotWidget.addShape` method to add `Shape` items (PR 2873, 2904, 2919, 2925, 3120)
* Added support of uint16 RGBA images (PR 2889)
* Improved interaction (PR 2909, 3014, 3033)
* Fixed `PlotWidget` (PR 2884, 2901, 2970, 3002)
* Fixed and cleaned-up backends (PR 2887, 2910, 2913, 2957, 2964, 2984, 2991, 3023, 3064, 3135)

* `silx.gui.plot.items`:

* Added `sigDragStarted` and `sigDragFinished` signals to marker items and `sigEditingStarted` and `sigEditingFinished` signals to region of interest items (PR 2754)
* Added `XAxisExtent` and `YAxisExtent` items in `silx.gui.plot.items` to control the plot data extent (PR 2932)
* Added `ImageStack` item (PR 2994)
* Added `Scatter` item histogram visualization mode (PR 2912, 2923)
* Added `isDragged` method to marker items (PR 3000)
* Improved performance of colormapped items by caching data min/max (PR 2876, 2886)
* Improved `Scatter` item regular grid (PR 2918) and irregular grid (PR 3108) visualizations

* `silx.gui.qt`:

* Changed behavior of `QObject` multiple-inheritance (PR 3052)
* Limit `silxGlobalThreadPool` function to use 4 threads maximum (PR 3072)

* `silx.gui.utils.glutils`: Added `isOpenGLAvailable` to check the availability of OpenGL (PR 2878)
* `silx.gui.widgets`:

* Added `ElidedLabel` widget (PR 3110, 3111)
* Fixed `LegendIconWidget` (PR 3112)

* `silx.io`:

* Added support of signal dataset name-based errors to NXdata (PR 2976)
* Added `dicttonx` function and support of HDF5 attibutes in `dicttoh5` function (PR 3013, 3017, 3031, 3093)
* Fixed `url.DataUrl.path` (PR 2973)

* `silx.opencl`:

* Fixed issue with Python 3.8 (PR 3036)
* Disable textures for Nvidia Fermi GPUs for `convolution` (PR 3101)

* Miscellaneous:

* Requires fabio >= 0.9 (PR 2937)
* Fixed compatibility with h5py<v2.9 (PR 3024), cython 3 (PR 3034)
* Avoid deprecation warnings (PR 3104) from Python 3.7 (PR 3012), Python 3.8 (PR 2891, 2934, 2989, 2993, 3127), h5py (PR 2854, 2893), matplotlib (PR 2890), fabio (PR 2930) and numpy (PR 3129)
* Use `numpy.errstate` to ignore warnings rather than the `warnings` module (PR 2920)

* Build, documentation and tests:

* Dropped Python2 support (PR 3119, 3140) and removed Python 2 tests and packaging (PR 2838, 2917)
* Added debian 11/Ubuntu 20.04 packaging (PR 2875)
* Improved test environment (PR 2870, 2949, 2995, 3009, 3061, 3086, 3087, 3122), documentation (PR 2872, 2894, 2937, 2987, 3042, 3053, 3068, 3091, 3103, 3115) and sample code (PR 2978, 3130, 3138)
* Fixed Windows "fat binary" build (PR 2971)