Silx

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

This is the first version of `silx` supporting `PySide6` (for `Qt6`) and using `pytest` to run the tests.

* `silx view`:

* Added Windows installer generation (PR 3548)
* Updated 'About' dialog (3547, 3475)
* Fixed: Keep curve legend selection with changing dimensions (PR 3529)
* Fixed: Increase max number of opened file at start-up (PR 3545)

* `silx.gui`:

* Added PySide6 support (PR 3486, 3528, 3479, 3542, 3549, 3478, 3481):
* Removed support of PyQt4 / Pyside (PR 3423, 3424, 3480, 3482)
* `silx.gui.colors`:

* Fixed duplicated logs when colormap vmin/vmax are not valid (PR 3471)

* `silx.gui.plot`:

* `silx.gui.plot.actions`:

* `silx.gui.plot.actions.fit`:

* Updated behaviour of fitted item auto update (PR 3532)

* `silx.gui.plot.actions.histogram`:

* Enhanced: Allow user to change histogram nbins and range (PR 3514, 3514)
* Updated `PixelIntensitiesHistoAction` to use `PlotWidget.selection` (PR 3408)
* Fixed issue when the whole image is masked (PR 3544)
* Fixed error on macOS 11 with 3D display in `silx view` (PR 3544)

* `silx.gui.plot.CompareImages`:

* Fixed `colormap`: avoid forcing vmin and vmax when not in 'HORIZONTAL_LINE' or 'VERTICAL_LINE' mode (PR 3510)

* `silx.gui.plot.items`:

* Added 'image_aggregated.ImageDataAggregated': item allowing to aggregate image data before display (PR 3503)
* Fixed `ArcROI.setGeometry` (fix 3492)

* `silx.gui.plot.ImageStack`:

* Enhanced management of the `animation thread` (PR 3440, PR 3441)

* `silx.gui.plot.ImageView`:

* Added action to show/hide the side histogram (PR 3488)
* Added 'resetzoom' parameter to 'ImageView.setImage' (PR 3488)
* Added empty array support to 'ImageView.setImage' (PR 3530)
* Added aggregation mode action (PR 3536)
* Added support of RGB and RGBA images (PR 3487)
* Updated 'imageview' example with a '--live' option (PR 3488)
* Fixed profile window, added `setProfileWindowBehavior` method (PR 3457)
* Fixed issue with profile window size (PR 3455)

* `silx.gui.plot.PlotWidget`:

* Fixed update of `Scatter` item binned statistics visualization (PR 3452)
* Fixed OpenGL backend memory leak (PR 3453)
* Enhanced: Optimized scatter when rendered as regular grid with the OpenGL backend (PR 3447)
* Enhanced axis limits management by the OpenGL backend (PR 3504)
* Enhanced control of repaint (PR 3449)
* Enhanced text label background rendering with OpenGL backend (PR 3565)

* `silx.gui.plot.PlotWindow`:

* Fixed returned action from 'getKeepDataAspectRatioAction' (PR 3500)

* `silx.gui.plot3d`:

* Fixed picking on highdpi screen (PR 3550)
* Fixed issue in parameter tree (PR 3550)

* `silx.io`:

* Added read support for FIO files (PR 3539) thanks to tifuchs contribution
* `silx.io.dictdump`:

* Fixed missing conversion of the key (PR 3505) thanks to rnwatanabe contribution
* Extract update modes list to a constant global variable (PR 3460) thanks to jpcbertoldo

* `silx.io.convert`:

* Enhanced `write_to_h5`: `infile` parameter can now also be a HDF5 file as input (PR 3511)

* `silx.io.h5py_utils`:

* Added support of `locking` argument from the h5py.File when possible (PR 3554)
* Added log a critical message for unsupported versions of libhdf5 (PR 3533)

* `silx.io.spech5`:

* Enhanced: Improve robustness (PR 3507, 3463)

* `silx.io.url`:

* Fixed `is_absolute` in the case the `file_path()` returns None (PR 3437)

* `silx.io.utils`:

* Added 'silx.io.utils.visitall': provides a visitor of all items including links that works for both `commonh5` and `h5py` (PR 3511)

* `silx.math`:

* `silx.math.colormap`:

* Added `apply_colormap` function (PR 3525)
* Enhanced `cmap` error messages (PR 3522)

* `silx.opencl`:

* Added description of compute capabilities for Ampere generation GPU from Nvidia (PR 3535)
* Added doubleword OpenCL library (PR 3466, PR 3472)

* Miscellaneous:

* Enhanced: Setup the project to use `pytest` (PR 3431, 3516, 3526)
* Enhanced: Minor test clean up (PR 3515, 3508)
* Updated project structure: move `silx` sources in `src/silx` (PR 3412)
* Fixed 'run_test.py --qt-binding' option (PR 3527)
* Fixed support of numpy 1.21rc1 (PR 3476)
* Removed `six` dependency (PR 3483)

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

Minor release:

* `silx.io`:

* `silx.io.spech5`: Enhanced robustness for missing positioner values (PR 3477)
* `silx.io.url`: Fixed `DataUrl.is_absolute` (PR 3467)

* `silx.gui`:

* Fixed naming of some loggers (PR 3477)
* Fixed assert on `ImageStack` when length of urls > 0 (PR 3491)
* `silx.gui.plot`: Fixed `ArcROI.setGeometry` (PR 3493)

* `silx.opencl`: Expose the double-word library and include it in tests (PR 3466)
* Misc: Fixed support of `numpy` 1.21rc1 (PR 3477)

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

Minor release:

* silx.gui.plot.PlotWidget: Fixed `PlotWidget` OpenGL backend memory leak (PR 3448)
* silx.gui.plot.ImageView:

* Fixed profile window default behavior (PR 3458)
* Added `setProfileWindowBehavior` method (PR 3458)

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

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)