silx

First release candidate of v0.13.0

https://pypi.org/project/silx/0.13.0b2/

• silx view application:

  • Improved HDF5TableView information table to make text selectable and ease copy (PR #2903)
  • Fixed expand/collapse tree actions (PR #2881)
  • Fixed display of chunk infomation (PR #2902)

• silx.gui:

  • silx.gui.colors.Colormap: Added mean+/-3*std autscale mode (PR #2877, #2900)

  • silx.gui.utils.glutils: Added isOpenGLAvailable to check the availability of OpenGL (PR #2878)

  • silx.gui.dialog.ColormapDialog: Improved widget (PR #2874, #2915, #2924)

  • silx.gui.plot:

    • silx.gui.plot.PlotWidget:

      • Renamed PlotWidget.addItem to PlotWidget.addShape to add Shape items (PR #2873)
      • Change behavior of PlotWidget.addItem and PlotWidget.removeItem to handle object items (previous behavior deprecated, not removed) (PR #2904, #2919)
      • Added pan with middle button pressed (PR #2909)
      • Fixed avoid display of offset for axis ticks (PR #2884)
      • Fixed crosshair position offset with right axis on (PR #2901)
      • Fixed image picking inconsitency between backends (PR #2913)
      • Fixed image profile window position being reset each time data is updated (PR #2933)
      • Cleaned-up backends (PR #2887, #2910)

    • 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)
      • Improved performance of colormapped items by caching data min/max (PR #2876, #2886)
      • Improved Scatter item regular grid visualization to be more resilient (PR #2918)

• Miscellaneous:

  • Requires fabio >= 0.9 (PR #2937)
  • Avoid deprecation warnings from Python 3.8 (PR #2891, #2934), h5py (PR #2854, #2893), matplotlib (PR #2890) and fabio (PR #2930)
  • Use numpy.errstate to ignore warnings rather than the warnings module (PR #2920)

• Build, documentation and tests:

  • Added debian 11/Ubuntu 20.04 packaging (PR #2875)
  • Removed Python 2 tests and packaging (PR #2838, #2917)
  • Improved test environement (PR #2870) and documentation (PR #2872, #2894, #2937)

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)

First release candidate for v0.12.0

• 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.

Bug fix release

0.10.0: 2019/02/19

• 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.

• Plot:

  • Fix logarithmic axes, broken by new matplotlib version 2.1.0.
  • Fix axis limits changed signal, not emitted with matplotlib 1.5.x and 2.0.x
    when the widget is resized.
  • Support displaying float128 data with matplotlib < 2.1.0.
  • Fix minor bugs with the crosshair cursor and the legends widget.

• Update documentation on Zenodo DOI and Debian packages installation.

• Fix the Debian packaging script for Ubuntu distributions.

0.6.0: 2017/10/06

• 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: new wrapping modes

• 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))

• Image: Add tomography utils: phantomgenerator, calc_center_corr, calc_center_centroid

• Commands:

  • silx view:

    • Add command line option --use-opengl-plot, --debug
    • 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

• 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.

• Added OpenCL management
• Added isosurface marching cubes
• Added sift algorithm for image alignement
• Added octaveh5 module to insure communication between octave and python using HDF5 file
• Added silx.utils module containing weakref and html-escape
• Added silx.sx for flat import (helper for interactive shell)
• Added HDF5 load API (supporting Spec files) to silx.io.utils module
• Added SpecFile support for multiple MCA headers
• Added HDF5 TreeView
• Added FitManager and FitWidget to the silx.math.fit module
• Added ThreadPoolPushButton to silx.gui.widgets
• Added getDataRange function to plot widget
• Added loadUi, Slot and Property to qt.py
• Added SVG icons and support
• Added examples for plot actions, HDF5 widget, helper widgets, converter from Spec to HDF5
• Added tutorials for plot actions, spech5, spectoh5, sift and fitmanager
• Improve right axis support for plot widget
• Improve mask tool
• Refactoring widgets constructor: first argument is now the parent widget
• Change plot documentation and add missing module to the documentation