Change Log

0.11.0: 2019/07/03

• 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.

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

0.9.0: 2018/10/23

• 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

0.8.0: 2018/07/04

• 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

0.7.0: 2018/02/27

• 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.

0.6.0: 2017/10/02

• 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.

0.5.0: 2017/05/12

• 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.

0.4.0: 2017/02/01

• Adds plot3D package (include visualization of 3-dimensional scalar fields)

• Adds data viewer (it can handle n-dimensional data)

• Adds StackView (ex. Visualization of stack of images)

• Adds depth profile calculation (ex. extract profile of a stack of images)

• Adds periodic table widget

• Adds ArrayTableWidget

• Adds pixel intensity histogram action

• Adds histogram parameter to addCurve

• Refactoring. Create silx.gui.data (include widgets for data)

• Refactoring. Rename utils.load as silx.io.open

• Changes active curve behavior in Plot. No default active curve is set by default

• Fit Action. Add polynomial functions and background customization

• PlotWindow. Provide API to access toolbar actions

• Handle SPEC, HDF5 and image formats through an unified API

• hdf5widget example. Inspect and visualize any datasets

• Improves mask tool

• Deprecates PlotWindow dock widgets attributes in favor of getter methods

0.3.0: 2016/10/12

• Adds OpenCL management

• Adds isosurface marching cubes

• Adds sift algorithm for image alignement

• Adds octaveh5 module to insure communication between octave and python using HDF5 file

• Adds silx.utils module containing weakref and html-escape

• Adds silx.sx for flat import (helper for interactive shell)

• Adds HDF5 load API (supporting Spec files) to silx.io.utils module

• Adds SpecFile support for multiple MCA headers

• Adds HDF5 TreeView

• Adds FitManager to silx.math.fit and FitWidget to silx.gui.fit

• Adds ThreadPoolPushButton to silx.gui.widgets

• Adds getDataRange function to plot widget

• Adds loadUi, Slot and Property to qt.py

• Adds SVG icons and support

• Adds examples for plot actions, HDF5 widget, helper widgets, converter from Spec to HDF5

• Adds tutorials for plot actions, spech5, spectoh5, sift and fitmanager

• Improves right axis support for plot widget

• Improves mask tool

• Refactors widgets constructor: first argument is now the parent widget

• Changes plot documentation and add missing module to the documentation

0.2.0: 2016/07/12

• Adds bilinear interpolator and line-profile for images to silx.image

• Adds Levenberg-Marquardt least-square fitting algorithm to silx.math.fit

• Histogramnd changed to become a class rather than a function, API and return values changed

• Adds HistogramndLut, using a lookup table to bin data onto a regular grid for several sets of data sharing the same coordinates

• Adds legend widget and bottom toolbar to PlotWindow

• Adds a line-profile toolbar to PlotWindow

• Adds ImageView widget with side histograms and profile toolbar

• Adds IPython console widget, to be started from PlotWindow toolbar

• Adds Plot1D widget for curves and Plot2D widget for images

• Adds ROI widget for curves in PlotWindow

• Adds a mask widget and toolbar to plot (2D)

• Renames silx.io.dicttoh5 to silx.io.dictdump

• Adds configuration dictionary dumping/loading to/from JSON and INI files in silx.io.configdict

• Adds specfile wrapper API compatible with legacy wrapper: silx.io.specfilewrapper

• Transposes scan data in specfile module to have detector as first index

• Set up nigthly build for sources package, debian packages (http://www.silx.org/pub/debian/) and documentation (http://www.silx.org/doc/)

0.1.0: 2016/04/14

• Adds project build, documentation and test structure

• Adds continuous integration set-up for Travis-CI and Appveyor

• Adds Debian packaging support

• Adds SPEC file reader, SPEC file conversion to HDF5 in silx.io

• Adds histogramnd function in silx.math

• Adds 1D, 2D plot widget with a toolbar, refactored from PyMca PlotWindow in silx.gui.plot