Change Log

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