Change Log¶

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