Release notes¶
v0.5¶
This is a major release recommended for all users. Your existing code to open files may need to be edited slightly – see the first change listed below.
API: all readers do not support the keyword arguments
process_func
,dtype
andas_grey
anymore. Please consult the documentation on Pipelines on how to convert videos. (see Pipelines) (PR 250)New built-in
as_grey
pipeline for convenient conversion to greyscale (PR 305)New built-in
crop
pipeline for making a cropped sequence (PR 247)Major speedup for random access in PyAVReaderIndexed (PR 340)
Bumped Bioformats version to 6.5.x (PR 301)
Added instructions for installing/updating Bioformats (PR 346)
Enhanced support for metadata in the CINE format (PR 317)
Enhanced documentation for PyAV video support (PR 334)
Added multidimensional capabilities to ImageIOReader (see Multidimensional Readers) (PR 320)
Added support for nd2reader as alternative reader for Nikon nd2 files (PR 272)
Removed fallback to scipy.misc.imread, which was removed from scipy (PR 359)
Fixed compatibility with PyAV 0.4.0 and newer (PR 300)
Fixed compatibility and bugs in PyAV export (PR 283, PR 313)
Fixed opening of PyAV videos with audio (PR 322)
Fixed compatibility with newer versions of tifffile (PR 314, PR 339)
Fixed response to missing ImageIO (PR 333)
v0.4¶
API: N-dimensional readers now smartly use
get_frame
methods; depending on thebundle_axes
settings, the reader optimizes whichget_frame
methods is optimal to use. Readers that derive fromFramesSequenceND
will need to callFramesSequenceND.__init__()
on initialization, and also will need to registerget_frame
methods using_register_get_frame(method, axes)
. (PR 227)API: Swap elements of
frame_shape
inSpeStack
to match frames’shape
. (PR 241)API: Swap elements of
frame_shape
inPyAVVideoReader
to match frames’shape
. (PR 251)API: Reimplement the
PyAVVideoReader
(or:Video
) into a reader that uses the frame timestamps and reader frame rate to compute the frame index. The new reader is namedPyAVReaderTimed
and the namesPyAVVideoReader
andVideo
refer to it. For the case when the video misses timestamps, the old implementation is available underPyAVReaderIndexed
.API: The video exporter (
export
) takes more arguments. The argument'format'
has been renamed to'pixel_format'
, while'format'
now refers to the container format. (PR 257)Fixed filename sorting when list is provided explicitely to
ImageSequence
(PR 252)Fixed
plot_to_frame
withsavefig.bbox == 'tight'
(PR 248)Added a reader that wraps ImageIO
ImageIOReader
(PR 233)Added a reader that wraps MoviePy
MoviePyReader
(PR 233)Added a reader for single images
ImageReader
andImageReaderND
(PR 249)Added a reader that stacks readers into a multidimensional reader
ReaderSequence
(PR 249)Added a video exporter based on MoviePy (PR 233)
Added
BioformatsReader.metadata.fields
that lists all metadata fields. (PR 230)
v0.3.4¶
API: Swap elements of
frame_shape
inSpeStack
to match frames’shape
.
v0.3.3¶
Fix compatibility with Pillow v0.3.0 (PR 204)
API:
plot_to_frame
andplots_to_frame
now takefig_size_inches
andbbox_inches
as keyword arguments instead of passing on all keyword arguments toimsave
(PR 206)Fix zipfile handling in Py3 (PR 199)
Fix CINE reader for Py2 (PR 219)
Support non-monochrome and packed-bits images in NorpixSeq (PR 218)
Update documentation
Update slicerator dependency to v0.9.7 (fixes pipeline nesting)
Update bioformats version to v5.1.7 (PR 224)
v0.3.2¶
Bug fixes
Build fixes and fewer required deps
v0.3.1¶
Fix build-related mistakes in v0.3.0.
v0.3.0¶
Refactor the slicing logic into a separate package, slicerator.
Extend the slicing logic to allow nested lazy slicing.
Add pipeline feature; deprecate process_func.
Support multispectral and multidimensional images.
Add Norpix reader.
v0.2.2¶
This is a simple maintenance release, introducing no functionality changes. The packaging and installation are simplified by adopting tifffile as a dependency rather than directly including the source PIMS.
Henceforth, to install PIMS on any platform, we recommend
conda install -c soft-matter pims
, but pip install pims
is also supported.
v0.2.1¶
Use PyAV for handling video files
Ships with Christoph Gohlke’s tifffile
Added support for .cine files
Added prototype of universal open function which tries to guess the correct class to use to handle a given file based on the extension
Added ability to create an ImageSequence from a list of paths