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@freeman-lab freeman-lab released this 04 Nov 06:52
v0.4.1
bd268aa

We are happy to announce the 0.4.1 release of Thunder. This is a maintenance / bug fix release.

The focus is ensuring consistent array indexing across all supported input types and internal data formats. For 3D image volumes, the z-plane will now be on the third array axis (e.g. ary[:,:,2]), and will be in the same position for Series indices and the dims attribute on Images and Series objects. Visualizing image data by matplotlib’s imshow() function will yield an image in the expected orientation, both for Images objects and for the arrays returned by a Series.pack() call. Other changes described below.

Changes and Bug Fixes

  • Handling of wildcards in path strings for the local filesystem and S3 is improved.
  • New Data.astype method for converting numerical type of values.
  • A dtype parameter has been added to the ThunderContext.load* methods.
  • Several exceptions thrown by uncommon edge cases in tif handling code have been resolved.
  • The Series.pack() method no longer automatically casts returned data to float16. This can instead be performed ahead of time using the new astype methods.
  • tsc.convertImagesToSeries() did not previously write output files with tif file input when shuffle=True.
  • A ValueError thrown by the random sampling methods with numpy 1.9 has been resolved (issue #41).
  • The thunder-ec2 script will now generate a ~/.boto configuration file containing AWS access keys on all nodes, allowing workers to access S3 with no additional configuration.
  • Test example data files are now copied out to all nodes in a cluster as part of the thunder-ec2 script.
  • Now compatible with boto 2.8.0 and later versions, for EC2 deployments (issue #40).
  • Fixed a dimension bug when colorizing 2D images with the indexed conversion type.
  • Fixed an issue with optimization approach being misspecified in colorization.

Thanks

  • Joseph Naegele: reporting path and data type bugs
  • Allan Wong: reporting random sampling bug
  • Sung Soo Kim: reporting colorization optimization issue
  • Thomas Sainsbury: reporting indexed colorization bug

Contributions

Thanks very much for your interest in Thunder. Questions and comments can be set to the mailing list.

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