Pyshepseg Release Notes

Version 2.0.5 (2026-01-28)

New Features

  • Support for RatZarr format RAT files for per-segment statistics columns (#83, #84, #85)

  • Built-in read worker support in per-segment statistics (i.e. no dependency on RIOS) (#86, #87, #88)

Deprecations

  • Both calcPerSegmentStatsRIOS and calcPerSegmentSpatialStatsRIOS are now deprecated, to be removed at a later date.

Version 2.0.4 (2025-10-17)

New Features

  • Integrated concurrency for tiled segmentation, supporting threads within process or AWS Fargate segmentation workers (#75, #76, #77, #79, #80). See SegmentationConcurrencyConfig for usage details. Eventually this will make the AWSBatch-based concurrency obsolete, but there may be more to do before then.

  • Improved flexibility of AWSBatch-based concurrency for per-segment stats (#69, #71, #72, #74).

Bug Fixes

  • Only open segmentation file as update when necessary, otherwise read-only (#73).

  • Avoid using repr on numpy scalars, as numpy-2.0 changed its behaviour too radically (#67).

Version 2.0.3 (2024-12-06)

New Features:

  • Support numpy 2.0

  • Use multiple RIOS readworkers while calculating statistics if recent RIOS available.

Bug fixes:

  • Allow GDAL dataset to be returned from doTiledShepherdSegmentation and histogram to be written to file by default.

  • More functions now support receiving a GDAL dataset as input

  • Add –noremove option to tiling jobs

Version 2.0.2 (2024-06-12)

New Features:

  • Setup is now fully controlled by pyproject.toml, with no setup.py

  • Add support for spatial stats within AWS Batch

  • Add –tileprefix in AWS Batch so all temporary S3 files are unique. This allows multiple concurrent runs.

Bug fixes:

  • Add guard against subsampling >100% of the data

  • Fix console_scripts syntax

Version 2.0.1 (2024-05-21)

New Features:

  • Many fixes and improvements to the AWS Batch support. Most notably, statistics can now be calculated before the “stitch” job finishes.

Bug Fixes:

  • Fix tiling code with recent scipy (>1.9.0).

Version 2.0.0 (2023-01-04)

New Features:

  • A test script (pyshepseg_runtests) that can be run to confirm the install is working as intended.

  • Split up the parts of doTiledSegmentation() so they can be run in parallel.

  • Check syntax with flake8 and run test script on new PRs in github.

  • Use entry points for the command line scripts rather than creating our own. Should make running on Windows easier.

  • Added ability to calculate “spatial” statistics on the segments.

  • Use numpydoc for creating Sphinx documentation.

  • Subset functionality is now in a separate “subset” module.

  • Statistics functionality now in a new “tilingstats” module.

Version 1.1.0 (2021-12-24)

Bug Fixes:

  • Guard against Float images being used for calculating statistics as the results were undefined.

  • Added other checks to ensure that the image having statistics calculated matches spatially with the segmented image.

  • Add the ability to add GDAL driver creation options for the output image of a segmentation.

  • Create the histogram column as a Real to match common GDAL usage.

  • Add checks to ensure histogram and colour columns aren’t created if they already exist.

  • Ensure the first segment of each RAT Page isn’t initally set to ‘complete’ before use.

  • Raise error if any incomplete RAT Pages are found during processing as this indicates the RAT contains more entries than unique values in the image.

  • When calculating statistics, open the file that the stats are calculated on in read only mode so /vsi filesystems can be used.

  • Increase default overlap for tiled segmentation as the old value could result in inconsistencies and segments that were missing from the image (but in the RAT).

  • Remove dependency on distutils which is now deprecated.

New Features:

  • New Sphinx documentation located at https://www.pyshepseg.org.

  • Added a new subsetImage() function to the tiling module that subsets an already segemented image and collapses the RAT so there are no redundant entries. Also added a test_pyshepseg_subset.py command line program to test this functionality.

  • Exclude any nodata pixels values during statistics calculation.

Version 1.0.0 (2021-04-08)

New Features:

  • Added pyshsep.tiling module to allow processing of large rasters in a memory-efficient manner.

  • Added pyshepseg.tiling.calcPerSegmentStatsTiled() function to enable calculation of per-segment statistics in a fast and memory-efficient manner.

  • Added pyshepseg.utils.writeColorTableFromRatColumns() function, to add colour table calculated from per-segment statistics

Version 0.1

Initial implementation of segmentation algorithm. Other facilities will be added as we get to them.