Fix offset #8
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Fix offset #8
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…nput image's chunk sizes
…maller than patch sizes
…ow overlapping patches extraction
…hes of the defined shape
…scales than image scale
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Aug 29, 2024
* Integration of CI/CD practices (#2) * Integration CI/CD pipeline to this project * Corrected github actions test workflow * Install the package before test it * Created empty __init__.py inside tests to record coverage * Changed name of sample_images_generator.py to utils.py for clarity * Updated test workflow to use a non-supported workaround for the multiple OpenMP runtime library issue * Updated test workflow to report coverage * Moved non-pytorch compatibility test to last position * Added test for datasets with zero expected samples * Changed PatchSampler to take as base the patche size instead of the input image's chunk sizes * Reverted change in the computation when masks elements are relative smaller than patch sizes * Fixed spatial chunk size computation when patch sizes are grater than the chunk size * Fixed missing patches from chunks smaller than the input image chunk size * Padding and stride added to PatchSampler and ImageBase classes to allow overlapping patches extraction * Added tests for stride and pad parameters of PatchSampler class * Fixed patch slices generation in PatchSampler to always retrieve patches of the defined shape * Standardized patch sampling method to handle smaller and bigger mask scales than image scale * Added example notebook to documentation * Fix offset (#8) * Changed PatchSampler to take as base the patche size instead of the input image's chunk sizes * Reverted change in the computation when masks elements are relative smaller than patch sizes * Fixed spatial chunk size computation when patch sizes are grater than the chunk size * Fixed missing patches from chunks smaller than the input image chunk size * Padding and stride added to PatchSampler and ImageBase classes to allow overlapping patches extraction * Added tests for stride and pad parameters of PatchSampler class * Fixed patch slices generation in PatchSampler to always retrieve patches of the defined shape * Standardized patch sampling method to handle smaller and bigger mask scales than image scale * Added example notebook to documentation * Fixed incorrect sampling of patches on masked regions * Updated documentation for version 0.0.2 * Updated tests/utils.py to use an example image from a public S3 bucket
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This fixes the incorrect sampling on masked regions mentioned in #7 by considering the chunk location as offset for mask coordinates.
This also corrects a typo in the example notebook for clarity of the documentation.