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Reference Implementation: Python (0.3)#6

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balbasty wants to merge 108 commits intomainneuroscales/nifti-zarr:mainfrom impl/0.3/pythonneuroscales/nifti-zarr:impl/0.3/pythonCopy head branch name to clipboard

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Commits on Dec 16, 2023

• Move python implementation to its own branch

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• Remove pycache

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• WIP: python converter

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• minor change

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• Fixed coordinate transforms + pyramid

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• Add skimage dependency

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• Fix axes order

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• Neuroglancer example

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• Forgot to save latest fileserver

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• Latest notebook

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• Move python implementation to its own branch

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• Remove pycache

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Commits on Jan 2, 2024

• FIX(python): label pyramid (untested) + neurglancer notebook

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• DOC(python): add README

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• DOC(python): typo

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Commits on Jan 29, 2024

• FIX(setup.cfg): typo in extra_require

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• FIX(setup.cfg): typo still

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Commits on Jan 30, 2024

• FEAT(python): command-line tools

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• FIX(python/cli): no args as input

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• FIX(python/cli): put back args as input

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• FIX(python/cli): description -> help

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• FEAT(cli) (#4)

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Commits on Feb 13, 2024

• ENH(nii2zarr): dimensions T or C in ome.zarr are not required so let's get rid of them when we can

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Commits on Mar 26, 2024

• Sync

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• Merge branch 'impl/python_cli' into impl/python

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• Store header in zarr-array form instead of bin64 form, following draft 0.2 spec

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Commits on Mar 27, 2024

• Fix: for nifti header, chunk=len(header) (not 1)

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Commits on Apr 2, 2024

• ENH(nii2zarr): add --label flag

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Commits on Apr 4, 2024

• FIX(nii2zarr): chunk sizes not properly propagated + ENH(nii2zarr)

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• MERGE

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• FIX(nii2zarr): fix label mode

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Commits on Apr 11, 2024

• Option to only perform in-plane pyramid

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• FIX(nii2zarr): reverse dim indices in no-pyramid since volume is already permuted

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Commits on Sep 16, 2024

• Adapt JSON specification to JNifTI

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• Add unit test

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• No more adding axis when ndim=4

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• Use hdr_size to check nifti version

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• Comply with JNifTI Specification

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• Comply with JNifTI Specification

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• Refactor to get nifti header from byte array in one function

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• Remove the loop that decreases dimensions

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• Add magic string validation

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  d7e7d1a

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• typo

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• cleanup

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Commits on Sep 17, 2024

• Strip excessive control character

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• Strip excessive control character

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• Add nifti extension support

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• Use sizeof_hdr to check nifti version

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Commits on Sep 18, 2024

• Strip excessive \0 when loading extensions

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• Add unit test for extension support

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• Add JSON schema complied with JNifti

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• Add unit test for JSON schema with output

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• Change exception to warning when magic string mismatch in loading nifti files

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• Optimize extensions loading process

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• Add dimension check when converting zarr2nii

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• Use nibabel to load extensions from bytes instead of our own implementation

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• cleanup

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• rename testcases

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• Remove settings.json

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• Add unit test for checking the data preserves after convertion roundtrip

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• Switch axis when ndim=2

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• cleanup

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Commits on Sep 19, 2024

• Use orientation field in JNifti spec

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• Change fsl-related intent value to lower case

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• fix intent value error

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• Comment out unused loading extension function.

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• Determine swapping byte or not when writing extension blob based on guessed header endian

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• Let datatype compatible with JNifti in JSON and convert it when interpreting the binary values

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• Check axis order use mutlscales axes in group attribute instead of the arrtibute from each level

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• Change named tuple datatype from tuple to array

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• Revert to tuple as list cannot be key in dict

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• Fix byteorder based on the header byteorder

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• Fix byteorder based on the header byteorder

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• Change extension name for testing file

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• Merge pull request #5 from calvinchai/impl/0.3/python

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• Refactor functions determines header version

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• Fix orientation field in JSON validation

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• Change FSL-related intent string to small case

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• Refactor

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• Refactor

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• Fix orientation field in JSON

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• cleanup

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• Revert "cleanup"

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• Revert "Fix orientation field in JSON"

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Commits on Sep 23, 2024

• cleanup

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  7cdf40f

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• fix datatype when writing to zarr

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• Use zarr spec when write header info to zarr

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• Fix extensions byte order

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Commits on Oct 3, 2024

• Add debug info when nifti data does not present in a zarr archive

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• Remove reference text

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• Update XFORM field according to JNIfTI update

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• Add TODO for Orientation field

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• Add NIFTIExtension field in JSON

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Commits on Oct 4, 2024

• Fix Byte Order

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• Remove control characters in JSON values

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• Fix errors when dtype is tuple, rgb and rgba data should work but there is no test

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Commits on Oct 7, 2024

• Add unit tests for endianess preservation

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• Rename json validation test class

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• Optimize process handling endianness

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Commits on Oct 15, 2024

• Fix type and cleanup

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Commits on Oct 17, 2024

• Change the default number of generated levels and add unit tests

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• cleanup

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• Add general conversion test

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• Fix typo

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Commits on Oct 24, 2024

• FIX: do not use structured numpy representation for simple (non RGB) types

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• Add unit test and test data for checking nii2zarr and zarr2nii always produces same result

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Commits on Oct 25, 2024

• Merge branch 'impl/0.3/python' into impl/0.3/python

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• Merge pull request #8 from calvinchai/impl/0.3/python

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