Read MMStack with Zarr v3#293
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The converter is still broken. |
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The converter also works now, merging. |
ziw-liu
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May 19, 2025
* wip * wip: 2025-02-27 * Undo reformatting * Remove unused imports * Fix miscellaneous failing tests. * Get rename_well working. * sort import * Read MMStack with Zarr v3 (#293) * use fsspec as a wrapper for ZarrTiffStore * update deprecated readers and tests * document the helper function * add back the binary check after a flag * use kwarg for file mode in reader * restore dtype attribute * restore opening zarr with dask * stringify path name * remove redundant dtype * add rich for zarr v3 print tree * skip tests that require ome-zarr-py * fix file list checking it doesn't matter what the order is * fix commas * stringify path names * `test_rename_well` no longer broken, remove mark * from_positions is actually broken this is not related to ome-zarr-py * write to stdout pallets/click#2874 * remove unused import * non-zero return code with no args pallets/click#1489 --------- Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
ziw-liu
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Jun 4, 2025
* wip * wip: 2025-02-27 * Undo reformatting * Remove unused imports * Fix miscellaneous failing tests. * Get rename_well working. * sort import * Read MMStack with Zarr v3 (#293) * use fsspec as a wrapper for ZarrTiffStore * update deprecated readers and tests * document the helper function * add back the binary check after a flag * use kwarg for file mode in reader * restore dtype attribute * restore opening zarr with dask * stringify path name * remove redundant dtype * add rich for zarr v3 print tree * skip tests that require ome-zarr-py * fix file list checking it doesn't matter what the order is * fix commas * stringify path names * detect ome key in reader * allow multiscales to not have version * wip: allow reading v0.5 images * normalize store path * update docstring * remove unused import * remove zarr-python synchronizer zarr-developers/zarr-python#1596 * allow empty zarr examples * add example json files * fixture for example v0.5 HCS dataset * unify ome container unwrapping * run PR tests for all target branches * test with absolute paths zarr-python 3.0.8 breakage * avoid big endian test cases * avoid yanked versions * fix zarr-python breakage * revert keyword argument name * fix version detection after zarr-python breakage * test with absolute path * Revert "allow empty zarr examples" This reverts commit 77146dd. * Test reading NGFF v0.5 with acquire-zarr * check binary values * simplify file mode switch Co-authored-by: Alan Liddell <alan.c.liddell@gmail.com> * remove redundant deletion --------- Co-authored-by: Alan Liddell <alan.c.liddell@gmail.com> Co-authored-by: Alan Liddell <aliddell@chanzuckerberg.com>
ziw-liu
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Aug 20, 2025
* wip * wip: 2025-02-27 * Undo reformatting * Remove unused imports * Fix miscellaneous failing tests. * Get rename_well working. * sort import * Read MMStack with Zarr v3 (#293) * use fsspec as a wrapper for ZarrTiffStore * update deprecated readers and tests * document the helper function * add back the binary check after a flag * use kwarg for file mode in reader * restore dtype attribute * restore opening zarr with dask * stringify path name * remove redundant dtype * add rich for zarr v3 print tree * skip tests that require ome-zarr-py * fix file list checking it doesn't matter what the order is * fix commas * stringify path names * `test_rename_well` no longer broken, remove mark * from_positions is actually broken this is not related to ome-zarr-py * enable tests against ome-zarr-py * from_positions is actually broken this is not related to ome-zarr-py * replace almost equal assertion in the ngff-zarr test * unskip ome-zarr-py tests * consolidate import paths * bump test requirement --------- Co-authored-by: Alan Liddell <alan.c.liddell@gmail.com> Co-authored-by: Alan Liddell <aliddell@chanzuckerberg.com>
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Fix #292 by wrapping the
ZarrTiffStore's storage mapping withfsspecso it can be used with zarr-python 3.Also fixed deprecated TIFF and Zarr readers.