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Author SHA1 Message Date
w.pomp 5ad9a44ecd - add doc strings 2026-08-07 17:00:28 +02:00
w.pomp b950f4a39d - silence java warnings 
- renam View -> Imread in Python
 2026-08-07 15:26:12 +02:00
w.pomp a0d2359e55 - various fixes 2026-08-07 15:14:16 +02:00
w.pomp e4de76f26c - as_array_dyn lru caching 2026-08-04 18:29:56 +02:00
w.pomp 9f5f9debc5 - frame caching 2026-08-04 14:35:24 +02:00
w.pomp c975b1943f - add __len__ and axes to PyShape stub 2026-07-24 10:29:15 +02:00
w.pomp c16e71bf30 - add __len__ to PyShape 2026-07-22 17:31:36 +02:00
w.pomp b063a63869 - fixing PyShape 2026-07-22 16:59:04 +02:00
w.pomp 1471ec00af - fixing PyShape 2026-07-22 16:13:54 +02:00
w.pomp 0ed70edd3e - small updates 2026-07-22 15:43:12 +02:00
w.pomp a5ec4125f9 - small cosmetic changes 2026-07-22 13:40:27 +02:00
w.pomp 0d347b7967 - suppress most java warnings 2026-07-14 12:49:16 +02:00
w.pomp 25d2070ac3 - better python errors 2026-07-13 17:53:52 +02:00
w.pomp 916d301f1b - open tiff seq folders with bioformats_java by finding the first tiff recursively 
- make PyView serializable by skipping the ome field
- fix python tests
 2026-07-13 15:16:10 +02:00
w.pomp 0ce1187a43 - metadata 2026-07-13 13:41:02 +02:00
w.pomp ff7cd562af - implement shape in Rust 
- implement more readers
- fix downloading of bioformats jar
- (mostly) compatible with python version
 2026-07-13 13:40:34 +02:00
w.pomp 705ca16379 start using semver, fix doc.rs issue 2026-02-23 19:54:58 +01:00
Wim Pomp d2c725440c - bump ome-metadata dependency 
- add extract-ome cli subcommand
 2026-01-04 17:03:14 +01:00
Wim Pomp b1f8dd998b - test ome reading from some example files 2026-01-04 15:13:35 +01:00
Wim Pomp 8db873c425 - bump ome-metadata dependency 
- make Reader::new error instead of panic if file cannot be read
 2026-01-04 15:09:23 +01:00
Wim Pomp 3c14168878 - implement custom error types 
- less restrictive dependency versions
- some extra features and bugfixes for movie writing
- make python tests work again
 2026-01-04 13:59:57 +01:00
Wim Pomp 3dc8e6af04 - bump bioformats to 8.3.0 
- rust: command line binary, save as mp4, save as tiff, ome metadata, more methods for View, bugfixes, less unsafe code
- python: ome as dict
 2025-08-21 19:45:02 +02:00
Wim Pomp 24af64ac7e - make modules public 2025-04-27 20:14:57 +02:00
Wim Pomp 5195ccfcb5 - implement sliced views, including min, max, sum and mean operations 2025-04-27 20:07:49 +02:00
Wim Pomp 87e9715f97 - remove all readers but bioformats 
- open folder with sequence
 2025-02-19 21:28:59 +01:00
Wim Pomp 2247a994be - change to MIT license 
- thread local image reader instances
- add keywords and categories
- add python dependencies
- README
 2025-02-17 19:53:34 +01:00
Wim Pomp e5c6361086 Merge remote-tracking branch 'origin/rs' into rs 2025-02-16 23:03:55 +01:00
Wim Pomp 83ea9722f6 - some workarounds to get jars and shared libs in the right place for python 
- add most ndbioimage python code and use rs code as bfread
 2025-02-16 23:03:48 +01:00
Wim Pomp 372b816f93 - some workarounds to get jars and shared libs in the right place for python 
- add most ndbioimage python code and use rs code as bfread
 2025-02-16 23:02:40 +01:00
Wim Pomp fefdd6448b - added ome_xml method 
- some pyo3 methods
 2025-02-08 20:22:45 +01:00
Wim Pomp a3dfc075a8 - do not try java things when building for docs.rs 2025-02-03 16:27:24 +01:00
Wim Pomp 15eae99272 - do not try java things when building for docs.rs 2025-02-03 16:22:49 +01:00
Wim Pomp b612d33a35 - do not try java things when building for docs.rs 2025-02-03 16:17:14 +01:00
Wim Pomp 3c22cf743a - rename ndbioimage 2025-02-03 15:52:03 +01:00
Wim Pomp dd5e2d393f - exclude tests on publish 2025-02-03 15:48:27 +01:00
Wim Pomp 45aa72d14c - exclude tests on publish 2025-02-03 15:45:29 +01:00
Wim Pomp 1aad79b441 - start rust rewrite 2025-02-03 15:41:25 +01:00
Wim Pomp 3db6dc8ee1 - start rust rewrite 2025-02-03 15:33:32 +01:00
Wim Pomp 4a6a15686c - slightly more robust czi metadata reading 2025-01-29 17:16:20 +01:00
Wim Pomp c34b52cb55 - bugfix: reading wrong frame in some cases when opened with custom axes argument 
- some more try except in czi metadata reading
- bugfix: Pos pattern in seqread
 2025-01-24 15:53:51 +01:00
Wim Pomp 00abb8a684 Merge remote-tracking branch 'origin/main' 
# Conflicts:
#	pyproject.toml
 2025-01-08 13:20:22 +01:00
Wim Pomp 8b280b3061 - make cache size configurable 2025-01-08 13:18:38 +01:00
Wim Pomp f75e1925b8 - make cache size configurable 2025-01-08 13:16:34 +01:00
Wim Pomp e6d5ec0928 - bump tiffwrite 2024-10-17 17:18:26 +02:00
Wim Pomp 814bb0da85 - slice notation for time argument on command line 
- fix seqread can_open
 2024-09-24 13:23:04 +02:00
Wim Pomp eea24e17ef - add metaseriesread 
- add function to get all positions/series in a file
- make sure mp4 dimensions are even
 2024-09-13 11:48:38 +02:00
Wim Pomp af600633cf - main: not parallel anymore (for now), make batch processing easier. 2024-09-11 14:23:41 +02:00
Wim Pomp be2c519951 - transforms bugfix: swap xy 
- save as movie: progress bar
- swap command line argument out for --write
 2024-07-11 10:13:19 +02:00
Wim Pomp 1d2cc951fa - save as mp4 or mkv movie 2024-06-04 19:11:40 +02:00
Wim Pomp e257ec326d - catch 0 timeinterval 
- better error handling in JVM
 2024-05-30 11:02:38 +02:00
Wim Pomp ff3a43d3c9 - OmeCache bugfix 2024-05-13 11:41:13 +02:00
Wim Pomp f70128e426 - czi ome bug fix, forgot channels, planes and annotations 2024-04-29 13:20:13 +02:00
Wim Pomp c13ae9d4ad - Make Imread __init__ signature more compatible with typing. 
- Support czi metadata version 1.1.
 2024-04-24 17:11:58 +02:00
Wim Pomp 8bf1646736 - Remove support for python <= 3.9. 2024-04-12 17:38:38 +02:00
Wim Pomp 1bfac6f26e - Some typing. 
- Ignore sitk on python3.12 on intel mac.
 2024-04-12 16:03:36 +02:00
Wim Pomp db4bd63b94 - OmeCache: detect changes in ome.xml 2024-04-10 15:20:12 +02:00
Wim Pomp 37364d9cfa - CachedPath bugfix, try 3 2024-04-03 14:56:06 +02:00
Wim Pomp 153355d736 - CachedPath bugfix, try 2 2024-04-03 14:32:52 +02:00
Wim Pomp 6041f8c72e - CachedPath bugfix 2024-04-03 10:52:06 +02:00
Wim Pomp 41658bea79 - replace "" with '' 
- bugfix in seqread finding images with pattern 00-Pos_000_000
- cache ome metadata
- detect faulty time delta data in czi files
- read ome from path.ome.xml if this file exists
- add extract-ome command line option
 2024-04-02 18:23:28 +02:00
Wim Pomp 7d06db4ecd - add physical_size_z if known but missing from ome. 2024-03-19 17:59:59 +01:00
Wim Pomp a805613390 - fix split_path_series. 2024-03-19 15:47:28 +01:00
Wim Pomp 5345e38d3c - read the correct metadata for series > 0 2024-03-18 16:43:26 +01:00
Wim Pomp 110cb6d9c1 - bugfix: swap xy. 2024-03-18 14:45:33 +01:00
Wim Pomp 5dafc31559 - flatten method for Imread. 2024-03-12 15:55:38 +01:00
Wim Pomp 06906b1d2c - Limit xsdata version (required by pydantic < ome-data). 2024-03-08 19:25:00 +01:00
Wim Pomp b5c308365d - Make layers optional in czi metadata. 2024-03-08 17:29:48 +01:00
Wim Pomp 8a66c570a6 - Fix bug wrt. supporting non-file images. 
- Make layers optional in czi metadata.
- Delta_t for tif.
 2024-02-13 17:46:23 +01:00
Wim Pomp 735523aba0 - Static __all__ for pyinstaller compatibility. 2023-12-07 13:52:06 +01:00
Wim Pomp cbeca59989 - Zstd decompression for czi files. 2023-12-05 13:45:56 +01:00
Wim Pomp 5508de14f8 - Transforms cast_image fix. 
- Prevent invalid value in log in is_noise.
- Fix bug when no bead_files found.
- Deal with some more czi files.
 2023-12-04 17:14:12 +01:00
Wim Pomp a6457ea497 - Slicing bugfix. 2023-11-21 16:08:57 +01:00
Wim Pomp 5a34adef7b - Slicing bugfix. 
- Sort imports.
- Make sitk-elastix optional again.
 2023-11-20 14:47:47 +01:00
Wim Pomp 2dccbf1cef - Include scikit-image dependency. 2023-11-02 15:09:16 +01:00
Wim Pomp d13b702481 - Improve transforms, implement drift correction transforms, require from_ methods for instantiation. 
- Replace transform, drift and beadfile arguments for Imread by with_transform method.
- Bring Imread.transpose in line with numpy.transpose.
- Fix seqread.lazy_property.
 2023-11-02 15:05:40 +01:00
Wim Pomp 2e56f45f3e - Improve speed of saving transformed images by parallelization. 
- Remove piezoval.
- cziread: make color optional.
 2023-10-30 16:53:09 +01:00
Wim Pomp 7797f38a59 - transforms bugfixes 2023-10-12 14:55:37 +02:00
Wim Pomp 96ab3174d7 - bugfix in czi metadata reader 
- cziread now gives empty frame if the frame wasn't saved in the file
- astype accepts extra arguments, but does not use them
- improved jvm handling
- tifread dtype fix
 2023-09-04 10:26:10 +02:00
Wim Pomp ef6116c6bc - some ome fixes 2023-08-21 11:14:32 +02:00
Wim Pomp cf7f2b6e1e - remove list of views from base 
- fix frame_decorator in views
- use transforms and frame_decorators as cache keys
 2023-08-19 12:08:04 +02:00
Wim Pomp 3dbed27078 - bump ome-types to 0.4 2023-08-18 18:30:15 +02:00
Wim Pomp bb1a710463 - github workflow 2023-08-18 18:12:53 +02:00
Wim Pomp ff6c1aa8a8 - base & view model for imread 
- transforms bugfix
- implement (nan)var and (nan)std
- add tests
 2023-08-18 18:10:42 +02:00
Wim Pomp bdd7a5399c - set dtype according to pixel type in file 
- cziread bugfix
- add reader for broken files saved by Fiji
- make ndread work for arrays with less dimensions than 5
- relative imports
- remove some old functions
- make bfread check if it can open the file
 2023-08-14 17:01:03 +02:00
Wim Pomp 0bd22d766a - fix seqread bug 2023-07-20 10:22:55 +02:00
Wim Pomp dbe80c495b - do_copy class attribute to force copy of ome 
- more ome parts optional
- reading closed file raises an error
 2023-07-11 17:20:03 +02:00
Wim Pomp b629f98727 - seqread: lazily read delta_t 
- calculate timeinterval more efficiently
- remove timeval field
- bugfix in retrieving laser wavelenghts and powers
- add series/pos to summary
- cziread: better assign lightsources to channels
 2023-07-05 12:34:43 +02:00
Wim Pomp 8a74698fa5 - seqread bugfix where dimensions were mixed up 
- seqread load metadata in parallel in
 2023-07-04 16:24:17 +02:00
Wim Pomp f40f7e501b - readme changes 2023-06-29 14:34:54 +02:00
Wim Pomp 506b449f4d - read metadata into ome structure 
- pytest
- use pathlib
- series as part of the path: path/PosN
- summary only shows some available metadata
- allow dict in Imread[dict(c=c, z=z, t=t)]
- bfread in different process so the user can start another jvm
- deal with multiple images (series/positions) in czi files
- use jpype instead of javabridge/bioformats
- poetry for install
 2023-06-29 14:23:03 +02:00
Wim Pomp 33ddb845ae - Bugfix for transforms. 
- Make a list of attributes not to copy --> faster slicing.
- isclosed attribute.
- disable __del__ for now because it doesn't play nice with multiprocessing
 2022-07-17 12:13:31 +02:00
Wim Pomp 7c35741450 - First commit 2022-07-15 14:18:43 +02:00