8ff52f5af5
- main_channel and default_transform arguments for Imread.with_transform
w.pomp
2026-01-26 17:03:27 +01:00
066a39719a
- match ome.tif sequence metadata based on position number, with backup by taking any metadata found (with warning)
w.pomp
2026-01-16 11:32:00 +01:00
b1f8dd998b
- test ome reading from some example files
Wim Pomp
2026-01-04 15:13:35 +01:00
8db873c425
- bump ome-metadata dependency - make Reader::new error instead of panic if file cannot be read
Wim Pomp
2026-01-04 15:09:23 +01:00
3c14168878
- implement custom error types - less restrictive dependency versions - some extra features and bugfixes for movie writing - make python tests work again
Wim Pomp
2026-01-04 13:59:57 +01:00
776b5204c4
- remove python 3.14 test as SimpleITK-SimpleElastix is not yet available
w.pomp
2025-11-27 15:45:55 +01:00
e27a0f2657
- cziread: deal with missing exposure times
w.pomp
2025-11-26 17:24:48 +01:00
7fe1d189e5
- fix reading time interval when defined not in s in ome - search all ome.tif for metadata in order
Wim Pomp
2025-10-15 20:29:07 +02:00
1b5febc35b
- add option to skip autoscaling brightness when saving as mp4 - let coords_pandas also deal with polars dataframes
w.pomp
2025-09-25 15:20:00 +02:00
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
Wim Pomp
2025-08-21 19:45:02 +02:00
1fe3b3c824
- Make bioformats optional because jpype can cause problems - Ruff format
Wim Pomp
2025-08-06 11:03:03 +02:00
24af64ac7e
- make modules public
Wim Pomp
2025-04-27 20:14:57 +02:00
5195ccfcb5
- implement sliced views, including min, max, sum and mean operations
Wim Pomp
2025-04-27 20:07:49 +02:00
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
Wim Pomp
2025-02-16 23:02:40 +01:00
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
Wim Pomp
2025-02-16 23:02:40 +01:00
6daa372ccf
- allow None in Transform.from_dict - None transform parameters -> unit parameters/matrix
Wim Pomp
2025-02-14 15:45:43 +01:00
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
Wim Pomp
2025-01-24 15:53:51 +01:00
814bb0da85
- slice notation for time argument on command line - fix seqread can_open
Wim Pomp
2024-09-24 13:23:04 +02:00
eea24e17ef
- add metaseriesread - add function to get all positions/series in a file - make sure mp4 dimensions are even
Wim Pomp
2024-09-13 11:48:38 +02:00
af600633cf
- main: not parallel anymore (for now), make batch processing easier.
Wim Pomp
2024-09-11 14:23:41 +02:00
be2c519951
- transforms bugfix: swap xy - save as movie: progress bar - swap command line argument out for --write
Wim Pomp
2024-07-11 10:13:19 +02:00
1d2cc951fa
- save as mp4 or mkv movie
Wim Pomp
2024-06-04 19:11:40 +02:00
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
Wim Pomp
2024-04-02 18:23:28 +02:00
7d06db4ecd
- add physical_size_z if known but missing from ome.
Wim Pomp
2024-03-19 17:59:59 +01:00
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.
Wim Pomp
2023-12-04 17:14:12 +01:00
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
Wim Pomp
2023-09-04 10:26:10 +02:00
ef6116c6bc
- some ome fixes
Wim Pomp
2023-08-21 11:14:32 +02:00
cf7f2b6e1e
- remove list of views from base - fix frame_decorator in views - use transforms and frame_decorators as cache keys
Wim Pomp
2023-08-19 12:08:04 +02:00
ff6c1aa8a8
- base & view model for imread - transforms bugfix - implement (nan)var and (nan)std - add tests
Wim Pomp
2023-08-18 18:10:42 +02:00
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
Wim Pomp
2023-08-14 17:01:03 +02:00
dbe80c495b
- do_copy class attribute to force copy of ome - more ome parts optional - reading closed file raises an error
Wim Pomp
2023-07-11 17:20:03 +02:00
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
Wim Pomp
2023-07-05 12:34:43 +02:00
8a74698fa5
- seqread bugfix where dimensions were mixed up - seqread load metadata in parallel in
Wim Pomp
2023-07-04 16:24:17 +02:00
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
Wim Pomp
2023-06-29 14:23:03 +02:00
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
Wim Pomp
2022-07-17 12:13:31 +02:00
7c35741450
- First commit
Wim Pomp
2022-07-15 14:18:43 +02:00
w.pomp