wim/ndbioimage
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56 Commits 2 Branches 0 Tags
3db6dc8ee11b1f270e45a4c99bb1ffbf102f3f9f
Commit Graph

50 Commits

Author SHA1 Message Date
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
8b280b3061 - make cache size configurable 2025-01-08 13:18:38 +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
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