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
w.pomp2026-07-13 15:16:10 +02:00
ff7cd562af
- implement shape in Rust - implement more readers - fix downloading of bioformats jar - (mostly) compatible with python version
w.pomp2026-07-13 13:40:34 +02:00
2f076bd7b8
- let tifread raise FileNotFoundError when series != 0
Wim Pomp2026-04-01 10:13:43 +02:00
46c511dd49
- let tifread raise FileNotFoundError when series != 0
Wim Pomp2026-04-01 10:13:43 +02:00
0ee456a064
- improve support for tiled czi's
w.pomp2026-03-30 11:35:25 +02:00
6123eeee8b
- add support for tiled czi's: bugfix 2
w.pomp2026-03-26 17:05:37 +01:00
e56ef334f4
- add support for tiled czi's: bugfix
w.pomp2026-03-26 16:52:18 +01:00
bba24f2156
- add support for tiled czi's
w.pomp2026-03-26 16:39:16 +01:00
7e9cf46d55
- limit imagecodecs version
w.pomp2026-03-11 21:00:53 +01:00
351f563867
- cziread: fallback for when tile indices do not work
w.pomp2026-03-11 20:51:32 +01:00
4563908254
- make paths absolute if possible - seqfind: read some metadata from display_and_comments.txt if needed and present
w.pomp2026-03-03 15:56:27 +01:00
705ca16379
start using semver, fix doc.rs issue
w.pomp2026-02-23 19:54:58 +01:00
8ff52f5af5
- main_channel and default_transform arguments for Imread.with_transform
w.pomp2026-01-26 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.pomp2026-01-16 11:32:00 +01:00
b1f8dd998b
- test ome reading from some example files
Wim Pomp2026-01-04 15:13:35 +01:00
8db873c425
- bump ome-metadata dependency - make Reader::new error instead of panic if file cannot be read
Wim Pomp2026-01-04 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 Pomp2026-01-04 13:59:57 +01:00
776b5204c4
- remove python 3.14 test as SimpleITK-SimpleElastix is not yet available
w.pomp2025-11-27 15:45:55 +01:00
e27a0f2657
- cziread: deal with missing exposure times
w.pomp2025-11-26 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 Pomp2025-10-15 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.pomp2025-09-25 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 Pomp2025-08-21 19:45:02 +02:00
1fe3b3c824
- Make bioformats optional because jpype can cause problems - Ruff format
Wim Pomp2025-08-06 11:03:03 +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 Pomp2025-02-16 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 Pomp2025-02-16 23:02:40 +01:00
6daa372ccf
- allow None in Transform.from_dict - None transform parameters -> unit parameters/matrix
Wim Pomp2025-02-14 15:45:43 +01:00
cb52e77c34
- allow None in Transform.from_dict
Wim Pomp2025-02-14 15:00:55 +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 Pomp2025-01-24 15:53:51 +01:00
814bb0da85
- slice notation for time argument on command line - fix seqread can_open
Wim Pomp2024-09-24 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 Pomp2024-09-13 11:48:38 +02:00
af600633cf
- main: not parallel anymore (for now), make batch processing easier.
Wim Pomp2024-09-11 14:23:41 +02:00
be2c519951
- transforms bugfix: swap xy - save as movie: progress bar - swap command line argument out for --write
Wim Pomp2024-07-11 10:13:19 +02:00
1d2cc951fa
- save as mp4 or mkv movie
Wim Pomp2024-06-04 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 Pomp2024-04-02 18:23:28 +02:00
7d06db4ecd
- add physical_size_z if known but missing from ome.
Wim Pomp2024-03-19 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 Pomp2023-12-04 17:14:12 +01:00
w.pomp