From 68e441d0d4910e9fad89263ab7233a9266ad167e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 26 Jan 2024 11:17:10 +0100
Subject: [PATCH] Script to export patch stacks from non-PA TREC data
---
.../chaeo/batch_jobs/20231023_Porto_4ch.py | 19 +++++++++++--------
1 file changed, 11 insertions(+), 8 deletions(-)
diff --git a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
index c252fd8f..0d99fe5f 100644
--- a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
+++ b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
@@ -22,15 +22,18 @@ if __name__ == '__main__':
# write single-position TIF color stacks
where_proc = Path(where_output) / 'proc'
- for pos in range(0, cf.shape[cf.axes.index('S')]):
- fname = f'{czi_filepath.stem}_p{pos:02d}.tif'
- write_accessor_data_to_file(
- where_proc / fname,
- get_accessor_from_multiposition_czi(cf, pos)
- )
- print(f'Wrote file {fname}')
+ # for pos in range(0, cf.shape[cf.axes.index('S')]):
+ # for pos in [0, 50, 100, 150, 200]:
+ # fname = f'{czi_filepath.stem}_p{pos:02d}.tif'
+ # write_accessor_data_to_file(
+ # where_proc / fname,
+ # get_accessor_from_multiposition_czi(cf, pos)
+ # )
+ # print(f'Wrote file {fname}')
- px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+ px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_4ch_02.ilp').__str__()
+
+ where_proc = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/output/batch-output-20240126-0003/proc')
params = {
'pxmap_threshold': 0.25,
--
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