From 95267652e9f73cf218d8aa45ae0c2aef6e9eeb0e Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Tue, 17 May 2022 15:19:31 +0200
Subject: [PATCH] save metadata, add lut limits
---
src/zarr_tools/__main__.py | 29 ++++++++++++++++++++++++++---
1 file changed, 26 insertions(+), 3 deletions(-)
diff --git a/src/zarr_tools/__main__.py b/src/zarr_tools/__main__.py
index 3ca4ef4..9ea2bec 100644
--- a/src/zarr_tools/__main__.py
+++ b/src/zarr_tools/__main__.py
@@ -16,15 +16,24 @@ def main(nd2_path:str, output:str=None, channel_axis:int=1, steps:int=5, dry_run
if output is None:
output = nd2_path.replace('.nd2', '.zarr')
+
+ out = to_zarr(
+ data,
+ output,
+ steps=steps,
+ dry_run=dry_run,
+ channel_axis=channel_axis,
+ sizes=d.sizes,
+ lut=get_lut(d))
+
+ assert os.path.exists(out), "Saving zarr failed..."
+
try:
meta_path = save_metadata(d, output)
print(f'Saved metadata to {meta_path}')
except Exception as e:
print(f'Saving metadata Failed due to {e}')
- out = to_zarr(data, output, steps=steps, dry_run=dry_run, channel_axis=channel_axis, sizes=d.sizes)
-
- assert os.path.exists(out), "Saving zarr failed..."
exit(0)
def save_metadata(data:nd2.ND2File, output:str):
@@ -37,5 +46,19 @@ def save_metadata(data:nd2.ND2File, output:str):
raise e
return meta_path
+def get_lut(data:nd2.ND2File):
+ try:
+ meta = data.custom_data
+ return \
+ [
+ [
+ meta['LUTDataV1_0']['LutParam']['CompLutParam'][f'{ch:02d}'][lim][0] \
+ for lim in ['MinSrc','MaxSrc']
+ ] for ch in range(data.sizes['C'])
+ ]
+ except Exception as e:
+ print(f'Unable to get LUT due to {e}')
+ return None
+
if __name__=="__main__":
fire.Fire(main)
--
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