From 1022d0735e66e6ff88bb1ba8bb085050ba937eab Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Sun, 29 May 2022 13:04:37 +0200
Subject: [PATCH] combine zarrs
---
combine.py | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
create mode 100644 combine.py
diff --git a/combine.py b/combine.py
new file mode 100644
index 0000000..753b50b
--- /dev/null
+++ b/combine.py
@@ -0,0 +1,25 @@
+import dask.array as da
+import os
+from zarr_tools.convert import to_zarr
+import fire
+
+def combine(BF_zarr_2D_path:str, TRITC_zarr_3D_path:str, out_zarr_path:str):
+ bd2d = da.from_zarr(os.path.join(BF_zarr_2D_path,'0/'))
+ print('Opened BF:', bd2d)
+ fd3d = da.from_zarr(os.path.join(TRITC_zarr_3D_path,'0/'))
+ print('Opened TRITC:', fd3d)
+ fd2d = fd3d.max(axis=1)
+ bd2d = da.stack([bd2d, fd2d], axis=1)
+ print('Resulting stack:', bd2d)
+ to_zarr(
+ bd2d,
+ path=out_zarr_path,
+ steps=4,
+ name=['BF','TRITC'],
+ colormap=['gray','orange'],
+ lut=((1000,30000),(440, 600)),
+ )
+
+# combine(snakemake.input[0], snakemake.input[1], snakemake.output[0])
+if __name__ == "__main__":
+ fire.Fire(combine)
\ No newline at end of file
--
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