combine zarrs

combine.py

+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)
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