forgot to bundle with last commit

khanlab · Jan 15, 2025 · db6b2ff · db6b2ff
1 parent 661b345
commit db6b2ff
Showing 1 changed file with 28 additions and 27 deletions.
diff --git a/workflow/scripts/imaris_to_ome_zarr.py b/workflow/scripts/imaris_to_ome_zarr.py
@@ -23,6 +23,7 @@
 uri = snakemake.params.uri
 
 
+
 # prepare metadata for ome-zarr
 with open(metadata_json) as fp:
     metadata = json.load(fp)
@@ -55,44 +56,44 @@
     fs = get_fsspec(uri,**fs_args)
     store = zarr.storage.FSStore(Path(uri).path,fs=fs,dimension_separator='/',mode='w')
 else:
-    store = zarr.DirectoryStore(out_zarr,dimension_separator='/') 
-
+    #store = zarr.DirectoryStore(out_zarr,dimension_separator='/') 
+    store = zarr.ZipStore(out_zarr,dimension_separator='/',mode='x') 
 
 
 
+with h5py.File(snakemake.input.ims, 'r') as h5_file:
 
-darr_list=[]
-for zarr_i,in_zarr in enumerate(snakemake.input.zarr):
-    #open zarr to get group name
-    zi = zarr.open(in_zarr)
-    darr_list.append(da.from_zarr(in_zarr,component='Data').rechunk(rechunk_size))
+    darr_list=[]
+    for zarr_i,stain in enumerate(stains):
+        h5_group=f'DataSet/ResolutionLevel 0/TimePoint 0/Channel {zarr_i}/Data'
+        darr_list.append(da.from_array(h5_file[h5_group]).rechunk(rechunk_size))
 
 
-    #append to omero metadata
-    channel_metadata={key:val for key,val in snakemake.config['ome_zarr']['omero_metadata']['channels']['defaults'].items()}
-    channel_name=stains[zarr_i]
-    channel_metadata['label'] = channel_name
-    default_color=snakemake.config['ome_zarr']['omero_metadata']['channels']['default_color']
-    color=snakemake.config['ome_zarr']['omero_metadata']['channels']['color_mapping'].get(channel_name,default_color)
-    channel_metadata['color'] = color
-    omero['channels'].append(channel_metadata)
-
+        #append to omero metadata
+        channel_metadata={key:val for key,val in snakemake.config['ome_zarr']['omero_metadata']['channels']['defaults'].items()}
+        channel_name=stain
+        channel_metadata['label'] = channel_name
+        default_color=snakemake.config['ome_zarr']['omero_metadata']['channels']['default_color']
+        color=snakemake.config['ome_zarr']['omero_metadata']['channels']['color_mapping'].get(channel_name,default_color)
+        channel_metadata['color'] = color
+        omero['channels'].append(channel_metadata)
+        
 
-darr_channels = da.stack(darr_list)
+    darr_channels = da.stack(darr_list)
 
 
 
-group = zarr.group(store,overwrite=True)
-scaler = Scaler(max_layer=max_layer,method=scaling_method)
+    group = zarr.group(store,overwrite=True)
+    scaler = Scaler(max_layer=max_layer,method=scaling_method)
 
 
-with ProgressBar():
-    write_image(image=darr_channels,
-                            group=group,
-                            scaler=scaler,
-                            coordinate_transformations=coordinate_transformations,
-                            axes=axes,
-                            metadata={'omero':omero}
-                                )
+    with ProgressBar():
+        write_image(image=darr_channels,
+                                group=group,
+                                scaler=scaler,
+                                coordinate_transformations=coordinate_transformations,
+                                axes=axes,
+                                metadata={'omero':omero}
+                                    )