WIP

em_workflows/czi/flow.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List
+from typing import List, Dict
 import SimpleITK as sitk
 from prefect import Flow, Parameter, task
 from pytools.HedwigZarrImage import HedwigZarrImage
@@ -46,10 +46,6 @@ def gen_imageSet(file_path: FilePath) -> List:
             # we don't care about the macro image
             continue
         assets.append(gen_thumb(image=image, file_path=file_path))
-        # TODO this might be no longer needed
-        #         if image_name == "":
-        #             image_elt["imageName"] = f"Scene {image.ome_idx}"
-        #         else:
         image_elt["imageName"] = image_name
 
         if image_name != "label image":
@@ -99,13 +95,21 @@ def bioformats_gen_zarr(file_path: FilePath):
     ]
     FilePath.run(cmd, log_fp)
     rechunk_zarr(zarr_fp=Path(output_zarr))
-    asset_fp = file_path.copy_to_assets_dir(fp_to_cp=Path(output_zarr))
-    print(asset_fp)
+    file_path.copy_to_assets_dir(fp_to_cp=Path(output_zarr))
     imageSet = gen_imageSet(file_path=file_path)
     # extract images from input file, used to create imageSet elements
     return imageSet
 
 
+@task
+def find_thumb_idx(callback: List[Dict]) -> List[Dict]:
+    for elt in callback:
+        for i, image_elt in enumerate(elt["imageSet"]):
+            if image_elt["imageName"] == "label image":
+                elt["thumbnailIndex"] = i
+    return callback
+
+
 with Flow(
     "czi_to_zarr",
     state_handlers=[utils.notify_api_completion, utils.notify_api_running],
@@ -129,9 +133,10 @@ def bioformats_gen_zarr(file_path: FilePath):
     )
     fps = utils.gen_fps(input_dir=input_dir_fp, fps_in=input_fps)
     prim_fps = utils.gen_prim_fps.map(fp_in=fps)
-    zarrs = bioformats_gen_zarr.map(file_path=fps)
-    callback_with_zarr = utils.add_asset.map(prim_fp=prim_fps, asset=zarrs)
-    filtered_callback = utils.filter_results(callback_with_zarr)
+    imageSets = bioformats_gen_zarr.map(file_path=fps)
+    callback_with_zarrs = utils.add_asset.map(prim_fp=prim_fps, asset=imageSets)
+    callback_with_zarrs = find_thumb_idx(callback=callback_with_zarrs)
+    filtered_callback = utils.filter_results(callback_with_zarrs)
     cb = utils.send_callback_body(
         token=token, callback_url=callback_url, files_elts=filtered_callback
     )