Working example for new channel-assignment scheme (ref #61)

Author: tcompa

examples/wf_params_uzh_1_well_2x2_sites.json

@@ -3,5 +3,6 @@
 "dims": [2, 2],
 "coarsening_xy": 3,
 "coarsening_z": 1,
-"num_levels": 5
+"num_levels": 5,
+"channel_file": "wf_params_uzh_1_well_2x2_sites_channels.json"
 }

examples/wf_params_uzh_1_well_2x2_sites_channels.json

@@ -0,0 +1,26 @@
+{
+    "A01_C01": {
+        "label": "DAPI",
+        "colormap": "00FFFF",
+        "start": 110,
+        "end": 600
+    },
+    "A01_C02": {
+        "label": "nanog",
+        "colormap": "FF00FF",
+        "start": 115,
+        "end": 200
+    },
+    "A02_C03": {
+        "label": "Lamin B1",
+        "colormap": "FFFF00",
+        "start": 115,
+        "end": 1000
+    },
+    "fake": {
+        "label": "Fake",
+        "colormap": "FFFFFF",
+        "start": 115,
+        "end": 1000
+    }
+}

fractal/fractal_cmd.py

@@ -442,6 +442,7 @@ def workflow_apply(
     num_levels = params["num_levels"]
     rows, cols = params["dims"]
     workflow_name = params["workflow_name"]
+    path_dict_channels = params["channel_file"]
     delete_input = params.get("delete_input", False)
 
     # FIXME validate tasks somewhere?
@@ -486,6 +487,7 @@ def collect_intermediate_results(inputs=[]):
         kwargs = dict(
             in_paths=resources_in,
             out_path=resource_out,
+            path_dict_channels=path_dict_channels,
             ext=ext,
             num_levels=num_levels,
         )

fractal/tasks/create_zarr_structure.py

@@ -30,35 +30,19 @@ def create_zarr_structure(
     :type num_levels: int
     """
 
-    # FIXME: remove hard-coded default (for None)
-    if path_dict_channels is None:
-        dict_channels = {
-            "A01_C01": dict(
-                label="DAPI", colormap="00FFFF", start=110, end=600
-            ),
-            "A01_C02": dict(
-                label="nanog", colormap="FF00FF", start=115, end=200
-            ),
-            "A02_C03": dict(
-                label="Lamin B1", colormap="FFFF00", start=115, end=1000
-            ),
-            "fake": dict(label="Fake", colormap="FFFFFF", start=115, end=1000),
-        }
-    else:
-        try:
-            with open(path_dict_channels, "r") as json_file:
-                dict_channels = json.load(json_file)
-        except FileNotFoundError:
-            raise Exception(
-                "ERROR in create_zarr_structure: "
-                f"{path_dict_channels} missing."
-            )
-        except TypeError:
-            raise Exception(
-                "ERROR in create_zarr_structure: "
-                f"{path_dict_channels} has wrong type "
-                "(probably a None instead of a string)."
-            )
+    try:
+        with open(path_dict_channels, "r") as json_file:
+            dict_channels = json.load(json_file)
+    except FileNotFoundError:
+        raise Exception(
+            "ERROR in create_zarr_structure: " f"{path_dict_channels} missing."
+        )
+    except TypeError:
+        raise Exception(
+            "ERROR in create_zarr_structure: "
+            f"{path_dict_channels} has wrong type "
+            "(probably a None instead of a string)."
+        )
 
     # Identify all plates and all channels, across all input folders
     plates = []