Merge pull request #35 from dominikl/row_column_names

Row column names
ome · Oct 23, 2020 · 310243e · 310243e
2 parents bef531c + ff7e300
commit 310243e
Showing 1 changed file with 19 additions and 2 deletions.
diff --git a/src/omero_zarr/raw_pixels.py b/src/omero_zarr/raw_pixels.py
@@ -132,15 +132,20 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
     name = os.path.join(target_dir, "%s.zarr" % plate.id)
     print(f"Exporting to {name}")
     root = open_group(name, mode="w")
-    plate_metadata = {"rows": n_rows, "columns": n_cols}
-    root.attrs["plate"] = plate_metadata
 
     count = 0
     t0 = time.time()
 
+    row_names = set()
+    col_names = set()
+    ac_names = set()
+    paths = set()
+
     for well in plate.listChildren():
         row = plate.getRowLabels()[well.row]
         col = plate.getColumnLabels()[well.column]
+        row_names.add(row)
+        col_names.add(col)
         for field in range(n_fields[0], n_fields[1] + 1):
             ws = well.getWellSample(field)
             field_name = "Field_{}".format(field + 1)
@@ -149,13 +154,25 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
                 img = ws.getImage()
                 ac = ws.getPlateAcquisition()
                 ac_name = ac.getName() if ac else "0"
+                ac_names.add(ac_name)
+                paths.add(f"{ac_name}/{row}/{col}/{field_name}")
                 ac_group = root.require_group(ac_name)
                 row_group = ac_group.require_group(row)
                 col_group = row_group.require_group(col)
                 field_group = col_group.require_group(field_name)
                 n_levels = add_image(img, field_group, cache_dir=cache_dir)
                 add_group_metadata(field_group, img, n_levels)
             print_status(int(t0), int(time.time()), count, total)
+
+    plate_metadata = {
+        "rows": n_rows,
+        "columns": n_cols,
+        "row_names": sorted(list(row_names)),
+        "column_names": sorted(list(col_names)),
+        "plateAcquisitions": [{"path": x} for x in ac_names],
+        "images": [{"path": x} for x in paths],
+    }
+    root.attrs["plate"] = plate_metadata
     print("Finished.")