Check if a plate or an image zarr_url is loaded

Translate label and rectangle position if the zarr_url contains a plate and but not if only a single well is loaded.
fractal-napari-plugins-collection · Oct 1, 2024 · e24850a · e24850a
1 parent 8dc1bed
commit e24850a
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Showing 3 changed files with 23 additions and 8 deletions.
diff --git a/src/napari_ome_zarr_navigator/img_browser.py b/src/napari_ome_zarr_navigator/img_browser.py
@@ -72,6 +72,11 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
     def initialize_filters(self):
         self.zarr_dict = parse_zarr_url(self.zarr_dir.value)
         self.zarr_root = self.zarr_dict["root"]
+
+        if self.zarr_root == self.zarr_dir.value:
+            self.is_plate = True
+        else:
+            self.is_plate = False
         if self.zarr_root:
             adt = self.load_table()
             if adt:
@@ -206,7 +211,11 @@ def load_roi(self):
                     self.viewer.window.remove_dock_widget(self.roi_widget)
 
             self.roi_loader = ROILoaderPlate(
-                self.viewer, str(self.zarr_root), row_alpha[0], col_str[0]
+                self.viewer,
+                str(self.zarr_root),
+                row_alpha[0],
+                col_str[0],
+                self.is_plate,
             )
             self.roi_widget = self.viewer.window.add_dock_widget(
                 widget=self.roi_loader,
@@ -233,7 +242,10 @@ def go_to_well(self):
                     top_left_corner,
                     bottom_right_corner,
                 ) = calculate_well_positions(
-                    plate_url=self.zarr_root, row=well[0], col=well[1]
+                    plate_url=self.zarr_root,
+                    row=well[0],
+                    col=well[1],
+                    is_plate=self.is_plate,
                 )
                 rec = np.array([top_left_corner, bottom_right_corner])
                 self.viewer.add_shapes(

diff --git a/src/napari_ome_zarr_navigator/roi_loader.py b/src/napari_ome_zarr_navigator/roi_loader.py
@@ -396,7 +396,12 @@ def update_image_selection(self):
 
 class ROILoaderPlate(ROILoader):
     def __init__(
-        self, viewer: napari.viewer.Viewer, plate_url: str, row: str, col: str
+        self,
+        viewer: napari.viewer.Viewer,
+        plate_url: str,
+        row: str,
+        col: str,
+        is_plate: bool,
     ):
         self._zarr_picker = ComboBox(label="Image")
         self.plate_url = plate_url.rstrip("/")
@@ -416,9 +421,7 @@ def __init__(
 
         # Calculate base translation for a given well
         self.translation, _ = calculate_well_positions(
-            plate_url=plate_url,
-            row=row,
-            col=col,
+            plate_url=plate_url, row=row, col=col, is_plate=is_plate
         )
 
         # # Handle defaults for plate loading

diff --git a/src/napari_ome_zarr_navigator/util.py b/src/napari_ome_zarr_navigator/util.py
@@ -56,7 +56,7 @@ def add_features_to_labels(
         pass
 
 
-def calculate_well_positions(plate_url, row, col, plate=True):
+def calculate_well_positions(plate_url, row, col, is_plate=True):
     dataset = 0
     level = 0
     zarr_url = f"{plate_url}/{row}/{col}/{dataset}"
@@ -70,7 +70,7 @@ def calculate_well_positions(plate_url, row, col, plate=True):
     row = rows.index(row)
     col = cols.index(col)
 
-    if plate:
+    if is_plate:
         top_left_corner = [
             row * scale[0] * shape[0],
             col * scale[1] * shape[1],