Fix export assertion and add label measurements

empanada_napari/_export_batch_segs.py

@@ -59,8 +59,8 @@ def widget(
         image = image_layer.data
         mask = labels_layer.data
 
-        assert image.shape[0] == image.shape[0], \
-        f"Image and labels layer must have the same number of images, got {image.shape} and {image.shape}"
+        assert image.shape[0] == mask.shape[0], \
+        f"Image and labels layer must have the same number of images, got {image.shape} and {mask.shape}"
 
         if image.ndim == 3:
             if isinstance(image, da.Array):

empanada_napari/_measure_labels.py

@@ -0,0 +1,128 @@
+import os
+import numpy as np
+import pandas as pd
+import dask.array as da
+
+import napari
+from napari.layers import Labels
+from magicgui import magicgui
+from skimage.measure import regionprops_table
+
+
+def _compute_metrics(label_slice: np.ndarray) -> pd.DataFrame:
+    """Compute morphometric features for each label in a 2D label image."""
+    props = regionprops_table(
+        label_slice.astype(np.int32),
+        properties=(
+            'label',
+            'area',
+            'perimeter',
+            'major_axis_length',
+            'minor_axis_length',
+            'eccentricity',
+            'feret_diameter_max',
+            'equivalent_diameter_area',
+        )
+    )
+    df = pd.DataFrame(props)
+    df = df[df['label'] != 0]
+
+    # circularity = 4π × area / perimeter²; guard against zero-perimeter edge labels
+    df['circularity'] = np.where(
+        df['perimeter'] > 0,
+        (4 * np.pi * df['area']) / (df['perimeter'] ** 2),
+        np.nan
+    )
+    # aspect ratio = major / minor axis length; guard against zero minor axis
+    df['aspect_ratio'] = np.where(
+        df['minor_axis_length'] > 0,
+        df['major_axis_length'] / df['minor_axis_length'],
+        np.nan
+    )
+    return df
+
+
+def measure_labels_widget():
+    apply_to_opts = {
+        'Current slice': 'Current slice',
+        'All slices (z-stack)': 'All slices (z-stack)',
+    }
+
+    @magicgui(
+        call_button='Measure Labels',
+        layout='vertical',
+        apply_to=dict(
+            widget_type='RadioButtons',
+            choices=list(apply_to_opts.keys()),
+            value='Current slice',
+            label='Apply to:',
+            tooltip='Measure the current 2D slice or every slice in the z-stack.',
+        ),
+        export_csv=dict(
+            widget_type='CheckBox',
+            value=False,
+            label='Export measurements (.csv)',
+            tooltip='Save per-label measurements as a CSV file.',
+        ),
+        save_dir=dict(
+            widget_type='FileEdit',
+            value='',
+            label='Save directory',
+            mode='d',
+            tooltip='Directory in which to save the CSV file.',
+        ),
+    )
+    def widget(
+        viewer: napari.viewer.Viewer,
+        labels_layer: Labels,
+        apply_to: str,
+        export_csv: bool,
+        save_dir: str,
+    ):
+        labels = labels_layer.data
+        if isinstance(labels, da.Array):
+            labels = labels.compute()
+
+        results = []
+
+        if apply_to == 'Current slice' or labels.ndim == 2:
+            if labels.ndim > 2:
+                axis = viewer.dims.order[0]
+                plane = int(viewer.dims.current_step[axis])
+                slices = [slice(None)] * labels.ndim
+                slices[axis] = plane
+                label_slice = labels[tuple(slices)]
+            else:
+                label_slice = labels
+                plane = 0
+
+            df = _compute_metrics(np.asarray(label_slice))
+            df.insert(0, 'slice', plane)
+            results.append(df)
+
+        else:
+            for plane in range(labels.shape[0]):
+                label_slice = labels[plane]
+                df = _compute_metrics(np.asarray(label_slice))
+                df.insert(0, 'slice', plane)
+                results.append(df)
+
+        combined = pd.concat(results, ignore_index=True)
+
+        cols = ['slice', 'label', 'area', 'perimeter', 'circularity',
+                'aspect_ratio', 'eccentricity', 'feret_diameter_max',
+                'equivalent_diameter_area', 'major_axis_length', 'minor_axis_length']
+        combined = combined[[c for c in cols if c in combined.columns]]
+
+        print(combined.to_string(index=False))
+        print(f'\nTotal labels measured: {len(combined)}')
+
+        if export_csv:
+            assert save_dir, "Please select a save directory!"
+            os.makedirs(save_dir, exist_ok=True)
+            filename = f'{labels_layer.name}_measurements.csv'
+            filepath = os.path.join(save_dir, filename)
+            combined.to_csv(filepath, index=False)
+            print(f'Saved measurements to {filepath}')
+
+    return widget

empanada_napari/napari.yaml

@@ -17,6 +17,9 @@ contributions:
   - id: empanada-napari.label_counter_widget
     title: Count Labels
     python_name: empanada_napari._label_counter_widget:label_counter_widget
+  - id: empanada-napari.measure_labels_widget
+    title: Measure Labels
+    python_name: empanada_napari._measure_labels:measure_labels_widget
   - id: empanada-napari.merge_labels
     title: Create Merge Labels
     python_name: empanada_napari._merge_split_widget:merge_labels
@@ -89,6 +92,8 @@ contributions:
     display_name: Export Segmentations
   - command: empanada-napari.label_counter_widget
     display_name: Count Labels
+  - command: empanada-napari.measure_labels_widget
+    display_name: Measure Labels
   - command: empanada-napari.merge_labels
     display_name: Merge Labels
   - command: empanada-napari.delete_labels

requirements.txt

@@ -15,6 +15,5 @@ numba>=0.58.1
 imagecodecs
 openpyxl
 imagehash
-mlflow
 simpleitk
-tqdm
+tqdm

setup.cfg

@@ -51,7 +51,6 @@ install_requires =
     imagecodecs
     openpyxl
     imagehash
-    mlflow
     simpleitk
     tqdm