Merge pull request #36 from BiAPoL/save_coordinates

add bbox to metadata

napari_crop/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = "0.1.6"
+__version__ = "0.1.7"
 
 
 

napari_crop/_function.py

@@ -110,12 +110,20 @@ def crop_region(
 
             # trim zeros
             non_zero = np.where(cropped_data != 0)
-            indices = [slice(min(i_nz), max(i_nz) + 1) for i_nz in non_zero]
+            slices = [slice(min(i_nz), max(i_nz) + 1) for i_nz in non_zero]
             if rgb:
-                indices[-1] = slice(None)
-            cropped_data = cropped_data[tuple(indices)]
+                slices[-1] = slice(None)
+            cropped_data = cropped_data[tuple(slices)]
 
         new_layer_props = layer_props.copy()
+        # Update start and stop values for bbox
+        start = [slc.start for slc in slices if slc is not None]
+        stop = [slc.stop for slc in slices if slc is not None]
+        # Add cropped coordinates as metadata
+        # bounding box: (min_row, max_row, min_col, max_col)
+        # Pixels belonging to the bounding box are in the half-open interval [min_row; max_row) and [min_col; max_col).
+        new_layer_props['metadata'] = {'bbox': (start[0], stop[0], start[1], stop[1])}
+
         # If layer name is in viewer or is about to be added,
         # increment layer name until it has a different name
         while True:

napari_crop/_tests/test_function.py

@@ -23,8 +23,10 @@
               [ 0,  6,  7,  8,  0],
               [10, 11, 12, 13, 14],
               [ 0,  0, 17,  0,  0]]),  # fmt: skip
-
 ]
+bbox_expected = [(1.0, 5.0, 1.0, 4.0),
+                   (1.0, 5.0, 1.0, 4.0),
+                   (0.0, 4.0, 0.0, 5.0)]
 
 # rectangle crop
 # array([[ 6,  7,  8],
@@ -62,6 +64,22 @@ def test_crop_function_values_2d(make_napari_viewer, shape, shape_type,
     assert np.array_equal(crop_expected, cropped_actual_arrays)
 
 
+@pytest.mark.parametrize(
+    "shape,shape_type,bbox_expected",
+    zip(shapes, shape_types, bbox_expected)
+)
+def test_bbox_values(make_napari_viewer, shape, shape_type,
+                                 bbox_expected):
+    """Test that the bbox returned in metadata is correct."""
+
+    viewer = make_napari_viewer()
+    img_layer = viewer.add_image(arr_2d)
+    shapes_layer = viewer.add_shapes(shape, shape_type=shape_type)
+    cropped_actual = crop_region(img_layer, shapes_layer)[0][1] # get layer properties
+    bbox = cropped_actual['metadata']['bbox']
+    assert np.array_equal(bbox_expected, bbox)
+
+
 def test_crop_multiple_shapes(make_napari_viewer):
     """Test that 'n' drawn shapes return 'n' new cropped layers"""
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-crop
-version = 0.1.6
+version = 0.1.7
 author = Robert Haase, Tim Morello, Marcelo Leomil Zoccoler, Johannes Muller
 author_email = [email protected]
 license = BSD-3-Clause