Merge pull request #21527 from kostrykin/patch-1

Extend `image_diff` and image content assertions to handle boolean images

lib/galaxy/tool_util/verify/__init__.py

@@ -595,6 +595,12 @@ def files_image_diff(file1: str, file2: str, attributes: Optional[Dict[str, Any]
     if arr1.shape != arr2.shape:
         raise AssertionError(f"Image dimensions did not match ({arr1.shape}, {arr2.shape}).")
 
+    # Handle `bool` images by converting them to `uint8`
+    if numpy.issubdtype(arr1.dtype, bool):
+        arr1 = arr1.astype(numpy.uint8)
+    if numpy.issubdtype(arr2.dtype, bool):
+        arr2 = arr2.astype(numpy.uint8)
+
     distance = get_image_metric(attributes)(arr1, arr2)
     distance_eps = attributes.get("eps", DEFAULT_EPS)
     if distance > distance_eps:

lib/galaxy/tool_util/verify/asserts/image.py

@@ -747,8 +747,14 @@ def _get_image_labels(
         label = label.strip()
         if numpy.issubdtype(im_arr.dtype, numpy.integer):
             return int(label)
-        if numpy.issubdtype(im_arr.dtype, float):
+        if numpy.issubdtype(im_arr.dtype, numpy.floating):
             return float(label)
+        if numpy.issubdtype(im_arr.dtype, bool):
+            label_lower = label.lower()
+            if label_lower in ("0", "1", "false", "true"):
+                return label_lower in ("1", "true")
+            else:
+                raise AssertionError(f'Label "{label}" incompatible with label type "{im_arr.dtype}"')
         raise AssertionError(f'Unsupported image label type: "{im_arr.dtype}"')
 
     # Determine labels present in the image.

test/functional/tools/image_diff.xml

@@ -27,6 +27,11 @@
       <param name="in" value="im4_float.tif" />
       <output name="out" value="im4_float.tif" compare="image_diff" />
     </test>
+    <!-- test pair of equal images (bool tiff) -->
+    <test>
+      <param name="in" value="im3_b_bool.tiff" />
+      <output name="out" value="im3_b_bool.tiff" compare="image_diff" metric="iou" pin_labels="0" />
+    </test>
     <!-- test pair of different images -->
     <test>
       <param name="in" value="im2_a.png" />

test/functional/tools/validation_image.xml

@@ -181,6 +181,20 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input" value="im3_b_bool.tiff" />
+            <output name="output">
+                <assert_contents>
+                    <has_image_width width="32" />
+                    <has_image_height height="32" />
+                    <has_image_channels channels="1" />
+                    <has_image_n_labels n="1" exclude_labels="0" />
+                    <has_image_n_labels n="1" exclude_labels="1" />
+                    <has_image_n_labels n="0" exclude_labels="0,1" />
+                    <has_image_mean_object_size mean_object_size="256" exclude_labels="0" />
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="input" value="im2_b.png" />
             <output name="output">

test/unit/tool_util/test_verify.py

@@ -87,6 +87,17 @@ F9 = _encode_image(
     ),
     format="PNG",
 )
+F10 = _encode_image(
+    numpy.array(
+        [
+            [True, True, True],
+            [True, False, True],
+            [True, True, True],
+        ],
+        dtype=bool,
+    ),
+    format="TIFF",
+)
 
 
 def _test_file_list():
@@ -102,6 +113,7 @@ def _test_file_list():
         (F7, ".tiff"),
         (F8, ".tiff"),
         (F9, ".png"),
+        (F10, ".tiff"),
     ]:
         with tempfile.NamedTemporaryFile(mode="wb", suffix=ext, delete=False) as out:
             if ext == ".txt.gz":
@@ -112,7 +124,7 @@ def _test_file_list():
 
 
 def generate_tests(multiline=False):
-    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9 = _test_file_list()
+    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9, f10 = _test_file_list()
     tests: List[TestDef]
     if multiline:
         tests = [(multiline_match, f1, {"lines_diff": 0, "sort": True}, None)]
@@ -130,7 +142,7 @@ def generate_tests(multiline=False):
 
 
 def generate_tests_sim_size():
-    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9 = _test_file_list()
+    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9, f10 = _test_file_list()
     # tests for equal files
     tests: List[TestDef] = [
         (f1, f1, None, None),  # pass default values
@@ -156,7 +168,7 @@ def generate_tests_sim_size():
 
 
 def generate_tests_image_diff():
-    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9 = _test_file_list()
+    f1, f2, f3, f4, multiline_match, f5, f6, f7, f8, f9, f10 = _test_file_list()
     metrics = ["mae", "mse", "rms", "fro", "iou"]
     # tests for equal files (uint8, PNG)
     tests: List[TestDef] = [(f6, f6, {"metric": metric}, None) for metric in metrics]
@@ -164,6 +176,8 @@ def generate_tests_image_diff():
     tests += [(f7, f7, {"metric": metric}, None) for metric in metrics]
     # tests for equal files (float, TIFF)
     tests += [(f8, f8, {"metric": metric}, None) for metric in metrics]
+    # tests for equal files (bool, TIFF)
+    tests += [(f10, f10, {"metric": metric}, None) for metric in metrics]
     # tests for pairs of different files
     tests += [(f6, f8, {"metric": metric}, AssertionError) for metric in metrics]  # uint8 vs float
     tests += [(f7, f8, {"metric": metric}, AssertionError) for metric in metrics]  # uint8 vs float