napari-tmidas 0.2.1__py3-none-any.whl → 0.2.4__py3-none-any.whl

napari_tmidas/_tests/test_intensity_label_filter.py

@@ -0,0 +1,222 @@
+# src/napari_tmidas/_tests/test_intensity_label_filter.py
+"""Tests for intensity-based label filtering functions."""
+
+import numpy as np
+import pytest
+
+# Try importing the functions - they may not be available if sklearn-extra is not installed
+try:
+    from napari_tmidas.processing_functions.intensity_label_filter import (
+        _calculate_label_mean_intensities,
+        _cluster_intensities,
+        _filter_labels_by_threshold,
+    )
+
+    HAS_KMEDOIDS = True
+except ImportError:
+    HAS_KMEDOIDS = False
+
+
+@pytest.mark.skipif(
+    not HAS_KMEDOIDS, reason="scikit-learn-extra not installed"
+)
+class TestIntensityLabelFilter:
+    """Test suite for intensity-based label filtering."""
+
+    def test_calculate_label_mean_intensities(self):
+        """Test mean intensity calculation for labels."""
+        # Create simple label image with 3 labels
+        label_image = np.array(
+            [
+                [1, 1, 2, 2],
+                [1, 1, 2, 2],
+                [3, 3, 0, 0],
+                [3, 3, 0, 0],
+            ]
+        )
+
+        # Create intensity image with different values for each label
+        intensity_image = np.array(
+            [
+                [10, 10, 50, 50],
+                [10, 10, 50, 50],
+                [100, 100, 0, 0],
+                [100, 100, 0, 0],
+            ],
+            dtype=np.float32,
+        )
+
+        result = _calculate_label_mean_intensities(
+            label_image, intensity_image
+        )
+
+        assert len(result) == 3
+        assert result[1] == pytest.approx(10.0)
+        assert result[2] == pytest.approx(50.0)
+        assert result[3] == pytest.approx(100.0)
+
+    def test_cluster_intensities_2medoids(self):
+        """Test 2-medoids clustering."""
+        # Create clear separation: low (10, 15, 20) and high (80, 85, 90)
+        intensities = np.array([10, 15, 20, 80, 85, 90])
+
+        labels, medoids, threshold = _cluster_intensities(
+            intensities, n_clusters=2
+        )
+
+        assert len(labels) == 6
+        assert len(medoids) == 2
+        assert medoids[0] < medoids[1]  # Sorted low to high
+        assert threshold > medoids[0]
+        assert threshold < medoids[1]
+        # Check threshold is between the two groups
+        assert threshold > 20
+        assert threshold < 80
+
+    def test_cluster_intensities_3medoids(self):
+        """Test 3-medoids clustering."""
+        # Create clear separation: low (10, 15), medium (50, 55), high (90, 95)
+        intensities = np.array([10, 15, 50, 55, 90, 95])
+
+        labels, medoids, threshold = _cluster_intensities(
+            intensities, n_clusters=3
+        )
+
+        assert len(labels) == 6
+        assert len(medoids) == 3
+        assert medoids[0] < medoids[1] < medoids[2]  # Sorted low to high
+        # Threshold should be between lowest and second-lowest
+        assert threshold > medoids[0]
+        assert threshold < medoids[1]
+
+    def test_filter_labels_by_threshold(self):
+        """Test label filtering based on threshold."""
+        label_image = np.array(
+            [
+                [1, 1, 2, 2],
+                [1, 1, 2, 2],
+                [3, 3, 0, 0],
+                [3, 3, 0, 0],
+            ]
+        )
+
+        label_intensities = {1: 10.0, 2: 50.0, 3: 100.0}
+        threshold = 40.0  # Should keep labels 2 and 3, remove label 1
+
+        result = _filter_labels_by_threshold(
+            label_image, label_intensities, threshold
+        )
+
+        # Label 1 should be removed (set to 0)
+        assert np.all(result[0:2, 0:2] == 0)
+        # Labels 2 and 3 should remain
+        assert np.all(result[0:2, 2:4] == 2)
+        assert np.all(result[2:4, 0:2] == 3)
+        # Background should remain
+        assert np.all(result[2:4, 2:4] == 0)
+
+    def test_filter_labels_2medoids_integration(self, tmp_path):
+        """Integration test for 2-medoids filtering."""
+        # Create test label image with 3 labels
+        label_image = np.zeros((100, 100), dtype=np.uint16)
+        label_image[10:40, 10:40] = 1  # Low intensity
+        label_image[50:80, 10:40] = 2  # High intensity
+        label_image[10:40, 50:80] = 3  # High intensity
+
+        # Create intensity image where label 1 has low intensity, 2 and 3 high
+        intensity_image = np.zeros((100, 100), dtype=np.float32)
+        intensity_image[10:40, 10:40] = 20  # Low
+        intensity_image[50:80, 10:40] = 100  # High
+        intensity_image[10:40, 50:80] = 110  # High
+
+        # Save intensity image to temporary file
+        intensity_folder = tmp_path / "intensity"
+        intensity_folder.mkdir()
+        intensity_file = intensity_folder / "test_image.tif"
+
+        # Use tifffile if available, otherwise numpy
+        try:
+            import tifffile
+
+            tifffile.imwrite(intensity_file, intensity_image)
+        except ImportError:
+            np.save(intensity_file.with_suffix(".npy"), intensity_image)
+            intensity_file = intensity_file.with_suffix(".npy")
+
+        # Create fake label file path
+        label_file = tmp_path / "labels" / intensity_file.name
+        label_file.parent.mkdir()
+
+        # Run filter (without actual file, just testing logic)
+        # Note: This would require mocking the file reader in a real test
+        # For now, we'll test the components separately
+
+    def test_empty_label_image(self):
+        """Test handling of empty label image."""
+        label_image = np.zeros((50, 50), dtype=np.uint16)
+        intensity_image = np.random.rand(50, 50).astype(np.float32)
+
+        result = _calculate_label_mean_intensities(
+            label_image, intensity_image
+        )
+
+        assert len(result) == 0
+
+    def test_single_label(self):
+        """Test handling of single label."""
+        label_image = np.ones((50, 50), dtype=np.uint16)
+        intensity_image = np.full((50, 50), 42.0, dtype=np.float32)
+
+        result = _calculate_label_mean_intensities(
+            label_image, intensity_image
+        )
+
+        assert len(result) == 1
+        assert result[1] == pytest.approx(42.0)
+
+    def test_filter_preserves_dtype(self):
+        """Test that filtering preserves label image dtype."""
+        for dtype in [np.uint8, np.uint16, np.uint32, np.int32]:
+            label_image = np.array(
+                [
+                    [1, 1, 2, 2],
+                    [1, 1, 2, 2],
+                ],
+                dtype=dtype,
+            )
+
+            label_intensities = {1: 10.0, 2: 50.0}
+            threshold = 40.0
+
+            result = _filter_labels_by_threshold(
+                label_image, label_intensities, threshold
+            )
+
+            assert result.dtype == dtype
+
+    def test_clustering_reproducibility(self):
+        """Test that clustering is reproducible due to random_state."""
+        intensities = np.array([10, 15, 20, 25, 80, 85, 90, 95])
+
+        labels1, medoids1, threshold1 = _cluster_intensities(
+            intensities, n_clusters=2
+        )
+        labels2, medoids2, threshold2 = _cluster_intensities(
+            intensities, n_clusters=2
+        )
+
+        np.testing.assert_array_equal(labels1, labels2)
+        np.testing.assert_array_almost_equal(medoids1, medoids2)
+        assert threshold1 == pytest.approx(threshold2)
+
+
+@pytest.mark.skipif(HAS_KMEDOIDS, reason="Test for missing dependency")
+def test_import_error_without_sklearn_extra():
+    """Test that appropriate error is raised when sklearn-extra is not installed."""
+    # This test only runs when sklearn-extra is NOT installed
+    with pytest.raises(ImportError):
+        from napari_tmidas.processing_functions.intensity_label_filter import (
+            _cluster_intensities,
+        )
+
+        _cluster_intensities(np.array([1, 2, 3]), n_clusters=2)

napari_tmidas/_tests/test_label_inspection.py

@@ -0,0 +1,86 @@
+# src/napari_tmidas/_tests/test_label_inspection.py
+import os
+import tempfile
+from unittest.mock import Mock, patch
+
+import numpy as np
+
+from napari_tmidas._label_inspection import (
+    LabelInspector,
+    label_inspector_widget,
+)
+
+
+class TestLabelInspector:
+    def setup_method(self):
+        """Setup test environment"""
+        self.temp_dir = tempfile.mkdtemp()
+        self.viewer = Mock()
+
+    def teardown_method(self):
+        """Cleanup"""
+        import shutil
+
+        shutil.rmtree(self.temp_dir)
+
+    def test_label_inspector_initialization(self):
+        """Test LabelInspector initialization"""
+        inspector = LabelInspector(self.viewer)
+        assert inspector.viewer == self.viewer
+        assert inspector.image_label_pairs == []
+        assert inspector.current_index == 0
+
+    def test_load_image_label_pairs_no_folder(self):
+        """Test loading pairs with non-existent folder"""
+        inspector = LabelInspector(self.viewer)
+        inspector.load_image_label_pairs("/nonexistent/folder", "_labels")
+        assert (
+            self.viewer.status
+            == "Folder path does not exist: /nonexistent/folder"
+        )
+
+    def test_load_image_label_pairs_no_labels(self):
+        """Test loading pairs with no label files"""
+        inspector = LabelInspector(self.viewer)
+
+        # Create empty folder
+        empty_dir = os.path.join(self.temp_dir, "empty")
+        os.makedirs(empty_dir)
+
+        inspector.load_image_label_pairs(empty_dir, "_labels")
+        assert self.viewer.status == "No files found with suffix '_labels'"
+
+    @patch("napari_tmidas._label_inspection.imread")
+    def test_load_image_label_pairs_valid(self, mock_imread):
+        """Test loading valid image-label pairs"""
+        inspector = LabelInspector(self.viewer)
+
+        # Create test files
+        test_dir = os.path.join(self.temp_dir, "test")
+        os.makedirs(test_dir)
+
+        # Create image and label files
+        image_path = os.path.join(test_dir, "test_image.tif")
+        label_path = os.path.join(test_dir, "test_image_labels.tif")
+
+        with open(image_path, "w") as f:
+            f.write("dummy")
+        with open(label_path, "w") as f:
+            f.write("dummy")
+
+        # Mock imread to return valid label data
+        mock_imread.return_value = np.ones((10, 10), dtype=np.uint32)
+
+        inspector.load_image_label_pairs(test_dir, "_labels")
+
+        # Check that pairs were loaded
+        assert len(inspector.image_label_pairs) == 1
+        assert inspector.image_label_pairs[0] == (image_path, label_path)
+
+
+class TestLabelInspectorWidget:
+    def test_widget_creation(self):
+        """Test that the label inspector widget can be imported and called"""
+        # Just test that the function exists and can be called
+        # (without actually creating the widget to avoid Qt issues)
+        assert callable(label_inspector_widget)