Merge pull request #52 from janelia-cellmap/copilot/sub-pr-51

Add comprehensive test coverage for base classes and refactored components

Author: rhoadesScholar

tests/test_base_classes.py

@@ -0,0 +1,219 @@
+"""Tests for base abstract classes."""
+
+import pytest
+import torch
+from abc import ABC
+
+from cellmap_data.base_dataset import CellMapBaseDataset
+from cellmap_data.base_image import CellMapImageBase
+
+
+class TestCellMapBaseDataset:
+    """Test the CellMapBaseDataset abstract base class."""
+
+    def test_cannot_instantiate_abstract_class(self):
+        """Test that CellMapBaseDataset cannot be instantiated directly."""
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            CellMapBaseDataset()
+
+    def test_incomplete_implementation_raises_error(self):
+        """Test that incomplete implementations cannot be instantiated."""
+        
+        # Missing all abstract methods
+        class IncompleteDataset(CellMapBaseDataset):
+            pass
+        
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            IncompleteDataset()
+        
+        # Missing some abstract methods
+        class PartialDataset(CellMapBaseDataset):
+            @property
+            def class_counts(self):
+                return {}
+            
+            @property
+            def class_weights(self):
+                return {}
+        
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            PartialDataset()
+
+    def test_complete_implementation_can_be_instantiated(self):
+        """Test that complete implementations can be instantiated."""
+        
+        class CompleteDataset(CellMapBaseDataset):
+            def __init__(self):
+                self.classes = ["class1", "class2"]
+                self.input_arrays = {"raw": {}}
+                self.target_arrays = {"labels": {}}
+            
+            @property
+            def class_counts(self):
+                return {"class1": 100.0, "class2": 200.0}
+            
+            @property
+            def class_weights(self):
+                return {"class1": 0.67, "class2": 0.33}
+            
+            @property
+            def validation_indices(self):
+                return [0, 1, 2]
+            
+            def to(self, device, non_blocking=True):
+                return self
+            
+            def set_raw_value_transforms(self, transforms):
+                pass
+            
+            def set_target_value_transforms(self, transforms):
+                pass
+        
+        # Should not raise
+        dataset = CompleteDataset()
+        assert isinstance(dataset, CellMapBaseDataset)
+        assert dataset.classes == ["class1", "class2"]
+        assert dataset.class_counts == {"class1": 100.0, "class2": 200.0}
+        assert dataset.class_weights == {"class1": 0.67, "class2": 0.33}
+        assert dataset.validation_indices == [0, 1, 2]
+        assert dataset.to("cpu") is dataset
+        dataset.set_raw_value_transforms(lambda x: x)
+        dataset.set_target_value_transforms(lambda x: x)
+
+    def test_attributes_are_defined(self):
+        """Test that expected attributes are defined in the base class."""
+        # Check type annotations exist
+        assert hasattr(CellMapBaseDataset, '__annotations__')
+        annotations = CellMapBaseDataset.__annotations__
+        assert 'classes' in annotations
+        assert 'input_arrays' in annotations
+        assert 'target_arrays' in annotations
+
+
+class TestCellMapImageBase:
+    """Test the CellMapImageBase abstract base class."""
+
+    def test_cannot_instantiate_abstract_class(self):
+        """Test that CellMapImageBase cannot be instantiated directly."""
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            CellMapImageBase()
+
+    def test_incomplete_implementation_raises_error(self):
+        """Test that incomplete implementations cannot be instantiated."""
+        
+        # Missing all abstract methods
+        class IncompleteImage(CellMapImageBase):
+            pass
+        
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            IncompleteImage()
+        
+        # Missing some abstract methods
+        class PartialImage(CellMapImageBase):
+            @property
+            def bounding_box(self):
+                return {"x": (0, 100), "y": (0, 100)}
+            
+            @property
+            def sampling_box(self):
+                return {"x": (10, 90), "y": (10, 90)}
+        
+        with pytest.raises(TypeError, match="Can't instantiate abstract class"):
+            PartialImage()
+
+    def test_complete_implementation_can_be_instantiated(self):
+        """Test that complete implementations can be instantiated."""
+        
+        class CompleteImage(CellMapImageBase):
+            def __getitem__(self, center):
+                return torch.zeros((1, 64, 64))
+            
+            @property
+            def bounding_box(self):
+                return {"x": (0.0, 100.0), "y": (0.0, 100.0)}
+            
+            @property
+            def sampling_box(self):
+                return {"x": (10.0, 90.0), "y": (10.0, 90.0)}
+            
+            @property
+            def class_counts(self):
+                return 1000.0
+            
+            def to(self, device, non_blocking=True):
+                pass
+            
+            def set_spatial_transforms(self, transforms):
+                pass
+        
+        # Should not raise
+        image = CompleteImage()
+        assert isinstance(image, CellMapImageBase)
+        center = {"x": 50.0, "y": 50.0}
+        result = image[center]
+        assert isinstance(result, torch.Tensor)
+        assert result.shape == (1, 64, 64)
+        assert image.bounding_box == {"x": (0.0, 100.0), "y": (0.0, 100.0)}
+        assert image.sampling_box == {"x": (10.0, 90.0), "y": (10.0, 90.0)}
+        assert image.class_counts == 1000.0
+        image.to("cpu")
+        image.set_spatial_transforms(None)
+
+    def test_class_counts_supports_dict_return_type(self):
+        """Test that class_counts can return a dictionary."""
+        
+        class MultiClassImage(CellMapImageBase):
+            def __getitem__(self, center):
+                return torch.zeros((1, 64, 64))
+            
+            @property
+            def bounding_box(self):
+                return {"x": (0.0, 100.0)}
+            
+            @property
+            def sampling_box(self):
+                return {"x": (10.0, 90.0)}
+            
+            @property
+            def class_counts(self):
+                return {"class1": 500.0, "class2": 300.0, "class3": 200.0}
+            
+            def to(self, device, non_blocking=True):
+                pass
+            
+            def set_spatial_transforms(self, transforms):
+                pass
+        
+        image = MultiClassImage()
+        counts = image.class_counts
+        assert isinstance(counts, dict)
+        assert counts == {"class1": 500.0, "class2": 300.0, "class3": 200.0}
+
+    def test_bounding_box_can_be_none(self):
+        """Test that bounding_box property can return None."""
+        
+        class UnboundedImage(CellMapImageBase):
+            def __getitem__(self, center):
+                return torch.zeros((1, 64, 64))
+            
+            @property
+            def bounding_box(self):
+                return None
+            
+            @property
+            def sampling_box(self):
+                return None
+            
+            @property
+            def class_counts(self):
+                return 1000.0
+            
+            def to(self, device, non_blocking=True):
+                pass
+            
+            def set_spatial_transforms(self, transforms):
+                pass
+        
+        image = UnboundedImage()
+        assert image.bounding_box is None
+        assert image.sampling_box is None