Fix vessel structure generation at tissue boundaries

simpa/utils/libraries/structure_library/VesselStructure.py

@@ -67,7 +67,7 @@ def calculate_vessel_samples(self, position, direction, bifurcation_length, radi
         radius_array = [radius]
         samples = 0
 
-        while torch.all(position < torch.tensor(volume_dimensions).to(self.torch_device)) and torch.all(0 <= position):
+        while True:
             if samples >= bifurcation_length:
                 vessel_branch_positions1 = position
                 vessel_branch_positions2 = position
@@ -101,6 +101,11 @@ def calculate_vessel_samples(self, position, direction, bifurcation_length, radi
                 break
 
             position = torch.add(position, direction)
+
+            # Check if the new position is within bounds before adding it
+            if not (torch.all(position < torch.tensor(volume_dimensions).to(self.torch_device)) and torch.all(0 <= position)):
+                break
+
             position_array.append(position)
             radius_array.append(np.random.uniform(-1, 1) * radius_variation + radius)
 
@@ -188,3 +193,4 @@ def define_vessel_structure_settings(vessel_start_mm: list,
         Tags.ADHERE_TO_DEFORMATION: adhere_to_deformation,
         Tags.STRUCTURE_TYPE: Tags.VESSEL_STRUCTURE
     }
+# temp

simpa_tests/automatic_tests/structure_tests/test_vesseltree.py

@@ -113,3 +113,57 @@ def test_vessel_tree_geometrical_volume(self):
             assert 0 <= value <= 1
 
         self.assertTrue(np.sum(ts.geometrical_volume) > 0)
+
+    def test_vessel_starting_at_boundary(self):
+        """
+        Test that vessels starting exactly at a tissue boundary are created correctly.
+        This is a regression test for the issue where vessels starting at boundaries
+        (e.g., y=16 for a 16mm volume) would not create proper tube structures.
+        """
+        # Create settings for a vessel starting at the Y boundary
+        self.global_settings[Tags.SPACING_MM] = 0.5
+        self.global_settings[Tags.DIM_VOLUME_X_MM] = 16
+        self.global_settings[Tags.DIM_VOLUME_Y_MM] = 16
+        self.global_settings[Tags.DIM_VOLUME_Z_MM] = 10
+
+        # Vessel starting exactly at boundary (y=16)
+        vessel_settings_boundary = Settings()
+        vessel_settings_boundary[Tags.STRUCTURE_START_MM] = [10, 16, 0.2]
+        vessel_settings_boundary[Tags.STRUCTURE_DIRECTION] = [-1, -1, 0.0]
+        vessel_settings_boundary[Tags.STRUCTURE_RADIUS_MM] = 2.0
+        vessel_settings_boundary[Tags.STRUCTURE_CURVATURE_FACTOR] = 0.0
+        vessel_settings_boundary[Tags.STRUCTURE_RADIUS_VARIATION_FACTOR] = 1.0
+        vessel_settings_boundary[Tags.STRUCTURE_BIFURCATION_LENGTH_MM] = 1000.0
+        vessel_settings_boundary[Tags.MOLECULE_COMPOSITION] = TissueLibrary.muscle()
+        vessel_settings_boundary[Tags.CONSIDER_PARTIAL_VOLUME] = True
+        vessel_settings_boundary[Tags.ADHERE_TO_DEFORMATION] = False
+
+        # Vessel starting just inside boundary (y=15.99)
+        vessel_settings_inside = Settings()
+        vessel_settings_inside[Tags.STRUCTURE_START_MM] = [10, 15.99, 0.2]
+        vessel_settings_inside[Tags.STRUCTURE_DIRECTION] = [-1, -1, 0.0]
+        vessel_settings_inside[Tags.STRUCTURE_RADIUS_MM] = 2.0
+        vessel_settings_inside[Tags.STRUCTURE_CURVATURE_FACTOR] = 0.0
+        vessel_settings_inside[Tags.STRUCTURE_RADIUS_VARIATION_FACTOR] = 1.0
+        vessel_settings_inside[Tags.STRUCTURE_BIFURCATION_LENGTH_MM] = 1000.0
+        vessel_settings_inside[Tags.MOLECULE_COMPOSITION] = TissueLibrary.muscle()
+        vessel_settings_inside[Tags.CONSIDER_PARTIAL_VOLUME] = True
+        vessel_settings_inside[Tags.ADHERE_TO_DEFORMATION] = False
+
+        vessel_boundary = VesselStructure(self.global_settings, vessel_settings_boundary)
+        vessel_inside = VesselStructure(self.global_settings, vessel_settings_inside)
+
+        # Both vessels should have similar volumes (at least 80% similarity)
+        # The slight difference is due to randomness in vessel generation
+        volume_boundary = np.sum(vessel_boundary.geometrical_volume)
+        volume_inside = np.sum(vessel_inside.geometrical_volume)
+
+        # Ensure both vessels have substantial volume
+        self.assertGreater(volume_boundary, 100, "Vessel at boundary should have substantial volume")
+        self.assertGreater(volume_inside, 100, "Vessel inside should have substantial volume")
+
+        # Check that they are similar in size (within 20% tolerance)
+        ratio = volume_boundary / volume_inside
+        self.assertGreater(
+            ratio, 0.8, f"Vessel at boundary should be at least 80% of inside vessel size, got {ratio:.2%}")
+        self.assertLess(ratio, 1.2, f"Vessel at boundary should be at most 120% of inside vessel size, got {ratio:.2%}")