fix tests and lint

Author: JLBegin

pytissueoptics/examples/rayscattering/ex06.py

@@ -14,18 +14,17 @@ def exampleCode():
 
     material = ScatteringMaterial(mu_s=10, mu_a=1, g=0.98, n=1.0)
 
-    cube = Cuboid(
-        a=3, b=3, c=3, position=Vector(0, 0, 0), material=material, label="cube"
-    )
+    cube = Cuboid(a=3, b=3, c=3, position=Vector(0, 0, 0), material=material, label="cube")
     detector = Circle(
-        radius=0.25, orientation=Vector(0, 0, -1), position=Vector(0, 0.5, 1.501), label="detector",
+        radius=0.25,
+        orientation=Vector(0, 0, -1),
+        position=Vector(0, 0.5, 1.501),
+        label="detector",
     ).asDetector(halfAngle=np.pi / 4)
     scene = ScatteringScene([cube, detector])
 
     logger = EnergyLogger(scene)
-    source = DirectionalSource(
-        position=Vector(0, -0.5, -2), direction=Vector(0, 0, 1), N=N, diameter=0.5
-    )
+    source = DirectionalSource(position=Vector(0, -0.5, -2), direction=Vector(0, 0, 1), N=N, diameter=0.5)
 
     source.propagate(scene, logger)
 

pytissueoptics/rayscattering/display/viewer.py

@@ -219,7 +219,9 @@ def _addPointCloud(self, style: PointCloudStyle):
         logger = self._logger if style.detectedBy is None else self._logger.getFiltered(style.detectedBy)
 
         pointCloud = PointCloudFactory(logger).getPointCloud(
-            solidLabel=style.solidLabel, surfaceLabel=style.surfaceLabel, energyType=style.energyType,
+            solidLabel=style.solidLabel,
+            surfaceLabel=style.surfaceLabel,
+            energyType=style.energyType,
         )
 
         self._drawPointCloudOfSolids(pointCloud, style)

pytissueoptics/rayscattering/energyLogging/energyLogger.py

@@ -3,7 +3,7 @@
 import json
 import os
 import pickle
-from typing import List, Optional, TextIO, Union, Dict
+from typing import Dict, List, Optional, TextIO, Union
 
 import numpy as np
 
@@ -409,9 +409,7 @@ def export(self, exportName: str):
 
         self._exportSceneInfo(f"{exportName}.json", solidLabels)
 
-    def _writeKeyData(
-        self, file: TextIO, key: InteractionKey, solidIndex: int, surfaceIndex: int
-    ):
+    def _writeKeyData(self, file: TextIO, key: InteractionKey, solidIndex: int, surfaceIndex: int):
         if key not in self._data or self._data[key].dataPoints is None:
             return
 

pytissueoptics/rayscattering/photon.py

@@ -30,7 +30,7 @@ def __init__(self, position: Vector, direction: Vector, ID: int = 0):
         self._intersectionFinder: Optional[IntersectionFinder] = None
         self._logger: Optional[Logger] = None
 
-        self._lastIntersectedDetector: Optional[str] = None  # Prevent intersecting with a detector when passing through it.
+        self._lastIntersectedDetector: Optional[str] = None
 
     @property
     def isAlive(self) -> bool:
@@ -99,7 +99,7 @@ def step(self, distance=0) -> float:
                 # Prevent re-intersecting with the same detector when passing through it.
                 self._lastIntersectedDetector = intersection.insideEnvironment.solid.getLabel()
 
-                # skipping vertex check for now. TODO? Unclear stepCorrection and implications.
+                # skipping vertex check if detector
                 return intersection.distanceLeft
             else:
                 distanceLeft = self.reflectOrRefract(intersection)

pytissueoptics/rayscattering/tests/display/testViewer.py

@@ -8,7 +8,7 @@
 from pytissueoptics.rayscattering.display.profiles import Profile1D, ProfileFactory
 from pytissueoptics.rayscattering.display.viewer import PointCloudStyle, Viewer, Visibility
 from pytissueoptics.rayscattering.display.views import View2D
-from pytissueoptics.rayscattering.energyLogging import EnergyLogger, PointCloud, PointCloudFactory
+from pytissueoptics.rayscattering.energyLogging import EnergyLogger, PointCloud
 from pytissueoptics.rayscattering.scatteringScene import ScatteringScene
 from pytissueoptics.rayscattering.source import Source
 from pytissueoptics.scene.geometry import BoundingBox
@@ -112,14 +112,11 @@ def testWhenShow3DWithSource_shouldDisplaySource(self):
         self.mock3DViewer.show.assert_called_once()
 
     def testWhenShow3DWithDefaultPointCloud_shouldDisplayPointCloudOfSolidsAndSurfaceLeaving(self):
-        mockPointCloudFactory = mock(PointCloudFactory)
         aPointCloud = PointCloud(
-            solidPoints=np.array([[0.5, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0], [-1, 0, 0, 0]])
+            solidPoints=np.array([[0.5, 0, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0, 0], [-1, 0, 0, 0, 0]])
         )
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn(aPointCloud)
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        self.viewer.show3D(visibility=Visibility.POINT_CLOUD)
+        with self._mockPointCloud(aPointCloud):
+            self.viewer.show3D(visibility=Visibility.POINT_CLOUD)
 
         self.mock3DViewer.addDataPoints.assert_called()
         addedSolidPoints = self.mock3DViewer.addDataPoints.call_args_list[0][0][0]
@@ -130,25 +127,21 @@ def testWhenShow3DWithDefaultPointCloud_shouldDisplayPointCloudOfSolidsAndSurfac
         self.mock3DViewer.show.assert_called_once()
 
     def testGivenNoData_whenShow3DWithPointCloud_shouldNotDisplayPointCloud(self):
-        mockPointCloudFactory = mock(PointCloudFactory)
         aPointCloud = PointCloud()
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn(aPointCloud)
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        self.viewer.show3D(visibility=Visibility.POINT_CLOUD)
+        with self._mockPointCloud(aPointCloud):
+            self.viewer.show3D(visibility=Visibility.POINT_CLOUD)
 
         self.mock3DViewer.addDataPoints.assert_not_called()
         self.mock3DViewer.show.assert_called_once()
 
     def testWhenShow3DWithSurfacePointCloud_shouldOnlyDisplaySurfacePoints(self):
-        mockPointCloudFactory = mock(PointCloudFactory)
         aPointCloud = PointCloud(
-            solidPoints=np.array([[0.5, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0], [-1, 0, 0, 0]])
+            solidPoints=np.array([[0.5, 0, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0, 0], [-1, 0, 0, 0, 0]])
         )
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn(aPointCloud)
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        self.viewer.show3D(visibility=Visibility.POINT_CLOUD, pointCloudStyle=PointCloudStyle(showSolidPoints=False))
+        with self._mockPointCloud(aPointCloud):
+            self.viewer.show3D(
+                visibility=Visibility.POINT_CLOUD, pointCloudStyle=PointCloudStyle(showSolidPoints=False)
+            )
 
         self.mock3DViewer.addDataPoints.assert_called_once()
         self.assertTrue(
@@ -157,19 +150,16 @@ def testWhenShow3DWithSurfacePointCloud_shouldOnlyDisplaySurfacePoints(self):
         self.mock3DViewer.show.assert_called_once()
 
     def testWhenShow3DWithEnteringSurfacePointCloud_shouldOnlyDisplayEnteringSurfacePoints(self):
-        mockPointCloudFactory = mock(PointCloudFactory)
         aPointCloud = PointCloud(
-            solidPoints=np.array([[0.5, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0], [-1, 1, 1, 1]])
-        )
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn(aPointCloud)
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        self.viewer.show3D(
-            visibility=Visibility.POINT_CLOUD,
-            pointCloudStyle=PointCloudStyle(
-                showSolidPoints=False, showSurfacePointsLeaving=False, showSurfacePointsEntering=True
-            ),
+            solidPoints=np.array([[0.5, 0, 0, 0, 0]]), surfacePoints=np.array([[1, 0, 0, 0, 0], [-1, 1, 1, 0, 1]])
         )
+        with self._mockPointCloud(aPointCloud):
+            self.viewer.show3D(
+                visibility=Visibility.POINT_CLOUD,
+                pointCloudStyle=PointCloudStyle(
+                    showSolidPoints=False, showSurfacePointsLeaving=False, showSurfacePointsEntering=True
+                ),
+            )
 
         self.mock3DViewer.addDataPoints.assert_called_once()
         self.assertTrue(
@@ -206,49 +196,38 @@ def testWhenShow3DWithViewsIndexList_shouldAdd2DImageOfTheseViewsInThe3DDisplay(
         self.mock3DViewer.show.assert_called_once()
 
     def testGiven3DLogger_whenShow3DDefault_shouldDisplayEverythingExceptViews(self):
-        mockPointCloudFactory = mock(PointCloudFactory)
         aPointCloud = PointCloud()
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn(aPointCloud)
-        self.viewer._pointCloudFactory = mockPointCloudFactory
 
-        self.viewer.show3D()
+        with self._mockPointCloud(aPointCloud):
+            self.viewer.show3D()
 
         verify(self.source, times=1).addToViewer(...)
         verify(self.scene, times=1).addToViewer(...)
-        verify(mockPointCloudFactory, times=1).getPointCloud(...)
         self.mock3DViewer.addImage.assert_not_called()
         self.mock3DViewer.show.assert_called_once()
 
     def testGiven2DLogger_whenShow3DDefault_shouldDisplayEverythingExceptPointCloud(self):
         self._givenLoggerWithXSceneView()
         self.logger.has3D = False
 
-        mockPointCloudFactory = mock(PointCloudFactory)
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn()
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        self.viewer.show3D()
+        with self._mockPointCloud(PointCloud()):
+            self.viewer.show3D()
 
         verify(self.source, times=1).addToViewer(...)
         verify(self.scene, times=1).addToViewer(...)
-        verify(mockPointCloudFactory, times=0).getPointCloud(...)
         self.mock3DViewer.addImage.assert_called()
         self.mock3DViewer.show.assert_called_once()
 
     def testGiven2DLogger_whenShow3DWithDefault3DVisibility_shouldWarnAndDisplayDefault2D(self):
         self._givenLoggerWithXSceneView()
         self.logger.has3D = False
 
-        mockPointCloudFactory = mock(PointCloudFactory)
-        when(mockPointCloudFactory).getPointCloud(...).thenReturn()
-        self.viewer._pointCloudFactory = mockPointCloudFactory
-
-        with self.assertWarns(UserWarning):
-            self.viewer.show3D(visibility=Visibility.DEFAULT_3D)
+        with self._mockPointCloud(PointCloud()):
+            with self.assertWarns(UserWarning):
+                self.viewer.show3D(visibility=Visibility.DEFAULT_3D)
 
         verify(self.source, times=1).addToViewer(...)
         verify(self.scene, times=1).addToViewer(...)
-        verify(mockPointCloudFactory, times=0).getPointCloud(...)
         self.mock3DViewer.addImage.assert_called()
         self.mock3DViewer.show.assert_called_once()
 
@@ -260,3 +239,10 @@ def _givenLoggerWithXSceneView(self):
         self.logger.views = [sceneView]
         when(self.logger).updateView(sceneView).thenReturn()
         when(self.scene).getBoundingBox().thenReturn(BoundingBox([-2, 2], [-2, 2], [0, 5]))
+
+    @staticmethod
+    def _mockPointCloud(pointCloud: PointCloud):
+        return patch(
+            "pytissueoptics.rayscattering.display.viewer.PointCloudFactory.getPointCloud",
+            return_value=pointCloud,
+        )

pytissueoptics/rayscattering/tests/energyLogging/testEnergyLogger.py

@@ -296,10 +296,10 @@ def testWhenExport_shouldExport3DDataPointsToFile(self):
         self.logger = EnergyLogger(scene)
 
         # Log entering surface event, world scattering event and scattering event in both solids.
-        self.logger.logDataPoint(0.1, Vector(0.7, 0.8, 0.8), InteractionKey("middleLayer"))
-        self.logger.logDataPoint(-0.9, Vector(0.5, 1.0, 0.75), InteractionKey("frontLayer", "interface1"))
-        self.logger.logDataPoint(0.4, Vector(0, 5, 0), InteractionKey("sphere"))
-        self.logger.logDataPoint(0.2, Vector(0, 0, 0), InteractionKey(WORLD_SOLID_LABEL))
+        self.logger.logDataPoint(0.1, Vector(0.7, 0.8, 0.8), InteractionKey("middleLayer"), ID=1)
+        self.logger.logDataPoint(-0.9, Vector(0.5, 1.0, 0.75), InteractionKey("frontLayer", "interface1"), ID=0)
+        self.logger.logDataPoint(0.4, Vector(0, 5, 0), InteractionKey("sphere"), ID=0)
+        self.logger.logDataPoint(0.2, Vector(0, 0, 0), InteractionKey(WORLD_SOLID_LABEL), ID=0)
 
         with tempfile.TemporaryDirectory() as tempDir:
             filePath = os.path.join(tempDir, "test_sim")
@@ -309,12 +309,15 @@ def testWhenExport_shouldExport3DDataPointsToFile(self):
             with open(filePath + ".csv", "r") as f:
                 lines = f.readlines()
 
+            def parse_line(line):
+                return list(map(float, line.strip().split(",")))
+
             self.assertEqual(5, len(lines))
-            self.assertEqual("energy,x,y,z,solid_index,surface_index\n", lines[0])
-            self.assertEqual("0.2,0.0,0.0,0.0,-1,-1\n", lines[1])
-            self.assertEqual("-0.9,0.5,1.0,0.75,1,5\n", lines[2])
-            self.assertEqual("0.1,0.7,0.8,0.8,2,-1\n", lines[3])
-            self.assertEqual("0.4,0.0,5.0,0.0,3,-1\n", lines[4])
+            self.assertEqual("energy,x,y,z,photon_index,solid_index,surface_index\n", lines[0])
+            self.assertEqual(parse_line(lines[1]), [0.2, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0])
+            self.assertEqual(parse_line(lines[2]), [-0.9, 0.5, 1.0, 0.75, 0.0, 1.0, 5.0])
+            self.assertEqual(parse_line(lines[3]), [0.1, 0.7, 0.8, 0.8, 1.0, 2.0, -1.0])
+            self.assertEqual(parse_line(lines[4]), [0.4, 0.0, 5.0, 0.0, 0.0, 3.0, -1.0])
 
     def testWhenExport_shouldExportMetadataToFile(self):
         scene = PhantomTissue(worldMaterial=ScatteringMaterial(0.1, 0.1, 0.99))

pytissueoptics/rayscattering/tests/opencl/src/testCLFresnel.py

@@ -55,6 +55,8 @@ def _setUpWith(self, n1=1.0, n2=1.5, normal=Vector(0, 0, 1)):
                     self.INSIDE_SOLID_ID,
                     self.OUTSIDE_SOLID_ID,
                     False,
+                    False,
+                    0,
                 )
             ]
         )