Add tracing support and detectors

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
   "Pygments",
   "siphash24; python_version < '3.13'",
   "pyopencl",
-  "vtk>=9.4",
+  "vtk>=9.4,<9.5",
   "mayavi-dev",
   "pyqt5",
 ]
@@ -67,3 +67,14 @@ ignore = [
 [tool.ruff.format]
 quote-style = "double"
 indent-style = "space"
+
+[tool.coverage.run]
+source = ["pytissueoptics"]
+omit = [
+    "*/tests/*",
+    "*/test*.py",
+    "*/examples/*",
+]
+
+[tool.coverage.report]
+show_missing = true

pytissueoptics/examples/rayscattering/ex06.py

@@ -0,0 +1,54 @@
+import env  # noqa: F401
+
+from pytissueoptics import *  # noqa: F403
+
+TITLE = "Detectors"
+
+DESCRIPTION = """ Sampling volume simulation with a directional source and two circle detectors. """
+
+
+def exampleCode():
+    import numpy as np
+
+    N = 1000000 if hardwareAccelerationIsAvailable() else 1000
+
+    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")
+
+    detectorA = Circle(
+        radius=0.25,
+        orientation=Vector(0, 0, -1),
+        position=Vector(0, 1, 1.501),
+        label="detectorA",
+    ).asDetector(halfAngle=np.pi / 4)
+
+    detectorB = Circle(
+        radius=0.25,
+        orientation=Vector(0, 0, -1),
+        position=Vector(0, -1, 1.501),
+        label="detectorB",
+    ).asDetector(halfAngle=np.pi / 4)
+
+    scene = ScatteringScene([cube, detectorA, detectorB])
+
+    logger = EnergyLogger(scene)
+    source = DirectionalSource(position=Vector(0, 0, -2), direction=Vector(0, 0, 1), N=N, diameter=0.5)
+
+    source.propagate(scene, logger)
+
+    viewer = Viewer(scene, source, logger)
+    viewer.reportStats()
+
+    # Either filter the whole logger
+    logger.filter(detectedBy=["detectorA", "detectorB"])
+    viewer.show2D(View2DProjectionX())
+    viewer.show3D()
+
+    # ... or keep the logger intact and filter individual views
+    # viewer.show2D(View2DProjectionX(detectedBy="detectorA"))
+    # viewer.show3D(pointCloudStyle=PointCloudStyle(detectedBy=["detectorA", "detectorB"]))
+
+
+if __name__ == "__main__":
+    exampleCode()

pytissueoptics/examples/scene/example2.py

@@ -9,9 +9,9 @@
 def exampleCode():
     from pytissueoptics.scene import Cuboid, Vector, get3DViewer
 
-    cuboid1 = Cuboid(1, 1, 1, position=Vector(2, 0, 0))
-    cuboid2 = Cuboid(2, 1, 1, position=Vector(0, 2, 0))
-    cuboid3 = Cuboid(3, 1, 1, position=Vector(0, 0, 2))
+    cuboid1 = Cuboid(1, 1, 1, position=Vector(2, 0, 0), label="1")
+    cuboid2 = Cuboid(2, 1, 1, position=Vector(0, 2, 0), label="2")
+    cuboid3 = Cuboid(3, 1, 1, position=Vector(0, 0, 2), label="3")
 
     viewer = get3DViewer()
     viewer.add(cuboid1, cuboid2, cuboid3, representation="wireframe", lineWidth=5)

pytissueoptics/rayscattering/display/viewer.py

@@ -66,6 +66,7 @@ def __init__(
         showSurfacePointsLeaving: bool = True,
         showSurfacePointsEntering: bool = False,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
         showPointsAsSpheres: bool = False,
         pointSize: float = 0.15,
         scaleWithValue: bool = True,
@@ -82,6 +83,7 @@ def __init__(
         self.showSurfacePointsLeaving = showSurfacePointsLeaving
         self.showSurfacePointsEntering = showSurfacePointsEntering
         self.energyType = energyType
+        self.detectedBy = detectedBy
         self.showPointsAsSpheres = showPointsAsSpheres
 
         self.pointSize = pointSize
@@ -103,7 +105,6 @@ def __init__(self, scene: ScatteringScene, source: Source, logger: EnergyLogger)
         self._logger = logger
 
         self._viewer3D = None
-        self._pointCloudFactory = PointCloudFactory(logger)
         self._profileFactory = ProfileFactory(scene, logger)
 
     def listViews(self):
@@ -169,7 +170,7 @@ def show3DVolumeSlicer(
                 f"Consider using a larger binSize or tighter limits."
             )
 
-        points = self._pointCloudFactory.getPointCloudOfSolids(energyType=energyType).solidPoints
+        points = PointCloudFactory(self._logger).getPointCloudOfSolids(energyType=energyType).solidPoints
         try:
             hist, _ = np.histogramdd(points[:, 1:], bins=bins, weights=points[:, 0], range=limits)
         except MemoryError:
@@ -215,8 +216,12 @@ def reportStats(self, solidLabel: str = None, saveToFile: str = None, verbose=Tr
         stats.report(solidLabel=solidLabel, saveToFile=saveToFile, verbose=verbose)
 
     def _addPointCloud(self, style: PointCloudStyle):
-        pointCloud = self._pointCloudFactory.getPointCloud(
-            solidLabel=style.solidLabel, surfaceLabel=style.surfaceLabel, energyType=style.energyType
+        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,
         )
 
         self._drawPointCloudOfSolids(pointCloud, style)
@@ -241,7 +246,7 @@ def _drawPointCloudOfSurfaces(self, pointCloud: PointCloud, style: PointCloudSty
         if pointCloud.surfacePoints is None:
             return
 
-        surfacePoints = np.empty((0, 4))
+        surfacePoints = np.empty((0, 5))
 
         if style.showSurfacePointsLeaving:
             surfacePoints = np.vstack((surfacePoints, pointCloud.leavingSurfacePoints))

pytissueoptics/rayscattering/display/views/defaultViews.py

@@ -21,6 +21,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             projectionDirection,
@@ -29,6 +30,7 @@ def __init__(
             limits=limits,
             binSize=binSize,
             energyType=energyType,
+            detectedBy=detectedBy,
         )
 
     def _filter(self, dataPoints: np.ndarray) -> np.ndarray:
@@ -42,9 +44,15 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
-            *DEFAULT_X_VIEW_DIRECTIONS, solidLabel=solidLabel, limits=limits, binSize=binSize, energyType=energyType
+            *DEFAULT_X_VIEW_DIRECTIONS,
+            solidLabel=solidLabel,
+            limits=limits,
+            binSize=binSize,
+            energyType=energyType,
+            detectedBy=detectedBy,
         )
 
 
@@ -55,9 +63,15 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
-            *DEFAULT_Y_VIEW_DIRECTIONS, solidLabel=solidLabel, limits=limits, binSize=binSize, energyType=energyType
+            *DEFAULT_Y_VIEW_DIRECTIONS,
+            solidLabel=solidLabel,
+            limits=limits,
+            binSize=binSize,
+            energyType=energyType,
+            detectedBy=detectedBy,
         )
 
 
@@ -68,9 +82,15 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
-            *DEFAULT_Z_VIEW_DIRECTIONS, solidLabel=solidLabel, limits=limits, binSize=binSize, energyType=energyType
+            *DEFAULT_Z_VIEW_DIRECTIONS,
+            solidLabel=solidLabel,
+            limits=limits,
+            binSize=binSize,
+            energyType=energyType,
+            detectedBy=detectedBy,
         )
 
 
@@ -84,6 +104,7 @@ def __init__(
         surfaceEnergyLeaving: bool = True,
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             projectionDirection,
@@ -93,6 +114,7 @@ def __init__(
             surfaceEnergyLeaving=surfaceEnergyLeaving,
             limits=limits,
             binSize=binSize,
+            detectedBy=detectedBy,
         )
 
     def _filter(self, dataPoints: np.ndarray) -> np.ndarray:
@@ -116,6 +138,7 @@ def __init__(
         surfaceEnergyLeaving: bool = True,
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_X_VIEW_DIRECTIONS,
@@ -124,6 +147,7 @@ def __init__(
             surfaceEnergyLeaving=surfaceEnergyLeaving,
             limits=limits,
             binSize=binSize,
+            detectedBy=detectedBy,
         )
 
 
@@ -135,6 +159,7 @@ def __init__(
         surfaceEnergyLeaving: bool = True,
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_Y_VIEW_DIRECTIONS,
@@ -143,6 +168,7 @@ def __init__(
             surfaceEnergyLeaving=surfaceEnergyLeaving,
             limits=limits,
             binSize=binSize,
+            detectedBy=detectedBy,
         )
 
 
@@ -154,6 +180,7 @@ def __init__(
         surfaceEnergyLeaving: bool = True,
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_Z_VIEW_DIRECTIONS,
@@ -162,6 +189,7 @@ def __init__(
             surfaceEnergyLeaving=surfaceEnergyLeaving,
             limits=limits,
             binSize=binSize,
+            detectedBy=detectedBy,
         )
 
 
@@ -176,6 +204,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             projectionDirection,
@@ -186,6 +215,7 @@ def __init__(
             limits=limits,
             binSize=binSize,
             energyType=energyType,
+            detectedBy=detectedBy,
         )
 
     def setContext(self, limits3D: List[Tuple[float, float]], binSize3D: Tuple[float, float, float]):
@@ -210,6 +240,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_X_VIEW_DIRECTIONS,
@@ -219,6 +250,7 @@ def __init__(
             limits=limits,
             binSize=binSize,
             energyType=energyType,
+            detectedBy=detectedBy,
         )
 
 
@@ -231,6 +263,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_Y_VIEW_DIRECTIONS,
@@ -240,6 +273,7 @@ def __init__(
             limits=limits,
             binSize=binSize,
             energyType=energyType,
+            detectedBy=detectedBy,
         )
 
 
@@ -252,6 +286,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         super().__init__(
             *DEFAULT_Z_VIEW_DIRECTIONS,
@@ -261,4 +296,5 @@ def __init__(
             limits=limits,
             binSize=binSize,
             energyType=energyType,
+            detectedBy=detectedBy,
         )

pytissueoptics/rayscattering/display/views/view2D.py

@@ -50,6 +50,7 @@ def __init__(
         limits: Tuple[Tuple[float, float], Tuple[float, float]] = None,
         binSize: Union[float, Tuple[int, int]] = None,
         energyType=EnergyType.DEPOSITION,
+        detectedBy: Union[str, List[str]] = None,
     ):
         """
         The 2D view plane is obtained by looking towards the 'projectionDirection'. The 'horizontalDirection'
@@ -78,6 +79,7 @@ def __init__(
         self._position = position
         self._thickness = thickness
         self._energyType = energyType
+        self._detectedBy = detectedBy
 
         limits = [sorted(limit) for limit in limits] if limits else [None, None]
         self._limitsU, self._limitsV = limits
@@ -103,6 +105,7 @@ def setContext(self, limits3D: List[Tuple[float, float]], binSize3D: Tuple[float
 
         limits = [self._limitsU, self._limitsV]
         self._binsU, self._binsV = [int((limit[1] - limit[0]) / bin_) for limit, bin_ in zip(limits, self._binSize)]
+        self._binsU, self._binsV = max(1, self._binsU), max(1, self._binsV)
 
         if self._verticalIsNegative:
             self._limitsV = self._limitsV[::-1]
@@ -121,6 +124,10 @@ def setContext(self, limits3D: List[Tuple[float, float]], binSize3D: Tuple[float
     def energyType(self) -> EnergyType:
         return self._energyType
 
+    @property
+    def detectedBy(self) -> Union[str, List[str], None]:
+        return self._detectedBy
+
     def extractData(self, dataPoints: np.ndarray):
         """
         Used internally by Logger2D to store 3D datapoints into this 2D view.
@@ -245,6 +252,8 @@ def isEqualTo(self, other: "View2D") -> bool:
             return False
         if self._energyType != other._energyType:
             return False
+        if self._detectedBy != other._detectedBy:
+            return False
         return True
 
     def isContainedBy(self, other: "View2D") -> bool:
@@ -260,6 +269,8 @@ def isContainedBy(self, other: "View2D") -> bool:
             return False
         if self._thickness != other._thickness:
             return False
+        if self._detectedBy != other._detectedBy:
+            return False
 
         # TODO: change/remove the following once the algorithm can extract a view contained inside a bigger view.
         isTransposed = self.axisU != other.axisU