Updated default values and UI. Added visualization for debugging

HarryHeres · May 2, 2024 · 00880e2 · 00880e2
1 parent 835ea1f
commit 00880e2
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Showing 3 changed files with 37 additions and 12 deletions.
diff --git a/SlicerBoneMorphing/Resources/UI/SlicerBoneMorphing.ui b/SlicerBoneMorphing/Resources/UI/SlicerBoneMorphing.ui
@@ -97,10 +97,10 @@
       <string>Preprocessing parameters</string>
      </property>
      <property name="checked">
-      <bool>false</bool>
+      <bool>true</bool>
      </property>
      <property name="collapsed">
-      <bool>true</bool>
+      <bool>false</bool>
      </property>
      <layout class="QFormLayout" name="formLayout_16">
       <item row="0" column="0" colspan="2">
@@ -112,7 +112,7 @@
          <item row="0" column="0">
           <widget class="QLabel" name="preprocessingDownsamplingDistanceThresholdLabel">
            <property name="toolTip">
-            <string>The higher the number, the lower the distance threshold for a neighbour point to be considered</string>
+            <string>Maximum distance in which points are considered neighbouring</string>
            </property>
            <property name="text">
             <string>Downsampling distance threshold:</string>
@@ -1107,7 +1107,7 @@
       <string>Postprocessing parameters</string>
      </property>
      <property name="checked">
-      <bool>true</bool>
+      <bool>false</bool>
      </property>
      <layout class="QFormLayout" name="formLayout_19">
       <item row="0" column="0">

diff --git a/SlicerBoneMorphing/src/logic/Constants.py b/SlicerBoneMorphing/src/logic/Constants.py
@@ -91,10 +91,10 @@
 PREPROCESSING_KEY_MAX_NN_NORMALS = "mnnn"
 PREPROCESSING_KEY_MAX_NN_FPFH = "mnf"
 
-PREPROCESSING_DEFAULT_VALUE_DOWNSAMPLING_DISTANCE_THRESHOLD = 0.1
-PREPROCESSING_DEFAULT_VALUE_RADIUS_NORMAL_SCALE = 4
+PREPROCESSING_DEFAULT_VALUE_DOWNSAMPLING_DISTANCE_THRESHOLD = 0.05
+PREPROCESSING_DEFAULT_VALUE_RADIUS_NORMAL_SCALE = 0.5
 PREPROCESSING_DEFAULT_VALUE_RADIUS_FEATURE_SCALE = 10
-PREPROCESSING_DEFAULT_VALUE_MAX_NN_NORMALS = 30
+PREPROCESSING_DEFAULT_VALUE_MAX_NN_NORMALS = 10
 PREPROCESSING_DEFAULT_VALUE_MAX_NN_FPFH = 100
 
 ### REGISTRATION PARAMETERS ###

diff --git a/SlicerBoneMorphing/src/logic/SlicerBoneMorphingLogic.py b/SlicerBoneMorphing/src/logic/SlicerBoneMorphingLogic.py
@@ -31,11 +31,30 @@
 elif platform == "win32":
     BCPD_EXEC += "bcpd_win32.exe"
 
+SOURCE_VISUALIZATION_COLOR = [0, 1, 0]
+TARGET_VISUALIZATION_COLOR = [1, 0, 0]
+
 
 class SlicerBoneMorphingLogic(ScriptedLoadableModuleLogic):
     def __init__(self, parent):
         ScriptedLoadableModuleLogic.__init__(self, parent)
 
+    def __visualize(self, source, target):
+        """
+        Only for debugging purposes
+        """
+        models = []
+
+        if (source != None):
+            source.paint_uniform_color(SOURCE_VISUALIZATION_COLOR)
+            models.append(source)
+
+        if (target != None):
+            target.paint_uniform_color(TARGET_VISUALIZATION_COLOR)
+            models.append(target)
+
+        o3d.visualization.draw_geometries(models)
+
     def generate_model(
             self,
             source_model: vtkMRMLModelNode,
@@ -71,11 +90,17 @@ def generate_model(
             print("Cannot continue with generating. Aborting...")
             return EXIT_FAILURE, None, None
 
+        source_mesh.transform(result_icp.transformation)
+
+        # self.__visualize(source_mesh, target_mesh)
+
         # BCPD stage
-        deformed = self.__deformable_registration(source_mesh.transform(result_icp.transformation), target_mesh, parameters[BCPD_KEY])
+        deformed = self.__deformable_registration(source_mesh, target_mesh, parameters[BCPD_KEY])
         if (deformed == None):
             return EXIT_FAILURE, None, None
 
+        # self.__visualize(deformed, None)
+
         generated_polydata, merged_polydata = self.__postprocess_meshes(deformed, target_mesh, parameters[POSTPROCESSING_KEY])
 
         return EXIT_OK, generated_polydata, merged_polydata
@@ -240,14 +265,14 @@ def __preprocess_point_cloud(
             max_nn_normals: int,
             max_nn_fpfh: int
     ) -> Tuple[o3d.geometry.PointCloud, o3d.pipelines.registration.Feature]:
-        ''' 
+        '''
             Perform downsampling of a mesh, normal estimation and computing FPFH feature of the point cloud.
 
             Parameters
             ----------
             o3d.geometry.PointCloud pcd: Source point cloud
             float downsampling_distance_threshold: Distance threshold for downsampling
-            float normals_estimation_radius: Radius for estimating normals 
+            float normals_estimation_radius: Radius for estimating normals
             float fpfh_estimation_radius: Radius for the FPFH computation
             int max_nn_normals: Maximum number of neighbours considered for normals estimation
             int max_nn_fpfh: Maximum number of neighbours considered for the FPFH calculation
@@ -339,12 +364,12 @@ def __deformable_registration(
             Parameters
             ----------
             o3d.geometry.PointCloud sourcePcd: source point cloud
-            o3d.geometry.PointCloud targetPcd: target point cloud 
+            o3d.geometry.PointCloud targetPcd: target point cloud
             string bcpdParameters: parameters for the BCPD algorithm
 
             Returns
             -------
-            o3d.geometry.TriangleMesh representing the new deformed mesh 
+            o3d.geometry.TriangleMesh representing the new deformed mesh
         """
         source_array = np.asarray(source_pcd.vertices, dtype=np.float32)
         target_array = np.asarray(target_pcd.vertices, dtype=np.float32)