Merge pull request #78 from KVSlab/hotfix-prepare-output-surface

Hotfix for prepare_output_surface

Author: hkjeldsberg

.circleci/config.yml

@@ -7,7 +7,7 @@ workflows:
 jobs:
   install-and-test:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.10.6
     working_directory: ~/repo
     steps:
       - checkout
@@ -23,14 +23,15 @@ jobs:
             # Export path
             export PATH="$HOME/miniconda/bin:$PATH"
             hash -r
-
+            
             # Set conda parameters
             conda config --set always_yes yes --set changeps1 no
             conda config --add channels conda-forge
             conda config --set channel_priority strict
-
+            
             # Set up environment
-            conda create -n morphman morphman 
+            conda install mamba
+            mamba create -n morphman morphman 
 
             # Activate environment
             source activate morphman

morphman/common/surface_operations.py

@@ -503,10 +503,10 @@ def prepare_output_surface(surface, original_surface, new_centerline, output_fil
         # Get relevant points
         tmp_points = points[region_id == i]
 
-        # Get normal
+        # Get slightly downscaled normal
         tmp_normal = np.cross(tmp_points[0] - tmp_points[-1],
                               tmp_points[0] - tmp_points[tmp_points.shape[0] // 2])
-        normal = tmp_normal / np.sqrt(np.sum(tmp_normal ** 2))
+        normal = tmp_normal / np.sqrt(np.sum(tmp_normal ** 2) * 1.02)
 
         # Get Center
         center = np.mean(tmp_points, axis=0)
@@ -532,7 +532,7 @@ def prepare_output_surface(surface, original_surface, new_centerline, output_fil
             in_dir = np.array(line.GetPoint(line.GetNumberOfPoints() - 5)) - \
                      np.array(line.GetPoint(line.GetNumberOfPoints() - 1))
 
-        in_dir = in_dir / np.sqrt(np.sum(in_dir ** 2))
+        in_dir = in_dir / np.sqrt(np.sum(in_dir ** 2) * 1.02)
         angle = np.arccos(np.dot(in_dir, normal)) * 180 / np.pi
         normal = -normal if 90 < angle < 270 else normal