Improved 'direct method' for converting contours to meshes

.github/workflows/main.yml

@@ -27,6 +27,7 @@ jobs:
              rsync -avP /out/ ./Windows/
              strip ./Windows/usr/bin/*exe
              strip ./Windows/usr/lib/*a
+             git config --global --add safe.directory '*' || true
       - name: test
         run: |
              export DEBIAN_FRONTEND='noninteractive'
@@ -47,7 +48,7 @@ jobs:
              ./integration_tests/Run.sh -v
       - name: create_zip
         run: |
-             export short_sha="$(git rev-parse --short HEAD)"
+             export short_sha="$(git rev-parse --short HEAD || printf 'unknown')"
              export DEBIAN_FRONTEND="noninteractive"
              apt-get update --yes
              apt-get install --yes --no-install-recommends coreutils binutils findutils rsync openssh-client patchelf zip
@@ -86,6 +87,7 @@ jobs:
         run: |
              ( ( while true ; do sleep 225 ; printf '\n\n' ; df -h ; printf '\n\n' ; free || true ; printf '\n\n' ; done ) &)
              ./docker/builders/ci/implementation_ci_debian_oldstable.sh
+             git config --global --add safe.directory '*' || true
       - name: test
         run: |
              ./integration_tests/Run.sh -v

compile_and_install.sh

@@ -16,8 +16,8 @@ shopt -s nocasematch
 
 # The temporary location in which to build.
 #BUILDROOT="/home/hal/Builds/DICOMautomaton/"
-BUILDROOT="/tmp/dcma_build"
-#BUILDROOT="build"
+# BUILDROOT="/tmp/dcma_build"
+BUILDROOT="build"
 
 DISTRIBUTION="auto" # used to tailor the build process for specific distributions/environments.
 
@@ -190,6 +190,7 @@ elif [[ "${DISTRIBUTION}" =~ .*debian.* ]] ; then
           -DWITH_ASAN=OFF \
           -DWITH_TSAN=OFF \
           -DWITH_MSAN=OFF \
+          -DCMAKE_EXPORT_COMPILE_COMMANDS=1 \
           ../
     fi
     JOBS=$(nproc)

scripts/compare_all_meshes.sh

@@ -0,0 +1,138 @@
+#!/bin/bash
+POSITIONAL_ARGS=()
+OPERATIONS=""
+VERBOSE=0
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -s|--show)
+      OPERATIONS+="-o SDL_Viewer"
+      shift # past argument
+      ;;
+    -v|--verbose)
+      VERBOSE=1
+      shift # past argument
+      ;;
+    -*|--*)
+      echo "Unknown option $1"
+      exit 1
+      ;;
+    *)
+      POSITIONAL_ARGS+=("$1") # save positional arg
+      shift # past argument
+      ;;
+  esac
+done
+
+tri_force_shape="
+subtract(){
+  join(){
+    plane(0,0,0, 1,1,0, 10);
+    plane(0,0,0, 0,1,1, 10);
+    plane(0,0,0, 1,0,1, 10);
+
+    plane(10,10,10, -1,-1,-0, 10);
+    plane(10,10,10, -0,-1,-1, 10);
+    plane(10,10,10, -1,-0,-1, 10);
+  };
+
+  join(){
+    plane(0,0,0, 1,2,0, 10);
+    plane(0,0,0, 0,1,2, 10);
+    plane(0,0,0, 2,0,1, 10);  
+
+    plane(10,10,10, -2,-1,-0, 10);
+    plane(10,10,10, -0,-2,-1, 10);
+    plane(10,10,10, -1,-0,-2, 10);
+  };
+};
+"
+
+default_res="0.25,0.25,0.25"
+
+declare -a shape_labels=("Sphere(10)" "aa_box(1.0,2.0,4.0)" "tri-force" "chamfered(box-sphere)")
+declare -a shapes=("Sphere(10)" "aa_box(1.0,2.0,4.0)" "$tri_force_shape" "chamfer_subtract(2.0){aa_box(8.0,20.0,20.0);sphere(12.0);}")
+declare -a resolutions=("$default_res" "0.25,0.25,0.75" "0.25,0.25,0.75" "$default_res")
+
+printf "| %-20s | %-13s | %-13s | %-15s | %-15s | %-10s | %-10s | %-10s | %-10s| %-8s | %-8s | \n\n" Shape "Hausdorff 1" "Hausdorff 2" "Surface Area 1" "Surface Area 2" "Area Diff" "Vol 1" "Vol 2" "Vol Diff" "Manifold 1" "Manifold 2"
+
+for i in ${!shapes[@]}
+do
+  shape=${shapes[$i]}
+  res=${resolutions[$i]}
+  shape_label=${shape_labels[$i]}
+
+  OUTPUT="$(dicomautomaton_dispatcher \
+    -v \
+    -o GenerateMeshes \
+      -p resolution=$res \
+      -p MeshLabel="original" \
+      -p Objects="$shape" \
+    -o GenerateSyntheticImages \
+      -p NumberOfImages='128' \
+      -p NumberOfRows='64', \
+      -p NumberOfColumns='64' \
+      -p NumberOfChannels='1' \
+      -p SliceThickness='1' \
+      -p SpacingBetweenSlices='1' \
+      -p VoxelWidth='1.0' \
+      -p VoxelHeight='1.0' \
+      -p ImageAnchor='-14.0, -14.0, -14.0' \
+      -p ImagePosition='0.0, 0.0, 0.0' \
+      -p ImageOrientationColumn='1.0, 0.0, 0.0' \
+      -p ImageOrientationRow='0.0, 1.0, 0.0' \
+      -p InstanceNumber='1' \
+      -p AcquisitionNumber='1' \
+      -p VoxelValue='0.0' \
+      -p StipleValue='nan' \
+    -o ConvertMeshesToContours \
+      -p ROILabel="original contours" \
+      -p MeshSelection="last" \
+      -p ImageSelection="last" \
+    -o ConvertContoursToMeshes \
+      -p NormalizedROILabelRegex=".*" \
+      -p ROILabelRegex=".*" \
+      -p MeshLabel="reconstructed" \
+      -p Method="direct" \
+    -o CompareMeshes \
+      -p MeshSelection1="#-0" \
+      -p MeshSelection2="#-1" \
+    $OPERATIONS 2>&1)"
+  if [ "$VERBOSE" == 1 ]; then
+    echo "$OUTPUT"
+  fi
+  HD_LINE=$(grep "HAUSDORFF DISTANCE" <<< "$OUTPUT")
+  SA_LINE=$(grep "SURFACE AREA: First mesh" <<< "$OUTPUT")
+  SA_DIFF_LINE=$(grep "SURFACE AREA (%) difference" <<< "$OUTPUT")
+  VOL_LINE=$(grep "VOLUME: First mesh" <<< "$OUTPUT")
+  VOL_DIFF_LINE=$(grep "VOLUME (%) difference" <<< "$OUTPUT")
+  MA_LINE=$(grep "MANIFOLD: First mesh" <<< "$OUTPUT")
+
+  HD1=$(sed -r "s/.*([0-9]+\.[0-9]+) or.*/\1/g" <<< $HD_LINE)
+  HD2=$(sed -r "s/.*or ([0-9]+\.[0-9]+).*/\1/g" <<< $HD_LINE)
+
+  SA1=$(sed -r "s/.*First mesh = ([0-9]+\.[0-9]+).*/\1/g" <<< $SA_LINE)
+  SA2=$(sed -r "s/.*second mesh = ([0-9]+\.[0-9]+).*/\1/g" <<< $SA_LINE)
+
+  SA_DIFF=$(sed -r "s/.*difference: (-?[0-9]+\.[0-9]+).*/\1/g" <<< $SA_DIFF_LINE)
+
+  V1=$(sed -r "s/.*First mesh = ([0-9]+\.[0-9]+).*/\1/g" <<< $VOL_LINE)
+  V2=$(sed -r "s/.*second mesh = ([0-9]+\.[0-9]+).*/\1/g" <<< $VOL_LINE)
+
+  V_DIFF=$(sed -r "s/.*difference: (-?[0-9]+\.[0-9]+).*/\1/g" <<< $VOL_DIFF_LINE)
+
+  MA1=$(sed -r "s/.*First mesh = ([0-9]+).*/\1/g" <<< $MA_LINE)
+  MA2=$(sed -r "s/.*second mesh = ([0-9]+).*/\1/g" <<< $MA_LINE)
+
+  printf "| %-20s | %-13.3f | %-13.3f | %-15.3f | %-15.3f | %-10.3f | %-10.3f | %-10.3f | %-10.3f | %-8s | %-8s |\n\n" $shape_label $HD1 $HD2 $SA1 $SA2 $SA_DIFF $V1 $V2 $V_DIFF $MA1 $MA2
+
+done
+
+
+
+
+
+
+
+
+

src/CMakeLists.txt

@@ -149,6 +149,9 @@ set_target_properties(  Standard_Scripts_obj PROPERTIES POSITION_INDEPENDENT_COD
 add_library(            Surface_Meshes_obj OBJECT Surface_Meshes.cc )
 set_target_properties(  Surface_Meshes_obj PROPERTIES POSITION_INDEPENDENT_CODE TRUE )
 
+add_library(            Complex_Branching_Meshing_obj OBJECT Complex_Branching_Meshing.cc )
+set_target_properties(  Complex_Branching_Meshing_obj PROPERTIES POSITION_INDEPENDENT_CODE TRUE )
+
 add_library(            Simple_Meshing_obj OBJECT Simple_Meshing.cc )
 set_target_properties(  Simple_Meshing_obj PROPERTIES POSITION_INDEPENDENT_CODE TRUE )
 
@@ -368,6 +371,7 @@ add_executable (dicomautomaton_dispatcher
     $<TARGET_OBJECTS:Insert_Contours_obj>
     $<TARGET_OBJECTS:Surface_Meshes_obj>
     $<TARGET_OBJECTS:Simple_Meshing_obj>
+    $<TARGET_OBJECTS:Complex_Branching_Meshing_obj>
     $<TARGET_OBJECTS:Regex_Selectors_obj>
     $<TARGET_OBJECTS:String_Parsing_obj>
     $<TARGET_OBJECTS:Metadata_obj>
@@ -463,6 +467,7 @@ if(WITH_WT)
         $<TARGET_OBJECTS:Insert_Contours_obj>
         $<TARGET_OBJECTS:Surface_Meshes_obj>
         $<TARGET_OBJECTS:Simple_Meshing_obj>
+        $<TARGET_OBJECTS:Complex_Branching_Meshing_obj>
         $<TARGET_OBJECTS:Regex_Selectors_obj>
         $<TARGET_OBJECTS:String_Parsing_obj>
         $<TARGET_OBJECTS:Metadata_obj>