Ensure images are axis aligned when loading

.github/workflows/build-linux-debug.yml

@@ -61,13 +61,30 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
+    - name: Restore Dependencies Cache
+      id: cache-deps-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: /github/home/install
+        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
     - name: Check space4
       run: df -h
 
     - name: Build Dependencies
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
+    - name: Save Dependencies Cache
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: /github/home/install
+        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+
     - name: Check space5
       run: df -h
 

.github/workflows/build-linux.yml

@@ -59,14 +59,32 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
+    - name: Restore Dependencies Cache
+      id: cache-deps-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: /github/home/install
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
     - name: try import vtk
       shell: bash -l {0}
       run: conda activate shapeworks && python -c "import vtk"
 
+
     - name: Build Dependencies
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
+    - name: Save Dependencies Cache
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: /github/home/install
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+
     - name: Check space4
       run: df -h
 

.github/workflows/build-mac-arm64.yml

@@ -50,10 +50,27 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
+    - name: Restore Dependencies Cache
+      id: cache-deps-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: /Users/runner/install
+        key: ${{ runner.os }}-arm64-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
     - name: Build Dependencies
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
+    - name: Save Dependencies Cache
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: /Users/runner/install
+        key: ${{ runner.os }}-arm64-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+
     - name: cmake
       shell: bash -l {0}
       run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_LIBTOOL=/usr/bin/libtool -DCMAKE_CXX_FLAGS="-g -Wno-enum-constexpr-conversion" -DCMAKE_PREFIX_PATH=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DPython3_ROOT_DIR:FILEPATH=${CONDA_PREFIX} -DUSE_OPENMP=OFF -DBuild_Studio=ON -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DBUILD_DOCUMENTATION=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..

.github/workflows/build-mac.yml

@@ -51,10 +51,27 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
+    - name: Restore Dependencies Cache
+      id: cache-deps-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: /Users/runner/install
+        key: ${{ runner.os }}-intel-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
     - name: Build Dependencies
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
+    - name: Save Dependencies Cache
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: /Users/runner/install
+        key: ${{ runner.os }}-intel-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+
     - name: cmake
       shell: bash -l {0}
       run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_LIBTOOL=/usr/bin/libtool -DCMAKE_CXX_FLAGS=-g -DCMAKE_PREFIX_PATH=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DPython3_ROOT_DIR:FILEPATH=${CONDA_PREFIX} -DUSE_OPENMP=OFF -DBuild_Studio=ON -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DBUILD_DOCUMENTATION=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..

.github/workflows/build-windows.yml

@@ -87,9 +87,26 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
+    - name: Restore Dependencies Cache
+      id: cache-deps-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: C:\deps
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
     - name: Build Dependencies
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
+
+    - name: Save Dependencies Cache
+      if: steps.cache-deps-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: C:\deps
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Create Build Environment
       # Some projects don't allow in-source building, so create a separate build directory
@@ -167,4 +184,4 @@ jobs:
         prerelease: true
         title: "Development Build for Windows"
         files: |
-             d:/a/ShapeWorks/ShapeWorks/artifacts/*.exe
+             d:/a/ShapeWorks/ShapeWorks/artifacts/*.exe

Libs/Groom/Groom.cpp

@@ -216,9 +216,6 @@ bool Groom::image_pipeline(std::shared_ptr<Subject> subject, size_t domain) {
 
 //---------------------------------------------------------------------------
 bool Groom::run_image_pipeline(Image& image, GroomParameters params) {
-  // ensure axis aligned
-  image.toAxisAligned();
-
   // isolate
   if (params.get_isolate_tool()) {
     image.isolate();
@@ -1141,17 +1138,13 @@ Mesh Groom::get_mesh(int subject, int domain, bool transformed, MeshSource sourc
     }
     path = subjects[subject]->get_original_filenames()[domain];
     domain_type = project_->get_original_domain_types()[domain];
-    SW_DEBUG("Getting original mesh for subject {}, domain {}: {}", subject, domain, path);
-    SW_DEBUG("Domain type: {}", static_cast<int>(domain_type));
   } else {
     if (domain >= subjects[subject]->get_groomed_filenames().size()) {
       throw std::out_of_range("domain index out of range");
     }
     path = subjects[subject]->get_groomed_filenames()[domain];
 
     domain_type = ProjectUtils::determine_domain_type(path);
-    SW_DEBUG("Getting groomed mesh for subject {}, domain {}: {}", subject, domain, path);
-    SW_DEBUG("Domain type: {}", static_cast<int>(domain_type));
   }
 
   auto constraint_filename = subjects[subject]->get_constraints_filenames();

Libs/Groom/Groom.h

@@ -87,7 +87,6 @@ class Groom {
 
   Mesh get_mesh(int subject, int domain, bool transformed = false, MeshSource source = MeshSource::Groomed);
 
-
   vtkSmartPointer<vtkPoints> get_landmarks(int subject, int domain);
 
   int find_reference_landmarks(std::vector<vtkSmartPointer<vtkPoints>> landmarks);

Libs/Image/Image.cpp

@@ -140,6 +140,8 @@ Image::ImageType::Pointer Image::read(const std::string& pathname) {
     img = orienter->GetOutput();
   }
 
+  img = ImageUtils::make_axis_aligned(img);
+
   return img;
 }
 
@@ -431,90 +433,6 @@ Image& Image::resize(Dims dims, Image::InterpolationType interp) {
   return resample(IdentityTransform::New(), origin(), dims, spacing, coordsys(), interp);
 }
 
-
-Image& Image::toAxisAligned(InterpolationType interp) {
-  // Check if image is already axis-aligned
-  auto direction = itk_image_->GetDirection();
-  bool is_oblique = false;
-  for (unsigned int i = 0; i < 3; i++) {
-    for (unsigned int j = 0; j < 3; j++) {
-      double expected = (i == j) ? 1.0 : 0.0;
-      if (std::abs(direction(i, j) - expected) > 1e-6) {
-        is_oblique = true;
-        break;
-      }
-    }
-  }
-
-  // If already axis-aligned, return immediately
-  if (!is_oblique) {
-    return *this;
-  }
-
-  // The key insight: we need to create a transform that represents
-  // the DIFFERENCE between the oblique and axis-aligned coordinate systems
-
-  using TransformType = itk::AffineTransform<double, 3>;
-  auto transform = TransformType::New();
-
-  // The direction matrix rotates from index space to physical space
-  // To go from new axis-aligned indices to old oblique physical space,
-  // we need: newPhysical = identity * newIndex
-  //          oldIndex = direction^-1 * oldPhysical
-  // So: oldIndex = direction^-1 * identity * newIndex = direction^-1 * newIndex
-
-  TransformType::MatrixType matrix;
-  for (int i = 0; i < 3; i++) {
-    for (int j = 0; j < 3; j++) {
-      matrix(i, j) = direction(i, j);
-    }
-  }
-  transform->SetMatrix(matrix);
-
-  // Get bounding box
-  auto size = itk_image_->GetLargestPossibleRegion().GetSize();
-  auto spacing = itk_image_->GetSpacing();
-  auto origin = itk_image_->GetOrigin();
-
-  Point3 minPt, maxPt;
-  for (int i = 0; i < 3; i++) {
-    minPt[i] = std::numeric_limits<double>::max();
-    maxPt[i] = std::numeric_limits<double>::lowest();
-  }
-
-  for (int corner = 0; corner < 8; corner++) {
-    Coord index;
-    index[0] = (corner & 1) ? size[0] - 1 : 0;
-    index[1] = (corner & 2) ? size[1] - 1 : 0;
-    index[2] = (corner & 4) ? size[2] - 1 : 0;
-
-    Point3 point;
-    itk_image_->TransformIndexToPhysicalPoint(index, point);
-
-    for (int dim = 0; dim < 3; dim++) {
-      minPt[dim] = std::min(minPt[dim], point[dim]);
-      maxPt[dim] = std::max(maxPt[dim], point[dim]);
-    }
-  }
-
-  ImageType::DirectionType identityDir;
-  identityDir.SetIdentity();
-
-  ImageType::SizeType outputSize;
-  for (int i = 0; i < 3; i++) {
-    outputSize[i] = static_cast<size_t>(std::ceil((maxPt[i] - minPt[i]) / spacing[i])) + 1;
-  }
-
-  Vector3 spacingVec;
-  Dims dims;
-  for (int i = 0; i < 3; i++) {
-    spacingVec[i] = spacing[i];
-    dims[i] = outputSize[i];
-  }
-
-  return resample(transform, minPt, dims, spacingVec, identityDir, interp);
-}
-
 bool Image::compare(const Image& other, bool verifyall, double tolerance, double precision) const {
   if (tolerance > 1 || tolerance < 0) {
     throw std::invalid_argument("tolerance value must be between 0 and 1 (inclusive)");

Libs/Image/Image.h

@@ -105,9 +105,6 @@ class Image {
   /// resamples image using isotropic physical spacing
   Image& resample(double isoSpacing = 1.0, InterpolationType interp = Linear);
 
-  /// resamples image to be axis-aligned (i.e., identity direction matrix) if needed
-  Image& toAxisAligned(InterpolationType interp = NearestNeighbor);
-
   /// changes logical image size, computing new physical spacing based on this size (i.e., physical image size remains
   /// the same)
   Image& resize(Dims logicalDims, InterpolationType interp = Linear);