cgoates · colbyj427 · Jul 30, 2025 · Jul 30, 2025 · Jul 30, 2025 · Jul 31, 2025
diff --git a/.github/workflows/build_and_run_tests_macos.yaml b/.github/workflows/build_and_run_tests_macos.yaml
@@ -9,6 +9,14 @@ jobs:
         uses: actions/checkout@v4
       - name: Install OpenMP
         run: brew install libomp
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install Python Dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install numpy
       - name: Use cmake
         run: |
           mkdir build
@@ -20,6 +28,9 @@ jobs:
             -DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" \
             -DCMAKE_SHARED_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp"
           make -j10
+      - name: Build ScaleUntrim
+        run : |
+          python3 scripts/scaleUntrimBuilder.py
       - name: Run tests
         run: |
           cd build

diff --git a/.github/workflows/ubuntu_build_and_run_tests.yaml b/.github/workflows/ubuntu_build_and_run_tests.yaml
@@ -18,6 +18,10 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: '3.11'
+      - name: Install Python Dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install numpy
       - name: Setup Mold
         uses: rui314/setup-mold@v1
         with:
@@ -30,6 +34,15 @@ jobs:
           echo "CXX=g++-10" >> $GITHUB_ENV
           cmake .. -DCMAKE_BUILD_TYPE=Release
           make -j10
+      - name: Install Fortran
+        run: |
+          apt-get update
+          apt-get install -y gfortran-12
+          update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-12 100
+      - name: Build ScaleUntrim
+        run : |
+          uname -a
+          python3 scripts/scaleUntrimBuilder.py
       - name: Run tests
         run: |
           cd build

diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@ build
 deps
 .DS_Store
 scripts/*.vtu
+__pycache__/
diff --git a/scripts/quadMeshingFunctions.py b/scripts/quadMeshingFunctions.py
@@ -0,0 +1,123 @@
+# A python script meant to run the process of taking a tet mesh and creating a quad mesh of one of the boundaries.
+# The resulting vtk file path can be returned, along with a list of points and quads from the vtk file.
+
+import sys
+import subprocess
+from pathlib import Path
+import numpy as np
+SCRIPT_DIR = Path(__file__).resolve().parent
+if str(SCRIPT_DIR) not in sys.path:
+    sys.path.insert(0, str(SCRIPT_DIR))
+SWEEPS_DIR = SCRIPT_DIR.parent
+
+path_to_api = Path(__file__).parent.parent / "build" / "src" / "api"
+sys.path.insert(0, str(path_to_api))
+import sweeps
+
+def runQuadriflowProgram(input_file: str):
+    """
+    Runs the quadriflow program to create a quad mesh from a tet mesh input file.
+    input_file: str - Path to the tet mesh file.
+    """
+    quadriflow_executable = SWEEPS_DIR / "deps" / "ScaleUntrim" / "build" / "QuadriFlow"
+    config_path = SWEEPS_DIR / "deps" / "ScaleUntrim" / "setting.config"
+    if not quadriflow_executable.exists():
+        raise FileNotFoundError(f"C++ executable not found at {quadriflow_executable}")
+
+    command = [str(quadriflow_executable), input_file, config_path]
+    try:
+        result = subprocess.run(command, check=True, capture_output=True, text=True)
+        print("OUTPUT:")
+        print(result.stdout)
+    except subprocess.CalledProcessError as e:
+        print(f"Error running command: {e.cmd}")
+        print(f"Return code: {e.returncode}")
+        print(f"OUTPUT: {e.output}")
+        print("END OF OUTPUT MESSAGE")
+        print(f"ERROR OUTPUT: {e.stderr}")
+        print("END OF ERROR MESSAGE")
+        raise Exception("Error while running Quadriflow.")
+    except Exception as e:
+        print(f"An error occurred: {e}")
+        raise Exception("Could not run Quadriflow.")
+
+def generateQuadMesh(tri_mesh: sweeps.TriMesh):
+    """
+    Takes a sweeps.TriMesh object and creates an obj using the data. The obj is used to create a quad mesh vtk file.
+    The vtk file is used to generate a sweeps.QuadMesh object which is then returned.
+    tri_mesh: sweeps.TriMesh - A TriMesh object containing points and face data for the mesh to be generated.
+    Returns: a sweeps.QuadMesh object containing the points and face (quads) data from the vtk output.
+    """
+    tri_mesh_base_path = Path(__file__).resolve().parent / "MeshBase_new.obj"
+    saveTriMeshAsObj(tri_mesh, str(tri_mesh_base_path))
+    runQuadriflowProgram(tri_mesh_base_path)
+    vtk_path = SWEEPS_DIR / "deps" / "ScaleUntrim" / "build" / "tempDir" / "quad.vtk"
+    if not vtk_path.exists():
+        raise FileNotFoundError("The generated quadrilateral vtk file does not exist.")
+    return createQuadMeshObjectFromVtk(str(vtk_path))
+
+def createQuadMeshObjectFromVtk(vtk_path: str):
+    """
+    Takes a file path to a quad mesh as a vtk file and returns a sweeps.QuadMesh object derived from that vtk file.
+    vtk_path: str - path to the vtk file to use in creating the sweeps.QuadMesh object.
+    """
+    f = open(vtk_path, "r")
+    lines = f.readlines()
+    f.close()
+    num_points = -1
+    points_start_index = -1
+    num_quads = -1
+    quads_start_index = -1
+    for line in range(len(lines)):
+        if lines[line].startswith("POINTS"):
+            points_line = lines[line].split()
+            num_points = int(points_line[1])
+            points_start_index = line
+        elif lines[line].startswith("CELLS"):
+            quads_line = lines[line].split()
+            num_quads = int(quads_line[1])
+            quads_start_index = line
+    if (num_points < 0) or (num_quads < 0) or (points_start_index < 0) or (quads_start_index < 0):
+        raise Exception("Given Vtk file is empty or formatted incorrectly.")
+    point_lines = lines[points_start_index+1:points_start_index+num_points+1]
+    quad_lines = lines[quads_start_index+1:quads_start_index+num_quads+1]
+    points = getPoints(point_lines)
+    quads = getQuads(quad_lines)
+    return sweeps.QuadMesh(points, quads)
+
+def getPoints(lines):
+    """
+    Given lines of a file which contain vertices in vtk format, returns all vertices as a list of np arrays.
+    lines: list - a list of lines, each line containing the 3 coordinates of a vertex.
+    return: [np.array]
+    """
+    points = []
+    for line in lines:
+        nums = line.split()
+        points.append(np.array(nums, dtype=float))
+    return points
+
+def getQuads(lines):
+    """
+    Given lines of a file which contain quadrilaterals in vtk format, returns all quads as a list of lists.
+    lines: list = a list of lines, each line containing the number of vertices, and the 4 indices of the vertices in the quad.
+    return: [list] - 2d list
+    """
+    quads = []
+    for line in lines:
+        nums = line.split()
+        quads.append(list(map(int, nums[1:])))
+    return quads
+
+def saveTriMeshAsObj(mesh_base_tri: sweeps.TriMesh, path_to_file: str):
+    """
+    Takes in a sweeps.TriMesh object and a desired file path to save to and
+    creates an obj file using the data from the TriMesh object.
+    mesh_base_tri: sweeps.TriMesh - a TriMesh object created using the sweeps api.
+    path_to_file: str - the path for the obj file to be saved to.
+    """
+    with open(path_to_file, "w") as file:
+        for vertex in mesh_base_tri.points:
+            file.write(f"v {vertex[0]} {vertex[1]} {vertex[2]}\n")
+        for face in mesh_base_tri.tris:
+            file.write(f"f {' '.join(str(idx + 1) for idx in face)}\n")