refactor(smread): broke sparse matrix debug utilities into smaller functions

utils/debugUtils/MFEMAnalysisUtils/SSEDebug/src/SSEDebug/smRead/__init__.py

@@ -1 +1 @@
-from .smread import loadSparseMatrixBinary, analyze_sparse_matrix, load_and_analyze_sparse_matrix
+from .smread import loadSparseMatrixBinary, analyze_sparse_matrix, load_and_analyze_sparse_matrix

utils/debugUtils/MFEMAnalysisUtils/SSEDebug/src/SSEDebug/smRead/smread.py

@@ -26,6 +26,9 @@ def loadSparseMatrixBinary(f):
     EXPECTED_MAGIC = b'CSRB'
     EXPECTED_VERSION = 1
 
+    if isinstance(f, str):
+        f = open(f, 'rb')
+
     try:
         # --- Read Header ---
         magic = f.read(4)

utils/debugUtils/MeshQuality/meshQuality.py

@@ -0,0 +1,106 @@
+#!/usr/bin/env python3
+
+import argparse
+import meshio
+import pyvista as pv
+import numpy as np
+import matplotlib.pyplot as plt
+import warnings
+
+def analyze_mesh_quality(mesh_filepath):
+    """
+    Reads a mesh file, computes various quality metrics using the current
+    PyVista API (cell_quality), and prints statistics.
+    """
+    print(f"--- Analyzing Mesh: {mesh_filepath} ---")
+
+    try:
+        mesh_mshio = meshio.read(mesh_filepath)
+    except FileNotFoundError:
+        print(f"ERROR: Mesh file '{mesh_filepath}' not found.")
+        return
+    except Exception as e:
+        print(f"ERROR: Could not read mesh file '{mesh_filepath}' with meshio: {e}")
+        return
+
+    points = mesh_mshio.points
+    cells_list = []
+    cell_types_list = []
+
+    supported_3d_types = {
+        "tetra": pv.CellType.TETRA,
+        "tetra10": pv.CellType.QUADRATIC_TETRA
+    }
+
+    found_3d_cells = False
+    for cells_block in mesh_mshio.cells:
+        if cells_block.type in supported_3d_types:
+            print(f"Found cell block of type '{cells_block.type}' with {len(cells_block.data)} cells.")
+            num_points_per_cell = cells_block.data.shape[1]
+            pv_cell_block = np.hstack((
+                np.full((len(cells_block.data), 1), num_points_per_cell, dtype=cells_block.data.dtype),
+                cells_block.data
+            )).ravel()
+            cells_list.append(pv_cell_block)
+            cell_types_list.extend([supported_3d_types[cells_block.type]] * len(cells_block.data))
+            found_3d_cells = True
+
+    if not found_3d_cells:
+        print("ERROR: No supported 3D cell types (e.g., tetra, tetra10, hexahedron) found in the mesh.")
+        print("Meshio cell types found in file:", [block.type for block in mesh_mshio.cells])
+        return
+
+    if len(cells_list) > 1:
+        print("Warning: Multiple 3D cell blocks found and concatenated. Ensure these are compatible for a single UnstructuredGrid.")
+        flat_cells = np.concatenate(cells_list)
+    elif len(cells_list) == 1:
+        flat_cells = cells_list[0]
+    else: # Should have been caught by "not found_3d_cells"
+        return
+
+    try:
+        mesh_pv = pv.UnstructuredGrid(flat_cells, cell_types_list, points)
+        print(f"\nSuccessfully converted to PyVista mesh with {mesh_pv.n_points} points and {mesh_pv.n_cells} cells.")
+    except Exception as e:
+        print(f"ERROR: Could not create PyVista UnstructuredGrid: {e}")
+        return
+
+    quality_measures_to_try = [
+        ('aspect_ratio', "Aspect Ratio"),
+        ('condition', "Condition Number of Element Jacobian"),
+        ('distortion', "Distortion (0=perfect, 1=degenerated)"),
+        ('jacobian', "Determinant of Element Jacobian (should be > 0)"),
+        ('radius_ratio', "Radius Ratio (for tets: inscribed/circumscribed, 1 is best)"),
+        ('scaled_jacobian', "Scaled Jacobian (1 is ideal, <0 bad)"),
+        ('skew', "Skewness (0 is ideal, higher is worse)"),
+        ('volume', "Volume (should be > 0)"),
+        ('min_angle', "Minimum Dihedral/Face Angle (larger is better)"),
+        ('max_angle', "Maximum Dihedral/Face Angle (smaller is better, less 'flat')")
+    ]
+
+    # Suppress common warnings for cleaner output, adjust as needed
+    warnings.filterwarnings("ignore", category=UserWarning, message="`quality_measure`.*not implemented for this cell type.")
+    warnings.filterwarnings("ignore", category=UserWarning, message="Cannot compute quality of a point cell.") # If points/lines exist
+    warnings.filterwarnings("ignore", category=UserWarning, message="Mesh contains non-tetrahedral cells. Radius ratio is only defined for tetrahedra.")
+    warnings.filterwarnings("ignore", category=RuntimeWarning) # For potential NaN in stats from empty arrays etc.
+
+
+    for measure, description in quality_measures_to_try:
+        if not mesh_pv.n_cells > 0:
+            continue
+        # Use the recommended cell_quality method
+        quality_array = mesh_pv.cell_quality(quality_measure=measure)
+        range = quality_array.get_data_range(measure)
+        print(f"Range for {measure} is: {range[0]:0.3E} → {range[1]:0.3E}")
+
+
+
+    warnings.resetwarnings()
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Analyze mesh quality using PyVista.")
+    parser.add_argument("mesh_filepath", type=str, help="Path to the mesh file (e.g., .msh, .vtk).")
+
+    args = parser.parse_args()
+
+    analyze_mesh_quality(args.mesh_filepath)