Calculating higher-order precision gradients using vmtk’s vtkvmtkUnstructuredGridGradientFilter in Python is relatively straightforward.
For an Anaconda environment, first create a virtual environment and install vmtk using the following commands:
conda create -n vmtk python=3.11
conda activate vmtk
conda install conda-forge::vmtk
Next, you can create a Hessian matrix by applying vtkvmtkUnstructuredGridGradientFilter twice to a variable with a Python program like the one below. However, this program requires modification as it takes a vtu file format as input. You will likely also need to customize the arguments and other settings.
#!/usr/bin/env python3
"""
VMTK Higher-Order Precision Gradient Calculator
This script calculates first and second-order gradients of a specified field
in a VTK unstructured grid file using VMTK's differential geometry filters.
"""
import argparse
import os
import sys
import vtk
from vmtk.vtkvmtkDifferentialGeometryPython import vtkvmtkUnstructuredGridGradientFilter
def parse_arguments():
"""Parse command line arguments."""
parser = argparse.ArgumentParser(
description="This program computes the Hessian matrix using vmtk's higher-order precision gradient calculation filter",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument(
'--input-file',
default='test.vtu',
help='Input VTK unstructured grid file'
)
parser.add_argument(
'--output-file',
default='out.vtu',
help='Output file for gradient results'
)
parser.add_argument(
'--input-array-name',
default='DistanceToCenter',
help='Scalar field to calculate gradients from'
)
parser.add_argument(
'--quadrature-order',
type=int,
default=3,
help='Quadrature order for gradient calculations'
)
return parser.parse_args()
def calculate_gradients(input_file, array_name, quadrature_order):
"""
Calculate first and second order gradients.
Args:
input_file: Path to input VTU file
array_name: Name of the scalar field for gradient calculation
quadrature_order: Order of quadrature for numerical integration
Returns:
VTK data object with calculated gradients
"""
# Check if input file exists
if not os.path.exists(input_file):
raise FileNotFoundError(f"Input file not found: {input_file}")
# Read the input file
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(input_file)
reader.Update()
# Calculate first-order gradient
gradient_filter1 = vtkvmtkUnstructuredGridGradientFilter()
gradient_filter1.SetInputConnection(reader.GetOutputPort())
gradient_filter1.SetInputArrayName(array_name)
gradient_filter1.SetGradientArrayName(f'{array_name}_grad1')
gradient_filter1.SetQuadratureOrder(quadrature_order)
# Calculate second-order gradient
gradient_filter2 = vtkvmtkUnstructuredGridGradientFilter()
gradient_filter2.SetInputConnection(gradient_filter1.GetOutputPort())
gradient_filter2.SetInputArrayName(f'{array_name}_grad1')
gradient_filter2.SetGradientArrayName(f'{array_name}_grad2')
gradient_filter2.SetQuadratureOrder(quadrature_order)
gradient_filter2.Update()
return gradient_filter2.GetOutput()
def save_results(data, output_file):
"""
Save the VTK data to an output file.
Args:
data: VTK data object to write
output_file: Path to output file
"""
# Ensure the output directory exists
output_dir = os.path.dirname(output_file)
if output_dir and not os.path.exists(output_dir):
os.makedirs(output_dir)
# Write the output file
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetFileName(output_file)
writer.SetInputData(data)
writer.Write()
print(f"Results successfully written to {output_file}")
def main():
"""Main execution function."""
try:
# Parse command line arguments
args = parse_arguments()
# Calculate gradients
result_data = calculate_gradients(
args.input_file,
args.input_array_name,
args.quadrature_order
)
# Save results
save_results(result_data, args.output_file)
except Exception as e:
print(f"Error: {e}", file=sys.stderr)
return 1
return 0
if __name__ == "__main__":
sys.exit(main())
vmtk_test.zip (88.7 KB)