https://github.com/Radiomics/pyradiomics
Tip revision: 7c53bde67d69f146d1980001f19b3443a52ddc60 authored by JoostJM on 17 May 2023, 09:16:06 UTC
DOC: Add long_description_content_type
DOC: Add long_description_content_type
Tip revision: 7c53bde
_cshape.c
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <stdlib.h>
#include <Python.h>
#include <numpy/arrayobject.h>
#include "cshape.h"
static char module_docstring[] = "This module links to C-compiled code for efficient calculation of the surface area "
"in the pyRadiomics package. It provides fast calculation using a marching cubes "
"algortihm, accessed via ""calculate_surfacearea"". Arguments for this function"
"are positional and consist of two numpy arrays, mask and pixelspacing, which must "
"be supplied in this order. Pixelspacing is a 3 element vector containing the pixel"
"spacing in z, y and x dimension, respectively. All non-zero elements in mask are "
"considered to be a part of the segmentation and are included in the algorithm.";
static char coefficients_docstring[] = "Arguments: Mask, PixelSpacing. Uses a marching cubes algorithm to calculate an "
"approximation to the total surface area, volume and maximum diameters. "
"The isovalue is considered to be situated midway between a voxel that is part "
"of the segmentation and a voxel that is not.";
static char coefficients2D_docstring[] = "Arguments: Mask, PixelSpacing. Uses an adapted 2D marching cubes algorithm "
"to calculate an approximation to the total perimeter, surface and maximum "
"diameter. The isovalue is considered to be situated midway between a pixel "
"that is part of the segmentation and a pixel that is not.";
static PyObject *cshape_calculate_coefficients(PyObject *self, PyObject *args);
static PyObject *cshape_calculate_coefficients2D(PyObject *self, PyObject *args);
int check_arrays(PyArrayObject *mask_arr, PyArrayObject *spacing_arr, int *size, int *strides, int dimension);
static PyMethodDef module_methods[] = {
//{"calculate_", cmatrices_, METH_VARARGS, _docstring},
{ "calculate_coefficients", cshape_calculate_coefficients, METH_VARARGS, coefficients_docstring },
{ "calculate_coefficients2D", cshape_calculate_coefficients2D, METH_VARARGS, coefficients2D_docstring },
{ NULL, NULL, 0, NULL }
};
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef moduledef = {
PyModuleDef_HEAD_INIT,
"_cshape", /* m_name */
module_docstring, /* m_doc */
-1, /* m_size */
module_methods, /* m_methods */
NULL, /* m_reload */
NULL, /* m_traverse */
NULL, /* m_clear */
NULL, /* m_free */
};
#endif
static PyObject *
moduleinit(void)
{
PyObject *m;
#if PY_MAJOR_VERSION >= 3
m = PyModule_Create(&moduledef);
#else
m = Py_InitModule3("_cshape",
module_methods, module_docstring);
#endif
if (m == NULL)
return NULL;
return m;
}
#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC
init_cshape(void)
{
// Initialize numpy functionality
import_array();
moduleinit();
}
#else
PyMODINIT_FUNC
PyInit__cshape(void)
{
// Initialize numpy functionality
import_array();
return moduleinit();
}
#endif
static PyObject *cshape_calculate_coefficients(PyObject *self, PyObject *args)
{
PyObject *mask_obj, *spacing_obj;
PyArrayObject *mask_arr, *spacing_arr;
int size[3];
int strides[3];
char *mask;
double *spacing;
double SA, Volume;
double diameters[4];
PyObject *diameter_obj;
// Parse the input tuple
if (!PyArg_ParseTuple(args, "OO", &mask_obj, &spacing_obj))
return NULL;
// Interpret the input as numpy arrays
mask_arr = (PyArrayObject *)PyArray_FROM_OTF(mask_obj, NPY_BYTE, NPY_ARRAY_FORCECAST | NPY_ARRAY_IN_ARRAY);
spacing_arr = (PyArrayObject *)PyArray_FROM_OTF(spacing_obj, NPY_DOUBLE, NPY_ARRAY_FORCECAST | NPY_ARRAY_IN_ARRAY);
if (check_arrays(mask_arr, spacing_arr, size, strides, 3) > 0) return NULL;
// Get arrays in Ctype
mask = (char *)PyArray_DATA(mask_arr);
spacing = (double *)PyArray_DATA(spacing_arr);
//Calculate Surface Area and volume
if (calculate_coefficients(mask, size, strides, spacing, &SA, &Volume, diameters))
{
// An error has occurred
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_SetString(PyExc_RuntimeError, "Calculation of Shape coefficients failed.");
return NULL;
}
// Clean up
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
diameter_obj = Py_BuildValue("ffff", diameters[0], diameters[1], diameters[2], diameters[3]);
return Py_BuildValue("ffN", SA, Volume, diameter_obj);
}
static PyObject *cshape_calculate_coefficients2D(PyObject *self, PyObject *args)
{
PyObject *mask_obj, *spacing_obj;
PyArrayObject *mask_arr, *spacing_arr;
int size[2];
int strides[2];
char *mask;
double *spacing;
double perimeter, surface, diameter;
// Parse the input tuple
if (!PyArg_ParseTuple(args, "OO", &mask_obj, &spacing_obj))
return NULL;
// Interpret the input as numpy arrays
mask_arr = (PyArrayObject *)PyArray_FROM_OTF(mask_obj, NPY_BYTE, NPY_ARRAY_FORCECAST | NPY_ARRAY_IN_ARRAY);
spacing_arr = (PyArrayObject *)PyArray_FROM_OTF(spacing_obj, NPY_DOUBLE, NPY_ARRAY_FORCECAST | NPY_ARRAY_IN_ARRAY);
if (check_arrays(mask_arr, spacing_arr, size, strides, 2) > 0) return NULL;
// Get arrays in Ctype
mask = (char *)PyArray_DATA(mask_arr);
spacing = (double *)PyArray_DATA(spacing_arr);
//Calculate Surface Area and volume
if (calculate_coefficients2D(mask, size, strides, spacing, &perimeter, &surface, &diameter))
{
// An error has occurred
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_SetString(PyExc_RuntimeError, "Calculation of Shape coefficients failed.");
return NULL;
}
// Clean up
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
return Py_BuildValue("fff", perimeter, surface, diameter);
}
int check_arrays(PyArrayObject *mask_arr, PyArrayObject *spacing_arr, int *size, int *strides, int dimension)
{
int i;
if (mask_arr == NULL || spacing_arr == NULL)
{
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_SetString(PyExc_RuntimeError, "Error parsing array arguments.");
return 1;
}
if (PyArray_NDIM(mask_arr) != dimension || PyArray_NDIM(spacing_arr) != 1)
{
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_Format(PyExc_ValueError, "Expected a %iD array for mask, 1D for spacing.", dimension);
return 2;
}
if ( !PyArray_IS_C_CONTIGUOUS(mask_arr) || !PyArray_IS_C_CONTIGUOUS(spacing_arr))
{
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_SetString(PyExc_ValueError, "Expecting input arrays to be C-contiguous.");
return 3;
}
if (PyArray_DIM(spacing_arr, 0) != PyArray_NDIM(mask_arr))
{
Py_XDECREF(mask_arr);
Py_XDECREF(spacing_arr);
PyErr_SetString(PyExc_ValueError, "Expecting spacing array to have shape (3,).");
return 4;
}
// Get sizes and strides of the arrays
for (i = 0; i < dimension; i++)
{
size[i] = (int)PyArray_DIM(mask_arr, i);
strides[i] = (int)(PyArray_STRIDE(mask_arr, i) / PyArray_ITEMSIZE(mask_arr));
}
return 0;
}