int
main(int argc, char **argv)
{
int status;
char* env = NULL;
env = getenv("GPAW_OFFLOAD");
if (env) {
errno = 0;
gpaw_offload_enabled = strtol(env, NULL, 10);
if (errno) {
fprintf(stderr,
"Wrong value for for GPAW_OFFLOAD.\nShould be either 0 or 1, but was %s\n",
env);
}
}
fprintf(stderr, "GPAW info: GPAW_OFFLOAD=%d\n", gpaw_offload_enabled);
#ifdef CRAYPAT
PAT_region_begin(1, "C-Initializations");
#endif
#ifndef GPAW_OMP
MPI_Init(&argc, &argv);
#else
int granted;
MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &granted);
if(granted != MPI_THREAD_MULTIPLE) exit(1);
#endif // GPAW_OMP
// Get initial timing
double t0 = MPI_Wtime();
#ifdef GPAW_PERFORMANCE_REPORT
gpaw_perf_init();
#endif
#ifdef GPAW_MPI_MAP
int tag = 99;
int myid, numprocs, i, procnamesize;
char procname[MPI_MAX_PROCESSOR_NAME];
MPI_Comm_size(MPI_COMM_WORLD, &numprocs );
MPI_Comm_rank(MPI_COMM_WORLD, &myid );
MPI_Get_processor_name(procname, &procnamesize);
if (myid > 0) {
MPI_Send(&procnamesize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
MPI_Send(procname, procnamesize, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
else {
printf("MPI_COMM_SIZE is %d \n", numprocs);
printf("%s \n", procname);
for (i = 1; i < numprocs; ++i) {
MPI_Recv(&procnamesize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
MPI_Recv(procname, procnamesize, MPI_CHAR, i, tag, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
printf("%s \n", procname);
}
}
#endif // GPAW_MPI_MAP
#ifdef GPAW_MPI_DEBUG
// Default Errhandler is MPI_ERRORS_ARE_FATAL
MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN);
#endif
// Progname seems to be needed in some circumstances to resolve
// correct default sys.path
Py_SetProgramName(argv[0]);
Py_Initialize();
#pragma offload target(mic) if(gpaw_offload_enabled)
{
init_openmp();
}
if (PyType_Ready(&MPIType) < 0)
return -1;
if (PyType_Ready(&LFCType) < 0)
return -1;
if (PyType_Ready(&LocalizedFunctionsType) < 0)
return -1;
if (PyType_Ready(&OperatorType) < 0)
return -1;
if (PyType_Ready(&SplineType) < 0)
return -1;
if (PyType_Ready(&TransformerType) < 0)
return -1;
if (PyType_Ready(&XCFunctionalType) < 0)
return -1;
if (PyType_Ready(&lxcXCFunctionalType) < 0)
return -1;
PyObject* m = Py_InitModule3("_gpaw", functions,
"C-extension for GPAW\n\n...\n");
if (m == NULL)
return -1;
Py_INCREF(&MPIType);
PyModule_AddObject(m, "Communicator", (PyObject *)&MPIType);
// Add initial time to _gpaw object
PyModule_AddObject(m, "time0", PyFloat_FromDouble(t0));
Py_INCREF(&LFCType);
Py_INCREF(&LocalizedFunctionsType);
Py_INCREF(&OperatorType);
Py_INCREF(&SplineType);
Py_INCREF(&TransformerType);
Py_INCREF(&XCFunctionalType);
Py_INCREF(&lxcXCFunctionalType);
#ifdef GPAW_WITH_HDF5
init_gpaw_hdf5();
#endif
import_array1(-1);
MPI_Barrier(MPI_COMM_WORLD);
#ifdef CRAYPAT
PAT_region_end(1);
PAT_region_begin(2, "all other");
#endif
status = Py_Main(argc, argv);
#ifdef CRAYPAT
PAT_region_end(2);
#endif
#ifdef GPAW_PERFORMANCE_REPORT
gpaw_perf_finalize();
#endif
MPI_Finalize();
return status;
}
inline int import_numpy()
{
#ifdef NUMPY_IMPORT_ARRAY
import_array1(-1);
import_umath1(-1);
#endif
return 0;
}
Bool
eval_jac_g(Index n, Number * x, Bool new_x,
Index m, Index nele_jac,
Index * iRow, Index * jCol, Number * values, UserDataPtr data)
{
logger("[Callback:E] eval_jac_g");
DispatchData *myowndata = (DispatchData *) data;
UserDataPtr user_data = (UserDataPtr) myowndata->userdata;
int i;
long *rowd = NULL;
long *cold = NULL;
/* int dims[1]; */
npy_intp dims[1];
dims[0] = n;
double *tempdata;
if (myowndata->eval_grad_f_python == NULL) /* Why??? */
PyErr_Print();
if (values == NULL) {
/* import_array (); */
import_array1(FALSE);
PyObject *arrayx =
PyArray_SimpleNewFromData(1, dims, PyArray_DOUBLE,
(char *)x);
if (!arrayx)
return FALSE;
PyObject *arglist;
if (user_data != NULL)
arglist = Py_BuildValue("(OOO)",
arrayx, Py_True,
(PyObject *) user_data);
else
arglist = Py_BuildValue("(OO)", arrayx, Py_True);
PyObject *result =
PyObject_CallObject(myowndata->eval_jac_g_python, arglist);
if (!result) {
logger("[PyIPOPT] return from eval_jac_g is null\n");
/* TODO: need to deal with reference counting here */
return FALSE;
}
if (!PyTuple_Check(result)) {
PyErr_Print();
}
PyArrayObject *row =
(PyArrayObject *) PyTuple_GetItem(result, 0);
PyArrayObject *col =
(PyArrayObject *) PyTuple_GetItem(result, 1);
if (!row || !col || !PyArray_Check(row) || !PyArray_Check(col)) {
logger
("[Error] there are problems with row or col in eval_jac_g.\n");
PyErr_Print();
}
rowd = (long *)row->data;
cold = (long *)col->data;
for (i = 0; i < nele_jac; i++) {
iRow[i] = (Index) rowd[i];
jCol[i] = (Index) cold[i];
}
Py_CLEAR(arrayx);
Py_DECREF(result);
Py_CLEAR(arglist);
logger("[Callback:R] eval_jac_g(1)");
} else {
PyObject *arrayx =
PyArray_SimpleNewFromData(1, dims, PyArray_DOUBLE,
(char *)x);
if (!arrayx)
return FALSE;
if (new_x && myowndata->apply_new_python) {
/* Call the python function to applynew */
PyObject *arg1 = Py_BuildValue("(O)", arrayx);
PyObject *tempresult =
PyObject_CallObject(myowndata->apply_new_python,
arg1);
if (!tempresult) {
logger
("[Error] Python function apply_new returns a None\n");
Py_DECREF(arg1);
return FALSE;
}
Py_DECREF(arg1);
Py_DECREF(tempresult);
}
PyObject *arglist;
if (user_data != NULL)
arglist = Py_BuildValue("(OOO)",
arrayx, Py_False,
(PyObject *) user_data);
else
arglist = Py_BuildValue("(OO)", arrayx, Py_False);
PyArrayObject *result = (PyArrayObject *)
PyObject_CallObject(myowndata->eval_jac_g_python, arglist);
if (!result || !PyArray_Check(result))
PyErr_Print();
/*
* Code is buggy here. We assume that result is a double
* array
*/
assert(result->descr->type == 'd');
tempdata = (double *)result->data;
for (i = 0; i < nele_jac; i++)
values[i] = tempdata[i];
Py_DECREF(result);
Py_CLEAR(arrayx);
Py_CLEAR(arglist);
logger("[Callback:R] eval_jac_g(2)");
}
logger("[Callback:R] eval_jac_g");
return TRUE;
}
Bool
eval_g(Index n, Number * x, Bool new_x, Index m, Number * g, UserDataPtr data)
{
logger("[Callback:E] eval_g");
DispatchData *myowndata = (DispatchData *) data;
UserDataPtr user_data = (UserDataPtr) myowndata->userdata;
if (myowndata->eval_g_python == NULL)
PyErr_Print();
/* int dims[1]; */
npy_intp dims[1];
int i;
double *tempdata;
dims[0] = n;
// import_array ();
import_array1(FALSE);
/*
* PyObject *arrayx = PyArray_FromDimsAndData(1, dims, PyArray_DOUBLE
* , (char*) x);
*/
PyObject *arrayx =
PyArray_SimpleNewFromData(1, dims, PyArray_DOUBLE, (char *)x);
if (!arrayx)
return FALSE;
if (new_x && myowndata->apply_new_python) {
/* Call the python function to applynew */
PyObject *arg1 = Py_BuildValue("(O)", arrayx);
PyObject *tempresult =
PyObject_CallObject(myowndata->apply_new_python, arg1);
if (!tempresult) {
logger
("[Error] Python function apply_new returns a None\n");
Py_DECREF(arg1);
return FALSE;
}
Py_DECREF(arg1);
Py_DECREF(tempresult);
}
PyObject *arglist;
if (user_data != NULL)
arglist = Py_BuildValue("(OO)", arrayx, (PyObject *) user_data);
else
arglist = Py_BuildValue("(O)", arrayx);
PyArrayObject *result =
(PyArrayObject *) PyObject_CallObject(myowndata->eval_g_python,
arglist);
if (!result)
PyErr_Print();
if (!PyArray_Check(result))
PyErr_Print();
tempdata = (double *)result->data;
for (i = 0; i < m; i++) {
g[i] = tempdata[i];
}
Py_DECREF(result);
Py_CLEAR(arrayx);
Py_CLEAR(arglist);
logger("[Callback:R] eval_g");
return TRUE;
}
Bool
eval_f(Index n, Number * x, Bool new_x, Number * obj_value, UserDataPtr data)
{
logger("[Callback:E] eval_f");
npy_intp dims[1];
dims[0] = n;
DispatchData *myowndata = (DispatchData *) data;
UserDataPtr user_data = (UserDataPtr) myowndata->userdata;
// import_array ();
import_array1(FALSE);
PyObject *arrayx =
PyArray_SimpleNewFromData(1, dims, PyArray_DOUBLE, (char *)x);
if (!arrayx)
return FALSE;
if (new_x && myowndata->apply_new_python) {
/* Call the python function to applynew */
PyObject *arg1;
arg1 = Py_BuildValue("(O)", arrayx);
PyObject *tempresult =
PyObject_CallObject(myowndata->apply_new_python, arg1);
if (!tempresult) {
logger
("[Error] Python function apply_new returns a None\n");
Py_DECREF(arg1);
return FALSE;
}
Py_DECREF(arg1);
Py_DECREF(tempresult);
}
PyObject *arglist;
if (user_data != NULL)
arglist = Py_BuildValue("(OO)", arrayx, (PyObject *) user_data);
else
arglist = Py_BuildValue("(O)", arrayx);
PyObject *result =
PyObject_CallObject(myowndata->eval_f_python, arglist);
if (!result) {
PyErr_Print();
Py_DECREF(result);
Py_DECREF(arrayx);
Py_CLEAR(arglist);
return FALSE;
}
if (!PyFloat_Check(result)) {
PyErr_Print();
Py_DECREF(result);
Py_DECREF(arrayx);
Py_CLEAR(arglist);
return FALSE;
}
*obj_value = PyFloat_AsDouble(result);
Py_DECREF(result);
Py_DECREF(arrayx);
Py_CLEAR(arglist);
logger("[Callback:R] eval_f");
return TRUE;
}
bool mitk::PythonService::CopyToPythonAsCvImage( mitk::Image* image, const std::string& stdvarName )
{
QString varName = QString::fromStdString( stdvarName );
QString command;
unsigned int* imgDim = image->GetDimensions();
int npy_nd = 1;
// access python module
PyObject *pyMod = PyImport_AddModule((char*)"__main__");
// global dictionary
PyObject *pyDict = PyModule_GetDict(pyMod);
mitk::PixelType pixelType = image->GetPixelType();
PyObject* npyArray = nullptr;
mitk::ImageReadAccessor racc(image);
void* array = (void*) racc.GetData();
// save the total number of elements here (since the numpy array is one dimensional)
npy_intp* npy_dims = new npy_intp[1];
npy_dims[0] = imgDim[0];
/**
* Build a string in the format [1024,1028,1]
* to describe the dimensionality. This is needed for simple itk
* to know the dimensions of the image
*/
QString dimensionString;
dimensionString.append(QString("["));
dimensionString.append(QString::number(imgDim[0]));
// ToDo: check if we need this
for (unsigned i = 1; i < 3; ++i)
// always three because otherwise the 3d-geometry gets destroyed
// (relevant for backtransformation of simple itk image to mitk.
{
dimensionString.append(QString(","));
dimensionString.append(QString::number(imgDim[i]));
npy_dims[0] *= imgDim[i];
}
dimensionString.append("]");
// the next line is necessary for vectorimages
npy_dims[0] *= pixelType.GetNumberOfComponents();
// default pixeltype: unsigned short
NPY_TYPES npy_type = NPY_USHORT;
if( pixelType.GetComponentType() == itk::ImageIOBase::DOUBLE ) {
npy_type = NPY_DOUBLE;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::FLOAT ) {
npy_type = NPY_FLOAT;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::SHORT) {
npy_type = NPY_SHORT;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::CHAR ) {
npy_type = NPY_BYTE;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::INT ) {
npy_type = NPY_INT;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::LONG ) {
npy_type = NPY_LONG;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UCHAR ) {
npy_type = NPY_UBYTE;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UINT ) {
npy_type = NPY_UINT;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::ULONG ) {
npy_type = NPY_LONG;
} else if( pixelType.GetComponentType() == itk::ImageIOBase::USHORT ) {
npy_type = NPY_USHORT;
}
else {
MITK_WARN << "not a recognized pixeltype";
return false;
}
// creating numpy array
import_array1 (true);
npyArray = PyArray_SimpleNewFromData(npy_nd,npy_dims,npy_type,array);
// add temp array it to the python dictionary to access it in python code
const int status = PyDict_SetItemString( pyDict,QString("%1_numpy_array")
.arg(varName).toStdString().c_str(),
npyArray );
// sanity check
if ( status != 0 )
return false;
command.append( QString("import numpy as np\n"));
//command.append( QString("if '%1' in globals():\n").arg(varName));
//command.append( QString(" del %1\n").arg(varName));
command.append( QString("%1_array_tmp=%1_numpy_array.copy()\n").arg(varName));
command.append( QString("%1_array_tmp=%1_array_tmp.reshape(%2,%3,%4)\n").arg( varName,
QString::number(imgDim[1]),
QString::number(imgDim[0]),
QString::number(pixelType.GetNumberOfComponents())));
command.append( QString("%1 = %1_array_tmp[:,...,::-1]\n").arg(varName));
command.append( QString("del %1_numpy_array\n").arg(varName) );
command.append( QString("del %1_array_tmp").arg(varName) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute( command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
return true;
}
bool mitk::PythonService::CopyToPythonAsSimpleItkImage(mitk::Image *image, const std::string &stdvarName)
{
QString varName = QString::fromStdString( stdvarName );
QString command;
unsigned int* imgDim = image->GetDimensions();
int npy_nd = 1;
// access python module
PyObject *pyMod = PyImport_AddModule((char*)"__main__");
// global dictionary
PyObject *pyDict = PyModule_GetDict(pyMod);
const mitk::Vector3D spacing = image->GetGeometry()->GetSpacing();
const mitk::Point3D origin = image->GetGeometry()->GetOrigin();
mitk::PixelType pixelType = image->GetPixelType();
itk::ImageIOBase::IOPixelType ioPixelType = image->GetPixelType().GetPixelType();
PyObject* npyArray = nullptr;
mitk::ImageReadAccessor racc(image);
void* array = (void*) racc.GetData();
mitk::Vector3D xDirection;
mitk::Vector3D yDirection;
mitk::Vector3D zDirection;
const vnl_matrix_fixed<ScalarType, 3, 3> &transform =
image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix();
mitk::Vector3D s = image->GetGeometry()->GetSpacing();
// ToDo: Check if this is a collumn or row vector from the matrix.
// right now it works but not sure for rotated geometries
mitk::FillVector3D(xDirection, transform[0][0]/s[0], transform[0][1]/s[1], transform[0][2]/s[2]);
mitk::FillVector3D(yDirection, transform[1][0]/s[0], transform[1][1]/s[1], transform[1][2]/s[2]);
mitk::FillVector3D(zDirection, transform[2][0]/s[0], transform[2][1]/s[1], transform[2][2]/s[2]);
// save the total number of elements here (since the numpy array is one dimensional)
npy_intp* npy_dims = new npy_intp[1];
npy_dims[0] = imgDim[0];
/**
* Build a string in the format [1024,1028,1]
* to describe the dimensionality. This is needed for simple itk
* to know the dimensions of the image
*/
QString dimensionString;
dimensionString.append(QString("["));
dimensionString.append(QString::number(imgDim[0]));
for (unsigned i = 1; i < 3; ++i)
// always three because otherwise the 3d-geometry gets destroyed
// (relevant for backtransformation of simple itk image to mitk.
{
dimensionString.append(QString(","));
dimensionString.append(QString::number(imgDim[i]));
npy_dims[0] *= imgDim[i];
}
dimensionString.append("]");
// the next line is necessary for vectorimages
npy_dims[0] *= pixelType.GetNumberOfComponents();
// default pixeltype: unsigned short
NPY_TYPES npy_type = NPY_USHORT;
std::string sitk_type = "sitkUInt8";
if( ioPixelType == itk::ImageIOBase::SCALAR )
{
if( pixelType.GetComponentType() == itk::ImageIOBase::DOUBLE ) {
npy_type = NPY_DOUBLE;
sitk_type = "sitkFloat64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::FLOAT ) {
npy_type = NPY_FLOAT;
sitk_type = "sitkFloat32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::SHORT) {
npy_type = NPY_SHORT;
sitk_type = "sitkInt16";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::CHAR ) {
npy_type = NPY_BYTE;
sitk_type = "sitkInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::INT ) {
npy_type = NPY_INT;
sitk_type = "sitkInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::LONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UCHAR ) {
npy_type = NPY_UBYTE;
sitk_type = "sitkUInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UINT ) {
npy_type = NPY_UINT;
sitk_type = "sitkUInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::ULONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkUInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::USHORT ) {
npy_type = NPY_USHORT;
sitk_type = "sitkUInt16";
}
}
else if ( ioPixelType == itk::ImageIOBase::VECTOR ||
ioPixelType == itk::ImageIOBase::RGB ||
ioPixelType == itk::ImageIOBase::RGBA
)
{
if( pixelType.GetComponentType() == itk::ImageIOBase::DOUBLE ) {
npy_type = NPY_DOUBLE;
sitk_type = "sitkVectorFloat64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::FLOAT ) {
npy_type = NPY_FLOAT;
sitk_type = "sitkVectorFloat32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::SHORT) {
npy_type = NPY_SHORT;
sitk_type = "sitkVectorInt16";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::CHAR ) {
npy_type = NPY_BYTE;
sitk_type = "sitkVectorInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::INT ) {
npy_type = NPY_INT;
sitk_type = "sitkVectorInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::LONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkVectorInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UCHAR ) {
npy_type = NPY_UBYTE;
sitk_type = "sitkVectorUInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UINT ) {
npy_type = NPY_UINT;
sitk_type = "sitkVectorUInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::ULONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkVectorUInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::USHORT ) {
npy_type = NPY_USHORT;
sitk_type = "sitkVectorUInt16";
}
}
else {
MITK_WARN << "not a recognized pixeltype";
return false;
}
// creating numpy array
import_array1 (true);
npyArray = PyArray_SimpleNewFromData(npy_nd,npy_dims,npy_type,array);
// add temp array it to the python dictionary to access it in python code
const int status = PyDict_SetItemString( pyDict,QString("%1_numpy_array")
.arg(varName).toStdString().c_str(),
npyArray );
// sanity check
if ( status != 0 )
return false;
command.append( QString("%1 = sitk.Image(%2,sitk.%3,%4)\n").arg(varName)
.arg(dimensionString)
.arg(QString(sitk_type.c_str())).arg(QString::number(pixelType.GetNumberOfComponents())) );
command.append( QString("%1.SetSpacing([%2,%3,%4])\n").arg(varName)
.arg(QString::number(spacing[0]))
.arg(QString::number(spacing[1]))
.arg(QString::number(spacing[2])) );
command.append( QString("%1.SetOrigin([%2,%3,%4])\n").arg(varName)
.arg(QString::number(origin[0]))
.arg(QString::number(origin[1]))
.arg(QString::number(origin[2])) );
command.append( QString("%1.SetDirection([%2,%3,%4,%5,%6,%7,%8,%9,%10])\n").arg(varName)
.arg(QString::number(xDirection[0]))
.arg(QString::number(xDirection[1]))
.arg(QString::number(xDirection[2]))
.arg(QString::number(yDirection[0]))
.arg(QString::number(yDirection[1]))
.arg(QString::number(yDirection[2]))
.arg(QString::number(zDirection[0]))
.arg(QString::number(zDirection[1]))
.arg(QString::number(zDirection[2]))
);
// directly access the cpp api from the lib
command.append( QString("_SimpleITK._SetImageFromArray(%1_numpy_array,%1)\n").arg(varName) );
command.append( QString("del %1_numpy_array").arg(varName) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute( command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
return true;
}
void CMAC_net::plot_contourf() {
Py_Initialize();
import_array1();
PyObject* p_name, *p_module, *p_dict, *p_func, *p_value, *format_expression,
*run_expression, *run_script, *traceback_module, *python_module,
*traceback_dictionary, *python_dictionary;
traceback_module = PyImport_ImportModule("traceback");
python_module = PyImport_ImportModule("python_fun");
if (traceback_module && python_module) {
traceback_dictionary = PyModule_GetDict(traceback_module);
python_dictionary = PyModule_GetDict(python_module);
format_expression =
PyDict_GetItemString(traceback_dictionary, "format_expression");
run_expression =
PyDict_GetItemString(python_dictionary, "run_expression");
run_script = PyDict_GetItemString(python_dictionary, "run_script");
if (format_expression && run_expression && run_script) {
if (PyCallable_Check(format_expression) &&
PyCallable_Check(run_expression) &&
PyCallable_Check(run_script)) {
}
}
}
fexcp = PyDict_GetItemString(dict1)
const int res = 4;
float** x = new float* [res];
float** y = new float* [res];
float** z = new float* [res];
x[0] = new float[res];
x[1] = x[0] + res;
x[2] = x[1] + res;
y[0] = new float[res];
y[1] = y[0] + res;
y[2] = y[1] + res;
z[0] = new float[res];
z[1] = z[0] + res;
z[2] = z[1] + res;
int mdim[] = {res, res};
float x_step =
interval_width[0] * (float)_tile_resolution / ((float)res - 1);
float y_step =
interval_width[1] * (float)_tile_resolution / ((float)res - 1);
float input_vals[2];
std::ofstream fout;
fout.open("plot_contourf_tmp.txt");
for (int i = 0; i < res; i++) {
for (int j = 0; j < res; j++) {
x[i][j] = _range_inputs[0][0] + x_step * (float)i;
y[i][j] = _range_inputs[0][0] + y_step * (float)j;
input_vals[0] = x[i][j];
input_vals[1] = y[i][j];
sim(&z[i][j], input_vals);
fout << x[i][j] << "," << y[i][j] << "," << z[i][j];
printf("(%.2f,%.2f,%.2f)", x[i][j], y[i][j], z[i][j]);
if (j < res - 1) {
fout << ",";
std::cout << ",";
}
}
fout << std::endl;
printf("\n");
}
fout.close();
PyObject* x_mat = PyArray_SimpleNewFromData(2, mdim, PyArray_DOUBLE, x[0]);
char full_path[256];
char p_path[256];
getcwd(full_path, 255);
strcpy(p_path, "sys.path.append(\"");
strcat(p_path, full_path);
strcat(p_path, "\")");
PyRun_SimpleString("import sys");
PyRun_SimpleString(p_path);
p_name = PyString_FromString("py_plot");
p_module = PyImport_Import(p_name);
if (p_module == NULL) {
printf("Failed to open py_plot.py");
}
p_dict = PyModule_GetDict(p_module);
p_func = PyDict_GetItemString(p_dict, "plot_contourf");
if (PyCallable_Check(p_func)) {
PyObject_CallObject(p_func, NULL);
} else {
PyErr_Print();
}
Py_DECREF(p_module);
Py_DECREF(p_name);
Py_Finalize();
}
bool mitk::PythonService::CopyToPythonAsSimpleItkImage(mitk::Image *image, const std::string &stdvarName)
{
QString varName = QString::fromStdString( stdvarName );
QString command;
unsigned int* imgDim = image->GetDimensions();
int npy_nd = 1;
npy_intp* npy_dims = new npy_intp[1];
npy_dims[0] = imgDim[0] * imgDim[1] * imgDim[2];
// access python module
PyObject *pyMod = PyImport_AddModule((char*)"__main__");
// global dictionarry
PyObject *pyDict = PyModule_GetDict(pyMod);
const mitk::Vector3D spacing = image->GetGeometry()->GetSpacing();
const mitk::Point3D origin = image->GetGeometry()->GetOrigin();
mitk::PixelType pixelType = image->GetPixelType();
itk::ImageIOBase::IOPixelType ioPixelType = image->GetPixelType().GetPixelType();
PyObject* npyArray = NULL;
mitk::ImageReadAccessor racc(image);
void* array = (void*) racc.GetData();
// default pixeltype: unsigned short
NPY_TYPES npy_type = NPY_USHORT;
std::string sitk_type = "sitkUInt8";
if( ioPixelType == itk::ImageIOBase::SCALAR )
{
if( pixelType.GetComponentType() == itk::ImageIOBase::DOUBLE ) {
npy_type = NPY_DOUBLE;
sitk_type = "sitkFloat64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::FLOAT ) {
npy_type = NPY_FLOAT;
sitk_type = "sitkFloat32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::SHORT) {
npy_type = NPY_SHORT;
sitk_type = "sitkInt16";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::CHAR ) {
npy_type = NPY_BYTE;
sitk_type = "sitkInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::INT ) {
npy_type = NPY_INT;
sitk_type = "sitkInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::LONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UCHAR ) {
npy_type = NPY_UBYTE;
sitk_type = "sitkUInt8";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::UINT ) {
npy_type = NPY_UINT;
sitk_type = "sitkUInt32";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::ULONG ) {
npy_type = NPY_LONG;
sitk_type = "sitkUInt64";
} else if( pixelType.GetComponentType() == itk::ImageIOBase::USHORT ) {
npy_type = NPY_USHORT;
sitk_type = "sitkUInt16";
}
} else {
MITK_WARN << "not a scalar pixeltype";
return false;
}
// creating numpy array
import_array1 (true);
npyArray = PyArray_SimpleNewFromData(npy_nd,npy_dims,npy_type,array);
// add temp array it to the python dictionary to access it in python code
const int status = PyDict_SetItemString( pyDict,QString("%1_numpy_array")
.arg(varName).toStdString().c_str(),
npyArray );
// sanity check
if ( status != 0 )
return false;
command.append( QString("%1 = sitk.Image(%2,%3,%4,sitk.%5)\n").arg(varName)
.arg(QString::number(imgDim[0]))
.arg(QString::number(imgDim[1]))
.arg(QString::number(imgDim[2]))
.arg(QString(sitk_type.c_str())) );
command.append( QString("%1.SetSpacing([%2,%3,%4])\n").arg(varName)
.arg(QString::number(spacing[0]))
.arg(QString::number(spacing[1]))
.arg(QString::number(spacing[2])) );
command.append( QString("%1.SetOrigin([%2,%3,%4])\n").arg(varName)
.arg(QString::number(origin[0]))
.arg(QString::number(origin[1]))
.arg(QString::number(origin[2])) );
// directly access the cpp api from the lib
command.append( QString("_SimpleITK._SetImageFromArray(%1_numpy_array,%1)\n").arg(varName) );
command.append( QString("del %1_numpy_array").arg(varName) );
MITK_DEBUG("PythonService") << "Issuing python command " << command.toStdString();
this->Execute( command.toStdString(), IPythonService::MULTI_LINE_COMMAND );
return true;
}
bool ImgProc::initNumPy()
{
import_array1(false);
return true;
}
