diff options
| -rw-r--r-- | src/Python/Matlab2Python_utils.cpp | 206 | ||||
| -rw-r--r-- | src/Python/fista_module.cpp | 315 | ||||
| -rw-r--r-- | src/Python/setup.py | 58 | ||||
| -rw-r--r-- | src/Python/setup_test.py | 58 |
4 files changed, 637 insertions, 0 deletions
diff --git a/src/Python/Matlab2Python_utils.cpp b/src/Python/Matlab2Python_utils.cpp new file mode 100644 index 0000000..138e8da --- /dev/null +++ b/src/Python/Matlab2Python_utils.cpp @@ -0,0 +1,206 @@ +/* +This work is part of the Core Imaging Library developed by +Visual Analytics and Imaging System Group of the Science Technology +Facilities Council, STFC + +Copyright 2017 Daniil Kazanteev +Copyright 2017 Srikanth Nagella, Edoardo Pasca + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +*/ + +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + +#include <iostream> +#include <cmath> + +#include <boost/python.hpp> +#include <boost/python/numpy.hpp> +#include "boost/tuple/tuple.hpp" + +#if defined(_WIN32) || defined(_WIN32) || defined(__WIN32__) || defined(_WIN64) +#include <windows.h> +// this trick only if compiler is MSVC +__if_not_exists(uint8_t) { typedef __int8 uint8_t; } +__if_not_exists(uint16_t) { typedef __int8 uint16_t; } +#endif + +namespace bp = boost::python; +namespace np = boost::python::numpy; + +/*! in the Matlab implementation this is called as +void mexFunction( +int nlhs, mxArray *plhs[], +int nrhs, const mxArray *prhs[]) +where: +prhs Array of pointers to the INPUT mxArrays +nrhs int number of INPUT mxArrays + +nlhs Array of pointers to the OUTPUT mxArrays +plhs int number of OUTPUT mxArrays + +*********************************************************** + +*********************************************************** +double mxGetScalar(const mxArray *pm); +args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray. +Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray. In C, mxGetScalar returns a double. +*********************************************************** +char *mxArrayToString(const mxArray *array_ptr); +args: array_ptr Pointer to mxCHAR array. +Returns: C-style string. Returns NULL on failure. Possible reasons for failure include out of memory and specifying an array that is not an mxCHAR array. +Description: Call mxArrayToString to copy the character data of an mxCHAR array into a C-style string. +*********************************************************** +mxClassID mxGetClassID(const mxArray *pm); +args: pm Pointer to an mxArray +Returns: Numeric identifier of the class (category) of the mxArray that pm points to.For user-defined types, +mxGetClassId returns a unique value identifying the class of the array contents. +Use mxIsClass to determine whether an array is of a specific user-defined type. + +mxClassID Value MATLAB Type MEX Type C Primitive Type +mxINT8_CLASS int8 int8_T char, byte +mxUINT8_CLASS uint8 uint8_T unsigned char, byte +mxINT16_CLASS int16 int16_T short +mxUINT16_CLASS uint16 uint16_T unsigned short +mxINT32_CLASS int32 int32_T int +mxUINT32_CLASS uint32 uint32_T unsigned int +mxINT64_CLASS int64 int64_T long long +mxUINT64_CLASS uint64 uint64_T unsigned long long +mxSINGLE_CLASS single float float +mxDOUBLE_CLASS double double double + +**************************************************************** +double *mxGetPr(const mxArray *pm); +args: pm Pointer to an mxArray of type double +Returns: Pointer to the first element of the real data. Returns NULL in C (0 in Fortran) if there is no real data. +**************************************************************** +mxArray *mxCreateNumericArray(mwSize ndim, const mwSize *dims, +mxClassID classid, mxComplexity ComplexFlag); +args: ndimNumber of dimensions. If you specify a value for ndim that is less than 2, mxCreateNumericArray automatically sets the number of dimensions to 2. +dims Dimensions array. Each element in the dimensions array contains the size of the array in that dimension. +For example, in C, setting dims[0] to 5 and dims[1] to 7 establishes a 5-by-7 mxArray. Usually there are ndim elements in the dims array. +classid Identifier for the class of the array, which determines the way the numerical data is represented in memory. +For example, specifying mxINT16_CLASS in C causes each piece of numerical data in the mxArray to be represented as a 16-bit signed integer. +ComplexFlag If the mxArray you are creating is to contain imaginary data, set ComplexFlag to mxCOMPLEX in C (1 in Fortran). Otherwise, set ComplexFlag to mxREAL in C (0 in Fortran). +Returns: Pointer to the created mxArray, if successful. If unsuccessful in a standalone (non-MEX file) application, returns NULL in C (0 in Fortran). +If unsuccessful in a MEX file, the MEX file terminates and returns control to the MATLAB prompt. The function is unsuccessful when there is not +enough free heap space to create the mxArray. +*/ + +void mexErrMessageText(char* text) { + std::cerr << text << std::endl; +} + +/* +double mxGetScalar(const mxArray *pm); +args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray. +Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray. In C, mxGetScalar returns a double. +*/ + +template<typename T> +double mxGetScalar(const np::ndarray plh) { + return (double)bp::extract<T>(plh[0]); +} + + + +template<typename T> +T * mxGetData(const np::ndarray pm) { + //args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray. + //Returns: Pointer to the value of the first real(nonimaginary) element of the mxArray.In C, mxGetScalar returns a double. + /*Access the numpy array pointer: + char * get_data() const; + Returns: Array’s raw data pointer as a char + Note: This returns char so stride math works properly on it.User will have to reinterpret_cast it. + probably this would work. + A = reinterpret_cast<float *>(prhs[0]); + */ + return reinterpret_cast<T *>(prhs[0]); +} + +template<typename T> +np::ndarray zeros(int dims , int * dim_array, T el) { + bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]); + np::dtype dtype = np::dtype::get_builtin<T>(); + np::ndarray zz = np::zeros(shape, dtype); + return zz; +} + + +bp::list mexFunction( np::ndarray input ) { + int number_of_dims = input.get_nd(); + int dim_array[3]; + + dim_array[0] = input.shape(0); + dim_array[1] = input.shape(1); + if (number_of_dims == 2) { + dim_array[2] = -1; + } + else { + dim_array[2] = input.shape(2); + } + + /**************************************************************************/ + np::ndarray zz = zeros(3, dim_array, (int)0); + np::ndarray fzz = zeros(3, dim_array, (float)0); + /**************************************************************************/ + + int * A = reinterpret_cast<int *>( input.get_data() ); + int * B = reinterpret_cast<int *>( zz.get_data() ); + float * C = reinterpret_cast<float *>(fzz.get_data()); + + //Copy data and cast + for (int i = 0; i < dim_array[0]; i++) { + for (int j = 0; j < dim_array[1]; j++) { + for (int k = 0; k < dim_array[2]; k++) { + int index = k + dim_array[2] * j + dim_array[2] * dim_array[1] * i; + int val = (*(A + index)); + float fval = (float)val; + std::memcpy(B + index , &val, sizeof(int)); + std::memcpy(C + index , &fval, sizeof(float)); + } + } + } + + + bp::list result; + + result.append<int>(number_of_dims); + result.append<int>(dim_array[0]); + result.append<int>(dim_array[1]); + result.append<int>(dim_array[2]); + result.append<np::ndarray>(zz); + result.append<np::ndarray>(fzz); + + //result.append<bp::tuple>(tup); + return result; + +} + + +BOOST_PYTHON_MODULE(fista) +{ + np::initialize(); + + //To specify that this module is a package + bp::object package = bp::scope(); + package.attr("__path__") = "fista"; + + np::dtype dt1 = np::dtype::get_builtin<uint8_t>(); + np::dtype dt2 = np::dtype::get_builtin<uint16_t>(); + + //import_array(); + //numpy_boost_python_register_type<float, 1>(); + //numpy_boost_python_register_type<float, 2>(); + //numpy_boost_python_register_type<float, 3>(); + //numpy_boost_python_register_type<double, 3>(); + def("mexFunction", mexFunction); +}
\ No newline at end of file diff --git a/src/Python/fista_module.cpp b/src/Python/fista_module.cpp new file mode 100644 index 0000000..5344083 --- /dev/null +++ b/src/Python/fista_module.cpp @@ -0,0 +1,315 @@ +/* +This work is part of the Core Imaging Library developed by +Visual Analytics and Imaging System Group of the Science Technology +Facilities Council, STFC + +Copyright 2017 Daniil Kazanteev +Copyright 2017 Srikanth Nagella, Edoardo Pasca + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +*/ + +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + +#include <iostream> +#include <cmath> + +#include <boost/python.hpp> +#include <boost/python/numpy.hpp> +#include "boost/tuple/tuple.hpp" + +// include the regularizers +#include "FGP_TV_core.h" +#include "LLT_model_core.h" +#include "PatchBased_Regul_core.h" +#include "SplitBregman_TV_core.h" +#include "TGV_PD_core.h" + +#if defined(_WIN32) || defined(_WIN32) || defined(__WIN32__) || defined(_WIN64) +#include <windows.h> +// this trick only if compiler is MSVC +__if_not_exists(uint8_t) { typedef __int8 uint8_t; } +__if_not_exists(uint16_t) { typedef __int8 uint16_t; } +#endif + +namespace bp = boost::python; +namespace np = boost::python::numpy; + + +/*! in the Matlab implementation this is called as +void mexFunction( +int nlhs, mxArray *plhs[], +int nrhs, const mxArray *prhs[]) +where: +prhs Array of pointers to the INPUT mxArrays +nrhs int number of INPUT mxArrays + +nlhs Array of pointers to the OUTPUT mxArrays +plhs int number of OUTPUT mxArrays + +*********************************************************** +mxGetData +args: pm Pointer to an mxArray +Returns: Pointer to the first element of the real data. Returns NULL in C (0 in Fortran) if there is no real data. +*********************************************************** +double mxGetScalar(const mxArray *pm); +args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray. +Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray. In C, mxGetScalar returns a double. +*********************************************************** +char *mxArrayToString(const mxArray *array_ptr); +args: array_ptr Pointer to mxCHAR array. +Returns: C-style string. Returns NULL on failure. Possible reasons for failure include out of memory and specifying an array that is not an mxCHAR array. +Description: Call mxArrayToString to copy the character data of an mxCHAR array into a C-style string. +*********************************************************** +mxClassID mxGetClassID(const mxArray *pm); +args: pm Pointer to an mxArray +Returns: Numeric identifier of the class (category) of the mxArray that pm points to.For user-defined types, +mxGetClassId returns a unique value identifying the class of the array contents. +Use mxIsClass to determine whether an array is of a specific user-defined type. + +mxClassID Value MATLAB Type MEX Type C Primitive Type +mxINT8_CLASS int8 int8_T char, byte +mxUINT8_CLASS uint8 uint8_T unsigned char, byte +mxINT16_CLASS int16 int16_T short +mxUINT16_CLASS uint16 uint16_T unsigned short +mxINT32_CLASS int32 int32_T int +mxUINT32_CLASS uint32 uint32_T unsigned int +mxINT64_CLASS int64 int64_T long long +mxUINT64_CLASS uint64 uint64_T unsigned long long +mxSINGLE_CLASS single float float +mxDOUBLE_CLASS double double double + +**************************************************************** +double *mxGetPr(const mxArray *pm); +args: pm Pointer to an mxArray of type double +Returns: Pointer to the first element of the real data. Returns NULL in C (0 in Fortran) if there is no real data. +**************************************************************** +mxArray *mxCreateNumericArray(mwSize ndim, const mwSize *dims, mxClassID classid, mxComplexity ComplexFlag); +args: ndim: Number of dimensions. If you specify a value for ndim that is less than 2, mxCreateNumericArray automatically sets the number of dimensions to 2. + dims: Dimensions array. Each element in the dimensions array contains the size of the array in that dimension. + For example, in C, setting dims[0] to 5 and dims[1] to 7 establishes a 5-by-7 mxArray. Usually there are ndim elements in the dims array. + classid: Identifier for the class of the array, which determines the way the numerical data is represented in memory. + For example, specifying mxINT16_CLASS in C causes each piece of numerical data in the mxArray to be represented as a 16-bit signed integer. + ComplexFlag: If the mxArray you are creating is to contain imaginary data, set ComplexFlag to mxCOMPLEX in C (1 in Fortran). + Otherwise, set ComplexFlag to mxREAL in C (0 in Fortran). + +Returns: Pointer to the created mxArray, if successful. If unsuccessful in a standalone (non-MEX file) application, returns NULL in C (0 in Fortran). + If unsuccessful in a MEX file, the MEX file terminates and returns control to the MATLAB prompt. The function is unsuccessful when there is not + enough free heap space to create the mxArray. +*/ + +template<typename T> +np::ndarray zeros(int dims, int * dim_array, T el) { + bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]); + np::dtype dtype = np::dtype::get_builtin<T>(); + np::ndarray zz = np::zeros(shape, dtype); + return zz; +} + + +bp::list SplitBregman_TV(np::ndarray input, double d_mu, , int niterations, double d_epsil, int TV_type) { + /* C-OMP implementation of Split Bregman - TV denoising-regularization model (2D/3D) + * + * Input Parameters: + * 1. Noisy image/volume + * 2. lambda - regularization parameter + * 3. Number of iterations [OPTIONAL parameter] + * 4. eplsilon - tolerance constant [OPTIONAL parameter] + * 5. TV-type: 'iso' or 'l1' [OPTIONAL parameter] + * + * Output: + * Filtered/regularized image + * + * All sanity checks and default values are set in Python + */ + int number_of_dims, iter, dimX, dimY, dimZ, ll, j, count, methTV; + const int dim_array[3]; + float *A, *U = NULL, *U_old = NULL, *Dx = NULL, *Dy = NULL, *Dz = NULL, *Bx = NULL, *By = NULL, *Bz = NULL, lambda, mu, epsil, re, re1, re_old; + + //number_of_dims = mxGetNumberOfDimensions(prhs[0]); + //dim_array = mxGetDimensions(prhs[0]); + number_of_dims = input.get_nd(); + + dim_array[0] = input.shape(0); + dim_array[1] = input.shape(1); + if (number_of_dims == 2) { + dim_array[2] = -11; + } + else { + dim_array[2] = input.shape(2); + } + + /*Handling Matlab input data*/ + //if ((nrhs < 2) || (nrhs > 5)) mexErrMsgTxt("At least 2 parameters is required: Image(2D/3D), Regularization parameter. The full list of parameters: Image(2D/3D), Regularization parameter, iterations number, tolerance, penalty type ('iso' or 'l1')"); + + /*Handling Matlab input data*/ + //A = (float *)mxGetData(prhs[0]); /*noisy image (2D/3D) */ + A = reinterpret_cast<float *>(input.get_data()); + + + //mu = (float)mxGetScalar(prhs[1]); /* regularization parameter */ + mu = (float)d_mu; + //iter = 35; /* default iterations number */ + iter = niterations; + //epsil = 0.0001; /* default tolerance constant */ + epsil = (float)d_epsil; + //methTV = 0; /* default isotropic TV penalty */ + methTV = TV_type; + //if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5)) iter = (int)mxGetScalar(prhs[2]); /* iterations number */ + //if ((nrhs == 4) || (nrhs == 5)) epsil = (float)mxGetScalar(prhs[3]); /* tolerance constant */ + //if (nrhs == 5) { + // char *penalty_type; + // penalty_type = mxArrayToString(prhs[4]); /* choosing TV penalty: 'iso' or 'l1', 'iso' is the default */ + // if ((strcmp(penalty_type, "l1") != 0) && (strcmp(penalty_type, "iso") != 0)) mexErrMsgTxt("Choose TV type: 'iso' or 'l1',"); + // if (strcmp(penalty_type, "l1") == 0) methTV = 1; /* enable 'l1' penalty */ + // mxFree(penalty_type); + //} + //if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input image must be in a single precision"); } + + lambda = 2.0f*mu; + count = 1; + re_old = 0.0f; + /*Handling Matlab output data*/ + dimY = dim_array[0]; dimX = dim_array[1]; dimZ = dim_array[2]; + + if (number_of_dims == 2) { + dimZ = 1; /*2D case*/ + /* + mxArray *mxCreateNumericArray(mwSize ndim, const mwSize *dims, mxClassID classid, mxComplexity ComplexFlag); +args: ndim: Number of dimensions. If you specify a value for ndim that is less than 2, mxCreateNumericArray automatically sets the number of dimensions to 2. + dims: Dimensions array. Each element in the dimensions array contains the size of the array in that dimension. + For example, in C, setting dims[0] to 5 and dims[1] to 7 establishes a 5-by-7 mxArray. Usually there are ndim elements in the dims array. + classid: Identifier for the class of the array, which determines the way the numerical data is represented in memory. + For example, specifying mxINT16_CLASS in C causes each piece of numerical data in the mxArray to be represented as a 16-bit signed integer. + ComplexFlag: If the mxArray you are creating is to contain imaginary data, set ComplexFlag to mxCOMPLEX in C (1 in Fortran). + Otherwise, set ComplexFlag to mxREAL in C (0 in Fortran). + + mxCreateNumericArray initializes all its real data elements to 0. +*/ + +/* + U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + U_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Dx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Dy = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Bx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + By = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); +*/ + //U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + U = A = reinterpret_cast<float *>input.get_data(); + U_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Dx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Dy = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + Bx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + By = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL)); + copyIm(A, U, dimX, dimY, dimZ); /*initialize */ + + /* begin outer SB iterations */ + for (ll = 0; ll<iter; ll++) { + + /*storing old values*/ + copyIm(U, U_old, dimX, dimY, dimZ); + + /*GS iteration */ + gauss_seidel2D(U, A, Dx, Dy, Bx, By, dimX, dimY, lambda, mu); + + if (methTV == 1) updDxDy_shrinkAniso2D(U, Dx, Dy, Bx, By, dimX, dimY, lambda); + else updDxDy_shrinkIso2D(U, Dx, Dy, Bx, By, dimX, dimY, lambda); + + updBxBy2D(U, Dx, Dy, Bx, By, dimX, dimY); + + /* calculate norm to terminate earlier */ + re = 0.0f; re1 = 0.0f; + for (j = 0; j<dimX*dimY*dimZ; j++) + { + re += pow(U_old[j] - U[j], 2); + re1 += pow(U_old[j], 2); + } + re = sqrt(re) / sqrt(re1); + if (re < epsil) count++; + if (count > 4) break; + + /* check that the residual norm is decreasing */ + if (ll > 2) { + if (re > re_old) break; + } + re_old = re; + /*printf("%f %i %i \n", re, ll, count); */ + + /*copyIm(U_old, U, dimX, dimY, dimZ); */ + } + printf("SB iterations stopped at iteration: %i\n", ll); + } + if (number_of_dims == 3) { + U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + U_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + Dx = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + Dy = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + Dz = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + Bx = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + By = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + Bz = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL)); + + copyIm(A, U, dimX, dimY, dimZ); /*initialize */ + + /* begin outer SB iterations */ + for (ll = 0; ll<iter; ll++) { + + /*storing old values*/ + copyIm(U, U_old, dimX, dimY, dimZ); + + /*GS iteration */ + gauss_seidel3D(U, A, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda, mu); + + if (methTV == 1) updDxDyDz_shrinkAniso3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda); + else updDxDyDz_shrinkIso3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda); + + updBxByBz3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ); + + /* calculate norm to terminate earlier */ + re = 0.0f; re1 = 0.0f; + for (j = 0; j<dimX*dimY*dimZ; j++) + { + re += pow(U[j] - U_old[j], 2); + re1 += pow(U[j], 2); + } + re = sqrt(re) / sqrt(re1); + if (re < epsil) count++; + if (count > 4) break; + + /* check that the residual norm is decreasing */ + if (ll > 2) { + if (re > re_old) break; + } + /*printf("%f %i %i \n", re, ll, count); */ + re_old = re; + } + printf("SB iterations stopped at iteration: %i\n", ll); + } + bp::list result; + return result; +} + + +BOOST_PYTHON_MODULE(fista) +{ + np::initialize(); + + //To specify that this module is a package + bp::object package = bp::scope(); + package.attr("__path__") = "fista"; + + np::dtype dt1 = np::dtype::get_builtin<uint8_t>(); + np::dtype dt2 = np::dtype::get_builtin<uint16_t>(); + + + def("mexFunction", mexFunction); +}
\ No newline at end of file diff --git a/src/Python/setup.py b/src/Python/setup.py new file mode 100644 index 0000000..ffb9c02 --- /dev/null +++ b/src/Python/setup.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +import setuptools +from distutils.core import setup +from distutils.extension import Extension +from Cython.Distutils import build_ext + +import os +import sys +import numpy +import platform + +cil_version=os.environ['CIL_VERSION'] +if cil_version == '': + print("Please set the environmental variable CIL_VERSION") + sys.exit(1) + +library_include_path = "" +library_lib_path = "" +try: + library_include_path = os.environ['LIBRARY_INC'] + library_lib_path = os.environ['LIBRARY_LIB'] +except: + library_include_path = os.environ['PREFIX']+'/include' + pass + +extra_include_dirs = [numpy.get_include(), library_include_path] +extra_library_dirs = [library_include_path+"/../lib", "C:\\Apps\\Miniconda2\\envs\\cil27\\Library\\lib"] +extra_compile_args = ['-fopenmp','-O2', '-funsigned-char', '-Wall', '-std=c++0x'] +extra_libraries = [] +if platform.system() == 'Windows': + extra_compile_args[0:] = ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB'] + extra_include_dirs += ["..\\ContourTree\\", "..\\win32\\" , "..\\Core\\","."] + if sys.version_info.major == 3 : + extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64'] + else: + extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64'] +else: + extra_include_dirs += ["../ContourTree/", "../Core/","."] + if sys.version_info.major == 3: + extra_libraries += ['boost_python3', 'boost_numpy3','gomp'] + else: + extra_libraries += ['boost_python', 'boost_numpy','gomp'] + +setup( + name='ccpi', + description='CCPi Core Imaging Library - FISTA Reconstruction Module', + version=cil_version, + cmdclass = {'build_ext': build_ext}, + ext_modules = [Extension("fista", + sources=[ "Matlab2Python_utils.cpp", + ], + include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries ), + + ], + zip_safe = False, + packages = {'ccpi','ccpi.reconstruction'}, +) diff --git a/src/Python/setup_test.py b/src/Python/setup_test.py new file mode 100644 index 0000000..ffb9c02 --- /dev/null +++ b/src/Python/setup_test.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +import setuptools +from distutils.core import setup +from distutils.extension import Extension +from Cython.Distutils import build_ext + +import os +import sys +import numpy +import platform + +cil_version=os.environ['CIL_VERSION'] +if cil_version == '': + print("Please set the environmental variable CIL_VERSION") + sys.exit(1) + +library_include_path = "" +library_lib_path = "" +try: + library_include_path = os.environ['LIBRARY_INC'] + library_lib_path = os.environ['LIBRARY_LIB'] +except: + library_include_path = os.environ['PREFIX']+'/include' + pass + +extra_include_dirs = [numpy.get_include(), library_include_path] +extra_library_dirs = [library_include_path+"/../lib", "C:\\Apps\\Miniconda2\\envs\\cil27\\Library\\lib"] +extra_compile_args = ['-fopenmp','-O2', '-funsigned-char', '-Wall', '-std=c++0x'] +extra_libraries = [] +if platform.system() == 'Windows': + extra_compile_args[0:] = ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB'] + extra_include_dirs += ["..\\ContourTree\\", "..\\win32\\" , "..\\Core\\","."] + if sys.version_info.major == 3 : + extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64'] + else: + extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64'] +else: + extra_include_dirs += ["../ContourTree/", "../Core/","."] + if sys.version_info.major == 3: + extra_libraries += ['boost_python3', 'boost_numpy3','gomp'] + else: + extra_libraries += ['boost_python', 'boost_numpy','gomp'] + +setup( + name='ccpi', + description='CCPi Core Imaging Library - FISTA Reconstruction Module', + version=cil_version, + cmdclass = {'build_ext': build_ext}, + ext_modules = [Extension("fista", + sources=[ "Matlab2Python_utils.cpp", + ], + include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries ), + + ], + zip_safe = False, + packages = {'ccpi','ccpi.reconstruction'}, +) |