wim/sitk-registration-sys
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

- add more tests

Browse Source 
- do not allow multiple registrations to run at once because it causes a memory error in the sitk code
This commit is contained in:
Wim Pomp
2025-03-03 09:40:46 +01:00
parent 0aeb3c8c7e
commit 934f038ea1
8 changed files with 378 additions and 167 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
cpp/CMakeLists.txt
View File

@@ -1,10 +1,8 @@
cmake_minimum_required(VERSION 3.16.3)
project(sitk_adapter)
set(ENV{Elastix_DIR} "../sitk/build/Elastix-build" )
set(ENV{ITK_DIR} "~/code/c/SimpleITK/build/ITK-build" )
set(ENV{SimpleITK_DIR} "~/code/c/SimpleITK/build/SimpleITK-build" )
set(ENV{ITK_DIR} "../sitk/build/ITK-build" )
set(ENV{SimpleITK_DIR} "~../sitk/build/SimpleITK-build" )
find_package(SimpleITK)
add_library(sitk_adapter SHARED sitk_adapter.cxx)
target_link_libraries (sitk_adapter ${SimpleITK_LIBRARIES})

148
cpp/sitk_adapter.cxx
View File

@@ -1,12 +1,29 @@
#include <SimpleITK.h>
#include <sitkImageOperators.h>
#include <cstring>
#include <filesystem>
namespace sitk = itk::simple;
using namespace std;
std::string gen_random(const int len) {
static const char alphanum[] =
"0123456789"
"ABCDEFGHIJKLMNOPQRSTUVWXYZ"
"abcdefghijklmnopqrstuvwxyz";
std::string tmp_s;
tmp_s.reserve(len);
for (int i = 0; i < len; ++i) {
tmp_s += alphanum[rand() % (sizeof(alphanum) - 1)];
}
return tmp_s;
}
template <typename T>
sitk::Image make_image(
unsigned int width,
@@ -45,7 +62,7 @@ sitk::Image make_image(
} else if (id == sitk::PixelIDValueEnum::sitkFloat64) {
double* b = im.GetBufferAsDouble();
memcpy(b, image, width * height * 8);
}
}
return im;
}
@@ -114,7 +131,7 @@ interp_u16(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkUInt16);
im = interp(transform, origin, im, bspline_or_nn);
uint16_t* c = im.GetBufferAsUInt16();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 2);
}
extern "C" void
@@ -129,7 +146,7 @@ interp_i16(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkInt16);
im = interp(transform, origin, im, bspline_or_nn);
int16_t* c = im.GetBufferAsInt16();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 2);
}
extern "C" void
@@ -144,7 +161,7 @@ interp_u32(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkUInt32);
im = interp(transform, origin, im, bspline_or_nn);
uint32_t* c = im.GetBufferAsUInt32();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 4);
}
extern "C" void
@@ -159,7 +176,7 @@ interp_i32(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkInt32);
im = interp(transform, origin, im, bspline_or_nn);
int32_t* c = im.GetBufferAsInt32();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 4);
}
extern "C" void
@@ -174,7 +191,7 @@ interp_u64(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkUInt64);
im = interp(transform, origin, im, bspline_or_nn);
uint64_t* c = im.GetBufferAsUInt64();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 8);
}
extern "C" void
@@ -189,7 +206,7 @@ interp_i64(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkInt64);
im = interp(transform, origin, im, bspline_or_nn);
int64_t* c = im.GetBufferAsInt64();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 8);
}
extern "C" void
@@ -204,7 +221,7 @@ interp_f32(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkFloat32);
im = interp(transform, origin, im, bspline_or_nn);
float* c = im.GetBufferAsFloat();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 4);
}
extern "C" void
@@ -219,48 +236,97 @@ interp_f64(
sitk::Image im = make_image(width, height, *image, sitk::PixelIDValueEnum::sitkFloat64);
im = interp(transform, origin, im, bspline_or_nn);
double* c = im.GetBufferAsDouble();
memcpy(*image, c, width * height);
memcpy(*image, c, width * height * 8);
}
void
reg2(
sitk::Image fixed,
sitk::Image moving,
bool t_or_a,
double** transform
) {
try {
string kind = (t_or_a == false) ? "translation" : "affine";
sitk::ImageRegistrationMethod R;
R.SetMetricAsMattesMutualInformation();
const double maxStep = 4.0;
const double minStep = 0.01;
const unsigned int numberOfIterations = 200;
const double relaxationFactor = 0.5;
// R.SetOptimizerAsLBFGSB(maxStep, minStep, numberOfIterations, relaxationFactor);
R.SetOptimizerAsRegularStepGradientDescent(maxStep, minStep, numberOfIterations, relaxationFactor);
// R.SetOptimizerAsLBFGS2();
vector<double> matrix = {1.0, 0.0, 0.0, 1.0};
vector<double> translation = {0., 0.};
vector<double> origin = {399.5, 299.5};
R.SetInitialTransform(sitk::AffineTransform(matrix, translation, origin));
R.SetInterpolator(sitk::sitkBSpline);
sitk::Transform outTx = R.Execute(fixed, moving);
vector<double> t = outTx.GetParameters();
for (int i = 0; i < t.size(); i++) {
cout << t[i] << " ";
(*transform)[i] = t[i];
}
} catch (const std::exception &exc) {
cerr << exc.what();
}
}
void
reg(
sitk::Image fixed,
sitk::Image moving,
bool t_or_a,
double** transform
sitk::Image fixed,
sitk::Image moving,
bool t_or_a,
double** transform
) {
try {
string kind = (t_or_a == false) ? "translation" : "affine";
sitk::ElastixImageFilter tfilter = sitk::ElastixImageFilter();
tfilter.LogToConsoleOff();
tfilter.SetFixedImage(fixed);
tfilter.SetMovingImage(moving);
tfilter.SetParameterMap(sitk::GetDefaultParameterMap(kind));
tfilter.Execute();
try {
string kind = (t_or_a == false) ? "translation" : "affine";
// std::filesystem::path output_path = std::filesystem::temp_directory_path() / gen_random(12);
std::filesystem::path output_path = std::filesystem::temp_directory_path();
// std::filesystem::create_directory(output_path);
sitk::ElastixImageFilter::ParameterMapType parameter_map = tfilter.GetTransformParameterMap(0);
for (sitk::ElastixImageFilter::ParameterMapType::iterator parameter = parameter_map.begin(); parameter != parameter_map.end(); ++parameter) {
if (parameter->first == "TransformParameters") {
vector<string> tp = parameter->second;
if (t_or_a == true) {
for (int j = 0; j < tp.size(); j++) {
(*transform)[j] = stod(tp[j]);
}
} else {
(*transform)[0] = 1.0;
(*transform)[1] = 0.0;
(*transform)[2] = 0.0;
(*transform)[3] = 1.0;
for (int j = 0; j < tp.size(); j++) {
(*transform)[j + 4] = stod(tp[j]);
sitk::ElastixImageFilter tfilter = sitk::ElastixImageFilter();
tfilter.LogToConsoleOff();
tfilter.LogToFileOff();
tfilter.SetLogToFile(false);
tfilter.SetFixedImage(fixed);
tfilter.SetMovingImage(moving);
tfilter.SetParameterMap(sitk::GetDefaultParameterMap(kind));
tfilter.SetParameter("WriteResultImage", "false");
tfilter.SetOutputDirectory(output_path);
// cout << "output_path: " << output_path << endl;
// tfilter.PrintParameterMap();
// cout << "r6 " << std::flush;
tfilter.Execute();
// cout << "r7 " << std::flush;
sitk::ElastixImageFilter::ParameterMapType parameter_map = tfilter.GetTransformParameterMap(0);
for (sitk::ElastixImageFilter::ParameterMapType::iterator parameter = parameter_map.begin(); parameter != parameter_map.end(); ++parameter) {
if (parameter->first == "TransformParameters") {
vector<string> tp = parameter->second;
if (t_or_a == true) {
for (int j = 0; j < tp.size(); j++) {
(*transform)[j] = stod(tp[j]);
}
} else {
(*transform)[0] = 1.0;
(*transform)[1] = 0.0;
(*transform)[2] = 0.0;
(*transform)[3] = 1.0;
for (int j = 0; j < tp.size(); j++) {
(*transform)[j + 4] = stod(tp[j]);
}
}
break;
}
}
}
}
} catch (const std::exception &exc) {
cerr << exc.what();
}
// cout << "r8 " << std::flush;
} catch (const std::exception &exc) {
cerr << exc.what();
}
}