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m2PythonWrapper.cpp
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m2PythonWrapper.cpp
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/*===================================================================
MSI applications for interactive analysis in MITK (M2aia)
Copyright (c) Jonas Cordes.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or https://www.github.com/jtfcordes/m2aia for details.
===================================================================*/
#include <M2aiaCoreExports.h>
#include <itksys/SystemTools.hxx>
#include <m2ImzMLImageIO.h>
#include <m2ImzMLSpectrumImage.h>
#include <mitkCoreServices.h>
#include <mitkIPreferencesService.h>
#include <mitkImageReadAccessor.h>
// PYTHON EXPORT
namespace m2
{
namespace sys
{
// This class holds smartpointer and additional data the handling of an ImzMlMassSpecImage object.
class ImageHandle
{
public:
m2::ImzMLSpectrumImage::Pointer Image;
};
} // namespace sys
} // namespace m2
extern "C"
{
unsigned int GetNumberOfPixelsInImage(m2::sys::ImageHandle *handle)
{
auto dims = handle->Image->GetDimensions();
auto validDims = handle->Image->GetDimension();
auto N = std::accumulate(dims, dims + validDims, 1, std::multiplies<>());
return N;
}
M2AIACORE_EXPORT void GetImageArrayFloat32(m2::sys::ImageHandle *handle, double mz, double tol, float *data)
{
handle->Image->GetImage(mz, tol, nullptr, handle->Image);
auto N = GetNumberOfPixelsInImage(handle);
mitk::ImageReadAccessor acc(handle->Image.GetPointer());
std::copy((m2::DisplayImagePixelType *)(acc.GetData()), (m2::DisplayImagePixelType *)(acc.GetData()) + N, data);
}
M2AIACORE_EXPORT void GetImageArrayFloat64(m2::sys::ImageHandle *handle, double mz, double tol, double *data)
{
handle->Image->GetImage(mz, tol, nullptr, handle->Image);
auto N = GetNumberOfPixelsInImage(handle);
mitk::ImageReadAccessor acc(handle->Image.GetPointer());
std::copy((m2::DisplayImagePixelType *)(acc.GetData()), (m2::DisplayImagePixelType *)(acc.GetData()) + N, data);
}
M2AIACORE_EXPORT void GetMaskArray(m2::sys::ImageHandle *handle, mitk::Label::PixelType *data)
{
auto mask = handle->Image->GetMaskImage();
auto N = GetNumberOfPixelsInImage(handle);
mitk::ImageReadAccessor acc(mask);
std::copy((mitk::Label::PixelType *)(acc.GetData()), (mitk::Label::PixelType *)(acc.GetData()) + N, data);
}
M2AIACORE_EXPORT void GetIndexArray(m2::sys::ImageHandle *handle, unsigned int *data)
{
auto indexImage = handle->Image->GetIndexImage();
auto N = GetNumberOfPixelsInImage(handle);
mitk::ImageReadAccessor acc(indexImage);
std::copy((unsigned int *)(acc.GetData()), (unsigned int *)(acc.GetData()) + N, data);
}
M2AIACORE_EXPORT void GetNormalizationArray(m2::sys::ImageHandle *handle,
const char *typeName,
m2::NormImagePixelType *data)
{
auto type = static_cast<m2::NormalizationStrategyType>(m2::NORMALIZATION_MAPPINGS.at(typeName));
if (!handle->Image->GetNormalizationImageStatus(type))
handle->Image->InitializeNormalizationImage(type);
auto normImage = handle->Image->GetNormalizationImage(type);
auto N = GetNumberOfPixelsInImage(handle);
mitk::ImageReadAccessor acc(normImage);
std::copy((m2::NormImagePixelType *)(acc.GetData()), (m2::NormImagePixelType *)(acc.GetData()) + N, data);
}
M2AIACORE_EXPORT unsigned int GetSpectrumType(m2::sys::ImageHandle *handle)
{
return (unsigned int)(handle->Image->GetSpectrumType().Format);
}
M2AIACORE_EXPORT unsigned int GetSizeInBytesOfYAxisType(m2::sys::ImageHandle *handle)
{
return m2::to_bytes(handle->Image->GetSpectrumType().YAxisType);
}
M2AIACORE_EXPORT void GetXAxis(m2::sys::ImageHandle *handle, double *data)
{
auto &xAxis = handle->Image->GetXAxis();
std::copy(xAxis.begin(), xAxis.end(), data);
}
M2AIACORE_EXPORT unsigned int GetXAxisDepth(m2::sys::ImageHandle *handle)
{
auto &xAxis = handle->Image->GetXAxis();
return xAxis.size();
}
M2AIACORE_EXPORT float GetTolerance(m2::sys::ImageHandle *handle)
{
return handle->Image->GetTolerance();
}
M2AIACORE_EXPORT void SetTolerance(m2::sys::ImageHandle *handle, float tol)
{
handle->Image->SetTolerance(tol);
}
M2AIACORE_EXPORT unsigned int GetYDataTypeSizeInBytes(m2::sys::ImageHandle *handle)
{
auto id = handle->Image->GetSpectrumType().YAxisType;
if (id == m2::NumericType::Float)
{
return sizeof(float);
}
else if (id == m2::NumericType::Double)
{
return sizeof(double);
}
else
{
return 0;
}
}
M2AIACORE_EXPORT void GetSpectrum(m2::sys::ImageHandle *handle, unsigned int id, float *xd, float *yd)
{
std::vector<float> xs, ys;
handle->Image->GetSpectrumFloat(id, xs, ys);
std::copy(xs.begin(), xs.end(), xd);
std::copy(ys.begin(), ys.end(), yd);
}
M2AIACORE_EXPORT void GetSpectra(m2::sys::ImageHandle *handle, unsigned int *id, unsigned int N, float *yd)
{
std::vector<float> ys;
for (unsigned int i = 0; i < N; ++i)
{
handle->Image->GetIntensitiesFloat(id[i], ys);
std::copy(ys.begin(), ys.end(), yd + i * ys.size());
}
}
M2AIACORE_EXPORT void GetIntensities(m2::sys::ImageHandle *handle, unsigned int id, float *yd)
{
std::vector<float> ys;
handle->Image->GetIntensitiesFloat(id, ys);
std::copy(ys.begin(), ys.end(), yd);
}
M2AIACORE_EXPORT unsigned int GetSpectrumDepth(m2::sys::ImageHandle *handle, unsigned int id)
{
const auto &spectrum = handle->Image->GetSpectra()[id];
return spectrum.mzLength;
}
M2AIACORE_EXPORT void GetSpectrumPosition(m2::sys::ImageHandle *handle,
unsigned int spectrumId,
unsigned int *pixelPosition)
{
auto &spectrum = handle->Image->GetSpectra()[spectrumId];
auto *p = spectrum.index.GetIndex();
std::copy(p, p + 3, pixelPosition);
}
M2AIACORE_EXPORT unsigned int GetNumberOfSpectra(m2::sys::ImageHandle *handle)
{
return handle->Image->GetSpectra().size();
}
M2AIACORE_EXPORT void GetMeanSpectrum(m2::sys::ImageHandle *handle, double *data)
{
auto &yMean = handle->Image->GetMeanSpectrum();
std::copy(yMean.begin(), yMean.end(), data);
}
M2AIACORE_EXPORT void GetMaxSpectrum(m2::sys::ImageHandle *handle, double *data)
{
auto &yMean = handle->Image->GetSkylineSpectrum();
std::copy(yMean.begin(), yMean.end(), data);
}
M2AIACORE_EXPORT void GetSize(m2::sys::ImageHandle *handle, uint32_t *data)
{
auto p = handle->Image->GetDimensions();
std::copy(p, p + 3, data);
}
M2AIACORE_EXPORT void GetSpacing(m2::sys::ImageHandle *handle, double *data)
{
auto v = handle->Image->GetGeometry()->GetSpacing();
auto p = v.GetDataPointer();
std::copy(p, p + 3, data);
}
M2AIACORE_EXPORT void GetOrigin(m2::sys::ImageHandle *handle, double *data)
{
auto v = handle->Image->GetGeometry()->GetOrigin();
auto p = v.GetDataPointer();
std::copy(p, p + 3, data);
}
M2AIACORE_EXPORT void SetSmoothing(m2::sys::ImageHandle *handle, const char *sm_s, unsigned int hws)
{
handle->Image->SetSmoothingStrategy(static_cast<m2::SmoothingType>(m2::SMOOTHING_MAPPINGS.at(sm_s)));
handle->Image->SetSmoothingHalfWindowSize(hws);
}
M2AIACORE_EXPORT void SetBaselineCorrection(m2::sys::ImageHandle *handle, const char *sm_s, unsigned int hws)
{
handle->Image->SetBaselineCorrectionStrategy(
static_cast<m2::BaselineCorrectionType>(m2::BASECOR_MAPPINGS.at(sm_s)));
handle->Image->SetBaseLineCorrectionHalfWindowSize(hws);
}
M2AIACORE_EXPORT void SetPooling(m2::sys::ImageHandle *handle, const char *sm_s)
{
handle->Image->SetRangePoolingStrategy(static_cast<m2::RangePoolingStrategyType>(m2::POOLING_MAPPINGS.at(sm_s)));
}
M2AIACORE_EXPORT void SetNormalization(m2::sys::ImageHandle *handle, const char *sm_s)
{
handle->Image->SetNormalizationStrategy(
static_cast<m2::NormalizationStrategyType>(m2::NORMALIZATION_MAPPINGS.at(sm_s)));
}
M2AIACORE_EXPORT void SetIntensityTransformation(m2::sys::ImageHandle *handle, const char *sm_s)
{
handle->Image->SetIntensityTransformationStrategy(
static_cast<m2::IntensityTransformationType>(m2::INTENSITYTRANSFORMATION_MAPPINGS.at(sm_s)));
}
M2AIACORE_EXPORT char *GetMetaDataDictionary(m2::sys::ImageHandle *handle)
{
auto v = handle->Image->GetPropertyList();
std::string s;
auto keys = v->GetPropertyKeys();
for (auto k : keys)
{
auto prop = v->GetProperty(k.c_str());
s += k;
s += "\t" + prop->GetValueAsString();
s += "\n";
}
auto data = new char[s.length() + 1];
std::copy(s.begin(), s.end(), data);
data[s.length()] = '\0';
return data;
}
M2AIACORE_EXPORT void DestroyCharBuffer(std::string *p)
{
delete p;
}
M2AIACORE_EXPORT void WriteContinuousCentroidImzML(m2::sys::ImageHandle *handle,
const char *s,
double *centroids,
int n)
{
m2::ImzMLImageIO io;
mitk::AbstractFileWriter *writer = &io;
auto intervals = m2::IntervalVector::New();
for (int i = 0; i < n; ++i)
intervals->GetIntervals().push_back(m2::Interval(centroids[i], 0));
writer->SetInput(handle->Image);
writer->SetOutputLocation(std::string(s));
io.SetIntervalVector(intervals);
io.SetSpectrumFormat(m2::SpectrumFormat::ContinuousCentroid);
io.Write();
}
M2AIACORE_EXPORT void Update(m2::sys::ImageHandle *p)
{
// p->Image->InitializeProcessor();
// p->Image->InitializeGeometry();
p->Image->InitializeImageAccess();
}
M2AIACORE_EXPORT m2::sys::ImageHandle *CreateImageHandle(const char *path)
{
if (auto *preferencesService = mitk::CoreServices::GetPreferencesService())
if (!preferencesService->GetSystemPreferences())
{
mitk::CoreServicePointer preferencesService(mitk::CoreServices::GetPreferencesService());
preferencesService->InitializeStorage(".pym2aia_prefs.xml");
}
if (!itksys::SystemTools::FileExists(path))
{
MITK_ERROR << "The given path does not exist!\n\t" << std::string(path);
return nullptr;
}
// std::string parameters;
// if(itksys::SystemTools::PathExists(s) && itksys::SystemTools::FileExists(s)){
// auto ifs = std::ifstream(s);
// parameters = std::string(std::istreambuf_iterator<char>{ifs}, {});
// }else{
// parameters = s;
// }
// using namespace std::string_literals;
// std::map<std::string, std::string> pMap;
// const auto bsc_s = m2::Find(parameters, "baseline-correction", "None"s, pMap);
// const auto bsc_hw = m2::Find(parameters, "baseline-correction-hw", int(50), pMap);
// const auto sm_s = m2::Find(parameters, "smoothing", "None"s, pMap);
// const auto sm_hw = m2::Find(parameters, "smoothing-hw", int(2), pMap);
// const auto norm = m2::Find(parameters, "normalization", "None"s, pMap);
// const auto pool = m2::Find(parameters, "pooling", "Maximum"s, pMap);
// const auto tol = m2::Find(parameters, "tolerance", double(0), pMap);
// const auto intTransform = m2::Find(parameters, "transform", "None"s, pMap);
// const auto threads = m2::Find(parameters, "threads",
// int(itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads()), pMap);
// MITK_INFO << "---------------------";
// MITK_INFO << "Image initialization:";
// MITK_INFO << "---------------------";
// for (auto &p : pMap)
// MITK_INFO << "\t" << p.first << " " << p.second;
m2::ImzMLImageIO io;
mitk::AbstractFileReader *reader = &io;
reader->SetInput(std::string(path));
// MITK_INFO << "ImzML Path " << path;
auto data = io.DoRead();
auto storage = new m2::sys::ImageHandle();
auto sImage = storage->Image = dynamic_cast<m2::ImzMLSpectrumImage *>(data.front().GetPointer());
return storage;
}
M2AIACORE_EXPORT void DestroyImageHandle(m2::sys::ImageHandle *p)
{
delete p;
}
}