Mercurial > hg > orthanc-client
diff OrthancCppClient/Series.cpp @ 0:ebc1e38ef615
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 01 Jun 2015 09:47:32 +0200 |
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children | d5027f9f676a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancCppClient/Series.cpp Mon Jun 01 09:47:32 2015 +0200 @@ -0,0 +1,527 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics + * Department, University Hospital of Liege, Belgium + * + * This program is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * In addition, as a special exception, the copyright holders of this + * program give permission to link the code of its release with the + * OpenSSL project's "OpenSSL" library (or with modified versions of it + * that use the same license as the "OpenSSL" library), and distribute + * the linked executables. You must obey the GNU General Public License + * in all respects for all of the code used other than "OpenSSL". If you + * modify file(s) with this exception, you may extend this exception to + * your version of the file(s), but you are not obligated to do so. If + * you do not wish to do so, delete this exception statement from your + * version. If you delete this exception statement from all source files + * in the program, then also delete it here. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + **/ + + +#include "../Core/PrecompiledHeaders.h" +#include "Series.h" + +#include "OrthancConnection.h" + +#include <set> +#include <boost/lexical_cast.hpp> + +namespace OrthancClient +{ + namespace + { + class SliceLocator + { + private: + float normal_[3]; + + public: + SliceLocator(Instance& someSlice) + { + /** + * Compute the slice normal from Image Orientation Patient. + * http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-z-from-slice + * http://dicomiseasy.blogspot.be/2013/06/getting-oriented-using-image-plane.html + * http://www.itk.org/pipermail/insight-users/2003-September/004762.html + **/ + + std::vector<float> cosines; + someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient"); // 0020-0037 + + if (cosines.size() != 6) + { + throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); + } + + normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; + normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; + normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; + } + + + /** + * Compute the distance of some slice along the slice normal. + **/ + float ComputeSliceLocation(Instance& instance) const + { + std::vector<float> ipp; + instance.SplitVectorOfFloats(ipp, "ImagePositionPatient"); // 0020-0032 + if (ipp.size() != 3) + { + throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); + } + + float dist = 0; + + for (int i = 0; i < 3; i++) + { + dist += normal_[i] * ipp[i]; + } + + return dist; + } + }; + + class ImageDownloadCommand : public Orthanc::ICommand + { + private: + Orthanc::PixelFormat format_; + Orthanc::ImageExtractionMode mode_; + Instance& instance_; + void* target_; + size_t lineStride_; + + public: + ImageDownloadCommand(Instance& instance, + Orthanc::PixelFormat format, + Orthanc::ImageExtractionMode mode, + void* target, + size_t lineStride) : + format_(format), + mode_(mode), + instance_(instance), + target_(target), + lineStride_(lineStride) + { + instance_.SetImageExtractionMode(mode); + } + + virtual bool Execute() + { + using namespace Orthanc; + + unsigned int width = instance_.GetHeight(); + + for (unsigned int y = 0; y < instance_.GetHeight(); y++) + { + uint8_t* p = reinterpret_cast<uint8_t*>(target_) + y * lineStride_; + + if (instance_.GetPixelFormat() == format_) + { + memcpy(p, instance_.GetBuffer(y), GetBytesPerPixel(instance_.GetPixelFormat()) * instance_.GetWidth()); + } + else if (instance_.GetPixelFormat() == PixelFormat_Grayscale8 && + format_ == PixelFormat_RGB24) + { + const uint8_t* s = reinterpret_cast<const uint8_t*>(instance_.GetBuffer(y)); + for (unsigned int x = 0; x < width; x++, s++, p += 3) + { + p[0] = *s; + p[1] = *s; + p[2] = *s; + } + } + else + { + throw OrthancClientException(ErrorCode_NotImplemented); + } + } + + // Do not keep the image in memory, as we are loading 3D images + instance_.DiscardImage(); + + return true; + } + }; + + + class ProgressToFloatListener : public Orthanc::ThreadedCommandProcessor::IListener + { + private: + float* target_; + + public: + ProgressToFloatListener(float* target) : target_(target) + { + } + + virtual void SignalProgress(unsigned int current, + unsigned int total) + { + if (total == 0) + { + *target_ = 0; + } + else + { + *target_ = static_cast<float>(current) / static_cast<float>(total); + } + } + + virtual void SignalSuccess(unsigned int total) + { + *target_ = 1; + } + + virtual void SignalFailure() + { + *target_ = 0; + } + + virtual void SignalCancel() + { + *target_ = 0; + } + }; + + } + + + void Series::Check3DImage() + { + if (!Is3DImage()) + { + throw OrthancClientException(Orthanc::ErrorCode_NotImplemented); + } + } + + bool Series::Is3DImageInternal() + { + try + { + if (GetInstanceCount() == 0) + { + // Empty image, use some default value (should never happen) + voxelSizeX_ = 1; + voxelSizeY_ = 1; + voxelSizeZ_ = 1; + sliceThickness_ = 1; + + return true; + } + + // Choose a reference slice + Instance& reference = GetInstance(0); + + // Check that all the child instances share the same 3D parameters + for (unsigned int i = 0; i < GetInstanceCount(); i++) + { + Instance& i2 = GetInstance(i); + + if (std::string(reference.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) || + std::string(reference.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) || + std::string(reference.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) || + std::string(reference.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) || + std::string(reference.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing"))) + { + return false; + } + } + + + // Extract X/Y voxel size and slice thickness + std::string s = GetInstance(0).GetTagAsString("PixelSpacing"); // 0028-0030 + size_t pos = s.find('\\'); + assert(pos != std::string::npos); + std::string sy = s.substr(0, pos); + std::string sx = s.substr(pos + 1); + + try + { + voxelSizeX_ = boost::lexical_cast<float>(sx); + voxelSizeY_ = boost::lexical_cast<float>(sy); + } + catch (boost::bad_lexical_cast) + { + throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); + } + + sliceThickness_ = GetInstance(0).GetTagAsFloat("SliceThickness"); // 0018-0050 + + + // Compute the location of each slice to extract the voxel size along Z + voxelSizeZ_ = std::numeric_limits<float>::infinity(); + + SliceLocator locator(reference); + float referenceSliceLocation = locator.ComputeSliceLocation(reference); + + std::set<float> l; + for (unsigned int i = 0; i < GetInstanceCount(); i++) + { + float location = locator.ComputeSliceLocation(GetInstance(i)); + float distanceToReferenceSlice = fabs(location - referenceSliceLocation); + + l.insert(location); + + if (distanceToReferenceSlice > std::numeric_limits<float>::epsilon() && + distanceToReferenceSlice < voxelSizeZ_) + { + voxelSizeZ_ = distanceToReferenceSlice; + } + } + + + // Make sure that 2 slices do not share the same Z location + return l.size() == GetInstanceCount(); + } + catch (OrthancClientException) + { + return false; + } + } + + void Series::ReadSeries() + { + Orthanc::HttpClient client(connection_.GetHttpClient()); + + client.SetUrl(std::string(connection_.GetOrthancUrl()) + "/series/" + id_); + Json::Value v; + if (!client.Apply(series_)) + { + throw OrthancClientException(Orthanc::ErrorCode_NetworkProtocol); + } + } + + Orthanc::IDynamicObject* Series::GetFillerItem(size_t index) + { + Json::Value::ArrayIndex tmp = static_cast<Json::Value::ArrayIndex>(index); + std::string id = series_["Instances"][tmp].asString(); + return new Instance(connection_, id.c_str()); + } + + Series::Series(const OrthancConnection& connection, + const char* id) : + connection_(connection), + id_(id), + instances_(*this) + { + ReadSeries(); + status_ = Status3DImage_NotTested; + url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_; + + voxelSizeX_ = 0; + voxelSizeY_ = 0; + voxelSizeZ_ = 0; + sliceThickness_ = 0; + + instances_.SetThreadCount(connection.GetThreadCount()); + } + + + bool Series::Is3DImage() + { + if (status_ == Status3DImage_NotTested) + { + status_ = Is3DImageInternal() ? Status3DImage_True : Status3DImage_False; + } + + return status_ == Status3DImage_True; + } + + unsigned int Series::GetInstanceCount() + { + return instances_.GetSize(); + } + + Instance& Series::GetInstance(unsigned int index) + { + return dynamic_cast<Instance&>(instances_.GetItem(index)); + } + + unsigned int Series::GetWidth() + { + Check3DImage(); + + if (GetInstanceCount() == 0) + return 0; + else + return GetInstance(0).GetTagAsInt("Columns"); + } + + unsigned int Series::GetHeight() + { + Check3DImage(); + + if (GetInstanceCount() == 0) + return 0; + else + return GetInstance(0).GetTagAsInt("Rows"); + } + + const char* Series::GetMainDicomTag(const char* tag, const char* defaultValue) const + { + if (series_["MainDicomTags"].isMember(tag)) + { + return series_["MainDicomTags"][tag].asCString(); + } + else + { + return defaultValue; + } + } + + + + void Series::Load3DImageInternal(void* target, + Orthanc::PixelFormat format, + size_t lineStride, + size_t stackStride, + Orthanc::ThreadedCommandProcessor::IListener* listener) + { + using namespace Orthanc; + + // Choose the extraction mode, depending on the format of the + // target image. + + uint8_t bytesPerPixel; + ImageExtractionMode mode; + + switch (format) + { + case PixelFormat_RGB24: + bytesPerPixel = 3; + mode = ImageExtractionMode_Preview; + break; + + case PixelFormat_Grayscale8: + bytesPerPixel = 1; + mode = ImageExtractionMode_UInt8; // Preview ??? + break; + + case PixelFormat_Grayscale16: + bytesPerPixel = 2; + mode = ImageExtractionMode_UInt16; + break; + + case PixelFormat_SignedGrayscale16: + bytesPerPixel = 2; + mode = ImageExtractionMode_UInt16; + format = PixelFormat_Grayscale16; + break; + + default: + throw OrthancClientException(ErrorCode_NotImplemented); + } + + + // Check that the target image is properly sized + unsigned int sx = GetWidth(); + unsigned int sy = GetHeight(); + + if (lineStride < sx * bytesPerPixel || + stackStride < sx * sy * bytesPerPixel) + { + throw OrthancClientException(ErrorCode_BadRequest); + } + + if (sx == 0 || sy == 0 || GetInstanceCount() == 0) + { + // Empty image, nothing to do + if (listener) + listener->SignalSuccess(0); + return; + } + + + /** + * Order the stacks according to their distance along the slice + * normal (using the "Image Position Patient" tag). This works + * even if the "SliceLocation" tag is absent. + **/ + SliceLocator locator(GetInstance(0)); + + typedef std::map<float, Instance*> Instances; + Instances instances; + for (unsigned int i = 0; i < GetInstanceCount(); i++) + { + float dist = locator.ComputeSliceLocation(GetInstance(i)); + instances[dist] = &GetInstance(i); + } + + if (instances.size() != GetInstanceCount()) + { + // Several instances have the same Z coordinate + throw OrthancClientException(ErrorCode_NotImplemented); + } + + + // Submit the download of each stack as a set of commands + ThreadedCommandProcessor processor(connection_.GetThreadCount()); + + if (listener != NULL) + { + processor.SetListener(*listener); + } + + uint8_t* stackTarget = reinterpret_cast<uint8_t*>(target); + for (Instances::iterator it = instances.begin(); it != instances.end(); ++it) + { + processor.Post(new ImageDownloadCommand(*it->second, format, mode, stackTarget, lineStride)); + stackTarget += stackStride; + } + + + // Wait for all the stacks to be downloaded + if (!processor.Join()) + { + throw OrthancClientException(ErrorCode_NetworkProtocol); + } + } + + float Series::GetVoxelSizeX() + { + Check3DImage(); // Is3DImageInternal() will compute the voxel sizes + return voxelSizeX_; + } + + float Series::GetVoxelSizeY() + { + Check3DImage(); // Is3DImageInternal() will compute the voxel sizes + return voxelSizeY_; + } + + float Series::GetVoxelSizeZ() + { + Check3DImage(); // Is3DImageInternal() will compute the voxel sizes + return voxelSizeZ_; + } + + float Series::GetSliceThickness() + { + Check3DImage(); // Is3DImageInternal() will compute the voxel sizes + return sliceThickness_; + } + + void Series::Load3DImage(void* target, + Orthanc::PixelFormat format, + int64_t lineStride, + int64_t stackStride, + float* progress) + { + ProgressToFloatListener listener(progress); + Load3DImageInternal(target, format, static_cast<size_t>(lineStride), + static_cast<size_t>(stackStride), &listener); + } +}