Mercurial > hg > orthanc
view OrthancCppClient/Series.cpp @ 1346:911a1ad5ebe8
re-fix issue #30
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 20 Apr 2015 17:26:02 +0200 |
parents | 6e7e5ed91c2d |
children |
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/** * 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); } }