orthanc-client: OrthancCppClient/Series.cpp comparison

comparison OrthancCppClient/Series.cpp @ 0:ebc1e38ef615

initial commit

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Mon, 01 Jun 2015 09:47:32 +0200
parents
children	d5027f9f676a

comparison

equal deleted inserted replaced

--1:000000000000
+:ebc1e38ef615
+/**
+* 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);
+}
+}

Mercurial > hg > orthanc-client

comparison OrthancCppClient/Series.cpp @ 0:ebc1e38ef615