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cxReconstructCore.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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32 
33 
34 #include "cxReconstructCore.h"
35 #include <vtkImageData.h>
36 #include "cxTime.h"
37 #include "cxTypeConversions.h"
39 #include "cxVolumeHelpers.h"
41 #include "cxTimeKeeper.h"
42 #include "cxLogger.h"
43 #include "cxUSFrameData.h"
45 #include "vtkPointData.h"
46 #include "vtkDataArray.h"
47 #include "cxPatientModelService.h"
48 
49 namespace cx
50 {
51 
52 
54  mInput(InputParams()),
55  mPatientModelService(patientModelService)
56 {
57 // mMaxTimeDiff = 100; // TODO: Change default value for max allowed time difference between tracking and image time tags
58  mSuccess = false;
59 }
60 
62 {
63 }
64 
66 {
67  mInput = input;
68  mAlgorithm = algorithm;
69 }
70 
72 {
73  mOutputVolumeParams = outputVolumeParams;
74  mFileData = fileData;
75 }
76 
78 {
79  this->threadedPreReconstruct();
80 // this->threadablePreReconstruct();
81  this->threadedReconstruct();
83  return mOutput;
84 }
85 
90 {
91  if (!this->validInputData())
92  return;
93  mRawOutput = this->generateRawOutputVolume();
94 }
95 
100 {
101  if (!this->validInputData())
102  return;
103  CX_ASSERT(mRawOutput);
104 
105  TimeKeeper timer;
106 
107  mSuccess = mAlgorithm->reconstruct(mFileData, mRawOutput, mInput.mAlgoSettings);
108 
109  timer.printElapsedSeconds("Reconstruct core time");
110 }
111 
116 {
117  if (!this->validInputData())
118  return;
119 
120  if (mSuccess)
121  {
122  mOutput = this->generateOutputVolume(mRawOutput);
123 
124  Eigen::Array3i outputDims(mRawOutput->GetDimensions());
125  int total = outputDims[0] * outputDims[1] * outputDims[2];
126  report(QString("US Reconstruction complete: %1Mb, output=%2, algo=%3, preset=%4, angio=%5")
127  .arg(total/1024/1024)
128  .arg(mOutput->getName())
129  .arg(mAlgorithm->getName())
130  .arg(mInput.mTransferFunctionPreset)
131  .arg(mInput.mAngio));
132 
133  mPatientModelService->insertData(mOutput);
134  }
135  else
136  {
137  reportError("Reconstruction failed");
138  }
139 }
140 
145 ImagePtr ReconstructCore::generateOutputVolume(vtkImageDataPtr rawOutput)
146 {
147  setDeepModified(rawOutput);
148 
149 // //If no output path is selecetd, use the same path as the input
150 // QString filePath;
151 // if (mInput.mOutputBasePath.isEmpty() && mInput.mOutputRelativePath.isEmpty())
152 // filePath = qstring_cast(mFileData->getFilePath());
153 // else
154 // filePath = mInput.mOutputRelativePath;
155 
156  QString uid = this->generateOutputUid();
157  QString name = this->generateImageName(uid);
158 
159  ImagePtr image = mPatientModelService->createSpecificData<Image>(uid + "_%1", name + " %1");
160  image->setVtkImageData(rawOutput);
161 
162 // ImagePtr image = mPatientModelService->createImage(rawOutput, uid + "_%1", name + " %1", filePath);
163  image->get_rMd_History()->setRegistration(mOutputVolumeParams.get_rMd());
164  image->setModality("US");
165  if (mInput.mAngio)
166  image->setImageType("Angio");
167  else
168  image->setImageType("B-Mode");
169 
170  PresetTransferFunctions3DPtr presets = mPatientModelService->getPresetTransferFunctions3D();
171  presets->load(mInput.mTransferFunctionPreset, image, true, false);//Only apply to 2D, not 3D
172  presets->load("US B-Mode", image, false, true);//Only apply to 3D, not 2D
173 
174  return image;
175 }
176 
181 vtkImageDataPtr ReconstructCore::generateRawOutputVolume()
182 {
183  Eigen::Array3i dim = mOutputVolumeParams.getDim();
184  Vector3D spacing = Vector3D(1, 1, 1) * mOutputVolumeParams.getSpacing();
185  vtkImageDataPtr data = generateVtkImageData(dim, spacing, 0);
186  return data;
187 }
188 
194 QString ReconstructCore::generateOutputUid()
195 {
196  QString base = mFileData->getUid();
197  QString name = mFileData->getFilePath().split("/").back();
198  name = name.split(".").front();
199 
200  QStringList split = name.split("_");
201  QStringList prefix = split.front().split("-");
202  if (prefix.size() == 2)
203  {
204  split[0] = prefix[0];
205  }
206  else
207  {
208  split[0] += "_rec";
209  }
210 
211  return split.join("_");
212 }
213 
219 QString ReconstructCore::generateImageName(QString uid) const
220 {
221  QString name = uid.split("/").back();
222  name = name.split(".").front();
223  QString prefix = name.split("_").front(); // retrieve US-Acq part
224  prefix = prefix.split("-").front(); // retrieve US part.
225  if (prefix.isEmpty())
226  prefix = "US";
227 
228 // std::cout << "reconstruct input uid " << uid << std::endl;
229  if (mInput.mAngio) // tag angio images as such
230  prefix += "A";
231 
232  // retrieve index counter from _99_
233  QString counter = "";
234  QRegExp countReg("_[0-9]{1,2}_");
235  if (countReg.indexIn(name) > 0)
236  {
237  counter = countReg.cap(0).remove("_");
238  }
239 
240  // retrieve timestamp as HH:MM
241  QRegExp tsReg("[0-9]{8}T[0-9]{6}");
242  if (tsReg.indexIn(name) > 0)
243  {
244  QString postfix = name.split("_").back();
245  QDateTime datetime = QDateTime::fromString(tsReg.cap(0), timestampSecondsFormat());
246  QString timestamp = datetime.toString("hh:mm");
247  return prefix + " " + counter + " " + postfix + " " + timestamp;
248  }
249 
250  return name;
251 }
252 
254 {
255  return mOutput;
256 }
257 
258 bool ReconstructCore::validInputData() const
259 {
260  return mAlgorithm!=0;
261 }
262 
263 } /* namespace cx */
void reportError(QString msg)
Definition: cxLogger.cpp:92
Abstract interface for reconstruction algorithm.
#define CX_ASSERT(statement)
Definition: cxLogger.h:131
virtual void setVtkImageData(const vtkImageDataPtr &data, bool resetTransferFunctions=true)
Definition: cxImage.cpp:289
boost::shared_ptr< class TransferFunctions3DPresets > PresetTransferFunctions3DPtr
Definition: cxDataManager.h:56
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
Helper struct for sending and controlling output volume properties.
QString timestampSecondsFormat()
Definition: cxTime.cpp:39
A volumetric data set.
Definition: cxImage.h:66
virtual QString getName() const =0
void initialize(InputParams input, ReconstructionMethodService *algorithm)
boost::shared_ptr< class PatientModelService > PatientModelServicePtr
virtual bool reconstruct(ProcessedUSInputDataPtr input, vtkImageDataPtr outputData, QDomElement settings)=0
vtkImageDataPtr generateVtkImageData(Eigen::Array3i dim, Vector3D spacing, const unsigned char initValue, int components)
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
void printElapsedSeconds(QString text="Elapsed time")
void report(QString msg)
Definition: cxLogger.cpp:90
void setDeepModified(vtkImageDataPtr image)
bool mAngio
true for angio data, false is B-mode.
ReconstructCore(PatientModelServicePtr patientModelService)
boost::shared_ptr< class ProcessedUSInputData > ProcessedUSInputDataPtr
vtkSmartPointer< class vtkImageData > vtkImageDataPtr