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cxUsReconstructionFileMaker.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
5 All rights reserved.
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7 Redistribution and use in source and binary forms, with or without
8 modification, are permitted provided that the following conditions are met:
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10 1. Redistributions of source code must retain the above copyright notice,
11  this list of conditions and the following disclaimer.
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13 2. Redistributions in binary form must reproduce the above copyright notice,
14  this list of conditions and the following disclaimer in the documentation
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19  without specific prior written permission.
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21 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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31 =========================================================================*/
32 
34 
35 #include <QTextStream>
36 #include <QDir>
37 #include <QFile>
38 #include <QFileInfo>
39 #include <vtkImageChangeInformation.h>
40 #include <vtkImageData.h>
41 #include "vtkImageAppend.h"
42 #include "vtkMetaImageWriter.h"
43 #include "cxTypeConversions.h"
44 #include "cxLogger.h"
45 #include "cxSettings.h"
46 #include "cxXmlOptionItem.h"
47 #include "cxTimeKeeper.h"
48 #include "cxDataReaderWriter.h"
49 #include "cxUSFrameData.h"
50 #include "cxSavingVideoRecorder.h"
51 #include "cxImageDataContainer.h"
53 #include "cxCustomMetaImage.h"
54 
55 
56 typedef vtkSmartPointer<vtkImageAppend> vtkImageAppendPtr;
57 
58 namespace cx
59 {
60 
62  mSessionDescription(sessionDescription)
63 {
64 }
65 
67 {
68 }
69 
71 {
72  return mReconstructData;
73 }
74 
80  std::vector<TimeInfo> imageTimestamps,
81  TimedTransformMap trackerRecordedData,
82  std::map<double, ToolPositionMetadata> trackerRecordedMetadata,
83  std::map<double, ToolPositionMetadata> referenceRecordedMetadata,
84  ToolPtr tool, QString streamUid,
85  bool writeColor, Transform3D rMpr)
86 {
87  if(trackerRecordedData.empty())
88  reportWarning("No tracking data for writing to reconstruction file.");
89 
91 
92  retval.mFilename = mSessionDescription; // not saved yet - no filename
93  retval.mUsRaw = USFrameData::create(mSessionDescription, imageData);
94  retval.rMpr = rMpr;
95  retval.mTrackerRecordedMetadata = trackerRecordedMetadata;
96  retval.mReferenceRecordedMetadata = referenceRecordedMetadata;
97 
98  for (TimedTransformMap::iterator it = trackerRecordedData.begin(); it != trackerRecordedData.end(); ++it)
99  {
100  TimedPosition current;
101  current.mTime = it->first;
102  current.mTimeInfo.setAcquisitionTime(it->first);
103  current.mPos = it->second;
104  retval.mPositions.push_back(current);
105  }
106 
107  std::vector<TimeInfo> fts = imageTimestamps;
108  for (unsigned i=0; i<fts.size(); ++i)
109  {
110  TimedPosition current;
111  current.mTimeInfo = fts[i];
112  current.mTime = current.mTimeInfo.getAcquisitionTime();
113  current.mPos = Transform3D::Identity();
114  // current.mPos = not written - will be found from track positions during reconstruction.
115  retval.mFrames.push_back(current);
116  }
117 
118  if (tool && tool->getProbe())
119  {
120  retval.mProbeDefinition.setData(tool->getProbe()->getProbeDefinition(streamUid));
121  }
122 
123  if (tool)
124  retval.mProbeUid = tool->getUid();
125 
126  this->fillFramePositions(&retval);
127 
128  return retval;
129 }
130 
135 void UsReconstructionFileMaker::fillFramePositions(USReconstructInputData* data) const
136 {
139 }
140 
141 bool UsReconstructionFileMaker::writeTrackerTimestamps(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
142 {
143  return this->writeTimestamps(reconstructionFolder+"/"+session+".tts",
144  ts, "tracking timestamps");
145 }
146 
147 bool UsReconstructionFileMaker::writeUSTimestamps(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
148 {
149  bool retval = true;
150 
151  retval = this->writeTimestamps(reconstructionFolder+"/"+session+".fts",
152  ts, "frame timestamps", Modified);
153 
154  retval &= this->writeTimestamps(reconstructionFolder+"/"+session+".scanner.frameTimestamps",
155  ts, "frame scanner timestamps", Scanner);
156 
157  retval &= this->writeTimestamps(reconstructionFolder+"/"+session+".softwareArrive.frameTimestamps",
158  ts, "frame arrive in software timestamps", SoftwareArrive);
159  return retval;
160 }
161 
162 bool UsReconstructionFileMaker::writeTimestamps(QString filename, std::vector<TimedPosition> ts, QString type, TimeStampType timeStampType)
163 {
164  bool success = false;
165 
166  QFile file(filename);
167  if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
168  {
169  reportError("Cannot open "+file.fileName());
170  return success;
171  }
172  QTextStream stream(&file);
173 
174  for (unsigned i=0; i<ts.size(); ++i)
175  {
176  switch(timeStampType)
177  {
178  case Modified:
179  stream << qstring_cast(ts[i].mTimeInfo.getAcquisitionTime());
180  break;
181  case SoftwareArrive:
182  stream << qstring_cast(ts[i].mTimeInfo.getSoftwareAcquisitionTime());
183  break;
184  case Scanner:
185  stream << qstring_cast(ts[i].mTimeInfo.getScannerAcquisitionTime());
186  break;
187  default:
188  stream << qstring_cast(ts[i].mTime); // Is the same as mTimeInfo.getAcquisitionTime()
189  break;
190  }
191  stream << endl;
192  }
193  file.close();
194  success = true;
195 
196  QFileInfo info(file);
197  mReport << QString("%1, %2 bytes, %3 %4.")
198  .arg(info.fileName())
199  .arg(info.size())
200  .arg(ts.size())
201  .arg(type);
202 // mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" frame timestamps.";
203 
204  return success;
205 }
206 
207 bool UsReconstructionFileMaker::writeUSTransforms(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
208 {
209  return this->writeTransforms(reconstructionFolder+"/"+session+".fp", ts, "frame transforms rMu");
210 }
211 
212 bool UsReconstructionFileMaker::writeTrackerMetadata(QString reconstructionFolder, QString session, const std::map<double, ToolPositionMetadata>& ts)
213 {
214  QString filename = reconstructionFolder+"/"+session+".probe.toolmeta";
215  return this->writeMetadata(filename, ts, "tracker metadata");
216 }
217 
218 bool UsReconstructionFileMaker::writeReferenceMetadata(QString reconstructionFolder, QString session, const std::map<double, ToolPositionMetadata>& ts)
219 {
220  QString filename = reconstructionFolder+"/"+session+".ref.toolmeta";
221  return this->writeMetadata(filename, ts, "tracker metadata");
222 }
223 
224 bool UsReconstructionFileMaker::writeMetadata(QString filename, const std::map<double, ToolPositionMetadata>& ts, QString type)
225 {
226  bool success = false;
227  QFile file(filename);
228  if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
229  {
230  reportError("Cannot open "+file.fileName());
231  return success;
232  }
233  QTextStream stream(&file);
234 
235  for (std::map<double, ToolPositionMetadata>::const_iterator i=ts.begin(); i!=ts.end(); ++i)
236  {
237  stream << i->second.toString() << endl;
238  }
239  file.close();
240  success = true;
241 
242  QFileInfo info(file);
243  mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" " + type + ".";
244 
245  return success;
246 }
247 
248 bool UsReconstructionFileMaker::writeTrackerTransforms(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
249 {
250  return this->writeTransforms(reconstructionFolder+"/"+session+".tp", ts, "tracking transforms prMt");
251 }
252 
253 bool UsReconstructionFileMaker::writeTransforms(QString filename, std::vector<TimedPosition> ts, QString type)
254 {
255  bool success = false;
256  QFile file(filename);
257  if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
258  {
259  reportError("Cannot open "+file.fileName());
260  return success;
261  }
262  QTextStream stream(&file);
263 
264  for (unsigned i=0; i<ts.size(); ++i)
265  {
266  Transform3D transform = ts[i].mPos;
267  stream << transform(0,0) << " ";
268  stream << transform(0,1) << " ";
269  stream << transform(0,2) << " ";
270  stream << transform(0,3);
271  stream << endl;
272  stream << transform(1,0) << " ";
273  stream << transform(1,1) << " ";
274  stream << transform(1,2) << " ";
275  stream << transform(1,3);
276  stream << endl;
277  stream << transform(2,0) << " ";
278  stream << transform(2,1) << " ";
279  stream << transform(2,2) << " ";
280  stream << transform(2,3);
281  stream << endl;
282  }
283  file.close();
284  success = true;
285 
286  QFileInfo info(file);
287  mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" " + type + ".";
288 
289  return success;
290 }
291 
295 void UsReconstructionFileMaker::writeProbeConfiguration(QString reconstructionFolder, QString session, ProbeDefinition data, QString uid)
296 {
297  XmlOptionFile file = XmlOptionFile(reconstructionFolder + "/" + session + ".probedata.xml");
298  data.addXml(file.getElement("configuration"));
299  file.getElement("tool").toElement().setAttribute("toolID", uid);
300  file.save();
301 }
302 
303 QString UsReconstructionFileMaker::createUniqueFolder(QString patientFolder, QString sessionDescription)
304 {
305  QString retval("");
306  QDir patientDir(patientFolder + "/US_Acq");
307 
308  QString subfolder = sessionDescription;
309  QString subfolderAbsolutePath = patientDir.absolutePath()+"/"+subfolder;
310  QString newPathName = subfolderAbsolutePath;
311  int i=1;
312  while(!findNewSubfolder(newPathName))
313  {
314  newPathName = subfolderAbsolutePath+"_"+QString::number(i++);
315  }
316  patientDir.mkpath(newPathName);
317  patientDir.cd(newPathName);
318 
319  retval = patientDir.absolutePath();
320  return retval;
321 }
322 
323 QString UsReconstructionFileMaker::createFolder(QString patientFolder, QString sessionDescription)
324 {
325  QString retval("");
326  QDir patientDir(patientFolder + "/US_Acq");
327 
328  QString subfolder = sessionDescription;
329  QString subfolderAbsolutePath = patientDir.absolutePath()+"/"+subfolder;
330  QString newPathName = subfolderAbsolutePath;
331  patientDir.mkpath(newPathName);
332  patientDir.cd(newPathName);
333 
334  retval = patientDir.absolutePath();
335  return retval;
336 }
337 
338 bool UsReconstructionFileMaker::findNewSubfolder(QString subfolderAbsolutePath)
339 {
340  QDir dir;
341  if(dir.exists(subfolderAbsolutePath))
342  return false;
343 
344  return true;
345 }
346 
347 void UsReconstructionFileMaker::report()
348 {
349  foreach(QString string, mReport)
350  {
351  reportSuccess(string);
352  }
353 }
354 
355 void UsReconstructionFileMaker::writeUSImages(QString path, ImageDataContainerPtr images, bool compression, std::vector<TimedPosition> pos)
356 {
357  CX_ASSERT(images->size()==pos.size());
358  vtkMetaImageWriterPtr writer = vtkMetaImageWriterPtr::New();
359 
360  for (unsigned i=0; i<images->size(); ++i)
361  {
362  vtkImageDataPtr currentImage = images->get(i);
363  QString filename = QString("%1/%2_%3.mhd").arg(path).arg(mSessionDescription).arg(i);
364 
365  writer->SetInputData(currentImage);
366  writer->SetFileName(cstring_cast(filename));
367  writer->SetCompression(compression);
368  {
369  StaticMutexVtkLocker lock;
370  writer->Write();
371  }
372 
373  CustomMetaImagePtr customReader = CustomMetaImage::create(filename);
374  customReader->setTransform(pos[i].mPos);
375  customReader->setModality("US");
376  customReader->setImageType(mSessionDescription);
377  }
378 }
379 
380 void UsReconstructionFileMaker::writeMask(QString path, QString session, vtkImageDataPtr mask)
381 {
382  QString filename = QString("%1/%2.mask.mhd").arg(path).arg(session);
383  if (!mask)
384  {
385  reportWarning(QString("No mask found, ignoring write to %1").arg(filename));
386  return;
387  }
388 
389  vtkMetaImageWriterPtr writer = vtkMetaImageWriterPtr::New();
390  writer->SetInputData(mask);
391  writer->SetFileName(cstring_cast(filename));
392  writer->SetCompression(false);
393  writer->Write();
394 }
395 
396 
397 void UsReconstructionFileMaker::writeREADMEFile(QString reconstructionFolder, QString session)
398 {
399  QString text = ""
400 "* ==== Format description \n"
401 "* Refer to \n"
402 "* http://custusx.org/uploads/developer_doc/nightly/org_custusx_acquisition.html \n"
403 "* for a description of the files. \n"
404 "*/ \n";
405 
406  QFile file(reconstructionFolder+"/"+session+".README.txt");
407  if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
408  {
409  reportError("Cannot open "+file.fileName());
410  return;
411  }
412  QTextStream stream(&file);
413  stream << text;
414  file.close();
415 }
416 
417 QString UsReconstructionFileMaker::writeToNewFolder(QString path, bool compression)
418 {
419  TimeKeeper timer;
420  mReconstructData.mFilename = path+"/"+mSessionDescription+".fts"; // use fts since this is a single unique file.
421 
422  mReport.clear();
423  mReport << "Made reconstruction folder: " + path;
424  QString session = mSessionDescription;
425 
426  this->writeTrackerMetadata(path, session, mReconstructData.mTrackerRecordedMetadata);
427  this->writeReferenceMetadata(path, session, mReconstructData.mReferenceRecordedMetadata);
428  this->writeTrackerTimestamps(path, session, mReconstructData.mPositions);
429  this->writeTrackerTransforms(path, session, mReconstructData.mPositions);
430  this->writeUSTimestamps(path, session, mReconstructData.mFrames);
431  this->writeUSTransforms(path, session, mReconstructData.mFrames);
432  this->writeProbeConfiguration(path, session, mReconstructData.mProbeDefinition.mData, mReconstructData.mProbeUid);
433  this->writeMask(path, session, mReconstructData.getMask());
434  this->writeREADMEFile(path, session);
435 
436  ImageDataContainerPtr imageData = mReconstructData.mUsRaw->getImageContainer();
437  if (imageData)
438  this->writeUSImages(path, imageData, compression, mReconstructData.mFrames);
439  else
440  mReport << "failed to find frame data, save failed.";
441 
442  int time = std::max(1, timer.getElapsedms());
443  mReport << QString("Completed save to %1. Spent %2s, %3fps").arg(mSessionDescription).arg(time/1000).arg(imageData->size()*1000/time);
444 
445  this->report();
446  mReport.clear();
447 
448  return mReconstructData.mFilename;
449 }
450 
451 
452 
453 }//namespace cx
QString qstring_cast(const T &val)
DoubleBoundingBox3D transform(const Transform3D &m, const DoubleBoundingBox3D &bb)
void reportError(QString msg)
Definition: cxLogger.cpp:92
std::map< double, ToolPositionMetadata > mTrackerRecordedMetadata
UsReconstructionFileMaker(QString sessionDescription)
#define CX_ASSERT(statement)
Definition: cxLogger.h:131
One position with timestamp.
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
vtkSmartPointer< vtkImageAppend > vtkImageAppendPtr
std::vector< TimedPosition > mFrames
cstring_cast_Placeholder cstring_cast(const T &val)
QString writeToNewFolder(QString path, bool compression)
std::map< double, ToolPositionMetadata > mReferenceRecordedMetadata
static std::vector< double > interpolateFramePositionsFromTracking(USReconstructInputData *data)
boost::shared_ptr< class CustomMetaImage > CustomMetaImagePtr
Transform3D rMpr
patient registration
void setAcquisitionTime(double mSecsSinceEpoch)
Definition: cxData.h:86
int getElapsedms() const
void reportWarning(QString msg)
Definition: cxLogger.cpp:91
double getAcquisitionTime() const
Definition: cxData.h:82
vtkSmartPointer< class vtkMetaImageWriter > vtkMetaImageWriterPtr
static QString createFolder(QString patientFolder, QString sessionDescription)
void reportSuccess(QString msg)
Definition: cxLogger.cpp:93
std::vector< TimedPosition > mPositions
ProbeDefinition mData
Definition: cxProbeSector.h:75
QString mFilename
filename used for current data read
vtkSmartPointer< class vtkImageData > vtkImageDataPtr
USFrameDataPtr mUsRaw
All imported US data frames with pointers to each frame.
static void transformFramePositionsTo_rMu(USReconstructInputData *data)
static USFrameDataPtr create(ImagePtr inputFrameData)
static QString createUniqueFolder(QString patientFolder, QString sessionDescription)
std::map< double, Transform3D > TimedTransformMap
static CustomMetaImagePtr create(QString filename)
void setData(ProbeDefinition data)
boost::shared_ptr< class ImageDataContainer > ImageDataContainerPtr
Definition: cxUSFrameData.h:45
boost::shared_ptr< class Tool > ToolPtr