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cxDataManagerImpl.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
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4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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32 
33 
34 #include "cxDataManagerImpl.h"
35 
36 #include <QtCore>
37 #include <QDomDocument>
38 #include <QFileInfo>
39 #include <QFile>
40 #include <QTextStream>
41 #include <QDir>
42 
43 #include "cxTransform3D.h"
45 #include "cxLogger.h"
46 #include "cxTypeConversions.h"
47 #include "cxUtilHelpers.h"
48 #include "cxVideoSource.h"
49 #include "cxDataLocations.h"
50 
51 #include "cxImageLUT2D.h"
52 #include "cxImageTF3D.h"
53 
54 #include "cxDataReaderWriter.h"
55 #include "cxSpaceProvider.h"
56 #include "cxDataFactory.h"
57 
58 #include "cxXmlOptionItem.h"
60 #include "cxProfile.h"
61 #include "cxSettings.h"
62 #include "cxDefinitionStrings.h"
63 #include "cxActiveData.h"
64 
65 
66 namespace cx
67 {
68 
70 {
71  DataManagerImplPtr retval;
72  retval.reset(new DataManagerImpl(activeData));
73  return retval;
74 }
75 
77  mClinicalApplication(mdNEUROLOGICAL),
78  mActiveData(activeData)
79 {
83 
84  connect(settings(), SIGNAL(valueChangedFor(QString)), this, SLOT(settingsChangedSlot(QString)));
85  this->readClinicalView();
86 
87  this->clear();
88 }
89 
91 {
92 }
93 
95 {
97 }
98 
100 {
101  mDataFactory = dataFactory;
102 }
103 
105 {
106  return mSpaceProvider;
107 }
108 
110 {
111  return mDataFactory;
112 }
113 
115 {
116  mData.clear();
117  mCenter = Vector3D(0, 0, 0);
118  mLandmarkProperties.clear();
119 
120  m_rMpr_History->clear();
121  mPatientLandmarks->clear();
122 
123  emit dataAddedOrRemoved();
124  emit centerChanged();
126 }
127 
129 {
130  return mPatientLandmarks;
131 }
132 
133 // streams
135 {
136  if (mStreams.count(uid))
137  return mStreams.find(uid)->second;
138  return VideoSourcePtr();
139 }
140 
142 {
143  return mStreams;
144 }
145 
147 {
148  if (!stream)
149  return;
150  mStreams[stream->getUid()] = stream;
151  emit streamLoaded();
152 }
153 
154 std::map<QString, VideoSourcePtr> mStreams;
155 
157 {
158  return mCenter;
159 }
161 {
162  mCenter = center;
163  emit centerChanged();
164 }
165 
166 void DataManagerImpl::setLandmarkNames(std::vector<QString> names)
167 {
168  mLandmarkProperties.clear();
169  for (unsigned i = 0; i < names.size(); ++i)
170  {
171  LandmarkProperty prop(qstring_cast(i + 1), names[i]); // generate 1-indexed uids (keep users happy)
172  mLandmarkProperties[prop.getUid()] = prop;
173  }
175 }
176 
178 {
179  int max = 0;
180  std::map<QString, LandmarkProperty>::iterator iter;
181  for (iter = mLandmarkProperties.begin(); iter != mLandmarkProperties.end(); ++iter)
182  {
183  //max = std::max(max, qstring_cast(iter->second.getName()).toInt());
184  max = std::max(max, qstring_cast(iter->first).toInt());
185  }
186  QString uid = qstring_cast(max + 1);
188 
190  return uid;
191 }
192 
193 void DataManagerImpl::setLandmarkName(QString uid, QString name)
194 {
195  mLandmarkProperties[uid].setName(name);
197 }
198 
199 std::map<QString, LandmarkProperty> DataManagerImpl::getLandmarkProperties() const
200 {
201  return mLandmarkProperties;
202 }
203 
204 void DataManagerImpl::setLandmarkActive(QString uid, bool active)
205 {
206  mLandmarkProperties[uid].setActive(active);
208 }
209 
210 DataPtr DataManagerImpl::loadData(const QString& uid, const QString& path)
211 {
212  if (mData.count(uid)) // dont load same image twice
213  return mData[uid];
214 
215  QString type = DataReaderWriter().findDataTypeFromFile(path);
216  if(!mDataFactory)
217  reportError("DataManagerImpl::loadData() Got no DataFactory");
218  DataPtr data = mDataFactory->create(type, uid);
219 
220  if (!data)
221  {
222  reportError("Failed to find loaded for: [" + path + "]");
223  return DataPtr();
224  }
225 
226  bool loaded = data->load(path);
227 
228  if (!loaded)
229  {
230  reportError("Failed to load file: [" + path + "]");
231  return DataPtr();
232  }
233 
234  this->loadData(data);
235  return data;
236 }
237 
239 {
240  if (data->getUid().contains('%'))
241  {
242  QString uid = data->getUid();
243  QString name = data->getName();
244  this->generateUidAndName(&uid, &name);
245  data->setName(name);
246  data->setUid(uid);
247  }
248 
249  if (data)
250  {
251  if (mData.count(data->getUid()) && mData[data->getUid()]!=data)
252  reportError(QString("Overwriting Data with uid=%1 with new object into PasM").arg(data->getUid()));
253 // this->verifyParentFrame(data);
254  mData[data->getUid()] = data;
255  emit dataAddedOrRemoved();
256  }
257 }
258 
259 DataPtr DataManagerImpl::getData(const QString& uid) const
260 {
261  DataMap::const_iterator iter = mData.find(uid);
262  if (iter == mData.end())
263  return DataPtr();
264  return iter->second;
265 }
266 
267 std::map<QString, DataPtr> DataManagerImpl::getData() const
268 {
269  return mData;
270 }
271 
272 std::map<QString, ImagePtr> DataManagerImpl::getImages() const
273 {
274  std::map<QString, ImagePtr> retval;
275  for (DataMap::const_iterator iter = mData.begin(); iter != mData.end(); ++iter)
276  {
277  ImagePtr image = this->getImage(iter->first);
278  if (!image)
279  continue;
280  retval[iter->first] = image;
281  }
282  return retval;
283 }
284 
285 std::map<QString, MeshPtr> DataManagerImpl::getMeshes() const
286 {
287  std::map<QString, MeshPtr> retval;
288  for (DataMap::const_iterator iter = mData.begin(); iter != mData.end(); ++iter)
289  {
290  MeshPtr mesh = this->getMesh(iter->first);
291  if (!mesh)
292  continue;
293  retval[iter->first] = mesh;
294  }
295  return retval;
296 }
297 
298 void DataManagerImpl::addXml(QDomNode& parentNode)
299 {
300  QDomDocument doc = parentNode.ownerDocument();
301  QDomElement dataManagerNode = doc.createElement("datamanager");
302  parentNode.appendChild(dataManagerNode);
303 
304  m_rMpr_History->addXml(dataManagerNode);
305 
306  QDomElement landmarkPropsNode = doc.createElement("landmarkprops");
307  LandmarkPropertyMap::iterator it = mLandmarkProperties.begin();
308  for (; it != mLandmarkProperties.end(); ++it)
309  {
310  QDomElement landmarkPropNode = doc.createElement("landmarkprop");
311  it->second.addXml(landmarkPropNode);
312  landmarkPropsNode.appendChild(landmarkPropNode);
313  }
314  dataManagerNode.appendChild(landmarkPropsNode);
315 
316  QDomElement landmarksNode = doc.createElement("landmarks");
317  mPatientLandmarks->addXml(landmarksNode);
318  dataManagerNode.appendChild(landmarksNode);
319 
320  QDomElement centerNode = doc.createElement("center");
321  centerNode.appendChild(doc.createTextNode(qstring_cast(mCenter)));
322  dataManagerNode.appendChild(centerNode);
323 
324  for (DataMap::const_iterator iter = mData.begin(); iter != mData.end(); ++iter)
325  {
326  QDomElement dataNode = doc.createElement("data");
327  dataManagerNode.appendChild(dataNode);
328  iter->second->addXml(dataNode);
329  }
330 }
331 
332 void DataManagerImpl::parseXml(QDomNode& dataManagerNode, QString rootPath)
333 {
334  // look in the toolmanager, for backwards compatibility (2014-02-21)
335  QDomNode toolManagerNode = dataManagerNode.parentNode().namedItem("toolManager");
336 
337  QDomNode registrationHistory = dataManagerNode.namedItem("registrationHistory");
338  if (registrationHistory.isNull())
339  registrationHistory = toolManagerNode.namedItem("registrationHistory");
340  m_rMpr_History->parseXml(registrationHistory);
341 
342  QDomNode landmarksNode = dataManagerNode.namedItem("landmarkprops");
343  QDomElement landmarkNode = landmarksNode.firstChildElement("landmarkprop");
344  for (; !landmarkNode.isNull(); landmarkNode = landmarkNode.nextSiblingElement("landmarkprop"))
345  {
346  LandmarkProperty landmarkProp;
347  landmarkProp.parseXml(landmarkNode);
348  mLandmarkProperties[landmarkProp.getUid()] = landmarkProp;
349  //std::cout << "Loaded landmarkprop with name: " << landmarkProp.getName() << std::endl;
351  }
352 
353  QDomNode patientLandmarksNode = dataManagerNode.namedItem("landmarks");
354  if (patientLandmarksNode.isNull())
355  patientLandmarksNode = toolManagerNode.namedItem("landmarks");
356  mPatientLandmarks->parseXml(patientLandmarksNode);
357 
358  // All images must be created from the DataManager, so the image nodes are parsed here
359  std::map<DataPtr, QDomNode> datanodes;
360 
361  QDomNode child = dataManagerNode.firstChild();
362  for (; !child.isNull(); child = child.nextSibling())
363  {
364  if (child.nodeName() == "data")
365  {
366  DataPtr data = this->loadData(child.toElement(), rootPath);
367  if (data)
368  datanodes[data] = child.toElement();
369  }
370  }
371 
372  // parse xml data separately: we want to first load all data
373  // because there might be interdependencies (cx::DistanceMetric)
374  for (std::map<DataPtr, QDomNode>::iterator iter = datanodes.begin(); iter != datanodes.end(); ++iter)
375  {
376  iter->first->parseXml(iter->second);
377  }
378 
379  emit dataAddedOrRemoved();
380 
381  //we need to make sure all images are loaded before we try to set an active image
382  child = dataManagerNode.firstChild();
383  while (!child.isNull())
384  {
385  if (child.toElement().tagName() == "center")
386  {
387  const QString centerString = child.toElement().text();
388  if (!centerString.isEmpty())
389  {
390  Vector3D center = Vector3D::fromString(centerString);
391  this->setCenter(center);
392  }
393  }
394  child = child.nextSibling();
395  }
396 }
397 
398 DataPtr DataManagerImpl::loadData(QDomElement node, QString rootPath)
399 {
400  QString uid = node.toElement().attribute("uid");
401  QString name = node.toElement().attribute("name");
402  QString type = node.toElement().attribute("type");
403 
404  QDir relativePath = this->findRelativePath(node, rootPath);
405  QString absolutePath = this->findAbsolutePath(relativePath, rootPath);
406 
407  if (mData.count(uid)) // dont load same image twice
408  return mData[uid];
409 
410  DataPtr data = mDataFactory->create(type, uid, name);
411  if (!data)
412  {
413  reportWarning(QString("Unknown type: %1 for file %2").arg(type).arg(absolutePath));
414  return DataPtr();
415  }
416  bool loaded = data->load(absolutePath);
417 
418  if (!loaded)
419  {
420  reportWarning("Unknown file: " + absolutePath);
421  return DataPtr();
422  }
423 
424  if (!name.isEmpty())
425  data->setName(name);
426  data->setFilename(relativePath.path());
427 
428  this->loadData(data);
429 
430  // conversion for change in format 2013-10-29
431  QString newPath = rootPath+"/"+data->getFilename();
432  if (QDir::cleanPath(absolutePath) != QDir::cleanPath(newPath))
433  {
434  reportWarning(QString("Detected old data format, converting from %1 to %2").arg(absolutePath).arg(newPath));
435  data->save(rootPath);
436  }
437 
438  return data;
439 }
440 
441 QDir DataManagerImpl::findRelativePath(QDomElement node, QString rootPath)
442 {
443  QString path = this->findPath(node);
444  QDir relativePath = QDir(QString(path));
445 
446  QDir patientDataDir(rootPath);
447  relativePath.setPath(patientDataDir.relativeFilePath(relativePath.path()));
448 
449  return relativePath;
450 }
451 
452 QString DataManagerImpl::findPath(QDomElement node)
453 {
454  QDomElement filePathNode = node.namedItem("filePath").toElement();
455 
456  if (filePathNode.isNull())
457  return QString();
458 
459  QString path = filePathNode.text();
460  if (path.isEmpty())
461  return QString();
462  return path;
463 }
464 
465 QString DataManagerImpl::findAbsolutePath(QDir relativePath, QString rootPath)
466 {
467  QString absolutePath = relativePath.path();
468  if (!rootPath.isEmpty())
469  absolutePath = rootPath + "/" + relativePath.path();
470  return absolutePath;
471 }
472 
474 {
475  return mClinicalApplication;
476 }
477 
478 void DataManagerImpl::setClinicalApplication(CLINICAL_VIEW application)
479 {
480  if (mClinicalApplication == application)
481  return;
482  mClinicalApplication = application;
483 
484  QString val = enum2string<CLINICAL_VIEW>(mClinicalApplication);
485  settings()->setValue("View/clinicalView", val);
486 
488 }
489 
490 void DataManagerImpl::settingsChangedSlot(QString key)
491 {
492  if (key == "View/clinicalView")
493  {
494  this->readClinicalView();
495  }
496 }
497 
499 {
500  QString defVal = enum2string<CLINICAL_VIEW>(mdNEUROLOGICAL);
501  QString val = settings()->value("View/clinicalView", defVal).toString();
502  CLINICAL_VIEW view = string2enum<CLINICAL_VIEW>(val);
503 
504  this->setClinicalApplication(view);
505 }
506 
507 
508 int DataManagerImpl::findUniqueUidNumber(QString uidBase) const
509 {
510  if (!uidBase.contains("%"))
511  return -1;
512  // Find an uid that is not used before
513  size_t numMatches = 1;
514  int recNumber = 0;
515 
516  if (numMatches != 0)
517  {
518  while (numMatches != 0)
519  {
520  QString newId = qstring_cast(uidBase).arg(++recNumber);
521  numMatches = mData.count(qstring_cast(newId));
522  }
523  }
524  return recNumber;
525 }
526 
531 void DataManagerImpl::generateUidAndName(QString* _uid, QString* _name)
532 {
533  QString& uid = *_uid;
534  QString& name = *_name;
535 
536  int recNumber = this->findUniqueUidNumber(uid);
537 
538  if (uid.contains("%"))
539  {
540  uid = uid.arg(recNumber);
541  }
542 
543  if (name.contains("%"))
544  {
545  if (recNumber == 1)
546  name = name.arg("");
547  else
548  name = name.arg(recNumber);
549  }
550 }
551 
552 void DataManagerImpl::removeData(const QString& uid, QString basePath)
553 {
554  DataPtr dataToBeRemoved = this->getData(uid);
555  mActiveData->remove(dataToBeRemoved);
556 
557  mData.erase(uid);
558 
559  this->deleteFiles(dataToBeRemoved, basePath);
560 
561  emit dataAddedOrRemoved(); // this should alert everybody interested in the data as a collection.
562  report("Removed data [" + uid + "].");
563 }
564 
565 void DataManagerImpl::deleteFiles(DataPtr data, QString basePath)
566 {
567  if (!data)
568  return;
569  ImagePtr image = boost::dynamic_pointer_cast<Image>(data);
570  QStringList files;
571  if (!data->getFilename().isEmpty())
572  {
573  files << QDir(basePath).absoluteFilePath(data->getFilename());
574  if (image)
575  files << changeExtension(files[0], "raw");
576  }
577 
578  for (int i=0; i<files.size(); ++i)
579  {
580  if (!QFileInfo(files[i]).exists())
581  continue;
582  report(QString("Removing %1 from disk").arg(files[i]));
583  QFile(files[i]).remove();
584  }
585 }
586 
588 {
589  return m_rMpr_History->getCurrentRegistration().mValue;
590 }
591 
593 {
594  m_rMpr_History->setRegistration(val);
595 }
596 
598 {
599  return m_rMpr_History;
600 }
601 
603 {
605  XmlOptionFile preset(DataLocations::findConfigFilePath("presets.xml", "/transferFunctions"));
606  XmlOptionFile custom = profile()->getXmlSettings().descend("presetTransferFunctions");
607 
609  mPresetTransferFunctions3D.reset(new TransferFunctions3DPresets(preset, custom));
610 
612 }
613 
614 } // namespace cx
615 
boost::shared_ptr< class SpaceProvider > SpaceProviderPtr
QString qstring_cast(const T &val)
DataFactoryPtr mDataFactory
cxResource_EXPORT ProfilePtr profile()
Definition: cxProfile.cpp:176
void rMprChanged()
emitted when the transformation between patient reference and (data) reference is set ...
int findUniqueUidNumber(QString uidBase) const
virtual void removeData(const QString &uid, QString basePath)
remove data from datamanger, emit signal
void reportError(QString msg)
Definition: cxLogger.cpp:92
virtual CLINICAL_VIEW getClinicalApplication() const
boost::shared_ptr< class RegistrationHistory > RegistrationHistoryPtr
Definition: cxDataManager.h:57
std::map< QString, VideoSourcePtr > mStreams
QString findDataTypeFromFile(QString filename)
std::map< QString, VideoSourcePtr > mStreams
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
virtual std::map< QString, LandmarkProperty > getLandmarkProperties() const
boost::shared_ptr< class TransferFunctions3DPresets > PresetTransferFunctions3DPtr
Definition: cxDataManager.h:56
virtual void setLandmarkName(QString uid, QString name)
QString getUid() const
Definition: cxLandmark.cpp:196
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
virtual VideoSourcePtr getStream(const QString &uid) const
boost::shared_ptr< class DataManagerImpl > DataManagerImplPtr
void deleteFiles(DataPtr data, QString basePath)
virtual void generateUidAndName(QString *_uid, QString *_name)
virtual MeshPtr getMesh(const QString &uid) const
boost::shared_ptr< class ActiveData > ActiveDataPtr
Definition: cxColorWidget.h:42
void landmarkPropertiesChanged()
emitted when global info about a landmark changed
QVariant value(const QString &key, const QVariant &defaultValue=QVariant()) const
Definition: cxSettings.cpp:87
void centerChanged()
emitted when center is changed.
ActiveDataPtr mActiveData
virtual LandmarksPtr getPatientLandmarks()
virtual void addXml(QDomNode &parentNode)
adds xml information about the datamanger and its variabels
boost::shared_ptr< class Landmarks > LandmarksPtr
Definition: cxData.h:61
PresetTransferFunctions3DPtr mPresetTransferFunctions3D
void setValue(const QString &key, const QVariant &value)
Definition: cxSettings.cpp:79
boost::shared_ptr< class Data > DataPtr
DataManagerImpl(ActiveDataPtr activeData)
virtual void parseXml(QDomNode &datamangerNode, QString absolutePath=QString())
Use a XML node to load data.
virtual StreamMap getStreams() const
static DataManagerImplPtr create(ActiveDataPtr activeData)
virtual std::map< QString, ImagePtr > getImages() const
virtual void setLandmarkNames(std::vector< QString > names)
void reportWarning(QString msg)
Definition: cxLogger.cpp:91
virtual void setClinicalApplication(CLINICAL_VIEW application)
std::map< QString, DataPtr > getData() const
void dataAddedOrRemoved()
A volumetric data set.
Definition: cxImage.h:66
void parseXml(QDomNode &dataNode)
Definition: cxLandmark.cpp:217
virtual PresetTransferFunctions3DPtr getPresetTransferFunctions3D() const
boost::shared_ptr< class VideoSource > VideoSourcePtr
virtual Transform3D get_rMpr() const
get the patient registration transform
static QString findConfigFilePath(QString fileName, QString pathRelativeToConfigRoot, QString alternativeAbsolutePath="")
RegistrationHistoryPtr m_rMpr_History
transform from the patient reference to the reference, along with historical data.
Settings * settings()
Shortcut for accessing the settings instance.
Definition: cxSettings.cpp:42
virtual void setLandmarkActive(QString uid, bool active)
static LandmarksPtr create()
Definition: cxLandmark.cpp:116
LandmarksPtr mPatientLandmarks
in space patient reference.
cxLogicManager_EXPORT SpaceProviderPtr spaceProvider()
virtual Vector3D getCenter() const
current common center point for user viewing.
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
virtual void setCenter(const Vector3D &center)
virtual ImagePtr getImage(const QString &uid) const
QString changeExtension(QString name, QString ext)
void report(QString msg)
Definition: cxLogger.cpp:90
void setDataFactory(DataFactoryPtr dataFactory)
mdNEUROLOGICAL
Definition: cxDefinitions.h:75
virtual SpaceProviderPtr getSpaceProvider()
virtual void set_rMpr(const Transform3D &val)
set the transform from patient to reference space
virtual std::map< QString, MeshPtr > getMeshes() const
virtual QString addLandmark()
CLINICAL_VIEW mClinicalApplication
LandmarkPropertyMap mLandmarkProperties
uid and name
SpaceProviderPtr mSpaceProvider
boost::shared_ptr< class DataFactory > DataFactoryPtr
boost::shared_ptr< class Mesh > MeshPtr
void loadData(DataPtr data)
void clinicalApplicationChanged()
virtual void loadStream(VideoSourcePtr stream)
A history of registration events.
void setSpaceProvider(SpaceProviderPtr spaceProvider)
Helper class for xml files used to store ssc/cx data.
Handles transfer function presets.
virtual void clear()
remove all stuff from manager
virtual DataFactoryPtr getDataFactory()
virtual RegistrationHistoryPtr get_rMpr_History() const
std::map< QString, VideoSourcePtr > StreamMap
Definition: cxDataManager.h:75