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cxImportDataDialog.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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31 =========================================================================*/
32 
33 #include "cxImportDataDialog.h"
34 
35 #include <cmath>
36 #include <QFileDialog>
37 #include <QPushButton>
38 #include <QVBoxLayout>
39 #include <QLabel>
40 #include <Qt>
41 #include <QCheckBox>
42 #include <QTimer>
43 #include <vtkImageData.h>
45 #include "cxLogger.h"
46 #include "cxTypeConversions.h"
47 #include "cxData.h"
49 #include "cxImageAlgorithms.h"
50 #include "cxImage.h"
51 #include "cxVolumeHelpers.h"
52 #include "cxImageTF3D.h"
53 #include "cxImageLUT2D.h"
54 #include "cxPatientModelService.h"
55 #include "cxMesh.h"
56 #include "cxViewService.h"
57 
58 
59 //TODO: remove
60 #include "cxLegacySingletons.h"
61 
62 namespace cx
63 {
64 
65 ImportDataDialog::ImportDataDialog(PatientModelServicePtr patientModelService, QString filename, QWidget* parent) :
66  QDialog(parent),
67  mFilename(filename),
68  mPatientModelService(patientModelService)
69 {
70  this->setAttribute(Qt::WA_DeleteOnClose);
71 
72  QVBoxLayout* layout = new QVBoxLayout(this);
73  this->setWindowTitle("Set properties for imported data");
74 
75  mUidLabel = new QLabel("Data uid: ");
76  mNameLabel = new QLabel("Data name: ");
77 
78  layout->addWidget(mUidLabel);
79  layout->addWidget(mNameLabel);
80 
81  mModalityAdapter = StringPropertyDataModality::New(mPatientModelService);
82  mModalityCombo = new LabeledComboBoxWidget(this, mModalityAdapter);
83  layout->addWidget(mModalityCombo);
84 
85  mImageTypeAdapter = StringPropertyImageType::New(mPatientModelService);
86  mImageTypeCombo = new LabeledComboBoxWidget(this, mImageTypeAdapter);
87  layout->addWidget(mImageTypeCombo);
88 
89  mParentFrameAdapter = StringPropertySetParentFrame::New(mPatientModelService);
90  mParentFrameCombo = new LabeledComboBoxWidget(this, mParentFrameAdapter);
91  layout->addWidget(mParentFrameCombo);
92 
93  mNiftiFormatCheckBox = new QCheckBox("Convert from RAS to LPS coordinates", this);
94  mNiftiFormatCheckBox->setToolTip(""
95  "Use RAS (X=Left->Right Y=Posterior->Anterior Z=Inferior->Superior), as in ITK-Snap.\n"
96  "This is different from DICOM/CustusX, which uses LPS (left-posterior-superior).");
97  mNiftiFormatCheckBox->setChecked(false);
98  mNiftiFormatCheckBox->setEnabled(false);
99  mTransformFromParentFrameCheckBox = new QCheckBox("Import transform from Parent", this);
100  mTransformFromParentFrameCheckBox->setToolTip("Replace data transform with that of the parent data.");
101  mTransformFromParentFrameCheckBox->setChecked(false);
102 
103  mConvertToUnsignedCheckBox = new QCheckBox("Convert to unsigned", this);
104  mConvertToUnsignedCheckBox->setToolTip("Convert imported data set to unsigned values.");
105  mConvertToUnsignedCheckBox->setChecked(false);
106 
107  layout->addWidget(mNiftiFormatCheckBox);
108  layout->addWidget(mTransformFromParentFrameCheckBox);
109  layout->addWidget(mConvertToUnsignedCheckBox);
110 
111  connect(mParentFrameAdapter.get(), &Property::changed, this, &ImportDataDialog::updateImportTransformButton);
112  this->updateImportTransformButton();
113 
114  mErrorLabel = new QLabel();
115  layout->addWidget(mErrorLabel);
116 
117  QHBoxLayout* buttons = new QHBoxLayout;
118  layout->addLayout(buttons);
119  mOkButton = new QPushButton("OK", this);
120  buttons->addStretch();
121  buttons->addWidget(mOkButton);
122  connect(mOkButton, &QPushButton::clicked, this, &QDialog::accept);
123  connect(this, &QDialog::accepted, this, &ImportDataDialog::acceptedSlot);
124  connect(this, &QDialog::rejected, this, &ImportDataDialog::finishedSlot);
125  mOkButton->setDefault(true);
126  mOkButton->setFocus();
127 
128  report("Importing data...");
129 }
130 
132 {
133 }
134 
135 void ImportDataDialog::showEvent(QShowEvent* event)
136 {
137  // the import operation takes up to a few seconds. Call it AFTER the dialog is up and running its own message loop,
138  // this avoids all problems related to modal vs right-click in the main window.
139  QTimer::singleShot(0, this, SLOT(importDataSlot()));
140 }
141 
142 void ImportDataDialog::importDataSlot()
143 {
144  QString infoText;
145  mData = mPatientModelService->importData(mFilename, infoText);
146  if (!infoText.isEmpty())
147  {
148  infoText += "<font color=red><br>If these warnings are not expected the import have probably failed.</font>";
149  if(infoText.contains("File already exists", Qt::CaseInsensitive))
150  infoText += "<font color=red><br>Importing two different volumes with the same name will lead to undesired effects.</font>";
151  mErrorLabel->setText(infoText);
152  }
153 
154  if (!mData)
155  {
156  mUidLabel->setText(mFilename);
157  mNameLabel->setText("Import failed");
158  mOkButton->setText("Exit");
159  return;
160  }
161 
162  mUidLabel->setText("Data uid: " + qstring_cast(mData->getUid()));
163  mNameLabel->setText("Data name: " + qstring_cast(mData->getName()));
164 
165  ImagePtr image = boost::dynamic_pointer_cast<Image>(mData);
166  mModalityAdapter->setData(image);
167  mModalityCombo->setEnabled(image!=0);
168  mImageTypeAdapter->setData(image);
169  mImageTypeCombo->setEnabled(image!=0);
170 
171  this->setInitialGuessForParentFrame();
172  mParentFrameAdapter->setData(mData);
173  mParentFrameCombo->setEnabled(mPatientModelService->getData().size()>1);
174 
175  // enable nifti imiport only for meshes. (as this is the only case we have seen)
176  mNiftiFormatCheckBox->setEnabled(mPatientModelService->getData<Mesh>(mData->getUid())!=0);
177 
178  mConvertToUnsignedCheckBox->setEnabled(false);
179  if (image && image->getBaseVtkImageData())
180  {
181 // vtkImageDataPtr img = image->getBaseVtkImageData();
182 // std::cout << "type " << img->GetScalarTypeAsString() << " -- " << img->GetScalarType() << std::endl;
183 // std::cout << "range " << img->GetScalarTypeMin() << " -- " << img->GetScalarTypeMax() << std::endl;
184  mConvertToUnsignedCheckBox->setEnabled( (image!=0) && (image->getBaseVtkImageData()->GetScalarTypeMin()<0) );
185  }
186 }
187 
188 
192 void ImportDataDialog::setInitialGuessForParentFrame()
193 {
194  if(!mData)
195  return;
196 
197  QString base = qstring_cast(mData->getName()).split(".")[0];
198 
199  std::map<QString, DataPtr> all = mPatientModelService->getData();
200  for (std::map<QString, DataPtr>::iterator iter=all.begin(); iter!=all.end(); ++iter)
201  {
202  if (iter->second==mData)
203  continue;
204  QString current = qstring_cast(iter->second->getName()).split(".")[0];
205  if (base.indexOf(current)>=0)
206  {
207  mData->get_rMd_History()->setParentSpace(iter->first);
208  break;
209  }
210  }
211 
212 }
213 
214 void ImportDataDialog::updateImportTransformButton()
215 {
216  DataPtr parent = mPatientModelService->getData(mParentFrameAdapter->getValue());
217  bool enabled = bool(parent);
218  mTransformFromParentFrameCheckBox->setEnabled(enabled);
219 }
220 
221 void ImportDataDialog::acceptedSlot()
222 {
223  this->importParentTransform();
224  this->convertFromNifti1Coordinates();
225  this->convertToUnsigned();
226 
227  mPatientModelService->autoSave();
228  viewService()->autoShowData(mData);
229  this->finishedSlot();
230 }
231 
232 void ImportDataDialog::finishedSlot()
233 {
234 }
235 
243 void ImportDataDialog::convertFromNifti1Coordinates()
244 {
245  if (!mNiftiFormatCheckBox->isChecked())
246  return;
247  if(!mData)
248  return;
249  Transform3D sMd = mData->get_rMd();
251 // rMd = createTransformRotateZ(M_PI) * rMd;
252  Transform3D rMd = sMr.inv() * sMd;
253  mData->get_rMd_History()->setRegistration(rMd);
254  report("Nifti import: Converted data " + mData->getName() + " from LPS to RAS coordinates.");
255 }
256 
260 void ImportDataDialog::importParentTransform()
261 {
262  if (!mTransformFromParentFrameCheckBox->isChecked())
263  return;
264  if(!mData)
265  return;
266  DataPtr parent = mPatientModelService->getData(mData->getParentSpace());
267  if (!parent)
268  return;
269  mData->get_rMd_History()->setRegistration(parent->get_rMd());
270  report("Assigned rMd from data [" + parent->getName() + "] to data [" + mData->getName() + "]");
271 }
272 
273 void ImportDataDialog::convertToUnsigned()
274 {
275  if (!mConvertToUnsignedCheckBox->isChecked())
276  return;
277 
278  ImagePtr image = boost::dynamic_pointer_cast<Image>(mData);
279  if (!image)
280  return;
281 
282  ImagePtr converted = convertImageToUnsigned(patientService(), image);
283 
284  image->setVtkImageData(converted->getBaseVtkImageData());
285 
286  ImageTF3DPtr TF3D = converted->getTransferFunctions3D()->createCopy();
287  ImageLUT2DPtr LUT2D = converted->getLookupTable2D()->createCopy();
288  image->setLookupTable2D(LUT2D);
289  image->setTransferFunctions3D(TF3D);
290  patientService()->insertData(image);
291 }
292 
293 
294 }//namespace cx
QString qstring_cast(const T &val)
pcsRAS
Right-Anterior-Superior, used by Slicer3D, ITK-Snap, nifti.
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
cxResource_EXPORT Transform3D createTransformFromReferenceToExternal(PATIENT_COORDINATE_SYSTEM external)
static StringPropertyDataModalityPtr New(PatientModelServicePtr patientModelService)
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
Composite widget for string selection.
ImagePtr convertImageToUnsigned(PatientModelServicePtr dataManager, ImagePtr image, vtkImageDataPtr suggestedConvertedVolume, bool verbose)
boost::shared_ptr< class Data > DataPtr
static StringPropertyImageTypePtr New(PatientModelServicePtr patientModelService)
boost::shared_ptr< class ImageLUT2D > ImageLUT2DPtr
void showEvent(QShowEvent *event)
ImportDataDialog(PatientModelServicePtr patientModelService, QString filename, QWidget *parent=NULL)
boost::shared_ptr< class PatientModelService > PatientModelServicePtr
static StringPropertySetParentFramePtr New(PatientModelServicePtr patientModelService)
void changed()
emit when the underlying data value is changed: The user interface will be updated.
cxLogicManager_EXPORT ViewServicePtr viewService()
void report(QString msg)
Definition: cxLogger.cpp:90
cxLogicManager_EXPORT PatientModelServicePtr patientService()
boost::shared_ptr< class ImageTF3D > ImageTF3DPtr