File: CiftiXMLWriter.cxx

package info (click to toggle)
caret 5.6.4~dfsg.1-3
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd, wheezy
  • size: 31,904 kB
  • ctags: 28,901
  • sloc: cpp: 378,050; python: 6,718; ansic: 5,507; makefile: 333; sh: 46
file content (274 lines) | stat: -rw-r--r-- 10,460 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
/*LICENSE_START*/
/*
 *  Copyright 1995-2002 Washington University School of Medicine
 *
 *  http://brainmap.wustl.edu
 *
 *  This file is part of CARET.
 *
 *  CARET 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 2 of the License, or
 *  (at your option) any later version.
 *
 *  CARET 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 CARET; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 */
/*LICENSE_END*/

#include "CiftiXMLWriter.h"
#include "iostream"

void writeCiftiXML(QXmlStreamWriter &xml, CiftiRootElement &rootElement)
{  
   xml.setAutoFormatting(true);
   xml.writeStartElement("CIFTI");
   if(rootElement.m_version.length() >0) xml.writeAttribute("Version",rootElement.m_version);
   else xml.writeAttribute("Version","1.0");
   xml.writeAttribute("NumberOfMatrices",QString::number(rootElement.m_numberOfMatrices));

   for(unsigned int i = 0;i<rootElement.m_numberOfMatrices;i++)
   {
      writeMatrixElement(xml, rootElement.m_matrices[i]);
   }
   
   xml.writeEndElement(); //CIFTI
   
}

void writeMatrixElement(QXmlStreamWriter &xml, CiftiMatrixElement &matrixElement)
{ 
   xml.writeStartElement("Matrix");
   if(matrixElement.m_userMetaData.count() > 0) writeMetaData(xml,matrixElement.m_userMetaData);
   if(matrixElement.m_volume.size() > 0) writeVolume(xml, matrixElement.m_volume[0]);
   if(matrixElement.m_labelTable.size() > 0) writeLabelTable(xml, matrixElement.m_labelTable);
   
   for(unsigned int i = 0;i<matrixElement.m_matrixIndicesMap.size();i++)
   {
      writeMatrixIndicesMap(xml,matrixElement.m_matrixIndicesMap[i]);
   }
   
   xml.writeEndElement();//Matrix
}

void writeMetaData(QXmlStreamWriter &xml, QHash<QString, QString> &metaData)
{     
   xml.writeStartElement("MetaData");
   
   QHash<QString, QString>::Iterator i;
   
   for (i = metaData.begin(); i != metaData.end(); ++i)
   {
      writeMetaDataElement(xml,i.key(),i.value());
   }
   xml.writeEndElement();
}

void writeMetaDataElement(QXmlStreamWriter &xml, const QString &name, const QString &value)
{     
   xml.writeStartElement("MD");
   
   xml.writeStartElement("Name");
   xml.writeCharacters(name);
   xml.writeEndElement();//Name
   
   xml.writeStartElement("Value");
   xml.writeCharacters(value);
   xml.writeEndElement();//Value
   
   xml.writeEndElement();//MD
}

void writeLabelTable(QXmlStreamWriter &xml, std::vector <CiftiLabelElement> &labelElement)
{     
   xml.writeStartElement("LabelTable");
   
   for(unsigned int i=0;i<labelElement.size();i++)
   {
         writeLabel(xml,labelElement[i]);
   }
   
   xml.writeEndElement();
}

void writeLabel(QXmlStreamWriter &xml, CiftiLabelElement &label)
{     
   xml.writeStartElement("Label");
   
   xml.writeAttribute("Key", QString::number(label.m_key));
   xml.writeAttribute("Red", QString::number(label.m_red));
   xml.writeAttribute("Green", QString::number(label.m_green));
   xml.writeAttribute("Blue", QString::number(label.m_blue));
   xml.writeAttribute("Alpha", QString::number(label.m_alpha));
   xml.writeAttribute("X", QString::number(label.m_x));
   xml.writeAttribute("Y", QString::number(label.m_y));
   xml.writeAttribute("Z", QString::number(label.m_z));   
   
   xml.writeEndElement();
}

void writeMatrixIndicesMap(QXmlStreamWriter &xml, CiftiMatrixIndicesMapElement &matrixIndicesMap)
{     
   xml.writeStartElement("MatrixIndicesMap");
   //TODO
   //xml.writeAttribute("AppliesToMatrixDimension", QString::number(matrixIndicesMap.m_appliesToMatrixDimension));
   QString indicesMapToDataType;
   if(matrixIndicesMap.m_indicesMapToDataType == CIFTI_INDEX_TYPE_BRAIN_MODELS) indicesMapToDataType = "CIFTI_INDEX_TYPE_BRAIN_MODELS";
   else if(matrixIndicesMap.m_indicesMapToDataType == CIFTI_INDEX_TYPE_FIBERS) indicesMapToDataType = "CIFTI_INDEX_TYPE_FIBERS";
   else if(matrixIndicesMap.m_indicesMapToDataType == CIFTI_INDEX_TYPE_PARCELS) indicesMapToDataType = "CIFTI_INDEX_TYPE_PARCELS";
   else if(matrixIndicesMap.m_indicesMapToDataType == CIFTI_INDEX_TYPE_TIME_POINTS) indicesMapToDataType = "CIFTI_INDEX_TYPE_TIME_POINTS";
   
   xml.writeAttribute("IndicesMapToDataType",indicesMapToDataType);
   
   
   QString timeStepUnits;
   
   if(matrixIndicesMap.m_timeStepUnits == NIFTI_UNITS_SEC) timeStepUnits = "NIFTI_UNITS_SEC";
   else if(matrixIndicesMap.m_timeStepUnits == NIFTI_UNITS_MSEC) timeStepUnits = "NIFTI_UNITS_MSEC";
   else if(matrixIndicesMap.m_timeStepUnits == NIFTI_UNITS_USEC) timeStepUnits = "NIFTI_UNITS_USEC";
     
   if(timeStepUnits.length()>0) {
      QString str;
      xml.writeAttribute("TimeStep",str.sprintf("%.1f",matrixIndicesMap.m_timeStep));
      xml.writeAttribute("TimeStepUnits",timeStepUnits);
   }
   if(matrixIndicesMap.m_appliesToMatrixDimension.size())
   {
      int lastElement = matrixIndicesMap.m_appliesToMatrixDimension.size() -1;
      QString appliesToMatrixDimension, str;
      for(int i = 0;i<lastElement;i++)
      {
         appliesToMatrixDimension.append(str.sprintf("%d,",matrixIndicesMap.m_appliesToMatrixDimension[i]));
      }
      appliesToMatrixDimension.append(str.sprintf("%d",matrixIndicesMap.m_appliesToMatrixDimension[lastElement]));
      xml.writeAttribute("AppliesToMatrixDimension", appliesToMatrixDimension);
   }
   
   for(unsigned int i=0;i<matrixIndicesMap.m_brainModels.size();i++)
   {
      writeBrainModel(xml, matrixIndicesMap.m_brainModels[i]);      
   }
   xml.writeEndElement();   
}

void writeBrainModel(QXmlStreamWriter &xml, CiftiBrainModelElement &brainModel)
{     
   xml.writeStartElement("BrainModel");
   
   xml.writeAttribute("IndexOffset", QString::number(brainModel.m_indexOffset));
   xml.writeAttribute("IndexCount", QString::number(brainModel.m_indexCount));
   QString modelType, brainStructure;
   getModelTypeString(brainModel.m_modelType,modelType);
   xml.writeAttribute("ModelType",modelType);
   xml.writeAttribute("BrainStructure", brainModel.m_brainStructure);
   if(brainModel.m_modelType == CIFTI_MODEL_TYPE_SURFACE) xml.writeAttribute("SurfaceNumberOfNodes",QString::number(brainModel.m_surfaceNumberOfNodes));
   
  
   unsigned long long lastnodeIndex= brainModel.m_nodeIndices.size();
   
   if(lastnodeIndex)
   {
      xml.writeStartElement("NodeIndices");
      lastnodeIndex--;
      for(unsigned int i = 0;i<lastnodeIndex;i++)
      {
         xml.writeCharacters(QString::number(brainModel.m_nodeIndices[i]));
         xml.writeCharacters(" ");
      }
      xml.writeCharacters(QString::number(brainModel.m_nodeIndices[lastnodeIndex]));      
      xml.writeEndElement();//NodeIndices
   }
   
   
   
   std::vector <voxelIndexType> &ind = brainModel.m_voxelIndicesIJK;
   unsigned long long lastVoxelIndex = ind.size();
   if(lastVoxelIndex)
   {
      xml.writeStartElement("VoxelIndicesIJK");   
      QString line( "%1 %2 %3\n");
      if((lastVoxelIndex%3))
      {
         std::cout << "Error writing BrainModel, invalid number of voxel indices:" << lastVoxelIndex << std::endl;
         return;//TODO throw exception      
      }
      //else
         //std::cout << "voxel indices ok:" << lastVoxelIndex<< std::endl;
      
      for(unsigned int i = 0;i < lastVoxelIndex;i+=3)
      {
         xml.writeCharacters(line.arg(QString::number(ind[i]),QString::number(ind[i+1]),QString::number(ind[i+2])));
      }
      xml.writeEndElement();//voxelIndicesIJK
   }
   
   xml.writeEndElement();
}

void writeVolume(QXmlStreamWriter &xml, CiftiVolume &volume)
{     
   xml.writeStartElement("Volume");
   
   QString str("%1,%2,%3");
   xml.writeAttribute("VolumeDimensions", str.arg(QString::number(volume.m_volumeDimensions[0]),QString::number(volume.m_volumeDimensions[1]),QString::number(volume.m_volumeDimensions[2])));
   for(unsigned int i = 0;i<volume.m_transformationMatrixVoxelIndicesIJKtoXYZ.size();i++)
   {
      writeTransformationMatrixVoxelIndicesIJKtoXYZ(xml,volume.m_transformationMatrixVoxelIndicesIJKtoXYZ[i]);
   }
   
   xml.writeEndElement();   
}

void writeTransformationMatrixVoxelIndicesIJKtoXYZ(QXmlStreamWriter &xml, TransformationMatrixVoxelIndicesIJKtoXYZ &transform)
{     
   xml.writeStartElement("TransformationMatrixVoxelIndicesIJKtoXYZ");
   
   QString dataSpaceString, transformedSpaceString, unitsXYZString;
   getDataSpaceString(transform.m_dataSpace, dataSpaceString);
   getDataSpaceString(transform.m_transformedSpace, transformedSpaceString);
   getUnitsXYZString(transform.m_unitsXYZ,unitsXYZString);
   
   if(dataSpaceString.length() > 0) xml.writeAttribute("DataSpace", dataSpaceString);
   if(transformedSpaceString.length() > 0) xml.writeAttribute("TransformedSpace", transformedSpaceString);
   if(unitsXYZString.length() > 0) xml.writeAttribute("UnitsXYZ", unitsXYZString);
   
   QString voxelIndices;
   QString s;
   for(int i = 0;i<15;i++)
   {      
      voxelIndices.append(s.sprintf("%.1f ",transform.m_transform[i]));      
   }
   voxelIndices.append(s.sprintf("%.1f", transform.m_transform[15]));   
   xml.writeCharacters(voxelIndices);
   
   xml.writeEndElement();  
   
}

void getModelTypeString(int modelType, QString &modelTypeString)
{
   if(modelType == CIFTI_MODEL_TYPE_SURFACE) modelTypeString = "CIFTI_MODEL_TYPE_SURFACE";
   else if(modelType == CIFTI_MODEL_TYPE_VOXELS) modelTypeString = "CIFTI_MODEL_TYPE_VOXELS";
}

void getDataSpaceString(int dataSpace, QString &dataSpaceString)
{
   if(dataSpace == NIFTI_XFORM_UNKNOWN) dataSpaceString = "NIFTI_XFORM_UNKNOWN";
   else if(dataSpace == NIFTI_XFORM_SCANNER_ANAT) dataSpaceString = "NIFTI_XFORM_SCANNER_ANAT";
   else if(dataSpace == NIFTI_XFORM_ALIGNED_ANAT) dataSpaceString = "NIFTI_XFORM_ALIGNED_ANAT";
   else if(dataSpace == NIFTI_XFORM_TALAIRACH) dataSpaceString = "NIFTI_XFORM_TALAIRACH";
   else if(dataSpace == NIFTI_XFORM_MNI_152) dataSpaceString = "NIFTI_XFORM_MNI_152";   
}

void getUnitsXYZString(int unitsXYZ, QString &unitsXYZString)
{
   if(unitsXYZ == NIFTI_UNITS_MM) unitsXYZString = "NIFTI_UNITS_MM";
   else if(unitsXYZ == NIFTI_UNITS_MICRON) unitsXYZString = "NIFTI_UNITS_MICRON";
}