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
|
/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2016 Univ. Grenoble Alpes, CNRS, TIMC-IMAG UMR 5525 (GMCAO)
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK 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 Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
#include "ItkImageComponentExtension.h"
#include "ItkImageComponent.h"
using namespace camitk;
// save to itk
#include <itkImageFileWriter.h>
#include <itkVTKImageToImageFilter.h>
//-- Qt
#include <QMessageBox>
// --------------- getName -------------------
QString ItkImageComponentExtension::getName() const {
return "ItkImages Component";
}
// --------------- getDescription -------------------
QString ItkImageComponentExtension::getDescription() const {
return QString("Manage any file type supported by itk and not by vtk in <b>CamiTK</b>.<br/>")
+ "For more info about image data format: <a href=\"http://www.dclunie.com/medical-image-faq/html\">http://www.dclunie.com/medical-image-faq/html</a><br/><ul>"
+ "<li>hdr is the Analyse header file format</li>"
+ "<li>spr is the Stimulate header file format</li>"
+ "<li>gipl is the Guys Image Processing Lab Format</li>"
+ "<li>pic is the Bio-Rad file format, used by confocal micropscopes like MRC 1024 and MRC 600</li>"
// + "<li>PAR/REC is the research Philips format</li>"
+ "<li>LSM is a line of confocal laser scanning microscopes produced by the Zeiss company</li>"
// + "<li>ima is the Siemens Vision image format</li>"
// + "<li>mnc (MINC / MINC2) is developed over the past 15 years at the Brain Imaging Centre (or Centre) at the Montreal Neurological Institute</li>"
+ "<li>Nrrd is the \"Nearly Raw Raster Data\"</li>"
// + "<li>cub see <a href=\"http://www.insight-journal.org/browse/publication/118\">http://www.insight-journal.org/browse/publication/118</a></li></ul><br/>"
+ "<li>NIfTI-1 (.nii) is adapted from the widely used ANALYZE 7.5 file format. For more info about image data format: <a href=\"http://nifti.nimh.nih.gov/nifti-1/\">http://nifti.nimh.nih.gov/nifti-1/</a> </li>"
// + "<li>cub see <a href=\"http://www.insight-journal.org/browse/publication/118\">http://www.insight-journal.org/browse/publication/118</a></li></ul><br/>"
+ "</ul>";
}
// --------------- getFileExtensions -------------------
QStringList ItkImageComponentExtension::getFileExtensions() const {
QStringList ext;
ext << "hdr" << "spr" << "gipl" << "pic" << "lsm" << "nrrd" << "hdr.gz" << "nii" << "nii.gz" << "img" << "img.gz";
return ext;
}
// --------------- open -------------------
Component * ItkImageComponentExtension::open(const QString & fileName) throw (AbortException) {
ItkImageComponent * res = NULL;
try {
res = new ItkImageComponent(fileName);
} catch (AbortException e) {
throw e;
}
return res;
}
// --------------- save -------------------
bool ItkImageComponentExtension::save(Component * c) const {
bool succeed = false;
ImageComponent *img = dynamic_cast<ImageComponent *>(c);
if (!img)
return succeed;
// Instanciate the template function saveImage
// according to the input image type.
// Here by default, the Ouput pixel type corresponds to the input pixel type.
int * dims = img->getImageData()->GetDimensions();
int dim = 0;
if (dims[2] == 0)
dim = 2;
else
dim = 3;
vtkSmartPointer<vtkImageData> data = img->getImageData();
int scalarType = data->GetScalarType();
switch (scalarType) {
case VTK_CHAR :
if (dim == 2) {
typedef itk::Image<char, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<char, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_UNSIGNED_CHAR :
if (dim == 2) {
typedef itk::Image<unsigned char, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<unsigned char, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_SIGNED_CHAR :
if (dim == 2) {
typedef itk::Image<signed char, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<signed char, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_SHORT :
if (dim == 2) {
typedef itk::Image<short, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<short, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_UNSIGNED_SHORT :
if (dim == 2) {
typedef itk::Image<unsigned short, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<unsigned short, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_INT :
if (dim == 2) {
typedef itk::Image<int, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<int, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_UNSIGNED_INT :
if (dim == 2) {
typedef itk::Image<unsigned int, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<unsigned int, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_LONG :
if (dim == 2) {
typedef itk::Image<long, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<long, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_UNSIGNED_LONG :
if (dim == 2) {
typedef itk::Image<unsigned long, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<unsigned long, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_FLOAT :
if (dim == 2) {
typedef itk::Image<float, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<float, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
case VTK_DOUBLE :
if (dim == 2) {
typedef itk::Image<double, 2> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
} else { // if dim == 3
typedef itk::Image<double, 3> ImageType;
succeed = ItkImageComponentExtension::saveImage<ImageType>(img);
}
break;
default :
break;
}
return succeed;
}
// --------------- saveImage -------------------
template<class ImageType> bool ItkImageComponentExtension::saveImage(ImageComponent * img) {
typedef itk::VTKImageToImageFilter<ImageType> VtkToItkFilterType;
typedef itk::ImageFileWriter< ImageType > WriterType;
QString filename = img->getFileName();
if (filename.isEmpty())
return false;
vtkSmartPointer<vtkImageData> vtkImage = img->getImageData();
typename VtkToItkFilterType::Pointer vtkToItkFilter = VtkToItkFilterType::New();
typename WriterType::Pointer writer = WriterType::New();
vtkToItkFilter->SetInput(vtkImage);
writer->SetFileName( filename.toUtf8() );
writer->SetInput( vtkToItkFilter->GetOutput() );
try {
writer->Update();
} catch (itk::ExceptionObject & err ) {
QMessageBox::warning(NULL,"Saving Error", "Problem while saving to file:<br/>" + filename +"<br/>ITK Exception:<br/>"+ err.what());
return false;
}
return true;
}
|
