1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
20 #include "clitkDicom2Image_ggo.h"
21 #include "clitkCommon.h"
22 #include "clitkImageCommon.h"
23 #include "vvImageReader.h"
24 #include "vvImageWriter.h"
26 #include <vtkImageChangeInformation.h>
27 #if GDCM_MAJOR_VERSION == 2
28 #include <gdcmImageHelper.h>
29 #include <gdcmAttribute.h>
30 #include <gdcmReader.h>
35 //====================================================================
36 int main(int argc, char * argv[])
39 GGO(clitkDicom2Image, args_info);
40 std::vector<std::string> input_files;
41 ///if std_input is given, read the input files from stdin
42 if (args_info.std_input_given) {
47 input_files.push_back(tmp);
50 args_info.inputs_num=input_files.size();
51 } else for (unsigned int i=0; i<args_info.inputs_num; i++)
52 input_files.push_back(args_info.inputs[i]);
55 //===========================================
56 /// Get slices locations ...
57 int series_number = -1;
58 std::set<int> series_numbers;
59 std::map< int, std::vector<double> > theorigin;
60 std::map< int, std::vector<double> > sliceLocations;
61 std::map< int, std::vector<std::string> > seriesFiles;
62 for(unsigned int i=0; i<args_info.inputs_num; i++) {
63 //std::cout << "Reading <" << input_files[i] << std::endl;
64 #if GDCM_MAJOR_VERSION == 2
65 if (args_info.verbose_flag)
66 std::cout << "Using GDCM-2.x" << std::endl;
68 hreader.SetFileName(input_files[i].c_str());
70 gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
72 if (args_info.extract_series_flag) {
73 gdcm::Attribute<0x20,0x11> series_number_att;
74 series_number_att.SetFromDataSet(hreader.GetFile().GetDataSet());
75 series_number = series_number_att.GetValue();
78 series_numbers.insert(series_number);
79 theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
80 sliceLocations[series_number].push_back(theorigin[series_number][2]);
81 seriesFiles[series_number].push_back(input_files[i]);
83 gdcm::Attribute<0x28, 0x100> pixel_size;
84 pixel_size.SetFromDataSet(ds);
85 /* if (pixel_size.GetValue() != 16)
87 std::cerr << "Pixel type not 2 bytes ! " << std::endl;
88 std::cerr << "In file " << input_files[i] << std::endl;
93 if (args_info.verbose_flag)
94 std::cout << "Not using GDCM-2.x" << std::endl;
95 gdcm::File *header = new gdcm::File();
96 header->SetFileName(input_files[i]);
97 header->SetMaxSizeLoadEntry(16384); // required ?
100 if (args_info.extract_series_flag) {
101 series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
104 series_numbers.insert(series_number);
105 theorigin[series_number].resize(3);
106 theorigin[series_number][0] = header->GetXOrigin();
107 theorigin[series_number][1] = header->GetYOrigin();
108 theorigin[series_number][2] = header->GetZOrigin();
109 sliceLocations[series_number].push_back(theorigin[series_number][2]);
110 seriesFiles[series_number].push_back(input_files[i]);
111 /*if (header->GetPixelSize() != 2) {
112 std::cerr << "Pixel type 2 bytes ! " << std::endl;
113 std::cerr << "In file " << input_files[i] << std::endl;
120 //===========================================
121 // Sort slices locations ...
122 std::set<int>::iterator sn = series_numbers.begin();
123 while ( sn != series_numbers.end() ) {
124 std::vector<double> locs = sliceLocations[*sn];
125 std::vector<double> origin = theorigin[*sn];
126 std::vector<std::string> files = seriesFiles[*sn];
127 std::vector<int> sliceIndex;
128 clitk::GetSortedIndex(locs, sliceIndex);
129 if (args_info.verboseSliceLocation_flag) {
130 std::cout << locs[sliceIndex[0]] << " -> "
131 << sliceIndex[0] << " / " << 0 << " => "
133 << files[sliceIndex[0]]
135 for(unsigned int i=1; i<sliceIndex.size(); i++) {
136 std::cout << locs[sliceIndex[i]] << " -> "
137 << sliceIndex[i] << " / " << i << " => "
138 << locs[sliceIndex[i]] - locs[sliceIndex[i-1]]
140 << files[sliceIndex[i]]
145 //===========================================
146 // Analyze slices locations ...
149 double tolerance = args_info.tolerance_arg;
150 double previous = locs[sliceIndex[0]];
151 for(unsigned int i=1; i<sliceIndex.size(); i++) {
152 currentDist = locs[sliceIndex[i]]-previous;
154 if (fabs(dist-currentDist) > tolerance) {
155 std::cout << "ERROR : " << std::endl
156 << "Current slice pos is = " << locs[sliceIndex[i]] << std::endl
157 << "Previous slice pos is = " << previous << std::endl
158 << "Current file is = " << files[sliceIndex[i]] << std::endl
159 << "Current index is = " << i << std::endl
160 << "Current sortindex is = " << sliceIndex[i] << std::endl
161 << "Current slice diff = " << dist << std::endl
162 << "Current error = " << fabs(dist-currentDist) << std::endl;
165 } else dist = currentDist;
166 previous = locs[sliceIndex[i]];
169 //===========================================
170 // Create ordered vector of filenames
171 std::vector<std::string> sorted_files;
172 sorted_files.resize(sliceIndex.size());
173 for(unsigned int i=0; i<sliceIndex.size(); i++)
174 sorted_files[i] = files[ sliceIndex[i] ];
176 //===========================================
178 vvImageReader::Pointer reader = vvImageReader::New();
179 reader->SetInputFilenames(sorted_files);
180 reader->Update(vvImageReader::DICOM);
181 if (reader->GetLastError().size() != 0) {
182 std::cerr << reader->GetLastError() << std::endl;
186 vvImage::Pointer image = reader->GetOutput();
187 vtkImageData* vtk_image = image->GetFirstVTKImageData();
188 vtkImageChangeInformation* modifier = vtkImageChangeInformation::New();
189 if (args_info.focal_origin_given) {
190 std::vector<double> spacing = image->GetSpacing();
191 std::vector<int> size = image->GetSize();
192 origin[0] = -spacing[0]*size[0]/2.0;
193 origin[1] = -spacing[1]*size[1]/2.0;
194 modifier->SetInput(vtk_image);
195 modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
197 vvImage::Pointer focal_image = vvImage::New();
198 focal_image->AddVtkImage(modifier->GetOutput());
203 if (series_numbers.size() == 1)
204 outfile = args_info.output_arg;
206 std::ostringstream name;
207 name << *sn << "_" << args_info.output_arg;
208 outfile = name.str();
210 vvImageWriter::Pointer writer = vvImageWriter::New();
211 writer->SetInput(image);
212 writer->SetOutputFileName(outfile);