1 /*=========================================================================
4 Module: $RCSfile: PcpdenseToDicom.cxx,v $
6 Date: $Date: 2011/08/25 14:36:02 $
7 Version: $Revision: 1.8 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
23 #if defined(__BORLANDC__)
28 #include "gdcmFileHelper.h"
29 #include "gdcmDebug.h"
30 #include "gdcmDirList.h"
32 #include "gdcmArgMgr.h"
36 * Converts the "pcpdense" ".txt" (2008 version) files into 16 bits Dicom Files,
37 * Hope they don't change soon!
40 void MakeDicomImage(unsigned short int *tabVal, int X, int Y, std::string dcmImageName, const char * patientName, int nbFrames,
41 std::string studyUID, std::string serieUID, std::string SerieDescr, int imgNum, bool m );
43 void LoadImage(std::ifstream &from, unsigned short int * );
45 void LoadImageX2(std::ifstream &from, unsigned short int * );
48 int main(int argc, char *argv[])
51 " \n pcpdenseToDicom :\n ",
52 " Converts the '.txt' files into 16 bits Dicom-like Files, ",
54 " pcpdenseToDicom rootfilename=... ",
55 " (e.g.. : meas_MID380_DENSE_stacked_slices_aif_FID81637)",
56 " numberOfSlices = (default : 3) ",
57 " X2 : multiply x 2 image size ",
58 " m :create multiframe files instead of image stacks ",
59 " [patientname = Patient's name] ",
60 " [verbose] [debug] ",
62 " verbose : user wants to run the program in 'verbose mode' ",
63 " debug : *developer* wants to run the program in 'debug mode' ",
66 // ----- Initialize Arguments Manager ------
68 GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
70 if (argc == 1 || am->ArgMgrDefined("usage"))
72 am->ArgMgrUsage(usage); // Display 'usage'
76 // Seems that ArgMgrWantString doesn't work on MacOS
77 if(!am->ArgMgrDefined("rootfilename"))
79 std::cout << "'rootfilename' is mandatory" << std::endl;
83 const char *rootfilename = am->ArgMgrWantString("rootfilename",usage);
84 int numberOfSlices = am->ArgMgrGetInt("numberOfSlices",3);
85 const char *patientName = am->ArgMgrGetString("patientname", "Patient^Name");
87 if (am->ArgMgrDefined("debug"))
88 GDCM_NAME_SPACE::Debug::DebugOn();
90 verbose = ( 0 != am->ArgMgrDefined("verbose") );
91 bool X2 = ( 0 != am->ArgMgrDefined("X2") );
92 bool multiframe = ( 0 != am->ArgMgrDefined("m") );
94 // if unused Param we give up
95 if ( am->ArgMgrPrintUnusedLabels() )
97 am->ArgMgrUsage(usage);
101 delete am; // we don't need Argument Manager any longer
103 // ----- Begin Processing -----
105 std::ostringstream Ecc;
106 std::ostringstream perf;
107 std::ostringstream WashoutTc;
109 std::string strSerieUID;
110 std::string strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
111 std::string dcmImageName, textFileName, patientname, serieDescr;
112 std::string deb(rootfilename);
114 unsigned short int *image;
122 Ecc.str(rootfilename);
123 Ecc << Ecc.str() << "_s0" << "_Ecc.txt";
125 std::ifstream fromEcc( Ecc.str().c_str() );
128 std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
138 std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
148 image = new unsigned short int[NX*NY*mult*numberOfSlices];
150 image = new unsigned short int[NX*NY*mult];
156 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
161 for (int i=0; i<numberOfSlices; i++)
163 Ecc.str(rootfilename);
164 Ecc << Ecc.str() << "_s" << i << "_Ecc.txt";
166 std::ifstream fromEcc( Ecc.str().c_str() );
169 std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
172 std::cout << "Open file [" << Ecc.str() << "] : OK" << std::endl;
173 dcmImageName = Ecc.str() + ".dcm";
177 LoadImageX2(fromEcc, image);
178 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
182 LoadImage(fromEcc, image);
183 MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
187 } // end : for (int i=0; i<numberOfSlices
191 for (int i=0; i<numberOfSlices; i++)
193 Ecc.str(rootfilename);
194 Ecc << Ecc.str() << "_s" << i << "_Ecc.txt";
196 std::ifstream fromEcc( Ecc.str().c_str() );
199 std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
203 std::cout << "Open file [" << Ecc.str() << "] : OK" << std::endl;
205 LoadImageX2(fromEcc ,&image[NX*NY*4*i] );
207 LoadImage(fromEcc, &image[NX*NY*i] );
210 } // end : for (int i=0; i<numberOfSlices
212 dcmImageName = deb + "_Ecc.dcm";
214 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
216 MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
217 } // end : if (multiframe)
223 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
228 for (int i=0; i<numberOfSlices; i++)
230 perf.str(rootfilename);
231 perf << perf.str() << "_s" << i << "_perf.txt";
233 std::ifstream fromperf( perf.str().c_str() );
236 std::cout << "Can't open file [" << perf.str() << "]" << std::endl;
239 std::cout << "Open file [" << perf.str() << "] : OK" << std::endl;
242 LoadImageX2(fromperf ,image );
244 LoadImage(fromperf, image );
248 dcmImageName = perf.str() + ".dcm";
251 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
253 MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
255 } // end : for (int i=0; i<numberOfSlices
260 for (int i=0; i<numberOfSlices; i++)
262 perf.str(rootfilename);
263 perf << perf.str() << "_s" << i << "_perf.txt";
265 std::ifstream fromperf( perf.str().c_str() );
268 std::cout << "Can't open file [" << perf.str() << "]" << std::endl;
271 std::cout << "Open file [" << perf.str() << "] : OK" << std::endl;
274 LoadImageX2(fromperf, &image[NX*NY*i*4]);
276 LoadImage(fromperf, &image[NX*NY*i] );
279 } // end : for (int i=0; i<numberOfSlices
281 dcmImageName = deb + "_perf.dcm";
283 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
285 MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
293 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
295 serieDescr = "WashoutTc";
299 for (int i1=0; i1<numberOfSlices; i1++)
301 WashoutTc.str(rootfilename);
302 WashoutTc << WashoutTc.str() << "_s" << i1 << "_WashoutTc.txt";
304 std::ifstream fromWashoutTc( WashoutTc.str().c_str() );
305 if ( !fromWashoutTc )
307 std::cout << "Can't open file [" << WashoutTc.str() << "]" << std::endl;
311 std::cout << "Open file [" << WashoutTc.str() << "] : OK" << std::endl;
313 LoadImageX2(fromWashoutTc,image );
315 LoadImage(fromWashoutTc,image );
316 fromWashoutTc.close();
318 dcmImageName = WashoutTc.str() + ".dcm";
320 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i1, multiframe );
322 MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i1, multiframe );
323 } // end : for (int i=0; i<numberOfSlices
327 for (int i=0; i<numberOfSlices; i++)
329 WashoutTc.str(rootfilename);
330 WashoutTc << WashoutTc.str() << "_s" << i << "_WashoutTc.txt";
332 std::ifstream fromWashoutTc( WashoutTc.str().c_str() );
333 if ( !fromWashoutTc )
335 std::cout << "Can't open file [" << WashoutTc.str() << "]" << std::endl;
338 std::cout << "Open file [" << WashoutTc.str() << "] : OK" << std::endl;
341 LoadImageX2(fromWashoutTc, &image[NX*NY*4*i]);
343 LoadImage(fromWashoutTc, &image[NX*NY*i] );
344 fromWashoutTc.close();
346 } // end : for (int i=0; i<numberOfSlices
348 dcmImageName = deb + "_WashoutTc.dcm";
350 MakeDicomImage(image, NX*2, NY*2, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
352 MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
359 // =====================================================================================================================
361 void LoadImage(std::ifstream &from, unsigned short int *image)
363 // in any file ".txt" :
367 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
382 std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
390 image[i*NX+j] = (unsigned short int)(pixelValue * 1000.); // Why do we multiply by 1000? // JPR
396 // =====================================================================================================================
398 void LoadImageX2(std::ifstream &from, unsigned short int *image )
400 // in any file ".txt" :
404 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
419 std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
422 for( k=0;k<NX*NY*4;k++)
432 pixelValue*=1000.; // Why do we multiply by 1000? // JPR
433 image[i*4*NX + j*2] = image[i*4*NX + j*2+1] = image[(i*4+2)*NX + j*2] = image[(i*4+2)*NX + j*2+1] = (unsigned short int)(pixelValue);
438 int lgrLigneNvlleImage = NX+NX;
439 int debLigneNvlleImage = 0;
443 pixelValue*=1000.; // Why do we multiply by 1000? // JPR
444 image[debLigneNvlleImage + j+j] =
445 image[debLigneNvlleImage + j+j +1] =
446 image[debLigneNvlleImage + lgrLigneNvlleImage +j+j] =
447 image[debLigneNvlleImage + lgrLigneNvlleImage + j+j +1] =
448 (unsigned short int)(pixelValue);
450 debLigneNvlleImage += 2*lgrLigneNvlleImage;
453 // =====================================================================================================================================
456 void MakeDicomImage(unsigned short int *tabVal, int X, int Y, std::string dcmImageName, const char * patientName, int nbFrames, std::string studyUID, std::string serieUID, std::string SerieDescr, int imgNum, bool m)
459 std::cout << "in MakeDicomImage : dcmImageName = [" << dcmImageName << "]" << std::endl;
460 // GDCM_NAME_SPACE::Debug::DebugOn();
462 std::ostringstream str;
464 GDCM_NAME_SPACE::File *file;
465 file = GDCM_NAME_SPACE::File::New();
467 // Set the image size
470 file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
473 file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
475 // Set the pixel type
477 file->InsertEntryString("16",0x0028,0x0100,"US"); // Bits Allocated
480 str << 16; // may be 12 or 16 if componentSize =16
481 file->InsertEntryString("16",0x0028,0x0101,"US"); // Bits Stored
482 file->InsertEntryString("15",0x0028,0x0102,"US"); // High Bit
484 // Set the pixel representation // 0/1 , 0=unsigned
485 file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
487 // Set the samples per pixel // 1:Grey level, 3:RGB
488 file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
495 file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
498 if (strlen(patientName) != 0)
499 file->InsertEntryString(patientName,0x0010,0x0010, "PN"); // Patient's Name
501 file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
502 file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
504 file->InsertEntryString(SerieDescr,0x0008,0x103e, "LO"); // Series Description
506 // 0020 0037 DS 6 Image Orientation (Patient)
507 file->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial (Tant pis!)
509 // 0020 0032 DS 3 Image Position (Patient)
510 char charImagePosition[256];
511 sprintf(charImagePosition,"0.0\\0.0\\%f",(float)imgNum);
512 file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
514 // 0020 0x1041 DS 1 Slice Location
515 sprintf(charImagePosition,"%f",float(imgNum));
516 file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
518 // Set Rescale Intercept
521 file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
526 file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
529 GDCM_NAME_SPACE::FileHelper *fileH;
530 fileH = GDCM_NAME_SPACE::FileHelper::New(file);
531 // cast is just to avoid warnings (*no* conversion is performed)
532 //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
534 fileH->SetImageData((uint8_t *)tabVal,X*Y*nbFrames*sizeof(uint16_t));
535 fileH->SetWriteModeToRaw();
536 fileH->SetWriteTypeToDcmExplVR();
538 if( !fileH->Write(dcmImageName))
539 std::cout << "Failed for [" << dcmImageName << "]\n"
540 << " File is unwrittable" << std::endl;
551 // =====================================================================================================================