1 #include "bruker2dicom.h"
2 #include <boost/filesystem/path.hpp>
3 #include <boost/filesystem/operations.hpp>
4 #include "brukerexception.h"
6 #ifndef PATH_MAX // If not defined yet : do it
12 bool Bruker2Dicom::Execute()
14 // ----- Check input values -----
16 bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
18 //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
19 if ( ! boost::filesystem::is_directory(InputDirName) )
21 std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
27 std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
30 std::string strDirNameOut(OutputDirName);
31 bool res=CreateDirectory(strDirNameOut);
33 std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
35 throw ( BrukerHopelessException ("Output directory creation failure "));
38 std::string strDirNamein(InputDirName);
39 GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
40 std::string strDirNameout(OutputDirName);
45 std::cout << "------------List of found files ------------" << std::endl;
47 std::cout << std::endl;
53 // e.g : at level 0, in : B67d1.Bp1
55 // 1 2 3 4 5 6 AdjStatePerStudy subject
58 GDCM_NAME_SPACE::DirListType fileNames;
59 fileNames = dirList.GetFilenames();
61 std::string outputFileName;
64 // BrukerDataSet br_subject;
66 subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
67 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
70 std::cout << " Subject : [" << subject << "]" << std::endl;
71 canOpen =br_subject.LoadFile(subject);
75 std::cout << "Hopeless! no 'subject' found" << std::endl;
76 throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
77 //exit(0); /// \TODO throw an exception !
83 //br_subject.PrintSelf();
85 // get info for 'Study Description'
87 BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
88 std::string subject_name = b_name.GetStringValue()[0];
89 strPatientName = subject_name;
90 cleanString(subject_name);
92 BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
93 std::string subject_entry = b_entry.GetStringValue()[0];
94 //cleanString(subject_entry);
95 subject_entry = subject_entry.substr(11, subject_entry.size()-11);
97 BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
98 std::string subject_position = b_position.GetStringValue()[0];
99 //cleanString(subject_position);
100 subject_position = subject_position.substr(9, subject_position.size()-9);
102 BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
103 std::string subject_date = b_date.GetStringValue()[0];
104 strStudyTimeDate = subject_date;
105 cleanString(subject_date);
107 BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
108 std::string subject_study_name = b_study_name.GetStringValue()[0];
109 subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
110 cleanString(subject_date);
112 // subject_name is already in 'Patient Name'
113 strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
115 char outputDirName[(unsigned int) PATH_MAX+2];
117 strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
120 // -----------------------------------------------------
121 // Iterate to ALL the objets(files/directories) found in the input directory
122 // (this is level ZERO)
123 // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
124 // -----------------------------------------------------
126 GDCM_NAME_SPACE::DirListType::iterator it;
128 for (it = fileNames.begin();
129 it != fileNames.end();
132 if ( boost::filesystem::is_directory(*it) )
135 std::cout << "[" << *it << "] is a directory" << std::endl;
137 //BrukerDataSet br_acqp;
140 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
143 br_acqp.LoadFile(strAcqp);
146 std::string acqp_scan_name;
147 std::string acqp_method;
148 std::string acqp_protocol_location;
150 BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
151 acqp_protocol_location = b_protocol_location.GetStringValue()[0];
152 cleanString(acqp_protocol_location);
154 BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
155 acqp_scan_name = b_scan_name.GetStringValue()[0];
156 cleanString(acqp_scan_name);
158 BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
159 acqp_method = b_method.GetStringValue()[0];
160 cleanString(acqp_method);
162 BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
163 //b_list_size.PrintSelf(); //JP
165 nbSlices = b_list_size.GetIntValue()[0];
167 strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
168 /* + "." + acqp_protocol_location */ // always the same (in each acquisition)
169 + "." + acqp_scan_name
170 + "." + acqp_method.c_str();
172 sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
173 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
174 strSerieDescr.c_str() );
176 std::cout << " ================================================================================\n"
177 << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
178 << " ================================================================================"
183 printf ("outputDirName [%s]\n", outputDirName);
185 DealWithNiveau1(*it, outputDirName);
187 catch (BrukerHopelessException &e)
189 std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
193 } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
197 // =====================================================================
199 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
201 // e.g. : at level 1, in B67d1.Bp1/6
203 // acqp fid imnd pdata pulseprogram spnam0 spnam1
205 bool res = CreateDirectory(currentOutputDirName);
208 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
209 throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
212 GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
213 GDCM_NAME_SPACE::DirListType fileNames;
214 fileNames = dirList.GetFilenames();
215 // -----------------------------------------------------
216 // Iterate to ALL the objets(files/directories) found in the input directory
217 // -----------------------------------------------------
218 GDCM_NAME_SPACE::DirListType::iterator it;
220 for (it = fileNames.begin();
221 it != fileNames.end();
224 if ( boost::filesystem::is_regular(*it) )
225 //if ( ! boost::filesystem::is_directory(*it) )
228 std::cout << "--- [" << *it << "] is a file." << std::endl;
232 char outputDirName[(unsigned int) PATH_MAX+2];
233 //std::string firstName;
235 for (it = fileNames.begin();
236 it != fileNames.end();
239 if ( boost::filesystem::is_directory(*it) )
241 // will be always "pdata" ...
243 std::cout << "--- [" << *it << "] is a directory" << std::endl;
246 if (FileLine.startsWith("##$ACQ_size=")) {
247 if (FileLine.startsWith("##$NI=")) {
248 if (FileLine.startsWith("##$NR=")) {
249 if (FileLine.startsWith("##$ACQ_obj_order=")) {
250 if (FileLine.startsWith("##$ACQ_word_size=")) {
251 if (FileLine.startsWith("##$BYTORDA=")) {
252 if (FileLine.startsWith("##$PULPROG=")) {
255 sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
256 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
257 GDCM_NAME_SPACE::Util::GetName(*it).c_str());
260 std::string strMethod;
261 //std::string firstName = *(fileNames.begin());
263 strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
264 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
266 // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
267 canOpen = br_method.LoadFile(strMethod);
270 strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
271 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
273 //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
274 canOpen = br_method.LoadFile(strMethod);
277 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
278 << level1Directory << "]; we skip it!" << std::endl;
280 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
281 //exit(0); /// \TODO throw an exception !
285 std::cout << "open => [" << strMethod << "] successfully" << std::endl;
289 ##$PVM_Fov (dimension)
292 dans method (pour perfusion seulement?) :
293 ##$PVM_ObjOrderList=( 8 )
296 ##$PVM_SPackArrNSlices=( 2 )
300 DealWithNiveau2(*it,outputDirName );
302 catch (BrukerHopelessException &e)
304 std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
311 // =====================================================================
313 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
315 // e.g. : at level 2 in B67d1.Bp1/6/pdata
317 // acqp fid imnd pdata pulseprogram spnam0 spnam1
320 bool res = CreateDirectory(currentOutputDirName);
323 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
324 throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
328 GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
330 GDCM_NAME_SPACE::DirListType fileNames;
331 fileNames = dirList.GetFilenames();
333 char outputDirName[(unsigned int) PATH_MAX+2];
335 // -----------------------------------------------------
336 // Iterate to ALL the objets(files/directories) found in the input directory
337 // -----------------------------------------------------
338 GDCM_NAME_SPACE::DirListType::iterator it;
342 for (it = fileNames.begin();
343 it != fileNames.end();
346 if ( ! boost::filesystem::is_directory(*it) )
348 std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
353 for (it = fileNames.begin();
354 it != fileNames.end();
357 if ( boost::filesystem::is_directory(*it) )
361 std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
363 // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
364 // GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
365 // GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
369 // (interest of previous method :
370 // If unaware user changed the pdata name, it goes on working
374 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
377 std::string str_isa_func_name;
378 canOpen = br_isa.LoadFile(str_isa);
381 sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
382 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
383 GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
388 BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
390 str_isa_func_name = b_isa_func_name.GetStringValue()[0];
391 cleanString(str_isa_func_name);
393 sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
394 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
395 GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
396 str_isa_func_name.c_str());
399 DealWithNiveau3(*it, outputDirName);
401 catch (BrukerHopelessException &e)
403 std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
404 << " We skip [" << level2Directory << "]" << std::endl;
407 catch (BrukerInitException &e)
409 std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
410 << " We skip [" << level2Directory << "]" << std::endl;
419 // =====================================================================
422 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
425 // e.g. at level 3, in
427 // just to be able to go on checking // JP
428 if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
431 bool res = CreateDirectory(currentOutputDirName);
435 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
436 throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
440 GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
441 GDCM_NAME_SPACE::DirListType::iterator it;
442 GDCM_NAME_SPACE::DirListType fileNames;
443 fileNames = dirList.GetFilenames();
445 char original2dseqName [(unsigned int) PATH_MAX+2];
446 char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
448 char outputMhdFileName [(unsigned int) PATH_MAX+2];
449 char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
450 char output2dseqName [(unsigned int) PATH_MAX+6];
451 char output2dseqCartoName [(unsigned int) PATH_MAX+6];
453 char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
456 //-------------- try d3proc;
457 char char_d3proc[(unsigned int) PATH_MAX+2];
459 sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
462 std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
463 std::string str_d3proc(char_d3proc);
464 canOpen = br_d3proc.LoadFile(str_d3proc);
468 std::cout << "Hopeless! no 'd3proc' found" << std::endl;
469 throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
470 //exit(0); /// \TODO throw an exception !
473 canOpen = br_d3proc.FillMap();
476 std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
477 throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
478 //exit(0); /// \TODO throw an exception !
481 //-------------- end try d3proc;
484 // -------------------try reco
486 char char_reco[(unsigned int) PATH_MAX+2];
488 sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
489 //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
490 // GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
493 std::cout << "reco --- => [" << char_reco << "]" << std::endl;
494 std::string str_reco(char_reco);
495 canOpen = br_reco.LoadFile(str_reco);
497 if (!canOpen) // we try in directory ../1
500 std::cout << "[" << str_reco << "] not found " << std::endl;
501 std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
502 //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
503 sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
505 canOpen = br_reco.LoadFile(str_reco);
508 std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
509 throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
510 //exit(0); /// \TODO throw an exception !
514 canOpen = br_reco.FillMap();
517 std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
518 throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
519 //exit(0); /// \TODO throw an exception !
521 //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
522 // br_reco.PrintSelf();
523 // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
525 // -------------------end try reco
528 BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
529 int NX = bX.GetIntValue()[0];
532 std::cout << "IM_SIX " << NX << std::endl;
533 BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
534 int NY = bY.GetIntValue()[0];
537 std::cout << "IM_SIY " << NY << std::endl;
538 /// \todo : check if there are actually 3 dimensions or only 2
540 BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
541 int nbFrames = bZ.GetIntValue()[0];
543 std::cout << "IM_SIZ " << nbFrames << std::endl;
545 // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
547 BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
549 std::string mhdDataPixelType;
551 getImhDataType(bDPT, mhdDataPixelType, pixelSize);
553 BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
554 double fovX = fov.GetDoubleValue()[0];
555 double fovY = fov.GetDoubleValue()[1];
557 std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
559 /// \TODO probabely a more sophisticated accessor will be necessary :
560 /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
561 BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
562 double sliceDistance = bsliceDistance.GetDoubleValue()[0];
566 sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
567 GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
568 res = CreateDirectory( currentOutputMhdDirName );
570 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
571 throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
576 std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl;
580 std::cout << "nbFrames " << nbFrames << std::endl;
582 std::cout << "nbSlices " << nbSlices << std::endl;
584 int nbInstants = nbFrames/nbSlices;
586 std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
589 FILE *fp; // for MHD files
591 sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
594 // \TODO : tenir compte du bazar precedent
596 // load 2dseq in memory
598 fp = fopen(original2dseqName, "rb");
601 std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
602 throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
606 unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
607 ///\ TODO : find a safer way to be sure to read everything!
608 size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
610 // This one will be important!
611 // ---------------------------
613 imageSet = CreateImageSet ( );
615 catch (BrukerInitException& e)
618 std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
619 << "catched in DealWithNiveau3" << std::endl;
625 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
626 if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
629 std::cout << "Single instant : do not split" << std::endl;
632 sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
633 GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
634 fp=fopen(outputMhdFileName, "w");
637 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
638 throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
643 fprintf(fp, "ObjectType = Image\n");
644 fprintf(fp, "NDims = 3\n" );
645 fprintf(fp, "BinaryData = True \n" );
646 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
647 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
648 fprintf(fp, "HeaderSize = %d\n", 0);
649 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
650 fprintf(fp, "Position = 0 0 %d\n", 0 );
651 fprintf(fp, "Offset = 0 0 0\n" );
652 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
653 fprintf(fp, "ElementNumberOfChannels = 1\n" );
654 fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
655 fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
658 sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
659 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
660 fp=fopen(output2dseqSliceFileName, "wb");
663 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
664 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
668 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
672 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
676 sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
677 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
679 /* ----------- Write Dicom Image ---------------*/
680 MakeDicomImage(buffer_2dseq,
685 fovX/NY, fovY/NY, sliceDistance,
686 output2dseqSliceFileName,
694 0,// index frame number
695 GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
698 } // end if nbInstants = 1
700 else // more than ONE instant
703 // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
705 unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
708 for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
712 sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
713 GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k );
715 std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
716 fp=fopen(outputMhdFileName, "w");
719 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
720 throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
725 /* ----------- Write MHD Image ---------------*/
727 // std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
728 fprintf(fp, "ObjectType = Image\n");
729 fprintf(fp, "NDims = 3\n" );
730 fprintf(fp, "BinaryData = True \n" );
731 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
732 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
733 fprintf(fp, "HeaderSize = %d\n", 0);
734 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
735 fprintf(fp, "Position = 0 0 %d\n", sliceNb );
736 fprintf(fp, "Offset = 0 0 0\n" );
737 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
738 fprintf(fp, "ElementNumberOfChannels = 1\n" );
739 fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
740 fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
744 sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
745 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
746 fp=fopen(output2dseqSliceFileName, "wb");
749 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
750 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
753 int frameSize = NX*NY*pixelSize;
754 for (instantNb=0; instantNb<nbInstants; instantNb++)
756 // std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
757 fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
762 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
769 sprintf(output2dseqSliceFileName, "%sdummy_buffer",
770 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
771 fp=fopen(output2dseqSliceFileName, "wb");
774 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
777 int frameSize = NX*NY*pixelSize;
778 for (instantNb=0; instantNb<nbInstants; instantNb++)
780 // std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
781 fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
787 fp=fopen(output2dseqSliceFileName, "rb");
790 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
793 fread( pixelsForCurrentSlice,
794 frameSize*nbInstants,
797 // end of desperate try !
800 /* ----------- Write Dicom Image ---------------*/
802 int frameSize = NX*NY*pixelSize;
803 for (instantNb=0; instantNb<nbInstants; instantNb++)
805 memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
808 int indOfFirsImageWithinImageSet = nbSlices*instantNb;
809 sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
810 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
813 pixelsForCurrentSlice,
818 fovX/NY, fovY/NY, sliceDistance,
819 output2dseqSliceFileName,
828 GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
831 std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
837 delete [] pixelsForCurrentSlice;
838 } // end nbInstants == 1
839 delete [] buffer_2dseq;
843 // -----------------------------------------------------
844 // deal with MatLab-generated Carto file.
845 // -----------------------------------------------------
847 dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance,
848 copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
852 // ===========================================================================================
854 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
855 double fovX, double fovY, double sliceDistance,
856 char *copyFile, std::string ¤tOutputDirName,
857 char *outputMhdFileName, char *output2dseqCartoName)
859 // -----------------------------------------------------
860 // deal with MatLab-generated Carto file.
861 // -----------------------------------------------------
863 char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
865 GDCM_NAME_SPACE::DirListType::iterator it;
866 char file_name_ident[500];
869 // Iterate to ALL the objets(files/directories) found in the input directory
870 for (it = fileNames.begin();
871 it != fileNames.end();
874 if ( boost::filesystem::is_regular(*it) )
875 //if ( ! boost::filesystem::is_directory(*it) )
878 std::cout << "--- [" << *it << "] is a file..." << std::endl;
882 while (code[icode][0] != 0)
884 sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g "2dseq_ADC"
885 std::string::size_type loc = (*it).rfind(file_name_ident);
887 if ( loc != std::string::npos )
890 ///\ TODO : find a safer way to be sure to read everything!
891 unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
892 fp = fopen ( (*it).c_str(), "rb");
894 std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
895 throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
897 fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
899 std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
900 << NX*NY*sizeof(double)*nbSlices << std::endl;
901 std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
904 // Copy the data file in the new directory
905 sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
906 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
908 sprintf(outputMhdFileName, "%s%c%s%s",
909 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
911 std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
914 fp=fopen(outputMhdFileName, "w");
917 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
921 fprintf(fp, "ObjectType = Image\n");
922 fprintf(fp, "NDims = 3\n" );
923 fprintf(fp, "BinaryData = True \n" );
924 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
925 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
926 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
927 fprintf(fp, "HeaderSize = %d\n", 0 );
928 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
929 fprintf(fp, "Position = 0 0 0\n" );
930 fprintf(fp, "Offset = 0 0 0\n" );
931 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
932 fprintf(fp, "ElementNumberOfChannels = 1\n" );
933 fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
934 fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
939 std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
942 // ----------- Write Dicom Image ---------------
946 sprintf(output2dseqCartoName, "%s%c%s%s",
947 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
949 std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
951 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
952 std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
953 MakeDicomImage(buffer_carto,
958 fovX/NY, fovY/NY, sliceDistance,
959 output2dseqCartoName,
968 GDCM_NAME_SPACE::CREATED_IMAGE
972 delete [] buffer_carto;
974 std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
975 break; // don't check for more ident on same file name!
981 } // end iterate on files
985 // ==========================================================================================================
987 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
989 std::string systemCommand;
992 std::cout << "Check for output directory :[" << OutputDirName << "]."
994 if ( ! boost::filesystem::is_directory(OutputDirName) ) // dirout not found
996 std::string strDirNameout(OutputDirName); // to please gcc 4
997 systemCommand = "mkdir " + strDirNameout; // create it!
999 std::cout << systemCommand << std::endl;
1000 system (systemCommand.c_str());
1001 if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1004 std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1006 throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1011 std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1017 std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1025 // ===========================================================================================
1027 /// \TODO move cleanString to 'crea' ?
1029 void Bruker2Dicom::cleanString(std::string &s)
1032 if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1037 if (s[l-1] == ' ' ) // blank space
1045 std::string repChar("_");
1046 GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1051 // ===========================================================================================
1054 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1056 if(bDPT.GetDataType() == "string")
1058 std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1060 std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1061 //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1063 if (brukerDataPixelType == "ip_short") {
1064 mhdDataPixelType = "MET_USHORT";
1067 if (brukerDataPixelType == "ip_int") {
1068 mhdDataPixelType = "MET_UINT";
1071 if (brukerDataPixelType == "ip_char") {
1072 mhdDataPixelType = "MET_UCHAR";
1075 /// \TODO : finish the list
1077 case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1079 case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1081 case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1083 case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1085 case 4 : fp << "ElementType = MET_INT" << std::endl;
1087 case 5 : fp << "ElementType = MET_UINT" << std::endl;
1089 case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1091 case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1096 int brukerDataPixelType = bDPT.GetIntValue()[0];
1098 std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1099 //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1101 // Cross your fingers !!!
1103 // pb : found values : 2, 3, 5
1105 if (brukerDataPixelType == 2) {
1106 mhdDataPixelType = "MET_USHORT";
1109 if (brukerDataPixelType == 3) {
1110 mhdDataPixelType = "MET_USHORT";
1113 if (brukerDataPixelType == 1) {
1114 mhdDataPixelType = "MET_UCHAR";
1120 // ===========================================================================================
1122 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1124 std::vector<BrukerImage> imageSet;
1125 br_acqp.SetLoopStructure();
1126 std::vector<int> tempVect = br_acqp.GetLoopStructure() ;
1127 std::map<std::string, BrukerFieldData> map = br_acqp.GetBrukerHeaderMap();
1129 bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1131 if (result == false)
1133 throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1136 br_acqp.SetImageLoopStructure();
1137 br_acqp.SetBrukerImageList();
1138 std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1140 BrukerImage image(br_acqp,br_reco);
1141 image.Init(br_acqp,br_reco,1);
1143 for(int i=0;i<brukerImageList.size();i++)
1145 image.Init(br_acqp,br_reco,i);
1146 imageSet.push_back(image);
1149 // Just for checking
1152 std::vector<std::vector <double> > imageOrientation;
1153 std::vector <double> imagePosition;
1154 for(int i=0;i<brukerImageList.size();i++)
1156 // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1158 imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1159 std::cout << "Position " << imagePosition[0] << " "
1160 << imagePosition[1] << " " << imagePosition[2] ;
1161 imageOrientation = imageSet[i].getRotationMatrixRPS2XYZ();
1162 std::cout << "\t Orientation " ;
1163 for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1164 std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1166 //std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
1167 std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
1169 std::cout << "\t [";
1170 for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1171 std::cout << " " << imageSet[i].getLoopStamp()[i3];
1172 std::cout << "]" << std::endl;
1178 // ===========================================================================================
1180 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1185 double spacingX, double spacingY, double sliceDistance,
1186 std::string dcmImageName,
1187 const std::string &patientName,
1189 std::string &studyUID,
1190 std::string &serieUID,
1191 std::string &studyDescr,
1192 std::string &serieDescr,
1193 std::string &strStudyTimeDate,
1195 GDCM_NAME_SPACE::ImageContentType contentType
1198 std::ostringstream str;
1200 GDCM_NAME_SPACE::File *file;
1201 file = GDCM_NAME_SPACE::File::New();
1203 // Set the image size
1206 file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1209 file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1215 file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1218 // Set the pixel type
1219 // //8, 16, 32, 64 (for double ?)
1222 file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1224 file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1227 str << pixelSize*8-1;
1228 file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1230 // Set the pixel representation // 0/1 , 0=unsigned
1231 file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1233 // Set the samples per pixel // 1:Grey level, 3:RGB
1234 file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1236 // 0028 0030 DS 2 Pixel Spacing
1238 str << spacingX << "\\" << spacingY;
1239 file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1241 // 0018 0050 DS 1 Slice Thickness
1243 str << sliceDistance;
1244 file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1246 // 0020 0011 IS 1 Series Number
1249 file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1251 // 0020|0013 [IS] [Instance Number]
1254 str << instanceNumber;
1255 file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1258 // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1259 // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
1260 // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
1263 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1265 // 1.2.840.10008.5.1.4.1.1.4 MR Image Storage
1266 file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
1267 file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
1269 // if (strlen(patientName) != 0)
1270 file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1272 file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1273 file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1275 // 0008 0020 DA 1 Study Date
1276 // 0008 0030 TM 1 Study Time
1278 /// \TODO split into 2 strings!
1279 file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1280 file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(), 0x0008,0x0030, "TM");
1282 file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO"); // Study Description
1283 file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO"); // Series Description
1285 //0008|0060 [CS] [Modality]
1286 file->InsertEntryString("MR",0x0008,0x0060, "CS");
1288 // 0020 0037 DS 6 Image Orientation (Patient)
1289 char charImageOrientation[256];
1292 std::cout << "charImageOrientation " <<
1293 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1294 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1295 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1296 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1297 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1298 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1300 sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1301 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1302 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1303 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1304 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1305 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1306 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1308 file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1311 // 0020 0032 DS 3 Image Position (Patient)
1313 char charImagePosition[256];
1314 sprintf(charImagePosition,"%f\\%f\\%f",
1315 imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1316 imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1317 imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1319 file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
1323 // 0020 0x1041 DS 1 Slice Location
1324 // sprintf(charImagePosition,"%f",float(imgNum));
1325 // file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1327 // Set Rescale Intercept
1330 file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1332 // Set Rescale Slope
1335 file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1338 GDCM_NAME_SPACE::FileHelper *fileH;
1339 fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1340 fileH->SetContentType(contentType);
1342 // cast is just to avoid warnings (*no* conversion is performed)
1343 //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1345 //std::cout << "-------------------------------- X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1347 fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1348 fileH->SetWriteModeToRaw();
1349 fileH->SetWriteTypeToDcmExplVR();
1350 if( !fileH->Write(dcmImageName)) {
1351 std::cout << "Failed for [" << dcmImageName << "]\n"
1352 << " File is unwrittable" << std::endl;
1355 throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));