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();
119 // -----------------------------------------------------
120 // Iterate to ALL the objets(files/directories) found in the input directory
121 // (this is level ZERO)
122 // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
123 // -----------------------------------------------------
125 GDCM_NAME_SPACE::DirListType::iterator it;
127 for (it = fileNames.begin();
128 it != fileNames.end();
131 if ( boost::filesystem::is_directory(*it) )
134 std::cout << "[" << *it << "] is a directory" << std::endl;
136 //BrukerDataSet br_acqp;
139 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
142 br_acqp.LoadFile(strAcqp);
145 std::string acqp_scan_name;
146 std::string acqp_method;
147 std::string acqp_protocol_location;
149 BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
150 acqp_protocol_location = b_protocol_location.GetStringValue()[0];
151 cleanString(acqp_protocol_location);
153 BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
154 acqp_scan_name = b_scan_name.GetStringValue()[0];
155 cleanString(acqp_scan_name);
157 BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
158 acqp_method = b_method.GetStringValue()[0];
159 cleanString(acqp_method);
161 BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
162 //b_list_size.PrintSelf(); //JP
164 nbSlices = b_list_size.GetIntValue()[0];
166 strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
167 /* + "." + acqp_protocol_location */ // always the same (in each acquisition)
168 + "." + acqp_scan_name
169 + "." + acqp_method.c_str();
171 sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
172 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
173 strSerieDescr.c_str() );
175 std::cout << " ================================================================================\n"
176 << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
177 << " ================================================================================"
182 printf ("outputDirName [%s]\n", outputDirName);
184 DealWithNiveau1(*it, outputDirName);
186 } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
190 // =====================================================================
192 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
194 // e.g. : at level 1, in B67d1.Bp1/6
196 // acqp fid imnd pdata pulseprogram spnam0 spnam1
198 bool res = CreateDirectory(currentOutputDirName);
201 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
202 throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
205 GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
206 GDCM_NAME_SPACE::DirListType fileNames;
207 fileNames = dirList.GetFilenames();
208 // -----------------------------------------------------
209 // Iterate to ALL the objets(files/directories) found in the input directory
210 // -----------------------------------------------------
211 GDCM_NAME_SPACE::DirListType::iterator it;
213 for (it = fileNames.begin();
214 it != fileNames.end();
217 if ( boost::filesystem::is_regular(*it) )
218 //if ( ! boost::filesystem::is_directory(*it) )
221 std::cout << "--- [" << *it << "] is a file." << std::endl;
225 char outputDirName[(unsigned int) PATH_MAX+2];
226 //std::string firstName;
228 for (it = fileNames.begin();
229 it != fileNames.end();
232 if ( boost::filesystem::is_directory(*it) )
234 // will be always "pdata" ...
236 std::cout << "--- [" << *it << "] is a directory" << std::endl;
239 if (FileLine.startsWith("##$ACQ_size=")) {
240 if (FileLine.startsWith("##$NI=")) {
241 if (FileLine.startsWith("##$NR=")) {
242 if (FileLine.startsWith("##$ACQ_obj_order=")) {
243 if (FileLine.startsWith("##$ACQ_word_size=")) {
244 if (FileLine.startsWith("##$BYTORDA=")) {
245 if (FileLine.startsWith("##$PULPROG=")) {
248 sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
249 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
250 GDCM_NAME_SPACE::Util::GetName(*it).c_str());
253 std::string strMethod;
254 //std::string firstName = *(fileNames.begin());
256 strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
257 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
259 // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
260 canOpen = br_method.LoadFile(strMethod);
263 strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
264 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
266 //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
267 canOpen = br_method.LoadFile(strMethod);
270 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
271 throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
272 //exit(0); /// \TODO throw an exception !
276 std::cout << "open => [" << strMethod << "] successfully" << std::endl;
280 ##$PVM_Fov (dimension)
283 dans method (pour perfusion seulement?) :
284 ##$PVM_ObjOrderList=( 8 )
287 ##$PVM_SPackArrNSlices=( 2 )
290 DealWithNiveau2(*it,outputDirName );
295 // =====================================================================
297 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
299 // e.g. : at level 2 in B67d1.Bp1/6/pdata
301 // acqp fid imnd pdata pulseprogram spnam0 spnam1
304 bool res = CreateDirectory(currentOutputDirName);
307 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
308 throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
312 GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
314 GDCM_NAME_SPACE::DirListType fileNames;
315 fileNames = dirList.GetFilenames();
317 char outputDirName[(unsigned int) PATH_MAX+2];
319 // -----------------------------------------------------
320 // Iterate to ALL the objets(files/directories) found in the input directory
321 // -----------------------------------------------------
322 GDCM_NAME_SPACE::DirListType::iterator it;
326 for (it = fileNames.begin();
327 it != fileNames.end();
330 if ( ! boost::filesystem::is_directory(*it) )
332 std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
337 for (it = fileNames.begin();
338 it != fileNames.end();
341 if ( boost::filesystem::is_directory(*it) )
345 std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
347 // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
348 // GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
349 // GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
353 // (interest of previous method :
354 // If unaware user changed the pdata name, it goes on working
358 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
361 std::string str_isa_func_name;
362 canOpen = br_isa.LoadFile(str_isa);
365 sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
366 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
367 GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
372 BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
374 str_isa_func_name = b_isa_func_name.GetStringValue()[0];
375 cleanString(str_isa_func_name);
377 sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
378 GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
379 GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
380 str_isa_func_name.c_str());
382 DealWithNiveau3(*it, outputDirName);
389 // =====================================================================
392 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
395 // e.g. at level 3, in
397 // just to be able to go on checking // JP
398 if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
401 bool res = CreateDirectory(currentOutputDirName);
405 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
406 throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
410 GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
411 GDCM_NAME_SPACE::DirListType::iterator it;
412 GDCM_NAME_SPACE::DirListType fileNames;
413 fileNames = dirList.GetFilenames();
415 char original2dseqName [(unsigned int) PATH_MAX+2];
416 char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
418 char outputMhdFileName [(unsigned int) PATH_MAX+2];
419 char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
420 char output2dseqName [(unsigned int) PATH_MAX+6];
421 char output2dseqCartoName [(unsigned int) PATH_MAX+6];
423 char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
426 //-------------- try d3proc;
427 char char_d3proc[(unsigned int) PATH_MAX+2];
429 sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
432 std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
433 std::string str_d3proc(char_d3proc);
434 canOpen = br_d3proc.LoadFile(str_d3proc);
438 std::cout << "Hopeless! no 'd3proc' found" << std::endl;
439 throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
440 //exit(0); /// \TODO throw an exception !
443 canOpen = br_d3proc.FillMap();
446 std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
447 throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
448 //exit(0); /// \TODO throw an exception !
451 //-------------- end try d3proc;
454 // -------------------try reco
456 char char_reco[(unsigned int) PATH_MAX+2];
458 sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
459 //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
460 // GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
463 std::cout << "reco --- => [" << char_reco << "]" << std::endl;
464 std::string str_reco(char_reco);
465 canOpen = br_reco.LoadFile(str_reco);
467 if (!canOpen) // we try in directory ../1
470 std::cout << "[" << str_reco << "] not found " << std::endl;
471 std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
472 //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
473 sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
475 canOpen = br_reco.LoadFile(str_reco);
478 std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
479 throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
480 //exit(0); /// \TODO throw an exception !
484 canOpen = br_reco.FillMap();
487 std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
488 throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
489 //exit(0); /// \TODO throw an exception !
491 //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
492 // br_reco.PrintSelf();
493 // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
495 // -------------------end try reco
498 BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
499 int NX = bX.GetIntValue()[0];
502 std::cout << "IM_SIX " << NX << std::endl;
503 BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
504 int NY = bY.GetIntValue()[0];
507 std::cout << "IM_SIY " << NY << std::endl;
508 /// \todo : check if there are actually 3 dimensions or only 2
510 BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
511 int nbFrames = bZ.GetIntValue()[0];
513 std::cout << "IM_SIZ " << nbFrames << std::endl;
515 // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
517 BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
519 std::string mhdDataPixelType;
521 getImhDataType(bDPT, mhdDataPixelType, pixelSize);
523 BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
524 double fovX = fov.GetDoubleValue()[0];
525 double fovY = fov.GetDoubleValue()[1];
527 std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
529 /// \TODO probabely a more sophisticated accessor will be necessary :
530 /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
531 BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
532 double sliceDistance = bsliceDistance.GetDoubleValue()[0];
536 sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
537 GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
538 res = CreateDirectory( currentOutputMhdDirName );
540 std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
541 throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
546 std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl;
550 std::cout << "nbFrames " << nbFrames << std::endl;
552 std::cout << "nbSlices " << nbSlices << std::endl;
554 int nbInstants = nbFrames/nbSlices;
556 std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
559 FILE *fp; // for MHD files
561 sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
564 // \TODO : tenir compte du bazar precedent
566 // load 2dseq in memory
568 fp = fopen(original2dseqName, "rb");
571 std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
572 throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
576 unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
577 ///\ TODO : find a safer way to be sure to read everything!
578 size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
580 // This one will be important!
581 // ---------------------------
583 imageSet = CreateImageSet ( );
585 catch (BrukerInitException& e)
587 std::cout << "Exception " << e.what() << std::endl;
592 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
593 if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
596 std::cout << "Single instant : do not split" << std::endl;
599 sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
600 GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
601 fp=fopen(outputMhdFileName, "w");
604 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
605 throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
610 fprintf(fp, "ObjectType = Image\n");
611 fprintf(fp, "NDims = 3\n" );
612 fprintf(fp, "BinaryData = True \n" );
613 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
614 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
615 fprintf(fp, "HeaderSize = %d\n", 0);
616 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
617 fprintf(fp, "Position = 0 0 %d\n", 0 );
618 fprintf(fp, "Offset = 0 0 0\n" );
619 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
620 fprintf(fp, "ElementNumberOfChannels = 1\n" );
621 fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
622 fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
625 sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
626 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
627 fp=fopen(output2dseqSliceFileName, "wb");
630 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
631 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
635 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
639 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
643 sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
644 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
646 /* ----------- Write Dicom Image ---------------*/
647 MakeDicomImage(buffer_2dseq,
652 fovX/NY, fovY/NY, sliceDistance,
653 output2dseqSliceFileName,
661 0,// index frame number
662 GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
665 } // end if nbInstants = 1
667 else // more than ONE instant
670 // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
672 unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
675 for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
679 sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
680 GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k );
682 std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
683 fp=fopen(outputMhdFileName, "w");
686 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
687 throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
692 /* ----------- Write MHD Image ---------------*/
694 // std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
695 fprintf(fp, "ObjectType = Image\n");
696 fprintf(fp, "NDims = 3\n" );
697 fprintf(fp, "BinaryData = True \n" );
698 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
699 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
700 fprintf(fp, "HeaderSize = %d\n", 0);
701 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
702 fprintf(fp, "Position = 0 0 %d\n", sliceNb );
703 fprintf(fp, "Offset = 0 0 0\n" );
704 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
705 fprintf(fp, "ElementNumberOfChannels = 1\n" );
706 fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
707 fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
711 sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
712 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
713 fp=fopen(output2dseqSliceFileName, "wb");
716 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
717 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
720 int frameSize = NX*NY*pixelSize;
721 for (instantNb=0; instantNb<nbInstants; instantNb++)
723 // std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
724 fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
729 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
736 sprintf(output2dseqSliceFileName, "%sdummy_buffer",
737 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
738 fp=fopen(output2dseqSliceFileName, "wb");
741 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
744 int frameSize = NX*NY*pixelSize;
745 for (instantNb=0; instantNb<nbInstants; instantNb++)
747 // std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
748 fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
754 fp=fopen(output2dseqSliceFileName, "rb");
757 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
760 fread( pixelsForCurrentSlice,
761 frameSize*nbInstants,
764 // end of desperate try !
767 /* ----------- Write Dicom Image ---------------*/
769 int frameSize = NX*NY*pixelSize;
770 for (instantNb=0; instantNb<nbInstants; instantNb++)
772 memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
775 int indOfFirsImageWithinImageSet = nbSlices*instantNb;
776 sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
777 currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
780 pixelsForCurrentSlice,
785 fovX/NY, fovY/NY, sliceDistance,
786 output2dseqSliceFileName,
795 GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
798 std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
804 delete [] pixelsForCurrentSlice;
805 } // end nbInstants == 1
806 delete [] buffer_2dseq;
810 // -----------------------------------------------------
811 // deal with MatLab-generated Carto file.
812 // -----------------------------------------------------
814 dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance,
815 copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
819 // ===========================================================================================
821 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
822 double fovX, double fovY, double sliceDistance,
823 char *copyFile, std::string ¤tOutputDirName,
824 char *outputMhdFileName, char *output2dseqCartoName)
826 // -----------------------------------------------------
827 // deal with MatLab-generated Carto file.
828 // -----------------------------------------------------
830 char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""}; // add more carto file name identifiers if necessary; end with ""
832 GDCM_NAME_SPACE::DirListType::iterator it;
833 char file_name_ident[500];
836 // Iterate to ALL the objets(files/directories) found in the input directory
837 for (it = fileNames.begin();
838 it != fileNames.end();
841 if ( boost::filesystem::is_regular(*it) )
842 //if ( ! boost::filesystem::is_directory(*it) )
845 std::cout << "--- [" << *it << "] is a file..." << std::endl;
849 while (code[icode][0] != 0)
851 sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g "2dseq_ADC"
852 std::string::size_type loc = (*it).rfind(file_name_ident);
854 if ( loc != std::string::npos )
857 ///\ TODO : find a safer way to be sure to read everything!
858 unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
859 fp = fopen ( (*it).c_str(), "rb");
861 std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
864 fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
866 std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
867 << NX*NY*sizeof(double)*nbSlices << std::endl;
868 std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
871 // Copy the data file in the new directory
872 sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
873 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
875 sprintf(outputMhdFileName, "%s%c%s%s",
876 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
878 std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
881 fp=fopen(outputMhdFileName, "w");
884 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
888 fprintf(fp, "ObjectType = Image\n");
889 fprintf(fp, "NDims = 3\n" );
890 fprintf(fp, "BinaryData = True \n" );
891 fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
892 fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
893 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
894 fprintf(fp, "HeaderSize = %d\n", 0 );
895 fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
896 fprintf(fp, "Position = 0 0 0\n" );
897 fprintf(fp, "Offset = 0 0 0\n" );
898 fprintf(fp, "CenterOfRotation = 0 0 0\n" );
899 fprintf(fp, "ElementNumberOfChannels = 1\n" );
900 fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
901 fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
906 std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
909 // ----------- Write Dicom Image ---------------
913 sprintf(output2dseqCartoName, "%s%c%s%s",
914 currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
916 std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
918 strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
919 std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
920 MakeDicomImage(buffer_carto,
925 fovX/NY, fovY/NY, sliceDistance,
926 output2dseqCartoName,
935 GDCM_NAME_SPACE::CREATED_IMAGE
939 delete [] buffer_carto;
941 std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
942 break; // don't check for more ident on same file name!
948 } // end iterate on files
952 // ==========================================================================================================
954 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
956 std::string systemCommand;
959 std::cout << "Check for output directory :[" << OutputDirName << "]."
961 if ( ! boost::filesystem::is_directory(OutputDirName) ) // dirout not found
963 std::string strDirNameout(OutputDirName); // to please gcc 4
964 systemCommand = "mkdir " + strDirNameout; // create it!
966 std::cout << systemCommand << std::endl;
967 system (systemCommand.c_str());
968 if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
971 std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
973 /// \todo : THROW AN EXCEPTION
978 std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
984 std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
992 // ===========================================================================================
994 /// \TODO move cleanString to 'crea' ?
996 void Bruker2Dicom::cleanString(std::string &s)
999 if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1004 if (s[l-1] == ' ' ) // blank space
1012 std::string repChar("_");
1013 GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1018 // ===========================================================================================
1021 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1023 if(bDPT.GetDataType() == "string")
1025 std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1027 std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1028 //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1030 if (brukerDataPixelType == "ip_short") {
1031 mhdDataPixelType = "MET_USHORT";
1034 if (brukerDataPixelType == "ip_int") {
1035 mhdDataPixelType = "MET_UINT";
1038 if (brukerDataPixelType == "ip_char") {
1039 mhdDataPixelType = "MET_UCHAR";
1042 /// \TODO : finish the list
1044 case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1046 case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1048 case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1050 case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1052 case 4 : fp << "ElementType = MET_INT" << std::endl;
1054 case 5 : fp << "ElementType = MET_UINT" << std::endl;
1056 case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1058 case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1063 int brukerDataPixelType = bDPT.GetIntValue()[0];
1065 std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1066 //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1068 // Cross your fingers !!!
1070 // pb : found values : 2, 3, 5
1072 if (brukerDataPixelType == 2) {
1073 mhdDataPixelType = "MET_USHORT";
1076 if (brukerDataPixelType == 3) {
1077 mhdDataPixelType = "MET_USHORT";
1080 if (brukerDataPixelType == 1) {
1081 mhdDataPixelType = "MET_UCHAR";
1087 // ===========================================================================================
1089 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1091 std::vector<BrukerImage> imageSet;
1092 br_acqp.SetLoopStructure();
1093 std::vector<int> tempVect = br_acqp.GetLoopStructure() ;
1094 std::map<std::string, BrukerFieldData> map = br_acqp.GetBrukerHeaderMap();
1095 bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1097 if (result == false)
1099 throw ( BrukerInitException ("Bruker2Dicom::CreateImageSet failure ") );
1102 br_acqp.SetImageLoopStructure();
1103 br_acqp.SetBrukerImageList();
1104 std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1106 BrukerImage image(br_acqp,br_reco);
1107 image.Init(br_acqp,br_reco,1);
1109 for(int i=0;i<brukerImageList.size();i++)
1111 image.Init(br_acqp,br_reco,i);
1112 imageSet.push_back(image);
1115 // Just for checking
1118 std::vector<std::vector <double> > imageOrientation;
1119 std::vector <double> imagePosition;
1120 for(int i=0;i<brukerImageList.size();i++)
1122 // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1124 imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1125 std::cout << "Position " << imagePosition[0] << " "
1126 << imagePosition[1] << " " << imagePosition[2] ;
1127 imageOrientation = imageSet[i].getRotationMatrixRPS2XYZ();
1128 std::cout << "\t Orientation " ;
1129 for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1130 std::cout << imageOrientation[i1][i2] << " ";
1132 //std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
1133 std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
1135 std::cout << "\t [";
1136 for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1137 std::cout << " " << imageSet[i].getLoopStamp()[i3];
1138 std::cout << "]" << std::endl;
1144 // ===========================================================================================
1146 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1151 double spacingX, double spacingY, double sliceDistance,
1152 std::string dcmImageName,
1153 const std::string &patientName,
1155 std::string &studyUID,
1156 std::string &serieUID,
1157 std::string &studyDescr,
1158 std::string &serieDescr,
1159 std::string &strStudyTimeDate,
1161 GDCM_NAME_SPACE::ImageContentType contentType
1164 std::ostringstream str;
1166 GDCM_NAME_SPACE::File *file;
1167 file = GDCM_NAME_SPACE::File::New();
1169 // Set the image size
1172 file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1175 file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1181 file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1184 // Set the pixel type
1185 // //8, 16, 32, 64 (for double ?)
1188 file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1190 file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1193 str << pixelSize*8-1;
1194 file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1196 // Set the pixel representation // 0/1 , 0=unsigned
1197 file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1199 // Set the samples per pixel // 1:Grey level, 3:RGB
1200 file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1202 // 0028 0030 DS 2 Pixel Spacing
1204 str << spacingX << "\\" << spacingY;
1205 file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1207 // 0018 0050 DS 1 Slice Thickness
1209 str << sliceDistance;
1210 file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1212 // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1213 // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
1214 // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
1217 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1218 // 1.2.840.10008.5.1.4.1.1.4 MR Image Storage
1219 file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
1220 file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
1222 // if (strlen(patientName) != 0)
1223 file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1225 file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1226 file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1228 // 0008 0020 DA 1 Study Date
1229 // 0008 0030 TM 1 Study Time
1231 /// \TODO split into 2 strings!
1232 file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1233 file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
1235 file->InsertEntryString(studyDescr,0x0008,0x1030, "LO"); // Study Description
1236 file->InsertEntryString(serieDescr,0x0008,0x103e, "LO"); // Series Description
1238 //0008|0060 [CS] [Modality]
1239 file->InsertEntryString("MR",0x0008,0x0060, "CS");
1241 // 0020 0037 DS 6 Image Orientation (Patient)
1242 char charImageOrientation[256];
1245 std::cout << "charImageOrientation " <<
1246 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1247 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1248 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1249 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1250 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1251 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1253 sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1254 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1255 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1256 imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1257 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1258 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1259 imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1261 file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1264 // 0020 0032 DS 3 Image Position (Patient)
1266 char charImagePosition[256];
1267 sprintf(charImagePosition,"%f\\%f\\%f",
1268 imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1269 imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1270 imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1272 file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
1276 // 0020 0x1041 DS 1 Slice Location
1277 // sprintf(charImagePosition,"%f",float(imgNum));
1278 // file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1280 // Set Rescale Intercept
1283 file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1285 // Set Rescale Slope
1288 file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1291 GDCM_NAME_SPACE::FileHelper *fileH;
1292 fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1293 fileH->SetContentType(contentType);
1295 // cast is just to avoid warnings (*no* conversion is performed)
1296 //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1298 //std::cout << "-------------------------------- X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1300 fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1301 fileH->SetWriteModeToRaw();
1302 fileH->SetWriteTypeToDcmExplVR();
1303 if( !fileH->Write(dcmImageName))
1304 std::cout << "Failed for [" << dcmImageName << "]\n"
1305 << " File is unwrittable" << std::endl;