1 /*=========================================================================
4 Module: $RCSfile: ToInTag.cxx,v $
6 Date: $Date: 2007/02/26 08:47:29 $
7 Version: $Revision: 1.10 $
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 =========================================================================*/
18 #include "gdcmDocEntry.h"
19 #include "gdcmDicomDir.h"
20 #include "gdcmDicomDirPatient.h"
22 #include "gdcmFileHelper.h"
23 #include "gdcmDirList.h"
24 #include "gdcmDebug.h"
25 #include "gdcmArgMgr.h"
27 #include "gdcmSerieHelper.h"
33 * - explores recursively the given directory
34 * - keeps the requested series
35 * - orders the gdcm-readable found Files
36 * according to their Patient/Study/Serie/Image characteristics
37 * - fills a single level Directory with *all* the files,
38 * converted into a Brucker-like Dicom, Intags compliant
41 typedef std::map<std::string, gdcm::File*> SortedFiles;
43 int main(int argc, char *argv[])
47 " - explores recursively the given directory, ",
48 " - keeps the requested series/ drops the unrequested series ",
49 " - orders the gdcm-readable found Files according to their ",
50 " (0x0010, 0x0010) Patient's Name ",
51 " (0x0020, 0x000e) Series Instance UID ",
52 " (0x0020, 0x0032) Image Position (Patient) ",
53 " (0x0018, 0x1060) Trigger Time ",
54 " (0x0018, 0x1312) In-plane Phase Encoding Direction ",
55 " - fills a single level (*) Directory with *all* the files, ",
56 " converted into a Brucker-like Dicom, InTags compliant ",
57 " (*) actually : creates as many directories as Patients ",
58 " -that shouldn't appear, but being carefull is better ! -",
60 " - fills a tree-like structure of directories as : ",
64 " Images are (sorted by Trigger Time / ",
65 " Encoding Direction (Row, Column) ",
67 " 0x0021, 0x1020 : 'SLICE INDEX' ",
68 " 0x0021, 0x1040 : 'FRAME INDEX' ",
69 " 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) ",
71 " ToInTag dirin=rootDirectoryName ",
72 " dirout=outputDirectoryName ",
73 " { [keep= list of seriesNumber to process] ",
74 " | [drop= list of seriesNumber to ignore] } ",
76 " [input = {ACR|DCM}] ",
77 " [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ",
78 " [listonly] [split] ",
79 " [noshadowseq][noshadow][noseq] [verbose] [debug] ",
81 " dirout : will be created if doesn't exist ",
82 " keep : if user wants to process a limited number of series ",
83 " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
84 " drop : if user wants to ignore a limited number of series ",
85 " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
86 " SeriesNumber are short enough to be human readable ",
87 " e.g : 1030,1035,1043 ",
88 " taggrid : user knows all the images are 'grid' -ie : not 'col', not 'raw'",
89 " extent : DO NOT forget the leading '.' ! ",
90 " skel: name skeleton eg : patName_1.nema -> skel=patName_ ",
91 " split: creates a tree-like structure of directories as : ",
95 " Images are (sorted by Trigger Time / ",
96 " Encoding Direction (Row, Column) ",
97 " noshadowseq: user doesn't want to load Private Sequences ",
98 " noshadow : user doesn't want to load Private groups (odd number) ",
99 " noseq : user doesn't want to load Sequences ",
100 " verbose : user wants to run the program in 'verbose mode' ",
101 " debug : *developer* wants to run the program in 'debug mode' ",
104 std::cout << "inside ToInTag" << std::endl;
106 // ----- Initialize Arguments Manager ------
108 gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
110 if (argc == 1 || am->ArgMgrDefined("usage"))
112 am->ArgMgrUsage(usage); // Display 'usage'
117 const char *dirNamein;
118 dirNamein = am->ArgMgrGetString("dirin",".");
120 const char *dirNameout;
121 dirNameout = am->ArgMgrGetString("dirout",".");
123 int loadMode = gdcm::LD_ALL;
124 if ( am->ArgMgrDefined("noshadowseq") )
125 loadMode |= gdcm::LD_NOSHADOWSEQ;
128 if ( am->ArgMgrDefined("noshadow") )
129 loadMode |= gdcm::LD_NOSHADOW;
130 if ( am->ArgMgrDefined("noseq") )
131 loadMode |= gdcm::LD_NOSEQ;
134 if (am->ArgMgrDefined("debug"))
135 gdcm::Debug::DebugOn();
137 int verbose = am->ArgMgrDefined("verbose");
138 int split = am->ArgMgrDefined("split");
139 int listonly = am->ArgMgrDefined("listonly");
142 int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
144 int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
146 if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
148 std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
153 int taggrid = am->ArgMgrDefined("taggrid");
155 int hasSkel = am->ArgMgrDefined("skel");
158 skel = am->ArgMgrGetString("skel");
160 const char *extent = am->ArgMgrGetString("extent",".DCM");
162 // if unused Param we give up
163 if ( am->ArgMgrPrintUnusedLabels() )
165 am->ArgMgrUsage(usage);
169 delete am; // we don't need Argument Manager any longer
171 // ----- Begin Processing -----
173 if ( ! gdcm::DirList::IsDirectory(dirNamein) )
175 std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
181 std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
184 std::string systemCommand;
186 std::cout << "Check for output directory :[" << dirNameout << "]."
188 if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // dirout not found
190 std::string strDirNameout(dirNameout); // to please gcc 4
191 systemCommand = "mkdir " +strDirNameout; // create it!
193 std::cout << systemCommand << std::endl;
194 system (systemCommand.c_str());
195 if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // be sure it worked
197 std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
203 std::cout << "Directory [" << dirNameout << "] created." << std::endl;
208 std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
211 std::string strDirNamein(dirNamein);
212 gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files
216 std::cout << "------------List of found files ------------" << std::endl;
218 std::cout << std::endl;
221 gdcm::DirListType fileNames;
222 fileNames = dirList.GetFilenames();
223 gdcm::SerieHelper *s; // Needed only to may use SerieHelper::AddSeriesDetail()
224 s = gdcm::SerieHelper::New();
226 std::string token = "%%%"; // Hope it's enough!
228 std::cout << "---------------Print Serie--------------" << std::endl;
229 s->SetDirectory(dirNamein, true); // true : recursive exploration
230 s->SetUseSeriesDetails(true);
231 s->AddSeriesDetail(0x0018, 0x1312);
236 gdcm::FileHelper *fh;
237 std::vector<std::string> tokens;
238 std::vector<std::string> tokensForFileName;
240 // For Siemens pb, we need Station Name
242 gdcm::DirListType::iterator it1 = fileNames.begin();
243 f = gdcm::File::New();
244 f->SetLoadMode(gdcm::LD_ALL);
245 f->SetFileName( *it1 );
247 std::string stationName = f->GetEntryString(0x0008,0x1010);
251 std::cout << "---------------Print Unique Series identifiers---------"
253 std::string uniqueSeriesIdentifier;
255 for (gdcm::DirListType::iterator it) = fileNames.begin();
256 it != fileNames.end();
259 std::cout << "File Name : " << *it << std::endl;
260 f = gdcm::File::New();
261 f->SetLoadMode(gdcm::LD_ALL);
262 f->SetFileName( *it );
265 uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
267 uniqueSeriesIdentifier << "]" << std::endl;
273 std::cout << "------------------Print Break levels-----------------" << std::endl;
275 std::string userFileIdentifier;
278 s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
279 if ( stationName != "MRC35150" ) // for Siemens MRC35150, don't deal with 'Series Instance UID'
280 s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
282 s->AddSeriesDetail(0x9999, 0x9999, false); // dirty trick to ignore 'Series Instance UID'
283 s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
284 s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order)
285 s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
286 s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
288 //uint8_t *imageData; // Useless : pixels will not be loaded
289 // (images are overwritten)
291 for (gdcm::DirListType::iterator it = fileNames.begin();
292 it != fileNames.end();
295 f = gdcm::File::New();
296 f->SetLoadMode(loadMode);
297 f->SetFileName( *it );
300 std::string strSeriesNumber;
304 // keep only requested Series
306 if (nbSeriesToKeep != 0)
308 strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
309 seriesNumber = atoi( strSeriesNumber.c_str() );
310 for (j=0;j<nbSeriesToKeep; j++)
312 if(seriesNumber == seriesToKeep[j])
324 // drop all unrequested Series
326 if (nbSeriesToDrop != 0)
328 strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
329 seriesNumber = atoi( strSeriesNumber.c_str() );
330 for (j=0;j<nbSeriesToDrop; j++)
332 if(seriesNumber == seriesToDrop[j])
345 userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
347 gdcm::Util::Tokenize (userFileIdentifier, tokens, token);
349 int imageNum; // Within FileName
352 if ( tokens[3] == "gdcmUnfound") // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
354 ///this is a trick to build up a lexicographical compliant name :
355 /// eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
356 std::string name = gdcm::Util::GetName( *it );
359 gdcm::Util::Tokenize (name, tokensForFileName, skel);
360 imageNum = atoi ( tokensForFileName[0].c_str() );
361 // probabely we could write something much more complicated using C++ !
362 sprintf (newName, "%s%06d%s", skel, imageNum, extent);
364 tokensForFileName.clear();
370 userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
371 + tokens[3] + token + tokens[4] + token + tokens[5] + token;
374 std::cout << "[" << userFileIdentifier << "] : " << *it << std::endl;
376 // storing in a map ensures automatic sorting !
377 sf[userFileIdentifier] = f;
381 std::cout << " " << std::endl;
383 std::string fullFilename, lastFilename;
384 std::string previousPatientName, currentPatientName;
385 std::string previousSerieInstanceUID, currentSerieInstanceUID;
386 std::string previousImagePosition, currentImagePosition;
387 std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
388 std::string previousTriggerTime, currentTriggerTime;
390 std::string currentStudyUID;
391 std::string seriesDescription;
393 std::string writeDir, currentWriteDir;
394 std::string currentPatientWriteDir, currentSerieWriteDir,
395 currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
397 std::string fullWriteFilename;
398 std::string strExtent(extent);
400 writeDir = gdcm::Util::NormalizePath(dirNameout);
401 SortedFiles::iterator it2;
403 previousPatientName = "";
404 previousSerieInstanceUID = "";
405 previousImagePosition = "";
406 previousPhaseEncodingDirection = "";
407 previousTriggerTime = "";
409 int sliceIndex = 0; // Is incremented *at the beginning* of processing
418 gdcm::File *currentFile;
420 std::string defaultStudyUID = gdcm::Util::CreateUniqueUID();
421 std::string defaultSerieUID;
423 for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
425 currentFile = it2->second;
427 fullFilename = currentFile->GetFileName();
428 lastFilename = gdcm::Util::GetName( fullFilename );
429 std::cout << " --------------------------------------------------"
430 << " Rewrite [" <<lastFilename << "]" << std::endl;
433 gdcm::Util::Tokenize (it2->first, tokens, token);
435 currentPatientName = tokens[0];
436 currentSerieInstanceUID = tokens[1];
437 currentImagePosition = tokens[2];
438 currentTriggerTime = tokens[3];
439 currentPhaseEncodingDirection = tokens[4];
440 seriesDescription = tokens[5]; // For Siemens pb
442 if ( currentImagePosition[0] == '-')
443 currentImagePosition[0] = 'M';
444 if ( currentImagePosition[0] == '+')
445 currentImagePosition[0] = 'P';
447 // Add a default ImagePositionPatient to avoid confusion at post processing time
448 if ( currentFile->GetEntryString(0x0020,0x0032) == gdcm::GDCM_UNFOUND &&
449 currentFile->GetEntryString(0x0020,0x0030) == gdcm::GDCM_UNFOUND )
451 currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
454 // Add a default ImagePositionPatient to avoid confusion at post processing time
455 if ( currentFile->GetEntryString(0x0020,0x0037) == gdcm::GDCM_UNFOUND &&
456 currentFile->GetEntryString(0x0020,0x0035) == gdcm::GDCM_UNFOUND )
458 currentFile->InsertEntryString("1.\\0.\\0.\\0.\\1.\\0.",0x0020, 0x0037, "DS" );
461 if (previousPatientName != currentPatientName)
463 if ( currentFile->GetEntryString(0x0020,0x000d) == gdcm::GDCM_UNFOUND)
466 std::cout << "--- new Study UID created" << std::endl;
467 defaultStudyUID = gdcm::Util::CreateUniqueUID();
468 currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
471 previousPatientName = currentPatientName;
473 std::cout << "==== new Patient [" << currentPatientName << "]" << std::endl;
475 previousPatientName = currentPatientName;
476 previousSerieInstanceUID = ""; //currentSerieInstanceUID;
477 previousImagePosition = ""; //currentImagePosition;
478 previousTriggerTime = "";
479 previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
481 currentPatientWriteDir = writeDir + currentPatientName;
482 //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
484 systemCommand = "mkdir " + currentPatientWriteDir;
486 std::cout << systemCommand << std::endl;
487 system ( systemCommand.c_str() );
491 if ( stationName != "MRC35150" ) // for Siemens MRC35150, don't deal with 'Series Instance UID'
493 if (previousSerieInstanceUID != currentSerieInstanceUID)
496 std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
499 if ( currentFile->GetEntryString(0x0020,0x000e) == gdcm::GDCM_UNFOUND)
502 std::cout << "--- --- new Serie UID created" << std::endl;
503 defaultSerieUID = gdcm::Util::CreateUniqueUID();
504 currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
509 currentSerieWriteDir = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
510 + currentSerieInstanceUID;
511 systemCommand = "mkdir " + currentSerieWriteDir;
512 system (systemCommand.c_str());
514 previousSerieInstanceUID = currentSerieInstanceUID;
515 previousImagePosition = ""; //currentImagePosition;
516 previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
518 // end of stationName != "MRC35150"
520 if (previousImagePosition != currentImagePosition)
525 std::cout << "=== === === new Position [" << currentImagePosition << "]"
529 currentPositionWriteDir = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
530 + currentImagePosition;
531 systemCommand = "mkdir " + currentPositionWriteDir;
532 system (systemCommand.c_str());
534 previousImagePosition = currentImagePosition;
535 previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
537 sliceIndex = 1; // only *one* slice in a given directory
542 std::cout << "Slice Index : " << sliceIndex << std::endl;
544 // We don't split on Row/Column!
546 if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
549 std::cout << "==== === === === new PhaseEncodingDirection ["
550 << currentPhaseEncodingDirection << "]" << std::endl;
554 currentPhaseEncodingDirectionWriteDir = currentPositionWriteDir
555 + gdcm::GDCM_FILESEPARATOR
556 + currentPhaseEncodingDirection;
557 systemCommand = "mkdir " + currentPhaseEncodingDirectionWriteDir;
558 system (systemCommand.c_str());
561 previousPhaseEncodingDirection = currentPhaseEncodingDirection;
566 std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
569 if ( gdcm::Debug::GetDebugFlag())
570 std::cout << "--- --- --- --- --- " << it2->first << " "
571 << (it2->second)->GetFileName() << " "
572 << gdcm::Util::GetName( fullFilename ) << std::endl;
574 // Transform the image to be 'Brucker-Like'
575 // ----------------------------------------
577 // Deal with 0x0019, 0x1000 : 'FOV'
578 int nX = currentFile->GetXSize();
579 int nY = currentFile->GetYSize();
580 float pxSzX = currentFile->GetXSpacing();
581 float pxSzY = currentFile->GetYSpacing();
583 sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
584 if (currentFile->IsVRCoherent(0x0019) == 1 )
585 currentFile->InsertEntryString(fov, 0x0019, 0x1000, " ");
587 currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
590 // Deal with 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number)
591 std::string chSessionIndex;
597 chSessionIndex = "1";
602 D 0008|1010 [SH] [Station Name ] [MRC35150]
603 we have to deal with :
605 D 0008|103e [LO] [Series Description ] [fl2d9_line PA 15 90deg]
606 D 0008|103e [LO] [Series Description ] [fl2d9_line PA 15 0deg ]
607 (everything is flagged as 'ROW')
609 if ( stationName == "MRC35150" )
611 if ( memcmp(seriesDescription.c_str(), "fl2d9linePA1590deg", 18) )
612 chSessionIndex = "1";
613 else if ( memcmp(seriesDescription.c_str(), "fl2d9linePA150deg", 18) )
614 chSessionIndex = "2";
617 std::cout << "====================== seriesDescription "
618 << " neither fl2d9_line PA 15 90deg nor fl2d9_line PA 15 0deg (?!?) : ["
619 << seriesDescription << "]" << std::endl;
620 chSessionIndex = "1";
623 else // for all other 'normal' cases
625 if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
626 chSessionIndex = "1";
627 else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
628 chSessionIndex = "2";
631 std::cout << "====================== PhaseEncodingDirection "
632 << " neither COL nor ROW (?!?) : [ "
633 << currentPhaseEncodingDirection << "]" << std::endl;
634 chSessionIndex = "1";
638 if (currentFile->IsVRCoherent(0x0020) == 1 )
639 currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, " ");
641 currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
643 // Deal with 0x0021, 0x1020 : 'SLICE INDEX'
644 char chSliceIndex[5];
645 sprintf(chSliceIndex, "%04d", sliceIndex);
646 std::string strChSliceIndex(chSliceIndex);
648 // Deal with 0x0021, 0x1040 : 'FRAME INDEX'
649 char chFrameIndex[5];
650 sprintf(chFrameIndex, "%04d", frameIndex);
652 std::string stringVR;
653 if (currentFile->IsVRCoherent(0x0021) == 1 )
658 currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
659 currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR);
662 std::string strImagePositionPatient = currentFile->GetEntryString(0x0020, 0x0032 );
663 if (strImagePositionPatient == gdcm::GDCM_UNFOUND)
666 std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
667 currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
670 std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
671 if (strImageOrientationPatient == gdcm::GDCM_UNFOUND)
674 std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
675 currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
693 std::cout << "Frame Index : " << frameIndex << std::endl;
697 //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
698 // + lastFilename + strExtent;
699 fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
700 + lastFilename + strExtent;
702 fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
703 + lastFilename + strExtent;
706 systemCommand = "cp " + fullFilename + " " + fullWriteFilename;
707 std::cout << systemCommand << std::endl;
708 system ( systemCommand.c_str() );
711 // Load the pixels in RAM.
713 fh = gdcm::FileHelper::New(currentFile);
714 uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
715 fh->SetWriteTypeToDcmExplVR();
716 // We didn't modify pixels -> keep unchanged the following :
717 // 'Media Storage SOP Class UID' (0x0002,0x0002)
718 // 'SOP Class UID' (0x0008,0x0016)
719 // 'Image Type' (0x0008,0x0008)
720 // 'Conversion Type' (0x0008,0x0064)
722 // Put to Black the burnt-in number.
723 nX = currentFile->GetXSize();
724 nY = currentFile->GetYSize();
725 for(int y=nY-15; y<nY; y++)
726 for(int x=nX/3; x<nX/2+50; x++)
727 imageData[ y*nX*2 + x ] = 0;
729 fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
730 if (!fh->Write(fullWriteFilename))
732 std::cout << "Fail to write :[" << fullWriteFilename << "]"