1 /*=========================================================================
4 Module: $RCSfile: PrintFile.cxx,v $
6 Date: $Date: 2007/11/09 17:52:59 $
7 Version: $Revision: 1.89 $
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 =========================================================================*/
19 #include "gdcmDocument.h"
20 #include "gdcmSeqEntry.h"
21 #include "gdcmSQItem.h"
22 #include "gdcmDataEntry.h"
24 #include "gdcmFileHelper.h"
25 #include "gdcmDebug.h"
26 #include "gdcmDirList.h"
27 #include "gdcmGlobal.h"
28 #include "gdcmDictSet.h"
29 #include "gdcmArgMgr.h"
30 #include "gdcmOrientation.h"
33 /// \todo : code factorization, for 'single file' an 'whole directory' processing
35 void ShowLutData(GDCM_NAME_SPACE::File *f);
37 // Nothing is written yet to get LUT Data user friendly
38 // The following is to be moved into a PixelReadConvert method
39 // Let here, waiting for a clever idea on the way to do it.
41 void ShowLutData(GDCM_NAME_SPACE::File *f)
43 GDCM_NAME_SPACE::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000);
46 GDCM_NAME_SPACE::SQItem *sqi= modLutSeq->GetFirstSQItem();
49 std::string lutDescriptor = sqi->GetEntryString(0x0028,0x3002);
50 if ( /*lutDescriptor == GDCM_UNFOUND*/ 0 )
52 std::cout << "LUT Descriptor is missing" << std::endl;
55 int length; // LUT length in Bytes
56 int deb; // Subscript of the first Lut Value
57 int nbits; // Lut item size (in Bits)
59 int nbRead; // nb of items in LUT descriptor (must be = 3)
61 nbRead = sscanf( lutDescriptor.c_str(),
63 &length, &deb, &nbits );
64 std::cout << "length " << length
70 std::cout << "Wrong LUT descriptor" << std::endl;
72 //LUT Data (CTX dependent)
73 GDCM_NAME_SPACE::DataEntry *b = sqi->GetDataEntry(0x0028,0x3006);
76 int BitsAllocated = f->GetBitsAllocated();
77 if ( BitsAllocated <= 8 )
80 if ( ( nbits == 16 ) && ( BitsAllocated == 8 ) )
82 // when LUT item size is different than pixel size
83 mult = 2; // high byte must be = low byte
87 // See PS 3.3-2003 C.11.1.1.2 p 619
90 uint8_t *lut = b->GetBinArea();
91 for( int i=0; i < length; ++i )
93 std::cout << i+deb << " : \t"
94 << (int) (lut[i*mult + 1]) << std::endl;
99 uint16_t *lut = (uint16_t *)(b->GetBinArea());
100 for( int i=0; i < length; ++i )
102 std::cout << i+deb << " : \t"
103 << (int) (((uint16_t *)lut)[i])
109 std::cout << "No LUT Data DataEntry (0x0028,0x3006) found?!? "
113 std::cout << "No First SQ Item within (0x0028,0x3000) ?!? "
117 std::cout << "No LUT Data SeqEntry (0x0028,0x3000) found "
121 int main(int argc, char *argv[])
125 " \n PrintFile : \n ",
126 " Display the header of a ACR-NEMA/PAPYRUS/DICOM File ",
127 " usage: PrintFile {filein=inputFileName|dirin=inputDirectoryName}[level=n]",
128 " [forceload=listOfElementsToForceLoad] [rec] [noex] ",
129 " [4DLoc= ][dict= privateDirectory] ",
130 " [ { [noshadowseq] | [noshadow][noseq] } ] ",
131 " [debug] [warning] ",
132 " level = 0,1,2 : depending on the amount of details user wants to see",
133 " rec : user wants to parse recursively the directory ",
134 " noex : user doen't want extra 'user friendly' info ",
135 " 4DLoc: group-elem(in hexa, no space) of the DataEntry holdind 4thDim",
136 " listOfElementsToForceLoad : group-elem,g2-e2,... (in hexa, no space)",
137 " of Elements to load whatever their length ",
138 " privateDirectory : source file full path name of Shadow Group elems ",
139 " noshadowseq: user doesn't want to load Private Sequences ",
140 " noshadow : user doesn't want to load Private groups (odd number) ",
141 " noseq : user doesn't want to load Sequences ",
142 " debug : user wants to run the program in 'debug mode' ",
143 " warning : user wants to be warned about any oddity in the File ",
144 " showlut :user wants to display the Palette Color (as an int array) ",
147 // Initialize Arguments Manager
148 GDCM_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv);
150 if (argc == 1 || am->ArgMgrDefined("usage") )
152 am->ArgMgrUsage(usage); // Display 'usage'
157 const char *fileName = am->ArgMgrGetString("filein");
158 const char *dirName = am->ArgMgrGetString("dirin");
160 if ( (fileName == 0 && dirName == 0) ||
161 (fileName != 0 && dirName != 0) )
163 std::cerr << std::endl
164 << "Either 'filein=' or 'dirin=' must be present;"
165 << std::endl << "Not both" << std::endl;
166 am->ArgMgrUsage(usage); // Display 'usage'
171 bool noex = ( 0 != am->ArgMgrDefined("noex") );
172 bool rec = ( 0 != am->ArgMgrDefined("rec") );
174 if (am->ArgMgrDefined("debug"))
175 GDCM_NAME_SPACE::Debug::DebugOn();
177 if (am->ArgMgrDefined("warning"))
178 GDCM_NAME_SPACE::Debug::WarningOn();
180 int loadMode = GDCM_NAME_SPACE::LD_ALL;
181 if ( am->ArgMgrDefined("noshadowseq") )
182 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
185 if ( am->ArgMgrDefined("noshadow") )
186 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
187 if ( am->ArgMgrDefined("noseq") )
188 loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
191 int level = am->ArgMgrGetInt("level", 1);
194 uint16_t *elemsToForceLoad
195 = am->ArgMgrGetXInt16Enum("forceload", &forceLoadNb);
198 uint16_t *FourthDimLoc;
199 if ( am->ArgMgrDefined("4DLoc") )
201 FourthDimLoc = am->ArgMgrGetXInt16Enum("4DLoc", &nbP);
205 std::cout << "4DLoc must have 2 and only 2 components!" << std::endl;
211 bool showlut = ( 0 != am->ArgMgrDefined("SHOWLUT") );
213 bool ddict = am->ArgMgrDefined("dict") ? true : false;
214 const char *dict = 0;
218 dict = am->ArgMgrGetString("dict",0);
221 /* if unused Param we give up */
222 if ( am->ArgMgrPrintUnusedLabels() )
224 am->ArgMgrUsage(usage);
229 delete am; // we don't need Argument Manager any longer
231 // ----------- End Arguments Manager ---------
236 GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->AddDict(dict);
239 if ( fileName != 0 ) // ====== Deal with a single file ======
241 GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
242 f->SetLoadMode(loadMode);
243 f->SetFileName( fileName );
244 f->SetMaxSizeLoadEntry(0xffff);
246 for (int ri=0; ri<forceLoadNb; ri++)
248 f->AddForceLoadElement((uint32_t)elemsToForceLoad[2*ri],
249 (uint32_t)elemsToForceLoad[2*ri+1] );
251 // TODO : find why such a polution
252 // To avoid polluting the output with messages
253 // 'Last system error was : No such file or directory'
263 catch(std::exception &ex)
265 std::cerr << "sorry an exception was thrown: " << ex.what() << std::endl;
267 // GDCM_NAME_SPACE::File::IsReadable() is no usable here, because we deal with
268 // any kind of gdcm-Parsable *document*
269 // not only GDCM_NAME_SPACE::File (as opposed to GDCM_NAME_SPACE::DicomDir)
272 std::cout << "Cannot process file [" << fileName << "]" << std::endl;
273 std::cout << "Either it doesn't exist, or it's read protected "
275 std::cout << "or it's not a Dicom File, or its 'header' is bugged"
277 std::cout << "use 'PrintFile filein=... debug' to try to guess the pb"
284 f->SetFourthDimensionLocation(FourthDimLoc[0],FourthDimLoc[1]);
287 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
288 fh->SetPrintLevel( level );
292 std::cout << "\n\n" << std::endl;
294 std::cout <<std::endl;
295 std::cout <<" dataSize " << fh->GetImageDataSize() << std::endl;
296 std::cout <<" dataSizeRaw " << fh->GetImageDataRawSize() << std::endl;
299 int nX,nY,nZ,nT,sPP,planarConfig;
300 std::string pixelType;
305 std::cout << " DIMX=" << nX << " DIMY=" << nY
306 << " DIMZ=" << nZ << " DIMT=" << nT
309 pixelType = f->GetPixelType();
310 sPP = f->GetSamplesPerPixel();
311 std::cout << " pixelType= [" << pixelType
312 << "] SamplesPerPixel= [" << sPP
317 planarConfig = f->GetPlanarConfiguration();
318 std::cout << " PlanarConfiguration= [" << planarConfig
321 std::cout << " PhotometricInterpretation= ["
322 << f->GetEntryString(0x0028,0x0004)
325 int numberOfScalarComponents=f->GetNumberOfScalarComponents();
326 std::cout << " NumberOfScalarComponents = " << numberOfScalarComponents
328 << " LUT = " << (f->HasLUT() ? "TRUE" : "FALSE")
331 if ( f->GetDataEntry(0x0002,0x0010) )
332 if ( f->GetDataEntry(0x0002,0x0010)->IsNotLoaded() )
334 std::cout << "Transfer Syntax not loaded. " << std::endl
335 << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE"
341 std::string transferSyntaxName = f->GetTransferSyntaxName();
342 std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
344 std::cout << " SwapCode= " << f->GetSwapCode() << std::endl;
345 std::cout << " ------" << std::endl;
347 std::cout << "\n\n" << std::endl;
348 std::cout << "X spacing " << f->GetXSpacing() << std::endl;
349 std::cout << "Y spacing " << f->GetYSpacing() << std::endl;
350 std::cout << "Z spacing " << f->GetZSpacing() << std::endl;
352 //------------------------------
354 // Let's get and print some usefull fields about 'Orientation'
355 // ------------------------------------------------------------
357 std::string strPatientPosition =
358 f->GetEntryString(0x0018,0x5100);
359 if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
360 && strPatientPosition != "" )
361 std::cout << "PatientPosition (0x0010,0x5100)= ["
362 << strPatientPosition << "]" << std::endl;
364 std::string strViewPosition =
365 f->GetEntryString(0x0018,0x5101);
366 if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
367 && strViewPosition != "" )
368 std::cout << "View Position (0x0018,0x5101)= ["
369 << strViewPosition << "]" << std::endl;
371 std::string strPatientOrientation =
372 f->GetEntryString(0x0020,0x0020);
373 if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND
374 && strPatientOrientation != "")
375 std::cout << "PatientOrientation (0x0020,0x0020)= ["
376 << strPatientOrientation << "]" << std::endl;
378 std::string strImageOrientationPatient =
379 f->GetEntryString(0x0020,0x0037);
380 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
381 && strImageOrientationPatient != "" )
382 std::cout << "ImageOrientationPatient (0x0020,0x0037)= ["
383 << strImageOrientationPatient << "]" << std::endl;
385 std::string strImageOrientationRET =
386 f->GetEntryString(0x0020,0x0035);
387 if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND
388 && strImageOrientationRET != "" )
389 std::cout << "ImageOrientationRET (0x0020,0x0035)= ["
390 << strImageOrientationRET << "]" << std::endl;
392 std::string strImagePositionPatient =
393 f->GetEntryString(0x0020,0x0032);
394 if ( strImagePositionPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
395 && strImagePositionPatient != "" )
396 std::cout << "ImagePositionPatient (0x0020,0x0032)= ["
397 << strImagePositionPatient << "]" << std::endl;
399 std::string strImagePositionPatientRET =
400 f->GetEntryString(0x0020,0x0030);
401 if ( strImagePositionPatientRET != GDCM_NAME_SPACE::GDCM_UNFOUND
402 && strImagePositionPatientRET != "" )
403 std::cout << "ImagePositionPatientRET (0x0020,0x0030)= ["
404 << strImagePositionPatientRET << "]" << std::endl;
407 /*bool riop = */f->GetImageOrientationPatient(iop);
409 /*bool ripp = */f->GetImagePositionPatient(ipp);
411 std::cout << "Image Position (0x0020,0x0032|0x0030) : "
412 << ipp[0] << " , " << ipp[1] << " , "<< ipp[2]
414 std::cout << "Image Orientation (0x0020,0x0037|0x0035) : "
415 << iop[0] << " , " << iop[1] << " , "<< iop[2] << " , "
416 << iop[3] << " , " << iop[4] << " , "<< iop[5]
420 // Let's compute 'user friendly' results about 'Orientation'
421 // ---------------------------------------------------------
423 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
425 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND ||
426 strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND )
429 GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f );
431 std::cout << "TypeOrientation = " << orient << " (-> "
432 << o->GetOrientationTypeString(orient) << " )" << std::endl;
435 std::string ori = o->GetOrientation ( f );
437 std::cout << "Orientation [" << ori << "]" << std::endl;
440 //------------------------------
443 // Display the LUT as an int array (for debugging purpose)
444 if ( f->HasLUT() && showlut )
446 uint8_t* lutrgba = fh->GetLutRGBA();
449 std::cout << "Lut RGBA (Palette Color) not built " << std::endl;
451 // Nothing is written yet to get LUT Data user friendly
452 // The following is to be moved into a PixelRedaConvert method
454 GDCM_NAME_SPACE::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000);
457 GDCM_NAME_SPACE::SQItem *sqi= modLutSeq->GetFirstSQItem();
460 std::string lutDescriptor = sqi->GetEntryString(0x0028,0x3002);
461 int length; // LUT length in Bytes
462 int deb; // Subscript of the first Lut Value
463 int nbits; // Lut item size (in Bits)
464 int nbRead; // nb of items in LUT descriptor (must be = 3)
466 nbRead = sscanf( lutDescriptor.c_str(),
468 &length, &deb, &nbits );
471 std::cout << "Wrong LUT descriptor" << std::endl;
473 GDCM_NAME_SPACE::DataEntry *b = sqi->GetDataEntry(0x0028,0x3006);
476 if ( b->GetLength() != 0 )
478 std::cout << "---------------------------------------"
479 << " We should never reach this point "
481 //LoadEntryBinArea(b); //LUT Data (CTX dependent)
487 std::cout << "No LUT Data (0x0028,0x3000) found " << std::endl;
491 if ( fh->GetLutItemSize() == 8 )
493 for (int i=0;i<fh->GetLutItemNumber();i++)
494 std::cout << i << " : \t"
495 << (int)(lutrgba[i*4]) << " "
496 << (int)(lutrgba[i*4+1]) << " "
497 << (int)(lutrgba[i*4+2]) << std::endl;
499 else // LutItemSize assumed to be = 16
501 uint16_t* lutrgba16 = (uint16_t*)lutrgba;
502 for (int i=0;i<fh->GetLutItemNumber();i++)
503 std::cout << i << " : \t"
504 << (int)(lutrgba16[i*4]) << " "
505 << (int)(lutrgba16[i*4+1]) << " "
506 << (int)(lutrgba16[i*4+2]) << std::endl;
512 std::cout << "Try LUT Data "<< std::endl;
516 // Parsability of the GDCM_NAME_SPACE::Document already checked, after Load() !
518 if ( f->IsReadable() )
520 std::cout <<std::endl<<fileName<<" is Readable"<<std::endl;
522 else if ( f->GetSeqEntry(0x0041,0x1010) )
524 std::cout <<std::endl<<fileName<<" looks like a 'PAPYRUS image' file"
527 else if ( f->GetSeqEntry(0x0004,0x1220) )
529 std::cout <<std::endl<<fileName<<" looks like a 'DICOMDIR file'"
534 std::cout <<std::endl<<fileName<<" doesn't look like an image file "
538 std::cout<<std::flush;
542 // ===========================================================================
543 else // =============================== Deal with a Directory =====================
544 { // ===========================================================================
545 std::cout << "dirName [" << dirName << "]" << std::endl;
547 GDCM_NAME_SPACE::DirList dirList(dirName,rec); // gets recursively (or not) the file list
548 GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
549 GDCM_NAME_SPACE::File *f;
552 if (fileList.size() == 0)
554 std::cout << "No file found in : [" << dirName << "]" << std::endl;
557 for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin();
558 it != fileList.end();
561 std::cout << std::endl<<" Start processing :[" << it->c_str() << "]"
563 f = GDCM_NAME_SPACE::File::New();
564 f->SetLoadMode(loadMode);
565 f->SetFileName( it->c_str() );
567 for (int ri=0; ri<forceLoadNb; ri++)
569 printf("%04x,%04x\n",elemsToForceLoad[2*ri],
570 elemsToForceLoad[2*ri+1]);
571 f->AddForceLoadElement((uint32_t)elemsToForceLoad[2*ri],
572 (uint32_t)elemsToForceLoad[2*ri+1]);
578 std::cout << "Cannot process file [" << it->c_str() << "]"
580 std::cout << "Either it doesn't exist, or it's read protected "
582 std::cout << "or it's not a Dicom File, or its 'header' is bugged"
584 std::cout << "use 'PrintFile filein=... debug' "
585 << "to try to guess the pb"
591 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
592 fh->SetPrintLevel( level );
595 //------------------------------
598 // Lets's get and print some usefull fields about 'Orientation'
599 // ------------------------------------------------------------
601 std::string strPatientPosition =
602 f->GetEntryString(0x0018,0x5100);
603 if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
604 && strPatientPosition != "" )
605 std::cout << "PatientPosition (0x0010,0x5100)= ["
606 << strPatientPosition << "]" << std::endl;
608 std::string strViewPosition =
609 f->GetEntryString(0x0018,0x5101);
610 if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
611 && strViewPosition != "" )
612 std::cout << "strViewPosition (0x0010,0x5101)= ["
613 << strViewPosition << "]" << std::endl;
615 std::string strPatientOrientation =
616 f->GetEntryString(0x0020,0x0020);
617 if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND
618 && strPatientOrientation != "")
619 std::cout << "PatientOrientation (0x0020,0x0020)= ["
620 << strPatientOrientation << "]" << std::endl;
622 std::string strImageOrientationPatient =
623 f->GetEntryString(0x0020,0x0037);
624 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
625 && strImageOrientationPatient != "" )
626 std::cout << "ImageOrientationPatient (0x0020,0x0037)= ["
627 << strImageOrientationPatient << "]" << std::endl;
629 std::string strImageOrientationRET =
630 f->GetEntryString(0x0020,0x0035);
631 if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND
632 && strImageOrientationRET != "" )
634 std::cout << "ImageOrientationRET (0x0020,0x0035)= ["
635 << strImageOrientationRET << "]" << std::endl;
638 // Let's compute 'user friendly' results about 'Orientation'
639 // ---------------------------------------------------------
641 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
644 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND ||
645 strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND )
648 GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f );
650 std::cout << "TypeOrientation = " << orient << " (-> "
651 << o->GetOrientationTypeString(orient) << " )" << std::endl;
654 std::string ori = o->GetOrientation ( f );
656 std::cout << "Orientation [" << ori << "]" << std::endl;
659 //-------------------------------
662 std::cout <<std::endl<<it->c_str()<<" is Readable"<<std::endl;
664 std::cout <<std::endl<<it->c_str()<<" is NOT Readable"<<std::endl;
665 std::cout << "\n\n" << std::endl;
669 std::cout<<std::flush;