1 /*=========================================================================
4 Module: $RCSfile: PrintFile.cxx,v $
6 Date: $Date: 2007/09/12 12:36:50 $
7 Version: $Revision: 1.85 $
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 );
245 for (int ri=0; ri<forceLoadNb; ri++)
247 f->AddForceLoadElement((uint32_t)elemsToForceLoad[2*ri],
248 (uint32_t)elemsToForceLoad[2*ri+1] );
250 // TODO : find why such a polution
251 // To avoid polluting the output with messages
252 // 'Last system error was : No such file or directory'
257 bool res = f->Load();
258 // GDCM_NAME_SPACE::File::IsReadable() is no usable here, because we deal with
259 // any kind of gdcm-Parsable *document*
260 // not only GDCM_NAME_SPACE::File (as opposed to GDCM_NAME_SPACE::DicomDir)
263 std::cout << "Cannot process file [" << fileName << "]" << std::endl;
264 std::cout << "Either it doesn't exist, or it's read protected "
266 std::cout << "or it's not a Dicom File, or its 'header' is bugged"
268 std::cout << "use 'PrintFile filein=... debug' to try to guess the pb"
274 f->SetFourthDimensionLocation(FourthDimLoc[0],FourthDimLoc[1]);
276 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
277 fh->SetPrintLevel( level );
281 std::cout << "\n\n" << std::endl;
283 std::cout <<std::endl;
284 std::cout <<" dataSize " << fh->GetImageDataSize() << std::endl;
285 std::cout <<" dataSizeRaw " << fh->GetImageDataRawSize() << std::endl;
288 int nX,nY,nZ,nT,sPP,planarConfig;
289 std::string pixelType;
294 std::cout << " DIMX=" << nX << " DIMY=" << nY
295 << " DIMZ=" << nZ << " DIMT=" << nT
298 pixelType = f->GetPixelType();
299 sPP = f->GetSamplesPerPixel();
300 std::cout << " pixelType= [" << pixelType
301 << "] SamplesPerPixel= [" << sPP
306 planarConfig = f->GetPlanarConfiguration();
307 std::cout << " PlanarConfiguration= [" << planarConfig
310 std::cout << " PhotometricInterpretation= ["
311 << f->GetEntryString(0x0028,0x0004)
314 int numberOfScalarComponents=f->GetNumberOfScalarComponents();
315 std::cout << " NumberOfScalarComponents = " << numberOfScalarComponents
317 << " LUT = " << (f->HasLUT() ? "TRUE" : "FALSE")
320 if ( f->GetDataEntry(0x0002,0x0010) )
321 if ( f->GetDataEntry(0x0002,0x0010)->IsNotLoaded() )
323 std::cout << "Transfer Syntax not loaded. " << std::endl
324 << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE"
330 std::string transferSyntaxName = f->GetTransferSyntaxName();
331 std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
333 std::cout << " SwapCode= " << f->GetSwapCode() << std::endl;
334 std::cout << " ------" << std::endl;
336 std::cout << "\n\n" << std::endl;
337 std::cout << "X spacing " << f->GetXSpacing() << std::endl;
338 std::cout << "Y spacing " << f->GetYSpacing() << std::endl;
339 std::cout << "Z spacing " << f->GetZSpacing() << std::endl;
341 //------------------------------
343 // Let's get and print some usefull fields about 'Orientation'
344 // ------------------------------------------------------------
346 std::string strPatientPosition =
347 f->GetEntryString(0x0018,0x5100);
348 if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
349 && strPatientPosition != "" )
350 std::cout << "PatientPosition (0x0010,0x5100)= ["
351 << strPatientPosition << "]" << std::endl;
353 std::string strViewPosition =
354 f->GetEntryString(0x0018,0x5101);
355 if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
356 && strViewPosition != "" )
357 std::cout << "View Position (0x0018,0x5101)= ["
358 << strViewPosition << "]" << std::endl;
360 std::string strPatientOrientation =
361 f->GetEntryString(0x0020,0x0020);
362 if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND
363 && strPatientOrientation != "")
364 std::cout << "PatientOrientation (0x0020,0x0020)= ["
365 << strPatientOrientation << "]" << std::endl;
367 std::string strImageOrientationPatient =
368 f->GetEntryString(0x0020,0x0037);
369 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
370 && strImageOrientationPatient != "" )
371 std::cout << "ImageOrientationPatient (0x0020,0x0037)= ["
372 << strImageOrientationPatient << "]" << std::endl;
374 std::string strImageOrientationRET =
375 f->GetEntryString(0x0020,0x0035);
376 if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND
377 && strImageOrientationRET != "" )
378 std::cout << "ImageOrientationRET (0x0020,0x0035)= ["
379 << strImageOrientationRET << "]" << std::endl;
381 std::string strImagePositionPatient =
382 f->GetEntryString(0x0020,0x0032);
383 if ( strImagePositionPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
384 && strImagePositionPatient != "" )
385 std::cout << "ImagePositionPatient (0x0020,0x0032)= ["
386 << strImagePositionPatient << "]" << std::endl;
388 std::string strImagePositionPatientRET =
389 f->GetEntryString(0x0020,0x0030);
390 if ( strImagePositionPatientRET != GDCM_NAME_SPACE::GDCM_UNFOUND
391 && strImagePositionPatientRET != "" )
392 std::cout << "ImagePositionPatientRET (0x0020,0x0030)= ["
393 << strImagePositionPatientRET << "]" << std::endl;
396 /*bool riop = */f->GetImageOrientationPatient(iop);
398 /*bool ripp = */f->GetImagePositionPatient(ipp);
400 std::cout << "Image Position (0x0020,0x0032|0x0030) : "
401 << ipp[0] << " , " << ipp[1] << " , "<< ipp[2]
403 std::cout << "Image Orientation (0x0020,0x0037|0x0035) : "
404 << iop[0] << " , " << iop[1] << " , "<< iop[2] << " , "
405 << iop[3] << " , " << iop[4] << " , "<< iop[5]
409 // Let's compute 'user friendly' results about 'Orientation'
410 // ---------------------------------------------------------
412 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
414 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND ||
415 strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND )
418 GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f );
420 std::cout << "TypeOrientation = " << orient << " (-> "
421 << o->GetOrientationTypeString(orient) << " )" << std::endl;
424 std::string ori = o->GetOrientation ( f );
426 std::cout << "Orientation [" << ori << "]" << std::endl;
429 //------------------------------
432 // Display the LUT as an int array (for debugging purpose)
433 if ( f->HasLUT() && showlut )
435 uint8_t* lutrgba = fh->GetLutRGBA();
438 std::cout << "Lut RGBA (Palette Color) not built " << std::endl;
440 // Nothing is written yet to get LUT Data user friendly
441 // The following is to be moved into a PixelRedaConvert method
443 GDCM_NAME_SPACE::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000);
446 GDCM_NAME_SPACE::SQItem *sqi= modLutSeq->GetFirstSQItem();
449 std::string lutDescriptor = sqi->GetEntryString(0x0028,0x3002);
450 int length; // LUT length in Bytes
451 int deb; // Subscript of the first Lut Value
452 int nbits; // Lut item size (in Bits)
453 int nbRead; // nb of items in LUT descriptor (must be = 3)
455 nbRead = sscanf( lutDescriptor.c_str(),
457 &length, &deb, &nbits );
460 std::cout << "Wrong LUT descriptor" << std::endl;
462 GDCM_NAME_SPACE::DataEntry *b = sqi->GetDataEntry(0x0028,0x3006);
465 if ( b->GetLength() != 0 )
467 std::cout << "---------------------------------------"
468 << " We should never reach this point "
470 //LoadEntryBinArea(b); //LUT Data (CTX dependent)
476 std::cout << "No LUT Data (0x0028,0x3000) found " << std::endl;
480 if ( fh->GetLutItemSize() == 8 )
482 for (int i=0;i<fh->GetLutItemNumber();i++)
483 std::cout << i << " : \t"
484 << (int)(lutrgba[i*4]) << " "
485 << (int)(lutrgba[i*4+1]) << " "
486 << (int)(lutrgba[i*4+2]) << std::endl;
488 else // LutItemSize assumed to be = 16
490 uint16_t* lutrgba16 = (uint16_t*)lutrgba;
491 for (int i=0;i<fh->GetLutItemNumber();i++)
492 std::cout << i << " : \t"
493 << (int)(lutrgba16[i*4]) << " "
494 << (int)(lutrgba16[i*4+1]) << " "
495 << (int)(lutrgba16[i*4+2]) << std::endl;
501 std::cout << "Try LUT Data "<< std::endl;
505 // Parsability of the GDCM_NAME_SPACE::Document already checked, after Load() !
507 if ( f->IsReadable() )
509 std::cout <<std::endl<<fileName<<" is Readable"<<std::endl;
511 else if ( f->GetSeqEntry(0x0041,0x1010) )
513 std::cout <<std::endl<<fileName<<" looks like a 'PAPYRUS image' file"
516 else if ( f->GetSeqEntry(0x0004,0x1220) )
518 std::cout <<std::endl<<fileName<<" looks like a 'DICOMDIR file'"
523 std::cout <<std::endl<<fileName<<" doesn't look like an image file "
527 std::cout<<std::flush;
531 else // ====== Deal with a Directory ======
533 std::cout << "dirName [" << dirName << "]" << std::endl;
535 GDCM_NAME_SPACE::DirList dirList(dirName,rec); // gets recursively (or not) the file list
536 GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
537 GDCM_NAME_SPACE::File *f;
540 for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin();
541 it != fileList.end();
544 std::cout << std::endl<<" Start processing :[" << it->c_str() << "]"
546 f = GDCM_NAME_SPACE::File::New();
547 f->SetLoadMode(loadMode);
548 f->SetFileName( it->c_str() );
550 for (int ri=0; ri<forceLoadNb; ri++)
552 printf("%04x,%04x\n",elemsToForceLoad[2*ri],
553 elemsToForceLoad[2*ri+1]);
554 f->AddForceLoadElement((uint32_t)elemsToForceLoad[2*ri],
555 (uint32_t)elemsToForceLoad[2*ri+1]);
561 std::cout << "Cannot process file [" << it->c_str() << "]"
563 std::cout << "Either it doesn't exist, or it's read protected "
565 std::cout << "or it's not a Dicom File, or its 'header' is bugged"
567 std::cout << "use 'PrintFile filein=... debug' "
568 << "to try to guess the pb"
574 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
575 fh->SetPrintLevel( level );
578 //------------------------------
581 // Lets's get and print some usefull fields about 'Orientation'
582 // ------------------------------------------------------------
584 std::string strPatientPosition =
585 f->GetEntryString(0x0018,0x5100);
586 if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
587 && strPatientPosition != "" )
588 std::cout << "PatientPosition (0x0010,0x5100)= ["
589 << strPatientPosition << "]" << std::endl;
591 std::string strViewPosition =
592 f->GetEntryString(0x0018,0x5101);
593 if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND
594 && strViewPosition != "" )
595 std::cout << "strViewPosition (0x0010,0x5101)= ["
596 << strViewPosition << "]" << std::endl;
598 std::string strPatientOrientation =
599 f->GetEntryString(0x0020,0x0020);
600 if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND
601 && strPatientOrientation != "")
602 std::cout << "PatientOrientation (0x0020,0x0020)= ["
603 << strPatientOrientation << "]" << std::endl;
605 std::string strImageOrientationPatient =
606 f->GetEntryString(0x0020,0x0037);
607 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND
608 && strImageOrientationPatient != "" )
609 std::cout << "ImageOrientationPatient (0x0020,0x0037)= ["
610 << strImageOrientationPatient << "]" << std::endl;
612 std::string strImageOrientationRET =
613 f->GetEntryString(0x0020,0x0035);
614 if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND
615 && strImageOrientationRET != "" )
617 std::cout << "ImageOrientationRET (0x0020,0x0035)= ["
618 << strImageOrientationRET << "]" << std::endl;
621 // Let's compute 'user friendly' results about 'Orientation'
622 // ---------------------------------------------------------
624 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
627 if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND ||
628 strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND )
631 GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f );
633 std::cout << "TypeOrientation = " << orient << " (-> "
634 << o->GetOrientationTypeString(orient) << " )" << std::endl;
637 std::string ori = o->GetOrientation ( f );
639 std::cout << "Orientation [" << ori << "]" << std::endl;
642 //-------------------------------
645 std::cout <<std::endl<<it->c_str()<<" is Readable"<<std::endl;
647 std::cout <<std::endl<<it->c_str()<<" is NOT Readable"<<std::endl;
648 std::cout << "\n\n" << std::endl;
652 std::cout<<std::flush;