1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2005/02/15 18:12:34 $
7 Version: $Revision: 1.224 $
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 =========================================================================*/
20 // -------------- Remember ! ----------------------------------
22 // Image Position Patient (0020,0032):
23 // If not found (ACR_NEMA) we try Image Position (0020,0030)
24 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
25 // or Location (0020,0050)
26 // as the Z coordinate,
27 // 0. for all the coordinates if nothing is found
29 // ---------------------------------------------------------------
32 #include "gdcmGlobal.h"
34 #include "gdcmDebug.h"
36 #include "gdcmValEntry.h"
37 #include "gdcmBinEntry.h"
38 #include "gdcmSeqEntry.h"
39 #include "gdcmRLEFramesInfo.h"
40 #include "gdcmJPEGFragmentsInfo.h"
42 #include <stdio.h> //sscanf
47 //-----------------------------------------------------------------------------
48 // Constructor / Destructor
51 * @param filename name of the file whose header we want to analyze
53 File::File( std::string const &filename )
56 RLEInfo = new RLEFramesInfo;
57 JPEGInfo = new JPEGFragmentsInfo;
59 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
60 // We may encounter the 'RETired' (0x0028, 0x0200) tag
61 // (Image Location") . This entry contains the number of
62 // the group that contains the pixel data (hence the "Pixel Data"
63 // is found by indirection through the "Image Location").
64 // Inside the group pointed by "Image Location" the searched element
65 // is conventionally the element 0x0010 (when the norm is respected).
66 // When the "Image Location" is missing we default to group 0x7fe0.
67 // Note: this IS the right place for the code
70 const std::string &imgLocation = GetEntryValue(0x0028, 0x0200);
71 if ( imgLocation == GDCM_UNFOUND )
78 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
81 // sometimes Image Location value doesn't follow
82 // the supposed processor endianness.
83 // see gdcmData/cr172241.dcm
84 if ( GrPixel == 0xe07f )
89 if ( GrPixel != 0x7fe0 )
91 // This is a kludge for old dirty Philips imager.
99 // Now, we know GrPixel and NumPixel.
100 // Let's create a VirtualDictEntry to allow a further VR modification
101 // and force VR to match with BitsAllocated.
102 DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
105 // Compute the RLE or JPEG info
107 std::string ts = GetTransferSyntax();
108 Fp->seekg( entry->GetOffset(), std::ios::beg );
109 if ( Global::GetTS()->IsRLELossless(ts) )
111 else if ( Global::GetTS()->IsJPEG(ts) )
112 ComputeJPEGFragmentInfo();
115 // Create a new BinEntry to change the the DictEntry
116 // The changed DictEntry will have
117 // - a correct PixelVR OB or OW)
119 // - the name to "Pixel Data"
120 BinEntry *oldEntry = dynamic_cast<BinEntry *>(entry);
124 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
125 // more than 8 (i.e 12, 16) is a 'O Words'
126 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
131 // Change only made if usefull
132 if( PixelVR != oldEntry->GetVR() )
134 DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
135 PixelVR,"1","Pixel Data");
137 BinEntry *newEntry = new BinEntry(newDict);
138 newEntry->Copy(entry);
139 newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
140 oldEntry->SetSelfArea(false);
142 RemoveEntry(oldEntry);
150 * \brief Constructor used when we want to generate dicom files from scratch
155 RLEInfo = new RLEFramesInfo;
156 JPEGInfo = new JPEGFragmentsInfo;
157 InitializeDefaultFile();
161 * \brief Canonical destructor.
171 //-----------------------------------------------------------------------------
174 * \brief This predicate, based on hopefully reasonable heuristics,
175 * decides whether or not the current File was properly parsed
176 * and contains the mandatory information for being considered as
177 * a well formed and usable Dicom/Acr File.
178 * @return true when File is the one of a reasonable Dicom/Acr file,
181 bool File::IsReadable()
183 if( !Document::IsReadable() )
188 const std::string &res = GetEntryValue(0x0028, 0x0005);
189 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
191 return false; // Image Dimensions
193 if ( !GetDocEntry(0x0028, 0x0100) )
195 return false; // "Bits Allocated"
197 if ( !GetDocEntry(0x0028, 0x0101) )
199 return false; // "Bits Stored"
201 if ( !GetDocEntry(0x0028, 0x0102) )
203 return false; // "High Bit"
205 if ( !GetDocEntry(0x0028, 0x0103) )
207 return false; // "Pixel Representation" i.e. 'Sign'
214 * \brief gets the info from 0020,0013 : Image Number else 0.
215 * @return image number
217 int File::GetImageNumber()
219 // The function i atoi() takes the address of an area of memory as
220 // parameter and converts the string stored at that location to an integer
221 // using the external decimal to internal binary conversion rules. This may
222 // be preferable to sscanf() since atoi() is a much smaller, simpler and
223 // faster function. sscanf() can do all possible conversions whereas
224 // atoi() can only do single decimal integer conversions.
225 //0020 0013 IS REL Image Number
226 std::string strImNumber = GetEntryValue(0x0020,0x0013);
227 if ( strImNumber != GDCM_UNFOUND )
229 return atoi( strImNumber.c_str() );
235 * \brief gets the info from 0008,0060 : Modality
236 * @return Modality Type
238 ModalityType File::GetModality()
240 // 0008 0060 CS ID Modality
241 std::string strModality = GetEntryValue(0x0008,0x0060);
242 if ( strModality != GDCM_UNFOUND )
244 if ( strModality.find("AU") < strModality.length()) return AU;
245 else if ( strModality.find("AS") < strModality.length()) return AS;
246 else if ( strModality.find("BI") < strModality.length()) return BI;
247 else if ( strModality.find("CF") < strModality.length()) return CF;
248 else if ( strModality.find("CP") < strModality.length()) return CP;
249 else if ( strModality.find("CR") < strModality.length()) return CR;
250 else if ( strModality.find("CT") < strModality.length()) return CT;
251 else if ( strModality.find("CS") < strModality.length()) return CS;
252 else if ( strModality.find("DD") < strModality.length()) return DD;
253 else if ( strModality.find("DF") < strModality.length()) return DF;
254 else if ( strModality.find("DG") < strModality.length()) return DG;
255 else if ( strModality.find("DM") < strModality.length()) return DM;
256 else if ( strModality.find("DS") < strModality.length()) return DS;
257 else if ( strModality.find("DX") < strModality.length()) return DX;
258 else if ( strModality.find("ECG") < strModality.length()) return ECG;
259 else if ( strModality.find("EPS") < strModality.length()) return EPS;
260 else if ( strModality.find("FA") < strModality.length()) return FA;
261 else if ( strModality.find("FS") < strModality.length()) return FS;
262 else if ( strModality.find("HC") < strModality.length()) return HC;
263 else if ( strModality.find("HD") < strModality.length()) return HD;
264 else if ( strModality.find("LP") < strModality.length()) return LP;
265 else if ( strModality.find("LS") < strModality.length()) return LS;
266 else if ( strModality.find("MA") < strModality.length()) return MA;
267 else if ( strModality.find("MR") < strModality.length()) return MR;
268 else if ( strModality.find("NM") < strModality.length()) return NM;
269 else if ( strModality.find("OT") < strModality.length()) return OT;
270 else if ( strModality.find("PT") < strModality.length()) return PT;
271 else if ( strModality.find("RF") < strModality.length()) return RF;
272 else if ( strModality.find("RG") < strModality.length()) return RG;
273 else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE;
274 else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE;
275 else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN;
276 else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT;
277 else if ( strModality.find("SM") < strModality.length()) return SM;
278 else if ( strModality.find("ST") < strModality.length()) return ST;
279 else if ( strModality.find("TG") < strModality.length()) return TG;
280 else if ( strModality.find("US") < strModality.length()) return US;
281 else if ( strModality.find("VF") < strModality.length()) return VF;
282 else if ( strModality.find("XA") < strModality.length()) return XA;
283 else if ( strModality.find("XC") < strModality.length()) return XC;
287 /// \todo throw error return value ???
288 /// specified <> unknown in our database
297 * \brief Retrieve the number of columns of image.
298 * @return The encountered size when found, 0 by default.
299 * 0 means the file is NOT USABLE. The caller will have to check
303 const std::string &strSize = GetEntryValue(0x0028,0x0011);
304 if ( strSize == GDCM_UNFOUND )
309 return atoi( strSize.c_str() );
313 * \brief Retrieve the number of lines of image.
314 * \warning The defaulted value is 1 as opposed to File::GetXSize()
315 * @return The encountered size when found, 1 by default
316 * (The ACR-NEMA file contains a Signal, not an Image).
320 const std::string &strSize = GetEntryValue(0x0028,0x0010);
321 if ( strSize != GDCM_UNFOUND )
323 return atoi( strSize.c_str() );
330 // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
331 // hence be a signal (1D image). So we default to 1:
336 * \brief Retrieve the number of planes of volume or the number
337 * of frames of a multiframe.
338 * \warning When present we consider the "Number of Frames" as the third
339 * dimension. When Missing we consider the third dimension as
340 * being the ACR-NEMA "Planes" tag content.
341 * @return The encountered size when found, 1 by default (single image).
345 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
346 // as the third dimension.
347 const std::string &strSize = GetEntryValue(0x0028,0x0008);
348 if ( strSize != GDCM_UNFOUND )
350 return atoi( strSize.c_str() );
353 // We then consider the "Planes" entry as the third dimension
354 const std::string &strSize2 = GetEntryValue(0x0028,0x0012);
355 if ( strSize2 != GDCM_UNFOUND )
357 return atoi( strSize2.c_str() );
364 * \brief gets the info from 0028,0030 : Pixel Spacing
366 * @return X dimension of a pixel
368 float File::GetXSpacing()
370 float xspacing = 1.0;
371 float yspacing = 1.0;
372 const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
374 if( strSpacing == GDCM_UNFOUND )
376 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
381 if( ( nbValues = sscanf( strSpacing.c_str(),
382 "%f\\%f", &yspacing, &xspacing)) != 2 )
384 // if no values, xspacing is set to 1.0
387 // if single value is found, xspacing is defaulted to yspacing
391 if ( xspacing == 0.0 )
398 // to avoid troubles with David Clunie's-like images
399 if ( xspacing == 0. && yspacing == 0.)
404 gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
405 // seems to be a bug in the header ...
406 nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
407 gdcmAssertMacro( nbValues == 2 );
414 * \brief gets the info from 0028,0030 : Pixel Spacing
416 * @return Y dimension of a pixel
418 float File::GetYSpacing()
421 std::string strSpacing = GetEntryValue(0x0028,0x0030);
423 if ( strSpacing == GDCM_UNFOUND )
425 gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
429 // if sscanf cannot read any float value, it won't affect yspacing
430 int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
432 // if no values, xspacing is set to 1.0
436 if ( yspacing == 0.0 )
443 * \brief gets the info from 0018,0088 : Space Between Slices
444 * else from 0018,0050 : Slice Thickness
446 * @return Z dimension of a voxel-to be
448 float File::GetZSpacing()
450 // Spacing Between Slices : distance entre le milieu de chaque coupe
451 // Les coupes peuvent etre :
452 // jointives (Spacing between Slices = Slice Thickness)
453 // chevauchantes (Spacing between Slices < Slice Thickness)
454 // disjointes (Spacing between Slices > Slice Thickness)
455 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
456 // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
457 // Si le Spacing Between Slices est Missing,
458 // on suppose que les coupes sont jointives
460 const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
462 if ( strSpacingBSlices == GDCM_UNFOUND )
464 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
465 const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
466 if ( strSliceThickness == GDCM_UNFOUND )
468 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
473 // if no 'Spacing Between Slices' is found,
474 // we assume slices join together
475 // (no overlapping, no interslice gap)
476 // if they don't, we're fucked up
477 return (float)atof( strSliceThickness.c_str() );
481 return (float)atof( strSpacingBSlices.c_str() );
485 * \brief gets the info from 0020,0032 : Image Position Patient
486 * else from 0020,0030 : Image Position (RET)
488 * @return up-left image corner X position
490 float File::GetXOrigin()
492 float xImPos, yImPos, zImPos;
493 std::string strImPos = GetEntryValue(0x0020,0x0032);
495 if ( strImPos == GDCM_UNFOUND )
497 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
498 strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
499 if ( strImPos == GDCM_UNFOUND )
501 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
506 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
515 * \brief gets the info from 0020,0032 : Image Position Patient
516 * else from 0020,0030 : Image Position (RET)
518 * @return up-left image corner Y position
520 float File::GetYOrigin()
522 float xImPos, yImPos, zImPos;
523 std::string strImPos = GetEntryValue(0x0020,0x0032);
525 if ( strImPos == GDCM_UNFOUND)
527 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
528 strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
529 if ( strImPos == GDCM_UNFOUND )
531 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
536 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
545 * \brief gets the info from 0020,0032 : Image Position Patient
546 * else from 0020,0030 : Image Position (RET)
547 * else from 0020,1041 : Slice Location
548 * else from 0020,0050 : Location
550 * @return up-left image corner Z position
552 float File::GetZOrigin()
554 float xImPos, yImPos, zImPos;
555 std::string strImPos = GetEntryValue(0x0020,0x0032);
557 if ( strImPos != GDCM_UNFOUND )
559 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
561 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
562 return 0.; // bug in the element 0x0020,0x0032
570 strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
571 if ( strImPos != GDCM_UNFOUND )
573 if( sscanf( strImPos.c_str(),
574 "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
576 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
577 return 0.; // bug in the element 0x0020,0x0032
585 std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
586 if ( strSliceLocation != GDCM_UNFOUND )
588 if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
590 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
591 return 0.; // bug in the element 0x0020,0x1041
598 gdcmWarningMacro( "Unfound Slice Location (0020,1041)");
600 std::string strLocation = GetEntryValue(0x0020,0x0050);
601 if ( strLocation != GDCM_UNFOUND )
603 if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
605 gdcmWarningMacro( "Wrong Location (0020,0050)");
606 return 0.; // bug in the element 0x0020,0x0050
613 gdcmWarningMacro( "Unfound Location (0020,0050)");
615 return 0.; // Hopeless
619 * \brief gets the info from 0020,0037 : Image Orientation Patient
620 * (needed to organize DICOM files based on their x,y,z position)
621 * @param iop adress of the (6)float aray to receive values
622 * @return cosines of image orientation patient
624 void File::GetImageOrientationPatient( float iop[6] )
626 std::string strImOriPat;
627 //iop is supposed to be float[6]
628 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
630 // 0020 0037 DS REL Image Orientation (Patient)
631 if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
633 if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
634 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
636 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
640 // 0020 0035 DS REL Image Orientation (RET)
641 else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
643 if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
644 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
646 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
652 * \brief Retrieve the number of Bits Stored (actually used)
653 * (as opposed to number of Bits Allocated)
654 * @return The encountered number of Bits Stored, 0 by default.
655 * 0 means the file is NOT USABLE. The caller has to check it !
657 int File::GetBitsStored()
659 std::string strSize = GetEntryValue( 0x0028, 0x0101 );
660 if ( strSize == GDCM_UNFOUND )
662 gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
663 return 0; // It's supposed to be mandatory
664 // the caller will have to check
666 return atoi( strSize.c_str() );
670 * \brief Retrieve the number of Bits Allocated
671 * (8, 12 -compacted ACR-NEMA files, 16, ...)
672 * @return The encountered number of Bits Allocated, 0 by default.
673 * 0 means the file is NOT USABLE. The caller has to check it !
675 int File::GetBitsAllocated()
677 std::string strSize = GetEntryValue(0x0028,0x0100);
678 if ( strSize == GDCM_UNFOUND )
680 gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
681 return 0; // It's supposed to be mandatory
682 // the caller will have to check
684 return atoi( strSize.c_str() );
688 * \brief Retrieve the high bit position.
689 * \warning The method defaults to 0 when information is Missing.
690 * The responsability of checking this value is left to the caller.
691 * @return The high bit positin when present. 0 when Missing.
693 int File::GetHighBitPosition()
695 std::string strSize = GetEntryValue( 0x0028, 0x0102 );
696 if ( strSize == GDCM_UNFOUND )
698 gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
701 return atoi( strSize.c_str() );
705 * \brief Retrieve the number of Samples Per Pixel
706 * (1 : gray level, 3 : RGB -1 or 3 Planes-)
707 * @return The encountered number of Samples Per Pixel, 1 by default.
708 * (Gray level Pixels)
710 int File::GetSamplesPerPixel()
712 const std::string &strSize = GetEntryValue(0x0028,0x0002);
713 if ( strSize == GDCM_UNFOUND )
715 gdcmWarningMacro( "(0028,0002) is supposed to be mandatory");
716 return 1; // Well, it's supposed to be mandatory ...
717 // but sometimes it's missing : *we* assume Gray pixels
719 return atoi( strSize.c_str() );
723 * \brief Retrieve the Planar Configuration for RGB images
724 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
725 * @return The encountered Planar Configuration, 0 by default.
727 int File::GetPlanarConfiguration()
729 std::string strSize = GetEntryValue(0x0028,0x0006);
730 if ( strSize == GDCM_UNFOUND )
732 gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
735 return atoi( strSize.c_str() );
739 * \brief Return the size (in bytes) of a single pixel of data.
740 * @return The size in bytes of a single pixel of data; 0 by default
741 * 0 means the file is NOT USABLE; the caller will have to check
743 int File::GetPixelSize()
745 // 0028 0100 US IMG Bits Allocated
746 // (in order no to be messed up by old RGB images)
747 // if (File::GetEntryValue(0x0028,0x0100) == "24")
750 std::string pixelType = GetPixelType();
751 if ( pixelType == "8U" || pixelType == "8S" )
755 if ( pixelType == "16U" || pixelType == "16S")
759 if ( pixelType == "32U" || pixelType == "32S")
763 if ( pixelType == "FD" )
767 gdcmWarningMacro( "Unknown pixel type");
772 * \brief Build the Pixel Type of the image.
773 * Possible values are:
774 * - 8U unsigned 8 bit,
776 * - 16U unsigned 16 bit,
777 * - 16S signed 16 bit,
778 * - 32U unsigned 32 bit,
779 * - 32S signed 32 bit,
780 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
781 * \warning 12 bit images appear as 16 bit.
782 * 24 bit images appear as 8 bit
783 * @return 0S if nothing found. NOT USABLE file. The caller has to check
785 std::string File::GetPixelType()
787 std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
788 if ( bitsAlloc == GDCM_UNFOUND )
790 gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
791 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
794 if ( bitsAlloc == "64" )
798 else if ( bitsAlloc == "12" )
800 // It will be unpacked
803 else if ( bitsAlloc == "24" )
805 // (in order no to be messed up
806 bitsAlloc = "8"; // by old RGB images)
809 std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation"
811 if (sign == GDCM_UNFOUND )
813 gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
814 sign = "U"; // default and arbitrary value, not to polute the output
816 else if ( sign == "0" )
824 return bitsAlloc + sign;
828 * \brief Check whether the pixels are signed or UNsigned data.
829 * \warning The method defaults to false (UNsigned) when information is Missing.
830 * The responsability of checking this value is left to the caller.
831 * @return True when signed, false when UNsigned
833 bool File::IsSignedPixelData()
835 std::string strSize = GetEntryValue( 0x0028, 0x0103 );
836 if ( strSize == GDCM_UNFOUND )
838 gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
841 int sign = atoi( strSize.c_str() );
850 * \brief Check whether this a monochrome picture (gray levels) or not,
851 * using "Photometric Interpretation" tag (0x0028,0x0004).
852 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
854 bool File::IsMonochrome()
856 const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
857 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
858 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
862 if ( PhotometricInterp == GDCM_UNFOUND )
864 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
870 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
871 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
872 * @return true when "MONOCHROME1" . False otherwise.
874 bool File::IsMonochrome1()
876 const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
877 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
881 if ( PhotometricInterp == GDCM_UNFOUND )
883 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
889 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
890 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
891 * @return true when "PALETTE COLOR". False otherwise.
893 bool File::IsPaletteColor()
895 std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
896 if ( PhotometricInterp == "PALETTE COLOR " )
900 if ( PhotometricInterp == GDCM_UNFOUND )
902 gdcmWarningMacro( "Not found : Palette color (0028,0004)");
908 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
909 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
910 * @return true when "YBR_FULL". False otherwise.
912 bool File::IsYBRFull()
914 std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
915 if ( PhotometricInterp == "YBR_FULL" )
919 if ( PhotometricInterp == GDCM_UNFOUND )
921 gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
927 * \brief tells us if LUT are used
928 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
929 * are NOT considered as LUT, since nobody knows
930 * how to deal with them
931 * Please warn me if you know sbdy that *does* know ... jprx
932 * @return true if LUT Descriptors and LUT Tables were found
936 // Check the presence of the LUT Descriptors, and LUT Tables
938 if ( !GetDocEntry(0x0028,0x1101) )
942 // LutDescriptorGreen
943 if ( !GetDocEntry(0x0028,0x1102) )
948 if ( !GetDocEntry(0x0028,0x1103) )
952 // Red Palette Color Lookup Table Data
953 if ( !GetDocEntry(0x0028,0x1201) )
957 // Green Palette Color Lookup Table Data
958 if ( !GetDocEntry(0x0028,0x1202) )
962 // Blue Palette Color Lookup Table Data
963 if ( !GetDocEntry(0x0028,0x1203) )
968 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
969 // NOT taken into account, but we don't know how to use it ...
974 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
976 * @return Lookup Table number of Bits , 0 by default
977 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
978 * @ return bit number of each LUT item
980 int File::GetLUTNbits()
982 std::vector<std::string> tokens;
985 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
986 // = Lookup Table Desc-Blue
987 // Consistency already checked in GetLUTLength
988 std::string lutDescription = GetEntryValue(0x0028,0x1101);
989 if ( lutDescription == GDCM_UNFOUND )
994 tokens.clear(); // clean any previous value
995 Util::Tokenize ( lutDescription, tokens, "\\" );
996 //LutLength=atoi(tokens[0].c_str());
997 //LutDepth=atoi(tokens[1].c_str());
999 lutNbits = atoi( tokens[2].c_str() );
1006 *\brief gets the info from 0028,1052 : Rescale Intercept
1007 * @return Rescale Intercept
1009 float File::GetRescaleIntercept()
1011 float resInter = 0.;
1012 /// 0028 1052 DS IMG Rescale Intercept
1013 const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
1014 if ( strRescInter != GDCM_UNFOUND )
1016 if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
1018 // bug in the element 0x0028,0x1052
1019 gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
1027 *\brief gets the info from 0028,1053 : Rescale Slope
1028 * @return Rescale Slope
1030 float File::GetRescaleSlope()
1032 float resSlope = 1.;
1033 //0028 1053 DS IMG Rescale Slope
1034 std::string strRescSlope = GetEntryValue(0x0028,0x1053);
1035 if ( strRescSlope != GDCM_UNFOUND )
1037 if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
1039 // bug in the element 0x0028,0x1053
1040 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
1048 * \brief This function is intended to user who doesn't want
1049 * to have to manage a LUT and expects to get an RBG Pixel image
1050 * (or a monochrome one ...)
1051 * \warning to be used with GetImagePixels()
1052 * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
1054 int File::GetNumberOfScalarComponents()
1056 if ( GetSamplesPerPixel() == 3 )
1061 // 0028 0100 US IMG Bits Allocated
1062 // (in order no to be messed up by old RGB images)
1063 if ( GetEntryValue(0x0028,0x0100) == "24" )
1068 std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
1070 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1072 if ( HasLUT() )// PALETTE COLOR is NOT enough
1082 // beware of trailing space at end of string
1083 // DICOM tags are never of odd length
1084 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1085 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1086 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1092 // we assume that *all* kinds of YBR are dealt with
1098 * \brief This function is intended to user that DOESN'T want
1099 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1100 * - the (vtk) user is supposed to know how deal with LUTs -
1101 * \warning to be used with GetImagePixelsRaw()
1102 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1104 int File::GetNumberOfScalarComponentsRaw()
1106 // 0028 0100 US IMG Bits Allocated
1107 // (in order no to be messed up by old RGB images)
1108 if ( File::GetEntryValue(0x0028,0x0100) == "24" )
1113 // we assume that *all* kinds of YBR are dealt with
1114 return GetSamplesPerPixel();
1118 * \brief Recover the offset (from the beginning of the file)
1119 * of *image* pixels (not *icone image* pixels, if any !)
1120 * @return Pixel Offset
1122 size_t File::GetPixelOffset()
1124 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1127 return pxlElement->GetOffset();
1131 gdcmDebugMacro( "Big trouble : Pixel Element ("
1132 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1138 * \brief Recover the pixel area length (in Bytes)
1139 * @return Pixel Element Length, as stored in the header
1140 * (NOT the memory space necessary to hold the Pixels
1141 * -in case of embeded compressed image-)
1142 * 0 : NOT USABLE file. The caller has to check.
1144 size_t File::GetPixelAreaLength()
1146 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1149 return pxlElement->GetLength();
1153 gdcmDebugMacro( "Big trouble : Pixel Element ("
1154 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1160 * \brief Adds the characteristics of a new element we want to anonymize
1163 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1164 std::string const &value)
1171 AnonymizeList.push_back(el);
1175 * \brief Overwrites in the file the values of the DicomElements
1178 void File::AnonymizeNoLoad()
1180 std::fstream *fp = new std::fstream(Filename.c_str(),
1181 std::ios::in | std::ios::out | std::ios::binary);
1184 // how to white out disk space if longer than 50 ?
1190 uint32_t valLgth = 0;
1191 std::string *spaces;
1192 for (ListElements::iterator it = AnonymizeList.begin();
1193 it != AnonymizeList.end();
1196 d = GetDocEntry( (*it).Group, (*it).Elem);
1201 if ( dynamic_cast<BinEntry *>(d)
1202 || dynamic_cast<SeqEntry *>(d) )
1205 offset = d->GetOffset();
1206 lgth = d->GetLength();
1209 spaces = new std::string( lgth-valLgth, ' ');
1210 (*it).Value = (*it).Value + *spaces;
1213 fp->seekp( offset, std::ios::beg );
1214 fp->write( (*it).Value.c_str(), lgth );
1222 * \brief anonymize a File (removes Patient's personal info passed with
1223 * AddAnonymizeElement()
1225 bool File::AnonymizeFile()
1227 // If Anonymisation list is empty, let's perform some basic anonymization
1228 if ( AnonymizeList.begin() == AnonymizeList.end() )
1230 // If exist, replace by spaces
1231 SetValEntry (" ",0x0010, 0x2154); // Telephone
1232 SetValEntry (" ",0x0010, 0x1040); // Adress
1233 SetValEntry (" ",0x0010, 0x0020); // Patient ID
1235 DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
1237 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1239 std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
1240 if ( studyInstanceUID != GDCM_UNFOUND )
1242 SetValEntry(studyInstanceUID, 0x0010, 0x0010);
1246 SetValEntry("anonymised", 0x0010, 0x0010);
1253 for (ListElements::iterator it = AnonymizeList.begin();
1254 it != AnonymizeList.end();
1257 d = GetDocEntry( (*it).Group, (*it).Elem);
1262 if ( dynamic_cast<BinEntry *>(d)
1263 || dynamic_cast<SeqEntry *>(d) )
1266 SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
1270 // In order to make definitively impossible any further identification
1271 // remove or replace all the stuff that contains a Date
1273 //0008 0012 DA ID Instance Creation Date
1274 //0008 0020 DA ID Study Date
1275 //0008 0021 DA ID Series Date
1276 //0008 0022 DA ID Acquisition Date
1277 //0008 0023 DA ID Content Date
1278 //0008 0024 DA ID Overlay Date
1279 //0008 0025 DA ID Curve Date
1280 //0008 002a DT ID Acquisition Datetime
1281 //0018 9074 DT ACQ Frame Acquisition Datetime
1282 //0018 9151 DT ACQ Frame Reference Datetime
1283 //0018 a002 DT ACQ Contribution Date Time
1284 //0020 3403 SH REL Modified Image Date (RET)
1285 //0032 0032 DA SDY Study Verified Date
1286 //0032 0034 DA SDY Study Read Date
1287 //0032 1000 DA SDY Scheduled Study Start Date
1288 //0032 1010 DA SDY Scheduled Study Stop Date
1289 //0032 1040 DA SDY Study Arrival Date
1290 //0032 1050 DA SDY Study Completion Date
1291 //0038 001a DA VIS Scheduled Admission Date
1292 //0038 001c DA VIS Scheduled Discharge Date
1293 //0038 0020 DA VIS Admitting Date
1294 //0038 0030 DA VIS Discharge Date
1295 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1296 //0040 0004 DA PRC Scheduled Procedure Step End Date
1297 //0040 0244 DA PRC Performed Procedure Step Start Date
1298 //0040 0250 DA PRC Performed Procedure Step End Date
1299 //0040 2004 DA PRC Issue Date of Imaging Service Request
1300 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1301 //0040 4011 DT PRC Expected Completion Date and Time
1302 //0040 a030 DT PRC Verification Date Time
1303 //0040 a032 DT PRC Observation Date Time
1304 //0040 a120 DT PRC DateTime
1305 //0040 a121 DA PRC Date
1306 //0040 a13a DT PRC Referenced Datetime
1307 //0070 0082 DA ??? Presentation Creation Date
1308 //0100 0420 DT ??? SOP Autorization Date and Time
1309 //0400 0105 DT ??? Digital Signature DateTime
1310 //2100 0040 DA PJ Creation Date
1311 //3006 0008 DA SSET Structure Set Date
1312 //3008 0024 DA ??? Treatment Control Point Date
1313 //3008 0054 DA ??? First Treatment Date
1314 //3008 0056 DA ??? Most Recent Treatment Date
1315 //3008 0162 DA ??? Safe Position Exit Date
1316 //3008 0166 DA ??? Safe Position Return Date
1317 //3008 0250 DA ??? Treatment Date
1318 //300a 0006 DA RT RT Plan Date
1319 //300a 022c DA RT Air Kerma Rate Reference Date
1320 //300e 0004 DA RT Review Date
1326 * \brief Performs some consistency checking on various 'File related'
1327 * (as opposed to 'DicomDir related') entries
1328 * then writes in a file all the (Dicom Elements) included the Pixels
1329 * @param fileName file name to write to
1330 * @param filetype Type of the File to be written
1331 * (ACR, ExplicitVR, ImplicitVR)
1333 bool File::Write(std::string fileName, FileType filetype)
1335 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1336 std::ios::out | std::ios::binary);
1339 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1343 // Entry : 0002|0000 = group length -> recalculated
1344 ValEntry *e0002 = GetValEntry(0x0002,0x0000);
1347 std::ostringstream sLen;
1348 sLen << ComputeGroup0002Length(filetype);
1349 e0002->SetValue(sLen.str());
1353 if ( GetEntryValue(0x0028,0x0100) == "12")
1355 SetValEntry("16", 0x0028,0x0100);
1358 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1361 // no (GrPixel, NumPixel) element
1362 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1363 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1364 InsertValEntry(s_lgPix,GrPixel, 0x0000);
1367 // FIXME : should be nice if we could move it to File
1368 // (or in future gdcmPixelData class)
1370 // Drop Palette Color, if necessary
1371 if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' )
1373 // if SamplesPerPixel = 3, sure we don't need any LUT !
1374 // Drop 0028|1101, 0028|1102, 0028|1103
1375 // Drop 0028|1201, 0028|1202, 0028|1203
1377 DocEntry *e = GetDocEntry(0x0028,0x01101);
1380 RemoveEntryNoDestroy(e);
1382 e = GetDocEntry(0x0028,0x1102);
1385 RemoveEntryNoDestroy(e);
1387 e = GetDocEntry(0x0028,0x1103);
1390 RemoveEntryNoDestroy(e);
1392 e = GetDocEntry(0x0028,0x01201);
1395 RemoveEntryNoDestroy(e);
1397 e = GetDocEntry(0x0028,0x1202);
1400 RemoveEntryNoDestroy(e);
1402 e = GetDocEntry(0x0028,0x1203);
1405 RemoveEntryNoDestroy(e);
1409 Document::WriteContent(fp, filetype);
1417 //-----------------------------------------------------------------------------
1420 * \brief Initialize a default DICOM File that should contain all the
1421 * field require by other reader. DICOM standard does not
1422 * explicitely defines those fields, heuristic has been choosen.
1423 * This is not perfect as we are writting a CT image...
1425 void File::InitializeDefaultFile()
1427 std::string date = Util::GetCurrentDate();
1428 std::string time = Util::GetCurrentTime();
1429 std::string uid = Util::CreateUniqueUID();
1430 std::string uidMedia = uid;
1431 std::string uidInst = uid;
1432 std::string uidClass = Util::CreateUniqueUID();
1433 std::string uidStudy = Util::CreateUniqueUID();
1434 std::string uidSerie = Util::CreateUniqueUID();
1436 // Meta Element Group Length
1437 InsertValEntry("146 ", 0x0002, 0x0000);
1438 // Media Storage SOP Class UID (CT Image Storage)
1439 InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002);
1440 // Media Storage SOP Instance UID
1441 InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003);
1442 // Transfer Syntax UID (Explicit VR Little Endian)
1443 InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010);
1444 // META Implementation Class UID
1445 InsertValEntry(uidClass.c_str(), 0x0002, 0x0012);
1446 // Source Application Entity Title
1447 InsertValEntry("GDCM", 0x0002, 0x0016);
1449 // Instance Creation Date
1450 InsertValEntry(date.c_str(), 0x0008, 0x0012);
1451 // Instance Creation Time
1452 InsertValEntry(time.c_str(), 0x0008, 0x0013);
1454 InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016);
1456 InsertValEntry(uidInst.c_str(), 0x0008, 0x0018);
1458 InsertValEntry("CT", 0x0008, 0x0060);
1460 InsertValEntry("GDCM", 0x0008, 0x0070);
1462 InsertValEntry("GDCM", 0x0008, 0x0080);
1463 // Institution Address
1464 InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081);
1467 InsertValEntry("GDCM", 0x0010, 0x0010);
1469 InsertValEntry("GDCMID", 0x0010, 0x0020);
1471 // Study Instance UID
1472 InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d);
1473 // Series Instance UID
1474 InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e);
1476 InsertValEntry("1", 0x0020, 0x0010);
1478 InsertValEntry("1", 0x0020, 0x0011);
1480 // Samples per pixel 1 or 3
1481 InsertValEntry("1", 0x0028, 0x0002);
1482 // photochromatic interpretation
1483 InsertValEntry("MONOCHROME1", 0x0028, 0x0004);
1485 InsertValEntry("0", 0x0028, 0x0010);
1487 InsertValEntry("0", 0x0028, 0x0011);
1488 // BitsAllocated 8 or 12 or 16
1489 InsertValEntry("8", 0x0028, 0x0100);
1490 // BitsStored <= BitsAllocated
1491 InsertValEntry("8", 0x0028, 0x0101);
1492 // HighBit <= BitsAllocated - 1
1493 InsertValEntry("7", 0x0028, 0x0102);
1494 // Pixel Representation 0(unsigned) or 1(signed)
1495 InsertValEntry("0", 0x0028, 0x0103);
1498 // Special case this is the image (not a string)
1501 InsertBinEntry(0, 0, GrPixel, NumPixel);
1504 //-----------------------------------------------------------------------------
1507 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1508 * Compute the RLE extra information and store it in \ref RLEInfo
1509 * for later pixel retrieval usage.
1511 void File::ComputeRLEInfo()
1513 std::string ts = GetTransferSyntax();
1514 if ( !Global::GetTS()->IsRLELossless(ts) )
1519 // Encoded pixel data: for the time being we are only concerned with
1520 // Jpeg or RLE Pixel data encodings.
1521 // As stated in PS 3.5-2003, section 8.2 p44:
1522 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1523 // value representation OB is used".
1524 // Hence we expect an OB value representation. Concerning OB VR,
1525 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1526 // "For the Value Representations OB and OW, the encoding shall meet the
1527 // following specifications depending on the Data element tag:"
1529 // - the first item in the sequence of items before the encoded pixel
1530 // data stream shall be basic offset table item. The basic offset table
1531 // item value, however, is not required to be present"
1532 ReadAndSkipEncapsulatedBasicOffsetTable();
1534 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1535 // Loop on the individual frame[s] and store the information
1536 // on the RLE fragments in a RLEFramesInfo.
1537 // Note: - when only a single frame is present, this is a
1539 // - when more than one frame are present, then we are in
1540 // the case of a multi-frame image.
1542 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
1544 // Parse the RLE Header and store the corresponding RLE Segment
1545 // Offset Table information on fragments of this current Frame.
1546 // Note that the fragment pixels themselves are not loaded
1547 // (but just skipped).
1548 long frameOffset = Fp->tellg();
1550 uint32_t nbRleSegments = ReadInt32();
1551 if ( nbRleSegments > 16 )
1553 // There should be at most 15 segments (refer to RLEFrame class)
1554 gdcmWarningMacro( "Too many segments.");
1557 uint32_t rleSegmentOffsetTable[16];
1558 for( int k = 1; k <= 15; k++ )
1560 rleSegmentOffsetTable[k] = ReadInt32();
1563 // Deduce from both the RLE Header and the frameLength the
1564 // fragment length, and again store this info in a
1566 long rleSegmentLength[15];
1567 // skipping (not reading) RLE Segments
1568 if ( nbRleSegments > 1)
1570 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1572 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1573 - rleSegmentOffsetTable[k];
1574 SkipBytes(rleSegmentLength[k]);
1578 rleSegmentLength[nbRleSegments] = frameLength
1579 - rleSegmentOffsetTable[nbRleSegments];
1580 SkipBytes(rleSegmentLength[nbRleSegments]);
1582 // Store the collected info
1583 RLEFrame *newFrame = new RLEFrame;
1584 newFrame->SetNumberOfFragments(nbRleSegments);
1585 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1587 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1588 newFrame->SetLength(uk,rleSegmentLength[uk]);
1590 RLEInfo->AddFrame(newFrame);
1593 // Make sure that at the end of the item we encounter a 'Sequence
1595 if ( !ReadTag(0xfffe, 0xe0dd) )
1597 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1602 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1603 * Compute the jpeg extra information (fragment[s] offset[s] and
1604 * length) and store it[them] in \ref JPEGInfo for later pixel
1607 void File::ComputeJPEGFragmentInfo()
1609 // If you need to, look for comments of ComputeRLEInfo().
1610 std::string ts = GetTransferSyntax();
1611 if ( ! Global::GetTS()->IsJPEG(ts) )
1616 ReadAndSkipEncapsulatedBasicOffsetTable();
1618 // Loop on the fragments[s] and store the parsed information in a
1620 long fragmentLength;
1621 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
1623 long fragmentOffset = Fp->tellg();
1625 // Store the collected info
1626 JPEGFragment *newFragment = new JPEGFragment;
1627 newFragment->SetOffset(fragmentOffset);
1628 newFragment->SetLength(fragmentLength);
1629 JPEGInfo->AddFragment(newFragment);
1631 SkipBytes(fragmentLength);
1634 // Make sure that at the end of the item we encounter a 'Sequence
1636 if ( !ReadTag(0xfffe, 0xe0dd) )
1638 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1643 * \brief Assuming the internal file pointer \ref Document::Fp
1644 * is placed at the beginning of a tag check whether this
1645 * tag is (TestGroup, TestElement).
1646 * \warning On success the internal file pointer \ref Document::Fp
1647 * is modified to point after the tag.
1648 * On failure (i.e. when the tag wasn't the expected tag
1649 * (TestGroup, TestElement) the internal file pointer
1650 * \ref Document::Fp is restored to it's original position.
1651 * @param testGroup The expected group of the tag.
1652 * @param testElement The expected Element of the tag.
1653 * @return True on success, false otherwise.
1655 bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
1657 long positionOnEntry = Fp->tellg();
1658 long currentPosition = Fp->tellg(); // On debugging purposes
1660 // Read the Item Tag group and element, and make
1661 // sure they are what we expected:
1662 uint16_t itemTagGroup;
1663 uint16_t itemTagElement;
1666 itemTagGroup = ReadInt16();
1667 itemTagElement = ReadInt16();
1669 catch ( FormatError e )
1671 //std::cerr << e << std::endl;
1674 if ( itemTagGroup != testGroup || itemTagElement != testElement )
1676 gdcmWarningMacro( "Wrong Item Tag found:"
1677 << " We should have found tag ("
1678 << std::hex << testGroup << "," << testElement << ")" << std::endl
1679 << " but instead we encountered tag ("
1680 << std::hex << itemTagGroup << "," << itemTagElement << ")"
1681 << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
1683 Fp->seekg(positionOnEntry, std::ios::beg);
1691 * \brief Assuming the internal file pointer \ref Document::Fp
1692 * is placed at the beginning of a tag (TestGroup, TestElement),
1693 * read the length associated to the Tag.
1694 * \warning On success the internal file pointer \ref Document::Fp
1695 * is modified to point after the tag and it's length.
1696 * On failure (i.e. when the tag wasn't the expected tag
1697 * (TestGroup, TestElement) the internal file pointer
1698 * \ref Document::Fp is restored to it's original position.
1699 * @param testGroup The expected group of the tag.
1700 * @param testElement The expected Element of the tag.
1701 * @return On success returns the length associated to the tag. On failure
1704 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement)
1707 if ( !ReadTag(testGroup, testElement) )
1712 //// Then read the associated Item Length
1713 long currentPosition = Fp->tellg();
1714 uint32_t itemLength = ReadInt32();
1716 gdcmWarningMacro( "Basic Item Length is: "
1717 << itemLength << std::endl
1718 << " at address: " << std::hex << (unsigned int)currentPosition);
1724 * \brief When parsing the Pixel Data of an encapsulated file, read
1725 * the basic offset table (when present, and BTW dump it).
1727 void File::ReadAndSkipEncapsulatedBasicOffsetTable()
1729 //// Read the Basic Offset Table Item Tag length...
1730 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1732 // When present, read the basic offset table itself.
1733 // Notes: - since the presence of this basic offset table is optional
1734 // we can't rely on it for the implementation, and we will simply
1735 // trash it's content (when present).
1736 // - still, when present, we could add some further checks on the
1737 // lengths, but we won't bother with such fuses for the time being.
1738 if ( itemLength != 0 )
1740 char *basicOffsetTableItemValue = new char[itemLength + 1];
1741 Fp->read(basicOffsetTableItemValue, itemLength);
1744 for (unsigned int i=0; i < itemLength; i += 4 )
1746 uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
1748 gdcmWarningMacro( "Read one length: " <<
1749 std::hex << individualLength );
1753 delete[] basicOffsetTableItemValue;
1757 //-----------------------------------------------------------------------------
1760 //-----------------------------------------------------------------------------
1761 } // end namespace gdcm