X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=c27a505a1769d6eeb695cc2198db3c56ce4ba52c;hb=fa5cf7cf67a3ea643dae69394ac8df512a4d4d2e;hp=ac3b4707f4d64010806a3bbd19ba81e912bbcd6d;hpb=b1ebe82627c2a83cc9dd1239b148779d9a7c32ce;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index ac3b4707..c27a505a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/02/05 01:31:36 $ - Version: $Revision: 1.211 $ + Date: $Date: 2005/03/02 17:18:32 $ + Version: $Revision: 1.228 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,7 +23,7 @@ // If not found (ACR_NEMA) we try Image Position (0020,0030) // If not found (ACR-NEMA), we consider Slice Location (0020,1041) // or Location (0020,0050) -// as the Z coordinate, +// as the Z coordinate, // 0. for all the coordinates if nothing is found // // --------------------------------------------------------------- @@ -35,6 +35,7 @@ #include "gdcmTS.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" @@ -114,7 +115,6 @@ File::File( std::string const &filename ) // Create a new BinEntry to change the the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) - // - a VM to "PXL" // - the name to "Pixel Data" BinEntry *oldEntry = dynamic_cast(entry); if(oldEntry) @@ -215,13 +215,7 @@ bool File::IsReadable() */ int File::GetImageNumber() { - // The function i atoi() takes the address of an area of memory as - // parameter and converts the string stored at that location to an integer - // using the external decimal to internal binary conversion rules. This may - // be preferable to sscanf() since atoi() is a much smaller, simpler and - // faster function. sscanf() can do all possible conversions whereas - // atoi() can only do single decimal integer conversions. - //0020 0013 IS REL Image Number + //0020 0013 : Image Number std::string strImNumber = GetEntryValue(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { @@ -236,7 +230,7 @@ int File::GetImageNumber() */ ModalityType File::GetModality() { - // 0008 0060 CS ID Modality + // 0008 0060 : Modality std::string strModality = GetEntryValue(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { @@ -366,12 +360,13 @@ int File::GetZSize() */ float File::GetXSpacing() { - float xspacing, yspacing; + float xspacing = 1.0; + float yspacing = 1.0; const std::string &strSpacing = GetEntryValue(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) + if( strSpacing == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); return 1.; } @@ -379,11 +374,12 @@ float File::GetXSpacing() if( ( nbValues = sscanf( strSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2 ) { + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + xspacing = 1.0; // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - { + if( nbValues == 1 ) xspacing = yspacing; - } if ( xspacing == 0.0 ) xspacing = 1.0; @@ -398,7 +394,7 @@ float File::GetXSpacing() if ( xspacing == 0.) { - gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem"); // seems to be a bug in the header ... nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); gdcmAssertMacro( nbValues == 2 ); @@ -419,12 +415,16 @@ float File::GetYSpacing() if ( strSpacing == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)"); + gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); return 1.; } // if sscanf cannot read any float value, it won't affect yspacing - sscanf( strSpacing.c_str(), "%f", &yspacing); + int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + yspacing = 1.0; if ( yspacing == 0.0 ) yspacing = 1.0; @@ -440,25 +440,25 @@ float File::GetYSpacing() */ float File::GetZSpacing() { - // Spacing Between Slices : distance entre le milieu de chaque coupe - // Les coupes peuvent etre : + // Spacing Between Slices : distance between the middle of 2 slices + // Slices may be : // jointives (Spacing between Slices = Slice Thickness) - // chevauchantes (Spacing between Slices < Slice Thickness) + // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal - // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... - // Si le Spacing Between Slices est Missing, - // on suppose que les coupes sont jointives + // It only concerns the MRI guys, not people wanting to visualize volmues + // If Spacing Between Slices is Missing, + // we suppose slices joint together const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)"); + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)"); + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); return 1.; } else @@ -487,11 +487,11 @@ float File::GetXOrigin() if ( strImPos == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.; } } @@ -517,11 +517,11 @@ float File::GetYOrigin() if ( strImPos == GDCM_UNFOUND) { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.; } } @@ -551,7 +551,7 @@ float File::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)"); + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -566,7 +566,7 @@ float File::GetZOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { - gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)"); + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -580,7 +580,7 @@ float File::GetZOrigin() { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - gdcmVerboseMacro( "Wrong Slice Location (0020,1041)"); + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -588,14 +588,14 @@ float File::GetZOrigin() return zImPos; } } - gdcmVerboseMacro( "Unfound Slice Location (0020,1041)"); + gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); std::string strLocation = GetEntryValue(0x0020,0x0050); if ( strLocation != GDCM_UNFOUND ) { if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) { - gdcmVerboseMacro( "Wrong Location (0020,0050)"); + gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -603,7 +603,7 @@ float File::GetZOrigin() return zImPos; } } - gdcmVerboseMacro( "Unfound Location (0020,0050)"); + gdcmWarningMacro( "Unfound Location (0020,0050)"); return 0.; // Hopeless } @@ -626,7 +626,7 @@ void File::GetImageOrientationPatient( float iop[6] ) if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); } } //For ACR-NEMA @@ -636,14 +636,14 @@ void File::GetImageOrientationPatient( float iop[6] ) if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); } } } /** * \brief Retrieve the number of Bits Stored (actually used) - * (as opposite to number of Bits Allocated) + * (as opposed to number of Bits Allocated) * @return The encountered number of Bits Stored, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ @@ -652,7 +652,7 @@ int File::GetBitsStored() std::string strSize = GetEntryValue( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro("(0028,0101) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } @@ -670,7 +670,7 @@ int File::GetBitsAllocated() std::string strSize = GetEntryValue(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } @@ -688,7 +688,7 @@ int File::GetHighBitPosition() std::string strSize = GetEntryValue( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); return 0; } return atoi( strSize.c_str() ); @@ -705,7 +705,7 @@ int File::GetSamplesPerPixel() const std::string &strSize = GetEntryValue(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } @@ -722,7 +722,7 @@ int File::GetPlanarConfiguration() std::string strSize = GetEntryValue(0x0028,0x0006); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)"); + gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return atoi( strSize.c_str() ); @@ -757,7 +757,7 @@ int File::GetPixelSize() { return 8; } - gdcmVerboseMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type"); return 0; } @@ -772,7 +772,7 @@ int File::GetPixelSize() * - 32S signed 32 bit, * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. - * 24 bit images appear as 8 bit + * 24 bit images appear as 8 bit + photochromatic interp ="RGB " * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() @@ -780,7 +780,7 @@ std::string File::GetPixelType() std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); + gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); bitsAlloc = "16"; // default and arbitrary value, not to polute the output } @@ -803,7 +803,7 @@ std::string File::GetPixelType() if (sign == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); sign = "U"; // default and arbitrary value, not to polute the output } else if ( sign == "0" ) @@ -828,7 +828,7 @@ bool File::IsSignedPixelData() std::string strSize = GetEntryValue( 0x0028, 0x0103 ); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); return false; } int sign = atoi( strSize.c_str() ); @@ -840,8 +840,8 @@ bool File::IsSignedPixelData() } /** - * \brief Check whether this a monochrome picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * \brief Check whether this a monochrome picture (gray levels) or not, + * using "Photometric Interpretation" tag (0x0028,0x0004). * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ bool File::IsMonochrome() @@ -854,7 +854,26 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; +} + +/** + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. + */ +bool File::IsMonochrome1() +{ + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); } return false; } @@ -873,7 +892,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); + gdcmWarningMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -892,7 +911,7 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); + gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -990,7 +1009,7 @@ float File::GetRescaleIntercept() if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { // bug in the element 0x0028,0x1052 - gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); } } @@ -1011,7 +1030,7 @@ float File::GetRescaleSlope() if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) { // bug in the element 0x0028,0x1053 - gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } @@ -1095,7 +1114,7 @@ int File::GetNumberOfScalarComponentsRaw() */ size_t File::GetPixelOffset() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -1117,7 +1136,7 @@ size_t File::GetPixelOffset() */ size_t File::GetPixelAreaLength() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -1131,33 +1150,118 @@ size_t File::GetPixelAreaLength() } /** - * \brief anonymize a File (removes Patient's personal info) - * (read the code to see which ones ...) + * \brief Adds the characteristics of a new element we want to anonymize + * */ -bool File::AnonymizeFile() +void File::AddAnonymizeElement (uint16_t group, uint16_t elem, + std::string const &value) + +{ + Element el; + el.Group = group; + el.Elem = elem; + el.Value = value; + AnonymizeList.push_back(el); +} + +/** + * \brief Overwrites in the file the values of the DicomElements + * held in the list + */ +void File::AnonymizeNoLoad() { - // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + std::fstream *fp = new std::fstream(Filename.c_str(), + std::ios::in | std::ios::out | std::ios::binary); + + // TODO : FIXME + // how to white out disk space if longer than 50 ? + + + gdcm::DocEntry *d; + uint32_t offset; + uint32_t lgth; + uint32_t valLgth = 0; + std::string *spaces; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); - DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); - - if ( patientNameHE ) // we replace it by Study Instance UID (why not) - { - std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); - if ( studyInstanceUID != GDCM_UNFOUND ) + if ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + offset = d->GetOffset(); + lgth = d->GetLength(); + if (valLgth < lgth) { - InsertValEntry(studyInstanceUID, 0x0010, 0x0010); + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } - else + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + + } + fp->close(); + delete fp; +} + +/** + * \brief anonymize a File (removes Patient's personal info passed with + * AddAnonymizeElement() + */ +bool File::AnonymizeFile() +{ + // If Anonymisation list is empty, let's perform some basic anonymization + if ( AnonymizeList.begin() == AnonymizeList.end() ) + { + // If exist, replace by spaces + SetValEntry (" ",0x0010, 0x2154); // Telephone + SetValEntry (" ",0x0010, 0x1040); // Adress + SetValEntry (" ",0x0010, 0x0020); // Patient ID + + DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { - InsertValEntry("anonymised", 0x0010, 0x0010); + std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + SetValEntry(studyInstanceUID, 0x0010, 0x0010); + } + else + { + SetValEntry("anonymised", 0x0010, 0x0010); + } } } + else + { + gdcm::DocEntry *d; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); - // Just for fun :-( - // (if any) remove or replace all the stuff that contains a Date + if ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + } +} + + // In order to make definitively impossible any further identification + // remove or replace all the stuff that contains a Date //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date @@ -1216,26 +1320,26 @@ bool File::AnonymizeFile() * (as opposed to 'DicomDir related') entries * then writes in a file all the (Dicom Elements) included the Pixels * @param fileName file name to write to - * @param filetype Type of the File to be written + * @param writetype Type of the File to be written * (ACR, ExplicitVR, ImplicitVR) */ -bool File::Write(std::string fileName, FileType filetype) +bool File::Write(std::string fileName, FileType writetype) { std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if (*fp == NULL) { - gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str()); + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); return false; } // Entry : 0002|0000 = group length -> recalculated - ValEntry *e0002 = GetValEntry(0x0002,0x0000); - if( e0002 ) + ValEntry*e0000 = GetValEntry(0x0002,0x0000); + if( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(filetype); - e0002->SetValue(sLen.str()); + sLen << ComputeGroup0002Length(writetype); + e0000->SetValue(sLen.str()); } // Bits Allocated @@ -1295,39 +1399,7 @@ bool File::Write(std::string fileName, FileType filetype) } } - -#ifdef GDCM_WORDS_BIGENDIAN - // Super Super hack that will make gdcm a BOMB ! but should - // Fix temporarily the dashboard - BinEntry *b = GetBinEntry(GrPixel,NumPixel); - if ( GetPixelSize() == 16 ) - { - uint16_t *im16 = (uint16_t *)b->GetBinArea(); - int lgr = b->GetLength(); - for( int i = 0; i < lgr / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - } -#endif //GDCM_WORDS_BIGENDIAN - - - Document::WriteContent(fp, filetype); - - -#ifdef GDCM_WORDS_BIGENDIAN - // Flip back the pixel ... I told you this is a hack - if ( GetPixelSize() == 16 ) - { - uint16_t *im16 = (uint16_t*)b->GetBinArea(); - int lgr = b->GetLength(); - for( int i = 0; i < lgr / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - } -#endif //GDCM_WORDS_BIGENDIAN - + Document::WriteContent(fp, writetype); fp->close(); delete fp; @@ -1339,12 +1411,18 @@ bool File::Write(std::string fileName, FileType filetype) // Protected /** * \brief Initialize a default DICOM File that should contain all the - * field require by other reader. DICOM standard does not + * fields required by other readers. DICOM standard does not * explicitely defines those fields, heuristic has been choosen. - * This is not perfect as we are writting a CT image... + * \todo some more tests to be performed to avoid collisions + * with FileHelper::CheckMandatoryElements() */ void File::InitializeDefaultFile() { + +/* + // CurrentTime will be set just before Writting + // whatever the source image is + std::string date = Util::GetCurrentDate(); std::string time = Util::GetCurrentTime(); std::string uid = Util::CreateUniqueUID(); @@ -1354,21 +1432,32 @@ void File::InitializeDefaultFile() std::string uidStudy = Util::CreateUniqueUID(); std::string uidSerie = Util::CreateUniqueUID(); + // Meta Elements are set just before writting + // Meta Element Group Length InsertValEntry("146 ", 0x0002, 0x0000); - // Media Storage SOP Class UID (CT Image Storage) - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002); + // Media Storage SOP Class UID (Secondary Capture Image Storage) + InsertValEntry("1.2.840.10008.5.1.4.1.1.7", 0x0002, 0x0002); // Media Storage SOP Instance UID - InsertValEntry(uidClass.c_str(), 0x0002, 0x0003); + InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003); // Transfer Syntax UID (Explicit VR Little Endian) InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010); // META Implementation Class UID InsertValEntry(uidClass.c_str(), 0x0002, 0x0012); // Source Application Entity Title InsertValEntry("GDCM", 0x0002, 0x0016); +*/ + +// Just to avoid further trouble if user asks to write the dile ACR-NEMA mode + InsertValEntry("", 0x0008, 0x0010); // Recognition Code (RET) + +/* +// Dicom related entries must be set by the user +// If they are missing, they are defaulted just bedfore writting // Instance Creation Date InsertValEntry(date.c_str(), 0x0008, 0x0012); + // Instance Creation Time InsertValEntry(time.c_str(), 0x0008, 0x0013); // SOP Class UID @@ -1376,16 +1465,18 @@ void File::InitializeDefaultFile() // SOP Instance UID InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); // Modality - InsertValEntry("CT", 0x0008, 0x0060); + InsertValEntry("OT", 0x0008, 0x0060); // Manufacturer InsertValEntry("GDCM", 0x0008, 0x0070); // Institution Name InsertValEntry("GDCM", 0x0008, 0x0080); // Institution Address InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081); +*/ +/* // Patient's Name - InsertValEntry("GDCM", 0x0010, 0x0010); + InsertValEntry("GDCM^patient", 0x0010, 0x0010); // Patient ID InsertValEntry("GDCMID", 0x0010, 0x0020); @@ -1395,13 +1486,18 @@ void File::InitializeDefaultFile() InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); // StudyID InsertValEntry("1", 0x0020, 0x0010); + + // Is 'Series number' mandatory ? // SeriesNumber InsertValEntry("1", 0x0020, 0x0011); +// None of these default value is meaningfull ! +// It *must be* up to the user to initialize them. + // Samples per pixel 1 or 3 InsertValEntry("1", 0x0028, 0x0002); // photochromatic interpretation - InsertValEntry("MONOCHROME1", 0x0028, 0x0004); + InsertValEntry("MONOCHROME2", 0x0028, 0x0004); // nbRows InsertValEntry("0", 0x0028, 0x0010); // nbCols @@ -1415,11 +1511,17 @@ void File::InitializeDefaultFile() // Pixel Representation 0(unsigned) or 1(signed) InsertValEntry("0", 0x0028, 0x0103); +*/ + + // It should be up to the user to do that! + // default value // Special case this is the image (not a string) + GrPixel = 0x7fe0; NumPixel = 0x0010; InsertBinEntry(0, 0, GrPixel, NumPixel); + } //----------------------------------------------------------------------------- @@ -1472,7 +1574,7 @@ void File::ComputeRLEInfo() if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) - gdcmVerboseMacro( "Too many segments."); + gdcmWarningMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; @@ -1515,7 +1617,7 @@ void File::ComputeRLEInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); + gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } } @@ -1556,7 +1658,7 @@ void File::ComputeJPEGFragmentInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); + gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } } @@ -1578,7 +1680,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) long positionOnEntry = Fp->tellg(); long currentPosition = Fp->tellg(); // On debugging purposes - //// Read the Item Tag group and element, and make + // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; uint16_t itemTagElement; @@ -1594,7 +1696,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) } if ( itemTagGroup != testGroup || itemTagElement != testElement ) { - gdcmVerboseMacro( "Wrong Item Tag found:" + gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" << std::hex << testGroup << "," << testElement << ")" << std::endl << " but instead we encountered tag (" @@ -1634,7 +1736,7 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { - gdcmVerboseMacro( "Basic Item Length is: " + gdcmWarningMacro( "Basic Item Length is: " << itemLength << std::endl << " at address: " << std::hex << (unsigned int)currentPosition); } @@ -1666,7 +1768,7 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() { uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], uint32_t); - gdcmVerboseMacro( "Read one length: " << + gdcmWarningMacro( "Read one length: " << std::hex << individualLength ); } #endif //GDCM_DEBUG