X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=c27a505a1769d6eeb695cc2198db3c56ce4ba52c;hb=fa5cf7cf67a3ea643dae69394ac8df512a4d4d2e;hp=064eb84a6d4b23a92dcb301db86e3caa80d929c0;hpb=33ea6274972a853d1214fc5e6ea31309ec7e2ad8;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 064eb84a..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: 2005/02/07 12:54:00 $ - Version: $Revision: 1.216 $ + 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 @@ -115,7 +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) @@ -216,13 +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 ) { @@ -237,7 +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 ) { @@ -367,7 +360,8 @@ 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 ) @@ -400,7 +394,7 @@ float File::GetXSpacing() if ( xspacing == 0.) { - gdcmWarningMacro("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 ); @@ -446,15 +440,15 @@ 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); @@ -778,7 +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() @@ -846,8 +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() @@ -865,6 +859,25 @@ bool File::IsMonochrome() 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; +} + /** * \brief Check whether this a "PALETTE COLOR" picture or not by accessing * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). @@ -1159,42 +1172,40 @@ void File::AnonymizeNoLoad() { 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 ? - char spaces[50] = " "; + gdcm::DocEntry *d; uint32_t offset; uint32_t lgth; - uint32_t lgtToWrite; + uint32_t valLgth = 0; + std::string *spaces; for (ListElements::iterator it = AnonymizeList.begin(); it != AnonymizeList.end(); ++it) - { + { d = GetDocEntry( (*it).Group, (*it).Elem); + if ( d == NULL) + continue; + if ( dynamic_cast(d) || dynamic_cast(d) ) continue; offset = d->GetOffset(); lgth = d->GetLength(); - fp->seekp( offset, std::ios::beg ); - - if ( (*it).Value == "" ) + if (valLgth < lgth) { - lgtToWrite = lgth > 50 ? 50 : lgth; - fp->write( spaces, lgtToWrite ); - } - else - { - // TODO : FIXME - // how to white out disk space if longer than 50 ? - (*it).Value = (*it).Value + spaces; - lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth; - fp->write( (char *)(*it).Value.c_str(), lgtToWrite ); - + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + } fp->close(); delete fp; @@ -1206,7 +1217,7 @@ void File::AnonymizeNoLoad() */ bool File::AnonymizeFile() { - // If Anonymisation list is empty, let's perform some basic anonymisation + // If Anonymisation list is empty, let's perform some basic anonymization if ( AnonymizeList.begin() == AnonymizeList.end() ) { // If exist, replace by spaces @@ -1238,6 +1249,9 @@ bool File::AnonymizeFile() { d = GetDocEntry( (*it).Group, (*it).Elem); + if ( d == NULL) + continue; + if ( dynamic_cast(d) || dynamic_cast(d) ) continue; @@ -1306,10 +1320,10 @@ 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); @@ -1320,12 +1334,12 @@ bool File::Write(std::string fileName, FileType filetype) } // 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 @@ -1385,39 +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 lgth = b->GetLength(); - for( int i = 0; i < lgth / 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 lgth = b->GetLength(); - for( int i = 0; i < lgth / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - } -#endif //GDCM_WORDS_BIGENDIAN - + Document::WriteContent(fp, writetype); fp->close(); delete fp; @@ -1429,12 +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(); @@ -1444,10 +1432,12 @@ 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(uidMedia.c_str(), 0x0002, 0x0003); // Transfer Syntax UID (Explicit VR Little Endian) @@ -1456,9 +1446,18 @@ void File::InitializeDefaultFile() 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 @@ -1466,16 +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); @@ -1485,13 +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 @@ -1505,11 +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); + } //-----------------------------------------------------------------------------