X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=d18ce400659f2308d23de69d412f952ed3bbef2a;hb=7ab309d561964c2ab5f9cd5d51d2fb212cd5dfcb;hp=71d26f6116b1d785f189daa13635fed0f3be710e;hpb=25c9af365d9221bd45f3fbe27275ff0f66a265b1;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 71d26f61..d18ce400 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 09:51:03 $ - Version: $Revision: 1.214 $ + Date: $Date: 2005/04/14 14:26:19 $ + Version: $Revision: 1.232 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -46,12 +46,25 @@ namespace gdcm { //----------------------------------------------------------------------------- // Constructor / Destructor + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +File::File(): + Document() +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; + NumPixel = 0x0010; +} + /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ File::File( std::string const &filename ) - :Document( filename ) + :Document(filename) { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; @@ -115,7 +128,6 @@ 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) @@ -146,16 +158,6 @@ File::File( std::string const &filename ) } } -/** - * \brief Constructor used when we want to generate dicom files from scratch - */ -File::File(): - Document() -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - InitializeDefaultFile(); -} /** * \brief Canonical destructor. @@ -170,6 +172,8 @@ File::~File () //----------------------------------------------------------------------------- // Public + + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -216,13 +220,7 @@ 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 +235,7 @@ int File::GetImageNumber() */ ModalityType File::GetModality() { - // 0008 0060 CS ID Modality + // 0008 0060 : Modality std::string strModality = GetEntryValue(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { @@ -270,10 +268,14 @@ ModalityType File::GetModality() else if ( strModality.find("PT") < strModality.length()) return PT; else if ( strModality.find("RF") < strModality.length()) return RF; else if ( strModality.find("RG") < strModality.length()) return RG; - else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; - else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; - else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; - else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("RTDOSE") + < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") + < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") + < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") + < strModality.length()) return RTSTRUCT; else if ( strModality.find("SM") < strModality.length()) return SM; else if ( strModality.find("ST") < strModality.length()) return ST; else if ( strModality.find("TG") < strModality.length()) return TG; @@ -367,7 +369,8 @@ 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 +403,7 @@ 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 +449,15 @@ 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 +781,7 @@ 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() @@ -824,20 +827,21 @@ std::string File::GetPixelType() } /** - * \brief Check whether the pixels are signed or UNsigned data. - * \warning The method defaults to false (UNsigned) when information is Missing. + * \brief Check whether the pixels are signed (1) or UNsigned (0) data. + * \warning The method defaults to false (UNsigned) when tag 0028|0103 + * is missing. * The responsability of checking this value is left to the caller. * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() { - std::string strSize = GetEntryValue( 0x0028, 0x0103 ); - if ( strSize == GDCM_UNFOUND ) + std::string strSign = GetEntryValue( 0x0028, 0x0103 ); + if ( strSign == GDCM_UNFOUND ) { gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); return false; } - int sign = atoi( strSize.c_str() ); + int sign = atoi( strSign.c_str() ); if ( sign == 0 ) { return false; @@ -846,8 +850,8 @@ 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 +869,25 @@ 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 ). @@ -1101,7 +1124,7 @@ int File::GetNumberOfScalarComponentsRaw() */ size_t File::GetPixelOffset() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -1123,7 +1146,7 @@ size_t File::GetPixelOffset() */ size_t File::GetPixelAreaLength() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -1136,13 +1159,12 @@ size_t File::GetPixelAreaLength() } } - /** * \brief Adds the characteristics of a new element we want to anonymize * */ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, - std::string const &value) + std::string const &value) { Element el; @@ -1159,46 +1181,39 @@ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, 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] = " "; - + std::ios::in | std::ios::out | std::ios::binary); 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 ); + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } - 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 ); - - } - fp->close(); - delete fp; + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + } + fp->close(); + delete fp; } /** @@ -1207,7 +1222,7 @@ 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 @@ -1239,6 +1254,9 @@ bool File::AnonymizeFile() { d = GetDocEntry( (*it).Group, (*it).Elem); + if ( d == NULL) + continue; + if ( dynamic_cast(d) || dynamic_cast(d) ) continue; @@ -1307,10 +1325,10 @@ 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); @@ -1321,12 +1339,12 @@ 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 @@ -1386,39 +1404,7 @@ 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; @@ -1428,90 +1414,7 @@ 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 - * explicitely defines those fields, heuristic has been choosen. - * This is not perfect as we are writting a CT image... - */ -void File::InitializeDefaultFile() -{ - std::string date = Util::GetCurrentDate(); - std::string time = Util::GetCurrentTime(); - std::string uid = Util::CreateUniqueUID(); - std::string uidMedia = uid; - std::string uidInst = uid; - std::string uidClass = Util::CreateUniqueUID(); - std::string uidStudy = Util::CreateUniqueUID(); - std::string uidSerie = Util::CreateUniqueUID(); - - // 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 Instance UID - InsertValEntry(uidClass.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); - - // Instance Creation Date - InsertValEntry(date.c_str(), 0x0008, 0x0012); - // Instance Creation Time - InsertValEntry(time.c_str(), 0x0008, 0x0013); - // SOP Class UID - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016); - // SOP Instance UID - InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); - // Modality - InsertValEntry("CT", 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); - // Patient ID - InsertValEntry("GDCMID", 0x0010, 0x0020); - - // Study Instance UID - InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d); - // Series Instance UID - InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); - // StudyID - InsertValEntry("1", 0x0020, 0x0010); - // SeriesNumber - InsertValEntry("1", 0x0020, 0x0011); - - // Samples per pixel 1 or 3 - InsertValEntry("1", 0x0028, 0x0002); - // photochromatic interpretation - InsertValEntry("MONOCHROME1", 0x0028, 0x0004); - // nbRows - InsertValEntry("0", 0x0028, 0x0010); - // nbCols - InsertValEntry("0", 0x0028, 0x0011); - // BitsAllocated 8 or 12 or 16 - InsertValEntry("8", 0x0028, 0x0100); - // BitsStored <= BitsAllocated - InsertValEntry("8", 0x0028, 0x0101); - // HighBit <= BitsAllocated - 1 - InsertValEntry("7", 0x0028, 0x0102); - // Pixel Representation 0(unsigned) or 1(signed) - InsertValEntry("0", 0x0028, 0x0103); - - // default value - // Special case this is the image (not a string) - GrPixel = 0x7fe0; - NumPixel = 0x0010; - InsertBinEntry(0, 0, GrPixel, NumPixel); -} + //----------------------------------------------------------------------------- // Private @@ -1669,7 +1572,7 @@ 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;