X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=fb738bd28fd8d9418232cbc4563423534eefd31c;hb=56ad78cdf3b5de32f0a94a38cd32ddc9f403ffc3;hp=91a9f8c69d7ae673fa6c737446b5c6e64a3bd9b4;hpb=0b08879e15d8a4fdda35046822de5bb83778ab55;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 91a9f8c6..fb738bd2 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2007/05/24 10:41:25 $ - Version: $Revision: 1.332 $ + Date: $Date: 2008/01/07 17:16:06 $ + Version: $Revision: 1.343 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -142,7 +142,6 @@ File::~File() * @return false if file cannot be open or no swap info was found, * or no tag was found. */ - bool File::Load( ) { if ( ! this->Document::Load( ) ) @@ -177,7 +176,6 @@ bool File::DoTheLoadingJob( ) } else { - GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } @@ -237,7 +235,7 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) - { + { //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, // PixelVR,"1","Pixel Data"); //DataEntry *newEntry = DataEntry::New(newDict); @@ -249,7 +247,6 @@ bool File::DoTheLoadingJob( ) //RemoveEntry(oldEntry); //AddEntry(newEntry); //newEntry->Delete(); - } } */ @@ -481,7 +478,7 @@ bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing) TS *ts = Global::GetTS(); std::string sopclassuid_used; // D 0002|0002 [UI] [Media Storage SOP Class UID] - + //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002); const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); @@ -540,10 +537,9 @@ bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing) } return true; } - return false; } - + /** * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. * User has to tell gdcm the location of this '4th Dimension component' @@ -559,7 +555,7 @@ int File::GetTSize() DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), FourthDimensionLocation.GetElement() ); - if( !entry ) + if( !entry ) { gdcmWarningMacro( " FourthDimensionLocation not found at : " << std::hex << FourthDimensionLocation.GetGroup() @@ -570,9 +566,7 @@ int File::GetTSize() { return (int)entry->GetValue(0); } -} - - +} /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing @@ -583,19 +577,18 @@ int File::GetTSize() float File::GetXSpacing() { float xspacing = 1.0; - float yspacing = 1.0; + float yspacing = 1.0; float zspacing = 1.0; - + uint32_t nbValue; DataEntry *entry; bool ok = false; - if ( GetSpacing(xspacing,yspacing,zspacing) ) { return xspacing; } - // else fallback - + // else fallback + /* From:David Clunie - view profile Date:Wed, May 24 2006 1:12 pm @@ -690,7 +683,7 @@ and if( nbValue !=2 ) gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " << "has a wrong number of values :" << nbValue); - + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) @@ -714,7 +707,7 @@ and if( nbValue !=2 ) gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " << "has a wrong number of values :" << nbValue); - + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) @@ -745,14 +738,12 @@ float File::GetYSpacing() uint32_t nbValue; DataEntry *entry; bool ok = false; - if ( GetSpacing(xspacing,yspacing,zspacing) ) { return yspacing; } - // else fallback - - + // else fallback + std::string SOPClassUID = GetEntryString(0x0008,0x0016); /// \todo check the various SOP Class @@ -1367,13 +1358,13 @@ std::string File::GetPixelType() // (in order no to be messed up by old RGB images) bitsAlloc = "8"; } - + int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers if ( i > 8 && i < 16 ) { bitsAlloc = "16"; } - + std::string sign; if( IsSignedPixelData() ) { @@ -1423,6 +1414,9 @@ bool File::IsMonochrome() { gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " << "mandatory"); + // to deal with old ACR-NEMA images + if (GetNumberOfScalarComponents() == 1) + return true; } return false; } @@ -1459,6 +1453,13 @@ bool File::IsPaletteColor() { return true; } + + // MONOCHROME + [Enhanced CT Image Storage] actually have Palettes + std::string sopClassUid = GetEntryString( 0x0008, 0x0016 ); + if (Util::DicomStringEqual( sopClassUid, "1.2.840.10008.5.1.4.1.1.2.1")) + { + return true; + } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmDebugMacro( "Not found : Palette color (0028,0004)"); @@ -1473,7 +1474,7 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; @@ -1512,7 +1513,13 @@ bool File::HasLUT() return false; } // Red Palette Color Lookup Table Data - if ( !GetDocEntry(0x0028,0x1201) ) + bool segmented; + segmented = GetDocEntry(0x0028,0x1221) && + GetDocEntry(0x0028,0x1222) && + GetDocEntry(0x0028,0x1223); + if( segmented ) return true; + + if( !GetDocEntry(0x0028,0x1201) ) { return false; } @@ -1630,13 +1637,12 @@ int File::GetLUTNbits() } return true; } - return false; } /** *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept. defaulted to 0.0 is not found or empty + * @return Rescale Intercept. defaulted to 0.0 if not found or empty */ double File::GetRescaleIntercept() { @@ -1653,7 +1659,7 @@ double File::GetRescaleIntercept() /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope. defaulted to 1.0 is not found or empty + * @return Rescale Slope. defaulted to 1.0 if not found or empty */ double File::GetRescaleSlope() { @@ -1836,7 +1842,7 @@ void File::AnonymizeNoLoad() gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } - + valLgth = (*it).Value.size(); if (valLgth == 0) continue; @@ -1907,12 +1913,13 @@ bool File::AnonymizeFile() gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } - +/* if ( dynamic_cast(d) ) { gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); continue; } +*/ else SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } @@ -1983,6 +1990,7 @@ bool File::AnonymizeFile() */ bool File::Write(std::string fileName, FileType writetype) { + gdcmDebugMacro(" File::Write "); std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if (*fp == NULL) @@ -2001,18 +2009,18 @@ bool File::Write(std::string fileName, FileType writetype) } /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx - if( writetype != JPEG ) + if( writetype != JPEG && writetype != JPEG2000) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -2) + if (i_lgPix != -2) /// \todo wtf "-2" ?!? { // no (GrPixel, NumPixel) element std::string s_lgPix = Util::Format("%d", i_lgPix+12); s_lgPix = Util::DicomString( s_lgPix.c_str() ); - InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); + InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); } } - Document::WriteContent(fp, writetype); + Document::WriteContent(fp, writetype,false,false); fp->close(); delete fp; @@ -2028,7 +2036,7 @@ bool File::Write(std::string fileName, FileType writetype) // Private /** * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. - * Compute the RLE extra information and store it in \ref RLEInfo + * Compute the RLE extra information and store it in RLEInfo * for later pixel retrieval usage. */ void File::ComputeRLEInfo() @@ -2140,7 +2148,7 @@ void File::ComputeRLEInfo() /** * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. * Compute the jpeg extra information (fragment[s] offset[s] and - * length) and store it[them] in \ref JPEGInfo for later pixel + * length) and store it[them] in JPEGInfo for later pixel * retrieval usage. */ void File::ComputeJPEGFragmentInfo() @@ -2203,14 +2211,14 @@ void File::ComputeJPEGFragmentInfo() } /** - * \brief Assuming the internal file pointer \ref Document::Fp + * \brief Assuming the internal file pointer Document::Fp * is placed at the beginning of a tag, check whether this * tag is (TestGroup, TestElem). - * \warning On success the internal file pointer \ref Document::Fp + * \warning On success the internal file pointer Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElem) the internal file pointer - * \ref Document::Fp is restored to its original position. + * Document::Fp is restored to its original position. * @param testGroup The expected group of the tag. * @param testElem The expected Element of the tag. * @return True on success, false otherwise. @@ -2231,8 +2239,9 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) } catch ( FormatError ) { - gdcmErrorMacro( "Can not read tag for " - << " We should have found tag (" + gdcmErrorMacro( "Can not read tag at 0x(" + << std::hex << positionOnEntry + << "). We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" ) ; @@ -2248,7 +2257,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) << " but instead we encountered tag (" << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" << " at address: " << " 0x(" << std::hex - << (unsigned int)positionOnEntry << std::dec << ")" + << (unsigned int)positionOnEntry << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -2258,14 +2267,14 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) } /** - * \brief Assuming the internal file pointer \ref Document::Fp + * \brief Assuming the internal file pointer Document::Fp * is placed at the beginning of a tag (TestGroup, TestElement), * read the length associated to the Tag. - * \warning On success the internal file pointer \ref Document::Fp + * \warning On success the internal file pointer Document::Fp * is modified to point after the tag and its length. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer - * \ref Document::Fp is restored to its original position. + * Document::Fp is restored to its original position. * @param testGroup The expected Group of the tag. * @param testElem The expected Element of the tag. * @return On success returns the length associated to the tag. On failure @@ -2285,7 +2294,7 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) } //// Then read the associated Item Length - + // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); gdcmDebugMacro( "Basic Item Length is: " << itemLength