X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmFile.cxx;h=1c0db8127a5b61e298c83688d6385a9a2338cda7;hb=21d241b3fdcf675d8d91a6daf6dfd6f448b68195;hp=13570e2196845545714e5805701b3f2917c0ef85;hpb=db42dcafe4dafd893c12b6d209870d66ec474a1b;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 13570e21..1c0db812 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/07/20 14:49:41 $ - Version: $Revision: 1.254 $ + Date: $Date: 2005/10/10 22:25:05 $ + Version: $Revision: 1.274 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,27 +26,65 @@ // as the Z coordinate, // 0. for all the coordinates if nothing is found // -// Image Position (Patient) (0020,0032) What is it used for? +// Image Position (Patient) (0020,0032) VM=3 What is it used for? // --> // The attribute Patient Orientation (0020,0020) from the General Image Module // is of type 2C and has the condition Required if image does not require // Image Orientation (0020,0037) and Image Position (0020,0032). -// However, if the image does require the attributes Image Orientation (0020,0037) -// and Image Position (0020,0032) then attribute Patient Orientation (0020,0020) -// should not be present in the images. +// However, if the image does require the attributes +// - Image Orientation (Patient) (0020,0037), VM=6 +// - Image Position Patient (0020,0032), VM=3 +// then attribute Patient Orientation (0020,0020) should not be present +// in the images. // // Remember also : -// Patient Position (0018,5100) values : HFP = Head First-Prone -// HFS = Head First-Supine -// HFDR = Head First-Decubitus Right -// HFDL = Head First-Decubitus Left -// FFDR = Feet First-Decubitus Right -// FFDL = Feet First-Decubitus Left -// FFP = Feet First-Prone -// FFS = Feet First-Supine +// Patient Position (0018,5100) values : + +// HFS = Head First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFP = Head First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFS = Feet First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterion direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFP = Feet First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the posterior-to-anterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFDR = Head First-Decubitus Right +// HFDL = Head First-Decubitus Left +// FFDR = Feet First-Decubitus Right +// FFDL = Feet First-Decubitus Left + +// we can also find + +// SEMIERECT +// SUPINE + // CS 2 Patient Orientation (0020 0020) -// When the coordinates of the image -// are always present, this field is almost never used +// When the coordinates of the image +// are always present, this field is almost never used. +// Better we don't trust it too much ... +// Found Values are : +// L\P +// L\FP +// P\F +// L\F +// P\FR +// R\F +// +// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] + + // --------------------------------------------------------------- // #include "gdcmFile.h" @@ -61,11 +99,12 @@ #include "gdcmJPEGFragmentsInfo.h" #include -#include //sscanf +#include //sscanf #include // for atoi namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor @@ -79,6 +118,7 @@ File::File(): JPEGInfo = new JPEGFragmentsInfo; GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; + BasicOffsetTableItemValue = 0; } @@ -91,6 +131,7 @@ File::~File () delete RLEInfo; if ( JPEGInfo ) delete JPEGInfo; + delete[] BasicOffsetTableItemValue; } //----------------------------------------------------------------------------- @@ -715,11 +756,13 @@ float File::GetZOrigin() /** * \brief gets the info from 0020,0037 : Image Orientation Patient + * or from 0020 0035 : Image Orientation (RET) * (needed to organize DICOM files based on their x,y,z position) * @param iop adress of the (6)float array to receive values - * @return cosines of image orientation patient + * @return true when one of the tag is found + * false when nothing is found */ -void File::GetImageOrientationPatient( float iop[6] ) +bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] @@ -731,7 +774,9 @@ 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 ) { - gdcmWarningMacro( "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." ); + return false; } } //For ACR-NEMA @@ -741,11 +786,16 @@ 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 ) { - gdcmWarningMacro( "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." ); + return false; } } + return true; } + + /** * \brief Retrieve the number of Bits Stored (actually used) * (as opposed to number of Bits Allocated) @@ -766,8 +816,8 @@ int File::GetBitsStored() /** * \brief Retrieve the number of Bits Allocated - * (8, 12 -compacted ACR-NEMA files-, 16, ...) - * @return The encountered number of Bits Allocated, 0 by default. + * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,) + * @return The encountered Number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ int File::GetBitsAllocated() @@ -844,6 +894,7 @@ int File::GetPixelSize() // (in order no to be messed up by old ACR-NEMA RGB images) // if (File::GetEntryValue(0x0028,0x0100) == "24") // return 3; + assert( !(GetEntryValue(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) @@ -901,8 +952,8 @@ std::string File::GetPixelType() } else if ( bitsAlloc == "24" ) { - // (in order no to be messed up - bitsAlloc = "8"; // by old RGB images) + // (in order no to be messed up by old RGB images) + bitsAlloc = "8"; } std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" @@ -1270,7 +1321,7 @@ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, el.Group = group; el.Elem = elem; el.Value = value; - AnonymizeList.push_back(el); + UserAnonymizeList.push_back(el); } /** @@ -1286,8 +1337,8 @@ void File::AnonymizeNoLoad() uint32_t lgth; uint32_t valLgth = 0; std::string *spaces; - for (ListElements::iterator it = AnonymizeList.begin(); - it != AnonymizeList.end(); + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); ++it) { d = GetDocEntry( (*it).Group, (*it).Elem); @@ -1295,11 +1346,11 @@ void File::AnonymizeNoLoad() if ( d == NULL) continue; - if ( dynamic_cast(d) ) - { - gdcmWarningMacro( "You cannot 'Anonymize a SeqEntry "); - continue; - } + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); + continue; + } offset = d->GetOffset(); lgth = d->GetLength(); @@ -1325,7 +1376,7 @@ void File::AnonymizeNoLoad() bool File::AnonymizeFile() { // If Anonymisation list is empty, let's perform some basic anonymization - if ( AnonymizeList.begin() == AnonymizeList.end() ) + if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) { // If exist, replace by spaces SetValEntry (" ",0x0010, 0x2154); // Telephone @@ -1343,15 +1394,15 @@ bool File::AnonymizeFile() } else { - SetValEntry("anonymised", 0x0010, 0x0010); + SetValEntry("anonymized", 0x0010, 0x0010); } } } else { gdcm::DocEntry *d; - for (ListElements::iterator it = AnonymizeList.begin(); - it != AnonymizeList.end(); + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); ++it) { d = GetDocEntry( (*it).Group, (*it).Elem); @@ -1453,7 +1504,7 @@ bool File::Write(std::string fileName, FileType writetype) if ( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(writetype); + sLen << ComputeGroup0002Length( ); e0000->SetValue(sLen.str()); } @@ -1506,7 +1557,7 @@ void File::ComputeRLEInfo() // - the first item in the sequence of items before the encoded pixel // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" - ReadAndSkipEncapsulatedBasicOffsetTable(); + ReadEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) // Loop on the individual frame[s] and store the information @@ -1516,8 +1567,24 @@ void File::ComputeRLEInfo() // - when more than one frame are present, then we are in // the case of a multi-frame image. long frameLength; + int i=0; + uint32_t sum = 0; while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + assert( individualLength == sum ); // REMOVE that if this is a problem + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" ); + } + sum += frameLength + 8; + i++; + } // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded @@ -1590,22 +1657,46 @@ void File::ComputeJPEGFragmentInfo() return; } - ReadAndSkipEncapsulatedBasicOffsetTable(); + ReadEncapsulatedBasicOffsetTable(); // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; + int i=0; + uint32_t sum = 0; while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { - long fragmentOffset = Fp->tellg(); + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + // A.4 Transfer syntaxes for encapsulation of encoded pixel data: + // When the Item Value is present, the Basic Offset Table Item Value shall contain + // concatenated 32-bit unsigned integer values that are byte offsets to the first + // byte of the Item Tag of the first fragment for each frame in the Sequence of + // Items. These offsets are measured from the first byte of the first Item Tag + // following the Basic Offset Table item (See Table A.4-2). + + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ?? + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" << + individualLength << " != " << sum ); + } + sum += fragmentLength + 8; + i++; + } - // Store the collected info - JPEGFragment *newFragment = new JPEGFragment; - newFragment->SetOffset(fragmentOffset); - newFragment->SetLength(fragmentLength); - JPEGInfo->AddFragment(newFragment); + long fragmentOffset = Fp->tellg(); + // Store the collected info + JPEGFragment *newFragment = new JPEGFragment; + newFragment->SetOffset(fragmentOffset); + newFragment->SetLength(fragmentLength); + JPEGInfo->AddFragment(newFragment); - SkipBytes(fragmentLength); + SkipBytes(fragmentLength); } // Make sure that we encounter a 'Sequence Delimiter Item' @@ -1643,7 +1734,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } - catch ( FormatError e ) + catch ( FormatError /*e*/ ) { //std::cerr << e << std::endl; return false; @@ -1701,7 +1792,7 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) * \brief When parsing the Pixel Data of an encapsulated file, read * the basic offset table (when present, and BTW dump it). */ -void File::ReadAndSkipEncapsulatedBasicOffsetTable() +void File::ReadEncapsulatedBasicOffsetTable() { //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); @@ -1714,20 +1805,26 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - char *basicOffsetTableItemValue = new char[itemLength + 1]; - Fp->read(basicOffsetTableItemValue, itemLength); + char *charBasicOffsetTableItemValue = new char[itemLength]; + Fp->read(charBasicOffsetTableItemValue, itemLength); + unsigned int nbEntries = itemLength/4; + assert( nbEntries*4 == itemLength); // Make sure this is a multiple + BasicOffsetTableItemValue = new uint32_t[nbEntries]; -#ifdef GDCM_DEBUG - for (unsigned int i=0; i < itemLength; i += 4 ) + for (unsigned int i=0; i < nbEntries; i++ ) { - uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], - uint32_t); - gdcmWarningMacro( "Read one length: " << - std::hex << individualLength ); + BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i])); +#if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) + uint32_t val = BasicOffsetTableItemValue[i]; + BasicOffsetTableItemValue[i] + = ( (val<<24) | ((val<<8) & 0x00ff0000) | + ((val>>8) & 0x0000ff00) | (val>>24) ); +#endif + gdcmWarningMacro( "Read one length for: " << + std::hex << BasicOffsetTableItemValue[i] ); } -#endif //GDCM_DEBUG - delete[] basicOffsetTableItemValue; + delete[] charBasicOffsetTableItemValue; } } @@ -1745,7 +1842,8 @@ File::File( std::string const &filename ) RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; - Load( filename ); // gdcm::Document is first Loaded, then the 'File part' + SetFileName( filename ); + Load( ); // gdcm::Document is first Loaded, then the 'File part' } /**