X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=1c0db8127a5b61e298c83688d6385a9a2338cda7;hb=21d241b3fdcf675d8d91a6daf6dfd6f448b68195;hp=9f0952357734feed925b307e5beda76556a0bd66;hpb=7a6f4850521b56e6b907cb8c7938471898613fa4;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 9f095235..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: 2005/07/23 01:27:57 $ - Version: $Revision: 1.258 $ + 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 @@ -38,30 +38,53 @@ // 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 -// can also find SEMIERECT -// 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. -// Better we don't tust it too much ... -// Found Values are : L\P -// L\FP -// P\F -// L\F -// P\FR -// R\F +// 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" @@ -76,12 +99,12 @@ #include "gdcmJPEGFragmentsInfo.h" #include -#include //sscanf +#include //sscanf #include // for atoi -#include // for pow namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor @@ -95,6 +118,7 @@ File::File(): JPEGInfo = new JPEGFragmentsInfo; GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; + BasicOffsetTableItemValue = 0; } @@ -107,6 +131,7 @@ File::~File () delete RLEInfo; if ( JPEGInfo ) delete JPEGInfo; + delete[] BasicOffsetTableItemValue; } //----------------------------------------------------------------------------- @@ -731,9 +756,11 @@ 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 */ bool File::GetImageOrientationPatient( float iop[6] ) { @@ -747,7 +774,8 @@ bool 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; } } @@ -758,13 +786,16 @@ bool 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) @@ -785,8 +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() @@ -863,6 +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" ) @@ -920,8 +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" @@ -1289,7 +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); } /** @@ -1305,8 +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); @@ -1314,11 +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(); @@ -1344,7 +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 @@ -1362,15 +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); @@ -1472,7 +1504,7 @@ bool File::Write(std::string fileName, FileType writetype) if ( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(writetype); + sLen << ComputeGroup0002Length( ); e0000->SetValue(sLen.str()); } @@ -1525,7 +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 @@ -1535,8 +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 @@ -1609,22 +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' @@ -1662,7 +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; @@ -1720,7 +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); @@ -1733,20 +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; } } @@ -1764,7 +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' } /** @@ -1786,178 +1865,6 @@ bool File::Load( std::string const &fileName ) } #endif -// ----------------------------------------------------------------------------------------- -// THERALYS Algorithm to determine the most similar basic orientation -// -// Transliterated from original Python code. -// Kept as close as possible to the original code -// in order to speed up any further modif of Python code :-( -// ------------------------------------------------------------------------------------------ - -/** - * \brief THERALYS' Algorithm to determine the most similar basic orientation - * (Axial, Coronal, Sagital) of the image - * \note Should be run on the first gdcm::File of a 'coherent' Serie - * @return orientation code - * @return orientation code - * # 0 : Not Applicable (neither 0020,0037 Image Orientation Patient - * # nor 0020,0032Image Position found ) - * # 1 : Axial - * # -1 : Axial invert - * # 2 : Coronal - * # -2 : Coronal invert - * # 3 : Sagital - * # -3 : Sagital invert - * # 4 : Heart Axial - * # -4 : Heart Axial invert - * # 5 : Heart Coronal - * # -5 : Heart Coronal invert - * # 6 : Heart Sagital - * # -6 : Heart Sagital invert - */ -float File::TypeOrientation( ) -{ - float *iop = new float[6]; - bool succ = GetImageOrientationPatient( iop ); - if ( !succ ) - { - delete iop; - return 0.; - } - - vector3D ori1; - vector3D ori2; - - ori1.x = iop[0]; ori1.y = iop[1]; ori1.z = iop[2]; - ori1.x = iop[3]; ori2.y = iop[4]; ori2.z = iop[5]; - - // two perpendicular vectors describe one plane - float dicPlane[6][2][3] = - { { {1, 0, 0 },{0, 1, 0 } }, // Axial - { {1, 0, 0 },{0, 0, -1 } }, // Coronal - { {0, 1, 0 },{0, 0, -1 } }, // Sagittal - { { 0.8, 0.5, 0.0 },{-0.1, 0.1 , -0.95 } }, // Axial - HEART - { { 0.8, 0.5, 0.0 },{-0.6674, 0.687, 0.1794} }, // Coronal - HEART - { {-0.1, 0.1, -0.95},{-0.6674, 0.687, 0.1794} } // Sagittal - HEART - }; - - vector3D refA; - vector3D refB; - int i = 0; - Res res; // [ , ] - res.first = 0; - res.second = 99999; - for (int numDicPlane=0; numDicPlane<6; numDicPlane++) - { - i = i + 1; - // refA=plane[0] - refA.x = dicPlane[numDicPlane][0][0]; - refA.y = dicPlane[numDicPlane][0][1]; - refA.z = dicPlane[numDicPlane][0][2]; - // refB=plane[1] - refB.x = dicPlane[numDicPlane][1][0]; - refB.y = dicPlane[numDicPlane][1][1]; - refB.z = dicPlane[numDicPlane][1][2]; - res=VerfCriterion( i, CalculLikelyhood2Vec(refA,refB,ori1,ori2), res ); - res=VerfCriterion( -i, CalculLikelyhood2Vec(refB,refA,ori1,ori2), res ); - } - delete iop; - return res.first; -/* -// i=0 -// res=[0,99999] ## [ , ] -// for plane in dicPlane: -// i=i+1 -// refA=plane[0] -// refB=plane[1] -// res=self.VerfCriterion( i , self.CalculLikelyhood2Vec(refA,refB,ori1,ori2) , res ) -// res=self.VerfCriterion( -i , self.CalculLikelyhood2Vec(refB,refA,ori1,ori2) , res ) -// return res[0] -*/ - -} - -Res File::VerfCriterion(int typeCriterion, float criterionNew, Res res) -{ - float type = res.first; - float criterion = res.second; - if (criterionNew < criterion) - { - res.first = criterionNew; - res.second = typeCriterion; - } -/* -// type = res[0] -// criterion = res[1] -// # if criterionNew<0.1 and criterionNew : - type : vector 3D (float) -// # - : - type : vector 3D (float) -// # - Description of the first plane -// # - : - type : vector 3D (float) -// # - : - type : vector 3D (float) -// # - Description of the second plane -// # ------------------------- Return : ------------------------------------ -// # float : 0 if the planes are perpendicular. While the difference of -// # the orientation between the planes are big more enlarge is -// # the criterion. -// # ------------------------- Other : ------------------------------------- -// # The calculus is based with vectors normalice - - vector3D ori3 = ProductVectorial(ori1,ori2); - vector3D refC = ProductVectorial(refA,refB); - float res = pow(refC.x-ori3.x, 2.) + - pow(refC.y-ori3.y, 2.) + - pow(refC.z-ori3.z, 2.); - -/* -// ori3=self.ProductVectorial(ori1,ori2) -// refC=self.ProductVectorial(refA,refB) -// res=math.pow(refC[0]-ori3[0],2) + math.pow(refC[1]-ori3[1],2) + math.pow(refC[2]-ori3[2],2) -// return math.sqrt(res) -*/ - return sqrt(res); -} - -vector3D File::ProductVectorial(vector3D vec1, vector3D vec2) -{ - -// # ------------------------- Purpose : ----------------------------------- -// # - Calculus of the poduct vectorial between two vectors 3D -// # ------------------------- Parameters : -------------------------------- -// # - : - type : vector 3D (float) -// # - : - type : vector 3D (float) -// # ------------------------- Return : ------------------------------------ -// # (vec) : - Vector 3D -// # ------------------------- Other : ------------------------------------- - - vector3D vec3; - vec3.x = vec1.y*vec2.z - vec1.z*vec2.y; - vec3.y = -( vec1.x*vec2.z - vec1.z*vec2.x); - vec3.z = vec1.x*vec2.y - vec1.y*vec2.x; -/* -// vec3=[0,0,0] -// vec3[0]=vec1[1]*vec2[2] - vec1[2]*vec2[1] -// vec3[1]=-( vec1[0]*vec2[2] - vec1[2]*vec2[0]) -// vec3[2]=vec1[0]*vec2[1] - vec1[1]*vec2[0] -*/ - return vec3; -} - //----------------------------------------------------------------------------- // Print