X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b26c57d831b59495ceb2d1c672dbccbe757b29c4;hb=2bfcd91b06ec416462da3f080917576cc8793c18;hp=66d2ffd848ce48783ac43300565096f759b994d6;hpb=39fbd17fa58bc80fb241a49f50aae236da7606fa;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 66d2ffd8..b26c57d8 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 02:01:37 $ - Version: $Revision: 1.260 $ + Date: $Date: 2005/10/23 15:26:43 $ + Version: $Revision: 1.289 $ 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" @@ -69,19 +92,18 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" -#include "gdcmValEntry.h" -#include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDataEntry.h" #include -#include //sscanf +#include //sscanf #include // for atoi -#include // for pow namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor @@ -95,6 +117,7 @@ File::File(): JPEGInfo = new JPEGFragmentsInfo; GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; + BasicOffsetTableItemValue = 0; } @@ -107,6 +130,7 @@ File::~File () delete RLEInfo; if ( JPEGInfo ) delete JPEGInfo; + delete[] BasicOffsetTableItemValue; } //----------------------------------------------------------------------------- @@ -143,7 +167,7 @@ bool File::DoTheLoadingJob( ) // Note: this IS the right place for the code // Image Location - const std::string &imgLocation = GetEntryValue(0x0028, 0x0200); + const std::string &imgLocation = GetEntryString(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -188,14 +212,14 @@ bool File::DoTheLoadingJob( ) ComputeJPEGFragmentInfo(); CloseFile(); - // Create a new BinEntry to change the DictEntry + // Create a new DataEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" - BinEntry *oldEntry = dynamic_cast(entry); + DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { - std::string PixelVR; + VRKey PixelVR; // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'O Words' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) @@ -206,10 +230,11 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) { - DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); + DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + PixelVR,"1","Pixel Data"); - BinEntry *newEntry = new BinEntry(newDict); + DataEntry *newEntry = new DataEntry(newDict); + newDict->Delete(); newEntry->Copy(entry); newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); oldEntry->SetSelfArea(false); @@ -236,7 +261,7 @@ bool File::IsReadable() return false; } - const std::string &res = GetEntryValue(0x0028, 0x0005); + const std::string &res = GetEntryString(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { gdcmWarningMacro("Wrong Image Dimensions" << res); @@ -293,7 +318,7 @@ bool File::IsReadable() int File::GetImageNumber() { //0020 0013 : Image Number - std::string strImNumber = GetEntryValue(0x0020,0x0013); + std::string strImNumber = GetEntryString(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -308,7 +333,7 @@ int File::GetImageNumber() ModalityType File::GetModality() { // 0008 0060 : Modality - std::string strModality = GetEntryValue(0x0008,0x0060); + std::string strModality = GetEntryString(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; @@ -373,12 +398,10 @@ ModalityType File::GetModality() */ int File::GetXSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0011); - if ( strSize == GDCM_UNFOUND ) - { - return 0; - } - return atoi( strSize.c_str() ); + DataEntry *entry = GetDataEntry(0x0028,0x0011); + if( entry ) + return (int)entry->GetValue(0); + return 0; } /** @@ -389,11 +412,10 @@ int File::GetXSize() */ int File::GetYSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0010); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0010); + if( entry ) + return (int)entry->GetValue(0); + if ( IsDicomV3() ) { return 0; @@ -417,18 +439,14 @@ int File::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - const std::string &strSize = GetEntryValue(0x0028,0x0008); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0008); + if( entry ) + return (int)entry->GetValue(0); // We then consider the "Planes" entry as the third dimension - const std::string &strSize2 = GetEntryValue(0x0028,0x0012); - if ( strSize2 != GDCM_UNFOUND ) - { - return atoi( strSize2.c_str() ); - } + entry = GetDataEntry(0x0028,0x0012); + if( entry ) + return (int)entry->GetValue(0); return 1; } @@ -441,65 +459,49 @@ int File::GetZSize() float File::GetXSpacing() { float xspacing = 1.0; - float yspacing = 1.0; - int nbValues; + uint32_t nbValue; // To follow David Clunie's advice, we first check ImagerPixelSpacing - const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); - if ( strImagerPixelSpacing != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(), - "%f\\%f", &yspacing, &xspacing)) != 2 ) - { - // if no values, xspacing is set to 1.0 - if ( nbValues == 0 ) - xspacing = 1.0; - // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - xspacing = yspacing; - - if ( xspacing == 0.0 ) - xspacing = 1.0; + nbValue = entry->GetValueCount(); + // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); - return xspacing; - } + if ( xspacing == 0.0 ) + xspacing = 1.0; + return xspacing; } - - const std::string &strSpacing = GetEntryValue(0x0028,0x0030); - - if ( strSpacing == GDCM_UNFOUND ) + else { - gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); - return 1.; + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } - if ( ( nbValues = sscanf( strSpacing.c_str(), - "%f \\%f ", &yspacing, &xspacing)) != 2 ) + entry = GetDataEntry(0x0028,0x0030); + if( entry ) { - // if no values, xspacing is set to 1.0 - if ( nbValues == 0 ) - xspacing = 1.0; - // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - xspacing = yspacing; + nbValue = entry->GetValueCount(); + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; - return xspacing; } - - // to avoid troubles with David Clunie's-like images (at least one) - if ( xspacing == 0. && yspacing == 0.) - return 1.; - - if ( xspacing == 0.) + else { - 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 ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return xspacing; @@ -513,41 +515,36 @@ float File::GetXSpacing() */ float File::GetYSpacing() { - float yspacing = 1.; - int nbValues; + float yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing - const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); - if ( strImagerPixelSpacing != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing); - - // if sscanf cannot read any float value, it won't affect yspacing - if ( nbValues == 0 ) - yspacing = 1.0; + yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) - yspacing = 1.0; - - return yspacing; + yspacing = 1.0; + return yspacing; } - - std::string strSpacing = GetEntryValue(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) + else { - gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); - return 1.; - } - - // if sscanf cannot read any float value, it won't affect yspacing - nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } - // if no values, yspacing is set to 1.0 - if ( nbValues == 0 ) - yspacing = 1.0; + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + yspacing = (float)entry->GetValue(0); - if ( yspacing == 0.0 ) - yspacing = 1.0; + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } return yspacing; } @@ -560,6 +557,17 @@ float File::GetYSpacing() */ float File::GetZSpacing() { + // ---> + // ---> Warning : + // ---> + // For *Dicom* images, ZSpacing should be calculated using + // XOrigin, YOrigin, ZOrigin (of the top left image corner) + // of 2 consecutive images, and the Orientation + // + // Computing ZSpacing on a single image is not really meaningfull ! + + float zspacing = 1.0f; + // Spacing Between Slices : distance between the middle of 2 slices // Slices may be : // jointives (Spacing between Slices = Slice Thickness) @@ -569,29 +577,35 @@ float File::GetZSpacing() // It only concerns the MRI guys, not people wanting to visualize volumes // If Spacing Between Slices is missing, // we suppose slices joint together - - const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); - - if ( strSpacingBSlices == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0018,0x0088); + if( entry ) { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); - if ( strSliceThickness == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return 1.; - } - else - { - // if no 'Spacing Between Slices' is found, - // we assume slices join together - // (no overlapping, no interslice gap) - // if they don't, we're fucked up - return (float)atof( strSliceThickness.c_str() ); - } + + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + // if they don't, we're fucked up + entry = GetDataEntry(0x0018,0x0050); + if( entry ) + { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; } - //else - return (float)atof( strSpacingBSlices.c_str() ); + else + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + + return zspacing; } /** @@ -602,26 +616,24 @@ float File::GetZSpacing() */ float File::GetXOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; + return 0.0f; } } - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); } - - return xImPos; + return 0.0f; } /** @@ -632,26 +644,24 @@ float File::GetXOrigin() */ float File::GetYOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; - } + return 0.0f; + } } - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(1); } - - return yImPos; + return 0.0f; } /** @@ -664,76 +674,64 @@ float File::GetYOrigin() */ float File::GetZOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( entry ) { - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3) - { - gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else + if( entry->GetValueCount() == 3 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.0f; } - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( entry ) { - if ( sscanf( strImPos.c_str(), - "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 ) + if( entry->GetValueCount() == 3 ) { - gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.0f; } // for *very* old ACR-NEMA images - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); - if ( strSliceLocation != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x1041); + if( entry ) { - if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) - { - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.; // bug in the element 0x0020,0x1041 - } - else + if( entry->GetValueCount() == 1 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); // VM=1 ! } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); - std::string strLocation = GetEntryValue(0x0020,0x0050); - if ( strLocation != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0050); + if( entry ) { - if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 ) - { - gdcmWarningMacro( "Wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } - else + if( entry->GetValueCount() == 1 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); } + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Location (0020,0050)"); - return 0.; // Hopeless } /** * \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] ) { @@ -742,23 +740,25 @@ bool File::GetImageOrientationPatient( float iop[6] ) iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) - if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) + if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { 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 // 0020 0035 DS REL Image Orientation (RET) - else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND ) { 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; } } @@ -773,32 +773,30 @@ bool File::GetImageOrientationPatient( float iop[6] ) */ int File::GetBitsStored() { - std::string strSize = GetEntryValue( 0x0028, 0x0101 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0101); + if( !entry ) { gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** * \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() { - std::string strSize = GetEntryValue(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0100); + if( !entry ) { - gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + gdcmWarningMacro("(0028,0100) is supposed to be mandatory"); + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -809,13 +807,13 @@ int File::GetBitsAllocated() */ int File::GetHighBitPosition() { - std::string strSize = GetEntryValue( 0x0028, 0x0102 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0102); + if( !entry ) { - gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0102) is supposed to be mandatory"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -826,14 +824,14 @@ int File::GetHighBitPosition() */ int File::GetSamplesPerPixel() { - const std::string &strSize = GetEntryValue(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0002); + if( !entry ) { - gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -843,13 +841,13 @@ int File::GetSamplesPerPixel() */ int File::GetPlanarConfiguration() { - std::string strSize = GetEntryValue(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0006); + if( !entry ) { gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -861,8 +859,7 @@ int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old ACR-NEMA RGB images) - // if (File::GetEntryValue(0x0028,0x0100) == "24") - // return 3; + assert( !(GetEntryString(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) @@ -881,7 +878,7 @@ int File::GetPixelSize() { return 8; } - gdcmWarningMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; } @@ -902,7 +899,7 @@ int File::GetPixelSize() */ std::string File::GetPixelType() { - std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); @@ -920,24 +917,18 @@ 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" - - if (sign == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); - sign = "U"; // default and arbitrary value, not to polute the output - } - else if ( sign == "0" ) + std::string sign; + if( IsSignedPixelData() ) { - sign = "U"; + sign = "S"; } else { - sign = "S"; + sign = "U"; } return bitsAlloc + sign; } @@ -952,18 +943,13 @@ std::string File::GetPixelType() */ bool File::IsSignedPixelData() { - std::string strSign = GetEntryValue( 0x0028, 0x0103 ); - if ( strSign == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); - return false; - } - int sign = atoi( strSign.c_str() ); - if ( sign == 0 ) + DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" + if( !entry ) { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); return false; } - return true; + return entry->GetValue(0) != 0; } /** @@ -973,7 +959,7 @@ bool File::IsSignedPixelData() */ bool File::IsMonochrome() { - const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { @@ -993,7 +979,7 @@ bool File::IsMonochrome() */ bool File::IsMonochrome1() { - const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) { return true; @@ -1012,7 +998,7 @@ bool File::IsMonochrome1() */ bool File::IsPaletteColor() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; @@ -1031,7 +1017,7 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; @@ -1105,7 +1091,7 @@ int File::GetLUTNbits() //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string lutDescription = GetEntryValue(0x0028,0x1101); + std::string lutDescription = GetEntryString(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) { return 0; @@ -1128,19 +1114,15 @@ int File::GetLUTNbits() */ float File::GetRescaleIntercept() { - float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryValue(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) + // 0028 1052 DS IMG Rescale Intercept + DataEntry *entry = GetDataEntry(0x0028, 0x1052); + if( !entry ) { - if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) - { - // bug in the element 0x0028,0x1052 - gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); - } + gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); + return 0.0f; } + return (float)entry->GetValue(0); - return resInter; } /** @@ -1149,19 +1131,14 @@ float File::GetRescaleIntercept() */ float File::GetRescaleSlope() { - float resSlope = 1.; - //0028 1053 DS IMG Rescale Slope - std::string strRescSlope = GetEntryValue(0x0028,0x1053); - if ( strRescSlope != GDCM_UNFOUND ) + // 0028 1053 DS IMG Rescale Slope + DataEntry *entry = GetDataEntry(0x0028, 0x1053); + if( !entry ) { - if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 ) - { - // bug in the element 0x0028,0x1053 - gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); - } + gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); + return 1.0f; } - - return resSlope; + return (float)entry->GetValue(0); } /** @@ -1177,15 +1154,15 @@ int File::GetNumberOfScalarComponents() { return 3; } - + // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( GetEntryValue(0x0028,0x0100) == "24" ) + if ( GetEntryString(0x0028,0x0100) == "24" ) { return 3; } - - std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); + + std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { @@ -1225,7 +1202,7 @@ int File::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + if ( File::GetEntryString(0x0028,0x0100) == "24" ) { return 3; } @@ -1285,11 +1262,11 @@ size_t File::GetPixelAreaLength() void File::AddAnonymizeElement (uint16_t group, uint16_t elem, std::string const &value) { - Element el; + DicomElement el; el.Group = group; el.Elem = elem; el.Value = value; - AnonymizeList.push_back(el); + UserAnonymizeList.push_back(el); } /** @@ -1305,8 +1282,8 @@ 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 +1291,11 @@ 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(); @@ -1339,38 +1316,38 @@ void File::AnonymizeNoLoad() /** * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() - * \note You cannot Anonymize a BinEntry (to be fixed) + * \note You cannot Anonymize a DataEntry (to be fixed) */ 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 - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + SetEntryString(" ",0x0010, 0x2154); // Telephone + SetEntryString(" ",0x0010, 0x1040); // Adress + SetEntryString(" ",0x0010, 0x0020); // Patient ID - DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { - std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { - SetValEntry(studyInstanceUID, 0x0010, 0x0010); + SetEntryString(studyInstanceUID, 0x0010, 0x0010); } else { - SetValEntry("anonymised", 0x0010, 0x0010); + SetEntryString("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); @@ -1384,13 +1361,13 @@ bool File::AnonymizeFile() continue; } - if ( dynamic_cast(d) ) + if ( dynamic_cast(d) ) { - gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) "); + gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); continue; } else - SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1468,22 +1445,26 @@ bool File::Write(std::string fileName, FileType writetype) } // Entry : 0002|0000 = group length -> recalculated - ValEntry*e0000 = GetValEntry(0x0002,0x0000); + DataEntry *e0000 = GetDataEntry(0x0002,0x0000); if ( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(writetype); - e0000->SetValue(sLen.str()); + sLen << ComputeGroup0002Length( ); + e0000->SetString(sLen.str()); } - int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -2) - { - // no (GrPixel, NumPixel) element - std::string s_lgPix = Util::Format("%d", i_lgPix+12); - s_lgPix = Util::DicomString( s_lgPix.c_str() ); - InsertValEntry(s_lgPix,GrPixel, 0x0000); - } + // Derma?.dcm does not have it...let's remove it FIXME FIXME + if( writetype != JPEG ) + { + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -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); + } + } Document::WriteContent(fp, writetype); @@ -1525,7 +1506,7 @@ 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 +1516,24 @@ 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 +1606,46 @@ 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' @@ -1662,19 +1683,24 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } - catch ( FormatError e ) + catch ( FormatError ) { - //std::cerr << e << std::endl; + gdcmErrorMacro( "Can not read tag for " + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" + ) ; + return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) { - gdcmWarningMacro( "Wrong Item Tag found:" + gdcmErrorMacro( "Wrong Item Tag found:" << " We should have found tag (" - << std::hex << testGroup << "," << testElem << ")" << std::endl + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElem << ")" - << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)currentPosition << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1702,17 +1728,17 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) if ( !ReadTag(testGroup, testElem) ) { + gdcmErrorMacro( "ReadTag did not succeed for (" + << DictEntry::TranslateToKey(testGroup,testElem) + << ")..." ); return 0; } //// Then read the associated Item Length long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); - { - gdcmWarningMacro( "Basic Item Length is: " - << itemLength << std::endl + gdcmDebugMacro( "Basic Item Length is: " << itemLength << " at address: " << std::hex << (unsigned int)currentPosition); - } return itemLength; } @@ -1720,7 +1746,7 @@ 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); @@ -1733,30 +1759,36 @@ 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; } } // These are the deprecated method that one day should be removed (after the next release) #ifndef GDCM_LEGACY_REMOVE -/** - * \brief Constructor (DEPRECATED : temporaryly kept not to break the API) - * @param filename name of the file whose header we want to analyze - * @deprecated do not use any longer +/* + * brief Constructor (DEPRECATED : temporaryly kept not to break the API) + * param filename name of the file whose header we want to analyze + * deprecated do not use any longer */ File::File( std::string const &filename ) :Document( ) @@ -1768,12 +1800,12 @@ File::File( std::string const &filename ) Load( ); // gdcm::Document is first Loaded, then the 'File part' } -/** - * \brief Loader. (DEPRECATED : temporaryly kept not to break the API) - * @param fileName file to be open for parsing - * @return false if file cannot be open or no swap info was found, +/* + * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) + * @ param fileName file to be open for parsing + * @ return false if file cannot be open or no swap info was found, * or no tag was found. - * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead + * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ bool File::Load( std::string const &fileName ) { @@ -1787,177 +1819,6 @@ 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 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