X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e21f6e0a81c76b5da44d9acf5c78db0776194fe4;hb=f88cd7e3127179d20920d54df75bff206be94a09;hp=64ecac83c7f242e744d2fafe6b082ce9b12fe4e5;hpb=f5a0c2260b3778606fd984cef9874fb9761f6eed;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 64ecac83..e21f6e0a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/06/22 08:11:23 $ - Version: $Revision: 1.243 $ + Date: $Date: 2005/07/24 02:10:48 $ + Version: $Revision: 1.262 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,6 +26,42 @@ // as the Z coordinate, // 0. for all the coordinates if nothing is found // +// 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 (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 +// 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 +// +// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] + + // --------------------------------------------------------------- // #include "gdcmFile.h" @@ -39,11 +75,14 @@ #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" -#include //sscanf #include +#include //sscanf +#include // for atoi +#include // for pow namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor @@ -59,18 +98,6 @@ File::File(): NumPixel = 0x0010; } -/** - * \brief Constructor - * @param filename name of the file whose header we want to analyze - */ -File::File( std::string const &filename ) - :Document(filename) -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - - Load( filename ); -} /** * \brief Canonical destructor. @@ -85,16 +112,26 @@ File::~File () //----------------------------------------------------------------------------- // Public - /** * \brief Loader - * @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. */ -bool File::Load( std::string const &fileName ) +bool File::Load( ) +{ + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::DoTheLoadingJob( ) { - this->Document::Load( fileName ); // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag @@ -206,26 +243,41 @@ bool File::IsReadable() gdcmWarningMacro("Wrong Image Dimensions" << res); return false; // Image Dimensions } + bool b0028_0100 = true; if ( !GetDocEntry(0x0028, 0x0100) ) { gdcmWarningMacro("Bits Allocated (0028|0100) not found"); - return false; // "Bits Allocated" + //return false; // "Bits Allocated" + b0028_0100 = false; } + bool b0028_0101 = true; if ( !GetDocEntry(0x0028, 0x0101) ) { gdcmWarningMacro("Bits Stored (0028|0101) not found"); - return false; // "Bits Stored" + //return false; // "Bits Stored" + b0028_0101 = false; } + bool b0028_0102 = true; if ( !GetDocEntry(0x0028, 0x0102) ) { gdcmWarningMacro("Hight Bit (0028|0102) not found"); - return false; // "High Bit" + //return false; // "High Bit" + b0028_0102 = false; } + bool b0028_0103 = true; if ( !GetDocEntry(0x0028, 0x0103) ) { gdcmWarningMacro("Pixel Representation (0028|0103) not found"); - return false; // "Pixel Representation" i.e. 'Sign' + //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) + b0028_0103 = false; } + + if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) + { + gdcmWarningMacro("Too much mandatory Tags missing !"); + return false; + } + if ( !GetDocEntry(GrPixel, NumPixel) ) { gdcmWarningMacro("Pixel Dicom Element " << std::hex << @@ -260,50 +312,50 @@ ModalityType File::GetModality() std::string strModality = GetEntryValue(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { - if ( strModality.find("AU") < strModality.length()) return AU; - else if ( strModality.find("AS") < strModality.length()) return AS; - else if ( strModality.find("BI") < strModality.length()) return BI; - else if ( strModality.find("CF") < strModality.length()) return CF; - else if ( strModality.find("CP") < strModality.length()) return CP; - else if ( strModality.find("CR") < strModality.length()) return CR; - else if ( strModality.find("CT") < strModality.length()) return CT; - else if ( strModality.find("CS") < strModality.length()) return CS; - else if ( strModality.find("DD") < strModality.length()) return DD; - else if ( strModality.find("DF") < strModality.length()) return DF; - else if ( strModality.find("DG") < strModality.length()) return DG; - else if ( strModality.find("DM") < strModality.length()) return DM; - else if ( strModality.find("DS") < strModality.length()) return DS; - else if ( strModality.find("DX") < strModality.length()) return DX; + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; else if ( strModality.find("ECG") < strModality.length()) return ECG; else if ( strModality.find("EPS") < strModality.length()) return EPS; - else if ( strModality.find("FA") < strModality.length()) return FA; - else if ( strModality.find("FS") < strModality.length()) return FS; - else if ( strModality.find("HC") < strModality.length()) return HC; - else if ( strModality.find("HD") < strModality.length()) return HD; - else if ( strModality.find("LP") < strModality.length()) return LP; - else if ( strModality.find("LS") < strModality.length()) return LS; - else if ( strModality.find("MA") < strModality.length()) return MA; - else if ( strModality.find("MR") < strModality.length()) return MR; - else if ( strModality.find("NM") < strModality.length()) return NM; - else if ( strModality.find("OT") < strModality.length()) return OT; - 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("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + 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; + < strModality.length()) return RTDOSE; else if ( strModality.find("RTIMAGE") - < strModality.length()) return RTIMAGE; + < strModality.length()) return RTIMAGE; else if ( strModality.find("RTPLAN") - < strModality.length()) return 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; - else if ( strModality.find("US") < strModality.length()) return US; - else if ( strModality.find("VF") < strModality.length()) return VF; - else if ( strModality.find("XA") < strModality.length()) return XA; - else if ( strModality.find("XC") < strModality.length()) return XC; + < 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; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; else { @@ -312,7 +364,6 @@ ModalityType File::GetModality() return Unknow; } } - return Unknow; } @@ -328,7 +379,6 @@ int File::GetXSize() { return 0; } - return atoi( strSize.c_str() ); } @@ -350,8 +400,9 @@ int File::GetYSize() return 0; } - // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1D image). So we default to 1: + // The Rows (0028,0010) entry was optional for ACR/NEMA. + // (at least some images didn't have it.) + // It might hence be a signal (1D image). So we default to 1: return 1; } @@ -359,7 +410,7 @@ int File::GetYSize() * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third - * dimension. When Missing we consider the third dimension as + * dimension. When missing we consider the third dimension as * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ @@ -379,13 +430,12 @@ int File::GetZSize() { return atoi( strSize2.c_str() ); } - return 1; } /** - * \brief gets the info from 0028,0030 : Pixel Spacing - * (first in 0018,1164 : ImagerPixelSpacing) + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ @@ -396,7 +446,6 @@ float File::GetXSpacing() int nbValues; // To follow David Clunie's advice, we first check ImagerPixelSpacing - // (never saw any image with that field :-( const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); if ( strImagerPixelSpacing != GDCM_UNFOUND ) @@ -418,7 +467,6 @@ float File::GetXSpacing() } } - const std::string &strSpacing = GetEntryValue(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) @@ -441,10 +489,9 @@ float File::GetXSpacing() xspacing = 1.0; return xspacing; - } - // to avoid troubles with David Clunie's-like images + // to avoid troubles with David Clunie's-like images (at least one) if ( xspacing == 0. && yspacing == 0.) return 1.; @@ -460,8 +507,8 @@ float File::GetXSpacing() } /** - * \brief gets the info from 0028,0030 : Pixel Spacing - * (first in 0018,1164 : ImagerPixelSpacing) + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ @@ -470,7 +517,6 @@ float File::GetYSpacing() float yspacing = 1.; int nbValues; // To follow David Clunie's advice, we first check ImagerPixelSpacing - // (never saw any image with that field :-( const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); if ( strImagerPixelSpacing != GDCM_UNFOUND ) @@ -521,8 +567,8 @@ float File::GetZSpacing() // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal - // It only concerns the MRI guys, not people wanting to visualize volmues - // If Spacing Between Slices is Missing, + // 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); @@ -650,7 +696,8 @@ float File::GetZOrigin() } } - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images + // for *very* old ACR-NEMA images + std::string strSliceLocation = GetEntryValue(0x0020,0x1041); if ( strSliceLocation != GDCM_UNFOUND ) { if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) @@ -686,10 +733,10 @@ float File::GetZOrigin() /** * \brief gets the info from 0020,0037 : Image Orientation Patient * (needed to organize DICOM files based on their x,y,z position) - * @param iop adress of the (6)float aray to receive values + * @param iop adress of the (6)float array to receive values * @return cosines of image orientation patient */ -void File::GetImageOrientationPatient( float iop[6] ) +bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] @@ -702,6 +749,7 @@ void File::GetImageOrientationPatient( float iop[6] ) &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." ); + return false; } } //For ACR-NEMA @@ -712,8 +760,10 @@ void File::GetImageOrientationPatient( float iop[6] ) &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." ); + return false; } } + return true; } /** @@ -736,7 +786,7 @@ int File::GetBitsStored() /** * \brief Retrieve the number of Bits Allocated - * (8, 12 -compacted ACR-NEMA files, 16, ...) + * (8, 12 -compacted ACR-NEMA files-, 16, ...) * @return The encountered number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ @@ -754,9 +804,9 @@ int File::GetBitsAllocated() /** * \brief Retrieve the high bit position. - * \warning The method defaults to 0 when information is Missing. + * \warning The method defaults to 0 when information is missing. * The responsability of checking this value is left to the caller. - * @return The high bit positin when present. 0 when Missing. + * @return The high bit position when present. 0 when missing. */ int File::GetHighBitPosition() { @@ -771,9 +821,9 @@ int File::GetHighBitPosition() /** * \brief Retrieve the number of Samples Per Pixel - * (1 : gray level, 3 : RGB -1 or 3 Planes-) + * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-) * @return The encountered number of Samples Per Pixel, 1 by default. - * (Gray level Pixels) + * (we assume Gray level Pixels) */ int File::GetSamplesPerPixel() { @@ -811,7 +861,7 @@ int File::GetPlanarConfiguration() int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) + // (in order no to be messed up by old ACR-NEMA RGB images) // if (File::GetEntryValue(0x0028,0x0100) == "24") // return 3; @@ -848,6 +898,7 @@ int File::GetPixelSize() * - 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 + photochromatic interp ="RGB " + * + Planar Configuration = 0 * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() @@ -896,7 +947,8 @@ std::string File::GetPixelType() * \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. + * The responsability of checking this value is left to the caller + * (NO transformation is performed on the pixels to make then >0) * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() @@ -1118,7 +1170,7 @@ float File::GetRescaleSlope() * to have to manage a LUT and expects to get an RBG Pixel image * (or a monochrome one ...) * \warning to be used with GetImagePixels() - * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ int File::GetNumberOfScalarComponents() { @@ -1227,11 +1279,12 @@ size_t File::GetPixelAreaLength() /** * \brief Adds the characteristics of a new element we want to anonymize - * + * @param group Group number of the target tag. + * @param elem Element number of the target tag. + * @param value new value (string) to substitute with */ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, std::string const &value) - { Element el; el.Group = group; @@ -1262,9 +1315,11 @@ void File::AnonymizeNoLoad() if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) - continue; + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize a SeqEntry "); + continue; + } offset = d->GetOffset(); lgth = d->GetLength(); @@ -1283,8 +1338,9 @@ void File::AnonymizeNoLoad() } /** - * \brief anonymize a File (removes Patient's personal info passed with + * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() + * \note You cannot Anonymize a BinEntry (to be fixed) */ bool File::AnonymizeFile() { @@ -1323,11 +1379,19 @@ bool File::AnonymizeFile() if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; + } - SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) "); + continue; + } + else + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1391,7 +1455,7 @@ 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 writetype 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 writetype) @@ -1493,9 +1557,9 @@ void File::ComputeRLEInfo() rleSegmentOffsetTable[k] = ReadInt32(); } - // Deduce from both the RLE Header and the frameLength the - // fragment length, and again store this info in a - // RLEFramesInfo. + // Deduce from both RLE Header and frameLength + // the fragment length, and again store this info + // in a RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) @@ -1523,8 +1587,8 @@ void File::ComputeRLEInfo() RLEInfo->AddFrame(newFrame); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); @@ -1564,8 +1628,8 @@ void File::ComputeJPEGFragmentInfo() SkipBytes(fragmentLength); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); @@ -1575,17 +1639,17 @@ void File::ComputeJPEGFragmentInfo() /** * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag check whether this - * tag is (TestGroup, TestElement). + * tag is (TestGroup, TestElem). * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag - * (TestGroup, TestElement) the internal file pointer + * (TestGroup, TestElem) the internal file pointer * \ref Document::Fp is restored to it's original position. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. + * @param testGroup The expected group of the tag. + * @param testElem The expected Element of the tag. * @return True on success, false otherwise. */ -bool File::ReadTag(uint16_t testGroup, uint16_t testElement) +bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { long positionOnEntry = Fp->tellg(); long currentPosition = Fp->tellg(); // On debugging purposes @@ -1593,24 +1657,24 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; - uint16_t itemTagElement; + uint16_t itemTagElem; try { - itemTagGroup = ReadInt16(); - itemTagElement = ReadInt16(); + itemTagGroup = ReadInt16(); + itemTagElem = ReadInt16(); } catch ( FormatError e ) { //std::cerr << e << std::endl; return false; } - if ( itemTagGroup != testGroup || itemTagElement != testElement ) + if ( itemTagGroup != testGroup || itemTagElem != testElem ) { gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" - << std::hex << testGroup << "," << testElement << ")" << std::endl + << std::hex << testGroup << "," << testElem << ")" << std::endl << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElement << ")" + << std::hex << itemTagGroup << "," << itemTagElem << ")" << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1629,15 +1693,15 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer * \ref Document::Fp is restored to it's original position. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. + * @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 * returns 0. */ -uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) { - if ( !ReadTag(testGroup, testElement) ) + if ( !ReadTag(testGroup, testElem) ) { return 0; } @@ -1687,6 +1751,210 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() } } +// 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 + */ +File::File( std::string const &filename ) + :Document( ) +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + + SetFileName( 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, + * or no tag was found. + * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead + */ +bool File::Load( std::string const &fileName ) +{ + GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", + File::Load()); + SetFileName( fileName ); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} +#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 + */ +double File::TypeOrientation( ) +{ + float iop[6]; + bool succ = GetImageOrientationPatient( iop ); + if ( !succ ) + { + 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 + double 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; + // 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 ); + } + 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, double criterionNew, Res const & in) +{ + Res res; + double criterion = in.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 (double) +//- : - type : vector 3D (double) +// - Description of the first plane +//- : - type : vector 3D (double) +//- : - type : vector 3D (double) +// - Description of the second plane +//------------------------- Return : ------------------------------------ +// double : 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 +double +File::CalculLikelyhood2Vec(vector3D const & refA, vector3D const & refB, + vector3D const & ori1, vector3D const & ori2 ) +{ + + vector3D ori3 = ProductVectorial(ori1,ori2); + vector3D refC = ProductVectorial(refA,refB); + double res = square_dist(refC, ori3); + + return sqrt(res); +} + +//------------------------- Purpose : ----------------------------------- +//- Calculus of the poduct vectorial between two vectors 3D +//------------------------- Parameters : -------------------------------- +//- : - type : vector 3D (double) +//- : - type : vector 3D (double) +//------------------------- Return : ------------------------------------ +// (vec) : - Vector 3D +//------------------------- Other : ------------------------------------- +vector3D +File::ProductVectorial(vector3D const & vec1, vector3D const & vec2) +{ + 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; + + return vec3; +} + //----------------------------------------------------------------------------- // Print