+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: gdcmHeader.cxx,v $
- Language: C++
- Date: $Date: 2005/01/20 11:39:49 $
- Version: $Revision: 1.236 $
-
- Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
- l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the above copyright notices for more information.
-
-=========================================================================*/
-
-#include "gdcmHeader.h"
-#include "gdcmGlobal.h"
-#include "gdcmUtil.h"
-#include "gdcmDebug.h"
-#include "gdcmTS.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
-#include <stdio.h> //sscanf
-
-#include <vector>
-
-namespace gdcm
-{
-//-----------------------------------------------------------------------------
-// Constructor / Destructor
-/**
- * \brief Constructor
- * @param filename name of the file whose header we want to analyze
- */
-Header::Header( std::string const &filename ):
- Document( filename )
-{
- // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
- // We may encounter the 'RETired' (0x0028, 0x0200) tag
- // (Image Location") . This Element contains the number of
- // the group that contains the pixel data (hence the "Pixel Data"
- // is found by indirection through the "Image Location").
- // Inside the group pointed by "Image Location" the searched element
- // is conventionally the element 0x0010 (when the norm is respected).
- // When the "Image Location" is Missing we default to group 0x7fe0.
- // Note: this IS the right place for the code
-
- // Image Location
- const std::string &imgLocation = GetEntry(0x0028, 0x0200);
- if ( imgLocation == GDCM_UNFOUND )
- {
- // default value
- GrPixel = 0x7fe0;
- }
- else
- {
- GrPixel = (uint16_t) atoi( imgLocation.c_str() );
- }
-
- // sometimes Image Location value doesn't follow
- // the supposed processor endianness.
- // see gdcmData/cr172241.dcm
- if ( GrPixel == 0xe07f )
- {
- GrPixel = 0x7fe0;
- }
-
- if ( GrPixel != 0x7fe0 )
- {
- // This is a kludge for old dirty Philips imager.
- NumPixel = 0x1010;
- }
- else
- {
- NumPixel = 0x0010;
- }
-
- // Now, we know GrPixel and NumPixel.
- // Let's create a VirtualDictEntry to allow a further VR modification
- // and force VR to match with BitsAllocated.
- DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
- if ( entry != 0 )
- {
-
- std::string 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 )
- PixelVR = "OB";
- else
- PixelVR = "OW";
-
- DictEntry* newEntry = NewVirtualDictEntry(
- GrPixel, NumPixel,
- PixelVR, "PXL", "Pixel Data");
-
- entry->SetDictEntry( newEntry );
- }
-}
-
-/**
- * \brief Constructor used when we want to generate dicom files from scratch
- */
-Header::Header()
- :Document()
-{
- InitializeDefaultHeader();
-}
-
-/**
- * \brief Canonical destructor.
- */
-Header::~Header ()
-{
-}
-
-/**
- * \brief Performs some consistency checking on various 'File related'
- * (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 filetype Type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- */
-bool Header::Write(std::string fileName, FileType filetype)
-{
- std::ofstream *fp = new std::ofstream(fileName.c_str(),
- std::ios::out | std::ios::binary);
- if (*fp == NULL)
- {
- gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
- return false;
- }
-
- // Bits Allocated
- if ( GetEntry(0x0028,0x0100) == "12")
- {
- SetEntry("16", 0x0028,0x0100);
- }
-
- /// \todo correct 'Pixel group' Length if necessary
-
- 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() );
- ReplaceOrCreate(s_lgPix,GrPixel, 0x0000);
- }
-
- // FIXME : should be nice if we could move it to File
- // (or in future gdcmPixelData class)
-
- // Drop Palette Color, if necessary
-
- if ( GetEntry(0x0028,0x0002).c_str()[0] == '3' )
- {
- // if SamplesPerPixel = 3, sure we don't need any LUT !
- // Drop 0028|1101, 0028|1102, 0028|1103
- // Drop 0028|1201, 0028|1202, 0028|1203
-
- DocEntry *e = GetDocEntry(0x0028,0x01101);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1102);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1103);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x01201);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1202);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1203);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- }
-
-/*
-#ifdef GDCM_WORDS_BIGENDIAN
- // Super Super hack that will make gdcm a BOMB ! but should
- // Fix temporarily the dashboard
- BinEntry *b = GetBinEntry(GrPixel,NumPixel);
- if ( GetPixelSize() == 16 )
- {
- uint16_t *im16 = (uint16_t*)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- }
-#endif //GDCM_WORDS_BIGENDIAN
-*/
-
- Document::WriteContent(fp,filetype);
-
-/*
-#ifdef GDCM_WORDS_BIGENDIAN
- // Flip back the pixel ... I told you this is a hack
- if ( GetPixelSize() == 16 )
- {
- uint16_t *im16 = (uint16_t*)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- }
-#endif //GDCM_WORDS_BIGENDIAN
-*/
-
- fp->close();
- delete fp;
-
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Print
-
-
-//-----------------------------------------------------------------------------
-// Public
-
-/**
- * \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current Header was properly parsed
- * and contains the mandatory information for being considered as
- * a well formed and usable Dicom/Acr File.
- * @return true when Header is the one of a reasonable Dicom/Acr file,
- * false otherwise.
- */
-bool Header::IsReadable()
-{
- if( !Document::IsReadable() )
- {
- return false;
- }
-
- const std::string &res = GetEntry(0x0028, 0x0005);
- if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
- {
- return false; // Image Dimensions
- }
- if ( !GetDocEntry(0x0028, 0x0100) )
- {
- return false; // "Bits Allocated"
- }
- if ( !GetDocEntry(0x0028, 0x0101) )
- {
- return false; // "Bits Stored"
- }
- if ( !GetDocEntry(0x0028, 0x0102) )
- {
- return false; // "High Bit"
- }
- if ( !GetDocEntry(0x0028, 0x0103) )
- {
- return false; // "Pixel Representation" i.e. 'Sign'
- }
-
- return true;
-}
-
-/**
- * \brief Retrieve the number of columns of image.
- * @return The encountered size when found, 0 by default.
- * 0 means the file is NOT USABLE. The caller will have to check
- */
-int Header::GetXSize()
-{
- const std::string &strSize = GetEntry(0x0028,0x0011);
- if ( strSize == GDCM_UNFOUND )
- {
- return 0;
- }
-
- return atoi( strSize.c_str() );
-}
-
-/**
- * \brief Retrieve the number of lines of image.
- * \warning The defaulted value is 1 as opposed to Header::GetXSize()
- * @return The encountered size when found, 1 by default
- * (The ACR-NEMA file contains a Signal, not an Image).
- */
-int Header::GetYSize()
-{
- const std::string &strSize = GetEntry(0x0028,0x0010);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
- if ( IsDicomV3() )
- {
- 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:
- return 1;
-}
-
-/**
- * \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
- * being the ACR-NEMA "Planes" tag content.
- * @return The encountered size when found, 1 by default (single image).
- */
-int Header::GetZSize()
-{
- // Both DicomV3 and ACR/Nema consider the "Number of Frames"
- // as the third dimension.
- const std::string &strSize = GetEntry(0x0028,0x0008);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
-
- // We then consider the "Planes" entry as the third dimension
- const std::string &strSize2 = GetEntry(0x0028,0x0012);
- if ( strSize2 != GDCM_UNFOUND )
- {
- return atoi( strSize2.c_str() );
- }
-
- return 1;
-}
-
-/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * else 1.0
- * @return X dimension of a pixel
- */
-float Header::GetXSpacing()
-{
- float xspacing, yspacing;
- const std::string &strSpacing = GetEntry(0x0028,0x0030);
-
- if ( strSpacing == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
- return 1.;
- }
-
- int nbValues;
- if( ( nbValues = sscanf( strSpacing.c_str(),
- "%f\\%f", &yspacing, &xspacing)) != 2 )
- {
- // if single value is found, xspacing is defaulted to yspacing
- if ( nbValues == 1 )
- {
- xspacing = yspacing;
- }
-
- if ( xspacing == 0.0 )
- xspacing = 1.0;
-
- return xspacing;
-
- }
-
- // to avoid troubles with David Clunie's-like images
- if ( xspacing == 0. && yspacing == 0.)
- return 1.;
-
- if ( xspacing == 0.)
- {
- gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
- // seems to be a bug in the header ...
- nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
- gdcmAssertMacro( nbValues == 2 );
- }
-
- return xspacing;
-}
-
-/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * else 1.0
- * @return Y dimension of a pixel
- */
-float Header::GetYSpacing()
-{
- float yspacing = 1.;
- std::string strSpacing = GetEntry(0x0028,0x0030);
-
- if ( strSpacing == GDCM_UNFOUND )
- {
- gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
- return 1.;
- }
-
- // if sscanf cannot read any float value, it won't affect yspacing
- sscanf( strSpacing.c_str(), "%f", &yspacing);
-
- if ( yspacing == 0.0 )
- yspacing = 1.0;
-
- return yspacing;
-}
-
-/**
- * \brief gets the info from 0018,0088 : Space Between Slices
- * else from 0018,0050 : Slice Thickness
- * else 1.0
- * @return Z dimension of a voxel-to be
- */
-float Header::GetZSpacing()
-{
- // Spacing Between Slices : distance entre le milieu de chaque coupe
- // Les coupes peuvent etre :
- // jointives (Spacing between Slices = Slice Thickness)
- // chevauchantes (Spacing between Slices < Slice Thickness)
- // disjointes (Spacing between Slices > Slice Thickness)
- // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
- // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
- // Si le Spacing Between Slices est Missing,
- // on suppose que les coupes sont jointives
-
- const std::string &strSpacingBSlices = GetEntry(0x0018,0x0088);
-
- if ( strSpacingBSlices == GDCM_UNFOUND )
- {
- gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
- const std::string &strSliceThickness = GetEntry(0x0018,0x0050);
- if ( strSliceThickness == GDCM_UNFOUND )
- {
- gdcmVerboseMacro("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() );
- }
- }
- //else
- return (float)atof( strSpacingBSlices.c_str() );
-}
-
-/**
- *\brief gets the info from 0028,1052 : Rescale Intercept
- * @return Rescale Intercept
- */
-float Header::GetRescaleIntercept()
-{
- float resInter = 0.;
- /// 0028 1052 DS IMG Rescale Intercept
- const std::string &strRescInter = GetEntry(0x0028,0x1052);
- if ( strRescInter != GDCM_UNFOUND )
- {
- if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
- {
- // bug in the element 0x0028,0x1052
- gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
- }
- }
-
- return resInter;
-}
-
-/**
- *\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope
- */
-float Header::GetRescaleSlope()
-{
- float resSlope = 1.;
- //0028 1053 DS IMG Rescale Slope
- std::string strRescSlope = GetEntry(0x0028,0x1053);
- if ( strRescSlope != GDCM_UNFOUND )
- {
- if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
- {
- // bug in the element 0x0028,0x1053
- gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
- }
- }
-
- return resSlope;
-}
-
-/**
- * \brief This function is intended to user who doesn't want
- * 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)
- */
-int Header::GetNumberOfScalarComponents()
-{
- if ( GetSamplesPerPixel() == 3 )
- {
- return 3;
- }
-
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if ( GetEntry(0x0028,0x0100) == "24" )
- {
- return 3;
- }
-
- std::string strPhotometricInterpretation = GetEntry(0x0028,0x0004);
-
- if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
- {
- if ( HasLUT() )// PALETTE COLOR is NOT enough
- {
- return 3;
- }
- else
- {
- return 1;
- }
- }
-
- // beware of trailing space at end of string
- // DICOM tags are never of odd length
- if ( strPhotometricInterpretation == GDCM_UNFOUND ||
- Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
- Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
- {
- return 1;
- }
- else
- {
- // we assume that *all* kinds of YBR are dealt with
- return 3;
- }
-}
-
-/**
- * \brief This function is intended to user that DOESN'T want
- * to get RGB pixels image when it's stored as a PALETTE COLOR image
- * - the (vtk) user is supposed to know how deal with LUTs -
- * \warning to be used with GetImagePixelsRaw()
- * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
- */
-int Header::GetNumberOfScalarComponentsRaw()
-{
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if ( Header::GetEntry(0x0028,0x0100) == "24" )
- {
- return 3;
- }
-
- // we assume that *all* kinds of YBR are dealt with
- return GetSamplesPerPixel();
-}
-
-//
-// -------------- Remember ! ----------------------------------
-//
-// Image Position Patient (0020,0032):
-// If not found (ACR_NEMA) we try Image Position (0020,0030)
-// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
-// or Location (0020,0050)
-// as the Z coordinate,
-// 0. for all the coordinates if nothing is found
-
-// \todo find a way to inform the caller nothing was found
-// \todo How to tell the caller a wrong number of values was found?
-//
-// ---------------------------------------------------------------
-//
-
-/**
- * \brief gets the info from 0020,0032 : Image Position Patient
- * else from 0020,0030 : Image Position (RET)
- * else 0.
- * @return up-left image corner X position
- */
-float Header::GetXOrigin()
-{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntry(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
- /// \todo How to tell the caller nothing was found ?
- return 0.;
- }
- }
-
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
- {
- return 0.;
- }
-
- return xImPos;
-}
-
-/**
- * \brief gets the info from 0020,0032 : Image Position Patient
- * else from 0020,0030 : Image Position (RET)
- * else 0.
- * @return up-left image corner Y position
- */
-float Header::GetYOrigin()
-{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntry(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND)
- {
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
- /// \todo How to tell the caller nothing was found ?
- return 0.;
- }
- }
-
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
- {
- return 0.;
- }
-
- return yImPos;
-}
-
-/**
- * \brief gets the info from 0020,0032 : Image Position Patient
- * else from 0020,0030 : Image Position (RET)
- * else from 0020,1041 : Slice Location
- * else from 0020,0050 : Location
- * else 0.
- * @return up-left image corner Z position
- */
-float Header::GetZOrigin()
-{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntry(0x0020,0x0032);
-
- if ( strImPos != GDCM_UNFOUND )
- {
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
- {
- gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
- }
- }
-
- strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos != GDCM_UNFOUND )
- {
- if( sscanf( strImPos.c_str(),
- "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
- {
- gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
- }
- }
-
- std::string strSliceLocation = GetEntry(0x0020,0x1041); // for *very* old ACR-NEMA images
- if ( strSliceLocation != GDCM_UNFOUND )
- {
- if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
- {
- gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
- return 0.; // bug in the element 0x0020,0x1041
- }
- else
- {
- return zImPos;
- }
- }
- gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
-
- std::string strLocation = GetEntry(0x0020,0x0050);
- if ( strLocation != GDCM_UNFOUND )
- {
- if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
- {
- gdcmVerboseMacro( "Wrong Location (0020,0050)");
- return 0.; // bug in the element 0x0020,0x0050
- }
- else
- {
- return zImPos;
- }
- }
- gdcmVerboseMacro( "Unfound Location (0020,0050)");
-
- return 0.; // Hopeless
-}
-
-/**
- * \brief gets the info from 0020,0013 : Image Number else 0.
- * @return image number
- */
-int Header::GetImageNumber()
-{
- // The function i atoi() takes the address of an area of memory as
- // parameter and converts the string stored at that location to an integer
- // using the external decimal to internal binary conversion rules. This may
- // be preferable to sscanf() since atoi() is a much smaller, simpler and
- // faster function. sscanf() can do all possible conversions whereas
- // atoi() can only do single decimal integer conversions.
- //0020 0013 IS REL Image Number
- std::string strImNumber = GetEntry(0x0020,0x0013);
- if ( strImNumber != GDCM_UNFOUND )
- {
- return atoi( strImNumber.c_str() );
- }
- return 0; //Hopeless
-}
-
-/**
- * \brief gets the info from 0008,0060 : Modality
- * @return Modality Type
- */
-ModalityType Header::GetModality()
-{
- // 0008 0060 CS ID Modality
- std::string strModality = GetEntry(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;
- 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("RTDOSE") < strModality.length()) return RTDOSE;
- else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE;
- else if ( strModality.find("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;
-
- else
- {
- /// \todo throw error return value ???
- /// specified <> unknown in our database
- return Unknow;
- }
- }
-
- return Unknow;
-}
-
-/**
- * \brief Retrieve the number of Bits Stored (actually used)
- * (as opposite to number of Bits Allocated)
- * @return The encountered number of Bits Stored, 0 by default.
- * 0 means the file is NOT USABLE. The caller has to check it !
- */
-int Header::GetBitsStored()
-{
- std::string strSize = GetEntry( 0x0028, 0x0101 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro("(0028,0101) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
- }
- return atoi( strSize.c_str() );
-}
-
-/**
- * \brief Retrieve the high bit position.
- * \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.
- */
-int Header::GetHighBitPosition()
-{
- std::string strSize = GetEntry( 0x0028, 0x0102 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
- return 0;
- }
- return atoi( strSize.c_str() );
-}
-
-/**
- * \brief Check whether the pixels are signed or UNsigned data.
- * \warning The method defaults to false (UNsigned) when information is Missing.
- * The responsability of checking this value is left to the caller.
- * @return True when signed, false when UNsigned
- */
-bool Header::IsSignedPixelData()
-{
- std::string strSize = GetEntry( 0x0028, 0x0103 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory");
- return false;
- }
- int sign = atoi( strSize.c_str() );
- if ( sign == 0 )
- {
- return false;
- }
- return true;
-}
-
-/**
- * \brief Retrieve the number of Bits Allocated
- * (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 !
- */
-int Header::GetBitsAllocated()
-{
- std::string strSize = GetEntry(0x0028,0x0100);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
- }
- return atoi( strSize.c_str() );
-}
-
-/**
- * \brief Retrieve the number of Samples Per Pixel
- * (1 : gray level, 3 : RGB -1 or 3 Planes-)
- * @return The encountered number of Samples Per Pixel, 1 by default.
- * (Gray level Pixels)
- */
-int Header::GetSamplesPerPixel()
-{
- const std::string& strSize = GetEntry(0x0028,0x0002);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "(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() );
-}
-
-/**
- * \brief Check whether this a monochrome picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
- */
-bool Header::IsMonochrome()
-{
- const std::string& PhotometricInterp = GetEntry( 0x0028, 0x0004 );
- if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
- || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)");
- }
- return false;
-}
-
-/**
- * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "PALETTE COLOR". False otherwise.
- */
-bool Header::IsPaletteColor()
-{
- std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 );
- if ( PhotometricInterp == "PALETTE COLOR " )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : Palette color (0028,0004)");
- }
- return false;
-}
-
-/**
- * \brief Check whether this a "YBR_FULL" color picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "YBR_FULL". False otherwise.
- */
-bool Header::IsYBRFull()
-{
- std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 );
- if ( PhotometricInterp == "YBR_FULL" )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
- }
- return false;
-}
-
-/**
- * \brief Retrieve the Planar Configuration for RGB images
- * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
- * @return The encountered Planar Configuration, 0 by default.
- */
-int Header::GetPlanarConfiguration()
-{
- std::string strSize = GetEntry(0x0028,0x0006);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
- return 0;
- }
- return atoi( strSize.c_str() );
-}
-
-/**
- * \brief Return the size (in bytes) of a single pixel of data.
- * @return The size in bytes of a single pixel of data; 0 by default
- * 0 means the file is NOT USABLE; the caller will have to check
- */
-int Header::GetPixelSize()
-{
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- // if (Header::GetEntry(0x0028,0x0100) == "24")
- // return 3;
-
- std::string pixelType = GetPixelType();
- if ( pixelType == "8U" || pixelType == "8S" )
- {
- return 1;
- }
- if ( pixelType == "16U" || pixelType == "16S")
- {
- return 2;
- }
- if ( pixelType == "32U" || pixelType == "32S")
- {
- return 4;
- }
- if ( pixelType == "FD" )
- {
- return 8;
- }
- gdcmVerboseMacro( "Unknown pixel type");
- return 0;
-}
-
-/**
- * \brief Build the Pixel Type of the image.
- * Possible values are:
- * - 8U unsigned 8 bit,
- * - 8S signed 8 bit,
- * - 16U unsigned 16 bit,
- * - 16S signed 16 bit,
- * - 32U unsigned 32 bit,
- * - 32S signed 32 bit,
- * - 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
- * @return 0S if nothing found. NOT USABLE file. The caller has to check
- */
-std::string Header::GetPixelType()
-{
- std::string bitsAlloc = GetEntry(0x0028, 0x0100); // Bits Allocated
- if ( bitsAlloc == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)");
- bitsAlloc = "16"; // default and arbitrary value, not to polute the output
- }
-
- if ( bitsAlloc == "64" )
- {
- return "FD";
- }
- else if ( bitsAlloc == "12" )
- {
- // It will be unpacked
- bitsAlloc = "16";
- }
- else if ( bitsAlloc == "24" )
- {
- // (in order no to be messed up
- bitsAlloc = "8"; // by old RGB images)
- }
-
- std::string sign = GetEntry(0x0028, 0x0103);//"Pixel Representation"
-
- if (sign == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)");
- sign = "U"; // default and arbitrary value, not to polute the output
- }
- else if ( sign == "0" )
- {
- sign = "U";
- }
- else
- {
- sign = "S";
- }
- return bitsAlloc + sign;
-}
-
-
-/**
- * \brief Recover the offset (from the beginning of the file)
- * of *image* pixels (not *icone image* pixels, if any !)
- * @return Pixel Offset
- */
-size_t Header::GetPixelOffset()
-{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
- {
- return pxlElement->GetOffset();
- }
- else
- {
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
- return 0;
- }
-}
-
-/// \todo TODO : unify those two (previous one and next one)
-/**
- * \brief Recover the pixel area length (in Bytes)
- * @return Pixel Element Length, as stored in the header
- * (NOT the memory space necessary to hold the Pixels
- * -in case of embeded compressed image-)
- * 0 : NOT USABLE file. The caller has to check.
- */
-size_t Header::GetPixelAreaLength()
-{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
- {
- return pxlElement->GetLength();
- }
- else
- {
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
- return 0;
- }
-}
-
-/**
- * \brief tells us if LUT are used
- * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
- * are NOT considered as LUT, since nobody knows
- * how to deal with them
- * Please warn me if you know sbdy that *does* know ... jprx
- * @return true if LUT Descriptors and LUT Tables were found
- */
-bool Header::HasLUT()
-{
- // Check the presence of the LUT Descriptors, and LUT Tables
- // LutDescriptorRed
- if ( !GetDocEntry(0x0028,0x1101) )
- {
- return false;
- }
- // LutDescriptorGreen
- if ( !GetDocEntry(0x0028,0x1102) )
- {
- return false;
- }
- // LutDescriptorBlue
- if ( !GetDocEntry(0x0028,0x1103) )
- {
- return false;
- }
- // Red Palette Color Lookup Table Data
- if ( !GetDocEntry(0x0028,0x1201) )
- {
- return false;
- }
- // Green Palette Color Lookup Table Data
- if ( !GetDocEntry(0x0028,0x1202) )
- {
- return false;
- }
- // Blue Palette Color Lookup Table Data
- if ( !GetDocEntry(0x0028,0x1203) )
- {
- return false;
- }
-
- // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
- // NOT taken into account, but we don't know how to use it ...
- return true;
-}
-
-/**
- * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
- * else 0
- * @return Lookup Table number of Bits , 0 by default
- * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- * @ return bit number of each LUT item
- */
-int Header::GetLUTNbits()
-{
- std::vector<std::string> tokens;
- int lutNbits;
-
- //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
- // = Lookup Table Desc-Blue
- // Consistency already checked in GetLUTLength
- std::string lutDescription = GetEntry(0x0028,0x1101);
- if ( lutDescription == GDCM_UNFOUND )
- {
- return 0;
- }
-
- tokens.clear(); // clean any previous value
- Util::Tokenize ( lutDescription, tokens, "\\" );
- //LutLength=atoi(tokens[0].c_str());
- //LutDepth=atoi(tokens[1].c_str());
-
- lutNbits = atoi( tokens[2].c_str() );
- tokens.clear();
-
- return lutNbits;
-}
-
-
-//-----------------------------------------------------------------------------
-// Protected
-
-/**
- * \brief anonymize a Header (removes Patient's personal info)
- * (read the code to see which ones ...)
- */
-bool Header::AnonymizeHeader()
-{
- // If exist, replace by spaces
- SetEntry (" ",0x0010, 0x2154); // Telephone
- SetEntry (" ",0x0010, 0x1040); // Adress
- SetEntry (" ",0x0010, 0x0020); // Patient ID
-
- DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
-
- if ( patientNameHE ) // we replace it by Study Instance UID (why not)
- {
- std::string studyInstanceUID = GetEntry (0x0020, 0x000d);
- if ( studyInstanceUID != GDCM_UNFOUND )
- {
- ReplaceOrCreate(studyInstanceUID, 0x0010, 0x0010);
- }
- else
- {
- ReplaceOrCreate("anonymised", 0x0010, 0x0010);
- }
- }
-
- // Just for fun :-(
- // (if any) remove or replace all the stuff that contains a Date
-
-//0008 0012 DA ID Instance Creation Date
-//0008 0020 DA ID Study Date
-//0008 0021 DA ID Series Date
-//0008 0022 DA ID Acquisition Date
-//0008 0023 DA ID Content Date
-//0008 0024 DA ID Overlay Date
-//0008 0025 DA ID Curve Date
-//0008 002a DT ID Acquisition Datetime
-//0018 9074 DT ACQ Frame Acquisition Datetime
-//0018 9151 DT ACQ Frame Reference Datetime
-//0018 a002 DT ACQ Contribution Date Time
-//0020 3403 SH REL Modified Image Date (RET)
-//0032 0032 DA SDY Study Verified Date
-//0032 0034 DA SDY Study Read Date
-//0032 1000 DA SDY Scheduled Study Start Date
-//0032 1010 DA SDY Scheduled Study Stop Date
-//0032 1040 DA SDY Study Arrival Date
-//0032 1050 DA SDY Study Completion Date
-//0038 001a DA VIS Scheduled Admission Date
-//0038 001c DA VIS Scheduled Discharge Date
-//0038 0020 DA VIS Admitting Date
-//0038 0030 DA VIS Discharge Date
-//0040 0002 DA PRC Scheduled Procedure Step Start Date
-//0040 0004 DA PRC Scheduled Procedure Step End Date
-//0040 0244 DA PRC Performed Procedure Step Start Date
-//0040 0250 DA PRC Performed Procedure Step End Date
-//0040 2004 DA PRC Issue Date of Imaging Service Request
-//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
-//0040 4011 DT PRC Expected Completion Date and Time
-//0040 a030 DT PRC Verification Date Time
-//0040 a032 DT PRC Observation Date Time
-//0040 a120 DT PRC DateTime
-//0040 a121 DA PRC Date
-//0040 a13a DT PRC Referenced Datetime
-//0070 0082 DA ??? Presentation Creation Date
-//0100 0420 DT ??? SOP Autorization Date and Time
-//0400 0105 DT ??? Digital Signature DateTime
-//2100 0040 DA PJ Creation Date
-//3006 0008 DA SSET Structure Set Date
-//3008 0024 DA ??? Treatment Control Point Date
-//3008 0054 DA ??? First Treatment Date
-//3008 0056 DA ??? Most Recent Treatment Date
-//3008 0162 DA ??? Safe Position Exit Date
-//3008 0166 DA ??? Safe Position Return Date
-//3008 0250 DA ??? Treatment Date
-//300a 0006 DA RT RT Plan Date
-//300a 022c DA RT Air Kerma Rate Reference Date
-//300e 0004 DA RT Review Date
-
- return true;
-}
-
-/**
- * \brief gets the info from 0020,0037 : Image Orientation Patient
- * @param iop adress of the (6)float aray to receive values
- * @return cosines of image orientation patient
- */
-void Header::GetImageOrientationPatient( float iop[6] )
-{
- std::string strImOriPat;
- //iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
-
- // 0020 0037 DS REL Image Orientation (Patient)
- if ( (strImOriPat = GetEntry(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 )
- {
- gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
- }
- }
- //For ACR-NEMA
- // 0020 0035 DS REL Image Orientation (RET)
- else if ( (strImOriPat = GetEntry(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 )
- {
- gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
- }
- }
-}
-
-/**
- * \brief Initialize a default DICOM header that should contain all the
- * field require by other reader. DICOM standard does not
- * explicitely defines those fields, heuristic has been choosen.
- * This is not perfect as we are writting a CT image...
- */
-void Header::InitializeDefaultHeader()
-{
- typedef struct
- {
- const char *value;
- uint16_t group;
- uint16_t elem;
- } DICOM_DEFAULT_VALUE;
-
- std::string date = Util::GetCurrentDate();
- std::string time = Util::GetCurrentTime();
- std::string uid = Util::CreateUniqueUID();
- std::string uidMedia = uid;
- std::string uidClass = uid + ".1";
- std::string uidInst = uid + ".10";
- std::string uidStudy = uid + ".100";
- std::string uidSerie = uid + ".1000";
-
- static DICOM_DEFAULT_VALUE defaultvalue[] = {
- { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
- { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
- { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
- { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian)
- { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
- { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
-
- { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
- { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
- { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
- { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
- { "CT", 0x0008, 0x0060}, // Modality
- { "GDCM", 0x0008, 0x0070}, // Manufacturer
- { "GDCM", 0x0008, 0x0080}, // Institution Name
- { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
-
- { "GDCM", 0x0010, 0x0010}, // Patient's Name
- { "GDCMID", 0x0010, 0x0020}, // Patient ID
-
- { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
- { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
- { "1", 0x0020, 0x0010}, // StudyID
- { "1", 0x0020, 0x0011}, // SeriesNumber
-
- { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
- { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
- { "0", 0x0028, 0x0010}, // nbRows
- { "0", 0x0028, 0x0011}, // nbCols
- { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
- { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
- { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
- { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
- { 0, 0, 0 }
- };
-
- // default value
- // Special case this is the image (not a string)
- GrPixel = 0x7fe0;
- NumPixel = 0x0010;
- ReplaceOrCreate(0, 0, GrPixel, NumPixel);
-
- // All remaining strings:
- unsigned int i = 0;
- DICOM_DEFAULT_VALUE current = defaultvalue[i];
- while( current.value )
- {
- ReplaceOrCreate(current.value, current.group, current.elem);
- current = defaultvalue[++i];
- }
-}
-
-
-//-----------------------------------------------------------------------------
-// Private
-
-//-----------------------------------------------------------------------------
-
-} // end namespace gdcm
projects / gdcm.git / commitdiff