-#include "gdcmlib.h"
-extern "C" {
-#include "glib.h"
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2004/09/01 16:23:59 $
+ Version: $Revision: 1.183 $
+
+ 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.htm 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 <vector>
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
+ */
+gdcmHeader::gdcmHeader( std::string const & filename ):
+ gdcmDocument( 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 absent we default to group 0x7fe0.
+ // Note: this IS the right place for the code
+
+ // Image Location
+ std::string imgLocation = GetEntryByNumber(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 endianity.
+ // 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;
+ }
+}
+
+/**
+ * \brief Constructor
+ */
+gdcmHeader::gdcmHeader()
+ :gdcmDocument()
+{
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Canonical destructor.
+ */
+gdcmHeader::~gdcmHeader ()
+{
+}
+
+
+/**
+ * \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 fp file pointer on an already open file
+ * @param filetype Type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ */
+void gdcmHeader::Write(FILE* fp,FileType filetype)
+{
+ // Bits Allocated
+ if ( GetEntryByNumber(0x0028,0x0100) == "12")
+ {
+ SetEntryByNumber("16", 0x0028,0x0100);
+ }
+
+ // correct Pixel group Length if necessary
+
+ // TODO : create a gdcmHeader::Write method and move this part.
+ // (only gdcmHeader knows GrPixel, NumPixel)
+
+ int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel);
+ if (i_lgPix != -2)
+ {
+ // no (GrPixel, NumPixel) element
+ char* dumm = new char[20];
+ sprintf(dumm ,"%d", i_lgPix+12);
+ std::string s_lgPix = dumm;
+ delete[] dumm;
+ ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
+ }
+
+ // Drop Palette Color, if necessary
+
+ if ( GetEntryByNumber(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
+
+ gdcmDocEntry* e = GetDocEntryByNumber(0x0028,0x01101);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntry(e);
+ }
+ }
+ gdcmDocument::Write(fp,filetype);
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current gdcmHeader was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool gdcmHeader::IsReadable()
+{
+ if( !gdcmDocument::IsReadable() )
+ {
+ return false;
+ }
+
+ std::string res = GetEntryByNumber(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
+ return false; // Image Dimensions
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0100) )
+ {
+ return false; // "Bits Allocated"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0101) )
+ {
+ return false; // "Bits Stored"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0102) )
+ {
+ return false; // "High Bit"
+ }
+ if ( !GetDocEntryByNumber(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 gdcmHeader::GetXSize()
+{
+ std::string strSize;
+ strSize = GetEntryByNumber(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
+ * @return The encountered size when found, 1 by default
+ * (The ACR-NEMA file contains a Signal, not an Image).
+ */
+int gdcmHeader::GetYSize()
+{
+ std::string strSize = GetEntryByNumber(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;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 absent 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 gdcmHeader::GetZSize()
+{
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ std::string strSize = GetEntryByNumber(0x0028,0x0008);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+
+ // We then consider the "Planes" entry as the third dimension
+ strSize = GetEntryByNumber(0x0028,0x0012);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float gdcmHeader::GetXSpacing()
+{
+ float xspacing, yspacing;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetXSpacing: 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 )
+ {
+ return yspacing;
+ }
+ }
+ if ( xspacing == 0.)
+ {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ }
+
+ return xspacing;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float gdcmHeader::GetYSpacing()
+{
+ float yspacing = 0;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: 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);
+
+ return yspacing;
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\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 gdcmHeader::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 absent,
+ // on suppose que les coupes sont jointives
+
+ std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
+
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
+ std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
+ {
+ 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 atof( strSliceThickness.c_str() );
+ }
+ }
+ else
+ {
+ return atof( strSpacingBSlices.c_str() );
+ }
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float gdcmHeader::GetRescaleIntercept()
+{
+ float resInter = 0.;
+ std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
+ if ( strRescInter != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ {
+ // bug in the element 0x0028,0x1052
+ dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
+ }
+ }
+
+ return resInter;
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+float gdcmHeader::GetRescaleSlope()
+{
+ float resSlope = 1.;
+ std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ {
+ // bug in the element 0x0028,0x1053
+ dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
+ }
+ }
+
+ return resSlope;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetNumberOfScalarComponents()
+{
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
+ }
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryByNumber(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryByNumber(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 ||
+ strPhotometricInterpretation == "MONOCHROME1 " ||
+ strPhotometricInterpretation == "MONOCHROME2 " )
+ {
+ return 1;
+ }
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( gdcmHeader::GetEntryByNumber(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 gdcmHeader::GetXOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: 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 gdcmHeader::GetYOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: 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;
}
-#include <stdio.h>
-// For nthos:
-#ifdef _MSC_VER
-#include <winsock.h>
-#else
-#include <netinet/in.h>
-#endif
-#define LGR_ENTETE_A_LIRE 256 // on ne lit plus que le debut
-#define DEBUG 1
+/**
+ * \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 gdcmHeader::GetZOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(),
+ "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images
+ if ( strSliceLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
+
+ std::string strLocation = GetEntryByNumber(0x0020,0x0050);
+ if ( strLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
+}
+
+/**
+ * \brief gets the info from 0020,0013 : Image Number
+ * \ else 0.
+ * @return image number
+ */
+int gdcmHeader::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.
+ std::string strImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
+ if ( strImNumber != GDCM_UNFOUND )
+ {
+ return atoi( strImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType gdcmHeader::GetModality()
+{
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntryByNumber(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 <> unknow in our database
+ return Unknow;
+ }
+ }
+
+ return Unknow;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetBitsStored()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0101);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetBitsAllocated()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
+}
-//FIXME: this looks dirty to me...
-#define str2num(str, typeNum) *((typeNum *)(str))
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetSamplesPerPixel()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetBitsStored: this 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() );
+}
/**
* \ingroup gdcmHeader
- * \brief La seule maniere sure que l'on aie pour determiner
- * si on est en LITTLE_ENDIAN, BIG-ENDIAN,
- * BAD-LITTLE-ENDIAN, BAD-BIG-ENDIAN
- * est de trouver l'element qui donne la longueur d'un 'GROUP'
- * (on sait que la longueur de cet element vaut 0x00000004)
- * et de regarder comment cette longueur est codee en memoire
- *
- * Le probleme vient de ce que parfois, il n'y en a pas ...
- *
- * On fait alors le pari qu'on a a faire a du LITTLE_ENDIAN propre.
- * (Ce qui est la norme -pas respectee- depuis ACR-NEMA)
- * Si ce n'est pas le cas, on ne peut rien faire.
- *
- * (il faudrait avoir des fonctions auxquelles
- * on passe le code Swap en parametre, pour faire des essais 'manuels')
+ * \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.
*/
-void gdcmHeader::CheckSwap()
-{
- guint32 s;
- guint32 x=4; // x : pour ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
-
- int lgrLue;
- char * entCur;
- char deb[LGR_ENTETE_A_LIRE];
-
- // On teste le processeur
- if (x==ntohs(x)) {
- net2host = true;
- } else {
- net2host = false;
- }
-
- // On commence par verifier si c'est du DICOM 'actuel'
- // -------------
- lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE, fp);
-
- entCur = deb+128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- filetype = TrueDicom;
- if (DEBUG) printf ("_IdDcmCheckSwap : C est du DICOM actuel \n");
- } else {
- filetype = Unknown;
- if (DEBUG) printf ("_IdDcmCheckSwap : Ce n'est PAS du DICOM actuel\n");
- }
-
- if(filetype == TrueDicom) {
- // on saute le File Preamble (souvent a ZERO) : 128 Octets
- // + le DICM (4), et le (0002, 0000) soit 4 (136 = 128 + 4 + 4)
- entCur = deb+136;
- if(memcmp(entCur, "UL", (size_t)2) == 0) {
- // les 2 premiers octets de la lgr peuvent valoir UL --> Explicit VR
- filetype = ExplicitVR;
- if (DEBUG) printf ("_IdDcmCheckSwap : Explicit VR\n");
- } else {
- filetype = ImplicitVR;
- if (DEBUG) printf ("_IdDcmCheckSwap : PAS Explicit VR\n");
- }
-
- if (net2host) { // HostByteOrder is different from NetworkByteOrder
- sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
- if (DEBUG) printf("HostByteOrder = NetworkByteOrder\n");
- } else { /* on est sur une Sun ou une SGI */
- sw = 4321;
- if (DEBUG) printf("HostByteOrder != NetworkByteOrder\n");
- }
-
- rewind(fp);
- fseek (fp, 132L, SEEK_SET); //On se positionne sur le debut des info
- offsetCourant=132;
- } // End of TrueDicom
-
- // Pas du TrueDicom : permiere hypothese c'est de l'ACR 'propre', auquel
- // cas la lgr du premier element du groupe est FORCEMENT 4
- entCur=deb + 4;
- s=str2num(entCur,int);
-
- switch (s) {
- case 0x00040000 :
- sw=3412; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x04000000 :
- sw=4321; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x00000400 :
- sw=2143; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x00000004 :
- sw=0; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- default :
- sw = -1;
- if (DEBUG) printf (" Pas trouve l info de Swap; On va parier\n");
- }
- if(sw!=-1) {
- rewind(fp); // les info commencent au debut
- offsetCourant=0;
- return;
- }
-
- // Deuxieme hypothese : c'est de l'ACR 'pas propre' i.e. il manque
- // la lgr du groupe
-
- // On n'a pas trouve l'info de swap.
- // Si c'est du VRAI ACR NEMA et
- // * si on est sur une DEC ou un PC alors swap=0,
- // * si on est sur SUN ou SGI, alors swap=4321
- // Si c'est du RAW, ca degagera + tard
- if (DEBUG) printf("On force la chance \n");
-
- if (x!=ntohs(x)) // HostByteOrder is different from NetworkByteOrder
- // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
- sw = 0;
- else
- // on est sur Sun ou SGI
- sw = 4321;
- rewind(fp); // les info commencent au debut
- offsetCourant=0;
- return;
+int gdcmHeader::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+ return atoi( strSize.c_str() );
}
/**
* \ingroup gdcmHeader
- * \brief Pour les fichiers non TrueDicom, si le recognition
- * code (0008,0010) s'avere etre "ACR_LIBIDO", alors
- * valide la reconnaissance du fichier en positionnant
- * filetype.
+ * \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
*/
-void gdcmHeader::setAcrLibido() {
- string RecCode;
-
- if ( filetype != TrueDicom) {
- printf("_setAcrLibido expects a presumably ACR file\n");
- // Recognition Code --> n'existe plus en DICOM V3 ...
- RecCode = GetPubElValByNumber(0x0008, 0x0010);
- // FIXME NOW
- if (RecCode == "ACRNEMA_LIBIDO" ||
- RecCode == "CANRME_AILIBOD" )
- filetype = ACR_LIBIDO;
- else
- filetype = ACR;
- }
- return;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief recupere la longueur d'un champ DICOM.
- * Preconditions:
- * 1/ le fichier doit deja avoir ete ouvert,
- * 2/ CheckSwap() doit avoir ete appele
- * 3/ la partie 'group' ainsi que la partie 'elem'
- * de l'acr_element doivent avoir ete lues.
- *
- * ACR-NEMA : we allways get
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
- * DICOM en implicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
- *
- * DICOM en explicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ValueRepresentation (2 Octets)
- * ElementSize (2 Octets)
- *
- * ATTENTION : dans le cas ou ValueRepresentation = OB, OW, SQ, UN
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ValueRepresentation (2 Octets)
- * zone reservee (2 Octets)
- * ElementSize (4 Octets)
- *
- * @param sw code swap
- * @param skippedLength pointeur sur nombre d'octets que l'on a saute qd
- * la lecture est finie
- * @param longueurLue pointeur sur longueur (en nombre d'octets)
- * effectivement lue
- * @return longueur retenue pour le champ
+int gdcmHeader::GetPixelSize()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ // if (gdcmHeader::GetEntryByNumber(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;
+ }
+ dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ bitsAlloc = "16";
+ }
+
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ 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)
+ }
-// FIXME sw n'est plus un argument necessaire
-long int gdcmHeader::RecupLgr(
- _ID_DCM_ELEM *pleCourant, int sw, int *skippedLength, int *longueurLue)
-{
- guint32 l_gr;
- unsigned short int l_gr_2;
- int i, trouve;
- char VR[5];
- int lgrLue;
-
- // FIX ME
- // ATTENTION : nbCode correspond au nombre d'elements dans la table
- // de type DICOM_VR. A nettoyer.
- //
- int nbCode=26;
-
- if (filetype == ExplicitVR) {
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
-
- // ATTENTION :
- // Ce n'est pas parce qu'on a trouve UL la premiere fois qu'on respecte
- // Explicit VR tout le temps (cf e=film ...)
-
- for(i=0,trouve=0;i<nbCode;i++) {
- if(memcmp(_ID_dicom_vr[i].dicom_VR,VR,(size_t)2)==0) {
- (pleCourant)->VR=_ID_dicom_vr[i].dicom_VR;
- trouve=1;
- break;
- }
- }
-
- if ( trouve == 0) {
-
- // On est mal : implicit VR repere
- // mais ce n'est pas un code connu ...
- // On reconstitue la longueur
-
- if(DEBUG)
- printf("IdDcmRecupLgr : Explicit VR, mais pas de code connu\n");
- memcpy(&l_gr, VR,(size_t)2);
-
- lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, fp);
-
- l_gr = SWAP_LONG((guint32)l_gr);
-
- if(DEBUG)
- printf("IdDcmRecupLgr : lgr deduite : %08x , %d\n",l_gr,l_gr);
-
- *longueurLue=l_gr;
- if ( (int)l_gr == -1)
- l_gr=0;
-
- *skippedLength = 4;
- if (DEBUG)
- printf(" 1 : lgr %08x (%d )skippedLength %d\n",
- l_gr,l_gr, *skippedLength);
- return(l_gr);
- }
-
- // On repart dans la sequence 'sensee'
-
- if(DEBUG)
- printf("VR : [%01x , %01x] (%c%c) en position %d du tableau\n",
- VR[0],VR[1],VR[0],VR[1],i);
-
- if ( (!memcmp( VR,"OB",(size_t)2 )) ||
- (!memcmp( VR,"OW",(size_t)2 )) ||
- (!memcmp( VR,"SQ",(size_t)2 )) ||
- (!memcmp( VR,"UN",(size_t)2 )) ) {
-
- // les 2 octets suivants sont reserves: on les saute
- if(DEBUG)
- printf("IdDcmRecupLgr : les 2 octets suivants sont reserves\n");
- fseek(fp, 2L,SEEK_CUR);
-
- //on lit la lgr sur QUATRE octets
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
- l_gr = SWAP_LONG((guint32)l_gr);
- *skippedLength = 8;
-
- } else {
- //on lit la lgr sur DEUX octets
- lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, fp);
-
- if(sw) l_gr_2 = _IdDcmSWAP_SHORT((unsigned short)l_gr_2,sw);
-
- *longueurLue=l_gr_2;
-
-
- if ( l_gr_2 == 0xffff) {
- l_gr = 0;
- } else {
- l_gr = l_gr_2;
- }
- *skippedLength = 4;
- }
- } else {
- // Explicit VR = 0
- //on lit la lgr sur QUATRE octets
-
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
-
- l_gr= SWAP_LONG((long)l_gr);
- *skippedLength = 4;
- }
-
- *longueurLue=l_gr;
-
- // Traitement des curiosites sur la longueur
-
- if ( (int)l_gr == 0xffffffff)
- l_gr=0;
-
- if(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?!
- l_gr=0; // on lira donc les items de la sequence
- if (DEBUG) printf(" SQ trouve : lgr %d \n",l_gr);
- }
-
- if (DEBUG)
- printf(" 2 : lgr %08x (%d) skippedLength %d\n",l_gr,l_gr, *skippedLength);
- return(l_gr);
+ std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
+
+ if (sign == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
+ bitsAlloc = "0";
+ }
+ if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
}
+
/**
* \ingroup gdcmHeader
- * \brief remet les octets dans un ordre compatible avec celui du processeur
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t gdcmHeader::GetPixelOffset()
+{
+ gdcmDocEntry* pxlElement = GetDocEntryByNumber(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;
+ }
+}
- * @return longueur retenue pour le champ
+// TODO : unify those two (previous one and next one)
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetPixelAreaLength()
+{
+ gdcmDocEntry* pxlElement = GetDocEntryByNumber(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;
+ }
+}
-guint32 gdcmHeader::SWAP_LONG(guint32 a) {
- // FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
- switch (sw) {
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- printf("\n\n\n *******\n erreur code swap ?!?\n\n\n");
- a=0;
- }
- return(a);
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetDocEntryByNumber(0x0028,0x1101) )
+ {
+ return false;
+ }
+ // LutDescriptorGreen
+ if ( !GetDocEntryByNumber(0x0028,0x1102) )
+ {
+ return false;
+ }
+ // LutDescriptorBlue
+ if ( !GetDocEntryByNumber(0x0028,0x1103) )
+ {
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(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;
}
+
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::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 = GetEntryByNumber(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+
+ tokens.clear(); // clean any previous value
+ 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;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * and (0028,1101),(0028,1102),(0028,1102)
+ * - xxx Palette Color Lookup Table Descriptor - are found
+ * and (0028,1201),(0028,1202),(0028,1202)
+ * - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * no known Dicom reader deals with them :-(
+ * @return a RGBA Lookup Table
+ */
+uint8_t* gdcmHeader::GetLUTRGBA()
+{
+ // Not so easy : see
+ // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+ if ( GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR " )
+ {
+ return NULL;
+ }
+
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
+
+ // Get info from Lut Descriptors
+ // (the 3 LUT descriptors may be different)
+ std::string lutDescriptionR = GetEntryByNumber(0x0028,0x1101);
+ if ( lutDescriptionR == GDCM_UNFOUND )
+ {
+ return NULL;
+ }
+
+ std::string lutDescriptionG = GetEntryByNumber(0x0028,0x1102);
+ if ( lutDescriptionG == GDCM_UNFOUND )
+ {
+ return NULL;
+ }
+
+ std::string lutDescriptionB = GetEntryByNumber(0x0028,0x1103);
+ if ( lutDescriptionB == GDCM_UNFOUND )
+ {
+ return NULL;
+ }
+
+ // lengthR: Red LUT length in Bytes
+ // debR: subscript of the first Lut Value
+ // nbitsR: Lut item size (in Bits)
+ int nbRead = sscanf( lutDescriptionR.c_str(), "%d\\%d\\%d",
+ &lengthR, &debR, &nbitsR );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading red LUT");
+ }
+
+ // lengthG: Green LUT length in Bytes
+ // debG: subscript of the first Lut Value
+ // nbitsG: Lut item size (in Bits)
+ nbRead = sscanf( lutDescriptionG.c_str(), "%d\\%d\\%d",
+ &lengthG, &debG, &nbitsG );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading green LUT");
+ }
+
+ // lengthB: Blue LUT length in Bytes
+ // debB: subscript of the first Lut Value
+ // nbitsB: Lut item size (in Bits)
+ nbRead = sscanf( lutDescriptionB.c_str(), "%d\\%d\\%d",
+ &lengthB, &debB, &nbitsB );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT");
+ }
+
+ // Load LUTs into memory, (as they were stored on disk)
+ uint8_t* lutR = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1201);
+ uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202);
+ uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203);
+
+ if ( !lutR || !lutG || !lutB )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT");
+ return NULL;
+ }
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+
+ uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LUTRGBA )
+ {
+ return NULL;
+ }
+ memset(LUTRGBA, 0, 1024);
+
+ // Bits Allocated
+ int nb;
+ std::string str_nb = GetEntryByNumber(0x0028,0x0100);
+ if ( str_nb == GDCM_UNFOUND )
+ {
+ nb = 16;
+ }
+ else
+ {
+ nb = atoi( str_nb.c_str() );
+ }
+ int mult;
+
+ if ( nbitsR == 16 && nb == 8)
+ {
+ // when LUT item size is different than pixel size
+ mult = 2; // high byte must be = low byte
+ }
+ else
+ {
+ // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult = 1;
+ }
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+1' and check again
+ // if it works, we shall have to check the 3 Palettes
+ // to see which byte is ==0 (first one, or second one)
+ // and fix the code
+ // We give up the checking to avoid some (useless ?)overhead
+ // (optimistic asumption)
+ uint8_t* a;
+ int i;
+
+ a = LUTRGBA + 0;
+ for( i=0; i < lengthR; ++i)
+ {
+ *a = lutR[i*mult+1];
+ a += 4;
+ }
+
+ a = LUTRGBA + 1;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = lutG[i*mult+1];
+ a += 4;
+ }
+
+ a = LUTRGBA + 2;
+ for(i=0; i < lengthB; ++i)
+ {
+ *a = lutB[i*mult+1];
+ a += 4;
+ }
+
+ a = LUTRGBA + 3;
+ for(i=0; i < 256; ++i)
+ {
+ *a = 1; // Alpha component
+ a += 4;
+ }
+
+ return LUTRGBA;
+}
+
+/**
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * else 1.
+ * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
+ */
+std::string gdcmHeader::GetTransfertSyntaxName()
+{
+ // use the gdcmTS (TS : Transfert Syntax)
+ std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010);
+
+ if ( transfertSyntax == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:"
+ " unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+
+ while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) )
+ {
+ transfertSyntax.erase(transfertSyntax.length()-1, 1);
+ }
+ // we do it only when we need it
+ gdcmTS* ts = gdcmGlobal::GetTS();
+ std::string tsName = ts->GetValue( transfertSyntax );
+
+ //delete ts; /// \todo Seg Fault when deleted ?!
+ return tsName;
+}
+
+/**
+ * \brief Sets the Pixel Area size in the Header
+ * --> not-for-rats function
+ * @param ImageDataSize new Pixel Area Size
+ * warning : nothing else is checked
+ */
+void gdcmHeader::SetImageDataSize(size_t ImageDataSize)
+{
+ char car[20];
+ sprintf(car,"%d",ImageDataSize);
+
+ gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
+ a->SetLength(ImageDataSize);
+
+ ImageDataSize += 8;
+ sprintf(car,"%d",ImageDataSize);
+
+ const std::string content1 = car;
+ SetEntryByNumber(content1, GrPixel, NumPixel);
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool gdcmHeader::AnonymizeHeader()
+{
+ gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
+
+ ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
+ ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
+ ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
+
+ if ( patientNameHE )
+ {
+ std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ ReplaceOrCreateByNumber(std::string("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 gdcmHeader::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 = GetEntryByNumber(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 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
+ // bug in the element 0x0020,0x0037
+ }
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryByNumber(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 )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
+ // bug in the element 0x0020,0x0035
+ }
+ }
+}
+
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff