+#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()
+{
+}
+
+/**
+ * \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);
+ }
+
+ /// \todo correct 'Pixel group' Length if necessary
+
+ int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel);
+ if (i_lgPix != -2)
+ {
+ // no (GrPixel, NumPixel) element
+ std::string s_lgPix;
+ s_lgPix = gdcmUtil::Format("%d", i_lgPix+12);
+ ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
+ }
+
+ // FIXME : should be nice if we could move it to gdcmFile
+ // (or in future gdcmPixelData class)
+
+ // 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)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(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() );
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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() );
+ }
+}
+
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float gdcmHeader::GetRescaleIntercept()
+{
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ std::string strRescInter = GetEntryByNumber(0x0028,0x1052);
+ 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;
+}
+
+/**
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+float gdcmHeader::GetRescaleSlope()
+{
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryByNumber(0x0028,0x1053);
+ 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;
+}
+
+/**
+ * \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;
+ }
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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.
+ //0020 0013 IS REL Image Number
+ std::string strImNumber = GetEntryByNumber(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 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;
+}
+
+/**
+ * \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() );
+}
+
+/**
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit positin when present. 0 when absent.
+ */
+int gdcmHeader::GetHighBitPosition()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::GetHighBitPosition: this is supposed "
+ "to be mandatory");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Check wether the pixels are signed or UNsigned data.
+ * \warning The method defaults to false (UNsigned) when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return True when signed, false when UNsigned
+ */
+bool gdcmHeader::IsSignedPixelData()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::IsSignedPixelData: this 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 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() );
+}
+
+/**
+ * \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() );
+}
+
+/**
+ * \brief Check wether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
+ */
+bool gdcmHeader::IsMonochrome()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "MONOCHROME1 "
+ || PhotometricInterp == "MONOCHROME2 " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::IsMonochrome: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
+ */
+bool gdcmHeader::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::IsPaletteColor: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool gdcmHeader::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "gdcmHeader::IsYBRFull: absent Photometric "
+ "Interpretation");
+ }
+ 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 gdcmHeader::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ 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 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;
+}
+
+/**
+ * \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)
+ }
+
+ 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;
+}
+
+
+/**
+ * \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;
+ }
+}
+
+/// \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 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;
+ }
+}
+
+/**
+ * \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;
+}
+
+/**
+ * \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
+ gdcmUtil::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;
+}
+
+/**
+ * \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*) GetEntryBinAreaByNumber(0x0028,0x1201);
+ uint8_t* lutG = (uint8_t*) GetEntryBinAreaByNumber(0x0028,0x1202);
+ uint8_t* lutB = (uint8_t*) GetEntryBinAreaByNumber(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;