-// gdcmHeader.cxx
-//-----------------------------------------------------------------------------
-#include "gdcmHeader.h"
-
-#include <stdio.h>
-#include <cerrno>
-#include <cctype> // for isalpha
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2004/10/18 12:49:22 $
+ Version: $Revision: 1.194 $
+
+ 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"
-//-----------------------------------------------------------------------------
-// Refer to gdcmHeader::CheckSwap()
-//const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
+#include <vector>
-// Refer to gdcmHeader::SetMaxSizeLoadEntry()
-//const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+namespace gdcm
+{
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \ingroup gdcmHeader
- * \brief
- * @param InFilename
- * @param exception_on_error
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * @param ignore_shadow = true if user wants to skip shadow groups
- during parsing, to save memory space
- *\TODO : may be we need one more bool,
- * to allow skipping the private elements while parsing the header
- * in order to save space
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
*/
-gdcmHeader::gdcmHeader(const char *InFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow):
- gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
-{
+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 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;
+ }
}
/**
- * \ingroup gdcmHeader
- * \brief
- * @param exception_on_error
+ * \brief Constructor
*/
-gdcmHeader::gdcmHeader(bool exception_on_error) :
- gdcmParser(exception_on_error)
+Header::Header()
+ :Document()
{
}
/**
- * \ingroup gdcmHeader
* \brief Canonical destructor.
*/
-gdcmHeader::~gdcmHeader (void) {
+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 fp file pointer on an already open file
+ * @param filetype Type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ */
+void Header::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 = Util::Format("%d", i_lgPix+12);
+ ReplaceOrCreateByNumber(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 ( 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
+
+ DocEntry* 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);
+ }
+ }
+ Document::Write(fp,filetype);
}
//-----------------------------------------------------------------------------
// Print
+
//-----------------------------------------------------------------------------
// Public
+
/**
- * \ingroup gdcmHeader
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmParser was properly parsed
+ * 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 gdcmParser is the one of a reasonable Dicom/Acr file,
+ * @return true when Header is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmHeader::IsReadable(void) {
- if(!gdcmParser::IsReadable())
- return(false);
+bool Header::IsReadable()
+{
+ if( !Document::IsReadable() )
+ {
+ return false;
+ }
std::string res = GetEntryByNumber(0x0028, 0x0005);
- if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
return false; // Image Dimensions
- if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0100) )
+ {
return false; // "Bits Allocated"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0101) )
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0101) )
+ {
return false; // "Bits Stored"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0102) )
+ {
return false; // "High Bit"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
- return false; // "Pixel Representation"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0103) )
+ {
+ return false; // "Pixel Representation" i.e. 'Sign'
+ }
+
return true;
}
/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGBaseLineProcess1 one.
- *
- * @return True when JPEGBaseLineProcess1found. False in all other cases.
+ * \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
*/
-bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+int Header::GetXSize()
+{
+ std::string strSize;
+ strSize = GetEntryByNumber(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.50" )
- return true;
- return false;
+ return atoi( strSize.c_str() );
}
/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGExtendedProcess2-4 one.
- *
- * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
+ * \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).
*/
-bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
- return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" );
+int Header::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 Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGExtendeProcess3-5 one.
- *
- * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
+ * \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).
*/
-bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+int Header::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() );
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.52" )
- return true;
- return false;
+ // 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 Header::GetXSpacing()
+{
+ float xspacing, yspacing;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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, "Header::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 Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
- *
- * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
- * other cases.
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float Header::GetYSpacing()
+{
+ float yspacing = 0;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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
*/
-bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+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 absent,
+ // on suppose que les coupes sont jointives
+
+ std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.53" )
- return true;
- return false;
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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 Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a RLE Lossless one.
- *
- * @return True when RLE Lossless found. False in all
- * other cases.
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
*/
-bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+float Header::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, "Header::GetRescaleIntercept: Rescale Slope "
+ "is empty");
+ }
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.5" ) {
- return true;
- }
- return false;
+ return resInter;
}
/**
- * \ingroup gdcmHeader
- * \brief Determines if Transfer Syntax was already encountered
- * and if it corresponds to a JPEG Lossless one.
- *
- * @return True when RLE Lossless found. False in all
- * other cases.
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-bool gdcmHeader::IsJPEGLossless(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- // faire qq chose d'intelligent a la place de ça
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+float Header::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, "Header::GetRescaleSlope: Rescale Slope is empty");
+ }
+ }
- const char * Transfert = Element->GetValue().c_str();
- if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true;
- if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true;
- if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true;
+ return resSlope;
+}
- return false;
+/**
+ * \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 ( 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 Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG200 one.0
- *
- * @return True when JPEG2000 (Lossly or LossLess) found. False in all
- * other cases.
+ * \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' -)
*/
-bool gdcmHeader::IsJPEG2000(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+int Header::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
- std::string Transfer = Element->GetValue();
- if ( (Transfer == "1.2.840.10008.1.2.4.90")
- || (Transfer == "1.2.840.10008.1.2.4.91") )
- return true;
- return false;
+ // 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?
+//
+// ---------------------------------------------------------------
+//
+
/**
- * \ingroup gdcmHeader
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
+ * \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
*/
-bool gdcmHeader::IsDicomV3(void) {
- // Checking if Transfert Syntax exists is enough
- return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
+float Header::GetXOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetXImagePosition: unfound Image "
+ "Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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;
}
/**
- * \ingroup gdcmHeader
- * \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
+ * \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
*/
-int gdcmHeader::GetXSize(void) {
- std::string StrSize;
- StrSize = GetEntryByNumber(0x0028,0x0011);
- if (StrSize == GDCM_UNFOUND)
- return 0;
- return atoi(StrSize.c_str());
+float Header::GetYOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Image "
+ "Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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;
}
/**
- * \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 file contains a Signal, not an Image).
+ * \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
*/
-int gdcmHeader::GetYSize(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0010);
- if (StrSize != GDCM_UNFOUND)
- return atoi(StrSize.c_str());
- if ( IsDicomV3() )
- return 0;
- else
- // 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;
+float Header::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, "Header::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, "Header::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, "Header::GetZImagePosition: wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "Header::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, "Header::GetZImagePosition: wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
}
/**
- * \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 "Planes" tag content.
- * @return The encountered size when found, 1 by default (single image).
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
*/
-int gdcmHeader::GetZSize(void) {
- // 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 [we
- // cannot retrieve by name since "Planes tag is present both in
- // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary].
- StrSize = GetEntryByNumber(0x0028,0x0012);
- if (StrSize != GDCM_UNFOUND)
- return atoi(StrSize.c_str());
- return 1;
+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 = 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 Header::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(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0101);
- if (StrSize == GDCM_UNFOUND)
+int Header::GetBitsStored()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0101 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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());
+ }
+ 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 Header::GetHighBitPosition()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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 Header::IsSignedPixelData()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed "
+ "to be mandatory");
+ return false;
+ }
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
+ {
+ return false;
+ }
+ return true;
}
/**
- * \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(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0100);
- if (StrSize == GDCM_UNFOUND)
+int Header::GetBitsAllocated()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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());
+ }
+ return atoi( strSize.c_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(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0002);
- if (StrSize == GDCM_UNFOUND)
+int Header::GetSamplesPerPixel()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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());
+ // 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 Header::IsMonochrome()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "MONOCHROME1 "
+ || PhotometricInterp == "MONOCHROME2 " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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 Header::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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 Header::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsYBRFull: absent Photometric "
+ "Interpretation");
+ }
+ return false;
}
/**
- * \ingroup gdcmHeader
* \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(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0006);
- if (StrSize == GDCM_UNFOUND)
+int Header::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
return 0;
- return atoi(StrSize.c_str());
+ }
+ return atoi( strSize.c_str() );
}
/**
- * \ingroup gdcmHeader
* \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
+ * 0 means the file is NOT USABLE; the caller will have to check
*/
-int gdcmHeader::GetPixelSize(void) {
- std::string PixelType = GetPixelType();
- if (PixelType == "8U" || PixelType == "8S")
+int Header::GetPixelSize()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ // if (Header::GetEntryByNumber(0x0028,0x0100) == "24")
+ // return 3;
+
+ std::string pixelType = GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
+ {
return 1;
- if (PixelType == "16U" || PixelType == "16S")
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
return 2;
- if (PixelType == "32U" || PixelType == "32S")
+ }
+ if ( pixelType == "32U" || pixelType == "32S")
+ {
return 4;
- dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ }
+ if ( pixelType == "FD" )
+ {
+ return 8;
+ }
+ dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type");
return 0;
}
/**
- * \ingroup gdcmHeader
* \brief Build the Pixel Type of the image.
* Possible values are:
* - 8U unsigned 8 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
+ * 24 bit images appear as 8 bit
* @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
-std::string gdcmHeader::GetPixelType(void) {
- std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
- if (BitsAlloc == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
- BitsAlloc = std::string("16");
- }
- if (BitsAlloc == "12") // It will be unpacked
- BitsAlloc = std::string("16");
- else if (BitsAlloc == "24") // (in order no to be messed up
- BitsAlloc = std::string("8"); // by old RGB images)
-
- std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
- if (Signed == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
- BitsAlloc = std::string("0");
- }
- if (Signed == "0")
- Signed = std::string("U");
- else
- Signed = std::string("S");
+std::string Header::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated");
+ bitsAlloc = "16";
+ }
- return( BitsAlloc + Signed);
+ 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, "Header::GetPixelType: unfound Pixel Representation");
+ bitsAlloc = "0";
+ }
+ if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
}
+
/**
- * \ingroup gdcmHeader
* \brief Recover the offset (from the beginning of the file)
- * \ of *image* pixels (not *icone image* pixels, if any !)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset(void) {
- // 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.
- //
- // If the element (0x0088,0x0200) 'icone image sequence' is found
- // (grPixel,numPixel) is stored twice : the first one for the icon
- // the second one for the image ...
- // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything*
- // see gdcmData/MxTwinLossLess.dcm ...
- guint16 grPixel;
- guint16 numPixel;
- std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
-
- if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
- grPixel = 0x7fe0; // default value
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
- }
-
- if (grPixel == 0xe07f) // sometimes Image Location value doesn't follow
- grPixel = 0x7fe0; // the supposed processor endianity.
- // see gdcmData/cr172241.dcm
-
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
-
- IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel);
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel,numPixel);
- gdcmHeaderEntry* PixelElement;
-
- if (tagHT.count(key) == 1)
- PixelElement = (it.first)->second;
- else
- PixelElement = (++it.first)->second;
-
- if (PixelElement) {
- return PixelElement->GetOffset();
+size_t Header::GetPixelOffset()
+{
+ DocEntry* 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 : unify those two (previous one and next one)
+
+/// \todo TODO : unify those two (previous one and next one)
/**
- * \ingroup gdcmHeader
* \brief Recover the pixel area length (in Bytes)
- * @return 0 by default. NOT USABLE file. The caller has to check.
+ * @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(void) {
- // If this file complies with the norm we should encounter the
- // "Image Location" tag (0x0028, 0x0200). This tag contains the
- // 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.
- guint16 grPixel;
- guint16 numPixel;
- std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
- if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
- grPixel = 0x7fe0; // default value
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
- }
- if (grPixel == 0xe07f) // sometimes group doesn't follow
- grPixel = 0x7fe0; // the supposed processor endianity. see cr172241.dcm
-
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
-
- IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel);
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel,numPixel);
- gdcmHeaderEntry* PixelElement;
-
- if (tagHT.count(key) == 1)
- PixelElement = (it.first)->second;
+size_t Header::GetPixelAreaLength()
+{
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
else
- PixelElement = (++it.first)->second;
-
- if (PixelElement)
- return PixelElement->GetLength();
- else {
+ {
+#ifdef GDCM_DEBUG
std::cout << "Big trouble : Pixel Element ("
- << std::hex << grPixel<<","<< numPixel<< ") NOT found"
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
<< std::endl;
+#endif //GDCM_DEBUG
return 0;
}
}
/**
- * \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
- * @return a Boolean
+ * 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(void) {
-
- // Check the presence of the LUT Descriptors
-
+bool Header::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
// LutDescriptorRed
- if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ if ( !GetDocEntryByNumber(0x0028,0x1101) )
+ {
return false;
+ }
// LutDescriptorGreen
- if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ if ( !GetDocEntryByNumber(0x0028,0x1102) )
+ {
return false;
+ }
// LutDescriptorBlue
- if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ if ( !GetDocEntryByNumber(0x0028,0x1103) )
+ {
return false;
-
- // It is not enough :
- // we check also
-
+ }
// Red Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
- return false;
+ if ( !GetDocEntryByNumber(0x0028,0x1201) )
+ {
+ return false;
+ }
// Green Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ if ( !GetDocEntryByNumber(0x0028,0x1202) )
+ {
return false;
+ }
// Blue Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
- return false;
+ 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
+ * else 0
* @return Lookup Table number of Bits , 0 by default
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
*/
-int gdcmHeader::GetLUTNbits(void) {
+int Header::GetLUTNbits()
+{
std::vector<std::string> tokens;
- //int LutLength;
- //int LutDepth;
- int LutNbits;
- //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ 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)
+ std::string lutDescription = GetEntryByNumber(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
return 0;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescription, tokens, "\\");
+ }
+
+ 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;
-}
-
-/**
- * \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
- */
-unsigned char * gdcmHeader::GetLUTRGBA(void) {
-// 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;
-
- std::vector<std::string> tokens;
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescriptionR, tokens, "\\");
- lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
- debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
- nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
- tokens.clear();
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescriptionG, tokens, "\\");
- lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
- debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value
- nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits)
- tokens.clear();
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescriptionB, tokens, "\\");
- lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
- debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value
- nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+
+ lutNbits = atoi( tokens[2].c_str() );
tokens.clear();
-
- // Load LUTs into memory, (as they were stored on disk)
- unsigned char *lutR = (unsigned char *)
- GetEntryVoidAreaByNumber(0x0028,0x1201);
- unsigned char *lutG = (unsigned char *)
- GetEntryVoidAreaByNumber(0x0028,0x1202);
- unsigned char *lutB = (unsigned char *)
- GetEntryVoidAreaByNumber(0x0028,0x1203);
-
- if (!lutR || !lutG || !lutB ) {
- return NULL;
- }
- // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
-
- unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 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)
- unsigned char *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;
- }
-
- //How to free the now useless LUTs?
- //free(LutR); free(LutB); free(LutG); // Seg Fault when used
- return(LUTRGBA);
-}
+
+ return lutNbits;
+}
/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax
- * \ else 1.
- * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS
+ * else 1.
+ * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
*/
-std::string gdcmHeader::GetTransfertSyntaxName(void) {
- // 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)");
+std::string Header::GetTransfertSyntaxName()
+{
+ // use the TS (TS : Transfert Syntax)
+ std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010);
+
+ if ( transfertSyntax == GDCM_NOTLOADED )
+ {
+ std::cout << "Transfert Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE"
+ << std::endl;
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transfertSyntax == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::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; // Seg Fault when deleted ?!
+ TS* ts = Global::GetTS();
+ std::string tsName = ts->GetValue( transfertSyntax );
+
+ //delete ts; /// \todo Seg Fault when deleted ?!
return tsName;
}
/**
- * \ingroup gdcmFile
* \brief Sets the Pixel Area size in the Header
* --> not-for-rats function
- *
- * \warning WARNING doit-etre etre publique ?
- * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
- *
* @param ImageDataSize new Pixel Area Size
* warning : nothing else is checked
*/
-void gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
- std::string content1;
- char car[20];
- // Assumes HeaderEntry (0x7fe0, 0x0010) exists ...
- // TODO define private members PixelGroupNumber, PicxelElementNumber
- // update them, use them (only necessary for ACR-NEMA, not DICOM)
- sprintf(car,"%d",ImageDataSize);
+void Header::SetImageDataSize(size_t ImageDataSize)
+{
+ ///FIXME I don't understand this code wh ydo we set two times 'car' ?
+ std::string car = Util::Format("%d", ImageDataSize);
- gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010);
+ DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetEntryByNumber(content1, 0x7fe0, 0x0000);
+
+ ImageDataSize += 8;
+ car = Util::Format("%d", ImageDataSize);
+
+ SetEntryByNumber(car, GrPixel, NumPixel);
}
//-----------------------------------------------------------------------------
// 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
+ SetEntryByNumber (" ",0x0010, 0x2154); // Telephone
+ SetEntryByNumber (" ",0x0010, 0x1040); // Adress
+ SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID
+
+ DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ {
+ 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 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 = 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, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0037)");
+ }
+ }
+ //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, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0035)");
+ }
+ }
+}
+
//-----------------------------------------------------------------------------
// Private
//-----------------------------------------------------------------------------
+
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff