-// gdcmHeader.cxx
-//-----------------------------------------------------------------------------
-#include <stdio.h>
-#include <cerrno>
-#include <cctype> // for isalpha
-#include <vector>
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2004/07/31 23:30:04 $
+ Version: $Revision: 1.181 $
+
+ 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 InFilename name of the file whose header we want to analyze
+ * @param filename name of the file whose header we want to analyze
* @param exception_on_error whether we want to throw an exception or not
- * @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
*/
-gdcmHeader::gdcmHeader(const char *InFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow):
- gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
-{
-
+gdcmHeader::gdcmHeader( std::string const & filename,
+ bool exception_on_error ):
+ gdcmDocument( filename,
+ exception_on_error )
+{
// 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
// 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.
-
- // This IS the right place for the code
+ // Note: this IS the right place for the code
- 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;
+ // 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;
+ }
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel);
- countGrPixel = GetEntry().count(key);
+ if ( GrPixel != 0x7fe0 )
+ {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ }
+ else
+ {
+ NumPixel = 0x0010;
+ }
}
/**
* @param exception_on_error whether we want to throw an exception or not
*/
gdcmHeader::gdcmHeader(bool exception_on_error) :
- gdcmParser(exception_on_error)
+ gdcmDocument( exception_on_error )
{
}
* \ingroup gdcmHeader
* \brief Canonical destructor.
*/
-gdcmHeader::~gdcmHeader (void) {
+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
-// see gdcmParser.cxx
+
//-----------------------------------------------------------------------------
// 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 gdcmHeader 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 gdcmHeader is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmHeader::IsReadable(void) {
- if(!gdcmParser::IsReadable()) {
- return(false);
+bool gdcmHeader::IsReadable()
+{
+ if( !gdcmDocument::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) )
+ }
+ 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 gdcmHeader::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 gdcmHeader::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 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 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 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() );
+ }
- 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;
}
/**
- * \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.
- */
-bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+ * \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);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.53" )
- return true;
- return false;
+ 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 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.
+ * \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
*/
-bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+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");
+ }
+ }
- 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.
+ *\ingroup gdcmHeader
+ *\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 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");
+ }
+ }
- 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;
+/**
+ * \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 Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG2000 one
- * @return True when JPEG2000 (Lossly or LossLess) found. False in all
- * other cases.
- */
-bool gdcmHeader::IsJPEG2000(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+ * \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.;
+ }
- 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;
+ return yImPos;
}
-/**
- * \ingroup gdcmHeader
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
- */
-bool gdcmHeader::IsDicomV3(void) {
- // Checking if Transfert Syntax exists is enough
- // Anyway, it's to late check if the 'Preamble' was found ...
- // And ... would it be a rich idea to check ?
- // (some 'no Preamble' DICOM images exist !)
- return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
+/**
+ * \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
}
/**
- * \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
- */
-int gdcmHeader::GetXSize(void) {
- std::string StrSize;
- StrSize = GetEntryByNumber(0x0028,0x0011);
- if (StrSize == GDCM_UNFOUND)
- return 0;
- return atoi(StrSize.c_str());
+ * \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
}
/**
- * \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-MEMA file contains a Signal, not an Image).
- */
-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;
-}
+ * \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;
-/**
- * \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(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());
+ else
+ {
+ /// \todo throw error return value ???
+ /// specified <> unknow in our database
+ return Unknow;
+ }
+ }
- // 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;
+ return Unknow;
}
/**
* @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 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());
+ }
+
+ return atoi( strSize.c_str() );
}
/**
* @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 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());
+ }
+
+ return atoi( strSize.c_str() );
}
/**
* @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 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());
+ }
+
+ return atoi( strSize.c_str() );
}
/**
* (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 gdcmHeader::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
return 0;
- return atoi(StrSize.c_str());
+ }
+
+ return atoi( strSize.c_str() );
}
/**
* @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(void) {
- std::string PixelType = GetPixelType();
- if (PixelType == "8U" || PixelType == "8S")
+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")
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
return 2;
- if (PixelType == "32U" || PixelType == "32S")
+ }
+ if ( pixelType == "32U" || pixelType == "32S")
+ {
return 4;
- if (PixelType == "FD")
- return 8;
+ }
+ if ( pixelType == "FD" )
+ {
+ return 8;
+ }
+
dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
return 0;
}
* 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) {
+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 = std::string("16");
- }
- if (BitsAlloc == "64") // )
- return ("FD");
- 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) {
+ 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 = std::string("0");
+ bitsAlloc = "0";
+ }
+ if ( sign == "0" )
+ {
+ sign = "U";
}
- if (Signed == "0")
- Signed = std::string("U");
else
- Signed = std::string("S");
+ {
+ sign = "S";
+ }
- return( BitsAlloc + Signed);
+ return bitsAlloc + sign;
}
* of *image* pixels (not *icone image* pixels, if any !)
* @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset(void) {
- //
- // 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 ...
-
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
-
- IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
- gdcmHeaderEntry* PixelElement;
- if (countGrPixel == 1)
- PixelElement = (it.first)->second;
- else {
- PixelElement = (++it.first)->second; // hope there are no more than 2 !
- }
- if (PixelElement) {
- return PixelElement->GetOffset();
- } else {
-/* std::cout << "Big trouble : Pixel Element ("
+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; */
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
- }
+ }
}
+
// TODO : unify those two (previous one and next one)
/**
* \ingroup gdcmHeader
* -in case of embeded compressed image-)
* 0 : NOT USABLE file. The caller has to check.
*/
-size_t gdcmHeader::GetPixelAreaLength(void) {
-
- IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
- gdcmHeaderEntry* PixelElement;
-
- if (countGrPixel==1)
- PixelElement = (it.first)->second;
+size_t gdcmHeader::GetPixelAreaLength()
+{
+ gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
else
- PixelElement = (++it.first)->second;
-
- if (PixelElement) {
- return PixelElement->GetLength();
- } else {
-/* std::cout << "Big trouble : Pixel Element ("
+ {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
<< std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;*/
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
}
}
* 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) {
-
+bool gdcmHeader::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) )
- return false;
+ if ( !GetDocEntryByNumber(0x0028,0x1103) )
+ {
+ return false;
+ }
// 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;
}
* when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
* @ return bit number of each LUT item
*/
-int gdcmHeader::GetLUTNbits(void) {
+int gdcmHeader::GetLUTNbits()
+{
std::vector<std::string> tokens;
- //int LutLength;
- //int LutDepth;
- int LutNbits;
+ 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
+ Tokenize ( lutDescription, tokens, "\\" );
//LutLength=atoi(tokens[0].c_str());
//LutDepth=atoi(tokens[1].c_str());
- LutNbits=atoi(tokens[2].c_str());
+
+ lutNbits = atoi( tokens[2].c_str() );
tokens.clear();
- return LutNbits;
+
+ return lutNbits;
}
/**
* 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
+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 ") {
+ 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)
+ // 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)
+ }
+
+ std::string lutDescriptionG = GetEntryByNumber(0x0028,0x1102);
+ if ( lutDescriptionG == 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();
+ }
+
+ 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");
+ }
- 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)
- tokens.clear();
+ // 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)
- 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 ) {
+ 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
-
- unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
- if (!LUTRGBA) {
+
+ 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 ) {
+ if ( str_nb == GDCM_UNFOUND )
+ {
nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
+ }
+ 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 ( 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
// and fix the code
// We give up the checking to avoid some (useless ?)overhead
// (optimistic asumption)
- unsigned char *a;
+ uint8_t* a;
int i;
- a = LUTRGBA+0;
- for(i=0;i<lengthR;i++) {
- *a = lutR[i*mult+1];
- a+=4;
+ 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 + 1;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = lutG[i*mult+1];
+ a += 4;
}
- a = LUTRGBA+3;
- for(i=0;i<256;i++) {
+
+ 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);
+ a += 4;
+ }
+
+ return LUTRGBA;
}
/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
* else 1.
- * @return the full Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
*/
-std::string gdcmHeader::GetTransfertSyntaxName(void) {
+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)");
+ 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; // Seg Fault when deleted ?!
+ gdcmTS* ts = gdcmGlobal::GetTS();
+ std::string tsName = ts->GetValue( transfertSyntax );
+
+ //delete ts; /// \todo Seg Fault when deleted ?!
return tsName;
}
/**
- * \ingroup gdcmHeader
* \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) {
- std::string content1;
+void gdcmHeader::SetImageDataSize(size_t ImageDataSize)
+{
char car[20];
-
- // Assumes HeaderEntry (GrPixel, NumPixel) is unique ...
- // TODO deal with multiplicity (see gdcmData/icone.dcm)
sprintf(car,"%d",ImageDataSize);
- gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel);
+ gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
a->SetLength(ImageDataSize);
- ImageDataSize+=8;
+ ImageDataSize += 8;
sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetEntryByNumber(content1, GrPixel, NumPixel);
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief compares 2 Headers, according to DICOMDIR rules
- * --> not-for-rats function
- * \warning does NOT work with ACR-NEMA files
- * \todo find a trick to solve the pb (use RET fields ?)
- * @param header
- * @return true if 'smaller'
- */
- bool gdcmHeader::operator<(gdcmHeader &header){
- std::string s1,s2;
-
- // Patient Name
- s1=this->GetEntryByNumber(0x0010,0x0010);
- s2=header.GetEntryByNumber(0x0010,0x0010);
- if(s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- else
- {
- // Patient ID
- s1=this->GetEntryByNumber(0x0010,0x0020);
- s2=header.GetEntryByNumber(0x0010,0x0020);
- if (s1 < s2)
- return(true);
- else if (s1 > s2)
- return(1);
- else
- {
- // Study Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000d);
- s2=header.GetEntryByNumber(0x0020,0x000d);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- else
- {
- // Serie Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000e);
- s2=header.GetEntryByNumber(0x0020,0x000e);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- }
- }
- }
- return(false);
-}
-bool gdcmHeader::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
-{
- guint32 length = tag->GetLength();
-
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
- if(length%2==1)
- {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
-
- WriteEntryTagVRLength(tag, _fp, type);
-
- // Pixels are never loaded in the element !
- // we stop writting when Pixel are processed
- // FIX : we loose trailing elements (RAB, right now)
- guint16 el = tag->GetElement();
- guint16 group = tag->GetGroup();
- int compte =0;
- if ((group == GrPixel) && (el == NumPixel) ) {
- compte++;
- if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
- return false;
- }
- }
- WriteEntryValue(tag, _fp, type);
- return true;
+ const std::string content1 = car;
+ SetEntryByNumber(content1, GrPixel, NumPixel);
}
//-----------------------------------------------------------------------------
// Protected
/**
- * \ingroup gdcmHeader
* \brief anonymize a Header (removes Patient's personal info)
* (read the code to see which ones ...)
*/
-bool gdcmHeader::anonymizeHeader() {
+bool gdcmHeader::AnonymizeHeader()
+{
+ gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
- gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010);
- // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020);
-
- 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);
- }
+ 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
//300a 0006 DA RT RT Plan Date
//300a 022c DA RT Air Kerma Rate Reference Date
//300e 0004 DA RT Review Date
- return true;
+
+ 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