-// gdcmHeader.cxx
-//-----------------------------------------------------------------------------
-#include "gdcmHeader.h"
-
-#include <stdio.h>
-#include <cerrno>
-// For nthos:
-#ifdef _MSC_VER
-#include <winsock.h>
-#else
-#include <netinet/in.h>
-#endif
-#include <cctype> // for isalpha
-
-#ifdef GDCM_NO_ANSI_STRING_STREAM
-# include <strstream>
-# define ostringstream ostrstream
-# else
-# include <sstream>
-#endif
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/01/06 20:03:28 $
+ Version: $Revision: 1.222 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#include "gdcmHeader.h"
+#include "gdcmGlobal.h"
#include "gdcmUtil.h"
+#include "gdcmDebug.h"
#include "gdcmTS.h"
+#include "gdcmValEntry.h"
+#include <stdio.h> //sscanf
-//-----------------------------------------------------------------------------
-// Refer to gdcmHeader::CheckSwap()
-const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
-
-// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
-const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+#include <vector>
+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
+ * \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 ) {
- if (enable_sequences)
- enableSequences = 1;
+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
+ const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( imgLocation == GDCM_UNFOUND )
+ {
+ // default value
+ GrPixel = 0x7fe0;
+ }
else
- enableSequences = 0;
-
- SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = InFilename;
- Initialise();
- if ( !OpenFile(exception_on_error))
- return;
- ParseHeader();
- LoadHeaderEntries();
- CloseFile();
+ {
+ 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;
+ }
+
+ // Now, we know GrPixel and NumPixel.
+ // Let's create a VirtualDictEntry to allow a further VR modification
+ // and force VR to match with BitsAllocated.
+
+ DocEntry *entry = GetDocEntryByNumber(GrPixel, NumPixel);
+ if ( entry != 0 )
+ {
+
+ std::string PixelVR;
+ // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
+ // more than 8 (i.e 12, 16) is a 'O Words'
+ if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
+ PixelVR = "OB";
+ else
+ PixelVR = "OW";
+
+ DictEntry* newEntry = NewVirtualDictEntry(
+ GrPixel, NumPixel,
+ PixelVR, "PXL", "Pixel Data");
+
+ entry->SetDictEntry( newEntry );
+ }
}
/**
- * \ingroup gdcmHeader
- * \brief
- * @param exception_on_error
+ * \brief Constructor used when we want to generate dicom files from scratch
*/
-gdcmHeader::gdcmHeader(bool exception_on_error) {
- SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
+Header::Header()
+ :Document()
+{
+ InitializeDefaultHeader();
}
/**
- * \ingroup gdcmHeader
* \brief Canonical destructor.
*/
-gdcmHeader::~gdcmHeader (void) {
- dicom_vr = (gdcmVR*)0;
- Dicts = (gdcmDictSet*)0;
- RefPubDict = (gdcmDict*)0;
- RefShaDict = (gdcmDict*)0;
- return;
+Header::~Header ()
+{
}
-//-----------------------------------------------------------------------------
-// Print
-
/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubEntry(std::ostream & os) {
- PubEntrySet.Print(os);
-}
+ * \brief Performs some consistency checking on various 'File related'
+ * (as opposed to 'DicomDir related') entries
+ * then writes in a file all the (Dicom Elements) included the Pixels
+ * @param fileName file name to write to
+ * @param filetype Type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ */
+bool Header::Write(std::string fileName, FileType filetype)
+{
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
+ {
+ dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
+ return false;
+ }
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
+ // 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 = Util::Format("%d", i_lgPix+12);
+ s_lgPix = Util::DicomString( s_lgPix.c_str() );
+ 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::WriteContent(fp,filetype);
+
+ fp->close();
+ delete fp;
+
+ return true;
}
+//-----------------------------------------------------------------------------
+// Print
+
+
//-----------------------------------------------------------------------------
// Public
+
/**
- * \ingroup gdcmHeader
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmHeader 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 image.
- * @return true when gdcmHeader is the one of a reasonable Dicom file,
+ * a well formed and usable Dicom/Acr File.
+ * @return true when Header is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmHeader::IsReadable(void) {
- std::string res = GetEntryByNumber(0x0028, 0x0005);
- if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) {
- return false; // Image Dimensions
+bool Header::IsReadable()
+{
+ if( !Document::IsReadable() )
+ {
+ return false;
}
- if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
+ const std::string &res = GetEntryByNumber(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
+ return false; // Image Dimensions
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0100) )
+ {
return false; // "Bits Allocated"
- if ( !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 ImplicitVRLittleEndian one.
- *
- * @return True when ImplicitVRLittleEndian found. 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::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+int Header::GetXSize()
+{
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2" )
- 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 ExplicitVRLittleEndian one.
- *
- * @return True when ExplicitVRLittleEndian 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::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+int Header::GetYSize()
+{
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0010);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+ if ( IsDicomV3() )
+ {
+ return 0;
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1" )
- return true;
- return false;
+ // 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 DeflatedExplicitVRLittleEndian one.
- *
- * @return True when DeflatedExplicitVRLittleEndian 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::IsDeflatedExplicitVRLittleEndianTransferSyntax(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.
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0008);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1.99" )
- return true;
- return false;
+ // We then consider the "Planes" entry as the third dimension
+ const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
+ {
+ return atoi( strSize2.c_str() );
+ }
+
+ return 1;
}
/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a Explicit VR Big Endian one.
- *
- * @return True when big endian found. False in all other cases.
- */
-bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float Header::GetXSpacing()
+{
+ float xspacing, yspacing;
+ const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
- return true;
- return false;
-}
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
-/**
- * \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.
- */
-bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+ int nbValues;
+ if( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
+ {
+ // if single value is found, xspacing is defaulted to yspacing
+ if ( nbValues == 1 )
+ {
+ xspacing = yspacing;
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.50" )
- return true;
- return false;
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
+ }
+
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
+ if ( xspacing == 0.)
+ {
+ dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ assert( nbValues == 2 );
+ }
+
+ return xspacing;
}
/**
- * \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.
- */
-bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float Header::GetYSpacing()
+{
+ float yspacing = 1.;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.51" )
- return true;
- return false;
-}
+ // if sscanf cannot read any float value, it won't affect yspacing
+ sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+}
/**
- * \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 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::IsJPEGExtendedProcess3_5TransferSyntax(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
+
+ const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.52" )
- return true;
- return false;
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices");
+ const 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 (float)atof( strSliceThickness.c_str() );
+ }
+ }
+ //else
+ return (float)atof( strSpacingBSlices.c_str() );
}
/**
- * \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 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
*/
-bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
+float Header::GetRescaleIntercept()
+{
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const 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 == "1.2.840.10008.1.2.4.53" )
- return true;
- return false;
+ return resInter;
}
/**
- * \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 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- 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");
+ }
+ }
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.5" )
- return true;
- return false;
+ return resSlope;
}
/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
+ * \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)
*/
-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);
+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);
- 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;
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
+ {
+ return 3;
+ }
+ else
+ {
+ return 1;
+ }
+ }
- return false;
+ // beware of trailing space at end of string
+ // DICOM tags are never of odd length
+ if ( strPhotometricInterpretation == GDCM_UNFOUND ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
+ {
+ return 1;
+ }
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
}
/**
- * \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) {
- if ( (filetype == ExplicitVR)
- || (filetype == ImplicitVR) )
- return true;
- return false;
+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
- * @return
+ * \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
*/
-FileType gdcmHeader::GetFileType(void)
+float Header::GetYOrigin()
{
- return(filetype);
+ 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 columns of image.
- * @return The encountered size when found, 0 by default.
+ * \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::GetXSize(void) {
- // We cannot check for "Columns" because the "Columns" tag is present
- // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary.
- std::string StrSize = GetEntryByNumber(0x0028,0x0011);
- if (StrSize == GDCM_UNFOUND)
- return 0;
- return atoi(StrSize.c_str());
+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 lines of image.
- * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
- * @return The encountered size when found, 1 by default.
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
*/
-int gdcmHeader::GetYSize(void) {
- // We cannot check for "Rows" because the "Rows" tag is present
- // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary.
- 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 is optional for ACR/NEMA. It might
- // hence be a signal (1d image). So we default to 1:
- 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
}
/**
- * \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.
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
*/
-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;
+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
+ * \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)
- return 1;
- return atoi(StrSize.c_str());
+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() );
}
/**
- * \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.
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit positin when present. 0 when absent.
*/
-int gdcmHeader::GetBitsAllocated(void) {
- std::string StrSize = GetEntryByNumber(0x0028,0x0100);
- if (StrSize == GDCM_UNFOUND)
- return 1;
- return atoi(StrSize.c_str());
+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;
+}
+
+/**
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ * @return The encountered number of Bits Allocated, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int Header::GetBitsAllocated()
+{
+ std::string strSize = 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() );
}
/**
- * \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()
+{
+ const 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 ...
- 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()
+{
+ const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(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.
- *
+ * @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 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
- * @return
+ * 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";
+ }
+
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ else if ( bitsAlloc == "12" )
+ {
+ // It will be unpacked
+ bitsAlloc = "16";
+ }
+ else if ( bitsAlloc == "24" )
+ {
+ // (in order no to be messed up
+ bitsAlloc = "8"; // by old RGB images)
+ }
+
+ std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation"
- return( BitsAlloc + Signed);
+ if (sign == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation");
+ bitsAlloc = "0";
+ }
+ else if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
}
+
/**
- * \ingroup gdcmHeader
- * \brief Recover the offset (from the beginning of the file) of the pixels.
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset(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;
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
+size_t Header::GetPixelOffset()
+{
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
}
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
-
- gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
- if (PixelElement)
- return PixelElement->GetOffset();
else
+ {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
+ }
}
+/// \todo TODO : unify those two (previous one and next one)
/**
- * \ingroup gdcmHeader
- * \brief Recover the pixel area length (in Bytes) .
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
*/
-size_t gdcmHeader::GetPixelAreaLength(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 ) {
- grPixel = 0x7fe0;
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
- }
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
-
- gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
- if (PixelElement)
- return PixelElement->GetLength();
+size_t Header::GetPixelAreaLength()
+{
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
else
+ {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
+ }
}
/**
- * \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 int acts as a Boolean
+ * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
+ * are NOT considered as LUT, since nobody knows
+ * how to deal with them
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
*/
-bool gdcmHeader::HasLUT(void) {
-
- // Check the presence of the LUT Descriptors
- if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+bool Header::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ 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;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1202) )
+ {
return false;
- // It is not enough
- // we check also
- if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
- return false;
- if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1203) )
+ {
return false;
- if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
- return false;
+ }
+
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
return true;
}
/**
- * \ingroup gdcmHeader
* \brief gets the info from 0028,1101 : Lookup Table Desc-Red
- * \ else 0
- * @return Lookup Table nBit
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
*/
-int gdcmHeader::GetLUTNbits(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 deails with them :-(
- * @return Lookup Table RGBA
- */
-unsigned char * gdcmHeader::GetLUTRGBA(void) {
-// Not so easy : see
-// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
-// and OT-PAL-8-face.dcm
-
-// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
- if (gdcmHeader::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());
- nbitsG =atoi(tokens[2].c_str());
- 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());
- nbitsB =atoi(tokens[2].c_str());
+ lutNbits = atoi( tokens[2].c_str() );
tokens.clear();
-
-// Load LUTs into memory, (as they were stored on disk)
- unsigned char *lutR = (unsigned char *)
- GetPubEntryVoidAreaByNumber(0x0028,0x1201);
- unsigned char *lutG = (unsigned char *)
- GetPubEntryVoidAreaByNumber(0x0028,0x1202);
- unsigned char *lutB = (unsigned char *)
- GetPubEntryVoidAreaByNumber(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 overhead
- 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);
- return(LUTRGBA);
-}
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax
- * \ else 1.
- * @return Transfert Syntax Name (as oposite 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)");
- return "Uncompressed ACR-NEMA";
- }
- // we do it only when we need it
- gdcmTS * ts = gdcmGlobal::GetTS();
- std::string tsName=ts->GetValue(TransfertSyntax);
- //delete ts; // Seg Fault when deleted ?!
- return tsName;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value of
- * a given tag.
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the elements parsed with the public dictionary for
- * the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryVRByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value of
- * a given tag.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryByNumber(guint16 group, guint16 element) {
- return PubEntrySet.GetEntryByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value
- * representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryVRByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
- if ( !elem )
- return GDCM_UNFOUND;
- return elem->GetVR();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry in the PubHeaderEntrySet of this instance
- * through tag name and modifies it's content with the given value.
- * @param content new value to substitute with
- * @param tagName name of the tag to be modified
- */
-bool gdcmHeader::SetPubEntryByName(std::string content, std::string tagName) {
- //return ( PubHeaderEntrySet.SetHeaderEntryByName (content, tagName) );
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return false;
- return(PubEntrySet.SetEntryByNumber(content,
- dictEntry->GetGroup(),
- dictEntry->GetElement()));
+ return lutNbits;
}
/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value to substitute with
- * @param group group of the Dicom Element to modify
- * @param element element of the Dicom Element to modify
+ * \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)
*/
-bool gdcmHeader::SetPubEntryByNumber(std::string content, guint16 group,
- guint16 element)
-
-//TODO : homogeneiser les noms : SetPubElValByNumber
-// qui appelle PubHeaderEntrySet.SetHeaderEntryByNumber
-// pourquoi pas SetPubHeaderEntryByNumber ??
+std::string Header::GetTransfertSyntaxName()
{
- return ( PubEntrySet.SetEntryByNumber (content, group, element) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry in the PubHeaderEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param length new length to substitute with
- * @param group group of the ElVal to modify
- * @param element element of the ElVal to modify
- * @return 1 on success, 0 otherwise.
- */
-
-bool gdcmHeader::SetPubEntryLengthByNumber(guint32 length, guint16 group,
- guint16 element) {
- return ( PubEntrySet.SetEntryLengthByNumber (length, group, element) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value of a given tag.
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryByName(std::string tagName) {
- return GetPubEntryByName(tagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryVRByName(std::string tagName) {
- return GetPubEntryVRByName(tagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value of a given tag.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryByNumber(guint16 group, guint16 element) {
- return GetPubEntryByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryVRByNumber(guint16 group, guint16 element) {
- return GetPubEntryVRByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Sets the value (string) of the target Dicom Element
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool gdcmHeader::SetEntryByName(std::string content,std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return false;
-
-
- TagKey key = gdcmDictEntry::TranslateToKey(dictEntry->GetGroup(),
- dictEntry->GetElement());
- if ( PubEntrySet.GetTagHT().count(key) == 0 )
- return false;
- int l = content.length();
- if(l%2) { // Odd length are padded with a space (020H).
- l++;
- content = content + '\0';
+ // 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";
}
-
- //tagHt[key]->SetValue(content);
- gdcmHeaderEntry * a;
- IterHT p;
- TagHeaderEntryHT::iterator p2;
- // DO NOT remove the following lines : they explain the stuff
- //p= tagHt.equal_range(key); // get a pair of iterators first-last synonym
- //p2=p.first; // iterator on the first synonym
- //a=p2->second; // H Table target column (2-nd col)
-
- // or, easier :
- a = ((PubEntrySet.GetTagHT().equal_range(key)).first)->second;
-
- a-> SetValue(content);
-
- //std::string vr = tagHt[key]->GetVR();
- std::string vr = a->GetVR();
-
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
- else
- lgr = l;
- //tagHt[key]->SetLength(lgr);
- a->SetLength(lgr);
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param exception_on_error
- * @return
- */
-FILE *gdcmHeader::OpenFile(bool exception_on_error)
- throw(gdcmFileError) {
- fp=fopen(filename.c_str(),"rb");
- if(exception_on_error) {
- if(!fp)
- throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
- }
-
- if ( fp ) {
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
-
- //ACR -- or DICOM with no Preamble
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
- return(fp);
-
- //DICOM
- fseek(fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- return(fp);
-
- fclose(fp);
- dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str());
- }
- else {
- dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
- }
- return(NULL);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return TRUE if the close was successfull
- */
-bool gdcmHeader::CloseFile(void) {
- int closed = fclose(fp);
- fp = (FILE *)0;
- if (! closed)
- return false;
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Parses the header of the file but WITHOUT loading element values.
- */
-void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
- gdcmHeaderEntry * newHeaderEntry = (gdcmHeaderEntry *)0;
-
- rewind(fp);
- CheckSwap();
- while ( (newHeaderEntry = ReadNextHeaderEntry()) ) {
- SkipHeaderEntry(newHeaderEntry);
- PubEntrySet.Add(newHeaderEntry);
+ if ( transfertSyntax == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetTransfertSyntaxName:"
+ " unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
}
-}
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return integer, acts as a Boolean
- */
-bool gdcmHeader::Write(FILE * fp, FileType type) {
-
- // TODO : move the following lines (and a lot of others, to be written)
- // to a future function CheckAndCorrectHeader
-
- if (type == ImplicitVR) {
- std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
- ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
-
- //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
- // values with a VR of UI shall be padded with a single trailing null
- // Dans le cas suivant on doit pader manuellement avec un 0
-
- PubEntrySet.SetEntryLengthByNumber(18, 0x0002, 0x0010);
- }
-
- if (type == ExplicitVR) {
- std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
- ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
-
- //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
- // values with a VR of UI shall be padded with a single trailing null
- // Dans le cas suivant on doit pader manuellement avec un 0
-
- PubEntrySet.SetEntryLengthByNumber(20, 0x0002, 0x0010);
+ while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) )
+ {
+ transfertSyntax.erase(transfertSyntax.length()-1, 1);
}
+ // we do it only when we need it
+ TS* ts = Global::GetTS();
+ std::string tsName = ts->GetValue( transfertSyntax );
- return PubEntrySet.Write(fp, type);
-}
-
-/**
- * \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 ...
- sprintf(car,"%d",ImageDataSize);
-
- gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubEntryByNumber(content1, 0x7fe0, 0x0000);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief TODO
- * @param Value
- * @param Group
- * @param Elem
- * \return integer acts as a boolean
- */
-bool gdcmHeader::ReplaceOrCreateByNumber(std::string Value,
- guint16 Group, guint16 Elem ) {
- // TODO : FIXME JPRx
- // curieux, non ?
- // on (je) cree une HeaderEntry ne contenant pas de valeur
- // on l'ajoute au HeaderEntrySet
- // on affecte une valeur a cette HeaderEntry a l'interieur du HeaderEntrySet
- // --> devrait pouvoir etre fait + simplement ???
- if (CheckIfExistByNumber(Group, Elem) == 0) {
- gdcmHeaderEntry* a =NewHeaderEntryByNumber(Group, Elem);
- if (a == NULL)
- return false;
- PubEntrySet.Add(a);
- }
- PubEntrySet.SetEntryByNumber(Value, Group, Elem);
- return(true);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Modify (or Creates if not found) an element
- * @param Value new value
- * @param Group
- * @param Elem
- * \return integer acts as a boolean
- *
- */
-bool gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
-
- gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem);
- // TODO : check if fails
- PubEntrySet.Add(nvHeaderEntry);
- std::string v = Value;
- PubEntrySet.SetEntryByNumber(v, Group, Elem);
- return(true);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
- * @param Value
- * @param Group
- * @param Elem
- * \return integer acts as a boolean
- */
-bool gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) {
-
- //gdcmHeaderEntry* HeaderEntry = PubHeaderEntrySet.GetElementByNumber(Group, Elem);
- std::string v = Value;
- PubEntrySet.SetEntryByNumber(v, Group, Elem);
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly swaped 32 bits integer.
- */
-guint32 gdcmHeader::SwapLong(guint32 a) {
- switch (sw) {
- case 0 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- dbg.Error(" gdcmHeader::SwapLong : unset swap code");
- a=0;
- }
- return(a);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Swaps the bytes so they agree with the processor order
- * @return The properly swaped 16 bits integer.
- */
-guint16 gdcmHeader::SwapShort(guint16 a) {
- if ( (sw==4321) || (sw==2143) )
- a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
+ //delete ts; /// \todo Seg Fault when deleted ?!
+ return tsName;
}
//-----------------------------------------------------------------------------
// Protected
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
-gdcmHeaderEntry *gdcmHeader::GetHeaderEntryByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry *HeaderEntry = PubEntrySet.GetHeaderEntryByNumber(Group, Elem);
- if (!HeaderEntry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return NULL;
- }
- return HeaderEntry;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
- gdcmHeaderEntry *gdcmHeader::GetHeaderEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return NULL;
-
- return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Checks if a given HeaderEntry (group,number)
- * \ exists in the Public HeaderEntrySet
- * @param Group
- * @param Elem
- * @return integer acts as a boolean
- */
-bool gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) {
- return (PubEntrySet.CheckIfExistByNumber(Group, Elem)>0);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) the offset of a 'non string' element value
- * \ (LoadElementValue has already be executed)
- * @param Group
- * @param Elem
- * @return File Offset of the Element Value
- */
-size_t gdcmHeader::GetPubEntryOffsetByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (size_t)0;
- }
- return Entry->GetOffset();
-}
/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) a 'non string' element value
- * \ (LoadElementValue has already be executed)
- * @param Group
- * @param Elem
- * @return Pointer to the 'non string' area
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
*/
-void * gdcmHeader::GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (NULL);
- }
- return Entry->GetVoidArea();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- */
-void * gdcmHeader::LoadEntryVoidArea(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem);
- if ( !Element )
- return NULL;
- size_t o =(size_t)Element->GetOffset();
- fseek(fp, o, SEEK_SET);
- int l=Element->GetLength();
- void * a = malloc(l);
- if(!a) {
- return NULL;
- }
-
- PubEntrySet.SetVoidAreaByNumber(a, Group, Elem);
- // TODO check the result
- size_t l2 = fread(a, 1, l ,fp);
- if(l != l2) {
- free(a);
- return NULL;
- }
- return a;
-}
-
-//-----------------------------------------------------------------------------
-// Private
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element values of all the elements present in the
- * public tag based hash table.
- */
-void gdcmHeader::LoadHeaderEntries(void) {
- rewind(fp);
-
- // We don't use any longer the HashTable, since a lot a stuff is missing
- // when SeQuences were encountered
- //
- //TagHeaderEntryHT ht = PubHeaderEntrySet.GetTagHT();
- //for (TagHeaderEntryHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
- // LoadElementValue(tag->second);
- //}
-
- for (ListTag::iterator i = GetPubListEntry().begin();
- i != GetPubListEntry().end();
- ++i){
- LoadHeaderEntry(*i);
- }
-
- rewind(fp);
-
- // Load 'non string' values
- std::string PhotometricInterpretation = GetPubEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " ){
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
-
- LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
- }
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
- //
- // if recognition code tells us we deal with a LibIDO image
- // we switch lineNumber and columnNumber
- //
- std::string RecCode;
- RecCode = GetPubEntryByNumber(0x0008, 0x0010);
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) {
- filetype = ACR_LIBIDO;
- std::string rows = GetPubEntryByNumber(0x0028, 0x0010);
- std::string columns = GetPubEntryByNumber(0x0028, 0x0011);
- SetPubEntryByNumber(columns, 0x0028, 0x0010);
- SetPubEntryByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element content if it's length is not bigger
- * than the value specified with
- * gdcmHeader::SetMaxSizeLoadElementValue()
- * @param ElVal string value of the Dicom Element
- */
-void gdcmHeader::LoadHeaderEntry(gdcmHeaderEntry * ElVal) {
- size_t item_read;
- guint16 group = ElVal->GetGroup();
- std::string vr= ElVal->GetVR();
- guint32 length = ElVal->GetLength();
- bool SkipLoad = false;
-
- fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
-
- // the test was commented out to 'go inside' the SeQuences
- // we don't any longer skip them !
-
- // if( vr == "SQ" )
- // SkipLoad = true;
-
- // A SeQuence "contains" a set of Elements.
- // (fffe e000) tells us an Element is beginning
- // (fffe e00d) tells us an Element just ended
- // (fffe e0dd) tells us the current SeQuence just ended
- if( group == 0xfffe )
- SkipLoad = true;
-
- if ( SkipLoad ) {
- ElVal->SetLength(0);
- ElVal->SetValue("gdcm::Skipped");
- return;
- }
-
- // When the length is zero things are easy:
- if ( length == 0 ) {
- ElVal->SetValue("");
- return;
- }
-
- // The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice of the offset of
- // the element content and it's length.
- if (length > MaxSizeLoadElementValue) {
- std::ostringstream s;
- s << "gdcm::NotLoaded.";
- s << " Address:" << (long)ElVal->GetOffset();
- s << " Length:" << ElVal->GetLength();
- s << " x(" << std::hex << ElVal->GetLength() << ")";
- ElVal->SetValue(s.str());
- return;
- }
-
- // When an integer is expected, read and convert the following two or
- // four bytes properly i.e. as an integer as opposed to a string.
-
- // Actually, elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- // Any compacter code suggested (?)
- if ( IsHeaderEntryAnInteger(ElVal) ) {
- guint32 NewInt;
- std::ostringstream s;
- int nbInt;
- if (vr == "US" || vr == "SS") {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
-
- } else if (vr == "UL" || vr == "SL") {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- ElVal->SetValue(s.str());
- return;
- }
-
- // We need an additional byte for storing \0 that is not on disk
- char* NewValue = (char*)malloc(length+1);
- if( !NewValue) {
- dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
- return;
- }
- NewValue[length]= 0;
-
- item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
- if ( item_read != 1 ) {
- free(NewValue);
- dbg.Verbose(1, "gdcmHeader::LoadElementValue","unread element value");
- ElVal->SetValue("gdcm::UnRead");
- return;
- }
- ElVal->SetValue(NewValue);
- free(NewValue);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadElementValue that modifies it.
- * @param ElVal Element whose value shall be loaded.
- * @return
- */
-void gdcmHeader::LoadHeaderEntrySafe(gdcmHeaderEntry * ElVal) {
- long PositionOnEntry = ftell(fp);
- LoadHeaderEntry(ElVal);
- fseek(fp, PositionOnEntry, SEEK_SET);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- void gdcmHeader::FindHeaderEntryLength (gdcmHeaderEntry * ElVal) {
- guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup();
- std::string vr = ElVal->GetVR();
- guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) ) {
- dbg.SetDebug(-1);
- dbg.Verbose(2, "gdcmHeader::FindLength: ",
- "we reached 7fe0 0010");
- }
-
- if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
- if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
-
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
- // skipped before proceeding on reading the length on 4 bytes.
- fseek(fp, 2L, SEEK_CUR);
-
- guint32 length32 = ReadInt32();
-
- if ( (vr == "OB") && (length32 == 0xffffffff) ) {
- ElVal->SetLength(FindHeaderEntryLengthOB());
- return;
- }
- FixHeaderEntryFoundLength(ElVal, length32);
- return;
- }
-
- // Length is encoded on 2 bytes.
- length16 = ReadInt16();
-
- // We can tell the current file is encoded in big endian (like
- // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
- // and it's value is the one of the encoding of a big endian file.
- // In order to deal with such big endian encoded files, we have
- // (at least) two strategies:
- // * when we load the "Transfer Syntax" tag with value of big endian
- // encoding, we raise the proper flags. Then we wait for the end
- // of the META group (0x0002) among which is "Transfer Syntax",
- // before switching the swap code to big endian. We have to postpone
- // the switching of the swap code since the META group is fully encoded
- // in little endian, and big endian coding only starts at the next
- // group. The corresponding code can be hard to analyse and adds
- // many additional unnecessary tests for regular tags.
- // * the second strategy consists in waiting for trouble, that shall
- // appear when we find the first group with big endian encoding. This
- // is easy to detect since the length of a "Group Length" tag (the
- // ones with zero as element number) has to be of 4 (0x0004). When we
- // encounter 1024 (0x0400) chances are the encoding changed and we
- // found a group with big endian encoding.
- // We shall use this second strategy. In order to make sure that we
- // can interpret the presence of an apparently big endian encoded
- // length of a "Group Length" without committing a big mistake, we
- // add an additional check: we look in the already parsed elements
- // for the presence of a "Transfer Syntax" whose value has to be "big
- // endian encoding". When this is the case, chances are we have got our
- // hands on a big endian encoded file: we switch the swap code to
- // big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) ) {
- if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
- dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
- errno = 1;
- return;
- }
- length16 = 4;
- SwitchSwapToBigEndian();
- // Restore the unproperly loaded values i.e. the group, the element
- // and the dictionary entry depending on them.
- guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
- guint16 CorrectElem = SwapShort(ElVal->GetElement());
- gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
- CorrectElem);
- if (!NewTag) {
- // This correct tag is not in the dictionary. Create a new one.
- NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
- }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
- ElVal->SetDictEntry(NewTag);
- }
-
- // Heuristic: well some files are really ill-formed.
- if ( length16 == 0xffff) {
- length16 = 0;
- //dbg.Verbose(0, "gdcmHeader::FindLength",
- // "Erroneous element length fixed.");
- // Actually, length= 0xffff means that we deal with
- // Unknown Sequence Length
- }
-
- FixHeaderEntryFoundLength(ElVal, (guint32)length16);
- return;
- }
-
- // Either implicit VR or a non DICOM conformal (see not below) explicit
- // VR that ommited the VR of (at least) this element. Farts happen.
- // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
- // on Data elements "Implicit and Explicit VR Data Elements shall
- // not coexist in a Data Set and Data Sets nested within it".]
- // Length is on 4 bytes.
- FixHeaderEntryFoundLength(ElVal, ReadInt32());
- return;
-}
+bool Header::AnonymizeHeader()
+{
+ // If exist, replace by spaces
+ SetEntryByNumber (" ",0x0010, 0x2154); // Telephone
+ SetEntryByNumber (" ",0x0010, 0x1040); // Adress
+ SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID
-/**
- * \ingroup gdcmHeader
- * \brief Find the value representation of the current tag.
- * @param ElVal
- */
-void gdcmHeader::FindHeaderEntryVR( gdcmHeaderEntry *ElVal) {
- if (filetype != ExplicitVR)
- return;
-
- char VR[3];
- std::string vr;
- int lgrLue;
- char msg[100]; // for sprintf. Sorry
-
- long PositionOnEntry = ftell(fp);
- // Warning: we believe this is explicit VR (Value Representation) because
- // we used a heuristic that found "UL" in the first tag. Alas this
- // doesn't guarantee that all the tags will be in explicit VR. In some
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // within an explicit VR file. Hence we make sure the present tag
- // is in explicit VR and try to fix things if it happens not to be
- // the case.
- bool RealExplicit = true;
-
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
- vr = std::string(VR);
-
- // Assume we are reading a falsely explicit VR file i.e. we reached
- // a tag where we expect reading a VR but are in fact we read the
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) )
- RealExplicit = false;
-
- // CLEANME searching the dicom_vr at each occurence is expensive.
- // PostPone this test in an optional integrity check at the end
- // of parsing or only in debug mode.
- if ( RealExplicit && !dicom_vr->Count(vr) )
- RealExplicit= false;
-
- if ( RealExplicit ) {
- if ( ElVal->IsVRUnknown() ) {
- // When not a dictionary entry, we can safely overwrite the vr.
- ElVal->SetVR(vr);
- return;
+ 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);
}
- if ( ElVal->GetVR() == vr ) {
- // The vr we just read and the dictionary agree. Nothing to do.
- return;
+ else
+ {
+ ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010);
}
- // The vr present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the vr of the file. Since it would
- // be unwise to overwrite the vr of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the vr for the read one.
- gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(),
- ElVal->GetElement(),
- vr,
- "FIXME",
- ElVal->GetName());
- ElVal->SetDictEntry(NewTag);
- return;
}
-
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
-
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- ElVal->GetGroup(),ElVal->GetElement());
- dbg.Verbose(1, "gdcmHeader::FindVR: ",msg);
-
- fseek(fp, PositionOnEntry, SEEK_SET);
- // When this element is known in the dictionary we shall use, e.g. for
- // the semantics (see the usage of IsAnInteger), the vr proposed by the
- // dictionary entry. Still we have to flag the element as implicit since
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( ElVal->IsVRUnknown() )
- ElVal->SetVR("Implicit");
- ElVal->SetImplicitVr();
-}
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param ElVal
- * @return
- */
-void gdcmHeader::SkipHeaderEntry(gdcmHeaderEntry * ElVal) {
- SkipBytes(ElVal->GetLength());
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief When the length of an element value is obviously wrong (because
- * the parser went Jabberwocky) one can hope improving things by
- * applying this heuristic.
- */
-void gdcmHeader::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 FoundLength) {
+ // 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
- ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found
-
- if ( FoundLength == 0xffffffff) {
- FoundLength = 0;
- }
-
- // Sorry for the patch!
- // XMedCom did the trick to read some nasty GE images ...
- else if (FoundLength == 13) {
- // The following 'if' will be removed when there is no more
- // images on Creatis HDs with a 13 length for Manufacturer...
- if ( (ElVal->GetGroup() != 0x0008) ||
- ( (ElVal->GetElement() != 0x0070) && (ElVal->GetElement() != 0x0080) ) ) {
- // end of remove area
- FoundLength =10;
- ElVal->SetReadLength(10); // a bug is to be fixed
- }
- }
- // to fix some garbage 'Leonardo' Siemens images
- // May be commented out to avoid overhead
- else if ( (ElVal->GetGroup() == 0x0009) &&
- ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){
- FoundLength =4;
- ElVal->SetReadLength(4); // a bug is to be fixed
- }
- // end of fix
-
- // to try to 'go inside' SeQuences (with length), and not to skip them
- else if ( ElVal->GetVR() == "SQ") {
- if (enableSequences) // only if the user does want to !
- FoundLength =0;
- }
-
- ElVal->SetUsableLength(FoundLength);
+ return true;
}
/**
- * \ingroup gdcmHeader
- * \brief Apply some heuristics to predict wether the considered
- * element value contains/represents an integer or not.
- * @param ElVal The element value on which to apply the predicate.
- * @return The result of the heuristical predicate.
- */
-bool gdcmHeader::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) {
- guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup();
- std::string vr = ElVal->GetVR();
- guint32 length = ElVal->GetLength();
-
- // When we have some semantics on the element we just read, and if we
- // a priori know we are dealing with an integer, then we shall be
- // able to swap it's element value properly.
- if ( element == 0 ) { // This is the group length of the group
- if (length == 4)
- return true;
- else {
- std::ostringstream s;
- s << "Erroneous Group Length element length on :" \
- << std::hex << group << " , " << element;
- dbg.Error("gdcmHeader::IsAnInteger",
- s.str().c_str());
+ * \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)");
}
}
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- guint32 gdcmHeader::FindHeaderEntryLengthOB(void) {
- // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- guint16 g;
- guint16 n;
- long PositionOnEntry = ftell(fp);
- bool FoundSequenceDelimiter = false;
- guint32 TotalLength = 0;
- guint32 ItemLength;
-
- while ( ! FoundSequenceDelimiter) {
- g = ReadInt16();
- n = ReadInt16();
- if (errno == 1)
- return 0;
- TotalLength += 4; // We even have to decount the group and element
-
- if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ {
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
- errno = 1;
- return 0;
- }
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 ){
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",
- n, g,n);
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
- errno = 1;
- return 0;
+ //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)");
}
- ItemLength = ReadInt32();
- TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
- SkipBytes(ItemLength);
- }
- fseek(fp, PositionOnEntry, SEEK_SET);
- return TotalLength;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Reads a supposed to be 16 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @return integer acts as a boolean
- */
-guint16 gdcmHeader::ReadInt16(void) {
- guint16 g;
- size_t item_read;
- item_read = fread (&g, (size_t)2,(size_t)1, fp);
- if ( item_read != 1 ) {
- // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :");
- // if(feof(fp))
- // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error");
- errno = 1;
- return 0;
}
- errno = 0;
- g = SwapShort(g);
- return g;
}
/**
- * \ingroup gdcmHeader
- * \brief Reads a supposed to be 32 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @return
+ * \brief Initialize a default DICOM header that should contain all the
+ * field require by other reader. DICOM standard does not
+ * explicitely defines those fields, heuristic has been choosen.
+ * This is not perfect as we are writting a CT image...
*/
-guint32 gdcmHeader::ReadInt32(void) {
- guint32 g;
- size_t item_read;
- item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 ) {
- //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :");
- //if(feof(fp))
- // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error");
- errno = 1;
- return 0;
- }
- errno = 0;
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
-void gdcmHeader::SkipBytes(guint32 NBytes) {
- //FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::Initialise(void) {
- dicom_vr = gdcmGlobal::GetVR();
- dicom_ts = gdcmGlobal::GetTS();
- Dicts = gdcmGlobal::GetDicts();
- RefPubDict = Dicts->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- *
- */
-void gdcmHeader::CheckSwap()
+void Header::InitializeDefaultHeader()
{
- // Fourth semantics:
- //
- // ---> Warning : This fourth field is NOT part
- // of the 'official' Dicom Dictionnary
- // and should NOT be used.
- // (Not defined for all the groups
- // may be removed in a future release)
- //
- // CMD Command
- // META Meta Information
- // DIR Directory
- // ID
- // PAT Patient
- // ACQ Acquisition
- // REL Related
- // IMG Image
- // SDY Study
- // VIS Visit
- // WAV Waveform
- // PRC
- // DEV Device
- // NMI Nuclear Medicine
- // MED
- // BFS Basic Film Session
- // BFB Basic Film Box
- // BIB Basic Image Box
- // BAB
- // IOB
- // PJ
- // PRINTER
- // RT Radio Therapy
- // DVH
- // SSET
- // RES Results
- // CRV Curve
- // OLY Overlays
- // PXL Pixels
- // DL Delimiters
- //
-
- // The only guaranted way of finding the swap code is to find a
- // group tag since we know it's length has to be of four bytes i.e.
- // 0x00000004. Finding the swap code in then straigthforward. Trouble
- // occurs when we can't find such group...
- guint32 s;
- guint32 x=4; // x : for ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
-
- int lgrLue;
- char * entCur;
- char deb[HEADER_LENGTH_TO_READ];
-
- // First, compare HostByteOrder and NetworkByteOrder in order to
- // determine if we shall need to swap bytes (i.e. the Endian type).
- if (x==ntohs(x))
- net2host = true;
- else
- net2host = false;
- //cout << net2host << endl;
-
- // The easiest case is the one of a DICOM header, since it possesses a
- // file preamble where it suffice to look for the string "DICM".
- lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
-
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
- // Next, determine the value representation (VR). Let's skip to the
- // first element (0002, 0000) and check there if we find "UL"
- // - or "OB" if the 1st one is (0002,0001) -,
- // in which case we (almost) know it is explicit VR.
- // WARNING: if it happens to be implicit VR then what we will read
- // is the length of the group. If this ascii representation of this
- // length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
- // We need to skip :
- // * the 128 bytes of File Preamble (often padded with zeroes),
- // * the 4 bytes of "DICM" string,
- // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
- // i.e. a total of 136 bytes.
- entCur = deb + 136;
- // FIXME
- // Use gdcmHeader::dicom_vr to test all the possibilities
- // instead of just checking for UL, OB and UI !?
- if( (memcmp(entCur, "UL", (size_t)2) == 0) ||
- (memcmp(entCur, "OB", (size_t)2) == 0) ||
- (memcmp(entCur, "UI", (size_t)2) == 0) )
- {
- filetype = ExplicitVR;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "explicit Value Representation");
- } else {
- filetype = ImplicitVR;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "not an explicit Value Representation");
- }
- if (net2host) {
- sw = 4321;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
- } else {
- sw = 0;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
- }
-
- // Position the file position indicator at first tag (i.e.
- // after the file preamble and the "DICM" string).
- rewind(fp);
- fseek (fp, 132L, SEEK_SET);
- return;
- } // End of DicomV3
-
- // Alas, this is not a DicomV3 file and whatever happens there is no file
- // preamble. We can reset the file position indicator to where the data
- // is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
- rewind(fp);
-
- // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
- // By clean we mean that the length of the first tag is written down.
- // If this is the case and since the length of the first group HAS to be
- // four (bytes), then determining the proper swap code is straightforward.
-
- entCur = deb + 4;
- // We assume the array of char we are considering contains the binary
- // representation of a 32 bits integer. Hence the following dirty
- // trick :
- s = *((guint32 *)(entCur));
-
- switch (s) {
- case 0x00040000 :
- sw = 3412;
- filetype = ACR;
- return;
- case 0x04000000 :
- sw = 4321;
- filetype = ACR;
- return;
- case 0x00000400 :
- sw = 2143;
- filetype = ACR;
- return;
- case 0x00000004 :
- sw = 0;
- filetype = ACR;
- return;
- default :
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "ACR/NEMA unfound swap info (time to raise bets)");
- }
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses. So, let's assume this file
- // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
- // not present. Then the only info we have is the net2host one.
- filetype = Unknown;
- if (! net2host )
- sw = 0;
- else
- sw = 4321;
- return;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::SwitchSwapToBigEndian(void) {
- dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( sw == 0 ) {
- sw = 4321;
- return;
- }
- if ( sw == 4321 ) {
- sw = 0;
- return;
- }
- if ( sw == 3412 ) {
- sw = 2143;
- return;
- }
- if ( sw == 2143 )
- sw = 3412;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param NewSize
- * @return
- */
-void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
- if (NewSize < 0)
- return;
- if ((guint32)NewSize >= (guint32)0xffffffff) {
- MaxSizeLoadElementValue = 0xffffffff;
- return;
- }
- MaxSizeLoadElementValue = NewSize;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given
- * group and element. The public dictionary has precedence on the
- * shadow one.
- * @param group group of the searched DictEntry
- * @param element element of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group,
- guint16 element) {
- gdcmDictEntry * found = (gdcmDictEntry*)0;
- if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "gdcmHeader::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict) {
- found = RefPubDict->GetTagByNumber(group, element);
- if (found)
- return found;
- }
- if (RefShaDict) {
- found = RefShaDict->GetTagByNumber(group, element);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given name.
- * The public dictionary has precedence on the shadow one.
- * @param Name name of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) {
- gdcmDictEntry * found = (gdcmDictEntry*)0;
- if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "gdcmHeader::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict) {
- found = RefPubDict->GetTagByName(Name);
- if (found)
- return found;
- }
- if (RefShaDict) {
- found = RefShaDict->GetTagByName(Name);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Read the next tag but WITHOUT loading it's value
- * @return On succes the newly created HeaderEntry, NULL on failure.
- */
-gdcmHeaderEntry * gdcmHeader::ReadNextHeaderEntry(void) {
-
- guint16 g,n;
- gdcmHeaderEntry * NewElVal;
-
- g = ReadInt16();
- n = ReadInt16();
-
- if (errno == 1)
- // We reached the EOF (or an error occured) and header parsing
- // has to be considered as finished.
- return (gdcmHeaderEntry *)0;
-
- NewElVal = NewHeaderEntryByNumber(g, n);
- FindHeaderEntryVR(NewElVal);
- FindHeaderEntryLength(NewElVal);
-
- if (errno == 1) {
- // Call it quits
- return (gdcmHeaderEntry *)0;
- }
- NewElVal->SetOffset(ftell(fp));
- //if ( (g==0x7fe0) && (n==0x0010) )
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Name Name of the underlying DictEntry
- */
-gdcmHeaderEntry* gdcmHeader::NewHeaderEntryByName(std::string Name) {
-
- gdcmDictEntry * NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name);
-
- gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::ObtainHeaderEntryByName",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry*)0;
+ typedef struct
+ {
+ const char *value;
+ uint16_t group;
+ uint16_t elem;
+ } DICOM_DEFAULT_VALUE;
+
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidClass = uid + ".1";
+ std::string uidInst = uid + ".10";
+ std::string uidStudy = uid + ".100";
+ std::string uidSerie = uid + ".1000";
+
+ static DICOM_DEFAULT_VALUE defaultvalue[] = {
+ { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
+ { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
+ { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
+ { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
+
+ { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
+ { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
+ { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
+ { "CT", 0x0008, 0x0060}, // Modality
+ { "GDCM", 0x0008, 0x0070}, // Manufacturer
+ { "GDCM", 0x0008, 0x0080}, // Institution Name
+ { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
+
+ { "GDCM", 0x0010, 0x0010}, // Patient's Name
+ { "GDCMID", 0x0010, 0x0020}, // Patient ID
+
+ { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
+ { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
+ { "1", 0x0020, 0x0010}, // StudyID
+ { "1", 0x0020, 0x0011}, // SeriesNumber
+
+ { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
+ { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
+ { "0", 0x0028, 0x0010}, // nbRows
+ { "0", 0x0028, 0x0011}, // nbCols
+ { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
+ { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
+ { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
+ { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
+ { 0, 0, 0 }
+ };
+
+ // default value
+ // Special case this is the image (not a string)
+ GrPixel = 0x7fe0;
+ NumPixel = 0x0010;
+ ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel);
+
+ // All remaining strings:
+ unsigned int i = 0;
+ DICOM_DEFAULT_VALUE current = defaultvalue[i];
+ while( current.value )
+ {
+ ReplaceOrCreateByNumber(current.value, current.group, current.elem);
+ current = defaultvalue[++i];
}
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group of the underlying DictEntry
- * @param Elem element of the underlying DictEntry
- */
-gdcmHeaderEntry* gdcmHeader::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) {
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem);
- if (!NewTag)
- NewTag = new gdcmDictEntry(Group, Elem);
-
- gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::NewHeaderEntryByNumber",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry*)0;
- }
- return NewElVal;
}
-/**
- * \ingroup gdcmHeader
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmHeaderEntry with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @ return The newly hand crafted Element Value.
- */
-gdcmHeaderEntry* gdcmHeader::NewManualHeaderEntryToPubDict(std::string NewTagName,
- std::string VR) {
- gdcmHeaderEntry* NewElVal = (gdcmHeaderEntry*)0;
- guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
- guint32 FreeElem = 0;
- gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
-
- FreeElem = PubEntrySet.GenerateFreeTagKeyInGroup(StuffGroup);
- if (FreeElem == UINT32_MAX) {
- dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict",
- "Group 0xffff in Public Dict is full");
- return (gdcmHeaderEntry*)0;
- }
- NewEntry = new gdcmDictEntry(StuffGroup, FreeElem,
- VR, "GDCM", NewTagName);
- NewElVal = new gdcmHeaderEntry(NewEntry);
- PubEntrySet.Add(NewElVal);
- return NewElVal;
-}
//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
+
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff