-// gdcmHeader.cxx
-//-----------------------------------------------------------------------------
-#include <stdio.h>
-#include <cerrno>
-#include <cctype> // for isalpha
-#include <vector>
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2004/06/23 09:30:22 $
+ Version: $Revision: 1.169 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
#include "gdcmHeader.h"
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmTS.h"
+#include "gdcmValEntry.h"
+
+#include <vector>
//-----------------------------------------------------------------------------
// Constructor / Destructor
* @param ignore_shadow = true if user wants to skip shadow groups
* during parsing, to save memory space
*/
-gdcmHeader::gdcmHeader(const char *InFilename,
+gdcmHeader::gdcmHeader(std::string const & filename,
bool exception_on_error,
bool enable_sequences,
bool ignore_shadow):
- gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
-{
-
+ gdcmDocument(filename,exception_on_error,enable_sequences,ignore_shadow)
+{
// 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
// This IS the right place for the code
- std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
- if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
- GrPixel = 0x7fe0; // default value
- } else {
- GrPixel = (guint16) atoi( ImageLocation.c_str() );
- }
- if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
- GrPixel = 0x7fe0; // the supposed processor endianity.
- // see gdcmData/cr172241.dcm
- if (GrPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- NumPixel = 0x1010;
- else
- NumPixel = 0x0010;
-
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel);
- countGrPixel = GetEntry().count(key);
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ GrPixel = 0x7fe0; // default value
+ } else {
+ GrPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
+ GrPixel = 0x7fe0; // the supposed processor endianity.
+ // see gdcmData/cr172241.dcm
+ if (GrPixel != 0x7fe0) {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ } else {
+ NumPixel = 0x0010;
+ }
}
/**
* @param exception_on_error whether we want to throw an exception or not
*/
gdcmHeader::gdcmHeader(bool exception_on_error) :
- gdcmParser(exception_on_error)
+ gdcmDocument(exception_on_error)
{
}
* \ingroup gdcmHeader
* \brief Canonical destructor.
*/
-gdcmHeader::~gdcmHeader (void) {
+gdcmHeader::~gdcmHeader () {
}
//-----------------------------------------------------------------------------
// Print
-// see gdcmParser.cxx
+
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmHeader
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmParser was properly parsed
+ * decides whether or not the current gdcmHeader was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable Dicom/Acr File.
- * @return true when gdcmParser is the one of a reasonable Dicom/Acr file,
+ * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmHeader::IsReadable(void) {
- if(!gdcmParser::IsReadable()) {
- return(false);
+bool gdcmHeader::IsReadable() {
+ if(!gdcmDocument::IsReadable()) {
+ return false;
}
std::string res = GetEntryByNumber(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
return false; // Image Dimensions
- if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
+ if ( !GetDocEntryByNumber(0x0028, 0x0100) )
return false; // "Bits Allocated"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0101) )
+ if ( !GetDocEntryByNumber(0x0028, 0x0101) )
return false; // "Bits Stored"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
+ if ( !GetDocEntryByNumber(0x0028, 0x0102) )
return false; // "High Bit"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
+ if ( !GetDocEntryByNumber(0x0028, 0x0103) )
return false; // "Pixel Representation" i.e. 'Sign'
return true;
}
/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGBaseLineProcess1 one.
- * @return True when JPEGBaseLineProcess1found. False in all other cases.
- */
-bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.50" )
- return true;
- return false;
-}
-
-/**
- * \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);
- return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" );
-}
-
-/**
- * \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.
- */
-bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.52" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
- * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
- * other cases.
- */
-bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.53" )
- return true;
- return false;
-}
-
-/**
- * \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.
- */
-bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.5" ) {
- return true;
- }
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if Transfer Syntax was already encountered
- * and if it corresponds to a JPEG Lossless one.
- * @return True when RLE Lossless found. False in all
- * other cases.
- */
-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);
-
- const char * Transfert = Element->GetValue().c_str();
- if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true;
- if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true;
- if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true;
-
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG2000 one
- * @return True when JPEG2000 (Lossly or LossLess) found. False in all
- * other cases.
- */
-bool gdcmHeader::IsJPEG2000(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- 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;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
- */
-bool gdcmHeader::IsDicomV3(void) {
- // Checking if Transfert Syntax exists is enough
- // Anyway, it's to late check if the 'Preamble' was found ...
- // And ... would it be a rich idea to check ?
- // (some 'no Preamble' DICOM images exist !)
- return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
-}
-
-/**
- * \ingroup gdcmHeader
* \brief Retrieve the number of columns of image.
* @return The encountered size when found, 0 by default.
* 0 means the file is NOT USABLE. The caller will have to check
*/
-int gdcmHeader::GetXSize(void) {
+int gdcmHeader::GetXSize() {
std::string StrSize;
StrSize = GetEntryByNumber(0x0028,0x0011);
if (StrSize == GDCM_UNFOUND)
* \brief Retrieve the number of lines of image.
* \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
* @return The encountered size when found, 1 by default
- * (The ACR-MEMA file contains a Signal, not an Image).
+ * (The ACR-NEMA file contains a Signal, not an Image).
*/
-int gdcmHeader::GetYSize(void) {
+int gdcmHeader::GetYSize() {
std::string StrSize = GetEntryByNumber(0x0028,0x0010);
if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
* being the ACR-NEMA "Planes" tag content.
* @return The encountered size when found, 1 by default (single image).
*/
-int gdcmHeader::GetZSize(void) {
+int gdcmHeader::GetZSize() {
// Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
std::string StrSize = GetEntryByNumber(0x0028,0x0008);
return 1;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float gdcmHeader::GetXSpacing() {
+ float xspacing, yspacing;
+ std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if (StrSpacing == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+ int nbValues;
+ if( (nbValues = sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2) {
+ if (nbValues==1) // if single value is found, xspacing is defaulted to yspacing
+ return yspacing;
+ }
+ if (xspacing == 0.) {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ }
+ return xspacing;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float gdcmHeader::GetYSpacing() {
+ float yspacing;
+ std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if (StrSpacing == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+ sscanf( StrSpacing.c_str(), "%f", &yspacing);
+ return yspacing;
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0018,0088 : Space Between Slices
+ * else from 0018,0050 : Slice Thickness
+ * else 1.0
+ * @return Z dimension of a voxel-to be
+ */
+float gdcmHeader::GetZSpacing() {
+ // Spacing Between Slices : distance entre le milieu de chaque coupe
+ // Les coupes peuvent etre :
+ // jointives (Spacing between Slices = Slice Thickness)
+ // chevauchantes (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
+ // Si le Spacing Between Slices est absent,
+ // on suppose que les coupes sont jointives
+
+ std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
+
+ if (StrSpacingBSlices == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
+ std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050);
+ if (StrSliceThickness == GDCM_UNFOUND)
+ return 1.;
+ else
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return atof(StrSliceThickness.c_str());
+ } else {
+ return atof(StrSpacingBSlices.c_str());
+ }
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float gdcmHeader::GetRescaleIntercept() {
+ float resInter = 0.;
+ std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
+ if (StrRescInter != GDCM_UNFOUND) {
+ if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) {
+ dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
+ // bug in the element 0x0028,0x1052
+ }
+ }
+ return resInter;
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+ float gdcmHeader::GetRescaleSlope() {
+ float resSlope = 1.;
+ std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
+ if (StrRescSlope != GDCM_UNFOUND) {
+ if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) {
+ dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
+ // bug in the element 0x0028,0x1053
+ }
+ }
+ return resSlope;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief This function is intended to user who doesn't want
+ * to have to manage a LUT and expects to get an RBG Pixel image
+ * (or a monochrome one ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
+ */
+int gdcmHeader::GetNumberOfScalarComponents() {
+ if (GetSamplesPerPixel() ==3)
+ return 3;
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
+ return 3;
+
+ std::string PhotometricInterpretation =
+ gdcmHeader::GetEntryByNumber(0x0028,0x0004);
+
+ if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) {
+ if (HasLUT()) // PALETTE COLOR is NOT enough
+ return 3;
+ else
+ return 1;
+ }
+
+ //beware of trailing space at end of string
+ if (PhotometricInterpretation.find(GDCM_UNFOUND) <
+ PhotometricInterpretation.length() ||
+ PhotometricInterpretation.find("MONOCHROME1") <
+ PhotometricInterpretation.length() ||
+ PhotometricInterpretation.find("MONOCHROME2") <
+ PhotometricInterpretation.length() )
+ return 1;
+ else
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief This function is intended to user that DOESN'T want
+ * to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * - the (vtk) user is supposed to know how deal with LUTs -
+ * \warning to be used with GetImagePixelsRaw()
+ * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
+ */
+int gdcmHeader::GetNumberOfScalarComponentsRaw() {
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
+ return 3;
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0020,000d : Study Instance UID
+ *\todo ? : return the ACR-NEMA element value if DICOM one is not found
+ * @return Study Instance UID
+ */
+//std::string gdcmHeader::GetStudyUID(){
+// return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID
+//}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0020,000e : Series Instance UID
+ *\todo ? : return the ACR-NEMA element value if DICOM one is not found
+ * @return Series Instance UID
+ */
+//std::string gdcmHeader::GetSeriesUID(){
+// return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID
+//}
+
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0008,0016 : SOP Class UID
+ *\todo ? : return the ACR-NEMA element value if DICOM one is not found
+ * @return SOP Class UID
+ */
+//std::string gdcmHeader::GetClassUID(){
+// return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID
+//}
+
+/**
+ *\brief gets the info from 0008,0018 : SOP Instance UID
+ *\todo ? : return the ACR-NEMA element value if DICOM one is not found
+ * @return SOP Instance UID
+ */
+//std::string gdcmHeader::GetInstanceUID(){
+// return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID
+//}
+//
+// -------------- Remember ! ----------------------------------
+//
+// Image Position Patient (0020,0032):
+// If not found (ACR_NEMA) we try Image Position (0020,0030)
+// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
+// or Location (0020,0050)
+// as the Z coordinate,
+// 0. for all the coordinates if nothing is found
+
+// \todo find a way to inform the caller nothing was found
+// \todo How to tell the caller a wrong number of values was found?
+//
+// ---------------------------------------------------------------
+//
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner X position
+ */
+
+float gdcmHeader::GetXOrigin() {
+ float xImPos, yImPos, zImPos;
+ std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if (StrImPos == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
+ StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ return 0.;
+ return xImPos;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner Y position
+ */
+float gdcmHeader::GetYOrigin() {
+ float xImPos, yImPos, zImPos;
+ std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if (StrImPos == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
+ StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ return 0.;
+ return yImPos;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * \ else from 0020,0030 : Image Position (RET)
+ * \ else from 0020,1041 : Slice Location
+ * \ else from 0020,0050 : Location
+ * \ else 0.
+ * @return up-left image corner Z position
+ */
+float gdcmHeader::GetZOrigin() {
+ float xImPos, yImPos, zImPos;
+ std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
+ if (StrImPos != GDCM_UNFOUND) {
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ } else {
+ return zImPos;
+ }
+ }
+ StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos != GDCM_UNFOUND) {
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ } else {
+ return zImPos;
+ }
+ }
+ std::string StrSliceLocation = GetEntryByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
+ if (StrSliceLocation != GDCM_UNFOUND) {
+ if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ } else {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
+ std::string StrLocation = GetEntryByNumber(0x0020,0x0050);
+ if (StrLocation != GDCM_UNFOUND) {
+ if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ } else {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
+ return 0.; // Hopeless
+}
+
+/**
+ * \brief gets the info from 0020,0013 : Image Number
+ * \ else 0.
+ * @return image number
+ */
+int gdcmHeader::GetImageNumber() {
+ // The function i atoi() takes the address of an area of memory as
+ // parameter and converts the string stored at that location to an integer
+ // using the external decimal to internal binary conversion rules. This may
+ // be preferable to sscanf() since atoi() is a much smaller, simpler and
+ // faster function. sscanf() can do all possible conversions whereas
+ // atoi() can only do single decimal integer conversions.
+ std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
+ if (StrImNumber != GDCM_UNFOUND) {
+ return atoi( StrImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType gdcmHeader::GetModality() {
+ // 0008 0060 CS ID Modality
+ std::string StrModality = GetEntryByNumber(0x0008,0x0060);
+ if (StrModality != GDCM_UNFOUND) {
+ if ( StrModality.find("AU") < StrModality.length()) return AU;
+ else if ( StrModality.find("AS") < StrModality.length()) return AS;
+ else if ( StrModality.find("BI") < StrModality.length()) return BI;
+ else if ( StrModality.find("CF") < StrModality.length()) return CF;
+ else if ( StrModality.find("CP") < StrModality.length()) return CP;
+ else if ( StrModality.find("CR") < StrModality.length()) return CR;
+ else if ( StrModality.find("CT") < StrModality.length()) return CT;
+ else if ( StrModality.find("CS") < StrModality.length()) return CS;
+ else if ( StrModality.find("DD") < StrModality.length()) return DD;
+ else if ( StrModality.find("DF") < StrModality.length()) return DF;
+ else if ( StrModality.find("DG") < StrModality.length()) return DG;
+ else if ( StrModality.find("DM") < StrModality.length()) return DM;
+ else if ( StrModality.find("DS") < StrModality.length()) return DS;
+ else if ( StrModality.find("DX") < StrModality.length()) return DX;
+ else if ( StrModality.find("ECG") < StrModality.length()) return ECG;
+ else if ( StrModality.find("EPS") < StrModality.length()) return EPS;
+ else if ( StrModality.find("FA") < StrModality.length()) return FA;
+ else if ( StrModality.find("FS") < StrModality.length()) return FS;
+ else if ( StrModality.find("HC") < StrModality.length()) return HC;
+ else if ( StrModality.find("HD") < StrModality.length()) return HD;
+ else if ( StrModality.find("LP") < StrModality.length()) return LP;
+ else if ( StrModality.find("LS") < StrModality.length()) return LS;
+ else if ( StrModality.find("MA") < StrModality.length()) return MA;
+ else if ( StrModality.find("MR") < StrModality.length()) return MR;
+ else if ( StrModality.find("NM") < StrModality.length()) return NM;
+ else if ( StrModality.find("OT") < StrModality.length()) return OT;
+ else if ( StrModality.find("PT") < StrModality.length()) return PT;
+ else if ( StrModality.find("RF") < StrModality.length()) return RF;
+ else if ( StrModality.find("RG") < StrModality.length()) return RG;
+ else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE;
+ else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE;
+ else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN;
+ else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT;
+ else if ( StrModality.find("SM") < StrModality.length()) return SM;
+ else if ( StrModality.find("ST") < StrModality.length()) return ST;
+ else if ( StrModality.find("TG") < StrModality.length()) return TG;
+ else if ( StrModality.find("US") < StrModality.length()) return US;
+ else if ( StrModality.find("VF") < StrModality.length()) return VF;
+ else if ( StrModality.find("XA") < StrModality.length()) return XA;
+ else if ( StrModality.find("XC") < StrModality.length()) return XC;
+
+ else
+ {
+ /// \todo throw error return value ???
+ /// specified <> unknow in our database
+ return Unknow;
+ }
+ }
+ return Unknow;
+}
+
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of Bits Stored (actually used)
* @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) {
+int gdcmHeader::GetBitsStored() {
std::string StrSize = GetEntryByNumber(0x0028,0x0101);
if (StrSize == GDCM_UNFOUND)
return 0; // It's supposed to be mandatory
* @return The encountered number of Bits Allocated, 0 by default.
* 0 means the file is NOT USABLE. The caller has to check it !
*/
-int gdcmHeader::GetBitsAllocated(void) {
+int gdcmHeader::GetBitsAllocated() {
std::string StrSize = GetEntryByNumber(0x0028,0x0100);
if (StrSize == GDCM_UNFOUND)
return 0; // It's supposed to be mandatory
* @return The encountered number of Samples Per Pixel, 1 by default.
* (Gray level Pixels)
*/
-int gdcmHeader::GetSamplesPerPixel(void) {
+int gdcmHeader::GetSamplesPerPixel() {
std::string StrSize = GetEntryByNumber(0x0028,0x0002);
if (StrSize == GDCM_UNFOUND)
return 1; // Well, it's supposed to be mandatory ...
* (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
* @return The encountered Planar Configuration, 0 by default.
*/
-int gdcmHeader::GetPlanarConfiguration(void) {
+int gdcmHeader::GetPlanarConfiguration() {
std::string StrSize = GetEntryByNumber(0x0028,0x0006);
if (StrSize == GDCM_UNFOUND)
return 0;
* @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) {
+int gdcmHeader::GetPixelSize() {
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+// if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
+// return 3;
+
std::string PixelType = GetPixelType();
if (PixelType == "8U" || PixelType == "8S")
return 1;
* 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 gdcmHeader::GetPixelType() {
std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
if (BitsAlloc == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
* of *image* pixels (not *icone image* pixels, if any !)
* @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset(void) {
- //
- // If the element (0x0088,0x0200) 'icone image sequence' is found
- // (grPixel,numPixel) is stored twice : the first one for the icon
- // the second one for the image ...
- // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything*
- // see gdcmData/MxTwinLossLess.dcm ...
-
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
+size_t gdcmHeader::GetPixelOffset() {
- IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
- gdcmHeaderEntry* PixelElement;
- if (countGrPixel == 1)
- PixelElement = (it.first)->second;
- else {
- PixelElement = (++it.first)->second; // hope there are no more than 2 !
- }
+ gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
+
if (PixelElement) {
return PixelElement->GetOffset();
} else {
-/* std::cout << "Big trouble : Pixel Element ("
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
<< std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl; */
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
}
}
* -in case of embeded compressed image-)
* 0 : NOT USABLE file. The caller has to check.
*/
-size_t gdcmHeader::GetPixelAreaLength(void) {
+size_t gdcmHeader::GetPixelAreaLength() {
- IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
- TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
- gdcmHeaderEntry* PixelElement;
-
- if (countGrPixel==1)
- PixelElement = (it.first)->second;
- else
- PixelElement = (++it.first)->second;
+ gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
if (PixelElement) {
return PixelElement->GetLength();
} else {
-/* std::cout << "Big trouble : Pixel Element ("
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
<< std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;*/
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
}
}
* Please warn me if you know sbdy that *does* know ... jprx
* @return true if LUT Descriptors and LUT Tables were found
*/
-bool gdcmHeader::HasLUT(void) {
+bool gdcmHeader::HasLUT() {
// Check the presence of the LUT Descriptors, and LUT Tables
// LutDescriptorRed
- if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ if ( !GetDocEntryByNumber(0x0028,0x1101) )
return false;
// LutDescriptorGreen
- if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ if ( !GetDocEntryByNumber(0x0028,0x1102) )
return false;
// LutDescriptorBlue
- if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ if ( !GetDocEntryByNumber(0x0028,0x1103) )
return false;
// Red Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
+ if ( !GetDocEntryByNumber(0x0028,0x1201) )
return false;
// Green Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ if ( !GetDocEntryByNumber(0x0028,0x1202) )
return false;
// Blue Palette Color Lookup Table Data
- if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
- return false;
+ if ( !GetDocEntryByNumber(0x0028,0x1203) )
+ return false;
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
return true;
}
* when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
* @ return bit number of each LUT item
*/
-int gdcmHeader::GetLUTNbits(void) {
+int gdcmHeader::GetLUTNbits() {
std::vector<std::string> tokens;
//int LutLength;
//int LutDepth;
* no known Dicom reader deals with them :-(
* @return a RGBA Lookup Table
*/
-unsigned char * gdcmHeader::GetLUTRGBA(void) {
+unsigned char * gdcmHeader::GetLUTRGBA() {
// Not so easy : see
// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
- if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
+ if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
return NULL;
}
int lengthR, debR, nbitsR;
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
GetEntryVoidAreaByNumber(0x0028,0x1202);
unsigned char *lutB = (unsigned char *)
GetEntryVoidAreaByNumber(0x0028,0x1203);
-
+
if (!lutR || !lutG || !lutB ) {
return NULL;
}
// forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
- unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ unsigned char *LUTRGBA = new unsigned char[1024]; // 256 * 4 (R, G, B, Alpha)
if (!LUTRGBA) {
return NULL;
}
}
/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
* else 1.
- * @return the full Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
*/
-std::string gdcmHeader::GetTransfertSyntaxName(void) {
+std::string gdcmHeader::GetTransfertSyntaxName() {
// use the gdcmTS (TS : Transfert Syntax)
std::string TransfertSyntax = GetEntryByNumber(0x0002,0x0010);
if (TransfertSyntax == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName: unfound Transfert Syntax (0002,0010)");
+ 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 ?!
+ //delete ts; /// \todo Seg Fault when deleted ?!
return tsName;
}
/**
- * \ingroup gdcmHeader
* \brief Sets the Pixel Area size in the Header
* --> not-for-rats function
* @param ImageDataSize new Pixel Area Size
std::string content1;
char car[20];
- // Assumes HeaderEntry (GrPixel, NumPixel) is unique ...
- // TODO deal with multiplicity (see gdcmData/icone.dcm)
sprintf(car,"%d",ImageDataSize);
- gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel);
+ gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
a->SetLength(ImageDataSize);
ImageDataSize+=8;
SetEntryByNumber(content1, GrPixel, NumPixel);
}
-
-/**
- * \ingroup gdcmHeader
- * \brief compares 2 Headers, according to DICOMDIR rules
- * --> not-for-rats function
- * \warning does NOT work with ACR-NEMA files
- * \todo find a trick to solve the pb (use RET fields ?)
- * @param header
- * @return true if 'smaller'
- */
- bool gdcmHeader::operator<(gdcmHeader &header){
- std::string s1,s2;
-
- // Patient Name
- s1=this->GetEntryByNumber(0x0010,0x0010);
- s2=header.GetEntryByNumber(0x0010,0x0010);
- if(s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- else
- {
- // Patient ID
- s1=this->GetEntryByNumber(0x0010,0x0020);
- s2=header.GetEntryByNumber(0x0010,0x0020);
- if (s1 < s2)
- return(true);
- else if (s1 > s2)
- return(1);
- else
- {
- // Study Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000d);
- s2=header.GetEntryByNumber(0x0020,0x000d);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- else
- {
- // Serie Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000e);
- s2=header.GetEntryByNumber(0x0020,0x000e);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
- }
- }
- }
- return(false);
-}
-
-bool gdcmHeader::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
-{
- guint32 length = tag->GetLength();
-
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
- if(length%2==1)
- {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
-
- WriteEntryTagVRLength(tag, _fp, type);
-
- // Pixels are never loaded in the element !
- // we stop writting when Pixel are processed
- // FIX : we loose trailing elements (RAB, right now)
- guint16 el = tag->GetElement();
- guint16 group = tag->GetGroup();
- int compte =0;
- if ((group == GrPixel) && (el == NumPixel) ) {
- compte++;
- if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
- return false;
- }
- }
- WriteEntryValue(tag, _fp, type);
- return true;
-}
-
//-----------------------------------------------------------------------------
// Protected
/**
- * \ingroup gdcmHeader
* \brief anonymize a Header (removes Patient's personal info)
* (read the code to see which ones ...)
*/
-bool gdcmHeader::anonymizeHeader() {
+bool gdcmHeader::AnonymizeHeader() {
- gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010);
- // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020);
+ gdcmDocEntry *patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
if (patientNameHE) {
- std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
- if (StudyInstanceUID !=GDCM_UNFOUND)
- ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010);
+ std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if (studyInstanceUID !=GDCM_UNFOUND)
+ ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
else
ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
}
//300e 0004 DA RT Review Date
return true;
}
+
+/**
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void gdcmHeader::GetImageOrientationPatient( float* iop ) {
+
+ //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)
+ std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037);
+ if (StrImOriPat != GDCM_UNFOUND) {
+ if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
+ dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
+ return ; // bug in the element 0x0020,0x0037
+ }
+ else
+ return ;
+ }
+
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ StrImOriPat = GetEntryByNumber(0x0020,0x0035);
+ if (StrImOriPat != GDCM_UNFOUND) {
+ if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
+ dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
+ return ; // bug in the element 0x0020,0x0035
+ }
+ else
+ return ;
+ }
+}
+
//-----------------------------------------------------------------------------
// Private
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff