Program: gdcm
Module: $RCSfile: gdcmHeader.cxx,v $
Language: C++
- Date: $Date: 2004/07/19 15:16:18 $
- Version: $Revision: 1.178 $
+ Date: $Date: 2004/10/18 12:49:22 $
+ Version: $Revision: 1.194 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+ 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
#include <vector>
+namespace gdcm
+{
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
* \brief Constructor
* @param filename name of the file whose header we want to analyze
- * @param exception_on_error whether we want to throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences, when they have an actual length
- * @param ignore_shadow = true if user wants to skip shadow groups
- * during parsing, to save memory space
*/
-gdcmHeader::gdcmHeader( std::string const & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow ):
- gdcmDocument( filename,
- exception_on_error,
- enable_sequences,
- ignore_shadow )
+Header::Header( std::string const & filename ):
+ Document( filename )
{
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
// Inside the group pointed by "Image Location" the searched element
// is conventionally the element 0x0010 (when the norm is respected).
// When the "Image Location" is absent we default to group 0x7fe0.
-
- // This IS the right place for the code
+ // Note: this IS the right place for the code
// Image Location
std::string imgLocation = GetEntryByNumber(0x0028, 0x0200);
/**
* \brief Constructor
- * @param exception_on_error whether we want to throw an exception or not
*/
-gdcmHeader::gdcmHeader(bool exception_on_error) :
- gdcmDocument( exception_on_error )
+Header::Header()
+ :Document()
{
}
/**
- * \ingroup gdcmHeader
* \brief Canonical destructor.
*/
-gdcmHeader::~gdcmHeader ()
+Header::~Header ()
{
}
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
-void gdcmHeader::Write(FILE* fp,FileType filetype) {
-
+void Header::Write(FILE* fp,FileType filetype)
+{
// Bits Allocated
- if ( GetEntryByNumber(0x0028,0x0100) == "12") {
+ if ( GetEntryByNumber(0x0028,0x0100) == "12")
+ {
SetEntryByNumber("16", 0x0028,0x0100);
}
- // correct Pixel group Length if necessary
-
- // TODO : create a gdcmHeader::Write method and move this part.
- // (only gdcmHeader knows GrPixel, NumPixel)
+ /// \todo correct 'Pixel group' Length if necessary
int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel);
- if (i_lgPix != -2) { // no (GrPixel, NumPixel) element
- char * dumm = new char[20];
- sprintf(dumm ,"%d", i_lgPix+12);
- std::string s_lgPix = dumm;
- delete dumm;
+ if (i_lgPix != -2)
+ {
+ // no (GrPixel, NumPixel) element
+ std::string s_lgPix;
+ s_lgPix = Util::Format("%d", i_lgPix+12);
ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
}
-
+
+ // FIXME : should be nice if we could move it to File
+ // (or in future gdcmPixelData class)
+
// Drop Palette Color, if necessary
- if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) {
- // if SamplesPerPixel = 3, sure we don't need any LUT !
- // Drop 0028|1101, 0028|1102, 0028|1103
- // Drop 0028|1201, 0028|1202, 0028|1203
-
- gdcmDocEntry *e;
- e=GetDocEntryByNumber(0x0028,0x01101);
- if (e)
- RemoveEntry(e);
- e=GetDocEntryByNumber(0x0028,0x1102);
- if (e)
- RemoveEntry(e);
- e=GetDocEntryByNumber(0x0028,0x1103);
-
- if (e)
- RemoveEntry(e);
- e=GetDocEntryByNumber(0x0028,0x01201);
- if (e)
- RemoveEntry(e);
- e=GetDocEntryByNumber(0x0028,0x1202);
- if (e)
- RemoveEntry(e);
- e=GetDocEntryByNumber(0x0028,0x1203);
- if (e)
- RemoveEntry(e);
- }
-
- gdcmDocument::Write(fp,filetype);
+ if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' )
+ {
+ // if SamplesPerPixel = 3, sure we don't need any LUT !
+ // Drop 0028|1101, 0028|1102, 0028|1103
+ // Drop 0028|1201, 0028|1202, 0028|1203
+
+ DocEntry* e = GetDocEntryByNumber(0x0028,0x01101);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ }
+ Document::Write(fp,filetype);
}
//-----------------------------------------------------------------------------
/**
* \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 Dicom/Acr File.
- * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
+ * @return true when Header is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmHeader::IsReadable()
+bool Header::IsReadable()
{
- if( !gdcmDocument::IsReadable() )
+ if( !Document::IsReadable() )
{
return false;
}
* @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()
+int Header::GetXSize()
{
std::string strSize;
strSize = GetEntryByNumber(0x0028,0x0011);
}
/**
- * \ingroup gdcmHeader
* \brief Retrieve the number of lines of image.
- * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
+ * \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).
*/
-int gdcmHeader::GetYSize()
+int Header::GetYSize()
{
std::string strSize = GetEntryByNumber(0x0028,0x0010);
if ( strSize != GDCM_UNFOUND )
}
/**
- * \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
* being the ACR-NEMA "Planes" tag content.
* @return The encountered size when found, 1 by default (single image).
*/
-int gdcmHeader::GetZSize()
+int Header::GetZSize()
{
// Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
}
/**
- * \ingroup gdcmHeader
* \brief gets the info from 0028,0030 : Pixel Spacing
* else 1.0
* @return X dimension of a pixel
*/
-float gdcmHeader::GetXSpacing()
+float Header::GetXSpacing()
{
float xspacing, yspacing;
std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
+ dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)");
return 1.;
}
}
if ( xspacing == 0.)
{
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ dbg.Verbose(0, "Header::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
// seems to be a bug in the header ...
sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
}
}
/**
- * \ingroup gdcmHeader
* \brief gets the info from 0028,0030 : Pixel Spacing
* else 1.0
* @return Y dimension of a pixel
*/
-float gdcmHeader::GetYSpacing()
+float Header::GetYSpacing()
{
float yspacing = 0;
std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
+ dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)");
return 1.;
}
}
/**
- *\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()
+ * \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 Header::GetZSpacing()
{
// Spacing Between Slices : distance entre le milieu de chaque coupe
// Les coupes peuvent etre :
if ( strSpacingBSlices == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
+ dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices");
std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050);
if ( strSliceThickness == GDCM_UNFOUND )
{
}
/**
- *\ingroup gdcmHeader
- *\brief gets the info from 0028,1052 : Rescale Intercept
- * @return Rescale Intercept
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
*/
-float gdcmHeader::GetRescaleIntercept()
+float Header::GetRescaleIntercept()
{
float resInter = 0.;
- std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
+ /// 0028 1052 DS IMG Rescale Intercept
+ std::string strRescInter = GetEntryByNumber(0x0028,0x1052);
if ( strRescInter != GDCM_UNFOUND )
{
if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
{
// bug in the element 0x0028,0x1052
- dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
+ dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope "
+ "is empty");
}
}
- return resInter;
+ return resInter;
}
/**
- *\ingroup gdcmHeader
- *\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-float gdcmHeader::GetRescaleSlope()
+float Header::GetRescaleSlope()
{
float resSlope = 1.;
- std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryByNumber(0x0028,0x1053);
if ( strRescSlope != GDCM_UNFOUND )
{
if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
{
// bug in the element 0x0028,0x1053
- dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
+ dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty");
}
}
}
/**
- * \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()
+ * \brief This function is intended to user who doesn't want
+ * to have to manage a LUT and expects to get an RBG Pixel image
+ * (or a monochrome one ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
+ */
+int Header::GetNumberOfScalarComponents()
{
if ( GetSamplesPerPixel() == 3 )
{
}
/**
- * \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()
+ * \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 Header::GetNumberOfScalarComponentsRaw()
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" )
+ if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" )
{
return 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
- */
-
-float gdcmHeader::GetXOrigin()
+ * \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 Header::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)");
+ 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, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
+ 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 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()
+ * \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 Header::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)");
+ 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, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Image "
+ "Position (RET) (0020,0030)");
/// \todo How to tell the caller nothing was found ?
return 0.;
}
}
/**
- * \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()
+ * \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 Header::GetZOrigin()
{
float xImPos, yImPos, zImPos;
std::string strImPos = GetEntryByNumber(0x0020,0x0032);
{
if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
{
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Image "
+ "Position Patient (0020,0032)");
return 0.; // bug in the element 0x0020,0x0032
}
else
if( sscanf( strImPos.c_str(),
"%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
{
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
return 0.; // bug in the element 0x0020,0x0032
}
else
{
if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
{
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
+ dbg.Verbose(0, "Header::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)");
+ 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, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
+ dbg.Verbose(0, "Header::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)");
+ dbg.Verbose(0, "Header::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()
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+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
// 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
+ //0020 0013 IS REL Image Number
+ std::string strImNumber = GetEntryByNumber(0x0020,0x0013);
if ( strImNumber != GDCM_UNFOUND )
{
return atoi( strImNumber.c_str() );
}
/**
- * \brief gets the info from 0008,0060 : Modality
- * @return Modality Type
- */
-ModalityType gdcmHeader::GetModality()
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType Header::GetModality()
{
// 0008 0060 CS ID Modality
std::string strModality = GetEntryByNumber(0x0008,0x0060);
}
/**
- * \ingroup gdcmHeader
* \brief Retrieve the number of Bits Stored (actually used)
* (as opposite to number of Bits Allocated)
* @return The encountered number of Bits Stored, 0 by default.
* 0 means the file is NOT USABLE. The caller has to check it !
*/
-int gdcmHeader::GetBitsStored()
+int Header::GetBitsStored()
{
- std::string strSize = GetEntryByNumber(0x0028,0x0101);
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0101 );
if ( strSize == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory");
+ 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() );
+}
+/**
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit positin when present. 0 when absent.
+ */
+int Header::GetHighBitPosition()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed "
+ "to be mandatory");
+ return 0;
+ }
return atoi( strSize.c_str() );
}
/**
- * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetBitsAllocated()
+int Header::GetBitsAllocated()
{
std::string strSize = GetEntryByNumber(0x0028,0x0100);
if ( strSize == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory");
+ 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()
+int Header::GetSamplesPerPixel()
{
std::string strSize = GetEntryByNumber(0x0028,0x0002);
if ( strSize == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory");
+ dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
+ "be mandatory");
return 1; // Well, it's supposed to be mandatory ...
// but sometimes it's missing : *we* assume Gray pixels
}
-
return atoi( strSize.c_str() );
}
/**
- * \ingroup gdcmHeader
+ * \brief Check wether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
+ */
+bool Header::IsMonochrome()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "MONOCHROME1 "
+ || PhotometricInterp == "MONOCHROME2 " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsMonochrome: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
+ */
+bool Header::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool Header::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsYBRFull: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
* \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()
+int Header::GetPlanarConfiguration()
{
std::string strSize = GetEntryByNumber(0x0028,0x0006);
if ( strSize == GDCM_UNFOUND )
{
return 0;
}
-
return atoi( strSize.c_str() );
}
/**
- * \ingroup gdcmHeader
* \brief Return the size (in bytes) of a single pixel of data.
* @return The size in bytes of a single pixel of data; 0 by default
- * 0 means the file is NOT USABLE; the caller will have to check
+ * 0 means the file is NOT USABLE; the caller will have to check
*/
-int gdcmHeader::GetPixelSize()
+int Header::GetPixelSize()
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
+ // if (Header::GetEntryByNumber(0x0028,0x0100) == "24")
// return 3;
std::string pixelType = GetPixelType();
{
return 8;
}
-
- dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ 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,
* 24 bit images appear as 8 bit
* @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
-std::string gdcmHeader::GetPixelType()
+std::string Header::GetPixelType()
{
std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
if ( bitsAlloc == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated");
bitsAlloc = "16";
}
bitsAlloc = "8"; // by old RGB images)
}
- std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
+ std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation"
if (sign == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
+ dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation");
bitsAlloc = "0";
}
if ( sign == "0" )
{
sign = "S";
}
-
return bitsAlloc + sign;
}
/**
- * \ingroup gdcmHeader
* \brief Recover the offset (from the beginning of the file)
* of *image* pixels (not *icone image* pixels, if any !)
* @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset()
+size_t Header::GetPixelOffset()
{
- gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
if ( pxlElement )
{
return pxlElement->GetOffset();
}
}
-// TODO : unify those two (previous one and next one)
+/// \todo TODO : unify those two (previous one and next one)
/**
- * \ingroup gdcmHeader
* \brief Recover the pixel area length (in Bytes)
* @return 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()
+size_t Header::GetPixelAreaLength()
{
- gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
if ( pxlElement )
{
return pxlElement->GetLength();
}
/**
- * \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
* Please warn me if you know sbdy that *does* know ... jprx
* @return true if LUT Descriptors and LUT Tables were found
*/
-bool gdcmHeader::HasLUT()
+bool Header::HasLUT()
{
// Check the presence of the LUT Descriptors, and LUT Tables
// LutDescriptorRed
}
/**
- * \ingroup gdcmHeader
* \brief gets the info from 0028,1101 : Lookup Table Desc-Red
* else 0
* @return Lookup Table number of Bits , 0 by default
* when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
* @ return bit number of each LUT item
*/
-int gdcmHeader::GetLUTNbits()
+int Header::GetLUTNbits()
{
std::vector<std::string> tokens;
int lutNbits;
- //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ //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 )
}
tokens.clear(); // clean any previous value
- Tokenize ( lutDescription, tokens, "\\" );
+ Util::Tokenize ( lutDescription, tokens, "\\" );
//LutLength=atoi(tokens[0].c_str());
//LutDepth=atoi(tokens[1].c_str());
}
/**
- * \ingroup gdcmHeader
- * \brief builts Red/Green/Blue/Alpha LUT from Header
- * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- * and (0028,1101),(0028,1102),(0028,1102)
- * - xxx Palette Color Lookup Table Descriptor - are found
- * and (0028,1201),(0028,1202),(0028,1202)
- * - xxx Palette Color Lookup Table Data - are found
- * \warning does NOT deal with :
- * 0028 1100 Gray Lookup Table Descriptor (Retired)
- * 0028 1221 Segmented Red Palette Color Lookup Table Data
- * 0028 1222 Segmented Green Palette Color Lookup Table Data
- * 0028 1223 Segmented Blue Palette Color Lookup Table Data
- * no known Dicom reader deals with them :-(
- * @return a RGBA Lookup Table
- */
-uint8_t* gdcmHeader::GetLUTRGBA()
-{
- // Not so easy : see
- // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
-
-// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
- if ( GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR " )
- {
- return NULL;
- }
-
- int lengthR, debR, nbitsR;
- int lengthG, debG, nbitsG;
- int lengthB, debB, nbitsB;
-
- // Get info from Lut Descriptors
- // (the 3 LUT descriptors may be different)
- std::string lutDescriptionR = GetEntryByNumber(0x0028,0x1101);
- if ( lutDescriptionR == GDCM_UNFOUND )
- {
- return NULL;
- }
-
- std::string lutDescriptionG = GetEntryByNumber(0x0028,0x1102);
- if ( lutDescriptionG == GDCM_UNFOUND )
- {
- return NULL;
- }
-
- std::string lutDescriptionB = GetEntryByNumber(0x0028,0x1103);
- if ( lutDescriptionB == GDCM_UNFOUND )
- {
- return NULL;
- }
-
- // lengthR: Red LUT length in Bytes
- // debR: subscript of the first Lut Value
- // nbitsR: Lut item size (in Bits)
- int nbRead = sscanf( lutDescriptionR.c_str(), "%d\\%d\\%d",
- &lengthR, &debR, &nbitsR );
- if( nbRead != 3 )
- {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading red LUT");
- }
-
- // lengthG: Green LUT length in Bytes
- // debG: subscript of the first Lut Value
- // nbitsG: Lut item size (in Bits)
- nbRead = sscanf( lutDescriptionG.c_str(), "%d\\%d\\%d",
- &lengthG, &debG, &nbitsG );
- if( nbRead != 3 )
- {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading green LUT");
- }
-
- // lengthB: Blue LUT length in Bytes
- // debB: subscript of the first Lut Value
- // nbitsB: Lut item size (in Bits)
- nbRead = sscanf( lutDescriptionB.c_str(), "%d\\%d\\%d",
- &lengthB, &debB, &nbitsB );
- if( nbRead != 3 )
- {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT");
- }
-
- // Load LUTs into memory, (as they were stored on disk)
- uint8_t* lutR = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1201);
- uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202);
- uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203);
-
- if ( !lutR || !lutG || !lutB )
- {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT");
- return NULL;
- }
- // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
-
- uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha)
- if ( !LUTRGBA )
- {
- return NULL;
- }
- memset(LUTRGBA, 0, 1024);
-
- // Bits Allocated
- int nb;
- std::string str_nb = GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
- {
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- }
- int mult;
-
- if ( nbitsR == 16 && nb == 8)
- {
- // when LUT item size is different than pixel size
- mult = 2; // high byte must be = low byte
- }
- else
- {
- // See PS 3.3-2003 C.11.1.1.2 p 619
- mult = 1;
- }
-
- // if we get a black image, let's just remove the '+1'
- // from 'i*mult+1' and check again
- // if it works, we shall have to check the 3 Palettes
- // to see which byte is ==0 (first one, or second one)
- // and fix the code
- // We give up the checking to avoid some (useless ?)overhead
- // (optimistic asumption)
- uint8_t* a;
- int i;
-
- 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;
- }
-
- return LUTRGBA;
-}
-
-/**
- * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS
* else 1.
* @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
*/
-std::string gdcmHeader::GetTransfertSyntaxName()
+std::string Header::GetTransfertSyntaxName()
{
- // use the gdcmTS (TS : Transfert Syntax)
+ // use the TS (TS : Transfert Syntax)
std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010);
+ if ( transfertSyntax == GDCM_NOTLOADED )
+ {
+ std::cout << "Transfert Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE"
+ << std::endl;
+ return "Uncompressed ACR-NEMA";
+ }
if ( transfertSyntax == GDCM_UNFOUND )
{
- dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:"
+ dbg.Verbose(0, "Header::GetTransfertSyntaxName:"
" unfound Transfert Syntax (0002,0010)");
return "Uncompressed ACR-NEMA";
}
transfertSyntax.erase(transfertSyntax.length()-1, 1);
}
// we do it only when we need it
- gdcmTS* ts = gdcmGlobal::GetTS();
+ TS* ts = Global::GetTS();
std::string tsName = ts->GetValue( transfertSyntax );
//delete ts; /// \todo Seg Fault when deleted ?!
* @param ImageDataSize new Pixel Area Size
* warning : nothing else is checked
*/
-void gdcmHeader::SetImageDataSize(size_t ImageDataSize)
+void Header::SetImageDataSize(size_t ImageDataSize)
{
- std::string content1;
- char car[20];
-
- sprintf(car,"%d",ImageDataSize);
+ ///FIXME I don't understand this code wh ydo we set two times 'car' ?
+ std::string car = Util::Format("%d", ImageDataSize);
- gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
+ DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
a->SetLength(ImageDataSize);
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetEntryByNumber(content1, GrPixel, NumPixel);
+ ImageDataSize += 8;
+ car = Util::Format("%d", ImageDataSize);
+
+ SetEntryByNumber(car, GrPixel, NumPixel);
}
//-----------------------------------------------------------------------------
* \brief anonymize a Header (removes Patient's personal info)
* (read the code to see which ones ...)
*/
-bool gdcmHeader::AnonymizeHeader()
+bool Header::AnonymizeHeader()
{
- gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
+ // If exist, replace by spaces
+ SetEntryByNumber (" ",0x0010, 0x2154); // Telephone
+ SetEntryByNumber (" ",0x0010, 0x1040); // Adress
+ SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID
- ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
- ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
- ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
+ DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
- if ( patientNameHE )
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not)
{
std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
if ( studyInstanceUID != GDCM_UNFOUND )
* @param iop adress of the (6)float aray to receive values
* @return cosines of image orientation patient
*/
-void gdcmHeader::GetImageOrientationPatient( float* iop )
+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;
+ 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 ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND )
{
if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
- return ; // bug in the element 0x0020,0x0037
- }
- else
- {
- return ;
+ dbg.Verbose(0, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0037)");
}
}
-
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
- strImOriPat = GetEntryByNumber(0x0020,0x0035);
- if ( strImOriPat != GDCM_UNFOUND )
+ else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND )
{
if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
- return ; // bug in the element 0x0020,0x0035
+ dbg.Verbose(0, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0035)");
}
}
- else
- {
- return;
- }
}
//-----------------------------------------------------------------------------
// Private
//-----------------------------------------------------------------------------
+
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff