Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/01/24 16:10:52 $
- Version: $Revision: 1.198 $
+ Date: $Date: 2005/02/06 14:39:35 $
+ Version: $Revision: 1.213 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
+//
+// -------------- 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
+//
+// ---------------------------------------------------------------
+//
#include "gdcmFile.h"
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmTS.h"
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
-#include <stdio.h> //sscanf
+#include "gdcmSeqEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+#include <stdio.h> //sscanf
#include <vector>
namespace gdcm
* \brief Constructor
* @param filename name of the file whose header we want to analyze
*/
-File::File( std::string const &filename ):
- Document( filename )
+File::File( std::string const &filename )
+ :Document( filename )
{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
// (Image Location") . This entry contains the number of
GrPixel = (uint16_t) atoi( imgLocation.c_str() );
}
- // sometimes Image Location value doesn't follow
- // the supposed processor endianness.
- // see gdcmData/cr172241.dcm
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianness.
+ // see gdcmData/cr172241.dcm
if ( GrPixel == 0xe07f )
{
GrPixel = 0x7fe0;
DocEntry *entry = GetDocEntry(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");
-
- // friend class hunting : should we *create* a new entry,
- // instead of modifying its DictEntry,in order not to use 'friend' ?
- entry->SetDictEntry( newEntry );
+ // Compute the RLE or JPEG info
+ OpenFile();
+ std::string ts = GetTransferSyntax();
+ Fp->seekg( entry->GetOffset(), std::ios::beg );
+ if ( Global::GetTS()->IsRLELossless(ts) )
+ ComputeRLEInfo();
+ else if ( Global::GetTS()->IsJPEG(ts) )
+ ComputeJPEGFragmentInfo();
+ CloseFile();
+
+ // Create a new BinEntry to change the the DictEntry
+ // The changed DictEntry will have
+ // - a correct PixelVR OB or OW)
+ // - a VM to "PXL"
+ // - the name to "Pixel Data"
+ BinEntry *oldEntry = dynamic_cast<BinEntry *>(entry);
+ if(oldEntry)
+ {
+ 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";
+
+ // Change only made if usefull
+ if( PixelVR != oldEntry->GetVR() )
+ {
+ DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
+ PixelVR,"1","Pixel Data");
+
+ BinEntry *newEntry = new BinEntry(newDict);
+ newEntry->Copy(entry);
+ newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
+ oldEntry->SetSelfArea(false);
+
+ RemoveEntry(oldEntry);
+ AddEntry(newEntry);
+ }
+ }
}
}
/**
* \brief Constructor used when we want to generate dicom files from scratch
*/
-File::File()
- :Document()
+File::File():
+ Document()
{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
InitializeDefaultFile();
}
*/
File::~File ()
{
+ if( RLEInfo )
+ delete RLEInfo;
+ if( JPEGInfo )
+ delete JPEGInfo;
}
-/**
- * \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, ExplicitVR, ImplicitVR)
- */
-bool File::Write(std::string fileName, FileType filetype)
-{
- std::ofstream *fp = new std::ofstream(fileName.c_str(),
- std::ios::out | std::ios::binary);
- if (*fp == NULL)
- {
- gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
- return false;
- }
-
- // Bits Allocated
- if ( GetEntryValue(0x0028,0x0100) == "12")
- {
- SetEntryValue("16", 0x0028,0x0100);
- }
-
- /// \todo correct 'Pixel group' Length if necessary
-
- int i_lgPix = GetEntryLength(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() );
- ReplaceOrCreate(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 ( GetEntryValue(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 = GetDocEntry(0x0028,0x01101);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1102);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1103);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x01201);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1202);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1203);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- }
-
-/*
-#ifdef GDCM_WORDS_BIGENDIAN
- // Super Super hack that will make gdcm a BOMB ! but should
- // Fix temporarily the dashboard
- BinEntry *b = GetBinEntry(GrPixel,NumPixel);
- if ( GetPixelSize() == 16 )
- {
- uint16_t *im16 = (uint16_t*)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- }
-#endif //GDCM_WORDS_BIGENDIAN
-*/
-
- Document::WriteContent(fp,filetype);
-
-/*
-#ifdef GDCM_WORDS_BIGENDIAN
- // Flip back the pixel ... I told you this is a hack
- if ( GetPixelSize() == 16 )
- {
- uint16_t *im16 = (uint16_t*)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- }
-#endif //GDCM_WORDS_BIGENDIAN
-*/
-
- fp->close();
- delete fp;
-
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Print
-
-
//-----------------------------------------------------------------------------
// Public
-
/**
* \brief This predicate, based on hopefully reasonable heuristics,
* decides whether or not the current File was properly parsed
return true;
}
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int File::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 = GetEntryValue(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
+ {
+ return atoi( strImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType File::GetModality()
+{
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntryValue(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 <> unknown in our database
+ return Unknow;
+ }
+ }
+
+ return Unknow;
+}
+
/**
* \brief Retrieve the number of columns of image.
* @return The encountered size when found, 0 by default.
if ( strSpacing == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
return 1.;
}
if ( xspacing == 0.)
{
- gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
+ gdcmWarningMacro("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);
gdcmAssertMacro( nbValues == 2 );
if ( strSpacing == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
+ gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
return 1.;
}
if ( strSpacingBSlices == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
if ( strSliceThickness == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)");
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
return 1.;
}
else
}
/**
- *\brief gets the info from 0028,1052 : Rescale Intercept
- * @return Rescale Intercept
+ * \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 File::GetRescaleIntercept()
+float File::GetXOrigin()
{
- float resInter = 0.;
- /// 0028 1052 DS IMG Rescale Intercept
- const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
- if ( strRescInter != GDCM_UNFOUND )
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND )
{
- if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
{
- // bug in the element 0x0028,0x1052
- gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.;
}
}
- return resInter;
-}
-
-/**
- *\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope
- */
-float File::GetRescaleSlope()
-{
- float resSlope = 1.;
- //0028 1053 DS IMG Rescale Slope
- std::string strRescSlope = GetEntryValue(0x0028,0x1053);
- if ( strRescSlope != GDCM_UNFOUND )
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
{
- if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
- {
- // bug in the element 0x0028,0x1053
- gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
- }
+ return 0.;
}
- return resSlope;
-}
-
-/**
- * \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 File::GetNumberOfScalarComponents()
-{
- if ( GetSamplesPerPixel() == 3 )
- {
- return 3;
- }
-
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if ( GetEntryValue(0x0028,0x0100) == "24" )
- {
- return 3;
- }
-
- std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
-
- if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
- {
- if ( HasLUT() )// PALETTE COLOR is NOT enough
- {
- return 3;
- }
- else
- {
- return 1;
- }
- }
-
- // beware of trailing space at end of string
- // DICOM tags are never of odd length
- if ( strPhotometricInterpretation == GDCM_UNFOUND ||
- Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
- Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
- {
- return 1;
- }
- else
- {
- // we assume that *all* kinds of YBR are dealt with
- return 3;
- }
-}
-
-/**
- * \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 File::GetNumberOfScalarComponentsRaw()
-{
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if ( File::GetEntryValue(0x0028,0x0100) == "24" )
- {
- return 3;
- }
-
- // we assume that *all* kinds of YBR are dealt with
- return GetSamplesPerPixel();
-}
-
-//
-// -------------- Remember ! ----------------------------------
-//
-// Image Position Patient (0020,0032):
-// If not found (ACR_NEMA) we try Image Position (0020,0030)
-// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
-// or Location (0020,0050)
-// as the Z coordinate,
-// 0. for all the coordinates if nothing is found
-
-// \todo find a way to inform the caller nothing was found
-// \todo How to tell the caller a wrong number of values was found?
-//
-// ---------------------------------------------------------------
-//
-
-/**
- * \brief gets the info from 0020,0032 : Image Position Patient
- * else from 0020,0030 : Image Position (RET)
- * else 0.
- * @return up-left image corner X position
- */
-float File::GetXOrigin()
-{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "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;
+ return xImPos;
}
/**
if ( strImPos == GDCM_UNFOUND)
{
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
- /// \todo How to tell the caller nothing was found ?
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
return 0.;
}
}
{
if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
{
- gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
+ gdcmWarningMacro( "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 )
{
- gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
+ gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
return 0.; // bug in the element 0x0020,0x0032
}
else
{
if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
{
- gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
return 0.; // bug in the element 0x0020,0x1041
}
else
return zImPos;
}
}
- gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
+ gdcmWarningMacro( "Unfound Slice Location (0020,1041)");
std::string strLocation = GetEntryValue(0x0020,0x0050);
if ( strLocation != GDCM_UNFOUND )
{
if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
{
- gdcmVerboseMacro( "Wrong Location (0020,0050)");
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
return 0.; // bug in the element 0x0020,0x0050
}
else
return zImPos;
}
}
- gdcmVerboseMacro( "Unfound Location (0020,0050)");
+ gdcmWarningMacro( "Unfound Location (0020,0050)");
return 0.; // Hopeless
}
/**
- * \brief gets the info from 0020,0013 : Image Number else 0.
- * @return image number
- */
-int File::GetImageNumber()
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * (needed to organize DICOM files based on their x,y,z position)
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void File::GetImageOrientationPatient( float iop[6] )
{
- // 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 = GetEntryValue(0x0020,0x0013);
- if ( strImNumber != GDCM_UNFOUND )
+ 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 = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
{
- return atoi( strImNumber.c_str() );
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ }
}
- return 0; //Hopeless
-}
-
-/**
- * \brief gets the info from 0008,0060 : Modality
- * @return Modality Type
- */
-ModalityType File::GetModality()
-{
- // 0008 0060 CS ID Modality
- std::string strModality = GetEntryValue(0x0008,0x0060);
- if ( strModality != GDCM_UNFOUND )
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != 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
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- /// \todo throw error return value ???
- /// specified <> unknown in our database
- return Unknow;
+ gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
}
}
-
- return Unknow;
}
/**
* \brief Retrieve the number of Bits Stored (actually used)
- * (as opposite to number of Bits Allocated)
+ * (as opposed 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 !
*/
std::string strSize = GetEntryValue( 0x0028, 0x0101 );
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro("(0028,0101) is supposed to be mandatory");
+ gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
return 0; // It's supposed to be mandatory
// the caller will have to check
}
}
/**
- * \brief Retrieve the high bit position.
- * \warning The method defaults to 0 when information is Missing.
- * The responsability of checking this value is left to the caller.
- * @return The high bit positin when present. 0 when Missing.
+ * \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 File::GetHighBitPosition()
+int File::GetBitsAllocated()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0102 );
+ std::string strSize = GetEntryValue(0x0028,0x0100);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
- return 0;
+ gdcmWarningMacro( "(0028,0100) 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 Check whether the pixels are signed or UNsigned data.
- * \warning The method defaults to false (UNsigned) when information is Missing.
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is Missing.
* The responsability of checking this value is left to the caller.
- * @return True when signed, false when UNsigned
- */
-bool File::IsSignedPixelData()
-{
- std::string strSize = GetEntryValue( 0x0028, 0x0103 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "(0028,0103) 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 !
+ * @return The high bit positin when present. 0 when Missing.
*/
-int File::GetBitsAllocated()
+int File::GetHighBitPosition()
{
- std::string strSize = GetEntryValue(0x0028,0x0100);
+ std::string strSize = GetEntryValue( 0x0028, 0x0102 );
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
+ gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
+ return 0;
}
return atoi( strSize.c_str() );
}
*/
int File::GetSamplesPerPixel()
{
- const std::string& strSize = GetEntryValue(0x0028,0x0002);
+ const std::string &strSize = GetEntryValue(0x0028,0x0002);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory");
+ gdcmWarningMacro( "(0028,0002) 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() );
}
-/**
- * \brief Check whether this a monochrome picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
- */
-bool File::IsMonochrome()
-{
- const std::string& PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
- if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
- || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)");
- }
- return false;
-}
-
-/**
- * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "PALETTE COLOR". False otherwise.
- */
-bool File::IsPaletteColor()
-{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
- if ( PhotometricInterp == "PALETTE COLOR " )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : Palette color (0028,0004)");
- }
- return false;
-}
-
-/**
- * \brief Check whether this a "YBR_FULL" color picture or not by accessing
- * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
- * @return true when "YBR_FULL". False otherwise.
- */
-bool File::IsYBRFull()
-{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
- if ( PhotometricInterp == "YBR_FULL" )
- {
- return true;
- }
- if ( PhotometricInterp == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
- }
- return false;
-}
-
/**
* \brief Retrieve the Planar Configuration for RGB images
* (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
std::string strSize = GetEntryValue(0x0028,0x0006);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
+ gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
return atoi( strSize.c_str() );
{
return 8;
}
- gdcmVerboseMacro( "Unknown pixel type");
+ gdcmWarningMacro( "Unknown pixel type");
return 0;
}
std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
if ( bitsAlloc == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)");
+ gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
bitsAlloc = "16"; // default and arbitrary value, not to polute the output
}
if (sign == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)");
+ gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
sign = "U"; // default and arbitrary value, not to polute the output
}
else if ( sign == "0" )
return bitsAlloc + sign;
}
+/**
+ * \brief Check whether the pixels are signed or UNsigned data.
+ * \warning The method defaults to false (UNsigned) when information is Missing.
+ * The responsability of checking this value is left to the caller.
+ * @return True when signed, false when UNsigned
+ */
+bool File::IsSignedPixelData()
+{
+ std::string strSize = GetEntryValue( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
+ return false;
+ }
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
+ {
+ return false;
+ }
+ return true;
+}
/**
- * \brief Recover the offset (from the beginning of the file)
- * of *image* pixels (not *icone image* pixels, if any !)
- * @return Pixel Offset
+ * \brief Check whether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
*/
-size_t File::GetPixelOffset()
+bool File::IsMonochrome()
{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
+ const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
- return pxlElement->GetOffset();
+ return true;
}
- else
+ if ( PhotometricInterp == GDCM_UNFOUND )
{
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
- return 0;
+ gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
}
+ return false;
}
-/// \todo TODO : unify those two (previous one and next one)
/**
- * \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.
+ * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
*/
-size_t File::GetPixelAreaLength()
+bool File::IsPaletteColor()
{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
{
- return pxlElement->GetLength();
+ return true;
}
- else
+ if ( PhotometricInterp == GDCM_UNFOUND )
{
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
- return 0;
+ gdcmWarningMacro( "Not found : Palette color (0028,0004)");
}
+ return false;
+}
+
+/**
+ * \brief Check whether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool File::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
}
/**
return lutNbits;
}
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float File::GetRescaleIntercept()
+{
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
+ if ( strRescInter != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ {
+ // bug in the element 0x0028,0x1052
+ gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
+ }
+ }
-//-----------------------------------------------------------------------------
-// Protected
+ return resInter;
+}
/**
- * \brief anonymize a File (removes Patient's personal info)
- * (read the code to see which ones ...)
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-bool File::AnonymizeFile()
+float File::GetRescaleSlope()
{
- // If exist, replace by spaces
- SetEntryValue (" ",0x0010, 0x2154); // Telephone
- SetEntryValue (" ",0x0010, 0x1040); // Adress
- SetEntryValue (" ",0x0010, 0x0020); // Patient ID
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryValue(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ {
+ // bug in the element 0x0028,0x1053
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
+ }
+ }
- DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
-
- if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ return resSlope;
+}
+
+/**
+ * \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 File::GetNumberOfScalarComponents()
+{
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
+ }
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryValue(0x0028,0x0100) == "24" )
{
- std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
- if ( studyInstanceUID != GDCM_UNFOUND )
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
{
- ReplaceOrCreate(studyInstanceUID, 0x0010, 0x0010);
+ return 3;
}
else
{
- ReplaceOrCreate("anonymised", 0x0010, 0x0010);
+ return 1;
}
}
- // Just for fun :-(
- // (if any) remove or replace all the stuff that contains a Date
+ // 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;
+ }
+}
+
+/**
+ * \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 File::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryValue(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
+
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t File::GetPixelOffset()
+{
+ DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
+ }
+ else
+ {
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \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 File::GetPixelAreaLength()
+{
+ DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+
+/**
+ * \brief Adds the characteristics of a new element we want to anonymize
+ *
+ */
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
+
+{
+ Element el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ AnonymizeList.push_back(el);
+}
+
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
+{
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ // TODO : FIXME
+ // how to white out disk space if longer than 50 ?
+ char spaces[50] = " ";
+
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t lgtToWrite;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
+
+ offset = d->GetOffset();
+ lgth = d->GetLength();
+ fp->seekp( offset, std::ios::beg );
+
+ if ( (*it).Value == "" )
+ {
+ lgtToWrite = lgth > 50 ? 50 : lgth;
+ fp->write( spaces, lgtToWrite );
+ }
+ else
+ {
+ // TODO : FIXME
+ // how to white out disk space if longer than 50 ?
+ (*it).Value = (*it).Value + spaces;
+ lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth;
+ fp->write( (char *)(*it).Value.c_str(), lgtToWrite );
+
+ }
+ fp->close();
+ delete fp;
+ }
+}
+
+/**
+ * \brief anonymize a File (removes Patient's personal info passed with
+ * AddAnonymizeElement()
+ */
+bool File::AnonymizeFile()
+{
+ // If Anonymisation list is empty, let's perform some basic anonymisation
+ if ( AnonymizeList.begin() == AnonymizeList.end() )
+ {
+ // If exist, replace by spaces
+ SetValEntry (" ",0x0010, 0x2154); // Telephone
+ SetValEntry (" ",0x0010, 0x1040); // Adress
+ SetValEntry (" ",0x0010, 0x0020); // Patient ID
+
+ DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
+ {
+ std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ SetValEntry(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ SetValEntry("anonymised", 0x0010, 0x0010);
+ }
+ }
+ }
+ else
+ {
+ gdcm::DocEntry *d;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
+
+ SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
+ }
+}
+
+ // In order to make definitively impossible any further identification
+ // remove or replace all the stuff that contains a Date
//0008 0012 DA ID Instance Creation Date
//0008 0020 DA ID Study Date
}
/**
- * \brief gets the info from 0020,0037 : Image Orientation Patient
- * (needed to organize DICOM files based on their x,y,z position)
- * @param iop adress of the (6)float aray to receive values
- * @return cosines of image orientation patient
- */
-void File::GetImageOrientationPatient( float iop[6] )
+ * \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, ExplicitVR, ImplicitVR)
+ */
+bool File::Write(std::string fileName, FileType filetype)
{
- std::string strImOriPat;
- //iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
+ {
+ gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
+ return false;
+ }
- // 0020 0037 DS REL Image Orientation (Patient)
- if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
+ // Entry : 0002|0000 = group length -> recalculated
+ ValEntry *e0002 = GetValEntry(0x0002,0x0000);
+ if( e0002 )
{
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ std::ostringstream sLen;
+ sLen << ComputeGroup0002Length(filetype);
+ e0002->SetValue(sLen.str());
+ }
+
+ // Bits Allocated
+ if ( GetEntryValue(0x0028,0x0100) == "12")
+ {
+ SetValEntry("16", 0x0028,0x0100);
+ }
+
+ int i_lgPix = GetEntryLength(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() );
+ InsertValEntry(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 ( GetEntryValue(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 = GetDocEntry(0x0028,0x01101);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1202);
+ if (e)
{
- gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
}
}
- //For ACR-NEMA
- // 0020 0035 DS REL Image Orientation (RET)
- else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
+
+
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Super Super hack that will make gdcm a BOMB ! but should
+ // Fix temporarily the dashboard
+ BinEntry *b = GetBinEntry(GrPixel,NumPixel);
+ if ( GetPixelSize() == 16 )
{
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ uint16_t *im16 = (uint16_t *)b->GetBinArea();
+ int lgth = b->GetLength();
+ for( int i = 0; i < lgth / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ }
+#endif //GDCM_WORDS_BIGENDIAN
+
+
+ Document::WriteContent(fp, filetype);
+
+
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Flip back the pixel ... I told you this is a hack
+ if ( GetPixelSize() == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)b->GetBinArea();
+ int lgth = b->GetLength();
+ for( int i = 0; i < lgth / 2; i++ )
{
- gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
}
+#endif //GDCM_WORDS_BIGENDIAN
+
+
+ fp->close();
+ delete fp;
+
+ return true;
}
+//-----------------------------------------------------------------------------
+// Protected
/**
* \brief Initialize a default DICOM File that should contain all the
* field require by other reader. DICOM standard does not
*/
void File::InitializeDefaultFile()
{
- 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
- { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian)
- { 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 }
- };
+ std::string uidInst = uid;
+ std::string uidClass = Util::CreateUniqueUID();
+ std::string uidStudy = Util::CreateUniqueUID();
+ std::string uidSerie = Util::CreateUniqueUID();
+
+ // Meta Element Group Length
+ InsertValEntry("146 ", 0x0002, 0x0000);
+ // Media Storage SOP Class UID (CT Image Storage)
+ InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002);
+ // Media Storage SOP Instance UID
+ InsertValEntry(uidClass.c_str(), 0x0002, 0x0003);
+ // Transfer Syntax UID (Explicit VR Little Endian)
+ InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010);
+ // META Implementation Class UID
+ InsertValEntry(uidClass.c_str(), 0x0002, 0x0012);
+ // Source Application Entity Title
+ InsertValEntry("GDCM", 0x0002, 0x0016);
+
+ // Instance Creation Date
+ InsertValEntry(date.c_str(), 0x0008, 0x0012);
+ // Instance Creation Time
+ InsertValEntry(time.c_str(), 0x0008, 0x0013);
+ // SOP Class UID
+ InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016);
+ // SOP Instance UID
+ InsertValEntry(uidInst.c_str(), 0x0008, 0x0018);
+ // Modality
+ InsertValEntry("CT", 0x0008, 0x0060);
+ // Manufacturer
+ InsertValEntry("GDCM", 0x0008, 0x0070);
+ // Institution Name
+ InsertValEntry("GDCM", 0x0008, 0x0080);
+ // Institution Address
+ InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081);
+
+ // Patient's Name
+ InsertValEntry("GDCM", 0x0010, 0x0010);
+ // Patient ID
+ InsertValEntry("GDCMID", 0x0010, 0x0020);
+
+ // Study Instance UID
+ InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d);
+ // Series Instance UID
+ InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e);
+ // StudyID
+ InsertValEntry("1", 0x0020, 0x0010);
+ // SeriesNumber
+ InsertValEntry("1", 0x0020, 0x0011);
+
+ // Samples per pixel 1 or 3
+ InsertValEntry("1", 0x0028, 0x0002);
+ // photochromatic interpretation
+ InsertValEntry("MONOCHROME1", 0x0028, 0x0004);
+ // nbRows
+ InsertValEntry("0", 0x0028, 0x0010);
+ // nbCols
+ InsertValEntry("0", 0x0028, 0x0011);
+ // BitsAllocated 8 or 12 or 16
+ InsertValEntry("8", 0x0028, 0x0100);
+ // BitsStored <= BitsAllocated
+ InsertValEntry("8", 0x0028, 0x0101);
+ // HighBit <= BitsAllocated - 1
+ InsertValEntry("7", 0x0028, 0x0102);
+ // Pixel Representation 0(unsigned) or 1(signed)
+ InsertValEntry("0", 0x0028, 0x0103);
// default value
// Special case this is the image (not a string)
GrPixel = 0x7fe0;
NumPixel = 0x0010;
- ReplaceOrCreate(0, 0, GrPixel, NumPixel);
+ InsertBinEntry(0, 0, GrPixel, NumPixel);
+}
- // All remaining strings:
- unsigned int i = 0;
- DICOM_DEFAULT_VALUE current = defaultvalue[i];
- while( current.value )
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
+ */
+void File::ComputeRLEInfo()
+{
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
+ {
+ return;
+ }
+
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a RLEFramesInfo.
+ // Note: - when only a single frame is present, this is a
+ // classical image.
+ // - when more than one frame are present, then we are in
+ // the case of a multi-frame image.
+ long frameLength;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // Parse the RLE Header and store the corresponding RLE Segment
+ // Offset Table information on fragments of this current Frame.
+ // Note that the fragment pixels themselves are not loaded
+ // (but just skipped).
+ long frameOffset = Fp->tellg();
+
+ uint32_t nbRleSegments = ReadInt32();
+ if ( nbRleSegments > 16 )
+ {
+ // There should be at most 15 segments (refer to RLEFrame class)
+ gdcmWarningMacro( "Too many segments.");
+ }
+
+ uint32_t rleSegmentOffsetTable[16];
+ for( int k = 1; k <= 15; k++ )
+ {
+ rleSegmentOffsetTable[k] = ReadInt32();
+ }
+
+ // Deduce from both the RLE Header and the frameLength the
+ // fragment length, and again store this info in a
+ // RLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ {
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
+ }
+ }
+
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+
+ // Store the collected info
+ RLEFrame *newFrame = new RLEFrame;
+ newFrame->SetNumberOfFragments(nbRleSegments);
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+ {
+ newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
+ newFrame->SetLength(uk,rleSegmentLength[uk]);
+ }
+ RLEInfo->AddFrame(newFrame);
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
+ }
+}
+
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void File::ComputeJPEGFragmentInfo()
+{
+ // If you need to, look for comments of ComputeRLEInfo().
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
{
- ReplaceOrCreate(current.value, current.group, current.elem);
- current = defaultvalue[++i];
+ return;
+ }
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = Fp->tellg();
+
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->SetOffset(fragmentOffset);
+ newFragment->SetLength(fragmentLength);
+ JPEGInfo->AddFragment(newFragment);
+
+ SkipBytes(fragmentLength);
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
+/**
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag check whether this
+ * tag is (TestGroup, TestElement).
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return True on success, false otherwise.
+ */
+bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
+{
+ long positionOnEntry = Fp->tellg();
+ long currentPosition = Fp->tellg(); // On debugging purposes
-//-----------------------------------------------------------------------------
-// Private
+ //// Read the Item Tag group and element, and make
+ // sure they are what we expected:
+ uint16_t itemTagGroup;
+ uint16_t itemTagElement;
+ try
+ {
+ itemTagGroup = ReadInt16();
+ itemTagElement = ReadInt16();
+ }
+ catch ( FormatError e )
+ {
+ //std::cerr << e << std::endl;
+ return false;
+ }
+ if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ {
+ gdcmWarningMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << " but instead we encountered tag ("
+ << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
+ ) ;
+ Fp->seekg(positionOnEntry, std::ios::beg);
+
+ return false;
+ }
+ return true;
+}
+
+/**
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag (TestGroup, TestElement),
+ * read the length associated to the Tag.
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag and it's length.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return On success returns the length associated to the tag. On failure
+ * returns 0.
+ */
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement)
+{
+
+ if ( !ReadTag(testGroup, testElement) )
+ {
+ return 0;
+ }
+
+ //// Then read the associated Item Length
+ long currentPosition = Fp->tellg();
+ uint32_t itemLength = ReadInt32();
+ {
+ gdcmWarningMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
+ }
+ return itemLength;
+}
+
+/**
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
+ */
+void File::ReadAndSkipEncapsulatedBasicOffsetTable()
+{
+ //// Read the Basic Offset Table Item Tag length...
+ uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
+
+ // When present, read the basic offset table itself.
+ // Notes: - since the presence of this basic offset table is optional
+ // we can't rely on it for the implementation, and we will simply
+ // trash it's content (when present).
+ // - still, when present, we could add some further checks on the
+ // lengths, but we won't bother with such fuses for the time being.
+ if ( itemLength != 0 )
+ {
+ char *basicOffsetTableItemValue = new char[itemLength + 1];
+ Fp->read(basicOffsetTableItemValue, itemLength);
+
+#ifdef GDCM_DEBUG
+ for (unsigned int i=0; i < itemLength; i += 4 )
+ {
+ uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
+ uint32_t);
+ gdcmWarningMacro( "Read one length: " <<
+ std::hex << individualLength );
+ }
+#endif //GDCM_DEBUG
+
+ delete[] basicOffsetTableItemValue;
+ }
+}
//-----------------------------------------------------------------------------
+// Print
+//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff