Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/02/17 11:02:47 $
- Version: $Revision: 1.225 $
+ Date: $Date: 2005/09/20 09:07:56 $
+ Version: $Revision: 1.269 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// as the Z coordinate,
// 0. for all the coordinates if nothing is found
//
+// Image Position (Patient) (0020,0032) VM=3 What is it used for?
+// -->
+// The attribute Patient Orientation (0020,0020) from the General Image Module
+// is of type 2C and has the condition Required if image does not require
+// Image Orientation (0020,0037) and Image Position (0020,0032).
+// However, if the image does require the attributes
+// - Image Orientation (Patient) (0020,0037), VM=6
+// - Image Position Patient (0020,0032), VM=3
+// then attribute Patient Orientation (0020,0020) should not be present
+// in the images.
+//
+// Remember also :
+// Patient Position (0018,5100) values :
+
+// HFS = Head First-Supine, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// HFP = Head First-Prone, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// FFS = Feet First-Supine, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterion direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// FFP = Feet First-Prone, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the posterior-to-anterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// HFDR = Head First-Decubitus Right
+// HFDL = Head First-Decubitus Left
+// FFDR = Feet First-Decubitus Right
+// FFDL = Feet First-Decubitus Left
+
+// we can also find
+
+// SEMIERECT
+// SUPINE
+
+// CS 2 Patient Orientation (0020 0020)
+// When the coordinates of the image
+// are always present, this field is almost never used.
+// Better we don't trust it too much ...
+// Found Values are :
+// L\P
+// L\FP
+// P\F
+// L\F
+// P\FR
+// R\F
+//
+// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
+
+
// ---------------------------------------------------------------
//
#include "gdcmFile.h"
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
-#include <stdio.h> //sscanf
#include <vector>
+#include <stdio.h> //sscanf
+#include <stdlib.h> // for atoi
namespace gdcm
{
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
+
/**
- * \brief Constructor
- * @param filename name of the file whose header we want to analyze
+ * \brief Constructor used when we want to generate dicom files from scratch
*/
-File::File( std::string const &filename )
- :Document( filename )
-{
+File::File():
+ Document()
+{
RLEInfo = new RLEFramesInfo;
JPEGInfo = new JPEGFragmentsInfo;
+ GrPixel = 0x7fe0; // to avoid further troubles
+ NumPixel = 0x0010;
+}
+
+
+/**
+ * \brief Canonical destructor.
+ */
+File::~File ()
+{
+ if ( RLEInfo )
+ delete RLEInfo;
+ if ( JPEGInfo )
+ delete JPEGInfo;
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Loader
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool File::Load( )
+{
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+
+/**
+ * \brief Does the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool File::DoTheLoadingJob( )
+{
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
{
// Compute the RLE or JPEG info
OpenFile();
- std::string ts = GetTransferSyntax();
+ const std::string &ts = GetTransferSyntax();
Fp->seekg( entry->GetOffset(), std::ios::beg );
if ( Global::GetTS()->IsRLELossless(ts) )
ComputeRLEInfo();
ComputeJPEGFragmentInfo();
CloseFile();
- // Create a new BinEntry to change the the DictEntry
+ // Create a new BinEntry to change the DictEntry
// The changed DictEntry will have
// - a correct PixelVR OB or OW)
// - the name to "Pixel Data"
BinEntry *oldEntry = dynamic_cast<BinEntry *>(entry);
- if(oldEntry)
+ if (oldEntry)
{
std::string PixelVR;
// 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
PixelVR = "OW";
// Change only made if usefull
- if( PixelVR != oldEntry->GetVR() )
+ if ( PixelVR != oldEntry->GetVR() )
{
DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
PixelVR,"1","Pixel Data");
}
}
}
+ return true;
}
-
-/**
- * \brief Constructor used when we want to generate dicom files from scratch
- */
-File::File():
- Document()
-{
- RLEInfo = new RLEFramesInfo;
- JPEGInfo = new JPEGFragmentsInfo;
- InitializeDefaultFile();
-}
-
-/**
- * \brief Canonical destructor.
- */
-File::~File ()
-{
- if( RLEInfo )
- delete RLEInfo;
- if( JPEGInfo )
- delete JPEGInfo;
-}
-
-//-----------------------------------------------------------------------------
-// Public
/**
* \brief This predicate, based on hopefully reasonable heuristics,
* decides whether or not the current File was properly parsed
*/
bool File::IsReadable()
{
- if( !Document::IsReadable() )
+ if ( !Document::IsReadable() )
{
return false;
}
const std::string &res = GetEntryValue(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
+ gdcmWarningMacro("Wrong Image Dimensions" << res);
return false; // Image Dimensions
}
+ bool b0028_0100 = true;
if ( !GetDocEntry(0x0028, 0x0100) )
{
- return false; // "Bits Allocated"
+ gdcmWarningMacro("Bits Allocated (0028|0100) not found");
+ //return false; // "Bits Allocated"
+ b0028_0100 = false;
}
+ bool b0028_0101 = true;
if ( !GetDocEntry(0x0028, 0x0101) )
{
- return false; // "Bits Stored"
+ gdcmWarningMacro("Bits Stored (0028|0101) not found");
+ //return false; // "Bits Stored"
+ b0028_0101 = false;
}
+ bool b0028_0102 = true;
if ( !GetDocEntry(0x0028, 0x0102) )
{
- return false; // "High Bit"
+ gdcmWarningMacro("Hight Bit (0028|0102) not found");
+ //return false; // "High Bit"
+ b0028_0102 = false;
}
+ bool b0028_0103 = true;
if ( !GetDocEntry(0x0028, 0x0103) )
{
- return false; // "Pixel Representation" i.e. 'Sign'
+ gdcmWarningMacro("Pixel Representation (0028|0103) not found");
+ //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
+ b0028_0103 = false;
+ }
+
+ if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
+ {
+ gdcmWarningMacro("Too much mandatory Tags missing !");
+ return false;
}
+ if ( !GetDocEntry(GrPixel, NumPixel) )
+ {
+ gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
+ GrPixel << "|" << NumPixel << "not found");
+ return false; // Pixel Dicom Element not found :-(
+ }
return true;
}
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;
+ 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 ( 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
{
return Unknow;
}
}
-
return Unknow;
}
{
return 0;
}
-
return atoi( strSize.c_str() );
}
return 0;
}
- // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
- // hence be a signal (1D image). So we default to 1:
+ // The Rows (0028,0010) entry was optional for ACR/NEMA.
+ // (at least some images didn't have it.)
+ // It might hence be a signal (1D image). So we default to 1:
return 1;
}
* \brief Retrieve the number of planes of volume or the number
* of frames of a multiframe.
* \warning When present we consider the "Number of Frames" as the third
- * dimension. When Missing we consider the third dimension as
+ * dimension. When missing we consider the third dimension as
* being the ACR-NEMA "Planes" tag content.
* @return The encountered size when found, 1 by default (single image).
*/
{
return atoi( strSize2.c_str() );
}
-
return 1;
}
/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
+ * \brief gets the info from 0018,1164 : ImagerPixelSpacing
+ * then 0028,0030 : Pixel Spacing
* else 1.0
* @return X dimension of a pixel
*/
{
float xspacing = 1.0;
float yspacing = 1.0;
+ int nbValues;
+
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
+ if ( strImagerPixelSpacing != GDCM_UNFOUND )
+ {
+ if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
+ {
+ // if no values, xspacing is set to 1.0
+ if ( nbValues == 0 )
+ xspacing = 1.0;
+ // if single value is found, xspacing is defaulted to yspacing
+ if ( nbValues == 1 )
+ xspacing = yspacing;
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+ }
+ }
+
const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
- if( strSpacing == GDCM_UNFOUND )
+ if ( strSpacing == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
return 1.;
}
- int nbValues;
- if( ( nbValues = sscanf( strSpacing.c_str(),
- "%f\\%f", &yspacing, &xspacing)) != 2 )
+ if ( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f \\%f ", &yspacing, &xspacing)) != 2 )
{
// if no values, xspacing is set to 1.0
- if( nbValues == 0 )
+ if ( nbValues == 0 )
xspacing = 1.0;
// if single value is found, xspacing is defaulted to yspacing
- if( nbValues == 1 )
+ if ( nbValues == 1 )
xspacing = yspacing;
if ( xspacing == 0.0 )
xspacing = 1.0;
return xspacing;
-
}
- // to avoid troubles with David Clunie's-like images
+ // to avoid troubles with David Clunie's-like images (at least one)
if ( xspacing == 0. && yspacing == 0.)
return 1.;
{
gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem");
// seems to be a bug in the header ...
- nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing);
gdcmAssertMacro( nbValues == 2 );
}
}
/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
+ * \brief gets the info from 0018,1164 : ImagerPixelSpacing
+ * then from 0028,0030 : Pixel Spacing
* else 1.0
* @return Y dimension of a pixel
*/
float File::GetYSpacing()
{
float yspacing = 1.;
- std::string strSpacing = GetEntryValue(0x0028,0x0030);
-
+ int nbValues;
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
+ if ( strImagerPixelSpacing != GDCM_UNFOUND )
+ {
+ nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing);
+
+ // if sscanf cannot read any float value, it won't affect yspacing
+ if ( nbValues == 0 )
+ yspacing = 1.0;
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+ }
+
+ std::string strSpacing = GetEntryValue(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
}
// if sscanf cannot read any float value, it won't affect yspacing
- int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
+ nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
- // if no values, xspacing is set to 1.0
- if( nbValues == 0 )
+ // if no values, yspacing is set to 1.0
+ if ( nbValues == 0 )
yspacing = 1.0;
if ( yspacing == 0.0 )
// overlapping (Spacing between Slices < Slice Thickness)
// disjointes (Spacing between Slices > Slice Thickness)
// Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
- // It only concerns the MRI guys, not people wanting to visualize volmues
- // If Spacing Between Slices is Missing,
+ // It only concerns the MRI guys, not people wanting to visualize volumes
+ // If Spacing Between Slices is missing,
// we suppose slices joint together
const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
}
}
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
{
return 0.;
}
}
}
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
{
return 0.;
}
if ( strImPos != GDCM_UNFOUND )
{
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3)
{
gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
return 0.; // bug in the element 0x0020,0x0032
strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos != GDCM_UNFOUND )
{
- if( sscanf( strImPos.c_str(),
- "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ if ( sscanf( strImPos.c_str(),
+ "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 )
{
gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
return 0.; // bug in the element 0x0020,0x0032
}
}
- std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
+ // for *very* old ACR-NEMA images
+ std::string strSliceLocation = GetEntryValue(0x0020,0x1041);
if ( strSliceLocation != GDCM_UNFOUND )
{
- if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
{
gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
return 0.; // bug in the element 0x0020,0x1041
std::string strLocation = GetEntryValue(0x0020,0x0050);
if ( strLocation != GDCM_UNFOUND )
{
- if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
+ if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 )
{
gdcmWarningMacro( "Wrong Location (0020,0050)");
return 0.; // bug in the element 0x0020,0x0050
/**
* \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
+ * @param iop adress of the (6)float array to receive values
* @return cosines of image orientation patient
*/
-void File::GetImageOrientationPatient( float iop[6] )
+bool File::GetImageOrientationPatient( float iop[6] )
{
std::string strImOriPat;
//iop is supposed to be float[6]
// 0020 0037 DS REL Image Orientation (Patient)
if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
{
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ 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 false;
}
}
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
{
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ 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 (0020,0035). Less than 6 values were found." );
+ 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.
+ * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
+ * @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::GetBitsAllocated()
{
std::string strSize = GetEntryValue(0x0028,0x0100);
- if ( strSize == GDCM_UNFOUND )
+ if ( strSize == GDCM_UNFOUND )
{
gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
return 0; // It's supposed to be mandatory
/**
* \brief Retrieve the high bit position.
- * \warning The method defaults to 0 when information is Missing.
+ * \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.
+ * @return The high bit position when present. 0 when missing.
*/
int File::GetHighBitPosition()
{
/**
* \brief Retrieve the number of Samples Per Pixel
- * (1 : gray level, 3 : RGB -1 or 3 Planes-)
+ * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
* @return The encountered number of Samples Per Pixel, 1 by default.
- * (Gray level Pixels)
+ * (we assume Gray level Pixels)
*/
int File::GetSamplesPerPixel()
{
int File::GetPixelSize()
{
// 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
+ // (in order no to be messed up by old ACR-NEMA RGB images)
// if (File::GetEntryValue(0x0028,0x0100) == "24")
// return 3;
* - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
* \warning 12 bit images appear as 16 bit.
* 24 bit images appear as 8 bit + photochromatic interp ="RGB "
+ * + Planar Configuration = 0
* @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
std::string File::GetPixelType()
}
else if ( bitsAlloc == "24" )
{
- // (in order no to be messed up
- bitsAlloc = "8"; // by old RGB images)
+ // (in order no to be messed up by old RGB images)
+ bitsAlloc = "8";
}
std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation"
}
/**
- * \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.
+ * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
+ * \warning The method defaults to false (UNsigned) when tag 0028|0103
+ * is missing.
+ * The responsability of checking this value is left to the caller
+ * (NO transformation is performed on the pixels to make then >0)
* @return True when signed, false when UNsigned
*/
bool File::IsSignedPixelData()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0103 );
- if ( strSize == GDCM_UNFOUND )
+ std::string strSign = GetEntryValue( 0x0028, 0x0103 );
+ if ( strSign == GDCM_UNFOUND )
{
gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
return false;
}
- int sign = atoi( strSize.c_str() );
+ int sign = atoi( strSign.c_str() );
if ( sign == 0 )
{
return false;
const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
if ( strRescInter != GDCM_UNFOUND )
{
- if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
{
// bug in the element 0x0028,0x1052
gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
std::string strRescSlope = GetEntryValue(0x0028,0x1053);
if ( strRescSlope != GDCM_UNFOUND )
{
- if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
{
// bug in the element 0x0028,0x1053
gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
* 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)
+ * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
*/
int File::GetNumberOfScalarComponents()
{
/**
* \brief Adds the characteristics of a new element we want to anonymize
- *
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value new value (string) to substitute with
*/
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);
+ UserAnonymizeList.push_back(el);
}
/**
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 ?
-
-
+ std::ios::in | std::ios::out | std::ios::binary);
gdcm::DocEntry *d;
uint32_t offset;
uint32_t lgth;
uint32_t valLgth = 0;
std::string *spaces;
- for (ListElements::iterator it = AnonymizeList.begin();
- it != AnonymizeList.end();
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
++it)
{
d = GetDocEntry( (*it).Group, (*it).Elem);
if ( d == NULL)
continue;
- if ( dynamic_cast<BinEntry *>(d)
- || dynamic_cast<SeqEntry *>(d) )
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
continue;
+ }
offset = d->GetOffset();
lgth = d->GetLength();
}
/**
- * \brief anonymize a File (removes Patient's personal info passed with
+ * \brief anonymize a File (remove Patient's personal info passed with
* AddAnonymizeElement()
+ * \note You cannot Anonymize a BinEntry (to be fixed)
*/
bool File::AnonymizeFile()
{
// If Anonymisation list is empty, let's perform some basic anonymization
- if ( AnonymizeList.begin() == AnonymizeList.end() )
+ if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
{
// If exist, replace by spaces
SetValEntry (" ",0x0010, 0x2154); // Telephone
}
else
{
- SetValEntry("anonymised", 0x0010, 0x0010);
+ SetValEntry("anonymized", 0x0010, 0x0010);
}
}
}
else
{
gdcm::DocEntry *d;
- for (ListElements::iterator it = AnonymizeList.begin();
- it != AnonymizeList.end();
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
++it)
{
d = GetDocEntry( (*it).Group, (*it).Elem);
if ( d == NULL)
continue;
- if ( dynamic_cast<BinEntry *>(d)
- || dynamic_cast<SeqEntry *>(d) )
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
continue;
+ }
- SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
+ if ( dynamic_cast<BinEntry *>(d) )
+ {
+ gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) ");
+ continue;
+ }
+ else
+ SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
}
}
* (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 writetype Type of the File to be written
+ * @param writetype type of the file to be written
* (ACR, ExplicitVR, ImplicitVR)
*/
bool File::Write(std::string fileName, FileType writetype)
// Entry : 0002|0000 = group length -> recalculated
ValEntry*e0000 = GetValEntry(0x0002,0x0000);
- if( e0000 )
+ if ( e0000 )
{
std::ostringstream sLen;
- sLen << ComputeGroup0002Length(writetype);
+ sLen << ComputeGroup0002Length( );
e0000->SetValue(sLen.str());
}
- // Bits Allocated
- if ( GetEntryValue(0x0028,0x0100) == "12")
- {
- SetValEntry("16", 0x0028,0x0100);
- }
-
int i_lgPix = GetEntryLength(GrPixel, NumPixel);
if (i_lgPix != -2)
{
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)
- {
- RemoveEntryNoDestroy(e);
- }
- e = GetDocEntry(0x0028,0x1203);
- if (e)
- {
- RemoveEntryNoDestroy(e);
- }
- }
-
Document::WriteContent(fp, writetype);
fp->close();
//-----------------------------------------------------------------------------
// Protected
-/**
- * \brief Initialize a default DICOM File that should contain all the
- * field require by other reader. DICOM standard does not
- * explicitely defines those fields, heuristic has been choosen.
- * This is not perfect as we are writting a Secondary Capture image...
- */
-void File::InitializeDefaultFile()
-{
- std::string date = Util::GetCurrentDate();
- std::string time = Util::GetCurrentTime();
- std::string uid = Util::CreateUniqueUID();
- std::string uidMedia = uid;
- 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 (Secondary Capture Image Storage)
- InsertValEntry("1.2.840.10008.5.1.4.1.1.7", 0x0002, 0x0002);
- // Media Storage SOP Instance UID
- InsertValEntry(uidMedia.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;
- InsertBinEntry(0, 0, GrPixel, NumPixel);
-}
+
//-----------------------------------------------------------------------------
// Private
// - 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)) )
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
{
// Parse the RLE Header and store the corresponding RLE Segment
// Offset Table information on fragments of this current Frame.
rleSegmentOffsetTable[k] = ReadInt32();
}
- // Deduce from both the RLE Header and the frameLength the
- // fragment length, and again store this info in a
- // RLEFramesInfo.
+ // Deduce from both RLE Header and frameLength
+ // the fragment length, and again store this info
+ // in a RLEFramesInfo.
long rleSegmentLength[15];
// skipping (not reading) RLE Segments
if ( nbRleSegments > 1)
RLEInfo->AddFrame(newFrame);
}
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the item :
if ( !ReadTag(0xfffe, 0xe0dd) )
{
gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
// Loop on the fragments[s] and store the parsed information in a
// JPEGInfo.
long fragmentLength;
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
{
long fragmentOffset = Fp->tellg();
SkipBytes(fragmentLength);
}
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the 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).
+ * tag is (TestGroup, TestElem).
* \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
+ * (TestGroup, TestElem) 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.
+ * @param testGroup The expected group of the tag.
+ * @param testElem The expected Element of the tag.
* @return True on success, false otherwise.
*/
-bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
+bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
{
long positionOnEntry = Fp->tellg();
long currentPosition = Fp->tellg(); // On debugging purposes
// Read the Item Tag group and element, and make
// sure they are what we expected:
uint16_t itemTagGroup;
- uint16_t itemTagElement;
+ uint16_t itemTagElem;
try
{
- itemTagGroup = ReadInt16();
- itemTagElement = ReadInt16();
+ itemTagGroup = ReadInt16();
+ itemTagElem = ReadInt16();
}
- catch ( FormatError e )
+ catch ( FormatError /*e*/ )
{
//std::cerr << e << std::endl;
return false;
}
- if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ if ( itemTagGroup != testGroup || itemTagElem != testElem )
{
gdcmWarningMacro( "Wrong Item Tag found:"
<< " We should have found tag ("
- << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << std::hex << testGroup << "," << testElem << ")" << std::endl
<< " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << std::hex << itemTagGroup << "," << itemTagElem << ")"
<< " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
) ;
Fp->seekg(positionOnEntry, std::ios::beg);
* 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.
+ * @param testGroup The expected Group of the tag.
+ * @param testElem 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)
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
{
- if ( !ReadTag(testGroup, testElement) )
+ if ( !ReadTag(testGroup, testElem) )
{
return 0;
}
}
}
+// These are the deprecated method that one day should be removed (after the next release)
+
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Constructor (DEPRECATED : temporaryly kept not to break the API)
+ * @param filename name of the file whose header we want to analyze
+ * @deprecated do not use any longer
+ */
+File::File( std::string const &filename )
+ :Document( )
+{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+
+ SetFileName( filename );
+ Load( ); // gdcm::Document is first Loaded, then the 'File part'
+}
+
+/**
+ * \brief Loader. (DEPRECATED : temporaryly kept not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
+ */
+bool File::Load( std::string const &fileName )
+{
+ GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
+ File::Load());
+ SetFileName( fileName );
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+#endif
+
//-----------------------------------------------------------------------------
// Print
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff