Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/07/07 10:12:32 $
- Version: $Revision: 1.248 $
+ Date: $Date: 2005/10/19 09:27:24 $
+ Version: $Revision: 1.280 $
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 "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmTS.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmDataEntry.h"
#include <vector>
-#include <stdio.h> //sscanf
+#include <stdio.h> //sscanf
#include <stdlib.h> // for atoi
namespace gdcm
{
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
JPEGInfo = new JPEGFragmentsInfo;
GrPixel = 0x7fe0; // to avoid further troubles
NumPixel = 0x0010;
+ BasicOffsetTableItemValue = 0;
}
-/**
- * \brief Constructor
- * @param filename name of the file whose header we want to analyze
- */
-File::File( std::string const &filename )
- :Document( )
-{
- RLEInfo = new RLEFramesInfo;
- JPEGInfo = new JPEGFragmentsInfo;
-
- Load( filename ); // gdcm::Document is first Loaded, then the 'File part'
-}
/**
* \brief Canonical destructor.
delete RLEInfo;
if ( JPEGInfo )
delete JPEGInfo;
+ delete[] BasicOffsetTableItemValue;
}
//-----------------------------------------------------------------------------
// Public
-
/**
* \brief Loader
- * @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.
*/
-bool File::Load( std::string const &fileName )
+bool File::Load( )
{
- if ( ! this->Document::Load( fileName ) )
+ 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
// (Image Location") . This entry contains the number of
// Note: this IS the right place for the code
// Image Location
- const std::string &imgLocation = GetEntryValue(0x0028, 0x0200);
+ const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
if ( imgLocation == GDCM_UNFOUND )
{
// default value
ComputeJPEGFragmentInfo();
CloseFile();
- // Create a new BinEntry to change the DictEntry
+ // Create a new DataEntry 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);
+ DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
if (oldEntry)
{
- std::string PixelVR;
+ VRKey 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 )
DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
PixelVR,"1","Pixel Data");
- BinEntry *newEntry = new BinEntry(newDict);
+ DataEntry *newEntry = new DataEntry(newDict);
newEntry->Copy(entry);
newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
oldEntry->SetSelfArea(false);
return false;
}
- const std::string &res = GetEntryValue(0x0028, 0x0005);
+ const std::string &res = GetEntryString(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
gdcmWarningMacro("Wrong Image Dimensions" << res);
int File::GetImageNumber()
{
//0020 0013 : Image Number
- std::string strImNumber = GetEntryValue(0x0020,0x0013);
+ std::string strImNumber = GetEntryString(0x0020,0x0013);
if ( strImNumber != GDCM_UNFOUND )
{
return atoi( strImNumber.c_str() );
ModalityType File::GetModality()
{
// 0008 0060 : Modality
- std::string strModality = GetEntryValue(0x0008,0x0060);
+ std::string strModality = GetEntryString(0x0008,0x0060);
if ( strModality != GDCM_UNFOUND )
{
if ( strModality.find("AU") < strModality.length()) return AU;
*/
int File::GetXSize()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0011);
- if ( strSize == GDCM_UNFOUND )
- {
- return 0;
- }
- return atoi( strSize.c_str() );
+ DataEntry *entry = GetDataEntry(0x0028,0x0011);
+ if( entry )
+ return (int)entry->GetValue(0);
+ return 0;
}
/**
*/
int File::GetYSize()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0010);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
+ DataEntry *entry = GetDataEntry(0x0028,0x0010);
+ if( entry )
+ return (int)entry->GetValue(0);
+
if ( IsDicomV3() )
{
return 0;
{
// Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
- const std::string &strSize = GetEntryValue(0x0028,0x0008);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
+ DataEntry *entry = GetDataEntry(0x0028,0x0008);
+ if( entry )
+ return (int)entry->GetValue(0);
// We then consider the "Planes" entry as the third dimension
- const std::string &strSize2 = GetEntryValue(0x0028,0x0012);
- if ( strSize2 != GDCM_UNFOUND )
- {
- return atoi( strSize2.c_str() );
- }
+ entry = GetDataEntry(0x0028,0x0012);
+ if( entry )
+ return (int)entry->GetValue(0);
return 1;
}
float File::GetXSpacing()
{
float xspacing = 1.0;
- float yspacing = 1.0;
- int nbValues;
+ uint32_t nbValue;
// To follow David Clunie's advice, we first check ImagerPixelSpacing
- const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
+ DataEntry *entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
+ {
+ nbValue = entry->GetValueCount();
+ if( nbValue >= 3 )
+ xspacing = (float)entry->GetValue(2);
+ if( nbValue >= 2 )
+ xspacing = (float)entry->GetValue(1);
+ else
+ xspacing = (float)entry->GetValue(0);
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+ return xspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" );
+ }
+
+/* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
if ( strImagerPixelSpacing != GDCM_UNFOUND )
{
if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(),
if ( xspacing == 0.0 )
xspacing = 1.0;
-
- return xspacing;
}
- }
+ return xspacing;
+ }*/
- const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
+ entry = GetDataEntry(0x0028,0x0030);
+ if( entry )
+ {
+ nbValue = entry->GetValueCount();
+ if( nbValue >= 3 )
+ xspacing = (float)entry->GetValue(2);
+ if( nbValue >= 2 )
+ xspacing = (float)entry->GetValue(1);
+ else
+ xspacing = (float)entry->GetValue(0);
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+ return xspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
+ }
+/* const std::string &strSpacing = GetEntryString(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
if ( xspacing == 0.0 )
xspacing = 1.0;
+ return xspacing;
- return xspacing;
- }
+ }*/
// to avoid troubles with David Clunie's-like images (at least one)
- if ( xspacing == 0. && yspacing == 0.)
- return 1.;
+/* if ( xspacing == 0.0 && yspacing == 0.0)
+ return 1.0;
- if ( xspacing == 0.)
+ if ( xspacing == 0.0)
{
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);
gdcmAssertMacro( nbValues == 2 );
}
-
+*/
return xspacing;
}
*/
float File::GetYSpacing()
{
- float yspacing = 1.;
- int nbValues;
+ float yspacing = 1.0;
// To follow David Clunie's advice, we first check ImagerPixelSpacing
- const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
+ DataEntry *entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(0);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+ return yspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
+ }
+/* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
if ( strImagerPixelSpacing != GDCM_UNFOUND )
{
nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing);
yspacing = 1.0;
return yspacing;
- }
+ }*/
+
+ entry = GetDataEntry(0x0028,0x0030);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(0);
- std::string strSpacing = GetEntryValue(0x0028,0x0030);
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+ return yspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
+ }
+/* std::string strSpacing = GetEntryString(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
yspacing = 1.0;
if ( yspacing == 0.0 )
- yspacing = 1.0;
+ yspacing = 1.0;*/
return yspacing;
}
*/
float File::GetZSpacing()
{
+ // --->
+ // ---> Warning :
+ // --->
+ // For *Dicom* images, ZSpacing should be calculated using
+ // XOrigin, YOrigin, ZOrigin (of the top left image corner)
+ // of 2 consecutive images, and the Orientation
+ //
+ // Computing ZSpacing on a single image is not really meaningfull !
+
+ float zspacing = 1.0f;
+
// Spacing Between Slices : distance between the middle of 2 slices
// Slices may be :
// jointives (Spacing between Slices = Slice Thickness)
// 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);
+ DataEntry *entry = GetDataEntry(0x0018,0x0088);
+ if( entry )
+ {
+ zspacing = (float)entry->GetValue(0);
+
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+ else
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
+
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ entry = GetDataEntry(0x0018,0x0050);
+ if( entry )
+ {
+ zspacing = (float)entry->GetValue(0);
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+ else
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
+
+ return zspacing;
+
+/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
if ( strSpacingBSlices == GDCM_UNFOUND )
{
gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
- const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
+ const std::string &strSliceThickness = GetEntryString(0x0018,0x0050);
if ( strSliceThickness == GDCM_UNFOUND )
{
gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
- return 1.;
+ return 1.0;
}
else
{
return (float)atof( strSliceThickness.c_str() );
}
}
- //else
- return (float)atof( strSpacingBSlices.c_str() );
+
+ float zsp = (float)atof( strSpacingBSlices.c_str());
+ if (zsp == 0.0) // last change not to break further computations ...
+ zsp = 1.0;
+ return zsp;*/
}
/**
*/
float File::GetXOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0f;
+ }
+ }
+
+ if( entry->GetValueCount() == 3 )
+ return (float)entry->GetValue(0);
+ return 0.0f;
+/* std::string strImPos = GetEntryString(0x0020,0x0032);
if ( strImPos == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
+ return 0.0;
}
}
if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
{
- return 0.;
+ return 0.0;
}
- return xImPos;
+ return xImPos;*/
}
/**
*/
float File::GetYOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0f;
+ }
+ }
+
+ if( entry->GetValueCount() == 3 )
+ return (float)entry->GetValue(1);
+ return 0.0f;
+/* float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryString(0x0020,0x0032);
if ( strImPos == GDCM_UNFOUND)
{
gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
return 0.;
}
- return yImPos;
+ return yImPos;*/
}
/**
*/
float File::GetZOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 3 )
+ return (float)entry->GetValue(0);
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.0f;
+ }
+/* float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryString(0x0020,0x0032);
if ( strImPos != GDCM_UNFOUND )
{
{
return zImPos;
}
- }
+ }*/
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ entry = GetDataEntry(0x0020,0x0030);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 3 )
+ return (float)entry->GetValue(0);
+ gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
+ return 0.0f;
+ }
+/* strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos != GDCM_UNFOUND )
{
if ( sscanf( strImPos.c_str(),
{
return zImPos;
}
- }
+ }*/
// for *very* old ACR-NEMA images
- std::string strSliceLocation = GetEntryValue(0x0020,0x1041);
+ entry = GetDataEntry(0x0020,0x1041);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 1 )
+ return (float)entry->GetValue(0);
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
+ return 0.0f;
+ }
+/* std::string strSliceLocation = GetEntryString(0x0020,0x1041);
if ( strSliceLocation != GDCM_UNFOUND )
{
if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
return zImPos;
}
}
- gdcmWarningMacro( "Unfound Slice Location (0020,1041)");
+ gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/
- std::string strLocation = GetEntryValue(0x0020,0x0050);
+ entry = GetDataEntry(0x0020,0x0050);
+ if( entry )
+ {
+ gdcmWarningMacro( "Unfound Location (0020,0050)");
+ if( entry->GetValueCount() == 1 )
+ return (float)entry->GetValue(0);
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
+ return 0.0f;
+ }
+/* std::string strLocation = GetEntryString(0x0020,0x0050);
if ( strLocation != GDCM_UNFOUND )
{
if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 )
return zImPos;
}
}
- gdcmWarningMacro( "Unfound Location (0020,0050)");
+ gdcmWarningMacro( "Unfound Location (0020,0050)");*/
return 0.; // Hopeless
}
/**
* \brief gets the info from 0020,0037 : Image Orientation Patient
+ * or from 0020 0035 : Image Orientation (RET)
* (needed to organize DICOM files based on their x,y,z position)
* @param iop adress of the (6)float array to receive values
- * @return cosines of image orientation patient
+ * @return true when one of the tag is found
+ * false when nothing is found
*/
-void File::GetImageOrientationPatient( float iop[6] )
+bool File::GetImageOrientationPatient( float iop[6] )
{
std::string strImOriPat;
//iop is supposed to be float[6]
iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
// 0020 0037 DS REL Image Orientation (Patient)
- if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
+ if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
{
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ 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 )
+ else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
{
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
+ gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
+ << "Less than 6 values were found." );
+ return false;
}
}
+ return true;
}
+
+
/**
* \brief Retrieve the number of Bits Stored (actually used)
* (as opposed to number of Bits Allocated)
*/
int File::GetBitsStored()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0101 );
+ DataEntry *entry = GetDataEntry(0x0028,0x0101);
+ if( !entry )
+ {
+ gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+
+/* std::string strSize = GetEntryString( 0x0028, 0x0101 );
if ( strSize == GDCM_UNFOUND )
{
gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
return 0; // It's supposed to be mandatory
// the caller will have to check
}
- return atoi( strSize.c_str() );
+ return atoi( strSize.c_str() );*/
}
/**
* \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);
+ DataEntry *entry = GetDataEntry(0x0028,0x0100);
+ if( !entry )
+ {
+ gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+
+/* std::string strSize = GetEntryString(0x0028,0x0100);
if ( strSize == GDCM_UNFOUND )
{
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() );
+ return atoi( strSize.c_str() );*/
}
/**
*/
int File::GetHighBitPosition()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0102 );
+ DataEntry *entry = GetDataEntry(0x0028,0x0102);
+ if( !entry )
+ {
+ gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+
+/* std::string strSize = GetEntryString( 0x0028, 0x0102 );
if ( strSize == GDCM_UNFOUND )
{
gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
return 0;
}
- return atoi( strSize.c_str() );
+ return atoi( strSize.c_str() );*/
}
/**
*/
int File::GetSamplesPerPixel()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0002);
+ DataEntry *entry = GetDataEntry(0x0028,0x0002);
+ if( !entry )
+ {
+ 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 (int)entry->GetValue(0);
+
+/* const std::string &strSize = GetEntryString(0x0028,0x0002);
if ( strSize == GDCM_UNFOUND )
{
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() );
+ return atoi( strSize.c_str() );*/
}
/**
*/
int File::GetPlanarConfiguration()
{
- std::string strSize = GetEntryValue(0x0028,0x0006);
+ DataEntry *entry = GetDataEntry(0x0028,0x0006);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+
+/* std::string strSize = GetEntryString(0x0028,0x0006);
if ( strSize == GDCM_UNFOUND )
{
gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
- return atoi( strSize.c_str() );
+ return atoi( strSize.c_str() );*/
}
/**
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old ACR-NEMA RGB images)
- // if (File::GetEntryValue(0x0028,0x0100) == "24")
- // return 3;
+ assert( !(GetEntryString(0x0028,0x0100) == "24") );
std::string pixelType = GetPixelType();
if ( pixelType == "8U" || pixelType == "8S" )
{
return 8;
}
- gdcmWarningMacro( "Unknown pixel type");
+ gdcmWarningMacro( "Unknown pixel type: " << pixelType);
return 0;
}
*/
std::string File::GetPixelType()
{
- std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
+ std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
if ( bitsAlloc == GDCM_UNFOUND )
{
gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
}
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"
+ std::string sign;
+ if( IsSignedPixelData() )
+ {
+ sign = "S";
+ }
+ else
+ {
+ sign = "U";
+ }
+
+/* std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
+
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ else if ( bitsAlloc == "12" )
+ {
+ // It will be unpacked
+ bitsAlloc = "16";
+ }
+ else if ( bitsAlloc == "24" )
+ {
+ // (in order no to be messed up by old RGB images)
+ bitsAlloc = "8";
+ }
+
+ std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation"
if (sign == GDCM_UNFOUND )
{
else
{
sign = "S";
- }
+ }*/
return bitsAlloc + sign;
}
*/
bool File::IsSignedPixelData()
{
- std::string strSign = GetEntryValue( 0x0028, 0x0103 );
+ DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
+ return false;
+ }
+ return entry->GetValue(0) != 0;
+/* std::string strSign = GetEntryString( 0x0028, 0x0103 );
if ( strSign == GDCM_UNFOUND )
{
gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
{
return false;
}
- return true;
+ return true;*/
}
/**
*/
bool File::IsMonochrome()
{
- const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
|| Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
*/
bool File::IsMonochrome1()
{
- const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
{
return true;
*/
bool File::IsPaletteColor()
{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( PhotometricInterp == "PALETTE COLOR " )
{
return true;
*/
bool File::IsYBRFull()
{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( PhotometricInterp == "YBR_FULL" )
{
return true;
//Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
// = Lookup Table Desc-Blue
// Consistency already checked in GetLUTLength
- std::string lutDescription = GetEntryValue(0x0028,0x1101);
+ std::string lutDescription = GetEntryString(0x0028,0x1101);
if ( lutDescription == GDCM_UNFOUND )
{
return 0;
*/
float File::GetRescaleIntercept()
{
- float resInter = 0.;
+ // 0028 1052 DS IMG Rescale Intercept
+ DataEntry *entry = GetDataEntry(0x0028, 0x1052);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
+ return 0.0f;
+ }
+ return (float)entry->GetValue(0);
+
+/* float resInter = 0.;
/// 0028 1052 DS IMG Rescale Intercept
- const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
+ const std::string &strRescInter = GetEntryString(0x0028,0x1052);
if ( strRescInter != GDCM_UNFOUND )
{
if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
}
}
- return resInter;
+ return resInter;*/
}
/**
*/
float File::GetRescaleSlope()
{
- float resSlope = 1.;
+ // 0028 1053 DS IMG Rescale Slope
+ DataEntry *entry = GetDataEntry(0x0028, 0x1053);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
+ return 1.0f;
+ }
+ return (float)entry->GetValue(0);
+/* float resSlope = 1.;
//0028 1053 DS IMG Rescale Slope
- std::string strRescSlope = GetEntryValue(0x0028,0x1053);
+ std::string strRescSlope = GetEntryString(0x0028,0x1053);
if ( strRescSlope != GDCM_UNFOUND )
{
if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
}
}
- return resSlope;
+ return resSlope;*/
}
/**
{
return 3;
}
-
+
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- if ( GetEntryValue(0x0028,0x0100) == "24" )
+ if ( GetEntryString(0x0028,0x0100) == "24" )
{
return 3;
}
-
- std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+
+ std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
{
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- if ( File::GetEntryValue(0x0028,0x0100) == "24" )
+ if ( File::GetEntryString(0x0028,0x0100) == "24" )
{
return 3;
}
el.Group = group;
el.Elem = elem;
el.Value = value;
- AnonymizeList.push_back(el);
+ UserAnonymizeList.push_back(el);
}
/**
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 (remove Patient's personal info passed with
* AddAnonymizeElement()
+ * \note You cannot Anonymize a DataEntry (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
- SetValEntry (" ",0x0010, 0x1040); // Adress
- SetValEntry (" ",0x0010, 0x0020); // Patient ID
+ SetEntryString(" ",0x0010, 0x2154); // Telephone
+ SetEntryString(" ",0x0010, 0x1040); // Adress
+ SetEntryString(" ",0x0010, 0x0020); // Patient ID
- DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+ DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
{
- std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
+ std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
if ( studyInstanceUID != GDCM_UNFOUND )
{
- SetValEntry(studyInstanceUID, 0x0010, 0x0010);
+ SetEntryString(studyInstanceUID, 0x0010, 0x0010);
}
else
{
- SetValEntry("anonymised", 0x0010, 0x0010);
+ SetEntryString("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<DataEntry *>(d) )
+ {
+ gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
+ continue;
+ }
+ else
+ SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
}
}
}
// Entry : 0002|0000 = group length -> recalculated
- ValEntry*e0000 = GetValEntry(0x0002,0x0000);
+ DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
if ( e0000 )
{
std::ostringstream sLen;
- sLen << ComputeGroup0002Length(writetype);
- e0000->SetValue(sLen.str());
+ sLen << ComputeGroup0002Length( );
+ e0000->SetString(sLen.str());
}
- 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);
- }
+ // Derma?.dcm does not have it...let's remove it FIXME FIXME
+ if( writetype != JPEG )
+ {
+ 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() );
+ InsertEntryString(s_lgPix,GrPixel, 0x0000);
+ }
+ }
Document::WriteContent(fp, writetype);
// - 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();
+ ReadEncapsulatedBasicOffsetTable();
// Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
// Loop on the individual frame[s] and store the information
// - when more than one frame are present, then we are in
// the case of a multi-frame image.
long frameLength;
+ int i=0;
+ uint32_t sum = 0;
while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
{
+ // Since we have read the basic offset table, let's check the value were correct
+ // or else produce a warning:
+ if ( BasicOffsetTableItemValue )
+ {
+ // If a BasicOffsetTableItemValue was read
+ uint32_t individualLength = BasicOffsetTableItemValue[i];
+ assert( individualLength == sum ); // REMOVE that if this is a problem
+ if( individualLength != sum )
+ {
+ gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
+ }
+ sum += frameLength + 8;
+ i++;
+ }
// 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
return;
}
- ReadAndSkipEncapsulatedBasicOffsetTable();
+ ReadEncapsulatedBasicOffsetTable();
// Loop on the fragments[s] and store the parsed information in a
// JPEGInfo.
long fragmentLength;
+ int i=0;
+ uint32_t sum = 0;
while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
{
- long fragmentOffset = Fp->tellg();
+ // Since we have read the basic offset table, let's check the value were correct
+ // or else produce a warning:
+ // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
+ // When the Item Value is present, the Basic Offset Table Item Value shall contain
+ // concatenated 32-bit unsigned integer values that are byte offsets to the first
+ // byte of the Item Tag of the first fragment for each frame in the Sequence of
+ // Items. These offsets are measured from the first byte of the first Item Tag
+ // following the Basic Offset Table item (See Table A.4-2).
+
+ if ( BasicOffsetTableItemValue )
+ {
+ // If a BasicOffsetTableItemValue was read
+ uint32_t individualLength = BasicOffsetTableItemValue[i];
+ //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
+ if( individualLength != sum )
+ {
+ gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
+ individualLength << " != " << sum );
+ }
+ sum += fragmentLength + 8;
+ i++;
+ }
- // Store the collected info
- JPEGFragment *newFragment = new JPEGFragment;
- newFragment->SetOffset(fragmentOffset);
- newFragment->SetLength(fragmentLength);
- JPEGInfo->AddFragment(newFragment);
+ long fragmentOffset = Fp->tellg();
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->SetOffset(fragmentOffset);
+ newFragment->SetLength(fragmentLength);
+ JPEGInfo->AddFragment(newFragment);
- SkipBytes(fragmentLength);
+ SkipBytes(fragmentLength);
}
// Make sure that we encounter a 'Sequence Delimiter Item'
itemTagGroup = ReadInt16();
itemTagElem = ReadInt16();
}
- catch ( FormatError e )
+ catch ( FormatError /*e*/ )
{
//std::cerr << e << std::endl;
return false;
{
gdcmWarningMacro( "Wrong Item Tag found:"
<< " We should have found tag ("
- << std::hex << testGroup << "," << testElem << ")" << std::endl
+ << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
<< " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElem << ")"
+ << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
<< " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
) ;
Fp->seekg(positionOnEntry, std::ios::beg);
if ( !ReadTag(testGroup, testElem) )
{
+ gdcmErrorMacro( "ReadTag did not succeed... for "
+ << DictEntry::TranslateToKey(testGroup,testElem) );
return 0;
}
//// Then read the associated Item Length
long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
- {
- gdcmWarningMacro( "Basic Item Length is: "
- << itemLength << std::endl
+ gdcmDebugMacro( "Basic Item Length is: " << itemLength
<< " 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()
+void File::ReadEncapsulatedBasicOffsetTable()
{
//// Read the Basic Offset Table Item Tag length...
uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
// 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);
+ char *charBasicOffsetTableItemValue = new char[itemLength];
+ Fp->read(charBasicOffsetTableItemValue, itemLength);
+ unsigned int nbEntries = itemLength/4;
+ assert( nbEntries*4 == itemLength); // Make sure this is a multiple
+ BasicOffsetTableItemValue = new uint32_t[nbEntries];
-#ifdef GDCM_DEBUG
- for (unsigned int i=0; i < itemLength; i += 4 )
+ for (unsigned int i=0; i < nbEntries; i++ )
{
- uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
- uint32_t);
- gdcmWarningMacro( "Read one length: " <<
- std::hex << individualLength );
+ BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
+#if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
+ uint32_t val = BasicOffsetTableItemValue[i];
+ BasicOffsetTableItemValue[i]
+ = ( (val<<24) | ((val<<8) & 0x00ff0000) |
+ ((val>>8) & 0x0000ff00) | (val>>24) );
+#endif
+ gdcmWarningMacro( "Read one length for: " <<
+ std::hex << BasicOffsetTableItemValue[i] );
}
-#endif //GDCM_DEBUG
- delete[] basicOffsetTableItemValue;
+ delete[] charBasicOffsetTableItemValue;
}
}
+// 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