Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/02/02 10:02:17 $
- Version: $Revision: 1.207 $
+ Date: $Date: 2005/10/18 21:19:57 $
+ Version: $Revision: 1.279 $
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
+//
+// 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 "gdcmGlobal.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 <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;
+ BasicOffsetTableItemValue = 0;
+}
+
+
+/**
+ * \brief Canonical destructor.
+ */
+File::~File ()
+{
+ if ( RLEInfo )
+ delete RLEInfo;
+ if ( JPEGInfo )
+ delete JPEGInfo;
+ delete[] BasicOffsetTableItemValue;
+}
+
+//-----------------------------------------------------------------------------
+// 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
// 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
{
// 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 DataEntry to change 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)
+ 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 )
PixelVR = "OW";
// Change only made if usefull
- if( PixelVR != oldEntry->GetVR() )
+ if ( PixelVR != oldEntry->GetVR() )
{
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);
}
}
}
-}
-
-/**
- * \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 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;
- }
-
- // Entry : 0002|0000 = group length -> recalculated
- ValEntry *e0002 = GetValEntry(0x0002,0x0000);
- if( e0002 )
- {
- 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)
- {
- 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;
}
-
/**
* \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);
+ const std::string &res = GetEntryString(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;
}
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int File::GetImageNumber()
+{
+ //0020 0013 : Image Number
+ std::string strImNumber = GetEntryString(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 : Modality
+ std::string strModality = GetEntryString(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.
*/
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;
}
- // 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).
*/
{
// 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;
}
/**
- * \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 File::GetXSpacing()
{
- float xspacing, yspacing;
- const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
+ float xspacing = 1.0;
+ uint32_t nbValue;
+
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ 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(),
+ "%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;
+ }*/
+
+ 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 )
{
- gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
+ 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 )
+ 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;
- return xspacing;
-
- }
+ }*/
- // to avoid troubles with David Clunie's-like images
- if ( xspacing == 0. && yspacing == 0.)
- return 1.;
+ // to avoid troubles with David Clunie's-like images (at least one)
+/* if ( xspacing == 0.0 && yspacing == 0.0)
+ return 1.0;
- if ( xspacing == 0.)
+ if ( xspacing == 0.0)
{
- gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
+ 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 );
}
-
+*/
return xspacing;
}
/**
- * \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);
-
+ float yspacing = 1.0;
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ 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);
+
+ // 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;
+ }*/
+
+ entry = GetDataEntry(0x0028,0x0030);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(0);
+
+ 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 )
{
- gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
+ gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
return 1.;
}
// if sscanf cannot read any float value, it won't affect yspacing
- sscanf( strSpacing.c_str(), "%f", &yspacing);
+ nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
- if ( yspacing == 0.0 )
+ // if no values, yspacing is set to 1.0
+ if ( nbValues == 0 )
yspacing = 1.0;
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;*/
+
return yspacing;
}
*/
float File::GetZSpacing()
{
- // Spacing Between Slices : distance entre le milieu de chaque coupe
- // Les coupes peuvent etre :
+ // --->
+ // ---> 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)
- // chevauchantes (Spacing between Slices < Slice Thickness)
+ // overlapping (Spacing between Slices < Slice Thickness)
// disjointes (Spacing between Slices > Slice Thickness)
// Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
- // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
- // Si le Spacing Between Slices est Missing,
- // on suppose que les coupes sont jointives
-
- const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
-
- if ( strSpacingBSlices == GDCM_UNFOUND )
+ // It only concerns the MRI guys, not people wanting to visualize volumes
+ // If Spacing Between Slices is missing,
+ // we suppose slices joint together
+ DataEntry *entry = GetDataEntry(0x0018,0x0088);
+ if( entry )
{
- gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
- const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
- if ( strSliceThickness == GDCM_UNFOUND )
- {
- gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)");
- return 1.;
- }
- else
- {
- // if no 'Spacing Between Slices' is found,
- // we assume slices join together
- // (no overlapping, no interslice gap)
- // if they don't, we're fucked up
- return (float)atof( strSliceThickness.c_str() );
- }
- }
- //else
- return (float)atof( strSpacingBSlices.c_str() );
-}
+ zspacing = (float)entry->GetValue(0);
-/**
- *\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
- gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
- }
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
}
+ else
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
- 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 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 )
{
- if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
- {
- // bug in the element 0x0028,0x1053
- gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
- }
- }
-
- return resSlope;
-}
+ zspacing = (float)entry->GetValue(0);
-/**
- * \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;
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
}
-
- std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+ else
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
- if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ return zspacing;
+
+/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
+ if ( strSpacingBSlices == GDCM_UNFOUND )
{
- if ( HasLUT() )// PALETTE COLOR is NOT enough
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
+ const std::string &strSliceThickness = GetEntryString(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
{
- return 3;
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
+ return 1.0;
}
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;
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return (float)atof( strSliceThickness.c_str() );
+ }
}
-
- // we assume that *all* kinds of YBR are dealt with
- return GetSamplesPerPixel();
+
+ float zsp = (float)atof( strSpacingBSlices.c_str());
+ if (zsp == 0.0) // last change not to break further computations ...
+ zsp = 1.0;
+ return zsp;*/
}
-//
-// -------------- 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
-//
-// ---------------------------------------------------------------
-//
-
/**
* \brief gets the info from 0020,0032 : Image Position Patient
* else from 0020,0030 : Image Position (RET)
*/
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 )
{
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0;
}
}
- 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.;
+ 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)
{
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
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.;
}
- 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 )
{
- if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ 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
{
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(),
- "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ 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
{
return zImPos;
}
- }
+ }*/
- std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
+ // for *very* old ACR-NEMA images
+ 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)
+ 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);
+ 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)
+ 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
+ * 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 true when one of the tag is found
+ * false when nothing is found
+ */
+bool 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 = GetEntryString(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 false;
+ }
}
- 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 = GetEntryString(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 false;
}
}
-
- return Unknow;
+ return true;
}
+
+
/**
* \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 !
*/
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 )
{
- 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
}
- return atoi( strSize.c_str() );
+ return atoi( strSize.c_str() );*/
}
/**
- * \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, 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::GetHighBitPosition()
+int File::GetBitsAllocated()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0102 );
- if ( strSize == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0028,0x0100);
+ if( !entry )
{
- gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
+ gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
return 0;
}
- return atoi( strSize.c_str() );
+ 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() );*/
}
/**
- * \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
+ * @return The high bit position when present. 0 when missing.
*/
-bool File::IsSignedPixelData()
+int File::GetHighBitPosition()
{
- 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 )
+ DataEntry *entry = GetDataEntry(0x0028,0x0102);
+ if( !entry )
{
- return false;
+ gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
+ return 0;
}
- return true;
-}
+ return (int)entry->GetValue(0);
-/**
- * \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::GetBitsAllocated()
-{
- std::string strSize = GetEntryValue(0x0028,0x0100);
+/* std::string strSize = GetEntryString( 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() );
+ return atoi( strSize.c_str() );*/
}
/**
* \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()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0002);
- if ( strSize == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0028,0x0002);
+ if( !entry )
{
- 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;
-}
+ return (int)entry->GetValue(0);
-/**
- * \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 )
+/* const std::string &strSize = GetEntryString(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
+ 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 false;
+ 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 )
{
- gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
+ gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
- return atoi( strSize.c_str() );
+ return atoi( strSize.c_str() );*/
}
/**
int File::GetPixelSize()
{
// 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;
+ // (in order no to be messed up by old ACR-NEMA RGB images)
+ assert( !(GetEntryString(0x0028,0x0100) == "24") );
std::string pixelType = GetPixelType();
if ( pixelType == "8U" || pixelType == "8S" )
{
return 8;
}
- gdcmVerboseMacro( "Unknown pixel type");
+ gdcmWarningMacro( "Unknown pixel type: " << pixelType);
return 0;
}
* - 32S signed 32 bit,
* - 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
+ * 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()
{
- 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)");
+ 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;
+ if( IsSignedPixelData() )
+ {
+ sign = "S";
+ }
+ else
+ {
+ sign = "U";
+ }
+
+/* std::string bitsAlloc = GetEntryString(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
}
}
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 = GetEntryString(0x0028, 0x0103);//"Pixel Representation"
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" )
else
{
sign = "S";
- }
+ }*/
return bitsAlloc + sign;
}
+/**
+ * \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()
+{
+ 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;
+ }
+ int sign = atoi( strSign.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 (gray levels) or not,
+ * using "Photometric Interpretation" tag (0x0028,0x0004).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
*/
-size_t File::GetPixelOffset()
+bool File::IsMonochrome()
+{
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ }
+ return false;
+}
+
+/**
+ * \brief Check whether this a MONOCHROME1 picture (high values = dark)
+ * or not using "Photometric Interpretation" tag (0x0028,0x0004).
+ * @return true when "MONOCHROME1" . False otherwise.
+ */
+bool File::IsMonochrome1()
+{
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "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()
{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
{
- 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 : Palette color (0028,0004)");
}
+ return false;
}
/**
- * \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 "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
*/
-size_t File::GetPixelAreaLength()
+bool File::IsYBRFull()
{
- DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
- if ( pxlElement )
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
{
- 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 : YBR Full (0028,0004)");
}
+ return false;
}
/**
//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;
}
/**
- * \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 gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float File::GetRescaleIntercept()
{
- std::string strImOriPat;
- //iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 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);
- // 0020 0037 DS REL Image Orientation (Patient)
- if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
+/* float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntryString(0x0028,0x1052);
+ if ( strRescInter != 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 )
+ if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
{
- gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ // bug in the element 0x0028,0x1052
+ gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
}
}
- //For ACR-NEMA
- // 0020 0035 DS REL Image Orientation (RET)
- else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
+
+ return resInter;*/
+}
+
+/**
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+float File::GetRescaleSlope()
+{
+ // 0028 1053 DS IMG Rescale Slope
+ DataEntry *entry = GetDataEntry(0x0028, 0x1053);
+ if( !entry )
{
- 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( "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 = GetEntryString(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
{
- gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
+ // bug in the element 0x0028,0x1053
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
}
}
+
+ return resSlope;*/
}
/**
- * \brief anonymize a File (removes Patient's personal info)
- * (read the code to see which ones ...)
+ * \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*)
*/
-bool File::AnonymizeFile()
+int File::GetNumberOfScalarComponents()
{
- // If exist, replace by spaces
- SetValEntry (" ",0x0010, 0x2154); // Telephone
- SetValEntry (" ",0x0010, 0x1040); // Adress
- SetValEntry (" ",0x0010, 0x0020); // Patient ID
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
+ }
- DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
-
- if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
+
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
{
- std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
- if ( studyInstanceUID != GDCM_UNFOUND )
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
{
- InsertValEntry(studyInstanceUID, 0x0010, 0x0010);
+ return 3;
}
else
{
- InsertValEntry("anonymised", 0x0010, 0x0010);
+ 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::GetEntryString(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
+ * @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;
+ UserAnonymizeList.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);
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t valLgth = 0;
+ std::string *spaces;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ continue;
+
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
+ continue;
+ }
+
+ offset = d->GetOffset();
+ lgth = d->GetLength();
+ if (valLgth < lgth)
+ {
+ spaces = new std::string( lgth-valLgth, ' ');
+ (*it).Value = (*it).Value + *spaces;
+ delete spaces;
+ }
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (*it).Value.c_str(), lgth );
+
+ }
+ fp->close();
+ delete fp;
+}
+
+/**
+ * \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 ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
+ {
+ // If exist, replace by spaces
+ SetEntryString(" ",0x0010, 0x2154); // Telephone
+ SetEntryString(" ",0x0010, 0x1040); // Adress
+ SetEntryString(" ",0x0010, 0x0020); // Patient ID
+
+ DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
+ {
+ std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ SetEntryString(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ SetEntryString("anonymized", 0x0010, 0x0010);
+ }
}
}
+ else
+ {
+ gdcm::DocEntry *d;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ continue;
- // Just for fun :-(
- // (if any) remove or replace all the stuff that contains a Date
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
+ continue;
+ }
+
+ if ( dynamic_cast<DataEntry *>(d) )
+ {
+ gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
+ continue;
+ }
+ else
+ SetEntryString ((*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
return true;
}
-//-----------------------------------------------------------------------------
-// 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 CT image...
+ * \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 writetype type of the file to be written
+ * (ACR, ExplicitVR, ImplicitVR)
*/
-void File::InitializeDefaultFile()
+bool File::Write(std::string fileName, FileType writetype)
{
- 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 uidInst = uid;
- std::string uidClass = Util::CreateUniqueUID();
- std::string uidStudy = Util::CreateUniqueUID();
- std::string uidSerie = Util::CreateUniqueUID();
-
- 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 }
- };
-
- // default value
- // Special case this is the image (not a string)
- GrPixel = 0x7fe0;
- NumPixel = 0x0010;
- InsertBinEntry(0, 0, GrPixel, NumPixel);
+ 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;
+ }
- // All remaining strings:
- unsigned int i = 0;
- DICOM_DEFAULT_VALUE current = defaultvalue[i];
- while( current.value )
+ // Entry : 0002|0000 = group length -> recalculated
+ DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
+ if ( e0000 )
{
- InsertValEntry(current.value, current.group, current.elem);
- current = defaultvalue[++i];
+ std::ostringstream sLen;
+ sLen << ComputeGroup0002Length( );
+ e0000->SetString(sLen.str());
}
+
+ // 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);
+
+ fp->close();
+ delete fp;
+
+ return true;
}
+//-----------------------------------------------------------------------------
+// Protected
+
+
//-----------------------------------------------------------------------------
// Private
/**
// - 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;
- while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ 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
if ( nbRleSegments > 16 )
{
// There should be at most 15 segments (refer to RLEFrame class)
- gdcmVerboseMacro( "Too many segments.");
+ gdcmWarningMacro( "Too many segments.");
}
uint32_t rleSegmentOffsetTable[16];
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) )
{
- gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
+ gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
}
}
return;
}
- ReadAndSkipEncapsulatedBasicOffsetTable();
+ ReadEncapsulatedBasicOffsetTable();
// Loop on the fragments[s] and store the parsed information in a
// JPEGInfo.
long fragmentLength;
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ 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 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) )
{
- gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
+ 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
+ // 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 )
{
- gdcmVerboseMacro( "Wrong Item Tag found:"
+ 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) )
{
+ gdcmErrorMacro( "ReadTag did not succeed..." );
return 0;
}
//// Then read the associated Item Length
long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
- {
- gdcmVerboseMacro( "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);
- gdcmVerboseMacro( "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