Program: gdcm
Module: $RCSfile: gdcmHeader.cxx,v $
Language: C++
- Date: $Date: 2004/10/22 03:05:41 $
- Version: $Revision: 1.195 $
+ Date: $Date: 2005/01/06 15:36:48 $
+ Version: $Revision: 1.220 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDebug.h"
#include "gdcmTS.h"
#include "gdcmValEntry.h"
+#include <stdio.h> //sscanf
#include <vector>
namespace gdcm
{
-
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
// Note: this IS the right place for the code
// Image Location
- std::string imgLocation = GetEntryByNumber(0x0028, 0x0200);
+ const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200);
if ( imgLocation == GDCM_UNFOUND )
{
// default value
{
NumPixel = 0x0010;
}
+
+ // Now, we know GrPixel and NumPixel.
+ // Let's create a VirtualDictEntry to allow a further VR modification
+ // and force VR to match with BitsAllocated.
+
+ DocEntry* entry = GetDocEntryByNumber(GrPixel, NumPixel);
+ if ( entry != 0 )
+ {
+
+ std::string PixelVR;
+ // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
+ // more than 8 (i.e 12, 16) is a 'O Words'
+ if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
+ PixelVR = "OB";
+ else
+ PixelVR = "OW";
+
+ DictEntry* newEntry = NewVirtualDictEntry(
+ GrPixel, NumPixel,
+ PixelVR, "PXL", "Pixel Data");
+
+ entry->SetDictEntry( newEntry );
+ }
}
/**
- * \brief Constructor
+ * \brief Constructor used when we want to generate dicom files from scratch
*/
Header::Header()
:Document()
{
+ InitializeDefaultHeader();
}
/**
{
}
-
/**
* \brief Performs some consistency checking on various 'File related'
* (as opposed to 'DicomDir related') entries
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
-void Header::Write(std::ofstream* fp,FileType filetype)
+bool Header::Write(std::string fileName, FileType filetype)
{
+ std::ofstream* fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
+ {
+ dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
+ return false;
+ }
+
// Bits Allocated
if ( GetEntryByNumber(0x0028,0x0100) == "12")
{
if (i_lgPix != -2)
{
// no (GrPixel, NumPixel) element
- std::string s_lgPix;
- s_lgPix = Util::Format("%d", i_lgPix+12);
+ std::string s_lgPix = Util::Format("%d", i_lgPix+12);
+ s_lgPix = Util::DicomString( s_lgPix.c_str() );
ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
}
RemoveEntryNoDestroy(e);
}
}
- Document::Write(fp,filetype);
+ Document::WriteContent(fp,filetype);
+
+ fp->close();
+ delete fp;
+
+ return true;
}
//-----------------------------------------------------------------------------
return false;
}
- std::string res = GetEntryByNumber(0x0028, 0x0005);
+ const std::string &res = GetEntryByNumber(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
return false; // Image Dimensions
*/
int Header::GetXSize()
{
- std::string strSize;
- strSize = GetEntryByNumber(0x0028,0x0011);
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0011);
if ( strSize == GDCM_UNFOUND )
{
return 0;
*/
int Header::GetYSize()
{
- std::string strSize = GetEntryByNumber(0x0028,0x0010);
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0010);
if ( strSize != GDCM_UNFOUND )
{
return atoi( strSize.c_str() );
}
// The Rows (0028,0010) entry was optional for ACR/NEMA. It might
- // hence be a signal (1d image). So we default to 1:
+ // hence be a signal (1D image). So we default to 1:
return 1;
}
{
// Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
- std::string strSize = GetEntryByNumber(0x0028,0x0008);
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0008);
if ( strSize != GDCM_UNFOUND )
{
return atoi( strSize.c_str() );
}
// We then consider the "Planes" entry as the third dimension
- strSize = GetEntryByNumber(0x0028,0x0012);
- if ( strSize != GDCM_UNFOUND )
+ const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
{
- return atoi( strSize.c_str() );
+ return atoi( strSize2.c_str() );
}
return 1;
float Header::GetXSpacing()
{
float xspacing, yspacing;
- std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
+ const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
{
// if single value is found, xspacing is defaulted to yspacing
if ( nbValues == 1 )
{
- return yspacing;
+ xspacing = yspacing;
}
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
}
+
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
if ( xspacing == 0.)
{
- dbg.Verbose(0, "Header::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
// seems to be a bug in the header ...
- sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ assert( nbValues == 2 );
}
return xspacing;
*/
float Header::GetYSpacing()
{
- float yspacing = 0;
+ float yspacing = 1.;
std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
// if sscanf cannot read any float value, it won't affect yspacing
sscanf( strSpacing.c_str(), "%f", &yspacing);
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
return yspacing;
}
/**
* \brief gets the info from 0018,0088 : Space Between Slices
- * else from 0018,0050 : Slice Thickness
- * else 1.0
+ * else from 0018,0050 : Slice Thickness
+ * else 1.0
* @return Z dimension of a voxel-to be
*/
float Header::GetZSpacing()
// Si le Spacing Between Slices est absent,
// on suppose que les coupes sont jointives
- std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
+ const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
if ( strSpacingBSlices == GDCM_UNFOUND )
{
dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices");
- std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050);
+ const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050);
if ( strSliceThickness == GDCM_UNFOUND )
{
return 1.;
// we assume slices join together
// (no overlapping, no interslice gap)
// if they don't, we're fucked up
- return atof( strSliceThickness.c_str() );
+ return (float)atof( strSliceThickness.c_str() );
}
}
- else
- {
- return atof( strSpacingBSlices.c_str() );
- }
+ //else
+ return (float)atof( strSpacingBSlices.c_str() );
}
/**
{
float resInter = 0.;
/// 0028 1052 DS IMG Rescale Intercept
- std::string strRescInter = GetEntryByNumber(0x0028,0x1052);
+ const std::string &strRescInter = GetEntryByNumber(0x0028,0x1052);
if ( strRescInter != GDCM_UNFOUND )
{
if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
// beware of trailing space at end of string
// DICOM tags are never of odd length
if ( strPhotometricInterpretation == GDCM_UNFOUND ||
- strPhotometricInterpretation == "MONOCHROME1 " ||
- strPhotometricInterpretation == "MONOCHROME2 " )
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
{
return 1;
}
*/
int Header::GetSamplesPerPixel()
{
- std::string strSize = GetEntryByNumber(0x0028,0x0002);
+ const std::string& strSize = GetEntryByNumber(0x0028,0x0002);
if ( strSize == GDCM_UNFOUND )
{
dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
*/
bool Header::IsMonochrome()
{
- std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
- if ( PhotometricInterp == "MONOCHROME1 "
- || PhotometricInterp == "MONOCHROME2 " )
+ const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
return true;
}
{
return "FD";
}
- if ( bitsAlloc == "12" )
+ else if ( bitsAlloc == "12" )
{
// It will be unpacked
bitsAlloc = "16";
dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation");
bitsAlloc = "0";
}
- if ( sign == "0" )
+ else if ( sign == "0" )
{
sign = "U";
}
return "Uncompressed ACR-NEMA";
}
- while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) )
+ while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) )
{
transfertSyntax.erase(transfertSyntax.length()-1, 1);
}
return tsName;
}
-/**
- * \brief Sets the Pixel Area size in the Header
- * --> not-for-rats function
- * @param ImageDataSize new Pixel Area Size
- * warning : nothing else is checked
- */
-void Header::SetImageDataSize(size_t ImageDataSize)
-{
- ///FIXME I don't understand this code wh ydo we set two times 'car' ?
- std::string car = Util::Format("%d", ImageDataSize);
-
- DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
- a->SetLength(ImageDataSize);
-
- ImageDataSize += 8;
- car = Util::Format("%d", ImageDataSize);
-
- SetEntryByNumber(car, GrPixel, NumPixel);
-}
-
//-----------------------------------------------------------------------------
// Protected
}
else
{
- ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
+ ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010);
}
}
}
}
+/**
+ * \brief Initialize a default DICOM header 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...
+ */
+void Header::InitializeDefaultHeader()
+{
+ typedef struct
+ {
+ const char *value;
+ uint16_t group;
+ uint16_t elem;
+ } DICOM_DEFAULT_VALUE;
+
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidClass = uid + ".1";
+ std::string uidInst = uid + ".10";
+ std::string uidStudy = uid + ".100";
+ std::string uidSerie = uid + ".1000";
+
+ static DICOM_DEFAULT_VALUE defaultvalue[] = {
+ { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
+ { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
+ { 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;
+ ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel);
+
+ // All remaining strings:
+ unsigned int i = 0;
+ DICOM_DEFAULT_VALUE current = defaultvalue[i];
+ while( current.value )
+ {
+ ReplaceOrCreateByNumber(current.value, current.group, current.elem);
+ current = defaultvalue[++i];
+ }
+}
+
+
//-----------------------------------------------------------------------------
// Private
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff