Program: gdcm
Module: $RCSfile: gdcmHeader.cxx,v $
Language: C++
- Date: $Date: 2004/12/07 17:28:50 $
- Version: $Revision: 1.214 $
+ Date: $Date: 2005/01/06 20:03:28 $
+ Version: $Revision: 1.222 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* \brief Constructor
* @param filename name of the file whose header we want to analyze
*/
-Header::Header( std::string const & filename ):
+Header::Header( std::string const &filename ):
Document( filename )
{
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
{
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 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 fp file pointer on an already open file
+ * @param fileName file name to write to
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
-bool Header::Write(std::string fileName,FileType filetype)
+bool Header::Write(std::string fileName, FileType filetype)
{
- std::ofstream* fp = new std::ofstream(fileName.c_str(),
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
std::ios::out | std::ios::binary);
- if (fp == NULL)
+ if (*fp == NULL)
{
dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
return false;
// Drop 0028|1101, 0028|1102, 0028|1103
// Drop 0028|1201, 0028|1202, 0028|1203
- DocEntry* e = GetDocEntryByNumber(0x0028,0x01101);
+ DocEntry *e = GetDocEntryByNumber(0x0028,0x01101);
if (e)
{
RemoveEntryNoDestroy(e);
}
// 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;
}
// 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()
/**
* \brief Initialize a default DICOM header that should contain all the
- * field require by other reader. DICOM standart does not
- * explicitely defines thoses fields, heuristic has been choosen.
+ * 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()
std::string date = Util::GetCurrentDate();
std::string time = Util::GetCurrentTime();
- std::string uid = Util::CreateUniqueUID();
+ 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[] = {
- { "76 ", 0x0002, 0x0000}, // MetaElementGroup Length // FIXME: how to recompute ?
- { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // MediaStorageSOPInstanceUID (CT Image Storage)
- { uid.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
- { "ISO_IR 100",0x0008, 0x0005}, // Specific Character Set
- { "DERIVED\\SECONDARY\\OTHER\\GDCM", 0x0008, 0x0008}, // Image Type
- { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
- { "", 0x0008, 0x0050}, // Accession Number
- { "GDCM", 0x0008, 0x0070}, // Manufacturer
- { "GDCM", 0x0008, 0x0080}, // Institution Name
- { "http://www-creatis.insa-lyon.fr/Public/Gdcm/", 0x0008, 0x0081}, // Institution Address
- { "", 0x0008, 0x0090}, // Refering Physician Name
- { "", 0x0008, 0x1030}, // Study Description
- { "", 0x0008, 0x1050}, // Performing Physician's Name
- { "", 0x0008, 0x1060}, // Name of Physician(s) Reading Study
- { "", 0x0010, 0x0040}, // Patient's Sex
- { uid.c_str(), 0x0020, 0x000d}, // StudyInstanceUID
- { uid.c_str(), 0x0020, 0x000e}, // SeriesInstanceUID
- { "", 0x0020, 0x0011}, // AcquisitionNumber
- { "1\\0\\0\\0\\1\\0", 0x0020, 0x0037}, // Image Orientation Patient
- { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
- { "MONOCHROME1",0x0028, 0x0004}, // photochromatic interpretation
-
-// Date and timeG
- { date.c_str(), 0x0008, 0x0012 } , // Instance Creation Date
- { time.c_str(), 0x0008, 0x0013 } , // Instance Creation Time
- { date.c_str(), 0x0008, 0x0020 } , // Study Date
- { date.c_str(), 0x0008, 0x0022 } , // Acquisition Date
- { date.c_str(), 0x0008, 0x0023 } , // Content Date
- { time.c_str(), 0x0008, 0x0030 } , // Study Time
- { "CT", 0x0008, 0x0060 } , // Modality
- { "GDCM", 0x0010, 0x0010 } , // Patient's Name
- { "GDCMID", 0x0010, 0x0020 } , // Patient ID
- { "1", 0x0020, 0x0010 } , // StudyID
- { "1", 0x0020, 0x0011 } , // SeriesNumber
- { "1.0", 0x0018, 0x0050 } , // slice Thickness
- { "1.0", 0x0018, 0x0088 } , // space between slices
- { "1.0\\1.0", 0x0028, 0x0030 } , // pixelSpacing
- { "64", 0x0028, 0x0010 } , // nbRows
- { "64", 0x0028, 0x0011 } , // nbCols
- { "16", 0x0028, 0x0100 } , // BitsAllocated 8 or 16
- { "12", 0x0028, 0x0101 } , // BitsStored 8 or 12 or 16
- { "11", 0x0028, 0x0102 } , // HighBit 7 or 11 or 15
- { "0", 0x0028, 0x0103 } , // Pixel Representation 0(unsigned) or 1(signed)
- { "1000.0", 0x0028, 0x1051 } , // Window Width
- { "500.0", 0x0028, 0x1050 } , // Window Center
- { 0, 0, 0 }
+ { "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
}
}
+
//-----------------------------------------------------------------------------
// Private