Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/10/18 12:58:28 $
- Version: $Revision: 1.277 $
+ Date: $Date: 2005/10/26 06:23:37 $
+ Version: $Revision: 1.297 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// Change only made if usefull
if ( PixelVR != oldEntry->GetVR() )
{
- DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
- PixelVR,"1","Pixel Data");
+ DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
+ PixelVR,"1","Pixel Data");
- DataEntry *newEntry = new DataEntry(newDict);
+ DataEntry *newEntry = DataEntry::New(newDict);
+ newDict->Delete();
newEntry->Copy(entry);
newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
oldEntry->SetSelfArea(false);
RemoveEntry(oldEntry);
AddEntry(newEntry);
+ newEntry->Delete();
}
}
}
if( entry )
{
nbValue = entry->GetValueCount();
+ // Can't use IsValueCountValid because of the complex heuristic.
if( nbValue >= 3 )
xspacing = (float)entry->GetValue(2);
if( nbValue >= 2 )
}
else
{
- gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" );
+ gdcmWarningMacro( "Unfound Imager 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 )
+ else if( nbValue >= 2 )
xspacing = (float)entry->GetValue(1);
else
xspacing = (float)entry->GetValue(0);
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
}
-/* const std::string &strSpacing = GetEntryString(0x0028,0x0030);
- if ( strSpacing == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
- return 1.;
- }
-
- 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;
-
- }*/
-
- // to avoid troubles with David Clunie's-like images (at least one)
-/* if ( xspacing == 0.0 && yspacing == 0.0)
- return 1.0;
-
- if ( xspacing == 0.0)
- {
- gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem");
- // seems to be a bug in the header ...
- nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing);
- gdcmAssertMacro( nbValues == 2 );
- }
-*/
return xspacing;
}
}
else
{
- gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" );
+ 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 )
{
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
}
-/* std::string strSpacing = GetEntryString(0x0028,0x0030);
- if ( strSpacing == GDCM_UNFOUND )
- {
- gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
- return 1.;
- }
-
- // if sscanf cannot read any float value, it won't affect yspacing
- nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
-
- // if no values, yspacing is set to 1.0
- if ( nbValues == 0 )
- yspacing = 1.0;
-
- if ( yspacing == 0.0 )
- yspacing = 1.0;*/
return yspacing;
}
gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
return zspacing;
-
-/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
- if ( strSpacingBSlices == GDCM_UNFOUND )
- {
- gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
- const std::string &strSliceThickness = GetEntryString(0x0018,0x0050);
- if ( strSliceThickness == GDCM_UNFOUND )
- {
- gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
- return 1.0;
- }
- 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() );
- }
- }
-
- float zsp = (float)atof( strSpacingBSlices.c_str());
- if (zsp == 0.0) // last change not to break further computations ...
- zsp = 1.0;
- return zsp;*/
}
/**
}
if( entry->GetValueCount() == 3 )
- return (float)entry->GetValue(0);
- return 0.0f;
-
-/* std::string strImPos = GetEntryString(0x0020,0x0032);
- if ( strImPos == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
+ if (!entry->IsValueCountValid() )
{
- gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.0;
+ gdcmErrorMacro( "Invalid Value Count" );
}
+ return (float)entry->GetValue(0);
}
-
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
- {
- return 0.0;
- }
-
- return xImPos;*/
+ return 0.0f;
}
/**
}
if( entry->GetValueCount() == 3 )
- return (float)entry->GetValue(1);
- return 0.0f;
-/* float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryString(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND)
{
- gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
+ if (!entry->IsValueCountValid() )
{
- gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
- }
- }
-
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
- {
- return 0.;
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(1);
}
-
- return yImPos;*/
+ return 0.0f;
}
/**
if( entry )
{
if( entry->GetValueCount() == 3 )
- return (float)entry->GetValue(0);
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(2);
+ }
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)
- {
- gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
- }
- }*/
entry = GetDataEntry(0x0020,0x0030);
if( entry )
{
if( entry->GetValueCount() == 3 )
- return (float)entry->GetValue(0);
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(2);
+ }
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 )
- {
- gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
- }
- }*/
// 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)
- {
- gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
- return 0.; // bug in the element 0x0020,0x1041
- }
- else
{
- return zImPos;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0); // VM=1 !
}
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
+ return 0.0f;
}
- gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/
entry = GetDataEntry(0x0020,0x0050);
if( entry )
{
- gdcmWarningMacro( "Unfound Location (0020,0050)");
if( entry->GetValueCount() == 1 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
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 )
- {
- gdcmWarningMacro( "Wrong Location (0020,0050)");
- return 0.; // bug in the element 0x0020,0x0050
- }
- else
- {
- return zImPos;
- }
- }
- gdcmWarningMacro( "Unfound Location (0020,0050)");*/
-
return 0.; // Hopeless
}
return true;
}
-
-
/**
* \brief Retrieve the number of Bits Stored (actually used)
* (as opposed to number of Bits Allocated)
return 0;
}
return (int)entry->GetValue(0);
-
-/* std::string strSize = GetEntryString( 0x0028, 0x0101 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
- }
- return atoi( strSize.c_str() );*/
}
/**
return 0;
}
return (int)entry->GetValue(0);
-
-/* std::string strSize = GetEntryString(0x0028,0x0100);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
- }
- return atoi( strSize.c_str() );*/
}
/**
return 0;
}
return (int)entry->GetValue(0);
-
-/* std::string strSize = GetEntryString( 0x0028, 0x0102 );
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
- return 0;
- }
- return atoi( strSize.c_str() );*/
}
/**
// but sometimes it's missing : *we* assume Gray pixels
}
return (int)entry->GetValue(0);
-
-/* const std::string &strSize = GetEntryString(0x0028,0x0002);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "(0028,0002) is supposed to be mandatory");
- return 1; // Well, it's supposed to be mandatory ...
- // but sometimes it's missing : *we* assume Gray pixels
- }
- return atoi( strSize.c_str() );*/
}
/**
return 0;
}
return (int)entry->GetValue(0);
-
-/* std::string strSize = GetEntryString(0x0028,0x0006);
- if ( strSize == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
- return 0;
- }
- return atoi( strSize.c_str() );*/
}
/**
{
sign = "U";
}
-
-/* std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
- if ( bitsAlloc == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
- bitsAlloc = "16"; // default and arbitrary value, not to polute the output
- }
-
- if ( bitsAlloc == "64" )
- {
- return "FD";
- }
- else if ( bitsAlloc == "12" )
- {
- // It will be unpacked
- bitsAlloc = "16";
- }
- else if ( bitsAlloc == "24" )
- {
- // (in order no to be messed up by old RGB images)
- bitsAlloc = "8";
- }
-
- std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation"
-
- if (sign == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
- sign = "U"; // default and arbitrary value, not to polute the output
- }
- else if ( sign == "0" )
- {
- sign = "U";
- }
- else
- {
- sign = "S";
- }*/
return bitsAlloc + sign;
}
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;*/
}
/**
}
return (float)entry->GetValue(0);
-/* float resInter = 0.;
- /// 0028 1052 DS IMG Rescale Intercept
- const std::string &strRescInter = GetEntryString(0x0028,0x1052);
- if ( strRescInter != GDCM_UNFOUND )
- {
- if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
- {
- // bug in the element 0x0028,0x1052
- gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
- }
- }
-
- return resInter;*/
}
/**
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 )
- {
- // bug in the element 0x0028,0x1053
- gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
- }
- }
-
- return resSlope;*/
}
/**
void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
std::string const &value)
{
- Element el;
+ DicomElement el;
el.Group = group;
el.Elem = elem;
el.Value = value;
e0000->SetString(sLen.str());
}
- int i_lgPix = GetEntryLength(GrPixel, NumPixel);
- if (i_lgPix != -2)
+ // Derma?.dcm does not have it...let's remove it FIXME FIXME
+ if( writetype != JPEG )
{
- // 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);
- }
+ 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);
/**
* \brief Assuming the internal file pointer \ref Document::Fp
- * is placed at the beginning of a tag check whether this
+ * is placed at the beginning of a tag, check whether this
* tag is (TestGroup, TestElem).
* \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag.
itemTagGroup = ReadInt16();
itemTagElem = ReadInt16();
}
- catch ( FormatError /*e*/ )
+ catch ( FormatError )
{
- //std::cerr << e << std::endl;
+ gdcmErrorMacro( "Can not read tag for "
+ << " We should have found tag ("
+ << DictEntry::TranslateToKey(testGroup,testElem) << ")"
+ ) ;
+
return false;
}
if ( itemTagGroup != testGroup || itemTagElem != testElem )
- {
- gdcmWarningMacro( "Wrong Item Tag found:"
- << " We should have found tag ("
- << std::hex << testGroup << "," << testElem << ")" << std::endl
- << " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElem << ")"
- << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
- ) ;
+ {
+ // in order not to pollute output we don't warn on 'delimitors'
+ if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
+ gdcmErrorMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
+ << " but instead we encountered tag ("
+ << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
+ << " at address: " << " 0x(" << std::hex
+ << (unsigned int)currentPosition << std::dec << ")"
+ ) ;
Fp->seekg(positionOnEntry, std::ios::beg);
return false;
if ( !ReadTag(testGroup, testElem) )
{
+ // Avoid polutting output
+ if ( testGroup != 0xfffe )
+ gdcmErrorMacro( "ReadTag did not succeed for ("
+ << DictEntry::TranslateToKey(testGroup,testElem)
+ << ")..." );
return 0;
}
//// Then read the associated Item Length
long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
- {
- gdcmWarningMacro( "Basic Item Length is: "
- << itemLength << std::endl
+ gdcmDebugMacro( "Basic Item Length is: " << itemLength
<< " at address: " << std::hex << (unsigned int)currentPosition);
- }
return itemLength;
}
// 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,
+/*
+ * \ 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
+ * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
*/
bool File::Load( std::string const &fileName )
{
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff