Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/10/25 14:52:34 $
- Version: $Revision: 1.295 $
+ Date: $Date: 2005/12/09 12:22:49 $
+ Version: $Revision: 1.311 $
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):
+// 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?
+// Image Position (Patient) (0020,0032) VM=3
// -->
// 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
+// - Image Position (Patient) (0020,0032), VM=3
// then attribute Patient Orientation (0020,0020) should not be present
// in the images.
//
// FFDR = Feet First-Decubitus Right
// FFDL = Feet First-Decubitus Left
-// we can also find
+// we can also find (non standard!)
// SEMIERECT
// SUPINE
*/
bool File::DoTheLoadingJob( )
{
-
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
// (Image Location") . This entry contains the number of
{
nbValue = entry->GetValueCount();
// Can't use IsValueCountValid because of the complex heuristic.
+ if( nbValue !=2 )
+ gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
+ << "has a wrong number of values :" << nbValue);
+
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);
if( entry )
{
nbValue = entry->GetValueCount();
+ if( nbValue !=2 )
+ gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
+ << "has a wrong number of values :" << nbValue);
+
if( nbValue >= 3 )
xspacing = (float)entry->GetValue(2);
else if( nbValue >= 2 )
* \brief gets the info from 0018,0088 : Space Between Slices
* else from 0018,0050 : Slice Thickness
* else 1.0
+ *
+ * When an element is missing, we suppose slices join together
+ * (no overlapping, no interslice gap) but we have no way to check it !
+ * 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 !
+
* @return Z dimension of a voxel-to be
*/
float File::GetZSpacing()
{
- // --->
- // ---> Warning :
- // --->
- // For *Dicom* images, ZSpacing should be calculated using
- // XOrigin, YOrigin, ZOrigin (of the top left image corner)
- // of 2 consecutive images, and the Orientation
- //
- // Computing ZSpacing on a single image is not really meaningfull !
float zspacing = 1.0f;
// 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 )
{
else
gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ entry = GetDataEntry(0x3004,0x000c);
+ if( entry )
+ {
+ float z1 = (float)entry->GetValue(0);
+ float z2 = (float)entry->GetValue(1);
+ zspacing = z2 - z1; // can be negative...
+
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+
return zspacing;
}
if( entry->GetValueCount() == 3 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(0);
}
return 0.0f;
if( entry->GetValueCount() == 3 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(1);
}
return 0.0f;
{
if( entry->GetValueCount() == 3 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(2);
}
gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
{
if( entry->GetValueCount() == 3 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(2);
}
gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
{
if( entry->GetValueCount() == 1 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(0); // VM=1 !
}
gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
{
if( entry->GetValueCount() == 1 )
{
- gdcmErrorMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
return (float)entry->GetValue(0);
}
gdcmWarningMacro( "Wrong Location (0020,0050)");
/**
* \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
+ *
+ * @param iop adress of the (6)float array to receive values.
+ * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff-
+ * is found.
+ * @return true when one of the tag -with consistent values- is found
+ * false when nothing or inconsistent stuff - is found
*/
bool File::GetImageOrientationPatient( float iop[6] )
{
std::string strImOriPat;
//iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
// 0020 0037 DS REL Image Orientation (Patient)
if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
+ iop[0] = iop[4] = 1.;
+ iop[1] = iop[2] = iop[3] = iop[5] = 0.;
gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
<< " Less than 6 values were found." );
return false;
}
+ else
+ return true;
}
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
+ iop[0] = iop[4] = 1.;
+ iop[1] = iop[2] = iop[3] = iop[5] = 0.;
gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
<< "Less than 6 values were found." );
return false;
}
+ else
+ return true;
}
- return true;
+ return false;
}
/**
DataEntry *entry = GetDataEntry(0x0028,0x0101);
if( !entry )
{
- gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
+ gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
return 0;
}
return (int)entry->GetValue(0);
DataEntry *entry = GetDataEntry(0x0028,0x0100);
if( !entry )
{
- gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
+ gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
return 0;
}
return (int)entry->GetValue(0);
DataEntry *entry = GetDataEntry(0x0028,0x0102);
if( !entry )
{
- gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
+ gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
return 0;
}
return (int)entry->GetValue(0);
DataEntry *entry = GetDataEntry(0x0028,0x0002);
if( !entry )
{
- gdcmWarningMacro("(0028,0002) is supposed to be mandatory");
+ gdcmWarningMacro("SamplesPerPixel (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
}
DataEntry *entry = GetDataEntry(0x0028,0x0006);
if( !entry )
{
- gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
return (int)entry->GetValue(0);
std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
if ( bitsAlloc == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
+ gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
bitsAlloc = "16"; // default and arbitrary value, not to polute the output
}
DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
if( !entry )
{
- gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
+ gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
+ << "mandatory");
return false;
}
return entry->GetValue(0) != 0;
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
+ << "mandatory");
}
return false;
}
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
+ << " be mandatory! ");
}
return false;
}
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : Palette color (0028,0004)");
+ gdcmDebugMacro( "Not found : Palette color (0028,0004)");
}
return false;
}
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
+ gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
}
return false;
}
DataEntry *entry = GetDataEntry(0x0028, 0x1053);
if( !entry )
{
- gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
+ gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
return 1.0f;
}
return (float)entry->GetValue(0);
}
else
{
- gdcmDebugMacro( "Big trouble : Pixel Element ("
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
<< std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
return 0;
}
}
else
{
- gdcmDebugMacro( "Big trouble : Pixel Element ("
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
<< std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
return 0;
}
e0000->SetString(sLen.str());
}
- // Derma?.dcm does not have it...let's remove it FIXME FIXME
+ // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
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);
- }
- }
-
+ {
+ 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();
{
// in order not to pollute output we don't warn on 'delimitors'
if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
- gdcmErrorMacro( "Wrong Item Tag found:"
+ gdcmWarningMacro( "Wrong Item Tag found:"
<< " We should have found tag ("
<< DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
<< " but instead we encountered tag ("
uint32_t val = BasicOffsetTableItemValue[i];
BasicOffsetTableItemValue[i]
= ( (val<<24) | ((val<<8) & 0x00ff0000) |
- ((val>>8) & 0x0000ff00) | (val>>24) );
+ ( (val>>8) & 0x0000ff00) | (val>>24) );
#endif
- gdcmWarningMacro( "Read one length for: " <<
+ gdcmDebugMacro( "Read one length for: " <<
std::hex << BasicOffsetTableItemValue[i] );
}
// These are the deprecated method that one day should be removed (after the next release)
-#ifndef GDCM_LEGACY_REMOVE
+//#ifndef GDCM_LEGACY_REMOVE
/*
* \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
* @ param fileName file to be open for parsing
* 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",
return DoTheLoadingJob( );
}
-#endif
+*/
+//#endif
//-----------------------------------------------------------------------------
// Print