Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/10/21 14:15:42 $
- Version: $Revision: 1.287 $
+ Date: $Date: 2006/04/11 16:03:26 $
+ Version: $Revision: 1.318 $
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
GrPixel = 0x7fe0; // to avoid further troubles
NumPixel = 0x0010;
BasicOffsetTableItemValue = 0;
+ FourthDimensionLocation = TagKey(0,0);
}
/**
* \brief Canonical destructor.
*/
-File::~File ()
+File::~File()
{
if ( RLEInfo )
delete RLEInfo;
*/
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
// The changed DictEntry will have
// - a correct PixelVR OB or OW)
// - the name to "Pixel Data"
+
+ //==>Take it easy!
+ //==> Just change the VR !
+
+/*
DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
if (oldEntry)
{
// Change only made if usefull
if ( PixelVR != oldEntry->GetVR() )
- {
- DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
- PixelVR,"1","Pixel Data");
-
- DataEntry *newEntry = new DataEntry(newDict);
- newDict->Delete();
- newEntry->Copy(entry);
- newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
- oldEntry->SetSelfArea(false);
-
- RemoveEntry(oldEntry);
- AddEntry(newEntry);
+ {
+ //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
+ // PixelVR,"1","Pixel Data");
+ //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();
+
}
}
+*/
+ 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 = "OB";
+ else
+ PixelVR = "OW";
+ // Change only made if usefull
+ if ( PixelVR != entry->GetVR() )
+ {
+ entry->SetVR(PixelVR);
+ }
}
return true;
}
+
/**
* \brief This predicate, based on hopefully reasonable heuristics,
* decides whether or not the current File was properly parsed
return 1;
}
+/**
+ * \brief Retrieve the -unnormalized- number of 'times' of '4D image'.
+ * User has to tell gdcm the location of this '4th Dimension component'
+ * using SetFourthDimensionLocation() method before.
+ * \warning The defaulted value is 1.
+ * @return The encountered size when found, 1 by default
+ * (The file doesn't contain a '4D image'.).
+ */
+int File::GetTSize()
+{
+ if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object
+ return 1;
+
+ DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(),
+ FourthDimensionLocation.GetElement() );
+ if( !entry )
+ {
+ gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
+ std::hex << FourthDimensionLocation.GetGroup()
+ << "|" << FourthDimensionLocation.GetElement());
+ return 1;
+ }
+ else
+ {
+ return (int)entry->GetValue(0);
+ }
+}
+
/**
* \brief gets the info from 0018,1164 : ImagerPixelSpacing
* then 0028,0030 : Pixel Spacing
{
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);
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 !=2 )
+ gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
+ << "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);
{
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;
}
{
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;
}
* \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)");
- return zspacing;
-
-/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
- if ( strSpacingBSlices == GDCM_UNFOUND )
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ entry = GetDataEntry(0x3004,0x000c);
+ if( entry )
{
- 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 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;
}
-
- float zsp = (float)atof( strSpacingBSlices.c_str());
- if (zsp == 0.0) // last change not to break further computations ...
- zsp = 1.0;
- return zsp;*/
+
+ return zspacing;
}
/**
if( entry->GetValueCount() == 3 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
- 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 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
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 )
- {
- gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
- }
- }
-
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
- {
- return 0.;
- }
-
- return yImPos;*/
}
/**
{
if( entry->GetValueCount() == 3 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
- 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 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
- 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->GetValueCount() == 1 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
- return (float)entry->GetValue(0);
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0); // VM=1 !
}
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;
- }
- }
- gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/
entry = GetDataEntry(0x0020,0x0050);
if( entry )
{
if( entry->GetValueCount() == 1 )
{
- gdcmAssertMacro( entry->IsValueCountValid() );
+ 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
}
/**
* \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.;
+ iop[0] = iop[4] = 1.;
+ iop[1] = iop[2] = iop[3] = iop[5] = 0.;
// 0020 0037 DS REL Image Orientation (Patient)
if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
<< " Less than 6 values were found." );
return false;
}
+ return true;
}
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
<< "Less than 6 values were found." );
return false;
}
+ return true;
}
- return true;
+ return false;
}
-
-
/**
* \brief Retrieve the number of Bits Stored (actually used)
* (as opposed to number of Bits Allocated)
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);
-
-/* 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() );*/
}
/**
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);
-
-/* 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() );*/
}
/**
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);
-
-/* 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() );*/
}
/**
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
}
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() );*/
}
/**
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 )
- {
- gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
- return 0;
- }
- return atoi( strSize.c_str() );*/
}
/**
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
}
{
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;
}
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;
-/* 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;*/
}
/**
}
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;
}
/**
*\brief gets the info from 0028,1052 : Rescale Intercept
- * @return Rescale Intercept
+ * @return Rescale Intercept. defaulted to 0.0 is not found or empty
*/
float File::GetRescaleIntercept()
{
}
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;*/
}
/**
*\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope
+ * @return Rescale Slope. defaulted to 1.0 is not found or empty
*/
float File::GetRescaleSlope()
{
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);
-/* 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;*/
}
/**
* \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 ...)
+ * (or a monochrome one, if no LUT found ...)
* \warning to be used with GetImagePixels()
* @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
*/
}
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
+ /// \todo 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, "UL");
+ }
+ }
Document::WriteContent(fp, writetype);
fp->close();
// Offset Table information on fragments of this current Frame.
// Note that the fragment pixels themselves are not loaded
// (but just skipped).
- long frameOffset = Fp->tellg();
+ long frameOffset = Fp->tellg(); // once per fragment
uint32_t nbRleSegments = ReadInt32();
if ( nbRleSegments > 16 )
// Make sure that we encounter a 'Sequence Delimiter Item'
// at the end of the item :
- if ( !ReadTag(0xfffe, 0xe0dd) )
+ if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
{
gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
}
i++;
}
- long fragmentOffset = Fp->tellg();
+ long fragmentOffset = Fp->tellg(); // Once per fragment
// Store the collected info
JPEGFragment *newFragment = new JPEGFragment;
newFragment->SetOffset(fragmentOffset);
/**
* \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.
*/
bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
{
- long positionOnEntry = Fp->tellg();
- long currentPosition = Fp->tellg(); // On debugging purposes
+ long positionOnEntry = Fp->tellg(); // Only when reading fragments
+ //long currentPosition = positionOnEntry; // On debugging purposes
// Read the Item Tag group and element, and make
// sure they are what we expected:
}
if ( itemTagGroup != testGroup || itemTagElem != testElem )
{
- 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 << ")"
- ) ;
+ // in order not to pollute output we don't warn on 'delimitors'
+ if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
+ gdcmWarningMacro( "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)positionOnEntry << std::dec << ")"
+ ) ;
Fp->seekg(positionOnEntry, std::ios::beg);
return false;
if ( !ReadTag(testGroup, testElem) )
{
- gdcmErrorMacro( "ReadTag did not succeed for ("
+ // 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();
+
+ // long currentPosition = Fp->tellg(); // save time // JPRx
uint32_t itemLength = ReadInt32();
gdcmDebugMacro( "Basic Item Length is: " << itemLength
- << " at address: " << std::hex << (unsigned int)currentPosition);
+// << " at address: " << std::hex << (unsigned int)currentPosition
+ );
return itemLength;
}
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
-/* *
- * \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
*/