Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/11/05 13:24:39 $
- Version: $Revision: 1.302 $
+ 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
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 = DataEntry::New(newDict);
- newDict->Delete();
- newEntry->Copy(entry);
- newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
- oldEntry->SetSelfArea(false);
-
- RemoveEntry(oldEntry);
- AddEntry(newEntry);
- newEntry->Delete();
+ {
+ //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
{
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
}
-
return xspacing;
}
* \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;
}
/**
* \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;
}
/**
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
}
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;
}
/**
*\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()
{
/**
*\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);
/**
* \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());
}
- // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
+ /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
if( writetype != JPEG )
{
int i_lgPix = GetEntryLength(GrPixel, NumPixel);
// 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);
+ InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL");
}
}
Document::WriteContent(fp, writetype);
// 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);
*/
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:
return false;
}
if ( itemTagGroup != testGroup || itemTagElem != testElem )
- {
+ {
// 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 ("
<< DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
<< " at address: " << " 0x(" << std::hex
- << (unsigned int)currentPosition << std::dec << ")"
+ << (unsigned int)positionOnEntry << std::dec << ")"
) ;
Fp->seekg(positionOnEntry, std::ios::beg);
}
//// 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;
}
* @ 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