Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2006/11/15 15:54:15 $
- Version: $Revision: 1.327 $
+ Date: $Date: 2009/05/19 15:08:36 $
+ Version: $Revision: 1.344 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
#include "gdcmDataEntry.h"
+#include "gdcmSQItem.h"
#include <vector>
#include <stdio.h> //sscanf
#include <stdlib.h> // for atoi
-namespace gdcm
-
+namespace GDCM_NAME_SPACE
{
//-----------------------------------------------------------------------------
* @return false if file cannot be open or no swap info was found,
* or no tag was found.
*/
-
bool File::Load( )
{
if ( ! this->Document::Load( ) )
}
else
{
-
GrPixel = (uint16_t) atoi( imgLocation.c_str() );
}
// Change only made if usefull
if ( PixelVR != oldEntry->GetVR() )
- {
+ {
//DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
// PixelVR,"1","Pixel Data");
//DataEntry *newEntry = DataEntry::New(newDict);
//RemoveEntry(oldEntry);
//AddEntry(newEntry);
//newEntry->Delete();
-
}
}
*/
return 1;
}
+// Special case:
+// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage";
+bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing)
+{
+ xspacing = yspacing = zspacing = 1.0;
+ TS *ts = Global::GetTS();
+ std::string sopclassuid_used;
+ // D 0002|0002 [UI] [Media Storage SOP Class UID]
+
+ //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002);
+ const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002);
+ const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str);
+ //D 0008|0016 [UI] [SOP Class UID]
+ const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016);
+ const std::string &sopclassuid = ts->GetValue(sopclassuid_str);
+ if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND )
+ {
+ return false;
+ }
+ else
+ {
+ if ( mediastoragesopclassuid == sopclassuid )
+ {
+ sopclassuid_used = mediastoragesopclassuid;
+ }
+ else
+ {
+ gdcmWarningMacro( "Inconsistant SOP Class UID: "
+ << mediastoragesopclassuid << " and " << sopclassuid );
+ return false;
+ }
+ }
+ // ok we have now the correct SOP Class UID
+ if( sopclassuid_used == "Enhanced MR Image Storage" )
+ {
+ SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230);
+ unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems();
+ if( !n ) return false;
+ SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem();
+ DocEntry *p = item1->GetDocEntry(0x0028,0x9110);
+ if( !p ) return false;
+ SeqEntry *seq = dynamic_cast<SeqEntry*>(p);
+ unsigned int n1 = seq->GetNumberOfSQItems();
+ if( !n1 ) return false;
+ SQItem *item2 = seq->GetFirstSQItem();
+ // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ]
+ DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030);
+ if( !p2 ) return false;
+ DataEntry *entry = dynamic_cast<DataEntry *>(p2);
+ std::string spacing = entry->GetString();
+ if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 )
+ {
+ xspacing = yspacing = 1.;
+ return false;
+ }
+ // D 0018|0050 [DS] [Slice Thickness] [1 ]
+ DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050);
+ if( !p3 ) return false;
+ DataEntry *entry2 = dynamic_cast<DataEntry *>(p3);
+ std::string thickness = entry2->GetString();
+ if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 )
+ {
+ zspacing = 1.;
+ return false;
+ }
+ return true;
+ }
+ return false;
+ }
+
/**
* \brief Retrieve the -unnormalized- number of 'times' of '4D image'.
* User has to tell gdcm the location of this '4th Dimension component'
DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(),
FourthDimensionLocation.GetElement() );
- if( !entry )
+ if( !entry )
{
gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
std::hex << FourthDimensionLocation.GetGroup()
{
return (int)entry->GetValue(0);
}
-}
+}
/**
* \brief gets the info from 0018,1164 : ImagerPixelSpacing
float File::GetXSpacing()
{
float xspacing = 1.0;
+ float yspacing = 1.0;
+ float zspacing = 1.0;
+
uint32_t nbValue;
DataEntry *entry;
- bool ok = false;
+ bool ok = false;
+ if ( GetSpacing(xspacing,yspacing,zspacing) )
+ {
+ return xspacing;
+ }
+ // else fallback
+
/*
From:David Clunie - view profile
Date:Wed, May 24 2006 1:12 pm
if( nbValue !=2 )
gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
<< "has a wrong number of values :" << nbValue);
-
+
if( nbValue >= 3 )
xspacing = (float)entry->GetValue(2);
else if( nbValue >= 2 )
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 )
*/
float File::GetYSpacing()
{
- float yspacing;
+ float xspacing = 1., yspacing = 1.0, zspacing = 1.;
uint32_t nbValue;
DataEntry *entry;
bool ok = false;
-
+ if ( GetSpacing(xspacing,yspacing,zspacing) )
+ {
+ return yspacing;
+ }
+ // else fallback
+
std::string SOPClassUID = GetEntryString(0x0008,0x0016);
/// \todo check the various SOP Class
float File::GetZSpacing()
{
- float zspacing = 1.0f;
+ float xspacing = 1.0;
+ float yspacing = 1.0;
+ float zspacing = 1.0;
+ if ( GetSpacing(xspacing,yspacing,zspacing) )
+ {
+ return zspacing;
+ }
// Spacing Between Slices : distance between the middle of 2 slices
// Slices may be :
// (in order no to be messed up by old RGB images)
bitsAlloc = "8";
}
-
+
int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers
if ( i > 8 && i < 16 )
{
bitsAlloc = "16";
}
-
+
std::string sign;
if( IsSignedPixelData() )
{
{
gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
<< "mandatory");
+ // to deal with old ACR-NEMA images
+ if (GetNumberOfScalarComponents() == 1)
+ return true;
}
return false;
}
{
return true;
}
+
+ // MONOCHROME + [Enhanced CT Image Storage] actually have Palettes
+ std::string sopClassUid = GetEntryString( 0x0008, 0x0016 );
+ if (Util::DicomStringEqual( sopClassUid, "1.2.840.10008.5.1.4.1.1.2.1"))
+ {
+ return true;
+ }
if ( PhotometricInterp == GDCM_UNFOUND )
{
gdcmDebugMacro( "Not found : Palette color (0028,0004)");
*/
bool File::IsYBRFull()
{
- std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( PhotometricInterp == "YBR_FULL" )
{
return true;
return false;
}
// Red Palette Color Lookup Table Data
- if ( !GetDocEntry(0x0028,0x1201) )
+ bool segmented;
+ segmented = GetDocEntry(0x0028,0x1221) &&
+ GetDocEntry(0x0028,0x1222) &&
+ GetDocEntry(0x0028,0x1223);
+ if( segmented ) return true;
+
+ if( !GetDocEntry(0x0028,0x1201) )
{
return false;
}
return lutNbits;
}
+// Special case:
+// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage";
+ bool File::GetRescaleSlopeIntercept(double &slope, double &intercept)
+ {
+ slope = 1.0;
+ intercept = 0.0;
+ TS *ts = Global::GetTS();
+ std::string sopclassuid_used;
+ // D 0002|0002 [UI] [Media Storage SOP Class UID]
+ const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002);
+ const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str);
+ //D 0008|0016 [UI] [SOP Class UID]
+ const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016);
+ const std::string &sopclassuid = ts->GetValue(sopclassuid_str);
+ if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND )
+ {
+ return false;
+ }
+ else
+ {
+ if( mediastoragesopclassuid == sopclassuid )
+ {
+ sopclassuid_used = mediastoragesopclassuid;
+ }
+ else
+ {
+ gdcmWarningMacro( "Inconsistant SOP Class UID: "
+ << mediastoragesopclassuid << " and " << sopclassuid );
+ return false;
+ }
+ }
+ // ok we have now the correc SOP Class UID
+ if( sopclassuid_used == "Enhanced MR Image Storage" )
+ {
+ SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230);
+ unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems();
+ if( !n ) return false;
+ SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem();
+ DocEntry *p = item1->GetDocEntry(0x0028,0x9145);
+ if( !p ) return false;
+ SeqEntry *seq = dynamic_cast<SeqEntry*>(p);
+ unsigned int n1 = seq->GetNumberOfSQItems();
+ if( !n1 ) return false;
+ SQItem *item2 = seq->GetFirstSQItem();
+ // D 0028|1052 [DS] [Rescale Intercept] [0 ]
+ DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052);
+ if( !p2 ) return false;
+ DataEntry *entry = dynamic_cast<DataEntry *>(p2);
+ std::string intercept_str = entry->GetString();
+ if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 )
+ {
+ intercept = 0.;
+ return false;
+ }
+ // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085]
+ DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053);
+ if( !p3 ) return false;
+ DataEntry *entry2 = dynamic_cast<DataEntry *>(p3);
+ std::string slope_str = entry2->GetString();
+ if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 )
+ {
+ slope = 1.;
+ return false;
+ }
+ return true;
+ }
+ return false;
+ }
+
/**
*\brief gets the info from 0028,1052 : Rescale Intercept
- * @return Rescale Intercept. defaulted to 0.0 is not found or empty
+ * @return Rescale Intercept. defaulted to 0.0 if not found or empty
*/
-float File::GetRescaleIntercept()
+double File::GetRescaleIntercept()
{
// 0028 1052 DS IMG Rescale Intercept
DataEntry *entry = GetDataEntry(0x0028, 0x1052);
/**
*\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope. defaulted to 1.0 is not found or empty
+ * @return Rescale Slope. defaulted to 1.0 if not found or empty
*/
-float File::GetRescaleSlope()
+double File::GetRescaleSlope()
{
- // 0028 1053 DS IMG Rescale Slope
- DataEntry *entry = GetDataEntry(0x0028, 0x1053);
- if( !entry )
- {
- gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
- return 1.0f;
+ double resInter = 0.;
+ double resSlope = 1.;
+ if ( GetRescaleSlopeIntercept(resSlope, resInter) )
+ {
+ return resSlope;
+ }
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryString(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 )
+ {
+ // bug in the element 0x0028,0x1053
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
+ }
}
- return (float)entry->GetValue(0);
+
+ return resSlope;
}
/**
{
std::fstream *fp = new std::fstream(Filename.c_str(),
std::ios::in | std::ios::out | std::ios::binary);
- gdcm::DocEntry *d;
+ GDCM_NAME_SPACE::DocEntry *d;
uint32_t offset;
uint32_t lgth;
uint32_t valLgth = 0;
gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
continue;
}
-
+
valLgth = (*it).Value.size();
if (valLgth == 0)
continue;
}
else
{
- gdcm::DocEntry *d;
+ GDCM_NAME_SPACE::DocEntry *d;
for (ListElements::iterator it = UserAnonymizeList.begin();
it != UserAnonymizeList.end();
++it)
gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
continue;
}
-
+/*
if ( dynamic_cast<DataEntry *>(d) )
{
gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
continue;
}
+*/
else
SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
}
*/
bool File::Write(std::string fileName, FileType writetype)
{
+ gdcmDebugMacro(" File::Write ");
std::ofstream *fp = new std::ofstream(fileName.c_str(),
std::ios::out | std::ios::binary);
if (*fp == NULL)
}
/// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
- if( writetype != JPEG )
+ if( writetype != JPEG && writetype != JPEG2000)
{
int i_lgPix = GetEntryLength(GrPixel, NumPixel);
- if (i_lgPix != -2)
+ if (i_lgPix != -2) /// \todo wtf "-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");
+ InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL");
}
}
- Document::WriteContent(fp, writetype);
+ Document::WriteContent(fp, writetype,false,false);
fp->close();
delete fp;
// Private
/**
* \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
- * Compute the RLE extra information and store it in \ref RLEInfo
+ * Compute the RLE extra information and store it in RLEInfo
* for later pixel retrieval usage.
*/
void File::ComputeRLEInfo()
/**
* \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
* Compute the jpeg extra information (fragment[s] offset[s] and
- * length) and store it[them] in \ref JPEGInfo for later pixel
+ * length) and store it[them] in JPEGInfo for later pixel
* retrieval usage.
*/
void File::ComputeJPEGFragmentInfo()
}
/**
- * \brief Assuming the internal file pointer \ref Document::Fp
+ * \brief Assuming the internal file pointer Document::Fp
* 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
+ * \warning On success the internal file pointer Document::Fp
* is modified to point after the tag.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElem) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
+ * Document::Fp is restored to its original position.
* @param testGroup The expected group of the tag.
* @param testElem The expected Element of the tag.
* @return True on success, false otherwise.
}
catch ( FormatError )
{
- gdcmErrorMacro( "Can not read tag for "
- << " We should have found tag ("
+ gdcmErrorMacro( "Can not read tag at 0x("
+ << std::hex << positionOnEntry
+ << "). We should have found tag ("
<< DictEntry::TranslateToKey(testGroup,testElem) << ")"
) ;
<< " but instead we encountered tag ("
<< DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
<< " at address: " << " 0x(" << std::hex
- << (unsigned int)positionOnEntry << std::dec << ")"
+ << (unsigned int)positionOnEntry << std::dec << ")"
) ;
Fp->seekg(positionOnEntry, std::ios::beg);
}
/**
- * \brief Assuming the internal file pointer \ref Document::Fp
+ * \brief Assuming the internal file pointer Document::Fp
* is placed at the beginning of a tag (TestGroup, TestElement),
* read the length associated to the Tag.
- * \warning On success the internal file pointer \ref Document::Fp
- * is modified to point after the tag and it's length.
+ * \warning On success the internal file pointer Document::Fp
+ * is modified to point after the tag and its length.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
+ * Document::Fp is restored to its original position.
* @param testGroup The expected Group of the tag.
* @param testElem The expected Element of the tag.
* @return On success returns the length associated to the tag. On failure
}
//// Then read the associated Item Length
-
+
// long currentPosition = Fp->tellg(); // save time // JPRx
uint32_t itemLength = ReadInt32();
gdcmDebugMacro( "Basic Item Length is: " << itemLength
// When present, read the basic offset table itself.
// Notes: - since the presence of this basic offset table is optional
// we can't rely on it for the implementation, and we will simply
- // trash it's content (when present).
+ // trash its content (when present).
// - still, when present, we could add some further checks on the
// lengths, but we won't bother with such fuses for the time being.
if ( itemLength != 0 )
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff