Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/10/10 22:25:05 $
- Version: $Revision: 1.274 $
+ 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
//
// -------------- 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
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmTS.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
#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
{
//-----------------------------------------------------------------------------
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
// Note: this IS the right place for the code
// Image Location
- const std::string &imgLocation = GetEntryValue(0x0028, 0x0200);
+ const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
if ( imgLocation == GDCM_UNFOUND )
{
// default value
ComputeJPEGFragmentInfo();
CloseFile();
- // Create a new BinEntry to change the DictEntry
+ // Create a new DataEntry to change the DictEntry
// The changed DictEntry will have
// - a correct PixelVR OB or OW)
// - the name to "Pixel Data"
- BinEntry *oldEntry = dynamic_cast<BinEntry *>(entry);
+
+ //==>Take it easy!
+ //==> Just change the VR !
+
+/*
+ DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
if (oldEntry)
{
- std::string PixelVR;
+ 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 )
// Change only made if usefull
if ( PixelVR != oldEntry->GetVR() )
{
- DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
- PixelVR,"1","Pixel Data");
-
- BinEntry *newEntry = new BinEntry(newDict);
- 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 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB)
+ // more than 8 (i.e 12, 16) is a 'OW(ords)'
+ 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 false;
}
- const std::string &res = GetEntryValue(0x0028, 0x0005);
+ const std::string &res = GetEntryString(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
gdcmWarningMacro("Wrong Image Dimensions" << res);
int File::GetImageNumber()
{
//0020 0013 : Image Number
- std::string strImNumber = GetEntryValue(0x0020,0x0013);
+ std::string strImNumber = GetEntryString(0x0020,0x0013);
if ( strImNumber != GDCM_UNFOUND )
{
return atoi( strImNumber.c_str() );
ModalityType File::GetModality()
{
// 0008 0060 : Modality
- std::string strModality = GetEntryValue(0x0008,0x0060);
+ std::string strModality = GetEntryString(0x0008,0x0060);
if ( strModality != GDCM_UNFOUND )
{
if ( strModality.find("AU") < strModality.length()) return AU;
*/
int File::GetXSize()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0011);
- if ( strSize == GDCM_UNFOUND )
- {
- return 0;
- }
- return atoi( strSize.c_str() );
+ DataEntry *entry = GetDataEntry(0x0028,0x0011);
+ if( entry )
+ return (int)entry->GetValue(0);
+ return 0;
}
/**
*/
int File::GetYSize()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0010);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
+ DataEntry *entry = GetDataEntry(0x0028,0x0010);
+ if( entry )
+ return (int)entry->GetValue(0);
+
if ( IsDicomV3() )
{
return 0;
{
// Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
- const std::string &strSize = GetEntryValue(0x0028,0x0008);
- if ( strSize != GDCM_UNFOUND )
- {
- return atoi( strSize.c_str() );
- }
+ DataEntry *entry = GetDataEntry(0x0028,0x0008);
+ if( entry )
+ return (int)entry->GetValue(0);
// We then consider the "Planes" entry as the third dimension
- const std::string &strSize2 = GetEntryValue(0x0028,0x0012);
- if ( strSize2 != GDCM_UNFOUND )
+ entry = GetDataEntry(0x0028,0x0012);
+ if( entry )
+ return (int)entry->GetValue(0);
+ 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'
+ * 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 )
{
- return atoi( strSize2.c_str() );
+ gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
+ std::hex << FourthDimensionLocation.GetGroup()
+ << "|" << FourthDimensionLocation.GetElement());
+ return 1;
}
- return 1;
+ else
+ {
+ return (int)entry->GetValue(0);
+ }
}
/**
{
float xspacing = 1.0;
float yspacing = 1.0;
- int nbValues;
+ float zspacing = 1.0;
- // To follow David Clunie's advice, we first check ImagerPixelSpacing
+ uint32_t nbValue;
+ DataEntry *entry;
+ bool ok = false;
+ if ( GetSpacing(xspacing,yspacing,zspacing) )
+ {
+ return xspacing;
+ }
+ // else fallback
- const std::string &strImagerPixelSpacing = GetEntryValue(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;
+/*
+From:David Clunie - view profile
+Date:Wed, May 24 2006 1:12 pm
+Email:David Clunie <dclu...@dclunie.com>
+Groups:comp.protocols.dicom
+
+The short answer is that:
+
+- (0018,1164) describes a spacing equivalent to that which
+ would be measured off a film in projection radiography
- if ( xspacing == 0.0 )
- xspacing = 1.0;
+- (0018,7022) does not describe the image pixels themselves,
+ since detector elements may have been binned to produce
+ pixels
+- (0018,7020) may be different from (0018,7022) since there
+ may be non-sensitive material separating individual
+ detectors (i.e. the size is smaller than the spacing
+ between centers)
+
+Only (0018,1164) is relevant when measuring things; the
+detector-specific attributes are there to describe the
+acquisition.
+
+David
+
+PS. For ultrasound you need to use Region Calibration.
+*/
+
+/*
+It *SHOULD* first find the IOD and then deduce which tags to read
+Eg: Cross section this is in Pixel Spacing (0028,0030)
+CR is in Imager Pixel Spacing (0018,1164)
+US is in Pixel Aspect Ratio (0028,0034)
+RT is in :
+(3002,0011) Image Plane Pixel Spacing
+(3002,0012) RT Image Position
+and
+(3004,000c) for deducing Z spacing
+*/
+
+ std::string SOPClassUID = GetEntryString(0x0008,0x0016);
+
+ /// \todo check the various SOP Class
+ /// to get the Pixel Spacing at the proper location
+
+ ///\todo find images to check if it *actually* works
+
+ if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6")
+ // Ultrasound Image Storage (Retired)
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1")
+ // Ultrasound Image Storage
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3")
+ // Ultrasound Multi-Frame Storage (Retired)
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") )
+ // Ultrasound Multi-FrameImage Storage
+ {
+ // - check if SOPClassUID contains 2 parts (e.g. "4\3")
+ // - guess how to deduce the spacing (FOV ?, ??)
+
+ entry = GetDataEntry(0x0028,0x0034);
+ if ( entry )
+ {
+ nbValue = entry->GetValueCount();
+ if( nbValue !=2 ) {
+ gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) "
+ << "has a wrong number of values :" << nbValue);
+ }
+ xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ...
+ ok = true;
+ }
+
+ if (ok)
return xspacing;
- }
}
+/*
+ if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") )
+ // Computed Radiography Image Storage
- const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
+ // CR is in Imager Pixel Spacing (0018,1164)//
- if ( strSpacing == GDCM_UNFOUND )
- {
- gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
- return 1.;
- }
+*/
+ // go on with old method ...
+ // ---------------------
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
- if ( ( nbValues = sscanf( strSpacing.c_str(),
- "%f \\%f ", &yspacing, &xspacing)) != 2 )
+ entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
{
- // 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;
+ 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);
+ else if( nbValue >= 2 )
+ xspacing = (float)entry->GetValue(1);
+ else
+ xspacing = (float)entry->GetValue(0);
if ( xspacing == 0.0 )
xspacing = 1.0;
-
return xspacing;
}
+ else
+ {
+ gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
+ }
- // to avoid troubles with David Clunie's-like images (at least one)
- if ( xspacing == 0. && yspacing == 0.)
- return 1.;
+ 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);
+ else if( nbValue >= 2 )
+ xspacing = (float)entry->GetValue(1);
+ else
+ xspacing = (float)entry->GetValue(0);
- if ( xspacing == 0.)
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+ return xspacing;
+ }
+ else
{
- 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 );
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
}
-
return xspacing;
}
*/
float File::GetYSpacing()
{
- float yspacing = 1.;
- int nbValues;
+ 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
+ /// to get the Pixel Spacing at the proper location
+
+ ///\todo find images to check if it *actually* works
+
+ if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6")
+ // Ultrasound Image Storage (Retired)
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1")
+ // Ultrasound Image Storage
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3")
+ // Ultrasound Multi-Frame Storage (Retired)
+ || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") )
+ // Ultrasound Multi-FrameImage Storage
+ {
+ // - check if SOPClassUID contains 2 parts (e.g. "4\3")
+ // - no way to deduce the spacing/
+
+ entry = GetDataEntry(0x0028,0x0034);
+ if ( entry )
+ {
+ nbValue = entry->GetValueCount();
+ if( nbValue ==2 ) {
+ yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1);
+ //std::cout << "ys " << yspacing << std::endl;
+ ok = true;
+ }
+ else
+ {
+ gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) "
+ << "has a wrong number of values :" << nbValue);
+ if (nbValue == 0 ) {
+ ok = false;
+ }
+ else if (nbValue == 1 ) {
+ yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ...
+ ok = true;
+ }
+ }
+ }
+
+ if (ok)
+ return yspacing;
+ }
+
+ // go on with old method ...
+ // ---------------------
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+ yspacing = 1.0;
// To follow David Clunie's advice, we first check ImagerPixelSpacing
- const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
- if ( strImagerPixelSpacing != GDCM_UNFOUND )
+ entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
{
- 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;
+ yspacing = (float)entry->GetValue(0);
if ( yspacing == 0.0 )
- yspacing = 1.0;
-
- return yspacing;
+ yspacing = 1.0;
+ return yspacing;
}
-
- std::string strSpacing = GetEntryValue(0x0028,0x0030);
- if ( strSpacing == GDCM_UNFOUND )
+ else
{
- 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);
+ gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
+ }
- // if no values, yspacing is set to 1.0
- if ( nbValues == 0 )
- yspacing = 1.0;
+ entry = GetDataEntry(0x0028,0x0030);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(0);
- if ( yspacing == 0.0 )
- yspacing = 1.0;
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+ return yspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
+ }
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()
{
+
+ 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 :
// jointives (Spacing between Slices = Slice Thickness)
// It only concerns the MRI guys, not people wanting to visualize volumes
// If Spacing Between Slices is missing,
// we suppose slices joint together
-
- const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
+ DataEntry *entry = GetDataEntry(0x0018,0x0088);
+ if( entry )
+ { zspacing = (float)entry->GetValue(0);
- if ( strSpacingBSlices == GDCM_UNFOUND )
- {
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+ else
gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
- const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
- if ( strSliceThickness == GDCM_UNFOUND )
- {
- gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
- return 1.;
- }
- 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() );
- }
+
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ entry = GetDataEntry(0x0018,0x0050);
+ if( entry )
+ {
+ zspacing = (float)entry->GetValue(0);
+
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+ 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;
}
- //else
- return (float)atof( strSpacingBSlices.c_str() );
+
+ return zspacing;
}
/**
*/
float File::GetXOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
{
gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
{
gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
+ return 0.0f;
}
}
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
+ if( entry->GetValueCount() == 3 )
{
- return 0.;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0);
}
-
- return xImPos;
+ return 0.0f;
}
/**
*/
float File::GetYOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
-
- if ( strImPos == GDCM_UNFOUND)
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
{
gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos == GDCM_UNFOUND )
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
{
gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
- return 0.;
- }
+ return 0.0f;
+ }
}
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
+ if( entry->GetValueCount() == 3 )
{
- return 0.;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(1);
}
-
- return yImPos;
+ return 0.0f;
}
/**
*/
float File::GetZOrigin()
{
- float xImPos, yImPos, zImPos;
- std::string strImPos = GetEntryValue(0x0020,0x0032);
-
- if ( strImPos != GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( entry )
{
- if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3)
+ if( entry->GetValueCount() == 3 )
{
- gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(2);
}
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.0f;
}
- strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
- if ( strImPos != GDCM_UNFOUND )
+ entry = GetDataEntry(0x0020,0x0030);
+ if( entry )
{
- if ( sscanf( strImPos.c_str(),
- "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 )
+ if( entry->GetValueCount() == 3 )
{
- gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
- return 0.; // bug in the element 0x0020,0x0032
- }
- else
- {
- return zImPos;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(2);
}
+ gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
+ return 0.0f;
}
// for *very* old ACR-NEMA images
- std::string strSliceLocation = GetEntryValue(0x0020,0x1041);
- if ( strSliceLocation != GDCM_UNFOUND )
+ entry = GetDataEntry(0x0020,0x1041);
+ if( entry )
{
- if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
+ if( entry->GetValueCount() == 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)");
- std::string strLocation = GetEntryValue(0x0020,0x0050);
- if ( strLocation != GDCM_UNFOUND )
+ entry = GetDataEntry(0x0020,0x0050);
+ if( entry )
{
- if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 )
- {
- gdcmWarningMacro( "Wrong Location (0020,0050)");
- return 0.; // bug in the element 0x0020,0x0050
- }
- else
+ if( entry->GetValueCount() == 1 )
{
- return zImPos;
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0);
}
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
+ return 0.0f;
}
- 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 = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
+ 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 )
<< " Less than 6 values were found." );
return false;
}
+ return true;
}
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
- else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
+ else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != 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 )
<< "Less than 6 values were found." );
return false;
}
+ return true;
}
- return true;
+ return false;
}
+/**
+ * \brief gets the cosine of image X axis, against patient X axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image X axis, against patient X axis
+ */
+float File::GetXCosineOnX()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[0]);
+}
+
+/**
+ * \brief gets the cosine of image X axis, against patient Y axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image X axis, against patient Y axis
+ */
+float File::GetXCosineOnY()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[1]);
+}
+/**
+ * \brief gets the cosine of image X axis, against patient Z axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image X axis, against patient Z axis
+ */
+float File::GetXCosineOnZ()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[2]);
+}
+
+/**
+ * \brief gets the cosine of image Y axis, against patient X axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image Y axis, against patient X axis
+ */
+float File::GetYCosineOnX()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[3]);
+}
+
+/**
+ * \brief gets the cosine of image Y axis, against patient Y axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image Y axis, against patient Y axis
+ */
+float File::GetYCosineOnY()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[4]);
+}
+
+/**
+ * \brief gets the cosine of image Y axis, against patient Z axis
+ * (Sorry, but Python needs it :-( )
+ * @return cosine of image Y axis, against patient Z axis
+ */
+float File::GetYCosineOnZ()
+{
+ float iop[6];
+ GetImageOrientationPatient( iop );
+ return(iop[5]);
+}
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * or from 0020 0030 : Image Position (RET)
+ *
+ * @param ipp adress of the (3)float array to receive values.
+ * (defaulted as 0.,0.,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::GetImagePositionPatient( float ipp[3] )
+{
+ std::string strImPosiPat;
+ //ipp is supposed to be float[3]
+ ipp[0] = ipp[1] = ipp[2] = 0.;
+
+ // 0020 0032 DS REL Image Position (Patient)
+ strImPosiPat = GetEntryString(0x0020,0x0032);
+ if ( strImPosiPat != GDCM_UNFOUND )
+ {
+ if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ",
+ &ipp[0], &ipp[1], &ipp[2]) != 3 )
+ {
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)."
+ << " Less than 3 values were found." );
+ return false;
+ }
+ return true;
+ }
+ //For ACR-NEMA
+ // 0020 0030 DS REL Image Position (RET)
+ else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND )
+ {
+ if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ",
+ &ipp[0], &ipp[1], &ipp[2]) != 3 )
+ {
+ gdcmWarningMacro( "wrong Image Position Patient (0020,0030). "
+ << "Less than 3 values were found." );
+ return false;
+ }
+ return true;
+ }
+ return false;
+}
/**
* \brief Retrieve the number of Bits Stored (actually used)
*/
int File::GetBitsStored()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0101 );
- if ( strSize == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0028,0x0101);
+ if( !entry )
{
- gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
+ gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
+ return 0;
}
- return atoi( strSize.c_str() );
+ return (int)entry->GetValue(0);
}
/**
*/
int File::GetBitsAllocated()
{
- std::string strSize = GetEntryValue(0x0028,0x0100);
- if ( strSize == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0028,0x0100);
+ if( !entry )
{
- gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
- return 0; // It's supposed to be mandatory
- // the caller will have to check
+ gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
+ return 0;
}
- return atoi( strSize.c_str() );
+ return (int)entry->GetValue(0);
}
/**
*/
int File::GetHighBitPosition()
{
- std::string strSize = GetEntryValue( 0x0028, 0x0102 );
- if ( strSize == GDCM_UNFOUND )
+ 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 atoi( strSize.c_str() );
+ return (int)entry->GetValue(0);
}
/**
*/
int File::GetSamplesPerPixel()
{
- const std::string &strSize = GetEntryValue(0x0028,0x0002);
- if ( strSize == GDCM_UNFOUND )
+ 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 atoi( strSize.c_str() );
+ return (int)entry->GetValue(0);
}
/**
*/
int File::GetPlanarConfiguration()
{
- std::string strSize = GetEntryValue(0x0028,0x0006);
- if ( strSize == GDCM_UNFOUND )
+ DataEntry *entry = GetDataEntry(0x0028,0x0006);
+ if( !entry )
{
- gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
- return atoi( strSize.c_str() );
+ return (int)entry->GetValue(0);
}
/**
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old ACR-NEMA RGB images)
- // if (File::GetEntryValue(0x0028,0x0100) == "24")
- // return 3;
- assert( !(GetEntryValue(0x0028,0x0100) == "24") );
+ assert( !(GetEntryString(0x0028,0x0100) == "24") );
std::string pixelType = GetPixelType();
if ( pixelType == "8U" || pixelType == "8S" )
{
return 8;
}
- gdcmWarningMacro( "Unknown pixel type");
+ gdcmWarningMacro( "Unknown pixel type: " << pixelType);
return 0;
}
*/
std::string File::GetPixelType()
{
- std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
+ 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
}
- if ( bitsAlloc == "64" )
+ else if ( bitsAlloc == "64" )
{
return "FD";
}
+ // useless since we have to bypass a bug ( >8 && < 16)
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 = GetEntryValue(0x0028, 0x0103);//"Pixel Representation"
-
- if (sign == GDCM_UNFOUND )
+ int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers
+ if ( i > 8 && i < 16 )
{
- gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
- sign = "U"; // default and arbitrary value, not to polute the output
+ bitsAlloc = "16";
}
- else if ( sign == "0" )
+
+ std::string sign;
+ if( IsSignedPixelData() )
{
- sign = "U";
+ sign = "S";
}
else
{
- sign = "S";
+ sign = "U";
}
return bitsAlloc + sign;
}
*/
bool File::IsSignedPixelData()
{
- std::string strSign = GetEntryValue( 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 )
+ DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
+ if( !entry )
{
+ gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
+ << "mandatory");
return false;
}
- return true;
+ return entry->GetValue(0) != 0;
}
/**
*/
bool File::IsMonochrome()
{
- const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
|| Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
+ << "mandatory");
+ // to deal with old ACR-NEMA images
+ if (GetNumberOfScalarComponents() == 1)
+ return true;
}
return false;
}
*/
bool File::IsMonochrome1()
{
- const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
{
return true;
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
+ << " be mandatory! ");
}
return false;
}
*/
bool File::IsPaletteColor()
{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( PhotometricInterp == "PALETTE COLOR " )
{
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 )
{
- gdcmWarningMacro( "Not found : Palette color (0028,0004)");
+ gdcmDebugMacro( "Not found : Palette color (0028,0004)");
}
return false;
}
*/
bool File::IsYBRFull()
{
- std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
if ( PhotometricInterp == "YBR_FULL" )
{
return true;
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
+ gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
}
return false;
}
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;
}
//Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
// = Lookup Table Desc-Blue
// Consistency already checked in GetLUTLength
- std::string lutDescription = GetEntryValue(0x0028,0x1101);
+ std::string lutDescription = GetEntryString(0x0028,0x1101);
if ( lutDescription == GDCM_UNFOUND )
{
return 0;
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
+ * @return Rescale Intercept. defaulted to 0.0 if not found or empty
*/
-float File::GetRescaleIntercept()
+double File::GetRescaleIntercept()
{
- float resInter = 0.;
- /// 0028 1052 DS IMG Rescale Intercept
- const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
- if ( strRescInter != GDCM_UNFOUND )
+ // 0028 1052 DS IMG Rescale Intercept
+ DataEntry *entry = GetDataEntry(0x0028, 0x1052);
+ if( !entry )
{
- if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
- {
- // bug in the element 0x0028,0x1052
- gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
- }
+ gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
+ return 0.0f;
}
+ return (float)entry->GetValue(0);
- return resInter;
}
/**
*\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope
+ * @return Rescale Slope. defaulted to 1.0 if not found or empty
*/
-float File::GetRescaleSlope()
+double File::GetRescaleSlope()
{
- float resSlope = 1.;
+ double resInter = 0.;
+ double resSlope = 1.;
+ if ( GetRescaleSlopeIntercept(resSlope, resInter) )
+ {
+ return resSlope;
+ }
//0028 1053 DS IMG Rescale Slope
- std::string strRescSlope = GetEntryValue(0x0028,0x1053);
+ std::string strRescSlope = GetEntryString(0x0028,0x1053);
if ( strRescSlope != GDCM_UNFOUND )
{
- if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
+ if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 )
{
// bug in the element 0x0028,0x1053
gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
/**
* \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*)
*/
{
return 3;
}
-
+
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- if ( GetEntryValue(0x0028,0x0100) == "24" )
+ if ( GetEntryString(0x0028,0x0100) == "24" )
{
return 3;
}
-
- std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+
+ std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
{
{
// 0028 0100 US IMG Bits Allocated
// (in order no to be messed up by old RGB images)
- if ( File::GetEntryValue(0x0028,0x0100) == "24" )
+ if ( File::GetEntryString(0x0028,0x0100) == "24" )
{
return 3;
}
}
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;
}
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;
{
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;
it != UserAnonymizeList.end();
++it)
{
+
+ //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<<
+ // (*it).Elem
+ // << "[" << (*it).Value << "] "<< std::dec << std::endl;
d = GetDocEntry( (*it).Group, (*it).Elem);
if ( d == NULL)
continue;
}
+ valLgth = (*it).Value.size();
+ if (valLgth == 0)
+ continue;
+
offset = d->GetOffset();
lgth = d->GetLength();
+
+ //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl;
if (valLgth < lgth)
{
spaces = new std::string( lgth-valLgth, ' ');
(*it).Value = (*it).Value + *spaces;
+ //std::cout << "[" << (*it).Value << "] " << lgth << std::endl;
delete spaces;
}
fp->seekp( offset, std::ios::beg );
/**
* \brief anonymize a File (remove Patient's personal info passed with
* AddAnonymizeElement()
- * \note You cannot Anonymize a BinEntry (to be fixed)
+ * \note You cannot Anonymize a DataEntry (to be fixed)
*/
bool File::AnonymizeFile()
{
if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
{
// If exist, replace by spaces
- SetValEntry (" ",0x0010, 0x2154); // Telephone
- SetValEntry (" ",0x0010, 0x1040); // Adress
- SetValEntry (" ",0x0010, 0x0020); // Patient ID
+ SetEntryString(" ",0x0010, 0x2154); // Telephone
+ SetEntryString(" ",0x0010, 0x1040); // Adress
+ SetEntryString(" ",0x0010, 0x0020); // Patient ID
- DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+ DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
{
- std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
+ std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
if ( studyInstanceUID != GDCM_UNFOUND )
{
- SetValEntry(studyInstanceUID, 0x0010, 0x0010);
+ SetEntryString(studyInstanceUID, 0x0010, 0x0010);
}
else
{
- SetValEntry("anonymized", 0x0010, 0x0010);
+ SetEntryString("anonymized", 0x0010, 0x0010);
}
}
}
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<BinEntry *>(d) )
+/*
+ if ( dynamic_cast<DataEntry *>(d) )
{
- gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) ");
+ gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
continue;
}
+*/
else
- SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
+ 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)
}
// Entry : 0002|0000 = group length -> recalculated
- ValEntry*e0000 = GetValEntry(0x0002,0x0000);
+ DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
if ( e0000 )
{
std::ostringstream sLen;
sLen << ComputeGroup0002Length( );
- e0000->SetValue(sLen.str());
+ e0000->SetString(sLen.str());
}
- int i_lgPix = GetEntryLength(GrPixel, NumPixel);
- if (i_lgPix != -2)
+ /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
+ if( writetype != JPEG && writetype != JPEG2000)
{
- // no (GrPixel, NumPixel) element
- std::string s_lgPix = Util::Format("%d", i_lgPix+12);
- s_lgPix = Util::DicomString( s_lgPix.c_str() );
- InsertValEntry(s_lgPix,GrPixel, 0x0000);
+ int i_lgPix = GetEntryLength(GrPixel, NumPixel);
+ 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");
+ }
}
-
- 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()
// 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");
}
/**
* \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()
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
+ * \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.
*/
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:
itemTagGroup = ReadInt16();
itemTagElem = ReadInt16();
}
- catch ( FormatError /*e*/ )
+ catch ( FormatError )
{
- //std::cerr << e << std::endl;
+ gdcmErrorMacro( "Can not read tag at 0x("
+ << std::hex << positionOnEntry
+ << "). 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 )
+ 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;
}
/**
- * \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
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();
+
+ // long currentPosition = Fp->tellg(); // save time // JPRx
uint32_t itemLength = ReadInt32();
- {
- gdcmWarningMacro( "Basic Item Length is: "
- << itemLength << std::endl
- << " at address: " << std::hex << (unsigned int)currentPosition);
- }
+ gdcmDebugMacro( "Basic Item Length is: " << itemLength
+// << " at address: " << std::hex << (unsigned int)currentPosition
+ );
return 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 )
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,
+//#ifndef GDCM_LEGACY_REMOVE
+/*
+ * \ 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
*/
+ /*
bool File::Load( std::string const &fileName )
{
GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
return DoTheLoadingJob( );
}
#endif
-
+*/
//-----------------------------------------------------------------------------
// Print
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff