+#include "gdcmTS.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_NAME_SPACE
+{
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+
+/**
+ * \brief Constructor used when we want to generate dicom files from scratch
+ */
+File::File():
+ Document()
+{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+ GrPixel = 0x7fe0; // to avoid further troubles
+ NumPixel = 0x0010;
+ BasicOffsetTableItemValue = 0;
+ FourthDimensionLocation = TagKey(0,0);
+}
+
+
+/**
+ * \brief Canonical destructor.
+ */
+File::~File()
+{
+ if ( RLEInfo )
+ delete RLEInfo;
+ if ( JPEGInfo )
+ delete JPEGInfo;
+ delete[] BasicOffsetTableItemValue;
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Loader
+ * @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( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+
+/**
+ * \brief Does the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+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 group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is missing we default to group 0x7fe0.
+ // Note: this IS the right place for the code
+
+ // Image Location
+ const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
+ if ( imgLocation == GDCM_UNFOUND )
+ {
+ // default value
+ GrPixel = 0x7fe0;
+ }
+ else
+ {
+ GrPixel = (uint16_t) atoi( imgLocation.c_str() );
+ }
+
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianness.
+ // see gdcmData/cr172241.dcm
+ if ( GrPixel == 0xe07f )
+ {
+ GrPixel = 0x7fe0;
+ }
+
+ if ( GrPixel != 0x7fe0 )
+ {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ }
+ else
+ {
+ NumPixel = 0x0010;
+ }
+
+ // Now, we know GrPixel and NumPixel.
+ // Let's create a VirtualDictEntry to allow a further VR modification
+ // and force VR to match with BitsAllocated.
+ DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
+ if ( entry != 0 )
+ {
+ // Compute the RLE or JPEG info
+ OpenFile();
+ const std::string &ts = GetTransferSyntax();
+ Fp->seekg( entry->GetOffset(), std::ios::beg );
+ if ( Global::GetTS()->IsRLELossless(ts) )
+ ComputeRLEInfo();
+ else if ( Global::GetTS()->IsJPEG(ts) )
+ ComputeJPEGFragmentInfo();
+ CloseFile();
+
+ // Create a new DataEntry to change the DictEntry
+ // 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)
+ {
+ 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 != 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();
+ }
+ }
+*/
+ 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
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when File is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool File::IsReadable()
+{
+ if ( !Document::IsReadable() )
+ {
+ return false;
+ }
+
+ const std::string &res = GetEntryString(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
+ gdcmWarningMacro("Wrong Image Dimensions" << res);
+ return false; // Image Dimensions
+ }
+ bool b0028_0100 = true;
+ if ( !GetDocEntry(0x0028, 0x0100) )
+ {
+ gdcmWarningMacro("Bits Allocated (0028|0100) not found");
+ //return false; // "Bits Allocated"
+ b0028_0100 = false;
+ }
+ bool b0028_0101 = true;
+ if ( !GetDocEntry(0x0028, 0x0101) )
+ {
+ gdcmWarningMacro("Bits Stored (0028|0101) not found");
+ //return false; // "Bits Stored"
+ b0028_0101 = false;
+ }
+ bool b0028_0102 = true;
+ if ( !GetDocEntry(0x0028, 0x0102) )
+ {
+ gdcmWarningMacro("Hight Bit (0028|0102) not found");
+ //return false; // "High Bit"
+ b0028_0102 = false;
+ }
+ bool b0028_0103 = true;
+ if ( !GetDocEntry(0x0028, 0x0103) )
+ {
+ gdcmWarningMacro("Pixel Representation (0028|0103) not found");
+ //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
+ b0028_0103 = false;
+ }
+
+ if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
+ {
+ gdcmWarningMacro("Too much mandatory Tags missing !");
+ return false;
+ }
+
+ if ( !GetDocEntry(GrPixel, NumPixel) )
+ {
+ gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
+ GrPixel << "|" << NumPixel << "not found");
+ return false; // Pixel Dicom Element not found :-(
+ }
+ return true;
+}
+
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int File::GetImageNumber()
+{
+ //0020 0013 : Image Number
+ std::string strImNumber = GetEntryString(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
+ {
+ return atoi( strImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType File::GetModality()
+{
+ // 0008 0060 : Modality
+ std::string strModality = GetEntryString(0x0008,0x0060);
+ if ( strModality != GDCM_UNFOUND )
+ {
+ if ( strModality.find("AU") < strModality.length()) return AU;
+ else if ( strModality.find("AS") < strModality.length()) return AS;
+ else if ( strModality.find("BI") < strModality.length()) return BI;
+ else if ( strModality.find("CF") < strModality.length()) return CF;
+ else if ( strModality.find("CP") < strModality.length()) return CP;
+ else if ( strModality.find("CR") < strModality.length()) return CR;
+ else if ( strModality.find("CT") < strModality.length()) return CT;
+ else if ( strModality.find("CS") < strModality.length()) return CS;
+ else if ( strModality.find("DD") < strModality.length()) return DD;
+ else if ( strModality.find("DF") < strModality.length()) return DF;
+ else if ( strModality.find("DG") < strModality.length()) return DG;
+ else if ( strModality.find("DM") < strModality.length()) return DM;
+ else if ( strModality.find("DS") < strModality.length()) return DS;
+ else if ( strModality.find("DX") < strModality.length()) return DX;
+ else if ( strModality.find("ECG") < strModality.length()) return ECG;
+ else if ( strModality.find("EPS") < strModality.length()) return EPS;
+ else if ( strModality.find("FA") < strModality.length()) return FA;
+ else if ( strModality.find("FS") < strModality.length()) return FS;
+ else if ( strModality.find("HC") < strModality.length()) return HC;
+ else if ( strModality.find("HD") < strModality.length()) return HD;
+ else if ( strModality.find("LP") < strModality.length()) return LP;
+ else if ( strModality.find("LS") < strModality.length()) return LS;
+ else if ( strModality.find("MA") < strModality.length()) return MA;
+ else if ( strModality.find("MR") < strModality.length()) return MR;
+ else if ( strModality.find("NM") < strModality.length()) return NM;
+ else if ( strModality.find("OT") < strModality.length()) return OT;
+ else if ( strModality.find("PT") < strModality.length()) return PT;
+ else if ( strModality.find("RF") < strModality.length()) return RF;
+ else if ( strModality.find("RG") < strModality.length()) return RG;
+ else if ( strModality.find("RTDOSE")
+ < strModality.length()) return RTDOSE;
+ else if ( strModality.find("RTIMAGE")
+ < strModality.length()) return RTIMAGE;
+ else if ( strModality.find("RTPLAN")
+ < strModality.length()) return RTPLAN;
+ else if ( strModality.find("RTSTRUCT")
+ < strModality.length()) return RTSTRUCT;
+ else if ( strModality.find("SM") < strModality.length()) return SM;
+ else if ( strModality.find("ST") < strModality.length()) return ST;
+ else if ( strModality.find("TG") < strModality.length()) return TG;
+ else if ( strModality.find("US") < strModality.length()) return US;
+ else if ( strModality.find("VF") < strModality.length()) return VF;
+ else if ( strModality.find("XA") < strModality.length()) return XA;
+ else if ( strModality.find("XC") < strModality.length()) return XC;
+
+ else
+ {
+ /// \todo throw error return value ???
+ /// specified <> unknown in our database
+ return Unknow;
+ }
+ }
+ return Unknow;
+}
+
+/**
+ * \brief Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ * 0 means the file is NOT USABLE. The caller will have to check
+ */
+int File::GetXSize()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0011);
+ if( entry )
+ return (int)entry->GetValue(0);
+ return 0;
+}
+
+/**
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to File::GetXSize()
+ * @return The encountered size when found, 1 by default
+ * (The ACR-NEMA file contains a Signal, not an Image).
+ */
+int File::GetYSize()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0010);
+ if( entry )
+ return (int)entry->GetValue(0);
+
+ if ( IsDicomV3() )
+ {
+ return 0;
+ }
+
+ // The Rows (0028,0010) entry was optional for ACR/NEMA.
+ // (at least some images didn't have it.)
+ // It might hence be a signal (1D image). So we default to 1:
+ return 1;
+}
+
+/**
+ * \brief Retrieve the number of planes of volume or the number
+ * of frames of a multiframe.
+ * \warning When present we consider the "Number of Frames" as the third
+ * dimension. When missing we consider the third dimension as
+ * being the ACR-NEMA "Planes" tag content.
+ * @return The encountered size when found, 1 by default (single image).
+ */
+int File::GetZSize()
+{
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ DataEntry *entry = GetDataEntry(0x0028,0x0008);
+ if( entry )
+ return (int)entry->GetValue(0);
+
+ // We then consider the "Planes" entry as the third dimension
+ 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 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(0x0028,0x9110);
+ 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 )
+ {
+ 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
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float File::GetXSpacing()
+{
+ float xspacing = 1.0;
+ float yspacing = 1.0;
+ float zspacing = 1.0;
+
+ uint32_t nbValue;
+ DataEntry *entry;
+ 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
+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
+
+- (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
+
+ // CR is in Imager Pixel Spacing (0018,1164)//
+
+*/
+ // go on with old method ...
+ // ---------------------
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
+ {
+ 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)" );
+ }
+
+ 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 == 0.0 )
+ xspacing = 1.0;
+ return xspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
+ }
+ return xspacing;
+}
+
+/**
+ * \brief gets the info from 0018,1164 : ImagerPixelSpacing
+ * then from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float File::GetYSpacing()
+{
+ 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
+
+ entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(0);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+ return yspacing;
+ }
+ else
+ {
+ gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
+ }
+
+ entry = GetDataEntry(0x0028,0x0030);
+ if( entry )
+ {
+ yspacing = (float)entry->GetValue(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)
+ // overlapping (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // It only concerns the MRI guys, not people wanting to visualize volumes
+ // If Spacing Between Slices is missing,
+ // we suppose slices joint together
+ DataEntry *entry = GetDataEntry(0x0018,0x0088);
+ if( entry )
+ { zspacing = (float)entry->GetValue(0);
+
+ if ( zspacing == 0.0 )
+ zspacing = 1.0;
+ return zspacing;
+ }
+ else
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
+
+ // 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;
+ }
+
+ return zspacing;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner X position
+ */
+float File::GetXOrigin()
+{
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0f;
+ }
+ }
+
+ if( entry->GetValueCount() == 3 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0);
+ }
+ return 0.0f;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner Y position
+ */
+float File::GetYOrigin()
+{
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0f;
+ }
+ }
+
+ if( entry->GetValueCount() == 3 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(1);
+ }
+ return 0.0f;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else from 0020,1041 : Slice Location
+ * else from 0020,0050 : Location
+ * else 0.
+ * @return up-left image corner Z position
+ */
+float File::GetZOrigin()
+{
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 3 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(2);
+ }
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.0f;
+ }
+
+ entry = GetDataEntry(0x0020,0x0030);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 3 )
+ {
+ 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
+ entry = GetDataEntry(0x0020,0x1041);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 1 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0); // VM=1 !
+ }
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
+ return 0.0f;
+ }
+
+ entry = GetDataEntry(0x0020,0x0050);
+ if( entry )
+ {
+ if( entry->GetValueCount() == 1 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0);
+ }
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
+ return 0.0f;
+ }
+ 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.
+ * (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[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 )
+ {
+ if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
+ << " Less than 6 values were found." );
+ return false;
+ }
+ return true;
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ 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 )
+ {
+ gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
+ << "Less than 6 values were found." );
+ return false;
+ }
+ 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)
+ * (as opposed to number of Bits Allocated)
+ * @return The encountered number of Bits Stored, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int File::GetBitsStored()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0101);
+ if( !entry )
+ {
+ gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+}
+
+/**
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
+ * @return The encountered Number of Bits Allocated, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int File::GetBitsAllocated()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0100);
+ if( !entry )
+ {
+ gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+}
+
+/**
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is missing.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit position when present. 0 when missing.
+ */
+int File::GetHighBitPosition()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0102);
+ if( !entry )
+ {
+ gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+}
+
+/**
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ * (we assume Gray level Pixels)
+ */
+int File::GetSamplesPerPixel()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0002);
+ if( !entry )
+ {
+ 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);
+}
+
+/**
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int File::GetPlanarConfiguration()
+{
+ DataEntry *entry = GetDataEntry(0x0028,0x0006);
+ if( !entry )
+ {
+ return 0;
+ }
+ return (int)entry->GetValue(0);
+}
+
+/**
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data; 0 by default
+ * 0 means the file is NOT USABLE; the caller will have to check
+ */
+int File::GetPixelSize()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old ACR-NEMA RGB images)
+ assert( !(GetEntryString(0x0028,0x0100) == "24") );
+
+ std::string pixelType = GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
+ {
+ return 1;
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
+ return 2;
+ }
+ if ( pixelType == "32U" || pixelType == "32S")
+ {
+ return 4;
+ }
+ if ( pixelType == "FD" )
+ {
+ return 8;
+ }
+ gdcmWarningMacro( "Unknown pixel type: " << pixelType);
+ return 0;
+}
+
+/**
+ * \brief Build the Pixel Type of the image.
+ * Possible values are:
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
+ * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
+ * \warning 12 bit images appear as 16 bit.
+ * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
+ * + Planar Configuration = 0
+ * @return 0S if nothing found. NOT USABLE file. The caller has to check
+ */
+std::string File::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
+
+ 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";
+ }