+//
+// -------------- Remember ! ----------------------------------
+//
+// 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
+// -->
+// 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
+// then attribute Patient Orientation (0020,0020) should not be present
+// in the images.
+//
+// Remember also :
+// Patient Position (0018,5100) values :
+
+// HFS = Head First-Supine, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// HFP = Head First-Prone, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// FFS = Feet First-Supine, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the anterior-to-posterion direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// FFP = Feet First-Prone, where increasing (positive axis direction) :
+// X -> to the direction pointed to by the patient's oustretched left arm
+// Y -> to the posterior-to-anterior direction in the patient's body
+// Z -> to the feet-to-head direction in the patient's body
+
+// HFDR = Head First-Decubitus Right
+// HFDL = Head First-Decubitus Left
+// FFDR = Feet First-Decubitus Right
+// FFDL = Feet First-Decubitus Left
+
+// we can also find (non standard!)
+
+// SEMIERECT
+// SUPINE
+
+// CS 2 Patient Orientation (0020 0020)
+// When the coordinates of the image
+// are always present, this field is almost never used.
+// Better we don't trust it too much ...
+// Found Values are :
+// L\P
+// L\FP
+// P\F
+// L\F
+// P\FR
+// R\F
+//
+// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
+
+
+// ---------------------------------------------------------------
+//
+#include "gdcmFile.h"
+#include "gdcmGlobal.h"
+#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmDataEntry.h"
+
+#include <vector>
+#include <stdio.h> //sscanf
+#include <stdlib.h> // for atoi
+
+namespace gdcm
+{
+
+//-----------------------------------------------------------------------------
+// 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;
+}
+
+
+/**
+ * \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"
+ 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();
+ }
+ }
+ }
+ 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;
+}
+
+/**
+ * \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;
+ uint32_t nbValue;
+
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ DataEntry *entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
+ {
+ nbValue = entry->GetValueCount();
+ // Can't use IsValueCountValid because of the complex heuristic.
+ if( nbValue >= 3 )
+ xspacing = (float)entry->GetValue(2);
+ 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 >= 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 yspacing = 1.0;
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ DataEntry *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
+ * @return Z dimension of a voxel-to be
+ */
+float File::GetZSpacing()
+{
+ // --->
+ // ---> Warning :
+ // --->
+ // For *Dicom* images, ZSpacing should be calculated using
+ // XOrigin, YOrigin, ZOrigin (of the top left image corner)
+ // of 2 consecutive images, and the Orientation
+ //
+ // Computing ZSpacing on a single image is not really meaningfull !
+
+ float zspacing = 1.0f;
+
+ // 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)
+ // if they don't, we're fucked up
+ 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)");
+
+ 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
+ * @return true when one of the tag is found
+ * false when nothing 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.;
+
+ // 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;
+ }
+ }
+ //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;
+}
+
+/**
+ * \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("(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("(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("(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("(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( "Missing Bits Allocated (0028,0100)");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
+
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ else if ( bitsAlloc == "12" )
+ {
+ // It will be unpacked
+ bitsAlloc = "16";
+ }
+ else if ( bitsAlloc == "24" )
+ {
+ // (in order no to be messed up by old RGB images)
+ bitsAlloc = "8";
+ }
+
+ std::string sign;
+ if( IsSignedPixelData() )
+ {
+ sign = "S";
+ }
+ else
+ {
+ sign = "U";
+ }
+ return bitsAlloc + sign;
+}
+
+/**
+ * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
+ * \warning The method defaults to false (UNsigned) when tag 0028|0103
+ * is missing.
+ * The responsability of checking this value is left to the caller
+ * (NO transformation is performed on the pixels to make then >0)
+ * @return True when signed, false when UNsigned
+ */
+bool File::IsSignedPixelData()
+{
+ DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
+ return false;
+ }
+ return entry->GetValue(0) != 0;
+}
+
+/**
+ * \brief Check whether this a monochrome picture (gray levels) or not,
+ * using "Photometric Interpretation" tag (0x0028,0x0004).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
+ */
+bool File::IsMonochrome()
+{
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
+ }
+ return false;
+}
+
+/**
+ * \brief Check whether this a MONOCHROME1 picture (high values = dark)
+ * or not using "Photometric Interpretation" tag (0x0028,0x0004).
+ * @return true when "MONOCHROME1" . False otherwise.
+ */
+bool File::IsMonochrome1()
+{
+ 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)");
+ }
+ return false;
+}
+
+/**
+ * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
+ */
+bool File::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : Palette color (0028,0004)");
+ }
+ return false;
+}
+
+/**
+ * \brief Check whether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool File::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
+}
+
+/**
+ * \brief tells us if LUT are used
+ * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
+ * are NOT considered as LUT, since nobody knows
+ * how to deal with them
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
+ */
+bool File::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetDocEntry(0x0028,0x1101) )
+ {
+ return false;
+ }
+ // LutDescriptorGreen
+ if ( !GetDocEntry(0x0028,0x1102) )
+ {
+ return false;
+ }
+ // LutDescriptorBlue
+ if ( !GetDocEntry(0x0028,0x1103) )
+ {
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1203) )
+ {
+ return false;
+ }
+
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
+}
+
+/**
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
+ */
+int File::GetLUTNbits()
+{
+ std::vector<std::string> tokens;
+ int lutNbits;
+
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
+ // = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string lutDescription = GetEntryString(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+
+ tokens.clear(); // clean any previous value
+ Util::Tokenize ( lutDescription, tokens, "\\" );
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+
+ lutNbits = atoi( tokens[2].c_str() );
+ tokens.clear();
+
+ return lutNbits;
+}
+
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float File::GetRescaleIntercept()
+{
+ // 0028 1052 DS IMG Rescale Intercept
+ DataEntry *entry = GetDataEntry(0x0028, 0x1052);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
+ return 0.0f;
+ }
+ return (float)entry->GetValue(0);
+
+}
+
+/**
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+float File::GetRescaleSlope()
+{
+ // 0028 1053 DS IMG Rescale Slope
+ DataEntry *entry = GetDataEntry(0x0028, 0x1053);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
+ return 1.0f;
+ }
+ return (float)entry->GetValue(0);