- /*=========================================================================
+/*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/11/26 10:55:04 $
- Version: $Revision: 1.166 $
+ Date: $Date: 2007/10/08 15:20:17 $
+ Version: $Revision: 1.340 $
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):
+// 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 "gdcmDocument.h"
-#include "gdcmDebug.h"
+#include "gdcmGlobal.h"
#include "gdcmUtil.h"
-#include "gdcmBinEntry.h"
-#include <fstream>
-
-namespace gdcm
+#include "gdcmDebug.h"
+#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
{
-typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-//-------------------------------------------------------------------------
+//-----------------------------------------------------------------------------
// 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 Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header only deals with the ... header)
- * Opens (in read only and when possible) an existing file and checks
- * for DICOM compliance. Returns NULL on failure.
- * It will be up to the user to load the pixels into memory
- * (see GetImageData, GetImageDataRaw)
- * \note the in-memory representation of all available tags found in
- * the DICOM header is post-poned to first header information access.
- * This avoid a double parsing of public part of the header when
- * user sets an a posteriori shadow dictionary (efficiency can be
- * seen as a side effect).
- * @param header already built Header
+ * \brief Canonical destructor.
*/
-File::File(Header *header)
+File::~File()
{
- HeaderInternal = header;
- SelfHeader = false;
- Initialise();
+ if ( RLEInfo )
+ delete RLEInfo;
+ if ( JPEGInfo )
+ delete JPEGInfo;
+ delete[] BasicOffsetTableItemValue;
}
+//-----------------------------------------------------------------------------
+// Public
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header only deals with the ... header)
- * Opens (in read only and when possible) an existing file and checks
- * for DICOM compliance. Returns NULL on failure.
- * It will be up to the user to load the pixels into memory
- * (see GetImageData, GetImageDataRaw)
- * \note the in-memory representation of all available tags found in
- * the DICOM header is post-poned to first header information access.
- * This avoid a double parsing of public part of the header when
- * one sets an a posteriori shadow dictionary (efficiency can be
- * seen as a side effect).
- * @param filename file to be opened for parsing
+ * \brief Loader
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
*/
-File::File(std::string const & filename )
+bool File::Load( )
{
- HeaderInternal = new Header( filename );
- SelfHeader = true;
- Initialise();
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
}
/**
- * \brief Factorization for various forms of constructors.
+ * \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.
*/
-void File::Initialise()
+bool File::DoTheLoadingJob( )
{
- WriteMode = WMODE_DECOMPRESSED;
- WriteType = WTYPE_IMPL_VR;
+ // 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() );
+ }
- PixelConverter = new PixelConvert;
- Archive = new DocEntryArchive( HeaderInternal );
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianness.
+ // see gdcmData/cr172241.dcm
+ if ( GrPixel == 0xe07f )
+ {
+ GrPixel = 0x7fe0;
+ }
- if ( HeaderInternal->IsReadable() )
+ if ( GrPixel != 0x7fe0 )
+ {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ }
+ else
{
- PixelConverter->GrabInformationsFromHeader( HeaderInternal );
+ NumPixel = 0x0010;
}
- Pixel_Data = 0;
- ImageDataSize = 0;
+ // 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 canonical destructor
- * \note If the Header was created by the File constructor,
- * it is destroyed by the File
+ * \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.
*/
-File::~File()
-{
- if( PixelConverter )
+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) )
{
- delete PixelConverter;
+ gdcmWarningMacro("Hight Bit (0028|0102) not found");
+ //return false; // "High Bit"
+ b0028_0102 = false;
}
- if( Archive )
+ bool b0028_0103 = true;
+ if ( !GetDocEntry(0x0028, 0x0103) )
{
- delete Archive;
+ gdcmWarningMacro("Pixel Representation (0028|0103) not found");
+ //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
+ b0028_0103 = false;
}
- if( SelfHeader )
+ if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
{
- delete HeaderInternal;
+ gdcmWarningMacro("Too much mandatory Tags missing !");
+ return false;
}
- HeaderInternal = 0;
+
+ if ( !GetDocEntry(GrPixel, NumPixel) )
+ {
+ gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
+ GrPixel << "|" << NumPixel << "not found");
+ return false; // Pixel Dicom Element not found :-(
+ }
+ return true;
}
-//-----------------------------------------------------------------------------
-// Print
+/**
+ * \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
+}
-//-----------------------------------------------------------------------------
-// Public
/**
- * \brief Get the size of the image data
- *
- * If the image can be RGB (with a lut or by default), the size
- * corresponds to the RGB image
- * @return The image size
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
*/
-size_t File::GetImageDataSize()
+ModalityType File::GetModality()
{
- return PixelConverter->GetRGBSize();
+ // 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 Get the size of the image data
- *
- * If the image can be RGB by transformation in a LUT, this
- * transformation isn't considered
- * @return The raw image size
+ * \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
*/
-size_t File::GetImageDataRawSize()
+int File::GetXSize()
{
- return PixelConverter->GetDecompressedSize();
+ DataEntry *entry = GetDataEntry(0x0028,0x0011);
+ if( entry )
+ return (int)entry->GetValue(0);
+ return 0;
}
/**
- * \brief - Allocates necessary memory,
- * - Reads the pixels from disk (uncompress if necessary),
- * - Transforms YBR pixels, if any, into RGB pixels
- * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * - Transforms single Grey plane + 3 Palettes into a RGB Plane
- * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
- * @return Pointer to newly allocated pixel data.
- * NULL if alloc fails
+ * \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).
*/
-uint8_t* File::GetImageData()
+int File::GetYSize()
{
- if ( ! GetDecompressed() )
+ DataEntry *entry = GetDataEntry(0x0028,0x0010);
+ if( entry )
+ return (int)entry->GetValue(0);
+
+ if ( IsDicomV3() )
{
- // If the decompression failed nothing can be done.
return 0;
}
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ // 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 )
{
- return PixelConverter->GetRGB();
+ gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
+ std::hex << FourthDimensionLocation.GetGroup()
+ << "|" << FourthDimensionLocation.GetElement());
+ return 1;
}
else
{
- // When no LUT or LUT conversion fails, return the decompressed
- return PixelConverter->GetDecompressed();
- }
-}
-
-/**
- * \brief
- * Read the pixels from disk (uncompress if necessary),
- * Transforms YBR pixels, if any, into RGB pixels
- * Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
- * Copies at most MaxSize bytes of pixel data to caller allocated
- * memory space.
- * \warning This function allows people that want to build a volume
- * from an image stack *not to* have, first to get the image pixels,
- * and then move them to the volume area.
- * It's absolutely useless for any VTK user since vtk chooses
- * to invert the lines of an image, that is the last line comes first
- * (for some axis related reasons?). Hence he will have
- * to load the image line by line, starting from the end.
- * VTK users have to call GetImageData
- *
- * @param destination Address (in caller's memory space) at which the
- * pixel data should be copied
- * @param maxSize Maximum number of bytes to be copied. When MaxSize
- * is not sufficient to hold the pixel data the copy is not
- * executed (i.e. no partial copy).
- * @return On success, the number of bytes actually copied. Zero on
- * failure e.g. MaxSize is lower than necessary.
- */
-size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
-{
- if ( ! GetDecompressed() )
- {
- // If the decompression failed nothing can be done.
- return 0;
- }
+ return (int)entry->GetValue(0);
+ }
+}
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+/**
+ * \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
{
- if ( PixelConverter->GetRGBSize() > maxSize )
+ // - check if SOPClassUID contains 2 parts (e.g. "4\3")
+ // - guess how to deduce the spacing (FOV ?, ??)
+
+ entry = GetDataEntry(0x0028,0x0034);
+ if ( entry )
{
- dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return 0;
+ 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;
}
- memcpy( destination,
- (void*)PixelConverter->GetRGB(),
- PixelConverter->GetRGBSize() );
- return PixelConverter->GetRGBSize();
+
+ 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)//
- // Either no LUT conversion necessary or LUT conversion failed
- if ( PixelConverter->GetDecompressedSize() > maxSize )
+*/
+ // go on with old method ...
+ // ---------------------
+ // To follow David Clunie's advice, we first check ImagerPixelSpacing
+
+ entry = GetDataEntry(0x0018,0x1164);
+ if( entry )
{
- dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return 0;
+ 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)" );
}
- memcpy( destination,
- (void*)PixelConverter->GetDecompressed(),
- PixelConverter->GetDecompressedSize() );
- return PixelConverter->GetDecompressedSize();
+ return xspacing;
}
/**
- * \brief Allocates necessary memory,
- * Transforms YBR pixels (if any) into RGB pixels
- * Transforms 3 planes R, G, B (if any) into a single RGB Plane
- * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
- * @return Pointer to newly allocated pixel data.
- * \ NULL if alloc fails
+ * \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
*/
-uint8_t* File::GetImageDataRaw ()
+float File::GetZSpacing()
{
- return GetDecompressed();
+
+ 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;
}
-uint8_t* File::GetDecompressed()
+/**
+ * \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()
{
- uint8_t* decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
+ DataEntry *entry = GetDataEntry(0x0020,0x0032);
+ if( !entry )
{
- // The decompressed image migth not be loaded yet:
- std::ifstream* fp = HeaderInternal->OpenFile();
- PixelConverter->ReadAndDecompressPixelData( fp );
- if(fp)
- HeaderInternal->CloseFile();
-
- decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ entry = GetDataEntry(0x0020,0x0030);
+ if( !entry )
{
- dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
- "pixel data apparently went wrong.");
- return 0;
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.0f;
}
}
- return decompressed;
+ if( entry->GetValueCount() == 3 )
+ {
+ if (!entry->IsValueCountValid() )
+ {
+ gdcmErrorMacro( "Invalid Value Count" );
+ }
+ return (float)entry->GetValue(0);
+ }
+ return 0.0f;
}
/**
- * \brief Points the internal Pixel_Data pointer to the callers inData
- * image representation, BUT WITHOUT COPYING THE DATA.
- * 'image' Pixels are presented as C-like 2D arrays : line per line.
- * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
- * \warning Since the pixels are not copied, it is the caller's responsability
- * not to deallocate it's data before gdcm uses them (e.g. with
- * the Write() method.
- * @param inData user supplied pixel area
- * @param expectedSize total image size, in Bytes
- *
- * @return boolean
+ * \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
*/
-bool File::SetImageData(uint8_t* inData, size_t expectedSize)
+float File::GetYOrigin()
{
-// FIXME : if already allocated, memory leak !
- Pixel_Data = inData;
- ImageDataSize = expectedSize;
-// FIXME : 7fe0, 0010 IS NOT set ...
- return true;
+ 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 Writes on disk A SINGLE Dicom file
- * NO test is performed on processor "Endiannity".
- * It's up to the user to call his Reader properly
- * @param fileName name of the file to be created
- * (any already existing file is over written)
- * @return false if write fails
+ * \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
+}
-bool File::WriteRawData(std::string const & fileName)
+/**
+ * \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::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
- if (!fp1)
+ 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 )
{
- dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
- return false;
+ 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;
}
- fp1.write((char*)Pixel_Data, ImageDataSize);
- fp1.close();
+ return false;
+}
- return true;
+/**
+ * \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 Writes on disk A SINGLE Dicom file,
- * using the Implicit Value Representation convention
- * NO test is performed on processor "Endiannity".
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
- */
+ * \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]);
+}
-bool File::WriteDcmImplVR (std::string const & fileName)
+/**
+ * \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] )
{
- SetWriteTypeToDcmImplVR();
- return Write(fileName);
+ 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 Writes on disk A SINGLE Dicom file,
- * using the Explicit Value Representation convention
- * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \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 !
*/
-
-bool File::WriteDcmExplVR (std::string const & fileName)
+int File::GetBitsStored()
{
- SetWriteTypeToDcmExplVR();
- return Write(fileName);
+ DataEntry *entry = GetDataEntry(0x0028,0x0101);
+ if( !entry )
+ {
+ gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
}
/**
- * \brief Writes on disk A SINGLE Dicom file,
- * using the ACR-NEMA convention
- * NO test is performed on processor "Endiannity".
- * (a l'attention des logiciels cliniques
- * qui ne prennent en entrée QUE des images ACR ...
- * \warning if a DICOM_V3 header is supplied,
- * groups < 0x0008 and shadow groups are ignored
- * \warning NO TEST is performed on processor "Endiannity".
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \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);
+}
-bool File::WriteAcr (std::string const & fileName)
+/**
+ * \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()
{
- SetWriteTypeToAcr();
- return Write(fileName);
+ DataEntry *entry = GetDataEntry(0x0028,0x0102);
+ if( !entry )
+ {
+ gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
+ return 0;
+ }
+ return (int)entry->GetValue(0);
}
-bool File::Write(std::string const& fileName)
+/**
+ * \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()
{
- switch(WriteType)
+ DataEntry *entry = GetDataEntry(0x0028,0x0002);
+ if( !entry )
{
- case WTYPE_IMPL_VR:
- return WriteBase(fileName,ImplicitVR);
- case WTYPE_EXPL_VR:
- return WriteBase(fileName,ExplicitVR);
- case WTYPE_ACR:
- return WriteBase(fileName,ACR);
+ 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(false);
+ return (int)entry->GetValue(0);
}
/**
- * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ * \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.
*/
-uint8_t* File::GetLutRGBA()
+int File::GetPlanarConfiguration()
{
- return PixelConverter->GetLutRGBA();
+ DataEntry *entry = GetDataEntry(0x0028,0x0006);
+ if( !entry )
+ {
+ return 0;
+ }
+ return (int)entry->GetValue(0);
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \brief NOT a end user inteded function
- * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
- * @return false if write fails
- */
-bool File::WriteBase (std::string const & fileName, FileType type)
-{
- switch(type)
- {
- case ImplicitVR:
- SetWriteFileTypeToImplicitVR();
- break;
- case ExplicitVR:
- SetWriteFileTypeToExplicitVR();
- break;
- case ACR:
- SetWriteFileTypeToACR();
- break;
- case ACR_LIBIDO:
- SetWriteFileTypeToACRLibido();
- break;
- default:
- SetWriteFileTypeToExplicitVR();
+ * \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;
}
-
- switch(WriteMode)
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
+ return 2;
+ }
+ if ( pixelType == "32U" || pixelType == "32S")
{
- case WMODE_NATIVE :
- SetWriteToNative();
- break;
- case WMODE_DECOMPRESSED :
- SetWriteToDecompressed();
- break;
- case WMODE_RGB :
- SetWriteToRGB();
- break;
+ return 4;
}
+ if ( pixelType == "FD" )
+ {
+ return 8;
+ }
+ gdcmWarningMacro( "Unknown pixel type: " << pixelType);
+ return 0;
+}
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // if recognition code tells us we dealt with a LibIDO image
- // we reproduce on disk the switch between lineNumber and columnNumber
- // just before writting ...
- /// \todo the best trick would be *change* the recognition code
- /// but pb expected if user deals with, e.g. COMPLEX images
-/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
+/**
+ * \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 )
{
- SetWriteToLibido();
- }*/
- // ----------------- End of Special Patch ----------------
+ gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
- bool check = CheckWriteIntegrity();
- if(check)
+ 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" )
{
- check = HeaderInternal->Write(fileName,type);
+ // (in order no to be messed up by old RGB images)
+ bitsAlloc = "8";
}
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // ...and we restore the Header to be Dicom Compliant again
- // just after writting
-/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+ int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers
+ if ( i > 8 && i < 16 )
{
- RestoreWriteFromLibido();
- }*/
- // ----------------- End of Special Patch ----------------
+ bitsAlloc = "16";
+ }
- RestoreWrite();
- RestoreWriteFileType();
+ std::string sign;
+ if( IsSignedPixelData() )
+ {
+ sign = "S";
+ }
+ else
+ {
+ sign = "U";
+ }
+ return bitsAlloc + sign;
+}
- return check;
+/**
+ * \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( "Pixel Representation (0028,0103) supposed to be "
+ << "mandatory");
+ return false;
+ }
+ return entry->GetValue(0) != 0;
}
/**
- * \brief Check the write integrity
- *
- * The tests made are :
- * - verify the size of the image to write with the possible write
- * when the user set an image data
- * @return true if the check successfulls
+ * \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::CheckWriteIntegrity()
+bool File::IsMonochrome()
{
- if(Pixel_Data)
+ const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
- if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
- {
- numberBitsAllocated = 16;
- }
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
+ << "mandatory");
+ // to deal with old ACR-NEMA images
+ if (GetNumberOfScalarComponents() == 1)
+ return true;
+ }
+ return false;
+}
- size_t decSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
- size_t rgbSize = decSize;
- if( HeaderInternal->HasLUT() )
- rgbSize = decSize * 3;
+/**
+ * \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( "Photometric Interpretation (0028,0004) : supposed to"
+ << " be mandatory! ");
+ }
+ return false;
+}
- switch(WriteMode)
- {
- case WMODE_NATIVE :
- break;
- case WMODE_DECOMPRESSED :
- if( decSize!=ImageDataSize )
- {
- dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
- //std::cerr<<"Dec : "<<decSize<<" | "<<ImageDataSize<<std::endl;
- return false;
- }
- break;
- case WMODE_RGB :
- if( rgbSize!=ImageDataSize )
- {
- dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
- //std::cerr<<"RGB : "<<decSize<<" | "<<ImageDataSize<<std::endl;
- return false;
- }
- break;
- }
+/**
+ * \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;
}
-
- return true;
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmDebugMacro( "Not found : Palette color (0028,0004)");
+ }
+ return false;
}
-void File::SetWriteToNative()
+/**
+ * \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()
{
- if(Pixel_Data)
+ std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
{
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(Pixel_Data,false);
- pixel->SetLength(ImageDataSize);
+ gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
+}
- Archive->Push(pixel);
+/**
+ * \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
+ bool segmented;
+ segmented = GetDocEntry(0x0028,0x1221) &&
+ GetDocEntry(0x0028,0x1222) &&
+ GetDocEntry(0x0028,0x1223);
+ if( segmented ) return true;
+
+ 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;
}
-void File::SetWriteToDecompressed()
+/**
+ * \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()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
+ 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 )
{
- SetWriteToRGB();
- }
- else
+ 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;
+}
+
+// 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)
{
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- if(HeaderInternal->HasLUT())
- {
- photInt->SetValue("PALETTE COLOR ");
- photInt->SetLength(14);
- }
+ 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
- {
- photInt->SetValue("MONOCHROME1 ");
- photInt->SetLength(12);
- }
+ {
+ 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;
+ }
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- if(Pixel_Data)
- {
- pixel->SetBinArea(Pixel_Data,false);
- pixel->SetLength(ImageDataSize);
- }
- else
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept. defaulted to 0.0 if not found or empty
+ */
+double 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. defaulted to 1.0 if not found or empty
+ */
+double File::GetRescaleSlope()
+{
+ double resInter = 0.;
+ double resSlope = 1.;
+ if ( GetRescaleSlopeIntercept(resSlope, resInter) )
+ {
+ return resSlope;
+ }
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryString(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 )
{
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
+ // bug in the element 0x0028,0x1053
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
}
-
- Archive->Push(photInt);
- Archive->Push(pixel);
}
+
+ return resSlope;
}
-void File::SetWriteToRGB()
+/**
+ * \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, if no LUT found ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
+ */
+int File::GetNumberOfScalarComponents()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ if ( GetSamplesPerPixel() == 3 )
{
- PixelConverter->BuildRGBImage();
-
- ValEntry* spp = CopyValEntry(0x0028,0x0002);
- spp->SetValue("3 ");
- spp->SetLength(2);
+ return 3;
+ }
- ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
- planConfig->SetValue("0 ");
- planConfig->SetLength(2);
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("RGB ");
- photInt->SetLength(4);
+ std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- if(Pixel_Data)
- {
- pixel->SetBinArea(Pixel_Data,false);
- pixel->SetLength(ImageDataSize);
- }
- else if(PixelConverter->GetRGB())
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
{
- pixel->SetBinArea(PixelConverter->GetRGB(),false);
- pixel->SetLength(PixelConverter->GetRGBSize());
+ return 3;
}
- else // Decompressed data
+ else
{
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
+ return 1;
}
+ }
- Archive->Push(spp);
- Archive->Push(planConfig);
- Archive->Push(photInt);
- Archive->Push(pixel);
-
- // Remove any LUT
- Archive->Push(0x0028,0x1101);
- Archive->Push(0x0028,0x1102);
- Archive->Push(0x0028,0x1103);
- Archive->Push(0x0028,0x1201);
- Archive->Push(0x0028,0x1202);
- Archive->Push(0x0028,0x1203);
-
- // For old ACR-NEMA
- // Thus, we have a RGB image and the bits allocated = 24 and
- // samples per pixels = 1 (in the read file)
- if(HeaderInternal->GetBitsAllocated()==24)
- {
- ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100);
- bitsAlloc->SetValue("8 ");
- bitsAlloc->SetLength(2);
-
- ValEntry* bitsStored = CopyValEntry(0x0028,0x0101);
- bitsStored->SetValue("8 ");
- bitsStored->SetLength(2);
-
- ValEntry* highBit = CopyValEntry(0x0028,0x0102);
- highBit->SetValue("7 ");
- highBit->SetLength(2);
-
- Archive->Push(bitsAlloc);
- Archive->Push(bitsStored);
- Archive->Push(highBit);
- }
+ // beware of trailing space at end of string
+ // DICOM tags are never of odd length
+ if ( strPhotometricInterpretation == GDCM_UNFOUND ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
+ {
+ return 1;
}
else
{
- SetWriteToDecompressed();
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
}
}
-void File::RestoreWrite()
+/**
+ * \brief This function is intended to user that DOESN'T want
+ * to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * - the (vtk) user is supposed to know how deal with LUTs -
+ * \warning to be used with GetImagePixelsRaw()
+ * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
+ */
+int File::GetNumberOfScalarComponentsRaw()
{
- Archive->Restore(0x0028,0x0002);
- Archive->Restore(0x0028,0x0004);
- Archive->Restore(0x0028,0x0006);
- Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
-
- // For old ACR-NEMA (24 bits problem)
- Archive->Restore(0x0028,0x0100);
- Archive->Restore(0x0028,0x0101);
- Archive->Restore(0x0028,0x0102);
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
- // For the LUT
- Archive->Restore(0x0028,0x1101);
- Archive->Restore(0x0028,0x1102);
- Archive->Restore(0x0028,0x1103);
- Archive->Restore(0x0028,0x1201);
- Archive->Restore(0x0028,0x1202);
- Archive->Restore(0x0028,0x1203);
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
}
-void File::SetWriteFileTypeToACR()
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t File::GetPixelOffset()
{
- Archive->Push(0x0002,0x0010);
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
+ }
+ else
+ {
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
}
-void File::SetWriteFileTypeToACRLibido()
+/**
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
+ */
+size_t File::GetPixelAreaLength()
{
- SetWriteFileTypeToACR();
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \brief Adds the characteristics of a new element we want to anonymize
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value new value (string) to substitute with
+ */
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
+{
+ DicomElement el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ UserAnonymizeList.push_back(el);
}
-void File::SetWriteFileTypeToExplicitVR()
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
{
- std::string ts = Util::DicomString(
- Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ GDCM_NAME_SPACE::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t valLgth = 0;
+ std::string *spaces;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ 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);
- ValEntry* tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
- tss->SetLength(ts.length());
+ if ( d == NULL)
+ continue;
- Archive->Push(tss);
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
+ 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 );
+ fp->write( (*it).Value.c_str(), lgth );
+
+ }
+ fp->close();
+ delete fp;
}
-void File::SetWriteFileTypeToImplicitVR()
+/**
+ * \brief anonymize a File (remove Patient's personal info passed with
+ * AddAnonymizeElement()
+ * \note You cannot Anonymize a DataEntry (to be fixed)
+ */
+bool File::AnonymizeFile()
{
- std::string ts = Util::DicomString(
- Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
+ // If Anonymisation list is empty, let's perform some basic anonymization
+ if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
+ {
+ // If exist, replace by spaces
+ SetEntryString(" ",0x0010, 0x2154); // Telephone
+ SetEntryString(" ",0x0010, 0x1040); // Adress
+ SetEntryString(" ",0x0010, 0x0020); // Patient ID
- ValEntry* tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
- tss->SetLength(ts.length());
+ DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
+ {
+ std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ SetEntryString(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ SetEntryString("anonymized", 0x0010, 0x0010);
+ }
+ }
+ }
+ else
+ {
+ GDCM_NAME_SPACE::DocEntry *d;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ continue;
+
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
+ continue;
+ }
+
+ if ( dynamic_cast<DataEntry *>(d) )
+ {
+ gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
+ continue;
+ }
+ else
+ SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
+ }
}
-void File::RestoreWriteFileType()
-{
- Archive->Restore(0x0002,0x0010);
+ // In order to make definitively impossible any further identification
+ // remove or replace all the stuff that contains a Date
+
+//0008 0012 DA ID Instance Creation Date
+//0008 0020 DA ID Study Date
+//0008 0021 DA ID Series Date
+//0008 0022 DA ID Acquisition Date
+//0008 0023 DA ID Content Date
+//0008 0024 DA ID Overlay Date
+//0008 0025 DA ID Curve Date
+//0008 002a DT ID Acquisition Datetime
+//0018 9074 DT ACQ Frame Acquisition Datetime
+//0018 9151 DT ACQ Frame Reference Datetime
+//0018 a002 DT ACQ Contribution Date Time
+//0020 3403 SH REL Modified Image Date (RET)
+//0032 0032 DA SDY Study Verified Date
+//0032 0034 DA SDY Study Read Date
+//0032 1000 DA SDY Scheduled Study Start Date
+//0032 1010 DA SDY Scheduled Study Stop Date
+//0032 1040 DA SDY Study Arrival Date
+//0032 1050 DA SDY Study Completion Date
+//0038 001a DA VIS Scheduled Admission Date
+//0038 001c DA VIS Scheduled Discharge Date
+//0038 0020 DA VIS Admitting Date
+//0038 0030 DA VIS Discharge Date
+//0040 0002 DA PRC Scheduled Procedure Step Start Date
+//0040 0004 DA PRC Scheduled Procedure Step End Date
+//0040 0244 DA PRC Performed Procedure Step Start Date
+//0040 0250 DA PRC Performed Procedure Step End Date
+//0040 2004 DA PRC Issue Date of Imaging Service Request
+//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
+//0040 4011 DT PRC Expected Completion Date and Time
+//0040 a030 DT PRC Verification Date Time
+//0040 a032 DT PRC Observation Date Time
+//0040 a120 DT PRC DateTime
+//0040 a121 DA PRC Date
+//0040 a13a DT PRC Referenced Datetime
+//0070 0082 DA ??? Presentation Creation Date
+//0100 0420 DT ??? SOP Autorization Date and Time
+//0400 0105 DT ??? Digital Signature DateTime
+//2100 0040 DA PJ Creation Date
+//3006 0008 DA SSET Structure Set Date
+//3008 0024 DA ??? Treatment Control Point Date
+//3008 0054 DA ??? First Treatment Date
+//3008 0056 DA ??? Most Recent Treatment Date
+//3008 0162 DA ??? Safe Position Exit Date
+//3008 0166 DA ??? Safe Position Return Date
+//3008 0250 DA ??? Treatment Date
+//300a 0006 DA RT RT Plan Date
+//300a 022c DA RT Air Kerma Rate Reference Date
+//300e 0004 DA RT Review Date
+
+ return true;
}
-void File::SetWriteToLibido()
+/**
+ * \brief Performs some consistency checking on various 'File related'
+ * (as opposed to 'DicomDir related') entries
+ * then writes in a file all the (Dicom Elements) included the Pixels
+ * @param fileName file name to write to
+ * @param writetype type of the file to be written
+ * (ACR, ExplicitVR, ImplicitVR)
+ */
+bool File::Write(std::string fileName, FileType writetype)
{
- ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
- ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
-
- if( oldRow && oldCol )
+ gdcmDebugMacro(" File::Write ");
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
{
- std::string rows, columns;
+ gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
+ return false;
+ }
- ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
- ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+ // Entry : 0002|0000 = group length -> recalculated
+ DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
+ if ( e0000 )
+ {
+ std::ostringstream sLen;
+ sLen << ComputeGroup0002Length( );
+ e0000->SetString(sLen.str());
+ }
- newRow->Copy(oldCol);
- newCol->Copy(oldRow);
+ /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
+ if( writetype != JPEG && writetype != JPEG2000)
+ {
+ 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,false,false);
- newRow->SetValue(oldCol->GetValue());
- newCol->SetValue(oldRow->GetValue());
+ fp->close();
+ delete fp;
- Archive->Push(newRow);
- Archive->Push(newCol);
- }
+ return true;
}
-void File::RestoreWriteFromLibido()
+//-----------------------------------------------------------------------------
+// Protected
+
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in RLEInfo
+ * for later pixel retrieval usage.
+ */
+void File::ComputeRLEInfo()
{
- Archive->Restore(0x0028,0x0010);
- Archive->Restore(0x0028,0x0011);
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
+ {
+ return;
+ }
+
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+ ReadEncapsulatedBasicOffsetTable();
+
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a RLEFramesInfo.
+ // Note: - when only a single frame is present, this is a
+ // classical image.
+ // - when more than one frame are present, then we are in
+ // the case of a multi-frame image.
+ long frameLength;
+ int i=0;
+ uint32_t sum = 0;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
+ {
+ // Since we have read the basic offset table, let's check the value were correct
+ // or else produce a warning:
+ if ( BasicOffsetTableItemValue )
+ {
+ // If a BasicOffsetTableItemValue was read
+ uint32_t individualLength = BasicOffsetTableItemValue[i];
+ assert( individualLength == sum ); // REMOVE that if this is a problem
+ if( individualLength != sum )
+ {
+ gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
+ }
+ sum += frameLength + 8;
+ i++;
+ }
+ // Parse the RLE Header and store the corresponding RLE Segment
+ // 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(); // once per fragment
+
+ uint32_t nbRleSegments = ReadInt32();
+ if ( nbRleSegments > 16 )
+ {
+ // There should be at most 15 segments (refer to RLEFrame class)
+ gdcmWarningMacro( "Too many segments.");
+ }
+
+ uint32_t rleSegmentOffsetTable[16];
+ for( int k = 1; k <= 15; k++ )
+ {
+ rleSegmentOffsetTable[k] = ReadInt32();
+ }
+
+ // Deduce from both RLE Header and frameLength
+ // the fragment length, and again store this info
+ // in a RLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ {
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
+ }
+ }
+
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+
+ // Store the collected info
+ RLEFrame *newFrame = new RLEFrame;
+ newFrame->SetNumberOfFragments(nbRleSegments);
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+ {
+ newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
+ newFrame->SetLength(uk,rleSegmentLength[uk]);
+ }
+ RLEInfo->AddFrame(newFrame);
+ }
+
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the item :
+ if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
+ {
+ gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
+ }
}
-ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
+/**
+ * \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 JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void File::ComputeJPEGFragmentInfo()
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- ValEntry* newE;
+ // If you need to, look for comments of ComputeRLEInfo().
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
+ {
+ return;
+ }
- if(oldE)
+ ReadEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ int i=0;
+ uint32_t sum = 0;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
+ {
+ // Since we have read the basic offset table, let's check the value were correct
+ // or else produce a warning:
+ // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
+ // When the Item Value is present, the Basic Offset Table Item Value shall contain
+ // concatenated 32-bit unsigned integer values that are byte offsets to the first
+ // byte of the Item Tag of the first fragment for each frame in the Sequence of
+ // Items. These offsets are measured from the first byte of the first Item Tag
+ // following the Basic Offset Table item (See Table A.4-2).
+
+ if ( BasicOffsetTableItemValue )
+ {
+ // If a BasicOffsetTableItemValue was read
+ uint32_t individualLength = BasicOffsetTableItemValue[i];
+ //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
+ if( individualLength != sum )
+ {
+ gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
+ individualLength << " != " << sum );
+ }
+ sum += fragmentLength + 8;
+ i++;
+ }
+
+ long fragmentOffset = Fp->tellg(); // Once per fragment
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->SetOffset(fragmentOffset);
+ newFragment->SetLength(fragmentLength);
+ JPEGInfo->AddFragment(newFragment);
+
+ SkipBytes(fragmentLength);
+ }
+
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the item :
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
- newE = new ValEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
+ gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
}
- else
+}
+
+/**
+ * \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 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
+ * 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(); // 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:
+ uint16_t itemTagGroup;
+ uint16_t itemTagElem;
+ try
{
- newE = GetHeader()->NewValEntryByNumber(group,element);
+ itemTagGroup = ReadInt16();
+ itemTagElem = ReadInt16();
}
+ catch ( FormatError )
+ {
+ gdcmErrorMacro( "Can not read tag for "
+ << " We should have found tag ("
+ << DictEntry::TranslateToKey(testGroup,testElem) << ")"
+ ) ;
+
+ return false;
+ }
+ if ( itemTagGroup != testGroup || itemTagElem != testElem )
+ {
+ // 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(newE);
+ return false;
+ }
+ return true;
}
-BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
+/**
+ * \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 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
+ * 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
+ * returns 0.
+ */
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- BinEntry* newE;
- if(oldE)
+ if ( !ReadTag(testGroup, testElem) )
{
- newE = new BinEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
+ // Avoid polutting output
+ if ( testGroup != 0xfffe )
+ gdcmErrorMacro( "ReadTag did not succeed for ("
+ << DictEntry::TranslateToKey(testGroup,testElem)
+ << ")..." );
+ return 0;
}
- else
+
+ //// Then read the associated Item Length
+
+ // long currentPosition = Fp->tellg(); // save time // JPRx
+ uint32_t itemLength = ReadInt32();
+ gdcmDebugMacro( "Basic Item Length is: " << itemLength
+// << " at address: " << std::hex << (unsigned int)currentPosition
+ );
+ return itemLength;
+}
+
+/**
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
+ */
+void File::ReadEncapsulatedBasicOffsetTable()
+{
+ //// Read the Basic Offset Table Item Tag length...
+ uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
+
+ // 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 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 )
{
- newE = GetHeader()->NewBinEntryByNumber(group,element);
- }
+ char *charBasicOffsetTableItemValue = new char[itemLength];
+ Fp->read(charBasicOffsetTableItemValue, itemLength);
+ unsigned int nbEntries = itemLength/4;
+ assert( nbEntries*4 == itemLength); // Make sure this is a multiple
+ BasicOffsetTableItemValue = new uint32_t[nbEntries];
+ for (unsigned int i=0; i < nbEntries; i++ )
+ {
+ BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
+#if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
+ uint32_t val = BasicOffsetTableItemValue[i];
+ BasicOffsetTableItemValue[i]
+ = ( (val<<24) | ((val<<8) & 0x00ff0000) |
+ ( (val>>8) & 0x0000ff00) | (val>>24) );
+#endif
+ gdcmDebugMacro( "Read one length for: " <<
+ std::hex << BasicOffsetTableItemValue[i] );
+ }
- return(newE);
+ delete[] charBasicOffsetTableItemValue;
+ }
}
+// These are the deprecated method that one day should be removed (after the next release)
+
+//#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",
+ File::Load());
+ SetFileName( fileName );
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+#endif
+*/
//-----------------------------------------------------------------------------
-// Private
+// Print
//-----------------------------------------------------------------------------
} // end namespace gdcm
-
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff