Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/01/13 22:30:11 $
- Version: $Revision: 1.192 $
+ Date: $Date: 2005/02/10 20:53:23 $
+ Version: $Revision: 1.223 $
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
+//
+// ---------------------------------------------------------------
+//
#include "gdcmFile.h"
#include "gdcmGlobal.h"
-#include "gdcmTS.h"
-#include "gdcmDocument.h"
-#include "gdcmDebug.h"
#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
-#include "gdcmHeader.h"
-#include "gdcmPixelReadConvert.h"
-#include "gdcmPixelWriteConvert.h"
-#include "gdcmDocEntryArchive.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
-#include <fstream>
+#include <stdio.h> //sscanf
+#include <vector>
namespace gdcm
{
-typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-
-//-------------------------------------------------------------------------
+//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \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).
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
*/
-File::File( )
-{
- HeaderInternal = new Header( );
- SelfHeader = true;
- Initialise();
+File::File( std::string const &filename )
+ :Document( filename )
+{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+
+ // 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 = GetEntryValue(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();
+ 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 BinEntry to change the the DictEntry
+ // The changed DictEntry will have
+ // - a correct PixelVR OB or OW)
+ // - a VM to "PXL"
+ // - the name to "Pixel Data"
+ BinEntry *oldEntry = dynamic_cast<BinEntry *>(entry);
+ if(oldEntry)
+ {
+ std::string 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 = NewVirtualDictEntry(GrPixel,NumPixel,
+ PixelVR,"1","Pixel Data");
+
+ BinEntry *newEntry = new BinEntry(newDict);
+ newEntry->Copy(entry);
+ newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
+ oldEntry->SetSelfArea(false);
+
+ RemoveEntry(oldEntry);
+ AddEntry(newEntry);
+ }
+ }
+ }
}
/**
- * \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 Constructor used when we want to generate dicom files from scratch
*/
-File::File(Header *header)
+File::File():
+ Document()
{
- HeaderInternal = header;
- SelfHeader = false;
- Initialise();
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+ InitializeDefaultFile();
}
/**
- * \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 Canonical destructor.
*/
-File::File(std::string const & filename )
+File::~File ()
{
- HeaderInternal = new Header( filename );
- SelfHeader = true;
- Initialise();
+ if( RLEInfo )
+ delete RLEInfo;
+ if( JPEGInfo )
+ delete JPEGInfo;
}
+//-----------------------------------------------------------------------------
+// Public
/**
- * \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( PixelReadConverter )
+bool File::IsReadable()
+{
+ if( !Document::IsReadable() )
+ {
+ return false;
+ }
+
+ const std::string &res = GetEntryValue(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
- delete PixelReadConverter;
+ return false; // Image Dimensions
}
- if( PixelWriteConverter )
+ if ( !GetDocEntry(0x0028, 0x0100) )
{
- delete PixelWriteConverter;
+ return false; // "Bits Allocated"
}
- if( Archive )
+ if ( !GetDocEntry(0x0028, 0x0101) )
{
- delete Archive;
+ return false; // "Bits Stored"
+ }
+ if ( !GetDocEntry(0x0028, 0x0102) )
+ {
+ return false; // "High Bit"
+ }
+ if ( !GetDocEntry(0x0028, 0x0103) )
+ {
+ return false; // "Pixel Representation" i.e. 'Sign'
}
- if( SelfHeader )
+ return true;
+}
+
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int File::GetImageNumber()
+{
+ // The function i atoi() takes the address of an area of memory as
+ // parameter and converts the string stored at that location to an integer
+ // using the external decimal to internal binary conversion rules. This may
+ // be preferable to sscanf() since atoi() is a much smaller, simpler and
+ // faster function. sscanf() can do all possible conversions whereas
+ // atoi() can only do single decimal integer conversions.
+ //0020 0013 IS REL Image Number
+ std::string strImNumber = GetEntryValue(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
{
- delete HeaderInternal;
+ return atoi( strImNumber.c_str() );
}
- HeaderInternal = 0;
+ return 0; //Hopeless
}
-//-----------------------------------------------------------------------------
-// Print
-void File::Print(std::ostream &os)
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType File::GetModality()
{
- HeaderInternal->SetPrintLevel(PrintLevel);
- HeaderInternal->Print(os);
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntryValue(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;
+ }
+ }
- PixelReadConverter->SetPrintLevel(PrintLevel);
- PixelReadConverter->Print(os);
+ return Unknow;
}
-//-----------------------------------------------------------------------------
-// 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
- * (use GetImageDataRawSize if you want to be sure to get *only*
- * the size of the pixels)
- * @return The 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::GetImageDataSize()
+int File::GetXSize()
{
- if ( PixelWriteConverter->GetUserData() )
+ const std::string &strSize = GetEntryValue(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
{
- return PixelWriteConverter->GetUserDataSize();
+ return 0;
}
- return PixelReadConverter->GetRGBSize();
+ return atoi( strSize.c_str() );
}
/**
- * \brief Get the size of the image data
- * If the image could be converted to RGB using a LUT,
- * this transformation is not taken into account by GetImageDataRawSize
- * (use GetImageDataSize if you wish)
- * @return The raw image size
+ * \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).
*/
-size_t File::GetImageDataRawSize()
+int File::GetYSize()
{
- if ( PixelWriteConverter->GetUserData() )
+ const std::string &strSize = GetEntryValue(0x0028,0x0010);
+ if ( strSize != GDCM_UNFOUND )
{
- return PixelWriteConverter->GetUserDataSize();
+ return atoi( strSize.c_str() );
+ }
+ if ( IsDicomV3() )
+ {
+ return 0;
}
- return PixelReadConverter->GetRawSize();
+ // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
+ // hence be a signal (1D image). So we default to 1:
+ return 1;
}
/**
- * \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 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).
*/
-uint8_t *File::GetImageData()
+int File::GetZSize()
{
- if ( PixelWriteConverter->GetUserData() )
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ const std::string &strSize = GetEntryValue(0x0028,0x0008);
+ if ( strSize != GDCM_UNFOUND )
{
- return PixelWriteConverter->GetUserData();
+ return atoi( strSize.c_str() );
}
- if ( ! GetRaw() )
+ // We then consider the "Planes" entry as the third dimension
+ const std::string &strSize2 = GetEntryValue(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
{
- // If the decompression failed nothing can be done.
- return 0;
+ return atoi( strSize2.c_str() );
+ }
+
+ return 1;
+}
+
+/**
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float File::GetXSpacing()
+{
+ float xspacing = 1.0;
+ float yspacing = 1.0;
+ const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
+
+ if( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
+ return 1.;
}
- if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ int nbValues;
+ if( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
{
- return PixelReadConverter->GetRGB();
+ // if no values, xspacing is set to 1.0
+ if( nbValues == 0 )
+ xspacing = 1.0;
+ // if single value is found, xspacing is defaulted to yspacing
+ if( nbValues == 1 )
+ xspacing = yspacing;
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
}
- else
+
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
+ if ( xspacing == 0.)
{
- // When no LUT or LUT conversion fails, return the Raw
- return PixelReadConverter->GetRaw();
+ gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ gdcmAssertMacro( nbValues == 2 );
}
+
+ 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
- */
-uint8_t *File::GetImageDataRaw ()
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float File::GetYSpacing()
{
- return GetRaw();
-}
+ float yspacing = 1.;
+ std::string strSpacing = GetEntryValue(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+
+ // if sscanf cannot read any float value, it won't affect yspacing
+ int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ // if no values, xspacing is set to 1.0
+ if( nbValues == 0 )
+ yspacing = 1.0;
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+}
/**
- * \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.
+ * \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
*/
-size_t File::GetImageDataIntoVector (void *destination, size_t maxSize)
+float File::GetZSpacing()
{
- if ( ! GetRaw() )
+ // Spacing Between Slices : distance entre le milieu de chaque coupe
+ // Les coupes peuvent etre :
+ // jointives (Spacing between Slices = Slice Thickness)
+ // chevauchantes (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
+ // Si le Spacing Between Slices est Missing,
+ // on suppose que les coupes sont jointives
+
+ const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
+
+ if ( strSpacingBSlices == GDCM_UNFOUND )
{
- // If the decompression failed nothing can be done.
- return 0;
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
+ const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
+ return 1.;
+ }
+ else
+ {
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return (float)atof( strSliceThickness.c_str() );
+ }
}
+ //else
+ return (float)atof( strSpacingBSlices.c_str() );
+}
+
+/**
+ * \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()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
- if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ if ( strImPos == GDCM_UNFOUND )
{
- if ( PixelReadConverter->GetRGBSize() > maxSize )
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
- return 0;
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.;
}
- memcpy( destination,
- (void*)PixelReadConverter->GetRGB(),
- PixelReadConverter->GetRGBSize() );
- return PixelReadConverter->GetRGBSize();
}
- // Either no LUT conversion necessary or LUT conversion failed
- if ( PixelReadConverter->GetRawSize() > maxSize )
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
{
- gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
- return 0;
+ return 0.;
}
- memcpy( destination,
- (void*)PixelReadConverter->GetRaw(),
- PixelReadConverter->GetRawSize() );
- return PixelReadConverter->GetRawSize();
+
+ return xImPos;
}
/**
- * \brief Points the internal 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
*/
-void File::SetImageData(uint8_t *inData, size_t expectedSize)
+float File::GetYOrigin()
{
- SetUserData(inData,expectedSize);
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ return 0.;
+ }
+ }
+
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ {
+ return 0.;
+ }
+
+ return yImPos;
}
/**
- * \brief Set the image datas defined by the user
- * \warning When writting the file, this datas are get as default datas to write
+ * \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
*/
-void File::SetUserData(uint8_t *data, size_t expectedSize)
+float File::GetZOrigin()
{
- PixelWriteConverter->SetUserData(data,expectedSize);
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
+
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ {
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(),
+ "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ {
+ gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
+ if ( strSliceLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ gdcmWarningMacro( "Unfound Slice Location (0020,1041)");
+
+ std::string strLocation = GetEntryValue(0x0020,0x0050);
+ if ( strLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ gdcmWarningMacro( "Unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
}
/**
- * \brief Get the image datas defined by the user
- * \warning When writting the file, this datas are get as default data to write
- */
-uint8_t *File::GetUserData()
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * (needed to organize DICOM files based on their x,y,z position)
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void File::GetImageOrientationPatient( float iop[6] )
{
- return PixelWriteConverter->GetUserData();
+ 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 = GetEntryValue(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." );
+ }
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryValue(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." );
+ }
+ }
}
/**
- * \brief Get the image data size defined by the user
- * \warning When writting the file, this datas are get as default data to write
+ * \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 !
*/
-size_t File::GetUserDataSize()
+int File::GetBitsStored()
{
- return PixelWriteConverter->GetUserDataSize();
+ std::string strSize = GetEntryValue( 0x0028, 0x0101 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
}
/**
- * \brief Get the image datas from the file.
- * If a LUT is found, the data are expanded to be RGB
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ * @return The encountered number of Bits Allocated, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
*/
-uint8_t *File::GetRGBData()
+int File::GetBitsAllocated()
{
- return PixelReadConverter->GetRGB();
+ std::string strSize = GetEntryValue(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
}
/**
- * \brief Get the image data size from the file.
- * If a LUT is found, the data are expanded to be RGB
+ * \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 positin when present. 0 when Missing.
*/
-size_t File::GetRGBDataSize()
+int File::GetHighBitPosition()
{
- return PixelReadConverter->GetRGBSize();
+ std::string strSize = GetEntryValue( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
}
/**
- * \brief Get the image datas from the file.
- * If a LUT is found, the datas are not expanded !
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB -1 or 3 Planes-)
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ * (Gray level Pixels)
*/
-uint8_t *File::GetRawData()
+int File::GetSamplesPerPixel()
{
- return PixelReadConverter->GetRaw();
+ const std::string &strSize = GetEntryValue(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ 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 atoi( strSize.c_str() );
}
/**
- * \brief Get the image data size from the file.
- * If a LUT is found, the data are not expanded !
+ * \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.
*/
-size_t File::GetRawDataSize()
+int File::GetPlanarConfiguration()
{
- return PixelReadConverter->GetRawSize();
+ std::string strSize = GetEntryValue(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
}
/**
- * \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 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
*/
-
-bool File::WriteRawData(std::string const &fileName)
+int File::GetPixelSize()
{
- std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
- if (!fp1)
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ // if (File::GetEntryValue(0x0028,0x0100) == "24")
+ // return 3;
+
+ std::string pixelType = GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
{
- gdcmVerboseMacro( "Fail to open (write) file:" << fileName.c_str());
- return false;
+ 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");
+ return 0;
+}
- if( PixelWriteConverter->GetUserData() )
+/**
+ * \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
+ * @return 0S if nothing found. NOT USABLE file. The caller has to check
+ */
+std::string File::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
{
- fp1.write( (char*)PixelWriteConverter->GetUserData(),
- PixelWriteConverter->GetUserDataSize() );
+ gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
}
- else if ( PixelReadConverter->GetRGB() )
+
+ if ( bitsAlloc == "64" )
{
- fp1.write( (char*)PixelReadConverter->GetRGB(),
- PixelReadConverter->GetRGBSize());
+ return "FD";
}
- else if ( PixelReadConverter->GetRaw() )
+ else if ( bitsAlloc == "12" )
{
- fp1.write( (char*)PixelReadConverter->GetRaw(),
- PixelReadConverter->GetRawSize());
+ // It will be unpacked
+ bitsAlloc = "16";
}
- else
+ else if ( bitsAlloc == "24" )
{
- gdcmErrorMacro( "Nothing written." );
+ // (in order no to be messed up
+ bitsAlloc = "8"; // by old RGB images)
}
- fp1.close();
+ std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation"
- return true;
+ if (sign == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
+ sign = "U"; // default and arbitrary value, not to polute the output
+ }
+ else if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
}
/**
- * \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 Check whether the pixels are signed or UNsigned data.
+ * \warning The method defaults to false (UNsigned) when information is Missing.
+ * The responsability of checking this value is left to the caller.
+ * @return True when signed, false when UNsigned
*/
-
-bool File::WriteDcmImplVR (std::string const &fileName)
+bool File::IsSignedPixelData()
{
- SetWriteTypeToDcmImplVR();
- return Write(fileName);
+ std::string strSize = GetEntryValue( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
+ return false;
+ }
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
+ {
+ return false;
+ }
+ return true;
}
/**
-* \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 Check whether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
*/
-
-bool File::WriteDcmExplVR (std::string const &fileName)
+bool File::IsMonochrome()
{
- SetWriteTypeToDcmExplVR();
- return Write(fileName);
+ const std::string &PhotometricInterp = GetEntryValue( 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 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 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::WriteAcr (std::string const &fileName)
+bool File::IsPaletteColor()
{
- SetWriteTypeToAcr();
- return Write(fileName);
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : Palette color (0028,0004)");
+ }
+ return false;
}
/**
- * \brief Writes on disk A SINGLE Dicom file,
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \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::Write(std::string const &fileName)
+bool File::IsYBRFull()
{
- switch(WriteType)
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
{
- case ImplicitVR:
- SetWriteFileTypeToImplicitVR();
- break;
- case ExplicitVR:
- SetWriteFileTypeToExplicitVR();
- break;
- case ACR:
- case ACR_LIBIDO:
- SetWriteFileTypeToACR();
- break;
- default:
- SetWriteFileTypeToExplicitVR();
+ return true;
}
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
+}
- // --------------------------------------------------------------
- // 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( WriteType == ACR_LIBIDO )
+/**
+ * \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) )
{
- SetWriteToLibido();
+ return false;
}
- else
+ // LutDescriptorGreen
+ if ( !GetDocEntry(0x0028,0x1102) )
{
- SetWriteToNoLibido();
+ return false;
}
- // ----------------- End of Special Patch ----------------
-
- switch(WriteMode)
+ // LutDescriptorBlue
+ if ( !GetDocEntry(0x0028,0x1103) )
{
- case WMODE_RAW :
- SetWriteToRaw();
- break;
- case WMODE_RGB :
- SetWriteToRGB();
- break;
+ return false;
}
-
- bool check = CheckWriteIntegrity();
- if(check)
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1201) )
{
- check = HeaderInternal->Write(fileName,WriteType);
+ 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;
}
- RestoreWrite();
- RestoreWriteFileType();
-
- // --------------------------------------------------------------
- // 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
- RestoreWriteOfLibido();
- // ----------------- End of Special Patch ----------------
-
- return check;
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (string) to substitute with
- * @param group group number of the Dicom Element to modify
- * @param elem element number of the Dicom Element to modify
- */
-bool File::SetEntry(std::string const &content,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->SetEntry(content,group,elem);
-}
-
-
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (void* -> uint8_t*) to substitute with
- * @param lgth new value length
- * @param group group number of the Dicom Element to modify
- * @param elem element number of the Dicom Element to modify
- */
-bool File::SetEntry(uint8_t *content, int lgth,
- uint16_t group, uint16_t elem)
+ * \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()
{
- return HeaderInternal->SetEntry(content,lgth,group,elem);
-}
+ 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 = GetEntryValue(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
+ return 0;
+ }
-/**
- * \brief Modifies the value of a given Doc Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param content (string) Value to be set
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-bool File::ReplaceOrCreate(std::string const &content,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->ReplaceOrCreate(content,group,elem) != NULL;
-}
+ tokens.clear(); // clean any previous value
+ Util::Tokenize ( lutDescription, tokens, "\\" );
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * A copy of the binArea is made to be kept in the Document.
- * @param binArea (binary) value to be set
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-bool File::ReplaceOrCreate(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->ReplaceOrCreate(binArea,lgth,group,elem) != NULL;
+ lutNbits = atoi( tokens[2].c_str() );
+ tokens.clear();
+
+ return lutNbits;
}
/**
- * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
*/
-uint8_t* File::GetLutRGBA()
+float File::GetRescaleIntercept()
{
- return PixelReadConverter->GetLutRGBA();
-}
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
+ if ( strRescInter != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ {
+ // bug in the element 0x0028,0x1052
+ gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
+ }
+ }
-//-----------------------------------------------------------------------------
-// Protected
+ return resInter;
+}
/**
- * \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 gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-bool File::CheckWriteIntegrity()
+float File::GetRescaleSlope()
{
- if(PixelWriteConverter->GetUserData())
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryValue(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
{
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
- if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
{
- numberBitsAllocated = 16;
- }
-
- size_t decSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
- size_t rgbSize = decSize;
- if( HeaderInternal->HasLUT() )
- rgbSize = decSize * 3;
-
- switch(WriteMode)
- {
- case WMODE_RAW :
- if( decSize!=PixelWriteConverter->GetUserDataSize() )
- {
- gdcmVerboseMacro( "Data size is incorrect (Raw)" << decSize
- << " / " << PixelWriteConverter->GetUserDataSize() );
- return false;
- }
- break;
- case WMODE_RGB :
- if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
- {
- gdcmVerboseMacro( "Data size is incorrect (RGB)" << decSize
- << " / " << PixelWriteConverter->GetUserDataSize() );
- return false;
- }
- break;
+ // bug in the element 0x0028,0x1053
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
}
}
-
- return true;
+
+ return resSlope;
}
-void File::SetWriteToRaw()
+/**
+ * \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 ...)
+ * \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
- && !HeaderInternal->HasLUT())
+ if ( GetSamplesPerPixel() == 3 )
{
- SetWriteToRGB();
- }
- else
+ return 3;
+ }
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryValue(0x0028,0x0100) == "24" )
{
- ValEntry *photInt = CopyValEntry(0x0028,0x0004);
- if(HeaderInternal->HasLUT())
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
{
- photInt->SetValue("PALETTE COLOR ");
+ return 3;
}
else
{
- photInt->SetValue("MONOCHROME1 ");
+ return 1;
}
+ }
- PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
- PixelReadConverter->GetRawSize());
-
- BinEntry *pixel =
- CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelWriteConverter->GetData(),false);
- pixel->SetLength(PixelWriteConverter->GetDataSize());
-
- Archive->Push(photInt);
- Archive->Push(pixel);
+ // 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
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
}
}
-void File::SetWriteToRGB()
+/**
+ * \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()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryValue(0x0028,0x0100) == "24" )
{
- PixelReadConverter->BuildRGBImage();
-
- ValEntry *spp = CopyValEntry(0x0028,0x0002);
- spp->SetValue("3 ");
-
- ValEntry *planConfig = CopyValEntry(0x0028,0x0006);
- planConfig->SetValue("0 ");
-
- ValEntry *photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("RGB ");
+ return 3;
+ }
- if(PixelReadConverter->GetRGB())
- {
- PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
- PixelReadConverter->GetRGBSize());
- }
- else // Raw data
- {
- PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
- PixelReadConverter->GetRawSize());
- }
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
- BinEntry *pixel =
- CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelWriteConverter->GetData(),false);
- pixel->SetLength(PixelWriteConverter->GetDataSize());
-
- 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 ");
-
- ValEntry *bitsStored = CopyValEntry(0x0028,0x0101);
- bitsStored->SetValue("8 ");
-
- ValEntry *highBit = CopyValEntry(0x0028,0x0102);
- highBit->SetValue("7 ");
-
- Archive->Push(bitsAlloc);
- Archive->Push(bitsStored);
- Archive->Push(highBit);
- }
+/**
+ * \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()
+{
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
}
else
{
- SetWriteToRaw();
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
}
}
-void File::RestoreWrite()
+/**
+ * \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()
{
- Archive->Restore(0x0028,0x0002);
- Archive->Restore(0x0028,0x0004);
- Archive->Restore(0x0028,0x0006);
- Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
- // For old ACR-NEMA (24 bits problem)
- Archive->Restore(0x0028,0x0100);
- Archive->Restore(0x0028,0x0101);
- Archive->Restore(0x0028,0x0102);
+/**
+ * \brief Adds the characteristics of a new element we want to anonymize
+ *
+ */
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
- // 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);
+{
+ Element el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ AnonymizeList.push_back(el);
}
-void File::SetWriteFileTypeToACR()
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
{
- Archive->Push(0x0002,0x0010);
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+
+ // TODO : FIXME
+ // how to white out disk space if longer than 50 ?
+
+
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t valLgth = 0;
+ std::string *spaces;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ continue;
+
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
+
+ offset = d->GetOffset();
+ lgth = d->GetLength();
+ if (valLgth < lgth)
+ {
+ spaces = new std::string( lgth-valLgth, ' ');
+ (*it).Value = (*it).Value + *spaces;
+ delete spaces;
+ }
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (*it).Value.c_str(), lgth );
+
+ }
+ fp->close();
+ delete fp;
}
-void File::SetWriteFileTypeToExplicitVR()
+/**
+ * \brief anonymize a File (removes Patient's personal info passed with
+ * AddAnonymizeElement()
+ */
+bool File::AnonymizeFile()
{
- std::string ts = Util::DicomString(
- Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
-
- ValEntry *tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
+ // If Anonymisation list is empty, let's perform some basic anonymization
+ if ( AnonymizeList.begin() == AnonymizeList.end() )
+ {
+ // If exist, replace by spaces
+ SetValEntry (" ",0x0010, 0x2154); // Telephone
+ SetValEntry (" ",0x0010, 0x1040); // Adress
+ SetValEntry (" ",0x0010, 0x0020); // Patient ID
- Archive->Push(tss);
-}
+ DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
+ {
+ std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ SetValEntry(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ SetValEntry("anonymised", 0x0010, 0x0010);
+ }
+ }
+ }
+ else
+ {
+ gdcm::DocEntry *d;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
-void File::SetWriteFileTypeToImplicitVR()
-{
- std::string ts = Util::DicomString(
- Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
+ if ( d == NULL)
+ continue;
- ValEntry *tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
- Archive->Push(tss);
+ SetValEntry ((*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 filetype Type of the File to be written
+ * (ACR, ExplicitVR, ImplicitVR)
+ */
+bool File::Write(std::string fileName, FileType filetype)
{
- ValEntry *oldRow = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0028, 0x0010));
- ValEntry *oldCol = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0028, 0x0011));
-
- if( oldRow && oldCol )
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
{
- std::string rows, columns;
-
- ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
- ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+ gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
+ return false;
+ }
- newRow->Copy(oldCol);
- newCol->Copy(oldRow);
+ // Entry : 0002|0000 = group length -> recalculated
+ ValEntry *e0002 = GetValEntry(0x0002,0x0000);
+ if( e0002 )
+ {
+ std::ostringstream sLen;
+ sLen << ComputeGroup0002Length(filetype);
+ e0002->SetValue(sLen.str());
+ }
- newRow->SetValue(oldCol->GetValue());
- newCol->SetValue(oldRow->GetValue());
+ // Bits Allocated
+ if ( GetEntryValue(0x0028,0x0100) == "12")
+ {
+ SetValEntry("16", 0x0028,0x0100);
+ }
- Archive->Push(newRow);
- Archive->Push(newCol);
+ int i_lgPix = GetEntryLength(GrPixel, NumPixel);
+ if (i_lgPix != -2)
+ {
+ // no (GrPixel, NumPixel) element
+ std::string s_lgPix = Util::Format("%d", i_lgPix+12);
+ s_lgPix = Util::DicomString( s_lgPix.c_str() );
+ InsertValEntry(s_lgPix,GrPixel, 0x0000);
}
- ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
- libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
- Archive->Push(libidoCode);
-}
+ // FIXME : should be nice if we could move it to File
+ // (or in future gdcmPixelData class)
-void File::SetWriteToNoLibido()
-{
- ValEntry *recCode = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0008,0x0010));
- if( recCode )
+ // Drop Palette Color, if necessary
+ if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' )
{
- if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ // if SamplesPerPixel = 3, sure we don't need any LUT !
+ // Drop 0028|1101, 0028|1102, 0028|1103
+ // Drop 0028|1201, 0028|1202, 0028|1203
+
+ DocEntry *e = GetDocEntry(0x0028,0x01101);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x01201);
+ if (e)
{
- ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
- libidoCode->SetValue("");
- Archive->Push(libidoCode);
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
}
}
+
+ Document::WriteContent(fp, filetype);
+
+ fp->close();
+ delete fp;
+
+ return true;
}
-void File::RestoreWriteOfLibido()
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Initialize a default DICOM File that should contain all the
+ * field require by other reader. DICOM standard does not
+ * explicitely defines those fields, heuristic has been choosen.
+ * This is not perfect as we are writting a CT image...
+ */
+void File::InitializeDefaultFile()
{
- Archive->Restore(0x0028,0x0010);
- Archive->Restore(0x0028,0x0011);
- Archive->Restore(0x0008,0x0010);
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidInst = uid;
+ std::string uidClass = Util::CreateUniqueUID();
+ std::string uidStudy = Util::CreateUniqueUID();
+ std::string uidSerie = Util::CreateUniqueUID();
+
+ // Meta Element Group Length
+ InsertValEntry("146 ", 0x0002, 0x0000);
+ // Media Storage SOP Class UID (CT Image Storage)
+ InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002);
+ // Media Storage SOP Instance UID
+ InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003);
+ // Transfer Syntax UID (Explicit VR Little Endian)
+ InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010);
+ // META Implementation Class UID
+ InsertValEntry(uidClass.c_str(), 0x0002, 0x0012);
+ // Source Application Entity Title
+ InsertValEntry("GDCM", 0x0002, 0x0016);
+
+ // Instance Creation Date
+ InsertValEntry(date.c_str(), 0x0008, 0x0012);
+ // Instance Creation Time
+ InsertValEntry(time.c_str(), 0x0008, 0x0013);
+ // SOP Class UID
+ InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016);
+ // SOP Instance UID
+ InsertValEntry(uidInst.c_str(), 0x0008, 0x0018);
+ // Modality
+ InsertValEntry("CT", 0x0008, 0x0060);
+ // Manufacturer
+ InsertValEntry("GDCM", 0x0008, 0x0070);
+ // Institution Name
+ InsertValEntry("GDCM", 0x0008, 0x0080);
+ // Institution Address
+ InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081);
+
+ // Patient's Name
+ InsertValEntry("GDCM", 0x0010, 0x0010);
+ // Patient ID
+ InsertValEntry("GDCMID", 0x0010, 0x0020);
+
+ // Study Instance UID
+ InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d);
+ // Series Instance UID
+ InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e);
+ // StudyID
+ InsertValEntry("1", 0x0020, 0x0010);
+ // SeriesNumber
+ InsertValEntry("1", 0x0020, 0x0011);
+
+ // Samples per pixel 1 or 3
+ InsertValEntry("1", 0x0028, 0x0002);
+ // photochromatic interpretation
+ InsertValEntry("MONOCHROME1", 0x0028, 0x0004);
+ // nbRows
+ InsertValEntry("0", 0x0028, 0x0010);
+ // nbCols
+ InsertValEntry("0", 0x0028, 0x0011);
+ // BitsAllocated 8 or 12 or 16
+ InsertValEntry("8", 0x0028, 0x0100);
+ // BitsStored <= BitsAllocated
+ InsertValEntry("8", 0x0028, 0x0101);
+ // HighBit <= BitsAllocated - 1
+ InsertValEntry("7", 0x0028, 0x0102);
+ // Pixel Representation 0(unsigned) or 1(signed)
+ InsertValEntry("0", 0x0028, 0x0103);
+
+ // default value
+ // Special case this is the image (not a string)
+ GrPixel = 0x7fe0;
+ NumPixel = 0x0010;
+ InsertBinEntry(0, 0, GrPixel, NumPixel);
}
-ValEntry *File::CopyValEntry(uint16_t group,uint16_t elem)
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
+ */
+void File::ComputeRLEInfo()
{
- DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
- ValEntry *newE;
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
+ {
+ return;
+ }
- if(oldE)
+ // 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"
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // 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;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // 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();
+
+ 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 the RLE Header and the 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 at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
- newE = new ValEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
+ gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
}
- else
+}
+
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void File::ComputeJPEGFragmentInfo()
+{
+ // If you need to, look for comments of ComputeRLEInfo().
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
{
- newE = GetHeader()->NewValEntry(group,elem);
+ return;
+ }
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = Fp->tellg();
+
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->SetOffset(fragmentOffset);
+ newFragment->SetLength(fragmentLength);
+ JPEGInfo->AddFragment(newFragment);
+
+ SkipBytes(fragmentLength);
}
- return newE;
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
+ }
}
-BinEntry *File::CopyBinEntry(uint16_t group,uint16_t elem)
+/**
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag check whether this
+ * tag is (TestGroup, TestElement).
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return True on success, false otherwise.
+ */
+bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
{
- DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
- BinEntry *newE;
-
- if(oldE)
+ long positionOnEntry = Fp->tellg();
+ long currentPosition = Fp->tellg(); // On debugging purposes
+
+ // Read the Item Tag group and element, and make
+ // sure they are what we expected:
+ uint16_t itemTagGroup;
+ uint16_t itemTagElement;
+ try
{
- newE = new BinEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
+ itemTagGroup = ReadInt16();
+ itemTagElement = ReadInt16();
}
- else
+ catch ( FormatError e )
{
- newE = GetHeader()->NewBinEntry(group,elem);
+ //std::cerr << e << std::endl;
+ return false;
}
+ if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ {
+ gdcmWarningMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << " but instead we encountered tag ("
+ << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
+ ) ;
+ Fp->seekg(positionOnEntry, std::ios::beg);
- return newE;
+ return false;
+ }
+ return true;
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \brief Factorization for various forms of constructors.
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag (TestGroup, TestElement),
+ * read the length associated to the Tag.
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag and it's length.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return On success returns the length associated to the tag. On failure
+ * returns 0.
*/
-void File::Initialise()
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- WriteMode = WMODE_RAW;
- WriteType = ExplicitVR;
- PixelReadConverter = new PixelReadConvert;
- PixelWriteConverter = new PixelWriteConvert;
- Archive = new DocEntryArchive( HeaderInternal );
-
- if ( HeaderInternal->IsReadable() )
+ if ( !ReadTag(testGroup, testElement) )
+ {
+ return 0;
+ }
+
+ //// Then read the associated Item Length
+ long currentPosition = Fp->tellg();
+ uint32_t itemLength = ReadInt32();
{
- PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ gdcmWarningMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
}
+ return itemLength;
}
-uint8_t *File::GetRaw()
+/**
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
+ */
+void File::ReadAndSkipEncapsulatedBasicOffsetTable()
{
- uint8_t *raw = PixelReadConverter->GetRaw();
- if ( ! raw )
+ //// 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 it's 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 )
{
- // The Raw image migth not be loaded yet:
- std::ifstream *fp = HeaderInternal->OpenFile();
- PixelReadConverter->ReadAndDecompressPixelData( fp );
- if(fp)
- HeaderInternal->CloseFile();
+ char *basicOffsetTableItemValue = new char[itemLength + 1];
+ Fp->read(basicOffsetTableItemValue, itemLength);
- raw = PixelReadConverter->GetRaw();
- if ( ! raw )
+#ifdef GDCM_DEBUG
+ for (unsigned int i=0; i < itemLength; i += 4 )
{
- gdcmVerboseMacro( "Read/decompress of pixel data apparently went wrong.");
- return 0;
+ uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
+ uint32_t);
+ gdcmWarningMacro( "Read one length: " <<
+ std::hex << individualLength );
}
- }
+#endif //GDCM_DEBUG
- return raw;
+ delete[] basicOffsetTableItemValue;
+ }
}
//-----------------------------------------------------------------------------
-// Private
+// Print
//-----------------------------------------------------------------------------
} // end namespace gdcm
-
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff