- /*=========================================================================
+/*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/10/08 17:24:54 $
- Version: $Revision: 1.137 $
+ Date: $Date: 2005/01/21 12:37:15 $
+ Version: $Revision: 1.196 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#include "gdcmFile.h"
+#include "gdcmGlobal.h"
+#include "gdcmUtil.h"
#include "gdcmDebug.h"
-#include "gdcmPixelConvert.h"
-#include "jpeg/ljpg/jpegless.h"
+#include "gdcmTS.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
+#include <stdio.h> //sscanf
-typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
+#include <vector>
-//-------------------------------------------------------------------------
+namespace gdcm
+{
+//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader 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 gdcmHeader
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
+ */
+File::File( std::string const &filename ):
+ Document( filename )
+{
+ // 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 = GetEntry(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 )
+ {
+
+ 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";
+
+ DictEntry* newEntry = NewVirtualDictEntry(
+ GrPixel, NumPixel,
+ PixelVR, "PXL", "Pixel Data");
+
+ entry->SetDictEntry( newEntry );
+ }
+}
+
+/**
+ * \brief Constructor used when we want to generate dicom files from scratch
*/
-gdcmFile::gdcmFile(gdcmHeader *header)
+File::File()
+ :Document()
{
- Header = header;
- SelfHeader = false;
- Initialise();
+ InitializeDefaultFile();
}
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader 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.
*/
-gdcmFile::gdcmFile(std::string const & filename )
+File::~File ()
{
- Header = new gdcmHeader( filename );
- SelfHeader = true;
- Initialise();
}
/**
- * \brief Factorization for various forms of constructors.
+ * \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-NEMA, ExplicitVR, ImplicitVR)
*/
-void gdcmFile::Initialise()
+bool File::Write(std::string fileName, FileType filetype)
{
- if ( Header->IsReadable() )
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
{
- ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( Header->HasLUT() )
+ gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
+ return false;
+ }
+
+ // Bits Allocated
+ if ( GetEntry(0x0028,0x0100) == "12")
+ {
+ SetEntry("16", 0x0028,0x0100);
+ }
+
+ /// \todo correct 'Pixel group' Length if necessary
+
+ 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() );
+ ReplaceOrCreate(s_lgPix,GrPixel, 0x0000);
+ }
+
+ // FIXME : should be nice if we could move it to File
+ // (or in future gdcmPixelData class)
+
+ // Drop Palette Color, if necessary
+
+ if ( GetEntry(0x0028,0x0002).c_str()[0] == '3' )
+ {
+ // 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)
{
- ImageDataSize = 3 * ImageDataSizeRaw;
+ RemoveEntryNoDestroy(e);
}
- else
+ e = GetDocEntry(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1202);
+ if (e)
{
- ImageDataSize = ImageDataSizeRaw;
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
}
}
- SaveInitialValues();
+
+/*
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Super Super hack that will make gdcm a BOMB ! but should
+ // Fix temporarily the dashboard
+ BinEntry *b = GetBinEntry(GrPixel,NumPixel);
+ if ( GetPixelSize() == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)b->GetBinArea();
+ int lgr = b->GetLength();
+ for( int i = 0; i < lgr / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ }
+#endif //GDCM_WORDS_BIGENDIAN
+*/
+
+ Document::WriteContent(fp,filetype);
+
+/*
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Flip back the pixel ... I told you this is a hack
+ if ( GetPixelSize() == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)b->GetBinArea();
+ int lgr = b->GetLength();
+ for( int i = 0; i < lgr / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ }
+#endif //GDCM_WORDS_BIGENDIAN
+*/
+
+ fp->close();
+ delete fp;
+
+ return true;
}
+//-----------------------------------------------------------------------------
+// Print
+
+
+//-----------------------------------------------------------------------------
+// Public
+
/**
- * \brief canonical destructor
- * \note If the gdcmHeader was created by the gdcmFile constructor,
- * it is destroyed by the gdcmFile
+ * \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.
*/
-gdcmFile::~gdcmFile()
-{
- if( SelfHeader )
+bool File::IsReadable()
+{
+ if( !Document::IsReadable() )
+ {
+ return false;
+ }
+
+ const std::string &res = GetEntry(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
+ return false; // Image Dimensions
+ }
+ if ( !GetDocEntry(0x0028, 0x0100) )
+ {
+ return false; // "Bits Allocated"
+ }
+ if ( !GetDocEntry(0x0028, 0x0101) )
+ {
+ return false; // "Bits Stored"
+ }
+ if ( !GetDocEntry(0x0028, 0x0102) )
+ {
+ return false; // "High Bit"
+ }
+ if ( !GetDocEntry(0x0028, 0x0103) )
{
- delete Header;
+ return false; // "Pixel Representation" i.e. 'Sign'
}
- Header = 0;
- DeleteInitialValues();
+ return true;
}
/**
- * \brief Sets some initial values for the Constructor
- * \warning not end user intended
+ * \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
*/
-void gdcmFile::SaveInitialValues()
-{
-
- PixelRead = -1; // no ImageData read yet.
- LastAllocatedPixelDataLength = 0;
- Pixel_Data = 0;
-
- InitialSpp = "";
- InitialPhotInt = "";
- InitialPlanConfig = "";
- InitialBitsAllocated = "";
- InitialHighBit = "";
-
- InitialRedLUTDescr = 0;
- InitialGreenLUTDescr = 0;
- InitialBlueLUTDescr = 0;
- InitialRedLUTData = 0;
- InitialGreenLUTData = 0;
- InitialBlueLUTData = 0;
-
- if ( Header->IsReadable() )
- {
- // the following values *may* be modified
- // by gdcmFile::GetImageDataIntoVectorRaw
- // we save their initial value.
- InitialSpp = Header->GetEntryByNumber(0x0028,0x0002);
- InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004);
- InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006);
-
- InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100);
- InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102);
-
- // the following entries *may* be removed from the H table
- // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw
- // we keep a pointer on them.
- InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101);
- InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102);
- InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103);
-
- InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201);
- InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202);
- InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203);
+int File::GetXSize()
+{
+ const std::string &strSize = GetEntry(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
}
+
+ return atoi( strSize.c_str() );
}
/**
- * \brief restores some initial values
- * \warning not end user intended
+ * \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).
*/
-void gdcmFile::RestoreInitialValues()
-{
- if ( Header->IsReadable() )
- {
- // the following values *may* have been modified
- // by gdcmFile::GetImageDataIntoVectorRaw
- // we restore their initial value.
- if ( InitialSpp != "")
- Header->SetEntryByNumber(InitialSpp,0x0028,0x0002);
- if ( InitialPhotInt != "")
- Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004);
- if ( InitialPlanConfig != "")
-
- Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006);
- if ( InitialBitsAllocated != "")
- Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100);
- if ( InitialHighBit != "")
- Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102);
-
- // the following entries *may* be have been removed from the H table
- // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw
- // we restore them.
-
- if (InitialRedLUTDescr)
- Header->AddEntry(InitialRedLUTDescr);
- if (InitialGreenLUTDescr)
- Header->AddEntry(InitialGreenLUTDescr);
- if (InitialBlueLUTDescr)
- Header->AddEntry(InitialBlueLUTDescr);
-
- if (InitialRedLUTData)
- Header->AddEntry(InitialBlueLUTDescr);
- if (InitialGreenLUTData)
- Header->AddEntry(InitialGreenLUTData);
- if (InitialBlueLUTData)
- Header->AddEntry(InitialBlueLUTData);
+int File::GetYSize()
+{
+ const std::string &strSize = GetEntry(0x0028,0x0010);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+ if ( IsDicomV3() )
+ {
+ return 0;
}
+
+ // 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 delete initial values (il they were saved)
- * of InitialLutDescriptors and InitialLutData
+ * \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).
*/
-void gdcmFile::DeleteInitialValues()
-{
+int File::GetZSize()
+{
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ const std::string &strSize = GetEntry(0x0028,0x0008);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
-// InitialLutDescriptors and InitialLutData
-// will have to be deleted if the don't belong any longer
-// to the Header H table when the header is deleted...
+ // We then consider the "Planes" entry as the third dimension
+ const std::string &strSize2 = GetEntry(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
+ {
+ return atoi( strSize2.c_str() );
+ }
- if ( InitialRedLUTDescr )
- delete InitialRedLUTDescr;
-
- if ( InitialGreenLUTDescr )
- delete InitialGreenLUTDescr;
-
- if ( InitialBlueLUTDescr )
- delete InitialBlueLUTDescr;
-
- if ( InitialRedLUTData )
- delete InitialRedLUTData;
-
- if ( InitialGreenLUTData != NULL)
- delete InitialGreenLUTData;
-
- if ( InitialBlueLUTData != NULL)
- delete InitialBlueLUTData;
+ return 1;
}
-//-----------------------------------------------------------------------------
-// Print
+/**
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float File::GetXSpacing()
+{
+ float xspacing, yspacing;
+ const std::string &strSpacing = GetEntry(0x0028,0x0030);
-//-----------------------------------------------------------------------------
-// Public
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
+ return 1.;
+ }
+
+ int nbValues;
+ if( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
+ {
+ // if single value is found, xspacing is defaulted to yspacing
+ if ( nbValues == 1 )
+ {
+ xspacing = yspacing;
+ }
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
+ }
+
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
+ if ( xspacing == 0.)
+ {
+ gdcmVerboseMacro("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 computes the length (in bytes) we must ALLOCATE to receive the
- * image(s) pixels (multiframes taken into account)
- * \warning : it is NOT the group 7FE0 length
- * (no interest for compressed images).
- */
-int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader()
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float File::GetYSpacing()
{
- // see PS 3.3-2003 : C.7.6.3.2.1
- //
- // MONOCHROME1
- // MONOCHROME2
- // PALETTE COLOR
- // RGB
- // HSV (Retired)
- // ARGB (Retired)
- // CMYK (Retired)
- // YBR_FULL
- // YBR_FULL_422 (no LUT, no Palette)
- // YBR_PARTIAL_422
- // YBR_ICT
- // YBR_RCT
-
- // LUT's
- // ex : gdcm-US-ALOKA-16.dcm
- // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
- // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
- // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
-
- // ex : OT-PAL-8-face.dcm
- // 0028|1201 [US] [Red Palette Color Lookup Table Data]
- // 0028|1202 [US] [Green Palette Color Lookup Table Data]
- // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
-
- // Number of "Bits Allocated"
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
- {
- numberBitsAllocated = 16;
- }
-
- int DecompressedSize = Header->GetXSize()
- * Header->GetYSize()
- * Header->GetZSize()
- * ( numberBitsAllocated / 8 )
- * Header->GetSamplesPerPixel();
-
- return DecompressedSize;
-}
+ float yspacing = 1.;
+ std::string strSpacing = GetEntry(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+
+ // if sscanf cannot read any float value, it won't affect yspacing
+ sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+}
/**
- * \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 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
*/
-uint8_t* gdcmFile::GetImageData()
+float File::GetZSpacing()
{
- // FIXME (Mathieu)
- // I need to deallocate Pixel_Data before doing any allocation:
+ // 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
- if ( Pixel_Data )
- if ( LastAllocatedPixelDataLength != ImageDataSize )
- free(Pixel_Data);
- if ( !Pixel_Data )
- Pixel_Data = new uint8_t[ImageDataSize];
-
- if ( Pixel_Data )
- {
- LastAllocatedPixelDataLength = ImageDataSize;
-
- // we load the pixels (and transform grey level + LUT into RGB)
- GetImageDataIntoVector(Pixel_Data, ImageDataSize);
-
- // We say the value *is* loaded.
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-
- // Will be 7fe0, 0010 in standard case
- GetHeader()->SetEntryBinAreaByNumber( Pixel_Data,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- }
- PixelRead = 0; // no PixelRaw
-
- return Pixel_Data;
+ const std::string &strSpacingBSlices = GetEntry(0x0018,0x0088);
+
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
+ const std::string &strSliceThickness = GetEntry(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("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
- * 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 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
*/
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
+float File::GetRescaleIntercept()
{
- GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // =0 : no ImageDataRaw
- if ( !Header->HasLUT() )
- {
- return ImageDataSize;
- }
-
- // from Lut R + Lut G + Lut B
- uint8_t *newDest = new uint8_t[ImageDataSize];
- uint8_t *a = (uint8_t *)destination;
- uint8_t *lutRGBA = Header->GetLUTRGBA();
-
- if ( lutRGBA )
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntry(0x0028,0x1052);
+ if ( strRescInter != GDCM_UNFOUND )
{
- int j;
- // move Gray pixels to temp area
- memmove(newDest, destination, ImageDataSizeRaw);
- for (size_t i=0; i<ImageDataSizeRaw; ++i)
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
{
- // Build RGB Pixels
- j = newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
+ // bug in the element 0x0028,0x1052
+ gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
}
- delete[] newDest;
-
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // FIXME : Better use CreateOrReplaceIfExist ?
-
- std::string spp = "3"; // Samples Per Pixel
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb = "RGB "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- std::string planConfig = "0"; // Planar Configuration
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- }
- else // GetLUTRGBA() failed
- {
- // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color
- // that are *more* than 65535 long ?!?
- // No idea how to manage such an image !
- // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!)
- // It seems that *no Dicom Viewer* has any idea :-(
-
- std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(photomInterp,0x0028,0x0004);
- }
-
- /// \todo Drop Palette Color out of the Header?
- return ImageDataSize;
+ }
+
+ return resInter;
}
/**
- * \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 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-uint8_t* gdcmFile::GetImageDataRaw ()
+float File::GetRescaleSlope()
{
- size_t imgDataSize;
- if ( Header->HasLUT() )
- /// \todo Let gdcmHeader user a chance to get the right value
- imgDataSize = ImageDataSizeRaw;
- else
- imgDataSize = ImageDataSize;
-
- // FIXME (Mathieu)
- // I need to deallocate Pixel_Data before doing any allocation:
-
- if ( Pixel_Data )
- if ( LastAllocatedPixelDataLength != imgDataSize )
- free(Pixel_Data);
- if ( !Pixel_Data )
- Pixel_Data = new uint8_t[imgDataSize];
-
- if ( Pixel_Data )
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntry(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
{
- LastAllocatedPixelDataLength = imgDataSize;
-
- // we load the pixels ( grey level or RGB, but NO transformation)
- GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize);
-
- // We say the value *is* loaded.
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-
- // will be 7fe0, 0010 in standard cases
- GetHeader()->SetEntryBinAreaByNumber(Pixel_Data,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- }
- PixelRead = 1; // PixelRaw
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ {
+ // bug in the element 0x0028,0x1053
+ gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
+ }
+ }
- return Pixel_Data;
+ return resSlope;
}
/**
- * \brief Copies at most MaxSize bytes of pixel data to caller's
- * memory space.
- * \warning This function was designed to avoid people that want to build
- * a volume from an image stack to need 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 hace to call GetImageData
- * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
- * into a single RGB Pixels Plane
- * the (VTK) user will manage the palettes
- *
- * @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 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)
*/
-size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
+int File::GetNumberOfScalarComponents()
{
- // we save the initial values of the following
- // in order to be able to restore the header in a disk-consistent state
- // (if user asks twice to get the pixels from disk)
-
- if ( PixelRead != -1 ) // File was "read" before
- {
- RestoreInitialValues();
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
}
-
- PixelRead = 1 ; // PixelRaw
-
- if ( ImageDataSize > maxSize )
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntry(0x0028,0x0100) == "24" )
{
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
+ return 3;
}
+
+ std::string strPhotometricInterpretation = GetEntry(0x0028,0x0004);
- ReadPixelData( destination );
-
- // Number of Bits Allocated for storing a Pixel
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( numberBitsAllocated == 0 )
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
{
- numberBitsAllocated = 16;
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
+ {
+ return 3;
+ }
+ else
+ {
+ return 1;
+ }
}
- // Number of Bits actually used
- int numberBitsStored = Header->GetBitsStored();
- if ( numberBitsStored == 0 )
+ // 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") )
{
- numberBitsStored = numberBitsAllocated;
+ return 1;
}
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
+}
- // High Bit Position
- int highBitPosition = Header->GetHighBitPosition();
- if ( highBitPosition == 0 )
+/**
+ * \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()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntry(0x0028,0x0100) == "24" )
{
- highBitPosition = numberBitsAllocated - 1;
+ return 3;
}
- bool signedPixel = Header->IsSignedPixelData();
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
- gdcmPixelConvert::ConvertReorderEndianity(
- (uint8_t*) destination,
- ImageDataSize,
- numberBitsStored,
- numberBitsAllocated,
- Header->GetSwapCode(),
- signedPixel );
+//
+// -------------- 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
+
+// \todo find a way to inform the caller nothing was found
+// \todo How to tell the caller a wrong number of values was found?
+//
+// ---------------------------------------------------------------
+//
- ConvertReArrangeBits( (uint8_t*) destination,
- ImageDataSize,
- numberBitsStored,
- numberBitsAllocated,
- highBitPosition );
+/**
+ * \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 = GetEntry(0x0020,0x0032);
-#ifdef GDCM_DEBUG
- FILE* DebugFile;
- DebugFile = fopen( "SpuriousFile.RAW", "wb" );
- fwrite( PixelConvertor.GetUncompressed(),
- PixelConvertor.GetUncompressedsSize(),
- 1, DebugFile );
- fclose( DebugFile );
-#endif //GDCM_DEBUG
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
-// SPLIT ME
-//////////////////////////////////
-// Deal with the color
-
- // Monochrome pictures don't require color intervention
- if ( Header->IsMonochrome() )
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
{
- return ImageDataSize;
+ return 0.;
}
-
- // Planar configuration = 0 : Pixels are already RGB
- // Planar configuration = 1 : 3 planes : R, G, B
- // Planar configuration = 2 : 1 gray Plane + 3 LUT
- // Well ... supposed to be !
- // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
- // PhotometricInterpretation=PALETTE COLOR
- // and heuristic has to be found :-(
+ return xImPos;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner Y position
+ */
+float File::GetYOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntry(0x0020,0x0032);
- int planConf = Header->GetPlanarConfiguration();
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
- // Planar configuration = 2 ==> 1 gray Plane + 3 LUT
- // ...and...
- // whatever the Planar Configuration might be, "PALETTE COLOR "
- // implies that we deal with the palette.
- if ( ( planConf == 2 ) || Header->IsPaletteColor() )
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
{
- return ImageDataSize;
+ return 0.;
}
- // When planConf is 0, pixels are allready in RGB
+ return yImPos;
+}
- if ( planConf == 1 )
+/**
+ * \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()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntry(0x0020,0x0032);
+
+ if ( strImPos != GDCM_UNFOUND )
{
- uint8_t* newDest = new uint8_t[ImageDataSize];
- // Warning : YBR_FULL_422 acts as RGB
- if ( Header->IsYBRFull() )
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
{
- ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest);
+ gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
}
else
{
- ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest);
+ return zImPos;
}
- memmove(destination, newDest, ImageDataSize);
- delete[] newDest;
}
-///////////////////////////////////////////////////
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // Droping Palette Color out of the Header
- // has been moved to the Write process.
-
- // TODO : move 'values' modification to the write process
- // : save also (in order to be able to restore)
- // : 'high bit' -when not equal to 'bits stored' + 1
- // : 'bits allocated', when it's equal to 12 ?!
-
- std::string spp = "3"; // Samples Per Pixel
- std::string photInt = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
-
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- Header->SetEntryByNumber(photInt,0x0028,0x0004);
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- return ImageDataSize;
-}
+ strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(),
+ "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ {
+ gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
-/**
- * \brief Re-arrange the bits within the bytes.
- */
-void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone,
- size_t imageDataSize,
- int numberBitsStored,
- int numberBitsAllocated,
- int highBitPosition)
- throw ( gdcmFormatError )
-{
- if ( numberBitsStored != numberBitsAllocated )
+ std::string strSliceLocation = GetEntry(0x0020,0x1041); // for *very* old ACR-NEMA images
+ if ( strSliceLocation != GDCM_UNFOUND )
{
- int l = (int)(imageDataSize / (numberBitsAllocated/8));
- if ( numberBitsAllocated == 16 )
+ if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
{
- uint16_t mask = 0xffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
- uint16_t* deb = (uint16_t*)pixelZone;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
- deb++;
- }
+ return zImPos;
}
- else if ( numberBitsAllocated == 32 )
+ }
+ gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
+
+ std::string strLocation = GetEntry(0x0020,0x0050);
+ if ( strLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
{
- uint32_t mask = 0xffffffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
- uint32_t* deb = (uint32_t*)pixelZone;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
- deb++;
- }
+ gdcmVerboseMacro( "Wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
}
else
{
- dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image");
- throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()",
- "weird image !?" );
+ return zImPos;
}
}
+ gdcmVerboseMacro( "Unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
}
/**
- * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
- * \warning Works on all the frames at a time
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
*/
-void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source,
- uint8_t* destination)
+int File::GetImageNumber()
{
- // to see the tricks about YBR_FULL, YBR_FULL_422,
- // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
- // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
- // and be *very* affraid
- //
- int l = Header->GetXSize() * Header->GetYSize();
- int nbFrames = Header->GetZSize();
-
- uint8_t* a = source;
- uint8_t* b = source + l;
- uint8_t* c = source + l + l;
- double R, G, B;
-
- /// \todo : Replace by the 'well known' integer computation
- /// counterpart. Refer to
- /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
- /// for code optimisation.
-
- for (int i = 0; i < nbFrames; i++)
+ // 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 = GetEntry(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
{
- for (int j = 0; j < l; j++)
- {
- R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
- G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
- B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
-
- if (R < 0.0) R = 0.0;
- if (G < 0.0) G = 0.0;
- if (B < 0.0) B = 0.0;
- if (R > 255.0) R = 255.0;
- if (G > 255.0) G = 255.0;
- if (B > 255.0) B = 255.0;
-
- *(destination++) = (uint8_t)R;
- *(destination++) = (uint8_t)G;
- *(destination++) = (uint8_t)B;
- a++;
- b++;
- c++;
- }
+ return atoi( strImNumber.c_str() );
}
+ return 0; //Hopeless
}
/**
- * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
- * \warning Works on all the frames at a time
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
*/
-void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source,
- uint8_t* destination)
+ModalityType File::GetModality()
{
- int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntry(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;
+ }
+ }
- uint8_t* a = source;
- uint8_t* b = source + l;
- uint8_t* c = source + l + l;
+ return Unknow;
+}
- for (int j = 0; j < l; j++)
+/**
+ * \brief Retrieve the number of Bits Stored (actually used)
+ * (as opposite to number of Bits Allocated)
+ * @return The encountered number of Bits Stored, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int File::GetBitsStored()
+{
+ std::string strSize = GetEntry( 0x0028, 0x0101 );
+ if ( strSize == GDCM_UNFOUND )
{
- *(destination++) = *(a++);
- *(destination++) = *(b++);
- *(destination++) = *(c++);
+ gdcmVerboseMacro("(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 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 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.
*/
-bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize)
+int File::GetHighBitPosition()
{
- Header->SetImageDataSize( expectedSize );
-// FIXME : if already allocated, memory leak !
- Pixel_Data = inData;
- ImageDataSize = ImageDataSizeRaw = expectedSize;
- PixelRead = 1;
-// FIXME : 7fe0, 0010 IS NOT set ...
- return true;
+ std::string strSize = GetEntry( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
+ 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 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 gdcmFile::WriteRawData(std::string const & fileName)
+bool File::IsSignedPixelData()
{
- FILE* fp1 = fopen(fileName.c_str(), "wb");
- if (fp1 == NULL)
+ std::string strSize = GetEntry( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory");
+ return false;
+ }
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
{
- printf("Fail to open (write) file [%s] \n", fileName.c_str());
return false;
}
- fwrite (Pixel_Data, ImageDataSize, 1, fp1);
- fclose (fp1);
-
return true;
}
/**
- * \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 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 !
*/
-
-bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+int File::GetBitsAllocated()
{
- return WriteBase(fileName, gdcmImplicitVR);
+ std::string strSize = GetEntry(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(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 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 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)
*/
-
-bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+int File::GetSamplesPerPixel()
{
- return WriteBase(fileName, gdcmExplicitVR);
+ const std::string& strSize = GetEntry(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(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 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 monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
*/
-
-bool gdcmFile::WriteAcr (std::string const & fileName)
+bool File::IsMonochrome()
{
- return WriteBase(fileName, gdcmACR);
+ const std::string& PhotometricInterp = GetEntry( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)");
+ }
+ return false;
}
-//-----------------------------------------------------------------------------
-// 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
+ * \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 gdcmFile::WriteBase (std::string const & fileName, FileType type)
+bool File::IsPaletteColor()
{
- if ( PixelRead == -1 && type != gdcmExplicitVR)
+ std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
{
- return false;
+ return true;
}
-
- FILE* fp1 = fopen(fileName.c_str(), "wb");
- if (fp1 == NULL)
+ if ( PhotometricInterp == GDCM_UNFOUND )
{
- printf("Failed to open (write) File [%s] \n", fileName.c_str());
- return false;
+ gdcmVerboseMacro( "Not found : Palette color (0028,0004)");
}
+ return false;
+}
- if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+/**
+ * \brief Check whether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool File::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
{
- // writing Dicom File Preamble
- uint8_t* filePreamble = new uint8_t[128];
- memset(filePreamble, 0, 128);
- fwrite(filePreamble, 128, 1, fp1);
- fwrite("DICM", 4, 1, fp1);
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
+}
- delete[] filePreamble;
+/**
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int File::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntry(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
+ return 0;
}
+ return atoi( strSize.c_str() );
+}
- // --------------------------------------------------------------
- // 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
+/**
+ * \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 RGB images)
+ // if (File::GetEntry(0x0028,0x0100) == "24")
+ // return 3;
- std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO)
+ std::string pixelType = GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
{
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
-
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ return 1;
}
- // ----------------- End of Special Patch ----------------
-
- uint16_t grPixel = Header->GetGrPixel();
- uint16_t numPixel = Header->GetNumPixel();;
-
- gdcmDocEntry* PixelElement =
- GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
-
- if ( PixelRead == 1 )
+ if ( pixelType == "16U" || pixelType == "16S")
{
- // we read pixel 'as is' (no tranformation LUT -> RGB)
- PixelElement->SetLength( ImageDataSizeRaw );
+ return 2;
}
- else if ( PixelRead == 0 )
+ if ( pixelType == "32U" || pixelType == "32S")
{
- // we tranformed GrayLevel pixels + LUT into RGB Pixel
- PixelElement->SetLength( ImageDataSize );
+ return 4;
}
-
- Header->Write(fp1, type);
-
- // --------------------------------------------------------------
- // 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 ( Header->GetFileType() == gdcmACR_LIBIDO )
+ if ( pixelType == "FD" )
{
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
+ return 8;
}
- // ----------------- End of Special Patch ----------------
-
- // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
- fclose (fp1);
-
- return true;
+ gdcmVerboseMacro( "Unknown pixel type");
+ return 0;
}
-//-----------------------------------------------------------------------------
-// Private
/**
- * \brief Read pixel data from disk (optionaly decompressing) into the
- * caller specified memory location.
- * @param destination where the pixel data should be stored.
- *
+ * \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
*/
-bool gdcmFile::ReadPixelData(void* destination)
+std::string File::GetPixelType()
{
- FILE* fp = Header->OpenFile();
+ std::string bitsAlloc = GetEntry(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
- if ( !fp )
+ if ( bitsAlloc == "64" )
{
- return false;
+ return "FD";
}
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 )
+ else if ( bitsAlloc == "12" )
{
- Header->CloseFile();
- return false;
+ // It will be unpacked
+ bitsAlloc = "16";
}
-
- if ( Header->GetBitsAllocated() == 12 )
+ else if ( bitsAlloc == "24" )
{
- gdcmPixelConvert::ConvertDecompress12BitsTo16Bits(
- (uint8_t*)destination,
- Header->GetXSize(),
- Header->GetYSize(),
- fp);
- Header->CloseFile();
- return true;
+ // (in order no to be messed up
+ bitsAlloc = "8"; // by old RGB images)
}
- // ---------------------- Uncompressed File
- if ( !Header->IsDicomV3() ||
- Header->IsImplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ std::string sign = GetEntry(0x0028, 0x0103);//"Pixel Representation"
+
+ if (sign == GDCM_UNFOUND )
{
- size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- Header->CloseFile();
- if ( ItemRead != 1 )
- {
- return false;
- }
- else
- {
- return true;
- }
+ gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)");
+ sign = "U"; // default and arbitrary value, not to polute the output
}
-
- // ---------------------- Run Length Encoding
- if ( Header->IsRLELossLessTransferSyntax() )
+ else if ( sign == "0" )
{
- bool res = gdcmPixelConvert::gdcm_read_RLE_file ( destination,
- Header->GetXSize(),
- Header->GetYSize(),
- Header->GetZSize(),
- Header->GetBitsAllocated(),
- &(Header->RLEInfo),
- fp );
- Header->CloseFile();
- return res;
- }
-
- // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
+ sign = "U";
+ }
+ else
{
- numberBitsAllocated = 16;
+ sign = "S";
}
+ return bitsAlloc + sign;
+}
- int nBytes= numberBitsAllocated/8;
- int taille = Header->GetXSize() * Header->GetYSize()
- * Header->GetSamplesPerPixel();
- long fragmentBegining; // for ftell, fseek
-
- bool jpg2000 = Header->IsJPEG2000();
- bool jpgLossless = Header->IsJPEGLossless();
- bool res = true;
- uint16_t ItemTagGr, ItemTagEl;
- int ln;
-
- // Position on begining of Jpeg Pixels
-
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(Header->GetSwapCode())
+/**
+ * \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 )
{
- ItemTagGr = Header->SwapShort(ItemTagGr);
- ItemTagEl = Header->SwapShort(ItemTagEl);
+ return pxlElement->GetOffset();
}
-
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
+ else
{
- ln = Header->SwapLong( ln ); // Basic Offset Table Item length
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
}
+}
- if ( ln != 0 )
+/// \todo TODO : unify those two (previous one and next one)
+/**
+ * \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()
+{
+ DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
{
- // What is it used for ?!?
- uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- //delete[] BasicOffsetTableItemValue;
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
}
+}
- // first Fragment initialisation
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if( Header->GetSwapCode() )
+/**
+ * \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) )
{
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1203) )
+ {
+ return false;
}
- // parsing fragments until Sequence Delim. Tag found
- while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd )
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
+}
+
+/**
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
+ */
+int File::GetLUTNbits()
+{
+ std::vector<std::string> tokens;
+ int lutNbits;
+
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
+ // = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string lutDescription = GetEntry(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
{
- // --- for each Fragment
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
- {
- ln = Header->SwapLong(ln); // Fragment Item length
- }
- fragmentBegining = ftell( fp );
+ 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;
+}
+
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief anonymize a File (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool File::AnonymizeFile()
+{
+ // If exist, replace by spaces
+ SetEntry (" ",0x0010, 0x2154); // Telephone
+ SetEntry (" ",0x0010, 0x1040); // Adress
+ SetEntry (" ",0x0010, 0x0020); // Patient ID
- if ( jpg2000 )
+ DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ {
+ std::string studyInstanceUID = GetEntry (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
{
- // JPEG 2000 : call to ???
- res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
- // ------------------------------------- endif (JPEG2000)
+ ReplaceOrCreate(studyInstanceUID, 0x0010, 0x0010);
}
- else if (jpgLossless)
- {
- // JPEG LossLess : call to xmedcom Lossless JPEG
- // Reading Fragment pixels
- JPEGLosslessDecodeImage (fp, (uint16_t*)destination,
- Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln);
- res = 1; // in order not to break the loop
-
- } // ------------------------------------- endif (JPEGLossless)
else
{
- // JPEG Lossy : call to IJG 6b
- if ( Header->GetBitsStored() == 8)
- {
- // Reading Fragment pixels
- res = gdcm_read_JPEG_file (fp,destination);
- }
- else if ( Header->GetBitsStored() == 12)
- {
- // Reading Fragment pixels
- res = gdcm_read_JPEG_file12 (fp,destination);
- }
- else
- {
- // other JPEG lossy not supported
- dbg.Error(" gdcmFile::ReadPixelData : unknown jpeg lossy compression");
- return 0;
- }
- // ------------------------------------- endif (JPEGLossy)
+ ReplaceOrCreate("anonymised", 0x0010, 0x0010);
}
+ }
+
+ // Just for fun :-(
+ // (if any) 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
- if ( !res )
+ return true;
+}
+
+/**
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void File::GetImageOrientationPatient( float iop[6] )
+{
+ std::string strImOriPat;
+ //iop is supposed to be float[6]
+ iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
+
+ // 0020 0037 DS REL Image Orientation (Patient)
+ if ( (strImOriPat = GetEntry(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 )
{
- break;
+ gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
}
-
- // location in user's memory
- // for next fragment (if any)
- destination = (uint8_t*)destination + taille * nBytes;
-
- fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
-
- ItemTagGr = ItemTagEl = 0;
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if( Header->GetSwapCode() )
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntry(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 )
{
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
+ gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
}
}
- // endWhile parsing fragments until Sequence Delim. Tag found
+}
- Header->CloseFile();
- return res;
+/**
+ * \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()
+{
+ typedef struct
+ {
+ const char *value;
+ uint16_t group;
+ uint16_t elem;
+ } DICOM_DEFAULT_VALUE;
+
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidClass = uid + ".1";
+ std::string uidInst = uid + ".10";
+ std::string uidStudy = uid + ".100";
+ std::string uidSerie = uid + ".1000";
+
+ static DICOM_DEFAULT_VALUE defaultvalue[] = {
+ { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
+ { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
+ { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian)
+ { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
+ { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
+
+ { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
+ { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
+ { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
+ { "CT", 0x0008, 0x0060}, // Modality
+ { "GDCM", 0x0008, 0x0070}, // Manufacturer
+ { "GDCM", 0x0008, 0x0080}, // Institution Name
+ { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
+
+ { "GDCM", 0x0010, 0x0010}, // Patient's Name
+ { "GDCMID", 0x0010, 0x0020}, // Patient ID
+
+ { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
+ { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
+ { "1", 0x0020, 0x0010}, // StudyID
+ { "1", 0x0020, 0x0011}, // SeriesNumber
+
+ { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
+ { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
+ { "0", 0x0028, 0x0010}, // nbRows
+ { "0", 0x0028, 0x0011}, // nbCols
+ { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
+ { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
+ { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
+ { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
+ { 0, 0, 0 }
+ };
+
+ // default value
+ // Special case this is the image (not a string)
+ GrPixel = 0x7fe0;
+ NumPixel = 0x0010;
+ ReplaceOrCreate(0, 0, GrPixel, NumPixel);
+
+ // All remaining strings:
+ unsigned int i = 0;
+ DICOM_DEFAULT_VALUE current = defaultvalue[i];
+ while( current.value )
+ {
+ ReplaceOrCreate(current.value, current.group, current.elem);
+ current = defaultvalue[++i];
+ }
}
+
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
+
+} // end namespace gdcm