Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/09/23 10:17:26 $
- Version: $Revision: 1.128 $
+ Date: $Date: 2005/01/06 20:03:27 $
+ Version: $Revision: 1.183 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
=========================================================================*/
#include "gdcmFile.h"
+#include "gdcmDocument.h"
#include "gdcmDebug.h"
-#include "jpeg/ljpg/jpegless.h"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmPixelWriteConvert.h"
+#include "gdcmDocEntryArchive.h"
+#include <fstream>
+
+namespace gdcm
+{
typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \ingroup gdcmFile
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader only deals with the ... header)
+ * 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).
+ */
+File::File( )
+{
+ HeaderInternal = new Header( );
+ SelfHeader = true;
+ Initialise();
+}
+
+/**
+ * \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
* 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
+ * @param header already built Header
*/
-gdcmFile::gdcmFile(gdcmHeader *header)
+File::File(Header *header)
{
- Header = header;
+ HeaderInternal = header;
SelfHeader = false;
- SaveInitialValues();
+ Initialise();
}
/**
- * \ingroup gdcmFile
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader only deals with the ... header)
+ * 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
* seen as a side effect).
* @param filename file to be opened for parsing
*/
-gdcmFile::gdcmFile(std::string const & filename )
+File::File(std::string const & filename )
{
- Header = new gdcmHeader( filename );
+ HeaderInternal = new Header( filename );
SelfHeader = true;
- SaveInitialValues();
+ Initialise();
}
/**
- * \ingroup gdcmFile
* \brief canonical destructor
- * \note If the gdcmHeader was created by the gdcmFile constructor,
- * it is destroyed by the gdcmFile
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
*/
-gdcmFile::~gdcmFile()
+File::~File()
{
- if( SelfHeader )
+ if( PixelReadConverter )
{
- delete Header;
+ delete PixelReadConverter;
}
- Header = 0;
-
- DeleteInitialValues();
-}
-
-/**
- * \ingroup gdcmFile
- * \brief Sets some initial values for the Constructor
- * \warning not end user intended
- */
-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() )
+ if( PixelWriteConverter )
{
- SetPixelDataSizeFromHeader();
-
- // 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);
+ delete PixelWriteConverter;
}
-}
-
-/**
- * \ingroup gdcmFile
- * \brief restores some initial values
- * \warning not end user intended
- */
-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);
+ if( Archive )
+ {
+ delete Archive;
}
-}
-
-/**
- * \ingroup gdcmFile
- * \brief delete initial values (il they were saved)
- * of InitialLutDescriptors and InitialLutData
- */
-void gdcmFile::DeleteInitialValues()
-{
-
-// 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...
- 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;
-}
-
-/**
- * \ingroup gdcmFile
- * \brief drop palette related initial values -if any-
- * (InitialLutDescriptors and InitialLutData)
- * out of header, to make it consistent with the Pixel_Data
- * as it's loaded in memory
- */
-
-//FIXME : Should be nice, if we could let it here.
-// will be moved to PixelData class
-// Now, the job is done in gdcmHeader.cxx
-
- /*
-void gdcmFile::DropInitialValues()
-{
- gdcmHeader* h=GetHeader();
- if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' )
+ if( SelfHeader )
{
- // if SamplesPerPixel = 3, sure we don't need any LUT !
- // Drop 0028|1101, 0028|1102, 0028|1103
- // Drop 0028|1201, 0028|1202, 0028|1203
-
- gdcmDocEntry* e = h->GetDocEntryByNumber(0x0028,0x01101);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
- e = h->GetDocEntryByNumber(0x0028,0x1102);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
- e = h->GetDocEntryByNumber(0x0028,0x1103);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
- e = h->GetDocEntryByNumber(0x0028,0x01201);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
- e = h->GetDocEntryByNumber(0x0028,0x1202);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
- e = h->GetDocEntryByNumber(0x0028,0x1203);
- if (e)
- {
- h->RemoveEntryNoDestroy(e);
- }
+ delete HeaderInternal;
}
+ HeaderInternal = 0;
}
-*/
//-----------------------------------------------------------------------------
// Print
+void File::Print(std::ostream &os)
+{
+ HeaderInternal->SetPrintLevel(PrintLevel);
+ HeaderInternal->Print(os);
+
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
+}
//-----------------------------------------------------------------------------
// Public
-
/**
- * \ingroup gdcmFile
- * \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).
- * \warning : not end user intended ?
+ * \brief Get the size of the image data
+ *
+ * If the image can be RGB (with a lut or by default), the size
+ * corresponds to the RGB image
+ * @return The image size
*/
-void gdcmFile::SetPixelDataSizeFromHeader()
+size_t File::GetImageDataSize()
{
- // 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 nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
-
- if ( str_nb == GDCM_UNFOUND )
+ if ( PixelWriteConverter->GetUserData() )
{
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- if (nb == 12)
- {
- nb =16;
- }
+ return PixelWriteConverter->GetUserDataSize();
}
- ImageDataSize =
- ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize()
- * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel();
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
-
- // if ( str_PhotometricInterpretation == "PALETTE COLOR " ),
- // pb when undealt Segmented Palette Color
-
- if ( Header->HasLUT() )
+
+ return PixelReadConverter->GetRGBSize();
+}
+
+/**
+ * \brief Get the size of the image data
+ *
+ * If the image can be RGB by transformation in a LUT, this
+ * transformation isn't considered
+ * @return The raw image size
+ */
+size_t File::GetImageDataRawSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
{
- ImageDataSize *= 3;
+ return PixelWriteConverter->GetUserDataSize();
}
+
+ return PixelReadConverter->GetRawSize();
}
/**
- * \ingroup gdcmFile
* \brief - Allocates necessary memory,
* - Reads the pixels from disk (uncompress if necessary),
* - Transforms YBR pixels, if any, into RGB pixels
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-uint8_t* gdcmFile::GetImageData()
+uint8_t *File::GetImageData()
{
- // FIXME (Mathieu)
- // I need to deallocate Pixel_Data before doing any allocation:
-
- if ( Pixel_Data )
- if ( LastAllocatedPixelDataLength != ImageDataSize )
- free(Pixel_Data);
- if ( !Pixel_Data )
- Pixel_Data = new uint8_t[ImageDataSize];
-
- if ( Pixel_Data )
+ if ( PixelWriteConverter->GetUserData() )
{
- 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;
-}
+ return PixelWriteConverter->GetUserData();
+ }
-/**
- * \ingroup gdcmFile
- * \brief
- * Read the pixels from disk (uncompress if necessary),
- * Transforms YBR pixels, if any, into RGB pixels
- * Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
- * Copies at most MaxSize bytes of pixel data to caller allocated
- * memory space.
- * \warning This function allows people that want to build a volume
- * from an image stack *not to* have, first to get the image pixels,
- * and then move them to the volume area.
- * It's absolutely useless for any VTK user since vtk chooses
- * to invert the lines of an image, that is the last line comes first
- * (for some axis related reasons?). Hence he will have
- * to load the image line by line, starting from the end.
- * VTK users have to call GetImageData
- *
- * @param destination Address (in caller's memory space) at which the
- * pixel data should be copied
- * @param maxSize Maximum number of bytes to be copied. When MaxSize
- * is not sufficient to hold the pixel data the copy is not
- * executed (i.e. no partial copy).
- * @return On success, the number of bytes actually copied. Zero on
- * failure e.g. MaxSize is lower than necessary.
- */
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
-{
- GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // =0 : no ImageDataRaw
- if ( !Header->HasLUT() )
+ if ( ! GetRaw() )
{
- return ImageDataSize;
+ // If the decompression failed nothing can be done.
+ return 0;
}
-
- // 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 )
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
- int j;
- // move Gray pixels to temp area
- memmove(newDest, destination, ImageDataSizeRaw);
- for (size_t i=0; i<ImageDataSizeRaw; ++i)
- {
- // Build RGB Pixels
- j = newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
- }
- 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);
-
+ return PixelReadConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
}
- 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;
}
/**
- * \ingroup gdcmFile
* \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
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-uint8_t* gdcmFile::GetImageDataRaw ()
+uint8_t *File::GetImageDataRaw ()
{
- 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 )
- {
- 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
-
- return Pixel_Data;
+ return GetRaw();
}
/**
- * \ingroup gdcmFile
- * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * \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 was designed to avoid people that want to build
- * a volume from an image stack to need first to get the image pixels
+ * \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 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
+ * VTK users have to call GetImageData
*
* @param destination Address (in caller's memory space) at which the
* pixel data should be copied
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize)
+size_t File::GetImageDataIntoVector (void *destination, size_t maxSize)
{
- int nb, nbu, highBit, sign;
-
- // 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();
- }
-
- PixelRead = 1 ; // PixelRaw
-
- if ( ImageDataSize > maxSize )
+ if ( ! GetRaw() )
{
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
+ // If the decompression failed nothing can be done.
+ return 0;
}
- ReadPixelData( destination );
-
- // Number of Bits Allocated for storing a Pixel
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- // FIXME
- // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated
- // separately, correct ?
- }
-
- // Number of Bits actually used
- std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101);
- if ( str_nbu == GDCM_UNFOUND )
- {
- nbu = nb;
- }
- else
- {
- nbu = atoi( str_nbu.c_str() );
- }
-
- // High Bit Position
- std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102);
- if ( str_highBit == GDCM_UNFOUND )
- {
- highBit = nb - 1;
- }
- else
- {
- highBit = atoi( str_highBit.c_str() );
- }
-
- // Pixel sign
- // 0 = Unsigned
- // 1 = Signed
- std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103);
- if ( str_sign == GDCM_UNFOUND )
- {
- sign = 0; // default is unsigned
- }
- else
- {
- sign = atoi( str_sign.c_str() );
- }
-
- // re arange bytes inside the integer (processor endianity)
- if ( nb != 8 )
- {
- SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb);
- }
-
- // to avoid pb with some xmedcon breakers images
- if ( nb == 16 && nbu < nb && sign == 0)
- {
- int l = (int)(ImageDataSize / (nb/8));
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
{
- if( *deb == 0xffff )
- {
- *deb = 0;
- }
- deb++;
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
}
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
}
- // re arange bits inside the bytes
- if ( nbu != nb )
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelReadConverter->GetRawSize() > maxSize )
{
- int l = (int)(ImageDataSize / (nb/8));
- if ( nb == 16 )
- {
- uint16_t mask = 0xffff;
- mask = mask >> (nb-nbu);
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
- deb++;
- }
- }
- else if ( nb == 32 )
- {
- uint32_t mask = 0xffffffff;
- mask = mask >> (nb - nbu);
- uint32_t *deb = (uint32_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
- deb++;
- }
- }
- else
- {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
- return 0;
- }
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
}
-// DO NOT remove this code commented out.
-// Nobody knows what's expecting you ...
-// Just to 'see' what was actually read on disk :-(
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
+}
-// FILE * f2;
-// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,ImageDataSize,1,f2);
-// fclose(f2);
+/**
+ * \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
+ */
+void File::SetImageData(uint8_t *inData, size_t expectedSize)
+{
+ SetUserData(inData,expectedSize);
+}
- // Deal with the color
- // -------------------
-
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
+/**
+ * \brief Set the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+void File::SetUserData(uint8_t *data, size_t expectedSize)
+{
+ PixelWriteConverter->SetUserData(data,expectedSize);
+}
- if ( str_PhotometricInterpretation == "MONOCHROME1 "
- || str_PhotometricInterpretation == "MONOCHROME2 " )
- {
- return ImageDataSize;
- }
-
- // Planar configuration = 0 : Pixels are already RGB
- // Planar configuration = 1 : 3 planes : R, G, B
- // Planar configuration = 2 : 1 gray Plane + 3 LUT
+/**
+ * \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()
+{
+ return PixelWriteConverter->GetUserData();
+}
- // Well ... supposed to be !
- // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
- // PhotometricInterpretation=PALETTE COLOR
- // and heuristic has to be 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
+ */
+size_t File::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
+}
- int planConf = Header->GetPlanarConfiguration(); // 0028,0006
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+uint8_t *File::GetRGBData()
+{
+ return PixelReadConverter->GetRGB();
+}
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if ( str_PhotometricInterpretation == "PALETTE COLOR ")
- {
- planConf = 2;
- }
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+size_t File::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
+}
- switch ( planConf )
- {
- case 0:
- // Pixels are already RGB
- break;
- case 1:
- if (str_PhotometricInterpretation == "YBR_FULL")
- {
- // Warning : YBR_FULL_422 acts as RGB
- // : we need to make RGB Pixels from Planes Y,cB,cR
-
- // 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* newDest = new uint8_t[ImageDataSize];
- uint8_t* x = newDest;
- uint8_t* a = (uint8_t*)destination;
- uint8_t* b = a + l;
- uint8_t* c = b + l;
- double R,G,B;
-
- /// \todo : Replace by the 'well known' integer computation
- /// counterpart
- /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
- /// for code optimisation
-
- for (int i = 0; i < nbFrames; i++)
- {
- 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;
-
- *(x++) = (uint8_t)R;
- *(x++) = (uint8_t)G;
- *(x++) = (uint8_t)B;
- a++; b++; c++;
- }
- }
- memmove(destination, newDest, ImageDataSize);
- delete[] newDest;
- }
- else
- {
- // need to make RGB Pixels from R,G,B Planes
- // (all the Frames at a time)
-
- int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
-
- uint8_t *newDest = new uint8_t[ImageDataSize];
- uint8_t *x = newDest;
- uint8_t *a = (uint8_t *)destination;
- uint8_t *b = a + l;
- uint8_t *c = b + l;
-
- for (int j = 0; j < l; j++)
- {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination, newDest, ImageDataSize);
- delete[] newDest;
- }
- break;
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return ImageDataSize;
- }
- // 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;
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
+ */
+uint8_t *File::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
}
/**
- * \ingroup gdcmFile
- * \brief performs a shalow copy (not a deep copy) of the user given
- * pixel area.
- * '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 user is kindly requested NOT TO 'free' the Pixel area
- * @param inData user supplied pixel area
- * @param expectedSize total image size, in Bytes
- *
- * @return boolean
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are not expanded !
*/
-bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize)
+size_t File::GetRawDataSize()
{
- 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;
+ return PixelReadConverter->GetRawSize();
}
/**
- * \ingroup gdcmFile
* \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
* @return false if write fails
*/
-bool gdcmFile::WriteRawData(std::string const & fileName)
+bool File::WriteRawData(std::string const &fileName)
{
- FILE *fp1 = fopen(fileName.c_str(), "wb");
- if (fp1 == NULL)
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
{
- printf("Fail to open (write) file [%s] \n", fileName.c_str());
+ dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
return false;
}
- fwrite (Pixel_Data, ImageDataSize, 1, fp1);
- fclose (fp1);
+
+ if(PixelWriteConverter->GetUserData())
+ fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize());
+ else if(PixelReadConverter->GetRGB())
+ fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize());
+ else if(PixelReadConverter->GetRaw())
+ fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize());
+
+ fp1.close();
return true;
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the Implicit Value Representation convention
* NO test is performed on processor "Endiannity".
* @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+bool File::WriteDcmImplVR (std::string const &fileName)
{
- return WriteBase(fileName, gdcmImplicitVR);
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
}
/**
- * \ingroup gdcmFile
* \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
+ * 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
*/
-bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+bool File::WriteDcmExplVR (std::string const &fileName)
{
- return WriteBase(fileName, gdcmExplicitVR);
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the ACR-NEMA convention
* NO test is performed on processor "Endiannity".
* @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string const & fileName)
+bool File::WriteAcr (std::string const &fileName)
{
- return WriteBase(fileName, gdcmACR);
+ SetWriteTypeToAcr();
+ return Write(fileName);
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \ingroup gdcmFile
- * \brief NOT a end user inteded function
- * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
+ * \brief Writes on disk A SINGLE Dicom file,
* @param fileName name of the file to be created
* (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
* @return false if write fails
*/
-bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+bool File::Write(std::string const &fileName)
{
- if ( PixelRead == -1 && type != gdcmExplicitVR)
- {
- return false;
- }
-
- FILE *fp1 = fopen(fileName.c_str(), "wb");
- if (fp1 == NULL)
- {
- printf("Failed to open (write) File [%s] \n", fileName.c_str());
- return false;
- }
-
- if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ switch(WriteType)
{
- // 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);
-
- delete[] filePreamble;
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
+ break;
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
+ break;
+ case ACR:
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACR();
+ break;
+ default:
+ SetWriteFileTypeToExplicitVR();
}
// --------------------------------------------------------------
// 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
-
- std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO)
+ if( WriteType == ACR_LIBIDO )
{
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
-
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ SetWriteToLibido();
+ }
+ else
+ {
+ SetWriteToNoLibido();
}
// ----------------- End of Special Patch ----------------
-
- uint16_t grPixel = Header->GetGrPixel();
- uint16_t numPixel = Header->GetNumPixel();;
-
- gdcmDocEntry* PixelElement =
- GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
-
- if ( PixelRead == 1 )
+
+ switch(WriteMode)
{
- // we read pixel 'as is' (no tranformation LUT -> RGB)
- PixelElement->SetLength( ImageDataSizeRaw );
+ case WMODE_RAW :
+ SetWriteToRaw();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
}
- else if ( PixelRead == 0 )
+
+ bool check = CheckWriteIntegrity();
+ if(check)
{
- // we tranformed GrayLevel pixels + LUT into RGB Pixel
- PixelElement->SetLength( ImageDataSize );
+ check = HeaderInternal->Write(fileName,WriteType);
}
-
- Header->Write(fp1, type);
+
+ 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
-
- if ( Header->GetFileType() == gdcmACR_LIBIDO )
- {
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
- }
+ RestoreWriteOfLibido();
// ----------------- End of Special Patch ----------------
-
- // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
- fclose (fp1);
- return true;
+ return check;
}
-//-----------------------------------------------------------------------------
-// Private
/**
- * \ingroup gdcmFile
- * \brief Swap the bytes, according to swap code.
- * \warning not end user intended
- * @param im area to deal with
- * @param swap swap code
- * @param lgr Area Length
- * @param nb Pixels Bit number
+ * \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 element element number of the Dicom Element to modify
+ */
+bool File::SetEntryByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,group,element);
+}
+
+
+/**
+ * \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 element element number of the Dicom Element to modify
*/
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb)
+bool File::SetEntryByNumber(uint8_t *content, int lgth,
+ uint16_t group, uint16_t element)
{
- int i;
+ return HeaderInternal->SetEntryByNumber(content,lgth,group,element);
+}
+
+/**
+ * \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 element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreateByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL;
+}
- if( nb == 16 )
+/*
+ * \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 element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreateByNumber(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL;
+}
+
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelReadConverter->GetLutRGBA();
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \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
+ */
+bool File::CheckWriteIntegrity()
+{
+ if(PixelWriteConverter->GetUserData())
{
- uint16_t* im16 = (uint16_t*)im;
- switch( swap )
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
{
- case 0:
- case 12:
- case 1234:
- break;
- case 21:
- case 3412:
- case 2143:
- case 4321:
- for(i=0; i < lgr/2; i++)
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- break;
- default:
- std::cout << "SWAP value (16 bits) not allowed :i" << swap <<
- std::endl;
+ numberBitsAllocated = 16;
}
- }
- else if( nb == 32 )
- {
- uint32_t s32;
- uint16_t fort, faible;
- uint32_t* im32 = (uint32_t*)im;
- switch ( swap )
+
+ 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 0:
- case 1234:
- break;
- case 4321:
- for(i = 0; i < lgr/4; i++)
- {
- faible = im32[i] & 0x0000ffff; // 4321
- fort = im32[i] >> 16;
- fort = ( fort >> 8 ) | ( fort << 8 );
- faible = ( faible >> 8 ) | ( faible << 8);
- s32 = faible;
- im32[i] = ( s32 << 16 ) | fort;
- }
- break;
- case 2143:
- for(i = 0; i < lgr/4; i++)
+ case WMODE_RAW :
+ if( decSize!=PixelWriteConverter->GetUserDataSize() )
{
- faible = im32[i] & 0x0000ffff; // 2143
- fort = im32[i] >> 16;
- fort = ( fort >> 8 ) | ( fort << 8 );
- faible = ( faible >> 8) | ( faible << 8);
- s32 = fort;
- im32[i] = ( s32 << 16 ) | faible;
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
}
break;
- case 3412:
- for(i = 0; i < lgr/4; i++)
+ case WMODE_RGB :
+ if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
{
- faible = im32[i] & 0x0000ffff; // 3412
- fort = im32[i] >> 16;
- s32 = faible;
- im32[i] = ( s32 << 16 ) | fort;
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
}
break;
- default:
- std::cout << "SWAP value (32 bits) not allowed : " << swap <<
- std::endl;
}
}
+
+ return true;
}
-/**
- * \ingroup gdcmFile
- * \brief Read pixel data from disk (optionaly decompressing) into the
- * caller specified memory location.
- * @param destination where the pixel data should be stored.
- *
- */
-bool gdcmFile::ReadPixelData(void *destination)
+void File::SetWriteToRaw()
{
- FILE *fp = Header->OpenFile();
-
- if ( !fp )
- {
- return false;
- }
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 )
+ if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
{
- Header->CloseFile();
- return false;
- }
-
- // ---------------------- Compacted File (12 Bits Per Pixel)
- // unpack 12 Bits pixels into 16 Bits pixels
- // 2 pixels 12bit = [0xABCDEF]
- // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
-
- if ( Header->GetBitsAllocated() == 12 )
+ SetWriteToRGB();
+ }
+ else
{
- int nbPixels = Header->GetXSize() * Header->GetYSize();
- uint8_t b0, b1, b2;
-
- uint16_t* pdestination = (uint16_t*)destination;
- for(int p = 0; p < nbPixels; p += 2 )
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
{
- fread(&b0,1,1,fp);
- fread(&b1,1,1,fp);
- fread(&b2,1,1,fp);
-
- //Two steps is necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
- // A B D
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- // F C E
-
- // Troubles expected on Big-Endian processors ?
+ photInt->SetValue("PALETTE COLOR ");
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
}
- Header->CloseFile();
- return true;
+ 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);
}
+}
- // ---------------------- Uncompressed File
- if ( !Header->IsDicomV3() ||
- Header->IsImplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+void File::SetWriteToRGB()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
{
- size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- Header->CloseFile();
- if ( ItemRead != 1 )
+ 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 ");
+
+ if(PixelReadConverter->GetRGB())
{
- return false;
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
}
- else
+ else // Raw data
{
- return true;
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
}
- }
- // ---------------------- Run Length Encoding
- if ( Header->IsRLELossLessTransferSyntax() )
- {
- bool res = gdcm_read_RLE_file (fp,destination);
- Header->CloseFile();
- return res;
- }
-
- // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
- int nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
- {
- nb = 16;
+ 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);
+ }
}
else
{
- nb = atoi( str_nb.c_str() );
- if ( nb == 12 )
- {
- nb = 16; // ?? 12 should be ACR-NEMA only
- }
+ SetWriteToRaw();
}
+}
- int nBytes= nb/8;
- int taille = Header->GetXSize() * Header->GetYSize()
- * Header->GetSamplesPerPixel();
- long fragmentBegining; // for ftell, fseek
+void File::RestoreWrite()
+{
+ Archive->Restore(0x0028,0x0002);
+ Archive->Restore(0x0028,0x0004);
+ Archive->Restore(0x0028,0x0006);
+ Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+
+ // For old ACR-NEMA (24 bits problem)
+ Archive->Restore(0x0028,0x0100);
+ Archive->Restore(0x0028,0x0101);
+ Archive->Restore(0x0028,0x0102);
+
+ // 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);
+}
- bool jpg2000 = Header->IsJPEG2000();
- bool jpgLossless = Header->IsJPEGLossless();
+void File::SetWriteFileTypeToACR()
+{
+ Archive->Push(0x0002,0x0010);
+}
- bool res = true;
- uint16_t ItemTagGr, ItemTagEl;
- int ln;
-
- // Position on begining of Jpeg Pixels
+void File::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
+}
+
+void File::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(Header->GetSwapCode())
+ if( oldRow && oldCol )
{
- ItemTagGr = Header->SwapShort(ItemTagGr);
- ItemTagEl = Header->SwapShort(ItemTagEl);
+ std::string rows, columns;
+
+ ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
+ ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+
+ newRow->Copy(oldCol);
+ newCol->Copy(oldRow);
+
+ newRow->SetValue(oldCol->GetValue());
+ newCol->SetValue(oldRow->GetValue());
+
+ Archive->Push(newRow);
+ Archive->Push(newCol);
}
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ Archive->Push(libidoCode);
+}
+
+void File::SetWriteToNoLibido()
+{
+ ValEntry *recCode = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010));
+ if( recCode )
{
- ln = Header->SwapLong( ln ); // Basic Offset Table Item length
+ if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ {
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("");
+ Archive->Push(libidoCode);
+ }
}
+}
+
+void File::RestoreWriteOfLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+ Archive->Restore(0x0008,0x0010);
+}
+
+ValEntry *File::CopyValEntry(uint16_t group,uint16_t element)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ ValEntry *newE;
- if ( ln != 0 )
+ if(oldE)
{
- // What is it used for ?!?
- uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- //delete[] BasicOffsetTableItemValue;
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
}
-
- // 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() )
+ else
{
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
+ newE = GetHeader()->NewValEntryByNumber(group,element);
}
- // parsing fragments until Sequence Delim. Tag found
- while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd )
+ return(newE);
+}
+
+BinEntry *File::CopyBinEntry(uint16_t group,uint16_t element)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ BinEntry *newE;
+
+ if(oldE)
{
- // --- for each Fragment
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
- {
- ln = Header->SwapLong(ln); // Fragment Item length
- }
- fragmentBegining = ftell( fp );
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntryByNumber(group,element);
+ }
- if ( jpg2000 )
- {
- // JPEG 2000 : call to ???
- res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
- // ------------------------------------- endif (JPEG2000)
- }
- 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
- {
- // Reading Fragment pixels
- res = gdcm_read_JPEG_file12 (fp,destination);
- }
- // ------------------------------------- endif (JPEGLossy)
- }
+ return(newE);
+}
- if ( !res )
- {
- break;
- }
-
- // location in user's memory
- // for next fragment (if any)
- destination = (uint8_t*)destination + taille * nBytes;
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
+{
+ WriteMode = WMODE_RAW;
+ WriteType = ExplicitVR;
- 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() )
+ PixelReadConverter = new PixelReadConvert;
+ PixelWriteConverter = new PixelWriteConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ }
+}
+
+uint8_t *File::GetRaw()
+{
+ uint8_t *raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ // The Raw image migth not be loaded yet:
+ std::ifstream *fp = HeaderInternal->OpenFile();
+ PixelReadConverter->ReadAndDecompressPixelData( fp );
+ if(fp)
+ HeaderInternal->CloseFile();
+
+ raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
{
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
+ dbg.Verbose(0, "File::GetRaw: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
}
}
- // endWhile parsing fragments until Sequence Delim. Tag found
- Header->CloseFile();
- return res;
+ return raw;
}
+
+//-----------------------------------------------------------------------------
+// Private
+
//-----------------------------------------------------------------------------
+} // end namespace gdcm
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff