-// gdcmFile.cxx
-//-----------------------------------------------------------------------------
+ /*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ Date: $Date: 2004/09/24 11:39:21 $
+ Version: $Revision: 1.129 $
+
+ 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.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
#include "gdcmFile.h"
#include "gdcmDebug.h"
#include "jpeg/ljpg/jpegless.h"
typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-//-----------------------------------------------------------------------------
+//-------------------------------------------------------------------------
// Constructor / Destructor
/**
* \ingroup gdcmFile
- * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
- * file (see SetFileName, SetDcmTag and Write)
+ * \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
+ * user sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
- * @param header file to be opened for reading datas
- * @return
+ * @param header already built gdcmHeader
*/
-gdcmFile::gdcmFile(gdcmHeader *header) {
- Header=header;
- SelfHeader=false;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+gdcmFile::gdcmFile(gdcmHeader *header)
+{
+ Header = header;
+ SelfHeader = false;
+ SaveInitialValues();
}
/**
* \ingroup gdcmFile
- * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
- * file (see SetFileName, SetDcmTag and Write)
+ * \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
- * @param exception_on_error whether we throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
*/
-gdcmFile::gdcmFile(std::string & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- Header=new gdcmHeader(filename.c_str(),
- exception_on_error,
- enable_sequences,
- ignore_shadow);
- SelfHeader=true;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+gdcmFile::gdcmFile(std::string const & filename )
+{
+ Header = new gdcmHeader( filename );
+ SelfHeader = true;
+ SaveInitialValues();
}
/**
* \ingroup gdcmFile
- * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
- * file (see SetFileName, SetDcmTag and Write)
- * Opens (in read only and when possible) an existing file and checks
- * for DICOM compliance. Returns NULL on failure.
- * \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
- * @param exception_on_error whether we throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
+ * \brief canonical destructor
+ * \note If the gdcmHeader was created by the gdcmFile constructor,
+ * it is destroyed by the gdcmFile
*/
- gdcmFile::gdcmFile(const char *filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- Header=new gdcmHeader(filename,
- exception_on_error,
- enable_sequences,
- ignore_shadow);
- SelfHeader=true;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
+gdcmFile::~gdcmFile()
+{
+ if( SelfHeader )
+ {
+ delete Header;
+ }
+ 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() )
+ {
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);
+ }
}
/**
* \ingroup gdcmFile
- * \brief canonical destructor
- * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
- * by the gdcmFile
+ * \brief restores some initial values
+ * \warning not end user intended
*/
-gdcmFile::~gdcmFile(void) {
- if(SelfHeader)
- delete Header;
- Header=NULL;
+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);
+ }
}
-//-----------------------------------------------------------------------------
-// Print
+/**
+ * \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;
+}
-//-----------------------------------------------------------------------------
-// Public
/**
* \ingroup gdcmFile
- * \brief returns the gdcmHeader *Header
- * @return
+ * \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
*/
-gdcmHeader *gdcmFile::GetHeader(void) {
- return(Header);
+
+//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 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);
+ }
+ }
}
+*/
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
/**
* \ingroup gdcmFile
- * \brief computes the length (in bytes) to ALLOCATE to receive the
- * image(s) pixels (multiframes taken into account)
+ * \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).
- * @return length to allocate
+ * \warning : not end user intended ?
*/
-void gdcmFile::SetPixelDataSizeFromHeader(void) {
+void gdcmFile::SetPixelDataSizeFromHeader()
+{
// see PS 3.3-2003 : C.7.6.3.2.1
//
// MONOCHROME1
// 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;
- str_nb=Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
+ std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+
+ if ( str_nb == GDCM_UNFOUND )
+ {
nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
+ }
+ else
+ {
+ nb = atoi( str_nb.c_str() );
+ if (nb == 12)
+ {
+ nb =16;
+ }
}
- lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize()
- * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
+ 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 " )*/
+
+ // if ( str_PhotometricInterpretation == "PALETTE COLOR " ),
// pb when undealt Segmented Palette Color
- if (Header->HasLUT()) {
- lgrTotale*=3;
+ if ( Header->HasLUT() )
+ {
+ ImageDataSize *= 3;
}
}
-/**
- * \ingroup gdcmFile
- * \brief Returns the size (in bytes) of required memory to hold
- * the pixel data represented in this file.
- * @return The size of pixel data in bytes.
- */
-size_t gdcmFile::GetImageDataSize(void) {
- return (lgrTotale);
-}
-
-/**
- * \ingroup gdcmFile
- * \brief Returns the size (in bytes) of required memory to hold
- * the pixel data represented in this file, when user 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 The size of pixel data in bytes.
- */
-size_t gdcmFile::GetImageDataSizeRaw(void) {
- return (lgrTotaleRaw);
-}
-
/**
* \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * \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
*/
-void * gdcmFile::GetImageData (void) {
- PixelData = new char[lgrTotale];
- if (PixelData) {
- GetImageDataIntoVector(PixelData, lgrTotale);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(),
- GetHeader()->GetNumPixel());
+uint8_t* gdcmFile::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 )
+ {
+ 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(PixelData);
+ PixelRead = 0; // no PixelRaw
+
+ return Pixel_Data;
}
/**
* \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
*
* @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
+ * @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) {
- //size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
- GetImageDataIntoVectorRaw (destination, MaxSize);
- PixelRead=0 ; // no PixelRaw
- if (!Header->HasLUT())
- return lgrTotale;
+size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
+{
+ GetImageDataIntoVectorRaw (destination, maxSize);
+ PixelRead = 0 ; // =0 : no ImageDataRaw
+ if ( !Header->HasLUT() )
+ {
+ return ImageDataSize;
+ }
// from Lut R + Lut G + Lut B
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *a = (unsigned char *)destination;
- unsigned char *lutRGBA = Header->GetLUTRGBA();
- if (lutRGBA) {
- int l = lgrTotaleRaw;
- memmove(newDest, destination, l);// move Gray pixels to temp area
- int j;
- for (int i=0;i<l; i++) { // Build RGB Pixels
- j=newDest[i]*4;
- *a++ = lutRGBA[j];
+ uint8_t *newDest = new uint8_t[ImageDataSize];
+ uint8_t *a = (uint8_t *)destination;
+ uint8_t *lutRGBA = Header->GetLUTRGBA();
+
+ if ( lutRGBA )
+ {
+ 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];
}
// now, it's an RGB image
// Lets's write it in the Header
- // CreateOrReplaceIfExist ?
-
+ // FIXME : Better use CreateOrReplaceIfExist ?
+
std::string spp = "3"; // Samples Per Pixel
Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb= "RGB "; // Photometric Interpretation
+ std::string rgb = "RGB "; // Photometric Interpretation
Header->SetEntryByNumber(rgb,0x0028,0x0004);
std::string planConfig = "0"; // Planar Configuration
Header->SetEntryByNumber(planConfig,0x0028,0x0006);
- } else {
- // need to make RGB Pixels (?)
- // from grey Pixels (?!)
- // and Gray Lut (!?!)
- // or Segmented xxx Palette Color Lookup Table Data and so on
-
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage such an image
- // It seems that *no Dicom Viewer* has any idea :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
-
- std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- }
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ }
+ 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, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * \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
*/
-void * gdcmFile::GetImageDataRaw (void) {
- if (Header->HasLUT())
- /// \todo Let gdcmHeadar user a chance to get the right value
- /// Create a member lgrTotaleRaw ???
- lgrTotale /= 3;
- PixelData = new char[lgrTotale];
-
- if (PixelData) {
- GetImageDataIntoVectorRaw(PixelData, lgrTotale);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(),
- GetHeader()->GetNumPixel());
- }
- PixelRead=1; // PixelRaw
- return(PixelData);
+uint8_t* gdcmFile::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;
}
/**
*
* @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
+ * @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::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) {
+size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
+{
+ int nb, nbu, highBit, sign;
- int nb, nbu, highBit, signe;
- std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
- PixelRead=1 ; // PixelRaw
-
- if ( lgrTotale > MaxSize ) {
+ // 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 )
+ {
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
"than caller's expected MaxSize");
- return (size_t)0;
+ return (size_t)0;
}
-
- (void)ReadPixelData(destination);
-
- // Number of Bits Allocated for storing a Pixel
- str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
+
+ ReadPixelData( destination );
+
+ // Number of Bits Allocated for storing a Pixel
+ std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+ if ( str_nb == GDCM_UNFOUND )
+ {
nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
- // Number of Bits actually used
- str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
- if (str_nbu == GDCM_UNFOUND ) {
+ }
+ 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
- str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
- if (str_highBit == GDCM_UNFOUND ) {
+ }
+ 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
- str_signe=Header->GetEntryByNumber(0x0028,0x0103);
- if (str_signe == GDCM_UNFOUND ) {
- signe = 0; // default is unsigned
- } else {
- signe = atoi(str_signe.c_str() );
+ }
+ 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(), lgrTotale, nb);
+ if ( nb != 8 )
+ {
+ SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb);
+ }
// to avoid pb with some xmedcon breakers images
- if (nb==16 && nbu<nb && signe==0) {
- int l = (int)lgrTotale / (nb/8);
- guint16 *deb = (guint16 *)destination;
- for(int i = 0; i<l; i++) {
- if(*deb == 0xffff)
- *deb=0;
- deb++;
+ 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( *deb == 0xffff )
+ {
+ *deb = 0;
}
- }
+ deb++;
+ }
+ }
+
// re arange bits inside the bytes
- if (nbu != nb){
- int l = (int)lgrTotale / (nb/8);
- if (nb == 16) {
- guint16 mask = 0xffff;
+ if ( nbu != nb )
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ if ( nb == 16 )
+ {
+ uint16_t mask = 0xffff;
mask = mask >> (nb-nbu);
- guint16 *deb = (guint16 *)destination;
- for(int i = 0; i<l; i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
+ uint16_t *deb = (uint16_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ deb++;
}
- } else if (nb == 32 ) {
- guint32 mask = 0xffffffff;
- mask = mask >> (nb-nbu);
- guint32 *deb = (guint32 *)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: wierd image");
- return (size_t)0;
}
- }
-// DO NOT remove this commented out code .
+ else
+ {
+ dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
+ return 0;
+ }
+ }
+// DO NOT remove this code commented out.
// Nobody knows what's expecting you ...
// Just to 'see' what was actually read on disk :-(
-// FILE * f2;
+// FILE* f2;
// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,lgrTotale,1,f2);
+// fwrite(destination,ImageDataSize,1,f2);
// fclose(f2);
// Deal with the color
// -------------------
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
-
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
- return lgrTotale;
- }
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ if ( str_PhotometricInterpretation == "MONOCHROME1 "
+ || str_PhotometricInterpretation == "MONOCHROME2 " )
+ {
+ return ImageDataSize;
+ }
// Planar configuration = 0 : Pixels are already RGB
// Planar configuration = 1 : 3 planes : R, G, B
// PhotometricInterpretation=PALETTE COLOR
// and heuristic has to be found :-(
- int planConf=Header->GetPlanarConfiguration(); // 0028,0006
+ int planConf = Header->GetPlanarConfiguration(); // 0028,0006
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if (str_PhotometricInterpretation == "PALETTE COLOR ")
- planConf=2;
+ // Whatever Planar Configuration is,
+ // "PALETTE COLOR " implies that we deal with the palette.
+ if ( str_PhotometricInterpretation == "PALETTE COLOR ")
+ {
+ planConf = 2;
+ }
- switch (planConf) {
- case 0:
- // Pixels are already RGB
+ switch ( planConf )
+ {
+ case 0:
+ // Pixels are already RGB
break;
-
case 1:
-
+ if (str_PhotometricInterpretation == "YBR_FULL")
{
- 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();
+ // 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();
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *x = newDest;
- unsigned char *a = (unsigned char *)destination;
- unsigned char *b = a + l;
- unsigned char *c = b + l;
+ 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
+ /// 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++) = (unsigned char)R;
- *(x++) = (unsigned char)G;
- *(x++) = (unsigned char)B;
+
+ 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,lgrTotale);
+ }
+ memmove(destination, newDest, ImageDataSize);
delete[] newDest;
+ }
+ else
+ {
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
- } 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();
+ int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
- char *newDest = new char[lgrTotale];
- char *x = newDest;
- char *a = (char *)destination;
- char *b = a + l;
- char *c = b + l;
+ 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++) {
+ for (int j = 0; j < l; j++)
+ {
*(x++) = *(a++);
*(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination,newDest,lgrTotale);
+ *(x++) = *(c++);
+ }
+ memmove(destination, newDest, ImageDataSize);
delete[] newDest;
- }
+ }
break;
- }
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return lgrTotale;
- }
+ 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.
- // CreateOrReplaceIfExist ?
+ // 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 spp = "3"; // Samples Per Pixel
+ std::string photInt = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+
Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
-
- std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(photInt,0x0028,0x0004);
Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+
+ return ImageDataSize;
}
/**
* \ingroup gdcmFile
- * \brief performs a shadow copy (not a deep copy) of the user given
+ * \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 : lane per plane
+ * '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
+ * @param expectedSize total image size, in Bytes
*
- * @return boolean
+ * @return boolean
*/
-bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) {
- Header->SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- PixelRead = 1;
- return(true);
+bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize)
+{
+ 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;
}
/**
* 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
+ * @return false if write fails
*/
-bool gdcmFile::WriteRawData (std::string fileName) {
- FILE *fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Fail to open (write) file [%s] \n",fileName.c_str());
- return (false);
- }
- fwrite (PixelData,lgrTotale, 1, fp1);
+bool gdcmFile::WriteRawData(std::string const & fileName)
+{
+ FILE* fp1 = fopen(fileName.c_str(), "wb");
+ if (fp1 == NULL)
+ {
+ printf("Fail to open (write) file [%s] \n", fileName.c_str());
+ return false;
+ }
+ fwrite (Pixel_Data, ImageDataSize, 1, fp1);
fclose (fp1);
- return(true);
+
+ return true;
}
/**
* 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
+ * @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string fileName) {
+bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+{
return WriteBase(fileName, gdcmImplicitVR);
}
-/**
- * \ingroup gdcmFile
- * \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
- */
-
-bool gdcmFile::WriteDcmImplVR (const char *fileName) {
- return WriteDcmImplVR (std::string (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
* (any already existing file is overwritten)
- * @return false if write fails
+ * @return false if write fails
*/
-bool gdcmFile::WriteDcmExplVR (std::string fileName) {
+bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+{
return WriteBase(fileName, gdcmExplicitVR);
}
-
+
/**
* \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* \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
+ * @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string fileName) {
+bool gdcmFile::WriteAcr (std::string const & fileName)
+{
return WriteBase(fileName, gdcmACR);
}
* @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
+ * @return false if write fails
*/
-bool gdcmFile::WriteBase (std::string fileName, FileType type) {
-
- FILE *fp1;
-
- if (PixelRead==-1 && type != gdcmExplicitVR) {
- return false;
+bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+{
+ if ( PixelRead == -1 && type != gdcmExplicitVR)
+ {
+ return false;
}
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Failed to open (write) File [%s] \n",fileName.c_str());
- 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) ) {
- char *filePreamble;
+ if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ {
// writing Dicom File Preamble
- filePreamble=new char[128];
- memset(filePreamble,0,128);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
+ uint8_t* filePreamble = new uint8_t[128];
+ memset(filePreamble, 0, 128);
+ fwrite(filePreamble, 128, 1, fp1);
+ fwrite("DICM", 4, 1, fp1);
+
delete[] filePreamble;
}
/// but pb expected if user deals with, e.g. COMPLEX images
std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO){
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
- }
+ if ( Header->GetFileType() == gdcmACR_LIBIDO)
+ {
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
+
+ Header->SetEntryByNumber(columns, 0x0028, 0x0010);
+ Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ }
// ----------------- End of Special Patch ----------------
-
- /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only)
-
- guint16 grPixel =Header->GetGrPixel();
- guint16 numPixel=Header->GetNumPixel();;
-
- // Update Pixel Data Length
- // the *last* of the (GrPixel, NumPixel), if many.
+
+ uint16_t grPixel = Header->GetGrPixel();
+ uint16_t numPixel = Header->GetNumPixel();;
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
- TagDocEntryHT::iterator p2;
- gdcmDocEntry *PixelElement;
-
- IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
-
- if (Header->GetEntry().count(key) == 1) // only the first is significant
- p2=it.first; // iterator on the first (unique) synonym
- else
- p2=it.second;// iterator on the last synonym
-
- PixelElement=p2->second; // H Table target column (2-nd col)
- // PixelElement->SetPrintLevel(2);
- // PixelElement->Print();
+ gdcmDocEntry* PixelElement =
+ GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
+
+ if ( PixelRead == 1 )
+ {
+ // we read pixel 'as is' (no tranformation LUT -> RGB)
+ PixelElement->SetLength( ImageDataSizeRaw );
+ }
+ else if ( PixelRead == 0 )
+ {
+ // we tranformed GrayLevel pixels + LUT into RGB Pixel
+ PixelElement->SetLength( ImageDataSize );
+ }
- if (PixelRead==1)
- PixelElement->SetLength(lgrTotaleRaw);
- else if (PixelRead==0)
- PixelElement->SetLength(lgrTotale);
-
- //PixelElement->SetPrintLevel(2);
- //PixelElement->Print();
Header->Write(fp1, type);
// --------------------------------------------------------------
// ...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);
- }
+ if ( Header->GetFileType() == gdcmACR_LIBIDO )
+ {
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
+ }
// ----------------- End of Special Patch ----------------
- fwrite(PixelData, lgrTotale, 1, fp1);
+ // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
fclose (fp1);
- return(true);
+
+ return true;
}
//-----------------------------------------------------------------------------
* @param lgr Area Length
* @param nb Pixels Bit number
*/
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
-
-if(nb == 16)
- switch(swap) {
- case 0:
- case 12:
- case 1234:
- break;
-
- case 21:
- case 3412:
- case 2143:
- case 4321:
-
- for(i=0;i<lgr/2;i++) {
- ((unsigned short int *)im)[i]= ((((unsigned short int *)im)[i])>>8)
- | ((((unsigned short int *)im)[i])<<8);
- }
- break;
-
- default:
- printf("SWAP value (16 bits) not allowed : %d\n", swap);
- }
-
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
-
- case 4321:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 4321 */
- fort =((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
-
- case 2143:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 2143 */
- fort=((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=fort;
- ((unsigned long int *)im)[i]=(s32<<16)|faible;
- }
- break;
-
- case 3412:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 3412 */
- fort=((unsigned long int *)im)[i]>>16;
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
-
- default:
- printf("SWAP value (32 bits) not allowed : %d\n", swap);
- }
-return;
+void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb)
+{
+ int i;
+
+ if( nb == 16 )
+ {
+ uint16_t* im16 = (uint16_t*)im;
+ switch( swap )
+ {
+ 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;
+ }
+ }
+ else if( nb == 32 )
+ {
+ uint32_t s32;
+ uint16_t fort, faible;
+ uint32_t* im32 = (uint32_t*)im;
+ switch ( swap )
+ {
+ 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++)
+ {
+ 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;
+ }
+ break;
+ case 3412:
+ for(i = 0; i < lgr/4; i++)
+ {
+ faible = im32[i] & 0x0000ffff; // 3412
+ fort = im32[i] >> 16;
+ s32 = faible;
+ im32[i] = ( s32 << 16 ) | fort;
+ }
+ break;
+ default:
+ std::cout << "SWAP value (32 bits) not allowed : " << swap <<
+ std::endl;
+ }
+ }
}
/**
* @param destination where the pixel data should be stored.
*
*/
-bool gdcmFile::ReadPixelData(void *destination) {
+bool gdcmFile::ReadPixelData(void* destination)
+{
+ FILE* fp = Header->OpenFile();
- FILE *fp;
-
- if ( !(fp=Header->OpenFile()))
+ if ( !fp )
+ {
return false;
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+ }
+ if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 )
+ {
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] */
+ // unpack 12 Bits pixels into 16 Bits pixels
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
- if (Header->GetBitsAllocated()==12) {
+ if ( Header->GetBitsAllocated() == 12 )
+ {
int nbPixels = Header->GetXSize() * Header->GetYSize();
- unsigned char b0, b1, b2;
+ uint8_t b0, b1, b2;
- unsigned short int *pdestination = (unsigned short int*)destination;
- for(int p=0;p<nbPixels;p+=2) {
+ uint16_t* pdestination = (uint16_t*)destination;
+ for(int p = 0; p < nbPixels; p += 2 )
+ {
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 */
+ // A B D
*pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- /* F */ /* C */ /* E */
-
- // Troubles expected on Big-Endian processors ?
+ // F C E
+
+ // Troubles expected on Big-Endian processors ?
}
Header->CloseFile();
- return(true);
- }
+ return true;
+ }
// ---------------------- Uncompressed File
if ( !Header->IsDicomV3() ||
Header->IsImplicitVRLittleEndianTransferSyntax() ||
Header->IsExplicitVRLittleEndianTransferSyntax() ||
Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ {
size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- if ( ItemRead != 1 ) {
- Header->CloseFile();
+ Header->CloseFile();
+ if ( ItemRead != 1 )
+ {
return false;
- } else {
- Header->CloseFile();
+ }
+ else
+ {
return true;
}
- }
+ }
// ---------------------- Run Length Encoding
- if (Header->IsRLELossLessTransferSyntax()) {
- bool res = (bool)gdcm_read_RLE_file (fp,destination);
+ 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 ) {
+ std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+ if ( str_nb == GDCM_UNFOUND )
+ {
nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
+ }
+ else
+ {
+ nb = atoi( str_nb.c_str() );
+ if ( nb == 12 )
+ {
+ nb = 16; // ?? 12 should be ACR-NEMA only
+ }
}
int nBytes= nb/8;
-
int taille = Header->GetXSize() * Header->GetYSize()
- * Header->GetSamplesPerPixel();
+ * Header->GetSamplesPerPixel();
long fragmentBegining; // for ftell, fseek
- bool jpg2000 = Header->IsJPEG2000();
+ bool jpg2000 = Header->IsJPEG2000();
bool jpgLossless = Header->IsJPEGLossless();
-
+
bool res = true;
- guint16 ItemTagGr,ItemTagEl;
+ 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()) {
- ItemTagGr=Header->SwapShort(ItemTagGr);
- ItemTagEl=Header->SwapShort(ItemTagEl);
+ if(Header->GetSwapCode())
+ {
+ ItemTagGr = Header->SwapShort(ItemTagGr);
+ ItemTagEl = Header->SwapShort(ItemTagEl);
}
- fread(&ln,4,1,fp);
- if(Header->GetSwapCode())
- ln=Header->SwapLong(ln); // Basic Offset Table Item length
-
- if (ln != 0) {
+
+ fread(&ln,4,1,fp);
+ if( Header->GetSwapCode() )
+ {
+ ln = Header->SwapLong( ln ); // Basic Offset Table Item length
+ }
+
+ if ( ln != 0 )
+ {
// What is it used for ?!?
- char *BasicOffsetTableItemValue = new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
+ uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1];
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ //delete[] BasicOffsetTableItemValue;
}
-
+
// 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()) {
- ItemTagGr=Header->SwapShort(ItemTagGr);
- ItemTagEl=Header->SwapShort(ItemTagEl);
+ if( Header->GetSwapCode() )
+ {
+ ItemTagGr = Header->SwapShort( ItemTagGr );
+ ItemTagEl = Header->SwapShort( ItemTagEl );
}
-
+
// parsing fragments until Sequence Delim. Tag found
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd )
+ {
// --- for each Fragment
+ fread(&ln,4,1,fp);
+ if( Header->GetSwapCode() )
+ {
+ ln = Header->SwapLong(ln); // Fragment Item length
+ }
+ fragmentBegining = ftell( fp );
- fread(&ln,4,1,fp);
- if(Header->GetSwapCode())
- ln=Header->SwapLong(ln); // Fragment Item length
-
- fragmentBegining=ftell(fp);
-
- if (jpg2000) { // JPEG 2000 : call to ???
-
- res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
-
- } // ------------------------------------- endif (JPEG2000)
-
- else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
-
- JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
- (unsigned short *)destination,
- Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(),
- ln);
- res=1; // in order not to break the loop
+ 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)
+ }
+
+ if ( !res )
+ {
+ break;
+ }
- else { // JPEG Lossy : call to IJG 6b
-
- if (Header->GetBitsStored() == 8) {
- res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
- }
- } // ------------------------------------- endif (JPEGLossy)
-
- if (!res) break;
-
- destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
-
- fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
+ // 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;
+ 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()) {
- ItemTagGr=Header->SwapShort(ItemTagGr);
- ItemTagEl=Header->SwapShort(ItemTagEl);
- }
-
- } // endWhile parsing fragments until Sequence Delim. Tag found
-
+ if( Header->GetSwapCode() )
+ {
+ ItemTagGr = Header->SwapShort( ItemTagGr );
+ ItemTagEl = Header->SwapShort( ItemTagEl );
+ }
+ }
+ // endWhile parsing fragments until Sequence Delim. Tag found
+
Header->CloseFile();
return res;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff