- /*=========================================================================
+/*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/10/20 14:30:40 $
- Version: $Revision: 1.146 $
+ Date: $Date: 2005/01/20 16:17:00 $
+ Version: $Revision: 1.194 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmGlobal.h"
+#include "gdcmTS.h"
+#include "gdcmDocument.h"
#include "gdcmDebug.h"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmPixelWriteConvert.h"
+#include "gdcmDocEntryArchive.h"
+
+#include <fstream>
namespace gdcm
{
//-------------------------------------------------------------------------
// Constructor / Destructor
+/**
+ * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * file (Header only deals with the ... header)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ */
+FileHelper::FileHelper( )
+{
+ 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)
* seen as a side effect).
* @param header already built Header
*/
-File::File(Header *header)
+FileHelper::FileHelper(Header *header)
{
HeaderInternal = header;
SelfHeader = false;
* seen as a side effect).
* @param filename file to be opened for parsing
*/
-File::File(std::string const & filename )
+FileHelper::FileHelper(std::string const & filename )
{
HeaderInternal = new Header( filename );
SelfHeader = true;
}
/**
- * \brief Factorization for various forms of constructors.
+ * \brief canonical destructor
+ * \note If the header (gdcm::File) was created by the FileHelper constructor,
+ * it is destroyed by the FileHelper
*/
-void File::Initialise()
-{
- if ( HeaderInternal->IsReadable() )
+FileHelper::~FileHelper()
+{
+ if( PixelReadConverter )
{
- ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( HeaderInternal->HasLUT() )
- {
- ImageDataSize = 3 * ImageDataSizeRaw;
- }
- else
- {
- ImageDataSize = ImageDataSizeRaw;
- }
-
- PixelConverter = new PixelConvert;
- PixelConverter->GrabInformationsFromHeader( HeaderInternal );
+ delete PixelReadConverter;
+ }
+ if( PixelWriteConverter )
+ {
+ delete PixelWriteConverter;
+ }
+ if( Archive )
+ {
+ delete Archive;
}
- SaveInitialValues();
-}
-/**
- * \brief canonical destructor
- * \note If the Header was created by the File constructor,
- * it is destroyed by the File
- */
-File::~File()
-{
if( SelfHeader )
{
delete HeaderInternal;
}
HeaderInternal = 0;
-
- DeleteInitialValues();
}
-/**
- * \brief Sets some initial values for the Constructor
- * \warning not end user intended
- */
-void File::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 ( HeaderInternal->IsReadable() )
- {
- // the following values *may* be modified
- // by File::GetImageDataIntoVectorRaw
- // we save their initial value.
- InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002);
- InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004);
- InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006);
-
- InitialBitsAllocated = HeaderInternal->GetEntryByNumber(0x0028,0x0100);
- InitialHighBit = HeaderInternal->GetEntryByNumber(0x0028,0x0102);
-
- // the following entries *may* be removed from the H table
- // (NOT deleted ...) by File::GetImageDataIntoVectorRaw
- // we keep a pointer on them.
- InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101);
- InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102);
- InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103);
+//-----------------------------------------------------------------------------
+// Print
+void FileHelper::Print(std::ostream &os, std::string const &)
+{
+ HeaderInternal->SetPrintLevel(PrintLevel);
+ HeaderInternal->Print(os);
- InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201);
- InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202);
- InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203);
- }
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
}
+//-----------------------------------------------------------------------------
+// Public
/**
- * \brief restores some initial values
- * \warning not end user intended
- */
-void File::RestoreInitialValues()
-{
- if ( HeaderInternal->IsReadable() )
- {
- // the following values *may* have been modified
- // by File::GetImageDataIntoVectorRaw
- // we restore their initial value.
- if ( InitialSpp != "")
- HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002);
- if ( InitialPhotInt != "")
- HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004);
- if ( InitialPlanConfig != "")
-
- HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006);
- if ( InitialBitsAllocated != "")
- HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100);
- if ( InitialHighBit != "")
- HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102);
-
- // the following entries *may* be have been removed from the H table
- // (NOT deleted ...) by File::GetImageDataIntoVectorRaw
- // we restore them.
-
- if (InitialRedLUTDescr)
- HeaderInternal->AddEntry(InitialRedLUTDescr);
- if (InitialGreenLUTDescr)
- HeaderInternal->AddEntry(InitialGreenLUTDescr);
- if (InitialBlueLUTDescr)
- HeaderInternal->AddEntry(InitialBlueLUTDescr);
-
- if (InitialRedLUTData)
- HeaderInternal->AddEntry(InitialBlueLUTDescr);
- if (InitialGreenLUTData)
- HeaderInternal->AddEntry(InitialGreenLUTData);
- if (InitialBlueLUTData)
- HeaderInternal->AddEntry(InitialBlueLUTData);
- }
-}
-
-/**
- * \brief delete initial values (il they were saved)
- * of InitialLutDescriptors and InitialLutData
+ * \brief Get the size of the image data
+ * If the image can be RGB (with a lut or by default), the size
+ * corresponds to the RGB image
+ * (use GetImageDataRawSize if you want to be sure to get *only*
+ * the size of the pixels)
+ * @return The image size
*/
-void File::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...
+size_t FileHelper::GetImageDataSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
- if ( InitialRedLUTDescr )
- delete InitialRedLUTDescr;
-
- if ( InitialGreenLUTDescr )
- delete InitialGreenLUTDescr;
-
- if ( InitialBlueLUTDescr )
- delete InitialBlueLUTDescr;
-
- if ( InitialRedLUTData )
- delete InitialRedLUTData;
-
- if ( InitialGreenLUTData != NULL)
- delete InitialGreenLUTData;
-
- if ( InitialBlueLUTData != NULL)
- delete InitialBlueLUTData;
+ return PixelReadConverter->GetRGBSize();
}
-//-----------------------------------------------------------------------------
-// Print
-
-//-----------------------------------------------------------------------------
-// Public
-
/**
- * \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).
+ * \brief Get the size of the image data
+ * If the image could be converted to RGB using a LUT,
+ * this transformation is not taken into account by GetImageDataRawSize
+ * (use GetImageDataSize if you wish)
+ * @return The raw image size
*/
-int File::ComputeDecompressedPixelDataSizeFromHeader()
+size_t FileHelper::GetImageDataRawSize()
{
- // 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]
-
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
- // Number of "Bits Allocated" is fixed to 16 when:
- // - it is not defined (i.e. it's value is 0)
- // - it's 12, since we will expand the image to 16 bits (see
- // PixelConvert::ConvertDecompress12BitsTo16Bits() )
- if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
- {
- numberBitsAllocated = 16;
- }
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
- int DecompressedSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
-
- return DecompressedSize;
+ return PixelReadConverter->GetRawSize();
}
/**
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-uint8_t* File::GetImageData()
+uint8_t *FileHelper::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();
+ }
-/**
- * \brief
- * Read the pixels from disk (uncompress if necessary),
- * Transforms YBR pixels, if any, into RGB pixels
- * Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
- * Copies at most MaxSize bytes of pixel data to caller allocated
- * memory space.
- * \warning This function allows people that want to build a volume
- * from an image stack *not to* have, first to get the image pixels,
- * and then move them to the volume area.
- * It's absolutely useless for any VTK user since vtk chooses
- * to invert the lines of an image, that is the last line comes first
- * (for some axis related reasons?). Hence he will have
- * to load the image line by line, starting from the end.
- * VTK users have to call GetImageData
- *
- * @param destination Address (in caller's memory space) at which the
- * pixel data should be copied
- * @param maxSize Maximum number of bytes to be copied. When MaxSize
- * is not sufficient to hold the pixel data the copy is not
- * executed (i.e. no partial copy).
- * @return On success, the number of bytes actually copied. Zero on
- * failure e.g. MaxSize is lower than necessary.
- */
-size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
-{
- GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // =0 : no ImageDataRaw
- if ( !HeaderInternal->HasLUT() )
+ if ( ! GetRaw() )
{
- return ImageDataSize;
+ // If the decompression failed nothing can be done.
+ return 0;
}
-
- FILE* fp = HeaderInternal->OpenFile();
- if ( PixelConverter->BuildRGBImage( fp ) )
- {
- memmove( destination,
- (void*)PixelConverter->GetRGB(),
- PixelConverter->GetRGBSize() );
-
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // FIXME : Better use CreateOrReplaceIfExist ?
-
- std::string spp = "3"; // Samples Per Pixel
- HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb = "RGB "; // Photometric Interpretation
- HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004);
- std::string planConfig = "0"; // Planar Configuration
- HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ return PixelReadConverter->GetRGB();
}
else
- {
- // PixelConverter->BuildRGBImage() failed probably because
- // PixelConverter->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
- HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004);
- }
- HeaderInternal->CloseFile();
-
- /// \todo Drop Palette Color out of the Header?
- return ImageDataSize;
+ {
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
+ }
}
/**
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-uint8_t* File::GetImageDataRaw ()
-{
- size_t imgDataSize;
- if ( HeaderInternal->HasLUT() )
- /// \todo Let Header 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;
+uint8_t *FileHelper::GetImageDataRaw ()
+{
+ return GetRaw();
}
/**
- * \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.
*/
-void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
+size_t FileHelper::GetImageDataIntoVector (void *destination, size_t 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 )
+ if ( ! GetRaw() )
{
- dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return;
+ // If the decompression failed nothing can be done.
+ return 0;
}
- FILE* fp = HeaderInternal->OpenFile();
- PixelConverter->ReadAndDecompressPixelData( fp );
- HeaderInternal->CloseFile();
- memmove( destination,
- (void*)PixelConverter->GetDecompressed(),
- PixelConverter->GetDecompressedSize() );
-
- if ( ! PixelConverter->IsDecompressedRGB() )
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
- return;
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
+ {
+ gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
}
-///////////////////////////////////////////////////
- // 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
-
- HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
- HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
- HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- return;
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelReadConverter->GetRawSize() > maxSize )
+ {
+ gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
}
/**
- * \brief Points the internal Pixel_Data pointer to the callers inData
+ * \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
*
* @return boolean
*/
-bool File::SetImageData(uint8_t* inData, size_t expectedSize)
-{
- HeaderInternal->SetImageDataSize( expectedSize );
-// FIXME : if already allocated, memory leak !
- Pixel_Data = inData;
- ImageDataSize = ImageDataSizeRaw = expectedSize;
- PixelRead = 1;
-// FIXME : 7fe0, 0010 IS NOT set ...
- return true;
+void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
+{
+ SetUserData(inData,expectedSize);
+}
+
+/**
+ * \brief Set the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+void FileHelper::SetUserData(uint8_t *data, size_t expectedSize)
+{
+ PixelWriteConverter->SetUserData(data,expectedSize);
+}
+
+/**
+ * \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 *FileHelper::GetUserData()
+{
+ return PixelWriteConverter->GetUserData();
+}
+
+/**
+ * \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 FileHelper::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
+}
+
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+uint8_t *FileHelper::GetRGBData()
+{
+ return PixelReadConverter->GetRGB();
+}
+
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+size_t FileHelper::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
+}
+
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
+ */
+uint8_t *FileHelper::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
+}
+
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are not expanded !
+ */
+size_t FileHelper::GetRawDataSize()
+{
+ return PixelReadConverter->GetRawSize();
}
/**
* @return false if write fails
*/
-bool File::WriteRawData(std::string const & fileName)
+bool FileHelper::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());
+ gdcmVerboseMacro( "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());
+ }
+ else
+ {
+ gdcmErrorMacro( "Nothing written." );
+ }
+
+ fp1.close();
return true;
}
* @return false if write fails
*/
-bool File::WriteDcmImplVR (std::string const & fileName)
+bool FileHelper::WriteDcmImplVR (std::string const &fileName)
{
- return WriteBase(fileName, ImplicitVR);
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
}
/**
* \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 File::WriteDcmExplVR (std::string const & fileName)
+bool FileHelper::WriteDcmExplVR (std::string const &fileName)
{
- return WriteBase(fileName, ExplicitVR);
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
/**
* @return false if write fails
*/
-bool File::WriteAcr (std::string const & fileName)
+bool FileHelper::WriteAcr (std::string const &fileName)
{
- return WriteBase(fileName, ACR);
+ SetWriteTypeToAcr();
+ return Write(fileName);
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \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 File::WriteBase (std::string const & fileName, FileType type)
+bool FileHelper::Write(std::string const &fileName)
{
- if ( PixelRead == -1 && type != ExplicitVR)
+ switch(WriteType)
{
- 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 == ImplicitVR || type == ExplicitVR )
- {
- // 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO)
+ if( WriteType == ACR_LIBIDO )
{
- rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010);
- columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011);
-
- HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010);
- HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011);
+ SetWriteToLibido();
+ }
+ else
+ {
+ SetWriteToNoLibido();
}
// ----------------- End of Special Patch ----------------
-
- uint16_t grPixel = HeaderInternal->GetGrPixel();
- uint16_t numPixel = HeaderInternal->GetNumPixel();;
-
- DocEntry* 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);
}
-
- HeaderInternal->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
+ RestoreWriteOfLibido();
+ // ----------------- End of Special Patch ----------------
+
+ return check;
+}
+
+/**
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (string) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
+ */
+bool FileHelper::SetEntry(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->SetEntry(content,group,elem);
+}
+
+
+/**
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param lgth new value length
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
+ */
+bool FileHelper::SetEntry(uint8_t *content, int lgth,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->SetEntry(content,lgth,group,elem);
+}
+
+/**
+ * \brief Modifies the value of a given Doc Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param content (string) Value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool FileHelper::ReplaceOrCreate(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->ReplaceOrCreate(content,group,elem) != NULL;
+}
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
+ * @param binArea (binary) value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool FileHelper::ReplaceOrCreate(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->ReplaceOrCreate(binArea,lgth,group,elem) != NULL;
+}
+
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ */
+uint8_t* FileHelper::GetLutRGBA()
+{
+ return PixelReadConverter->GetLutRGBA();
+}
- if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+//-----------------------------------------------------------------------------
+// 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 FileHelper::CheckWriteIntegrity()
+{
+ if(PixelWriteConverter->GetUserData())
{
- HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010);
- HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011);
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
+
+ size_t decSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+ size_t rgbSize = decSize;
+ if( HeaderInternal->HasLUT() )
+ rgbSize = decSize * 3;
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ if( decSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ gdcmVerboseMacro( "Data size is incorrect (Raw)" << decSize
+ << " / " << PixelWriteConverter->GetUserDataSize() );
+ return false;
+ }
+ break;
+ case WMODE_RGB :
+ if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ gdcmVerboseMacro( "Data size is incorrect (RGB)" << decSize
+ << " / " << PixelWriteConverter->GetUserDataSize() );
+ return false;
+ }
+ break;
+ }
}
- // ----------------- End of Special Patch ----------------
- // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
- fclose (fp1);
-
return true;
}
/**
- * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ * \brief
+ */
+void FileHelper::SetWriteToRaw()
+{
+ if( HeaderInternal->GetNumberOfScalarComponents() == 3
+ && !HeaderInternal->HasLUT())
+ {
+ SetWriteToRGB();
+ }
+ else
+ {
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
+ {
+ photInt->SetValue("PALETTE COLOR ");
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
+ }
+
+ 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);
+ }
+}
+
+
+/**
+ * \brief
+ */
+void FileHelper::SetWriteToRGB()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ {
+ 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())
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
+ }
+ else // Raw data
+ {
+ 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(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
+ {
+ SetWriteToRaw();
+ }
+}
+
+/**
+ * \brief
+ */
+void FileHelper::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);
+}
+
+/**
+ * \brief
+ */
+void FileHelper::SetWriteFileTypeToACR()
+{
+ Archive->Push(0x0002,0x0010);
+}
+
+/**
+ * \brief
+ */
+void FileHelper::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+/**
+ * \brief
+ */
+void FileHelper::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+
+/**
+ * \brief
+ */
+void FileHelper::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
+}
+
+void FileHelper::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0028, 0x0011));
+
+ if( oldRow && oldCol )
+ {
+ 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);
+ }
+
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ Archive->Push(libidoCode);
+}
+
+/**
+ * \brief
+ */
+void FileHelper::SetWriteToNoLibido()
+{
+ ValEntry *recCode = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0008,0x0010));
+ if( recCode )
+ {
+ if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ {
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("");
+ Archive->Push(libidoCode);
+ }
+ }
+}
+
+/**
+ * \brief
+ */
+void FileHelper::RestoreWriteOfLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+ Archive->Restore(0x0008,0x0010);
+}
+
+ValEntry *FileHelper::CopyValEntry(uint16_t group,uint16_t elem)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
+ ValEntry *newE;
+
+ if(oldE)
+ {
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewValEntry(group,elem);
+ }
+
+ return newE;
+}
+
+/**
+ * \brief Modifies the value of a given Bin Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param content (string) Value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * \return pointer to the modified/created Bin Entry (NULL when creation
+ * failed).
+ */
+BinEntry *FileHelper::CopyBinEntry(uint16_t group,uint16_t elem)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
+ BinEntry *newE;
+
+ if(oldE)
+ {
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntry(group,elem);
+ }
+
+ return newE;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Factorization for various forms of constructors.
*/
-uint8_t* File::GetLutRGBA()
+void FileHelper::Initialise()
+{
+ WriteMode = WMODE_RAW;
+ WriteType = ExplicitVR;
+
+ PixelReadConverter = new PixelReadConvert;
+ PixelWriteConverter = new PixelWriteConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ }
+}
+
+/**
+ * \brief
+ */
+uint8_t *FileHelper::GetRaw()
{
- return PixelConverter->GetLutRGBA();
+ 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 )
+ {
+ gdcmVerboseMacro( "Read/decompress of pixel data apparently went wrong.");
+ return 0;
+ }
+ }
+
+ return raw;
}
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff