Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/06/28 14:29:52 $
- Version: $Revision: 1.113 $
+ Date: $Date: 2004/09/01 16:23:59 $
+ Version: $Revision: 1.122 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
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
+ * @param header already built gdcmHeader
* @return
*/
gdcmFile::gdcmFile(gdcmHeader *header)
{
Header = header;
SelfHeader = false;
+
PixelRead = -1; // no ImageData read yet.
-
+ LastAllocatedPixelDataLength = 0;
+ PixelData = NULL;
+
+ InitialSpp = "";
+ InitialPhotInt = "";
+ InitialPlanConfig = "";
+ InitialBitsAllocated = "";
+
if (Header->IsReadable())
{
SetPixelDataSizeFromHeader();
/**
* \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 const & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
+gdcmFile::gdcmFile(std::string const & filename )
{
- Header = new gdcmHeader( filename,
- exception_on_error,
- enable_sequences,
- ignore_shadow );
+ Header = new gdcmHeader( filename );
SelfHeader = true;
+
PixelRead = -1; // no ImageData read yet.
-
+ LastAllocatedPixelDataLength = 0;
+ PixelData = NULL;
+
+ InitialSpp = "";
+ InitialPhotInt = "";
+ InitialPlanConfig = "";
+ InitialBitsAllocated = "";
+
if ( Header->IsReadable() )
{
SetPixelDataSizeFromHeader();
/**
* \ingroup gdcmFile
* \brief canonical destructor
- * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
- * by the gdcmFile
+ * \note If the gdcmHeader was created by the gdcmFile constructor,
+ * it is destroyed by the gdcmFile
*/
gdcmFile::~gdcmFile()
{
/**
* \ingroup gdcmFile
- * \brief computes the length (in bytes) to ALLOCATE to receive the
+ * \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
*/
void gdcmFile::SetPixelDataSizeFromHeader()
{
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() )
}
}
-/**
- * \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()
-{
- return ImageDataSize;
-}
/**
* \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
+ * the pixel data represented in this file, if 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-
+ * -the (vtk) user is supposed to know how to deal with LUTs-
* \warning to be used with GetImagePixelsRaw()
* @return The size of pixel data in bytes.
*/
/**
* \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()
{
- // FIXME
+ // FIXME (Mathieu)
// I need to deallocate PixelData before doing any allocation:
+
+ if ( PixelData )
+ if ( LastAllocatedPixelDataLength != ImageDataSize)
+ free (PixelData);
PixelData = new uint8_t[ImageDataSize];
if ( PixelData )
{
+ LastAllocatedPixelDataLength = ImageDataSize;
+
GetImageDataIntoVector(PixelData, ImageDataSize);
+ // Will be 7fe0, 0010 in standard case
GetHeader()->SetEntryVoidAreaByNumber( PixelData,
GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
}
/**
* \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
*/
size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
{
- //size_t l = GetImageDataIntoVectorRaw (destination, maxSize);
GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // no PixelRaw
+ PixelRead = 0 ; // =0 : no ImageDataRaw
if ( !Header->HasLUT() )
{
return ImageDataSize;
// from Lut R + Lut G + Lut B
uint8_t *newDest = new uint8_t[ImageDataSize];
uint8_t *a = (uint8_t *)destination;
- uint8_t *lutRGBA = Header->GetLUTRGBA();
+ uint8_t *lutRGBA = Header->GetLUTRGBA();
if ( lutRGBA )
{
int j;
- //int l = ImageDataSizeRaw; //loss of precision
// move Gray pixels to temp area
memmove(newDest, destination, ImageDataSizeRaw);
for (size_t i=0; i<ImageDataSizeRaw; ++i)
// 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 //why is there a 'else' when an allocation failed ?
- {
- // 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
+ 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 :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
-
- std::string rgb = "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
+
+ std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
+ Header->SetEntryByNumber(photomInterp,0x0028,0x0004);
}
/// \todo Drop Palette Color out of the Header?
/**
* \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
+ * \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 ()
{
- size_t imgDataSize = ImageDataSize;
+ size_t imgDataSize;
if ( Header->HasLUT() )
- {
/// \todo Let gdcmHeader user a chance to get the right value
- // ImageDataSize /= 3; //dangerous
imgDataSize = ImageDataSizeRaw;
- }
-
- // FIXME
+ else
+ imgDataSize = ImageDataSize;
+
+ // FIXME (Mathieu)
// I need to deallocate PixelData before doing any allocation:
+
+ if ( PixelData )
+ if ( LastAllocatedPixelDataLength != imgDataSize)
+ free (PixelData);
PixelData = new uint8_t[imgDataSize];
if ( PixelData )
{
- GetImageDataIntoVectorRaw(PixelData, ImageDataSize);
+ LastAllocatedPixelDataLength = imgDataSize;
+
+ GetImageDataIntoVectorRaw(PixelData, imgDataSize);
+ // will be 7fe0, 0010 in standard cases
GetHeader()->SetEntryVoidAreaByNumber(PixelData,
GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
}
*
* @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
size_t gdcmFile::GetImageDataIntoVectorRaw (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 never "read" before
+ {
+ InitialSpp = Header->GetEntryByNumber(0x0028,0x0002);
+ InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004);
+ InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006);
+ InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100);
+ }
+ else // File was already "read", the following *may* have been modified
+ // we restore them to be in a disk-consistent state
+ {
+ // FIXME : What happened with the LUTs ?
+ Header->SetEntryByNumber(InitialSpp,0x0028,0x0002);
+ Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004);
+ Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006);
+ Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100);
+ }
+
PixelRead = 1 ; // PixelRaw
-
+
if ( ImageDataSize > maxSize )
{
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
}
else if ( nb == 32 )
{
- guint32 mask = 0xffffffff;
+ uint32_t mask = 0xffffffff;
mask = mask >> (nb - nbu);
- guint32 *deb = (guint32 *)destination;
+ uint32_t *deb = (uint32_t *)destination;
for(int i = 0; i<l; i++)
{
*deb = (*deb >> (nbu - highBit - 1)) & mask;
// CreateOrReplaceIfExist ?
- std::string spp = "3"; // Samples Per Pixel
- std::string rgb = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
+ 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(rgb,0x0028,0x0004);
+ Header->SetEntryByNumber(photInt,0x0028,0x0004);
Header->SetEntryByNumber(planConfig,0x0028,0x0006);
/// \todo Drop Palette Color out of the Header?
* \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
*/
bool gdcmFile::SetImageData(void *inData, size_t expectedSize)
{
Header->SetImageDataSize( expectedSize );
+// FIXME : if already allocated, memory leak !
PixelData = inData;
- ImageDataSize = expectedSize;
+ ImageDataSize = ImageDataSizeRaw = expectedSize;
PixelRead = 1;
-
+// FIXME : 7fe0, 0010 IS NOT set ...
return true;
}
bool gdcmFile::WriteRawData(std::string const & fileName)
{
- FILE *fp1;
- fp1 = fopen(fileName.c_str(), "wb");
+ FILE *fp1 = fopen(fileName.c_str(), "wb");
if (fp1 == NULL)
{
printf("Fail to open (write) file [%s] \n", fileName.c_str());
return false;
}
- fwrite (PixelData,ImageDataSize, 1, fp1);
+ fwrite (PixelData, ImageDataSize, 1, fp1);
fclose (fp1);
return true;
*/
bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
{
- FILE *fp1;
-
if ( PixelRead == -1 && type != gdcmExplicitVR)
{
return false;
}
- fp1 = fopen(fileName.c_str(), "wb");
+ FILE *fp1 = fopen(fileName.c_str(), "wb");
if (fp1 == NULL)
{
printf("Failed to open (write) File [%s] \n", fileName.c_str());
uint16_t grPixel = Header->GetGrPixel();
uint16_t numPixel = Header->GetNumPixel();;
- gdcmDocEntry* PixelElement;
-
- PixelElement = GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
+ gdcmDocEntry* PixelElement =
+ GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
if ( PixelRead == 1 )
{
case 4321:
for(i=0; i < lgr/2; i++)
{
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
break;
default:
// ---------------------- Run Length Encoding
if ( Header->IsRLELossLessTransferSyntax() )
{
- bool res = (bool)gdcm_read_RLE_file (fp,destination);
+ bool res = gdcm_read_RLE_file (fp,destination);
Header->CloseFile();
return res;
}
if ( jpg2000 )
{
// JPEG 2000 : call to ???
- res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
+ res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
// ------------------------------------- endif (JPEG2000)
}
else if (jpgLossless)
if ( Header->GetBitsStored() == 8)
{
// Reading Fragment pixels
- res = (bool)gdcm_read_JPEG_file (fp,destination);
+ res = gdcm_read_JPEG_file (fp,destination);
}
else
{
// Reading Fragment pixels
- res = (bool)gdcm_read_JPEG_file12 (fp,destination);
+ res = gdcm_read_JPEG_file12 (fp,destination);
}
// ------------------------------------- endif (JPEGLossy)
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff