-#include "gdcmlib.h"
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ 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
+ 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.
+
+=========================================================================*/
-gdcmFile::gdcmFile(string & filename) {
-
+#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 deal with the *pixels* area of a ACR/DICOMV3
+ * file (gdcmHeader only deals with the ... header)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * user sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param header already built gdcmHeader
+ * @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 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
+ */
+gdcmFile::gdcmFile(std::string const & filename )
+{
+ 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 was created by the gdcmFile constructor,
+ * it is destroyed by the gdcmFile
+ */
+gdcmFile::~gdcmFile()
+{
+ if( SelfHeader )
+ {
+ delete Header;
+ }
+ Header = 0;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \ingroup gdcmFile
+ * \brief computes the length (in bytes) we must ALLOCATE to receive the
+ * image(s) pixels (multiframes taken into account)
+ * \warning : it is NOT the group 7FE0 length
+ * (no interest for compressed images).
+ */
+void gdcmFile::SetPixelDataSizeFromHeader()
+{
+ // see PS 3.3-2003 : C.7.6.3.2.1
+ //
+ // MONOCHROME1
+ // MONOCHROME2
+ // PALETTE COLOR
+ // RGB
+ // HSV (Retired)
+ // ARGB (Retired)
+ // CMYK (Retired)
+ // YBR_FULL
+ // YBR_FULL_422 (no LUT, no Palette)
+ // YBR_PARTIAL_422
+ // YBR_ICT
+ // YBR_RCT
+
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+
+ // Number of "Bits Allocated"
+ int nb;
+ std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+
+ if ( str_nb == GDCM_UNFOUND )
+ {
+ nb = 16;
+ }
+ else
+ {
+ nb = atoi( str_nb.c_str() );
+ if (nb == 12)
+ {
+ nb =16;
+ }
+ }
+ ImageDataSize = ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize()
+ * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel();
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ // if ( str_PhotometricInterpretation == "PALETTE COLOR " ),
+ // pb when undealt Segmented Palette Color
+
+ if ( Header->HasLUT() )
+ {
+ ImageDataSize *= 3;
+ }
+}
+
+
+/**
+ * \ingroup gdcmFile
+ * \brief Returns the size (in bytes) of required memory to hold
+ * 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 to deal with LUTs-
+ * \warning to be used with GetImagePixelsRaw()
+ * @return The size of pixel data in bytes.
+ */
+size_t gdcmFile::GetImageDataSizeRaw()
+{
+ return ImageDataSizeRaw;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \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 (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());
+ }
+ PixelRead = 0; // no PixelRaw
+
+ return PixelData;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * Read the pixels from disk (uncompress if necessary),
+ * Transforms YBR pixels, if any, into RGB pixels
+ * Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * Copies at most MaxSize bytes of pixel data to caller allocated
+ * memory space.
+ * \warning This function allows people that want to build a volume
+ * from an image stack *not to* have, first to get the image pixels,
+ * and then move them to the volume area.
+ * It's absolutely useless for any VTK user since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users have to call GetImageData
+ *
+ * @param destination Address (in caller's memory space) at which the
+ * pixel data should be copied
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
+ * is not sufficient to hold the pixel data the copy is not
+ * executed (i.e. no partial copy).
+ * @return On success, the number of bytes actually copied. Zero on
+ * failure e.g. MaxSize is lower than necessary.
+ */
+size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
+{
+ GetImageDataIntoVectorRaw (destination, maxSize);
+ PixelRead = 0 ; // =0 : no ImageDataRaw
+ if ( !Header->HasLUT() )
+ {
+ return ImageDataSize;
+ }
+
+ // from Lut R + Lut G + Lut B
+ uint8_t *newDest = new uint8_t[ImageDataSize];
+ uint8_t *a = (uint8_t *)destination;
+ uint8_t *lutRGBA = Header->GetLUTRGBA();
+
+ if ( lutRGBA )
+ {
+ int j;
+ // move Gray pixels to temp area
+ memmove(newDest, destination, ImageDataSizeRaw);
+ for (size_t i=0; i<ImageDataSizeRaw; ++i)
+ {
+ // Build RGB Pixels
+ j = newDest[i]*4;
+ *a++ = lutRGBA[j];
+ *a++ = lutRGBA[j+1];
+ *a++ = lutRGBA[j+2];
+ }
+ delete[] newDest;
+
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // FIXME : Better use CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb = "RGB "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
+ }
+ else // GetLUTRGBA() failed
+ {
+ // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color
+ // that are *more* than 65535 long ?!?
+ // No idea how to manage such an image !
+ // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!)
+ // It seems that *no Dicom Viewer* has any idea :-(
+
+ std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
+ Header->SetEntryByNumber(photomInterp,0x0028,0x0004);
+ }
+
+ /// \todo Drop Palette Color out of the Header?
+ return ImageDataSize;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Allocates necessary memory,
+ * Transforms YBR pixels (if any) into RGB pixels
+ * Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * 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;
+ 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 PixelData before doing any allocation:
+
+ if ( PixelData )
+ if ( LastAllocatedPixelDataLength != imgDataSize)
+ free (PixelData);
+ PixelData = new uint8_t[imgDataSize];
+ if ( PixelData )
+ {
+ LastAllocatedPixelDataLength = imgDataSize;
+
+ GetImageDataIntoVectorRaw(PixelData, imgDataSize);
+ // will be 7fe0, 0010 in standard cases
+ GetHeader()->SetEntryVoidAreaByNumber(PixelData,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ }
+ PixelRead = 1; // PixelRaw
+
+ return PixelData;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * memory space.
+ * \warning This function was designed to avoid people that want to build
+ * a volume from an image stack to need first to get the image pixels
+ * and then move them to the volume area.
+ * It's absolutely useless for any VTK user since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users hace to call GetImageData
+ * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
+ * into a single RGB Pixels Plane
+ * the (VTK) user will manage the palettes
+ *
+ * @param destination Address (in caller's memory space) at which the
+ * pixel data should be copied
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
+ * is not sufficient to hold the pixel data the copy is not
+ * executed (i.e. no partial copy).
+ * @return On success, the number of bytes actually copied. Zero on
+ * failure e.g. MaxSize is lower than necessary.
+ */
+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"
+ "than caller's expected MaxSize");
+ return (size_t)0;
+ }
+
+ 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() );
+ // FIXME
+ // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated
+ // separately, correct ?
+ }
+
+ // Number of Bits actually used
+ std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101);
+ if ( str_nbu == GDCM_UNFOUND )
+ {
+ nbu = nb;
+ }
+ else
+ {
+ nbu = atoi( str_nbu.c_str() );
+ }
+
+ // High Bit Position
+ std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102);
+ if ( str_highBit == GDCM_UNFOUND )
+ {
+ highBit = nb - 1;
+ }
+ else
+ {
+ highBit = atoi( str_highBit.c_str() );
+ }
+
+ // Pixel sign
+ // 0 = Unsigned
+ // 1 = Signed
+ std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103);
+ if ( str_sign == GDCM_UNFOUND )
+ {
+ sign = 0; // default is unsigned
+ }
+ else
+ {
+ sign = atoi( str_sign.c_str() );
+ }
+
+ // re arange bytes inside the integer (processor endianity)
+ if ( nb != 8 )
+ {
+ SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb);
+ }
+
+ // to avoid pb with some xmedcon breakers images
+ if ( nb == 16 && nbu < nb && sign == 0)
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ uint16_t *deb = (uint16_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
+
+ // re arange bits inside the bytes
+ if ( nbu != nb )
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ if ( nb == 16 )
+ {
+ uint16_t mask = 0xffff;
+ mask = mask >> (nb-nbu);
+ uint16_t *deb = (uint16_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ deb++;
+ }
+ }
+ else if ( nb == 32 )
+ {
+ uint32_t mask = 0xffffffff;
+ mask = mask >> (nb - nbu);
+ uint32_t *deb = (uint32_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
+ return 0;
+ }
+ }
+// DO NOT remove this code commented out.
+// Nobody knows what's expecting you ...
+// Just to 'see' what was actually read on disk :-(
+
+// FILE * f2;
+// f2 = fopen("SpuriousFile.RAW","wb");
+// 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 ImageDataSize;
+ }
+
+ // Planar configuration = 0 : Pixels are already RGB
+ // Planar configuration = 1 : 3 planes : R, G, B
+ // Planar configuration = 2 : 1 gray Plane + 3 LUT
+
+ // Well ... supposed to be !
+ // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
+ // PhotometricInterpretation=PALETTE COLOR
+ // and heuristic has to be found :-(
+
+ 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;
+ }
+
+ switch ( planConf )
+ {
+ case 0:
+ // Pixels are already RGB
+ break;
+ case 1:
+ if (str_PhotometricInterpretation == "YBR_FULL")
+ {
+ // Warning : YBR_FULL_422 acts as RGB
+ // : we need to make RGB Pixels from Planes Y,cB,cR
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = Header->GetXSize() * Header->GetYSize();
+ int nbFrames = Header->GetZSize();
+
+ uint8_t* newDest = new uint8_t[ImageDataSize];
+ uint8_t* x = newDest;
+ uint8_t* a = (uint8_t*)destination;
+ uint8_t* b = a + l;
+ uint8_t* c = b + l;
+ double R,G,B;
+
+ /// \todo : Replace by the 'well known' integer computation
+ /// counterpart
+ /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation
+
+ for (int i = 0; i < nbFrames; i++)
+ {
+ for (int j = 0; j < l; j++)
+ {
+ R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R < 0.0) R = 0.0;
+ if (G < 0.0) G = 0.0;
+ if (B < 0.0) B = 0.0;
+ if (R > 255.0) R = 255.0;
+ if (G > 255.0) G = 255.0;
+ if (B > 255.0) B = 255.0;
+
+ *(x++) = (uint8_t)R;
+ *(x++) = (uint8_t)G;
+ *(x++) = (uint8_t)B;
+ a++; b++; c++;
+ }
+ }
+ memmove(destination, newDest, ImageDataSize);
+ delete[] newDest;
+ }
+ else
+ {
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
+
+ int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
+
+ uint8_t *newDest = new uint8_t[ImageDataSize];
+ uint8_t *x = newDest;
+ uint8_t *a = (uint8_t *)destination;
+ uint8_t *b = a + l;
+ uint8_t *c = b + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(x++) = *(a++);
+ *(x++) = *(b++);
+ *(x++) = *(c++);
+ }
+ memmove(destination, newDest, ImageDataSize);
+ delete[] newDest;
+ }
+ break;
+ case 2:
+ // Palettes were found
+ // Let the user deal with them !
+ return ImageDataSize;
+ }
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ std::string photInt = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+
+
+
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ Header->SetEntryByNumber(photInt,0x0028,0x0004);
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
+ /// \todo Drop Palette Color out of the Header?
+ return ImageDataSize;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief performs a shalow copy (not a deep copy) of the user given
+ * pixel area.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \warning user is kindly requested NOT TO 'free' the Pixel area
+ * @param inData user supplied pixel area
+ * @param expectedSize total image size, in Bytes
+ *
+ * @return boolean
+ */
+bool gdcmFile::SetImageData(void *inData, size_t expectedSize)
+{
+ Header->SetImageDataSize( expectedSize );
+// FIXME : if already allocated, memory leak !
+ PixelData = inData;
+ ImageDataSize = ImageDataSizeRaw = expectedSize;
+ PixelRead = 1;
+// FIXME : 7fe0, 0010 IS NOT set ...
+ return true;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Writes on disk A SINGLE Dicom file
+ * NO test is performed on processor "Endiannity".
+ * It's up to the user to call his Reader properly
+ * @param fileName name of the file to be created
+ * (any already existing file is over written)
+ * @return false if write fails
+ */
+
+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 (PixelData, ImageDataSize, 1, fp1);
+ fclose (fp1);
+
+ return true;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Writes on disk A SINGLE Dicom file,
+ * using the Implicit Value Representation convention
+ * NO test is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmImplicitVR);
+}
+
+/**
+ * \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
+ */
+
+bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmExplicitVR);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Writes on disk A SINGLE Dicom file,
+ * using the ACR-NEMA convention
+ * NO test is performed on processor "Endiannity".
+ * (a l'attention des logiciels cliniques
+ * qui ne prennent en entrée QUE des images ACR ...
+ * \warning if a DICOM_V3 header is supplied,
+ * groups < 0x0008 and shadow groups are ignored
+ * \warning NO TEST is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteAcr (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmACR);
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \ingroup gdcmFile
+ * \brief NOT a end user inteded function
+ * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @param type file type (ExplicitVR, ImplicitVR, ...)
+ * @return false if write fails
+ */
+bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+{
+ if ( PixelRead == -1 && type != gdcmExplicitVR)
+ {
+ return false;
+ }
+
+ FILE *fp1 = fopen(fileName.c_str(), "wb");
+ if (fp1 == NULL)
+ {
+ printf("Failed to open (write) File [%s] \n", fileName.c_str());
+ return false;
+ }
+
+ if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ {
+ // 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;
+ }
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // if recognition code tells us we dealt with a LibIDO image
+ // we reproduce on disk the switch between lineNumber and columnNumber
+ // just before writting ...
+
+ /// \todo the best trick would be *change* the recognition code
+ /// but pb expected if user deals with, e.g. COMPLEX images
+
+ 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);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ uint16_t grPixel = Header->GetGrPixel();
+ uint16_t numPixel = Header->GetNumPixel();;
+
+ 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 );
+ }
+
+ Header->Write(fp1, type);
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // ...and we restore the Header to be Dicom Compliant again
+ // just after writting
+
+ if ( Header->GetFileType() == gdcmACR_LIBIDO )
+ {
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now
+ fclose (fp1);
+
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \ingroup gdcmFile
+ * \brief Swap the bytes, according to swap code.
+ * \warning not end user intended
+ * @param im area to deal with
+ * @param swap swap code
+ * @param lgr Area Length
+ * @param nb Pixels Bit number
+ */
+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;
+ }
+ }
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Read pixel data from disk (optionaly decompressing) into the
+ * caller specified memory location.
+ * @param destination where the pixel data should be stored.
+ *
+ */
+bool gdcmFile::ReadPixelData(void *destination)
+{
+ FILE *fp = Header->OpenFile();
+
+ if ( !fp )
+ {
+ return false;
+ }
+ 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]
+
+ if ( Header->GetBitsAllocated() == 12 )
+ {
+ int nbPixels = Header->GetXSize() * Header->GetYSize();
+ uint8_t b0, b1, b2;
+
+ uint16_t* pdestination = (uint16_t*)destination;
+ for(int p = 0; p < nbPixels; p += 2 )
+ {
+ fread(&b0,1,1,fp);
+ fread(&b1,1,1,fp);
+ fread(&b2,1,1,fp);
+
+ //Two steps is necessary to please VC++
+ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // A B D
+ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+ // F C E
+
+ // Troubles expected on Big-Endian processors ?
+ }
+
+ Header->CloseFile();
+ return true;
+ }
+
+ // ---------------------- Uncompressed File
+ if ( !Header->IsDicomV3() ||
+ Header->IsImplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRBigEndianTransferSyntax() ||
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ {
+ size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
+ Header->CloseFile();
+ if ( ItemRead != 1 )
+ {
+ return false;
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ // ---------------------- Run Length Encoding
+ if ( Header->IsRLELossLessTransferSyntax() )
+ {
+ bool res = gdcm_read_RLE_file (fp,destination);
+ Header->CloseFile();
+ return res;
+ }
+
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ int nb;
+ std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+ if ( str_nb == GDCM_UNFOUND )
+ {
+ nb = 16;
+ }
+ 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();
+ long fragmentBegining; // for ftell, fseek
+
+ bool jpg2000 = Header->IsJPEG2000();
+ bool jpgLossless = Header->IsJPEGLossless();
+
+ bool res = true;
+ uint16_t ItemTagGr, ItemTagEl;
+ int ln;
+
+ // Position on begining of Jpeg Pixels
+
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode())
+ {
+ 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 )
+ {
+ // What is it used for ?!?
+ 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 );
+ }
+
+ // parsing fragments until Sequence Delim. Tag found
+ 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 );
+
+ 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;
+ }
+
+ // location in user's memory
+ // for next fragment (if any)
+ destination = (uint8_t*)destination + taille * nBytes;
+
+ fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start
+ fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
+
+ ItemTagGr = ItemTagEl = 0;
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if( Header->GetSwapCode() )
+ {
+ ItemTagGr = Header->SwapShort( ItemTagGr );
+ ItemTagEl = Header->SwapShort( ItemTagEl );
+ }
+ }
+ // endWhile parsing fragments until Sequence Delim. Tag found
+
+ Header->CloseFile();
+ return res;
}
+//-----------------------------------------------------------------------------