-// gdcmFile.cxx
-
-//This is needed when compiling in debug mode
-#ifdef _MSC_VER
-// 'type' : forcing value to bool 'true' or 'false' (performance warning)
-//#pragma warning ( disable : 4800 )
-// 'identifier' : class 'type' needs to have dll-interface to be used by
-// clients of class 'type2'
-#pragma warning ( disable : 4251 )
-// 'identifier' : identifier was truncated to 'number' characters in the
-// debug information
-#pragma warning ( disable : 4786 )
-#endif //_MSC_VER
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ Date: $Date: 2004/08/26 15:29:53 $
+ Version: $Revision: 1.121 $
+
+ 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 "gdcmUtil.h"
-#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
+#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)
* 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
+ * \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
- *
- * @return
+ * @param header file to be opened for reading datas
+ * @return
*/
-
-gdcmFile::gdcmFile(std::string & filename)
- :gdcmHeader(filename.c_str())
+gdcmFile::gdcmFile(gdcmHeader *header)
{
- SetPixelDataSizeFromHeader();
-}
+ Header = header;
+ SelfHeader = false;
+ PixelRead = -1; // no ImageData read yet.
-gdcmFile::gdcmFile(const char * filename)
- :gdcmHeader(filename)
-{
- SetPixelDataSizeFromHeader();
+ if (Header->IsReadable())
+ {
+ SetPixelDataSizeFromHeader();
+ }
}
/**
* \ingroup gdcmFile
- * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les
- * pixels de l'image
- * ou DES images dans le cas d'un multiframe
- * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels
- * (dans le cas d'images compressees, elle n'a pas de sens).
- *
- * @return longueur a allouer
+ * \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
*/
-void gdcmFile::SetPixelDataSizeFromHeader(void) {
- int nb;
- std::string str_nb;
+gdcmFile::gdcmFile(std::string const & filename )
+{
+ Header = new gdcmHeader( filename );
+ SelfHeader = true;
+ PixelRead = -1; // no ImageData read yet.
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
+ if ( Header->IsReadable() )
+ {
+ SetPixelDataSizeFromHeader();
}
- lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();
-
- std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- if ( str_PhotometricInterpretation == "PALETTE COLOR "
- || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !!
- lgrTotale*=3;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief canonical destructor
+ * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
+ * by the gdcmFile
+ */
+gdcmFile::~gdcmFile()
+{
+ if( SelfHeader )
+ {
+ delete Header;
}
+ Header = 0;
}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \ingroup gdcmFile
+ * \brief computes the length (in bytes) to 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()
+{
// see PS 3.3-2003 : C.7.6.3.2.1
//
// MONOCHROME1
// 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]
+ // 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 : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm
- // 0028|1201 [OW] [Red Palette Color Lookup Table Data]
- // 0028|1202 [OW] [Green Palette Color Lookup Table Data]
- // 0028|1203 [OW] [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]
+ // 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.
* @return The size of pixel data in bytes.
*/
-
-size_t gdcmFile::GetImageDataSize(void) {
- return (lgrTotale);
+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
+ * 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()
+{
+ return ImageDataSizeRaw;
+}
-/////////////////////////////////////////////////////////////////
/**
* \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.
- *
+ * \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
+ * @return Pointer to newly allocated pixel data.
+ * NULL if alloc fails
*/
-bool gdcmFile::ReadPixelData(void* destination) {
+void *gdcmFile::GetImageData()
+{
+ // FIXME
+ // I need to deallocate PixelData before doing any allocation:
+ PixelData = new uint8_t[ImageDataSize];
+ if ( PixelData )
+ {
+ GetImageDataIntoVector(PixelData, ImageDataSize);
+ GetHeader()->SetEntryVoidAreaByNumber( PixelData,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ }
+ PixelRead = 0; // no PixelRaw
- if ( !OpenFile())
- return false;
-
- if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
- CloseFile();
- return false;
- }
+ return PixelData;
+}
-// ------------------------- Uncompressed File
-
- if ( !IsDicomV3() ||
- IsImplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRBigEndianTransferSyntax() ||
- IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- size_t ItemRead = fread(destination, lgrTotale, 1, fp);
- if ( ItemRead != 1 ) {
- CloseFile();
- return false;
- } else {
- CloseFile();
- return true;
+/**
+ * \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 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)
+{
+ //size_t l = GetImageDataIntoVectorRaw (destination, maxSize);
+ GetImageDataIntoVectorRaw (destination, maxSize);
+ PixelRead = 0 ; // no PixelRaw
+ 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;
+ //int l = ImageDataSizeRaw; //loss of precision
+ // 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;
- // ------------------------ Compressed File .
-
- int nb;
- std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
- }
- int nBytes= nb/8;
-
- int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
-
-
- // ------------------------------- JPEG LossLess : call to Jpeg Libido
-
- if (IsJPEGLossless() && GetZSize() == 1) {
-
- int ln; // Position on begining of Jpeg Pixels
- fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : Basic Offset Table Item
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Item length
- fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes)
- fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : First fragment Item Tag
- fread(&ln,4,1,fp); // First fragment length (just to know)
- if(GetSwapCode())
- ln=SwapLong(ln);
-
- ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
- // (We use the LibIDO one :-(
- if(jpg == NULL) {
- CloseFile();
- return false;
- }
- int * dataJpg = jpg->DataImg;
-
- switch (nBytes) {
- case 1:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned char *)dest+i) = *(dataJpg +i);
- }
- }
- break;
-
- case 2:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned short *)dest+i) = *(dataJpg +i);
- }
- }
- break;
- }
- _IdDcmJpegFree (jpg);
- return true;
- }
-
- // ------------------------------- RLE
+ // now, it's an RGB image
+ // Lets's write it in the Header
- if (gdcmHeader::IsRLELossLessTransferSyntax()) {
- int res = (bool)gdcm_read_RLE_file (destination);
- return res;
- }
+ // CreateOrReplaceIfExist ?
- // ------------------------------- JPEG Lossy : call to IJG 6b
-
- long fragmentBegining; // for ftell, fseek
- bool b = gdcmHeader::IsJPEG2000();
-
- bool res;
- guint16 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(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item length
-
- if (ln != 0) {
- // What is it used for ?!?
- char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
- fread(BasicOffsetTableItemValue,ln,1,fp);
- }
-
- // first Fragment initialisation
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
-
- // parsing fragments until Sequence Delim. Tag found
- //unsigned short *dest = (unsigned short *)destination;
-
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Fragment Item length
-
- // FIXME : multi fragments
- fragmentBegining=ftell(fp);
-
+ 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 //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
- if (b)
- res = (bool)gdcm_read_JPEG2000_file (destination); // Reading Fragment pixels
-
- else if (IsJPEGLossless()) {
- // ------------- call to LibIDO Jpeg for each Frame/fragment
-
- // Warning : Works only if there is one fragment per frame
- // (Or a single fragment for the multiframe file)
- ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
- // (We use the LibIDO one :-(
- if(jpg == NULL) {
- CloseFile();
- return false;
- }
- int * dataJpg = jpg->DataImg;
- unsigned short *dest = (unsigned short *)destination;
- switch (nBytes) {
- case 1:
- {
- for (int i=0; i<taille; i++) {
- *((unsigned char *)dest+i) = *(dataJpg +i);
- }
- break;
- }
-
- case 2:
- {
- for (int i=0; i<taille; i++) {
- *((unsigned short *)dest+i) = *(dataJpg +i);
- }
- break;
- }
- }
- _IdDcmJpegFree (jpg);
-
- } // ------------------------------------- endif (IsJPEGLossless())
-
- else
- if (GetBitsStored() == 8) {
- res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
- }
-
- if (!res) break;
-
- // FIXME : will work only when each fragment corresponds to a Frame :-(
-
- destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
- // TODO : find a suitable file (multifragment/single Frame Jpeg file) to check
-
- 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(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
-
- //(char *) destination += taille * nBytes;
- //std::cout << "destination" << destination << std::endl;
- }
-
- return res;
-}
+ // 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 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
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-void * gdcmFile::GetImageData (void) {
- PixelData = (void *) malloc(lgrTotale);
- if (PixelData)
- GetImageDataIntoVector(PixelData, lgrTotale);
- return(PixelData);
+void * gdcmFile::GetImageDataRaw ()
+{
+ size_t imgDataSize = ImageDataSize;
+ if ( Header->HasLUT() )
+ {
+ /// \todo Let gdcmHeader user a chance to get the right value
+ imgDataSize = ImageDataSizeRaw;
+ }
+
+ // FIXME
+ // I need to deallocate PixelData before doing any allocation:
+ PixelData = new uint8_t[imgDataSize];
+ if ( PixelData )
+ {
+ GetImageDataIntoVectorRaw(PixelData, ImageDataSize);
+ 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
+ * @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) {
-
- int nb, nbu, highBit, signe;
- std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
+size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize)
+{
+ int nb, nbu, highBit, sign;
+ PixelRead = 1 ; // PixelRaw
- if ( lgrTotale > MaxSize ) {
+ if ( ImageDataSize > maxSize )
+ {
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
"than caller's expected MaxSize");
- return (size_t)0;
- }
-
- (void)ReadPixelData(destination);
-
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb = GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
+ 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() );
}
-
- // Nombre de Bits Utilises
- str_nbu=GetPubElValByNumber(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() );
- }
-
- // Position du Bit de Poids Fort
- str_highBit=GetPubElValByNumber(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() );
}
-
- // Signe des Pixels
- str_signe=GetPubElValByNumber(0x0028,0x0103);
- if (str_signe == GDCM_UNFOUND ) {
- signe = 1;
- } 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
- if (nb != 8)
- SwapZone(destination, GetSwapCode(), lgrTotale, nb);
-
- // re arange bits inside the bytes
- if (nbu != nb){
- int l = (int)lgrTotale / (nb/8);
- if (nb == 16) {
- guint16 mask = 0xffff;
- mask = mask >> (nb-nbu);
- guint16 *deb = (guint16 *)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 ++;
+ // 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;
}
- } else {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
- return (size_t)0;
+ deb++;
}
- }
-
- // *Try* to deal with the color
- // --------------------------
-
- std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
-
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ")
- || (str_PhotometricInterpretation == "RGB")) {
- return lgrTotale;
}
- int planConf=GetPlanarConfiguration();
- if( str_PhotometricInterpretation!="PALETTE COLOR" && planConf == 0)
- planConf=2; // Sorry, this is an heuristic
-
- switch ( planConf) {
- case 0:
- // Pixels are already RGB
- break;
-
- case 1:
- // need to make RGB Pixels from Planes R,G,B
+ // re arange bits inside the bytes
+ if ( nbu != nb )
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ if ( nb == 16 )
{
- int l = lgrTotale/3 ;
-
- char * a = (char *)destination;
- char * b = a + l;
- char * c = b + l;
- char * newDest = (char*) malloc(lgrTotale);
- // TODO :
- // any trick not to have to allocate temporary buffer is welcome ...
- char *x = newDest;
- for (int j=0;j<l; j++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
+ 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++;
}
- memmove(destination,newDest,lgrTotale);
- free(newDest);
- // now, it's an RGB image
- std::string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB";
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
- break;
}
-
- case 2:
- // from Lut R + Lut G + Lut B
-
- // we no longer use gdcmHeader::GetLUTRGB
- // since a lot of images have wrong info
- // in the Lookup Table Descriptors (0028,1101),...
+ else if ( nb == 32 )
{
- unsigned char *lutR =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1201);
- unsigned char *lutG =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1202);
- unsigned char *lutB =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1203);
-
- if (lutR && lutG && lutB ) { // need to make RGB Pixels
- // from grey Pixels
- // and Lut R,Lut G,Lut B
- unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
- int l = lgrTotale/3;
- memmove(newDest, destination, l);// move Gray pixels to temp area
-
- unsigned char * x = newDest;
- unsigned char * a = (unsigned char *)destination;
- int j;
- for (int i=0;i<l; i++) {
- j=newDest[i]*2; // Who can explain *why* we have to skip bytes
- *a++ = lutR[j];
- *a++ = lutG[j];
- *a++ = lutB[j];
- }
- free(newDest);
-
- // now, it's an RGB image
- std::string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB";
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
-
- } else { // need to make RGB Pixels (?)
- // from grey Pixels (?!)
- // and Gray Lut (!?!)
- unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
- // Well . I'll wait till I find such an image
+ 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++;
}
- break;
}
- }
-
- return lgrTotale;
-}
+ 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 :-(
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
+// FILE * f2;
+// f2 = fopen("SpuriousFile.RAW","wb");
+// fwrite(destination,ImageDataSize,1,f2);
+// fclose(f2);
-/**
- * \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
- */
+ // Deal with the color
+ // -------------------
+
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
-void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
+ 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
-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;i++)
- ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
- | ((((unsigned short int*)im)[i])<<8);
- break;
-
- default:
- printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
- }
-
-if( nb == 32 )
- switch (swap) {
+ // 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:
- case 1234:
+ // 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;
- case 4321:
- for(i=0;i<lgr;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;
+ 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;
}
- break;
+ else
+ {
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
- case 2143:
- for(i=0;i<lgr;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;
+ 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 3412:
- for(i=0;i<lgr;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;
-}
-
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief TODO JPR
- * \warning doit-etre etre publique ?
- * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
- *
- * @param inData
- * @param ExpectedSize
- *
- * @return integer acts as a boolean
- */
-int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
- SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- return(1);
-}
+ 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 ?
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief Sets the Pixel Area size in the Header
- * --> not-for-rats function
- *
- * \warning WARNING doit-etre etre publique ?
- * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
- *
- * @param ImageDataSize new Pixel Area Size
- * warning : nothing else is checked
- */
+ std::string spp = "3"; // Samples Per Pixel
+ std::string rgb = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
-void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
- std::string content1;
- char car[20];
- // Assumes ElValue (0x7fe0, 0x0010) exists ...
- sprintf(car,"%d",ImageDataSize);
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
- gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+ /// \todo Drop Palette Color out of the Header?
+ return ImageDataSize;
}
-
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief Ecrit sur disque les pixels d'UNE image
- * Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca sera à l'utilisateur d'appeler son Reader correctement
- * (Equivalent a IdImaWriteRawFile)
+ * \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
+ * \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 fileName
- * @return
+ * @return boolean
*/
+bool gdcmFile::SetImageData(void *inData, size_t expectedSize)
+{
+ Header->SetImageDataSize( expectedSize );
+ PixelData = inData;
+ ImageDataSize = expectedSize;
+ PixelRead = 1;
-int gdcmFile::WriteRawData (std::string fileName) {
- FILE * fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
- return (0);
- }
- fwrite (PixelData,lgrTotale, 1, fp1);
- fclose (fp1);
- return(1);
+ return true;
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief Ecrit sur disque UNE image Dicom
- * Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca fonctionnera correctement (?) sur processeur Intel
- * (Equivalent a IdDcmWrite)
- *
- * @param fileName
- * @return int acts as a boolean
+ * \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
*/
-int gdcmFile::WriteDcmImplVR (std::string fileName) {
- return WriteBase(fileName, ImplicitVR);
+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
- * @param fileName
- * @return int acts as a boolean
+ * \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
*/
-
-int gdcmFile::WriteDcmImplVR (const char* fileName) {
- return WriteDcmImplVR (std::string (fileName));
+
+bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmImplicitVR);
}
-
-/////////////////////////////////////////////////////////////////
+
/**
* \ingroup gdcmFile
- * \brief
- * @param fileName
- * @return int acts as a boolean
+* \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
*/
-int gdcmFile::WriteDcmExplVR (std::string fileName) {
- return WriteBase(fileName, ExplicitVR);
+bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmExplicitVR);
}
-
-/////////////////////////////////////////////////////////////////
+
/**
* \ingroup gdcmFile
- * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
+ * \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 si un header DICOM est fourni en entree,
- * les groupes < 0x0008 et les groupes impairs sont ignores)
- * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca fonctionnera correctement (?) sur processeur Intel
- * (Equivalent a IdDcmWrite)
- *
- * @param fileName
- * @return int acts as a boolean
+ * \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
*/
-int gdcmFile::WriteAcr (std::string fileName) {
- return WriteBase(fileName, ACR);
+bool gdcmFile::WriteAcr (std::string const & fileName)
+{
+ return WriteBase(fileName, gdcmACR);
}
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Protected
/**
* \ingroup gdcmFile
- *
- * @param FileName
- * @param type
- *
- * @return int acts as a boolean
+ * \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
*/
-int gdcmFile::WriteBase (std::string FileName, FileType type) {
+bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+{
+ if ( PixelRead == -1 && type != gdcmExplicitVR)
+ {
+ return false;
+ }
- FILE * fp1;
- fp1 = fopen(FileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
- return (0);
+ 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) ) {
- char * filePreamble;
+ if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ {
// writing Dicom File Preamble
- filePreamble=(char*)calloc(128,1);
- 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;
}
// --------------------------------------------------------------
// 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 ( filetype == ACR_LIBIDO){
- rows = GetPubElValByNumber(0x0028, 0x0010);
- columns = GetPubElValByNumber(0x0028, 0x0011);
- SetPubElValByNumber(columns, 0x0028, 0x0010);
- SetPubElValByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
+ if ( Header->GetFileType() == gdcmACR_LIBIDO)
+ {
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
- gdcmHeader::Write(fp1, type);
+ 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 (filetype == ACR_LIBIDO){
- SetPubElValByNumber(rows , 0x0028, 0x0010);
- SetPubElValByNumber(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(PixelData, ImageDataSize, 1, fp1); // should be useless, now
fclose (fp1);
- return(1);
+
+ 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;
}
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff