-// gdcmFile.cxx
-//-----------------------------------------------------------------------------
+ /*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ Date: $Date: 2005/01/06 20:03:27 $
+ Version: $Revision: 1.183 $
+
+ 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.html 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 "gdcmDocument.h"
#include "gdcmDebug.h"
-#include "jpeg/ljpg/jpegless.h"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmPixelWriteConvert.h"
+#include "gdcmDocEntryArchive.h"
+#include <fstream>
+
+namespace gdcm
+{
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 (Header only deals with the ... header)
* Opens (in read only and when possible) an existing file and checks
* for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
* \note the in-memory representation of all available tags found in
* the DICOM header is post-poned to first header information access.
* This avoid a double parsing of public part of the header when
* one sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
- * @param header file to be opened for reading datas
- * @return
*/
-gdcmFile::gdcmFile(gdcmHeader *header) {
- Header=header;
- SelfHeader=false;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+File::File( )
+{
+ HeaderInternal = new Header( );
+ SelfHeader = true;
+ Initialise();
}
/**
- * \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 (Header only deals with the ... header)
* Opens (in read only and when possible) an existing file and checks
* for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
* \note the in-memory representation of all available tags found in
* the DICOM header is post-poned to first header information access.
* This avoid a double parsing of public part of the header when
- * one sets an a posteriori shadow dictionary (efficiency can be
+ * user 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')
+ * @param header already built Header
*/
-gdcmFile::gdcmFile(std::string & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- Header=new gdcmHeader(filename.c_str(),
- exception_on_error,
- enable_sequences,
- ignore_shadow);
- SelfHeader=true;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+File::File(Header *header)
+{
+ HeaderInternal = header;
+ SelfHeader = false;
+ Initialise();
}
/**
- * \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 (Header only deals with the ... header)
* Opens (in read only and when possible) an existing file and checks
* for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
* \note the in-memory representation of all available tags found in
* the DICOM header is post-poned to first header information access.
* This avoid a double parsing of public part of the header when
* one sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
* @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(const char *filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- Header=new gdcmHeader(filename,
- exception_on_error,
- enable_sequences,
- ignore_shadow);
- SelfHeader=true;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+File::File(std::string const & filename )
+{
+ HeaderInternal = new Header( filename );
+ SelfHeader = true;
+ Initialise();
}
/**
- * \ingroup gdcmFile
* \brief canonical destructor
- * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
- * by the gdcmFile
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
*/
-gdcmFile::~gdcmFile(void) {
- if(SelfHeader)
- delete Header;
- Header=NULL;
+File::~File()
+{
+ if( PixelReadConverter )
+ {
+ delete PixelReadConverter;
+ }
+ if( PixelWriteConverter )
+ {
+ delete PixelWriteConverter;
+ }
+ if( Archive )
+ {
+ delete Archive;
+ }
+
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
}
//-----------------------------------------------------------------------------
// Print
+void File::Print(std::ostream &os)
+{
+ HeaderInternal->SetPrintLevel(PrintLevel);
+ HeaderInternal->Print(os);
-//-----------------------------------------------------------------------------
-// Public
-/**
- * \ingroup gdcmFile
- * \brief returns the gdcmHeader *Header
- * @return
- */
-gdcmHeader *gdcmFile::GetHeader(void) {
- return(Header);
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
}
+//-----------------------------------------------------------------------------
+// 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
+ * \brief Get the size of the image data
+ *
+ * If the image can be RGB (with a lut or by default), the size
+ * corresponds to the RGB image
+ * @return The image size
*/
-void gdcmFile::SetPixelDataSizeFromHeader(void) {
- // see PS 3.3-2003 : C.7.6.3.2.1
- //
- // MONOCHROME1
- // MONOCHROME2
- // PALETTE COLOR
- // RGB
- // HSV (Retired)
- // ARGB (Retired)
- // CMYK (Retired)
- // YBR_FULL
- // YBR_FULL_422 (no LUT, no Palette)
- // YBR_PARTIAL_422
- // YBR_ICT
- // YBR_RCT
-
- // LUT's
- // ex : gdcm-US-ALOKA-16.dcm
- // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
- // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
- // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
-
- // ex : OT-PAL-8-face.dcm
- // 0028|1201 [US] [Red Palette Color Lookup Table Data]
- // 0028|1202 [US] [Green Palette Color Lookup Table Data]
- // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
-
- int nb;
- std::string str_nb;
- 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;
- }
- lgrTotale = lgrTotaleRaw = 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()) {
- lgrTotale*=3;
+size_t File::GetImageDataSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
}
-}
-/**
- * \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);
+ return PixelReadConverter->GetRGBSize();
}
/**
- * \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.
+ * \brief Get the size of the image data
+ *
+ * If the image can be RGB by transformation in a LUT, this
+ * transformation isn't considered
+ * @return The raw image size
*/
-size_t gdcmFile::GetImageDataSizeRaw(void) {
- return (lgrTotaleRaw);
+size_t File::GetImageDataRawSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
+
+ return PixelReadConverter->GetRawSize();
}
/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * \brief - Allocates necessary memory,
+ * - Reads the pixels from disk (uncompress if necessary),
+ * - Transforms YBR pixels, if any, into RGB pixels
+ * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * - Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-void * gdcmFile::GetImageData (void) {
- PixelData = new char[lgrTotale];
- if (PixelData)
- GetImageDataIntoVector(PixelData, lgrTotale);
-
- PixelRead=0; // no PixelRaw
- return(PixelData);
-}
+uint8_t *File::GetImageData()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserData();
+ }
-/**
- * \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 lgrTotale;
-
- // from Lut R + Lut G + Lut B
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *a = (unsigned char *)destination;
- unsigned char *lutRGBA = Header->GetLUTRGBA();
- if (lutRGBA) {
- int l = lgrTotaleRaw;
- memmove(newDest, destination, l);// move Gray pixels to temp area
- int j;
- for (int i=0;i<l; i++) { // Build RGB Pixels
- j=newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
- }
- delete[] newDest;
-
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // 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 {
- // need to make RGB Pixels (?)
- // from grey Pixels (?!)
- // and Gray Lut (!?!)
- // or Segmented xxx Palette Color Lookup Table Data and so on
-
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage such an image
- // It seems that *no Dicom Viewer* has any idea :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
-
- std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- }
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ if ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ return PixelReadConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
+ }
}
/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * \brief Allocates necessary memory,
+ * Transforms YBR pixels (if any) into RGB pixels
+ * Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
+ * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-void * gdcmFile::GetImageDataRaw (void) {
- if (Header->HasLUT())
- /// \todo Let gdcmHeadar user a chance to get the right value
- /// Create a member lgrTotaleRaw ???
- lgrTotale /= 3;
- PixelData = new char[lgrTotale];
- if (PixelData)
- GetImageDataIntoVectorRaw(PixelData, lgrTotale);
- PixelRead=1; // PixelRaw
- return(PixelData);
+uint8_t *File::GetImageDataRaw ()
+{
+ return GetRaw();
}
/**
- * \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
* (for some axis related reasons?). Hence he will have
* to load the image line by line, starting from the end.
- * VTK users hace to call GetImageData
- * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
- * into a single RGB Pixels Plane
- * the (VTK) user will manage the palettes
+ * VTK users have to call GetImageData
*
* @param destination Address (in caller's memory space) at which the
* pixel data should be copied
- * @param MaxSize Maximum number of bytes to be copied. When MaxSize
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
* is not sufficient to hold the pixel data the copy is not
* executed (i.e. no partial copy).
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) {
-
- int nb, nbu, highBit, signe;
- std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
- PixelRead=1 ; // PixelRaw
-
- if ( lgrTotale > MaxSize ) {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
- }
-
- (void)ReadPixelData(destination);
-
- // Number of Bits Allocated for storing a Pixel
- str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
- // Number of Bits actually used
- str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
- if (str_nbu == GDCM_UNFOUND ) {
- nbu = nb;
- } else {
- nbu = atoi(str_nbu.c_str() );
- }
- // High Bit Position
- str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
- if (str_highBit == GDCM_UNFOUND ) {
- highBit = nb - 1;
- } else {
- highBit = atoi(str_highBit.c_str() );
- }
- // Pixel sign
- // 0 = Unsigned
- // 1 = Signed
- str_signe=Header->GetEntryByNumber(0x0028,0x0103);
- if (str_signe == GDCM_UNFOUND ) {
- signe = 0; // default is unsigned
- } else {
- signe = atoi(str_signe.c_str() );
+size_t File::GetImageDataIntoVector (void *destination, size_t maxSize)
+{
+ if ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
}
- // re arange bytes inside the integer (processor endianity)
- if (nb != 8)
- SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
-
- // to avoid pb with some xmedcon breakers images
- if (nb==16 && nbu<nb && signe==0) {
- int l = (int)lgrTotale / (nb/8);
- guint16 *deb = (guint16 *)destination;
- for(int i = 0; i<l; i++) {
- if(*deb == 0xffff)
- *deb=0;
- deb++;
- }
- }
- // 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 ++;
- }
- } else {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
- return (size_t)0;
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
}
- }
-// DO NOT remove this commented out code .
-// Nobody knows what's expecting you ...
-// Just to 'see' what was actually read on disk :-(
-
-// FILE * f2;
-// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,lgrTotale,1,f2);
-// fclose(f2);
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
+ }
- // Deal with the color
- // -------------------
-
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
-
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
- return lgrTotale;
- }
-
- // Planar configuration = 0 : Pixels are already RGB
- // Planar configuration = 1 : 3 planes : R, G, B
- // Planar configuration = 2 : 1 gray Plane + 3 LUT
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelReadConverter->GetRawSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
+}
- // Well ... supposed to be !
- // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
- // PhotometricInterpretation=PALETTE COLOR
- // and heuristic has to be found :-(
+/**
+ * \brief Points the internal pointer to the callers inData
+ * image representation, BUT WITHOUT COPYING THE DATA.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \warning Since the pixels are not copied, it is the caller's responsability
+ * not to deallocate it's data before gdcm uses them (e.g. with
+ * the Write() method.
+ * @param inData user supplied pixel area
+ * @param expectedSize total image size, in Bytes
+ *
+ * @return boolean
+ */
+void File::SetImageData(uint8_t *inData, size_t expectedSize)
+{
+ SetUserData(inData,expectedSize);
+}
- int planConf=Header->GetPlanarConfiguration(); // 0028,0006
+/**
+ * \brief Set the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+void File::SetUserData(uint8_t *data, size_t expectedSize)
+{
+ PixelWriteConverter->SetUserData(data,expectedSize);
+}
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if (str_PhotometricInterpretation == "PALETTE COLOR ")
- planConf=2;
+/**
+ * \brief Get the image datas defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+uint8_t *File::GetUserData()
+{
+ return PixelWriteConverter->GetUserData();
+}
- 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();
-
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *x = newDest;
- unsigned char *a = (unsigned char *)destination;
- unsigned char *b = a + l;
- unsigned char *c = b + l;
- 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++) = (unsigned char)R;
- *(x++) = (unsigned char)G;
- *(x++) = (unsigned char)B;
- a++; b++; c++;
- }
- }
- memmove(destination,newDest,lgrTotale);
- 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();
-
- char *newDest = new char[lgrTotale];
- char *x = newDest;
- char *a = (char *)destination;
- char *b = a + l;
- char *c = b + l;
-
- for (int j=0;j<l; j++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination,newDest,lgrTotale);
- delete[] newDest;
- }
- break;
- }
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return lgrTotale;
- }
- // now, it's an RGB image
- // Lets's write it in the Header
+/**
+ * \brief Get the image data size defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+size_t File::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
+}
- // CreateOrReplaceIfExist ?
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+uint8_t *File::GetRGBData()
+{
+ return PixelReadConverter->GetRGB();
+}
- std::string spp = "3"; // Samples Per Pixel
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+size_t File::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
+}
- std::string planConfig = "0"; // Planar Configuration
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
+ */
+uint8_t *File::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
}
/**
- * \ingroup gdcmFile
- * \brief performs a shadow 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
- *
- * @return boolean
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are not expanded !
*/
-bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) {
- Header->SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- PixelRead = 1;
- return(true);
+size_t File::GetRawDataSize()
+{
+ return PixelReadConverter->GetRawSize();
}
/**
- * \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
+ * @return false if write fails
*/
-bool gdcmFile::WriteRawData (std::string fileName) {
- FILE *fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Fail to open (write) file [%s] \n",fileName.c_str());
- return (false);
- }
- fwrite (PixelData,lgrTotale, 1, fp1);
- fclose (fp1);
- return(true);
+bool File::WriteRawData(std::string const &fileName)
+{
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
+ {
+ dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
+ return false;
+ }
+
+ if(PixelWriteConverter->GetUserData())
+ fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize());
+ else if(PixelReadConverter->GetRGB())
+ fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize());
+ else if(PixelReadConverter->GetRaw())
+ fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize());
+
+ fp1.close();
+
+ 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
+ * @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string fileName) {
- return WriteBase(fileName, gdcmImplicitVR);
+bool File::WriteDcmImplVR (std::string const &fileName)
+{
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
}
/**
- * \ingroup gdcmFile
- * \brief Writes on disk A SINGLE Dicom file,
- * using the Implicit Value Representation convention
- * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
- */
-
-bool gdcmFile::WriteDcmImplVR (const char *fileName) {
- return WriteDcmImplVR (std::string (fileName));
-}
-
-/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the Explicit Value Representation convention
- * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
+ * NO test is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
* (any already existing file is overwritten)
- * @return false if write fails
+ * @return false if write fails
*/
-bool gdcmFile::WriteDcmExplVR (std::string fileName) {
- return WriteBase(fileName, gdcmExplicitVR);
+bool File::WriteDcmExplVR (std::string const &fileName)
+{
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
-
+
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the ACR-NEMA convention
* NO test is performed on processor "Endiannity".
* \warning NO TEST is performed on processor "Endiannity".
* @param fileName name of the file to be created
* (any already existing file is overwritten)
- * @return false if write fails
+ * @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string fileName) {
- return WriteBase(fileName, gdcmACR);
+bool File::WriteAcr (std::string const &fileName)
+{
+ SetWriteTypeToAcr();
+ return Write(fileName);
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \ingroup gdcmFile
- * \brief NOT a end user inteded function
- * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
+ * \brief Writes on disk A SINGLE Dicom file,
* @param fileName name of the file to be created
* (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
- * @return false if write fails
+ * @return false if write fails
*/
-bool gdcmFile::WriteBase (std::string fileName, FileType type) {
-
- FILE *fp1;
-
- if (PixelRead==-1 && type != gdcmExplicitVR) {
- return false;
- }
-
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Failed to open (write) File [%s] \n",fileName.c_str());
- return (false);
- }
-
- if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) {
- char *filePreamble;
- // writing Dicom File Preamble
- filePreamble=new char[128];
- memset(filePreamble,0,128);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- delete[] filePreamble;
+bool File::Write(std::string const &fileName)
+{
+ switch(WriteType)
+ {
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
+ break;
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
+ break;
+ case ACR:
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACR();
+ break;
+ default:
+ SetWriteFileTypeToExplicitVR();
}
// --------------------------------------------------------------
// if recognition code tells us we dealt with a LibIDO image
// we reproduce on disk the switch between lineNumber and columnNumber
// just before writting ...
-
/// \todo the best trick would be *change* the recognition code
/// but pb expected if user deals with, e.g. COMPLEX images
-
- std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO){
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
- }
+ if( WriteType == ACR_LIBIDO )
+ {
+ SetWriteToLibido();
+ }
+ else
+ {
+ SetWriteToNoLibido();
+ }
// ----------------- End of Special Patch ----------------
-
- /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only)
-
- guint16 grPixel =Header->GetGrPixel();
- guint16 numPixel=Header->GetNumPixel();;
-
- // Update Pixel Data Length
- // the *last* of the (GrPixel, NumPixel), if many.
-
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
- TagDocEntryHT::iterator p2;
- gdcmDocEntry *PixelElement;
-
- IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ SetWriteToRaw();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
+ }
- if (Header->GetEntry().count(key) == 1) // only the first is significant
- p2=it.first; // iterator on the first (unique) synonym
- else
- p2=it.second;// iterator on the last synonym
-
- PixelElement=p2->second; // H Table target column (2-nd col)
- // PixelElement->SetPrintLevel(2);
- // PixelElement->Print();
-
- if (PixelRead==1)
- PixelElement->SetLength(lgrTotaleRaw);
- else if (PixelRead==0)
- PixelElement->SetLength(lgrTotale);
-
- //PixelElement->SetPrintLevel(2);
- //PixelElement->Print();
- Header->Write(fp1, type);
+ bool check = CheckWriteIntegrity();
+ if(check)
+ {
+ check = HeaderInternal->Write(fileName,WriteType);
+ }
+
+ RestoreWrite();
+ RestoreWriteFileType();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//
// ...and we restore the Header to be Dicom Compliant again
// just after writting
-
- if (Header->GetFileType() == gdcmACR_LIBIDO){
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
- }
+ RestoreWriteOfLibido();
// ----------------- End of Special Patch ----------------
-
- fwrite(PixelData, lgrTotale, 1, fp1);
- fclose (fp1);
- return(true);
+
+ return check;
}
-//-----------------------------------------------------------------------------
-// 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
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (string) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
*/
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
-
-if(nb == 16)
- switch(swap) {
- case 0:
- case 12:
- case 1234:
- break;
-
- case 21:
- case 3412:
- case 2143:
- case 4321:
-
- for(i=0;i<lgr/2;i++) {
- ((unsigned short int *)im)[i]= ((((unsigned short int *)im)[i])>>8)
- | ((((unsigned short int *)im)[i])<<8);
- }
- break;
-
- default:
- printf("SWAP value (16 bits) not allowed : %d\n", swap);
- }
-
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
+bool File::SetEntryByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,group,element);
+}
- case 4321:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 4321 */
- fort =((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
- case 2143:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 2143 */
- fort=((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=fort;
- ((unsigned long int *)im)[i]=(s32<<16)|faible;
- }
- break;
-
- case 3412:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 3412 */
- fort=((unsigned long int *)im)[i]>>16;
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
-
- default:
- printf("SWAP value (32 bits) not allowed : %d\n", swap);
- }
-return;
+/**
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param lgth new value length
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
+ */
+bool File::SetEntryByNumber(uint8_t *content, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,lgth,group,element);
}
/**
- * \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 Modifies the value of a given Doc Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param content (string) Value to be set
+ * @param group Group number of the Entry
+ * @param element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreateByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL;
+}
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
+ * @param binArea (binary) value to be set
+ * @param group Group number of the Entry
+ * @param element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
*/
-bool gdcmFile::ReadPixelData(void *destination) {
+bool File::ReplaceOrCreateByNumber(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL;
+}
- FILE *fp;
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelReadConverter->GetLutRGBA();
+}
- if ( !(fp=Header->OpenFile()))
- return false;
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
- Header->CloseFile();
- return false;
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief Check the write integrity
+ *
+ * The tests made are :
+ * - verify the size of the image to write with the possible write
+ * when the user set an image data
+ * @return true if the check successfulls
+ */
+bool File::CheckWriteIntegrity()
+{
+ if(PixelWriteConverter->GetUserData())
+ {
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
+
+ size_t decSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+ size_t rgbSize = decSize;
+ if( HeaderInternal->HasLUT() )
+ rgbSize = decSize * 3;
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ if( decSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
+ }
+ break;
+ case WMODE_RGB :
+ if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
+ }
+ break;
+ }
}
- // ---------------------- 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();
- unsigned char b0, b1, b2;
-
- unsigned short int *pdestination = (unsigned short int*)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 ?
+ return true;
+}
+
+void File::SetWriteToRaw()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
+ {
+ SetWriteToRGB();
+ }
+ else
+ {
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
+ {
+ photInt->SetValue("PALETTE COLOR ");
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
}
- 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);
- if ( ItemRead != 1 ) {
- Header->CloseFile();
- return false;
- } else {
- Header->CloseFile();
- return true;
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+
+ BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
+
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+ }
+}
+
+void File::SetWriteToRGB()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ {
+ PixelReadConverter->BuildRGBImage();
+
+ ValEntry *spp = CopyValEntry(0x0028,0x0002);
+ spp->SetValue("3 ");
+
+ ValEntry *planConfig = CopyValEntry(0x0028,0x0006);
+ planConfig->SetValue("0 ");
+
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("RGB ");
+
+ if(PixelReadConverter->GetRGB())
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
+ }
+ else // Raw data
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
}
- }
- // ---------------------- Run Length Encoding
- if (Header->IsRLELossLessTransferSyntax()) {
- bool res = (bool)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 ?
+ BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
+
+ Archive->Push(spp);
+ Archive->Push(planConfig);
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+
+ // Remove any LUT
+ Archive->Push(0x0028,0x1101);
+ Archive->Push(0x0028,0x1102);
+ Archive->Push(0x0028,0x1103);
+ Archive->Push(0x0028,0x1201);
+ Archive->Push(0x0028,0x1202);
+ Archive->Push(0x0028,0x1203);
+
+ // For old ACR-NEMA
+ // Thus, we have a RGB image and the bits allocated = 24 and
+ // samples per pixels = 1 (in the read file)
+ if(HeaderInternal->GetBitsAllocated()==24)
+ {
+ ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100);
+ bitsAlloc->SetValue("8 ");
+
+ ValEntry *bitsStored = CopyValEntry(0x0028,0x0101);
+ bitsStored->SetValue("8 ");
+
+ ValEntry *highBit = CopyValEntry(0x0028,0x0102);
+ highBit->SetValue("7 ");
+
+ Archive->Push(bitsAlloc);
+ Archive->Push(bitsStored);
+ Archive->Push(highBit);
+ }
}
+ else
+ {
+ SetWriteToRaw();
+ }
+}
- 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;
- guint16 ItemTagGr,ItemTagEl;
- int ln;
-
- // Position on begining of Jpeg Pixels
+void File::RestoreWrite()
+{
+ Archive->Restore(0x0028,0x0002);
+ Archive->Restore(0x0028,0x0004);
+ Archive->Restore(0x0028,0x0006);
+ Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+
+ // For old ACR-NEMA (24 bits problem)
+ Archive->Restore(0x0028,0x0100);
+ Archive->Restore(0x0028,0x0101);
+ Archive->Restore(0x0028,0x0102);
+
+ // For the LUT
+ Archive->Restore(0x0028,0x1101);
+ Archive->Restore(0x0028,0x1102);
+ Archive->Restore(0x0028,0x1103);
+ Archive->Restore(0x0028,0x1201);
+ Archive->Restore(0x0028,0x1202);
+ Archive->Restore(0x0028,0x1203);
+}
+
+void File::SetWriteFileTypeToACR()
+{
+ Archive->Push(0x0002,0x0010);
+}
+
+void File::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
+}
+
+void File::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(Header->GetSwapCode()) {
- ItemTagGr=Header->SwapShort(ItemTagGr);
- ItemTagEl=Header->SwapShort(ItemTagEl);
+ if( oldRow && oldCol )
+ {
+ std::string rows, columns;
+
+ ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
+ ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+
+ newRow->Copy(oldCol);
+ newCol->Copy(oldRow);
+
+ newRow->SetValue(oldCol->GetValue());
+ newCol->SetValue(oldRow->GetValue());
+
+ Archive->Push(newRow);
+ Archive->Push(newCol);
}
- fread(&ln,4,1,fp);
- if(Header->GetSwapCode())
- ln=Header->SwapLong(ln); // Basic Offset Table Item length
-
- if (ln != 0) {
- // What is it used for ?!?
- char *BasicOffsetTableItemValue = new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
+
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ Archive->Push(libidoCode);
+}
+
+void File::SetWriteToNoLibido()
+{
+ ValEntry *recCode = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010));
+ if( recCode )
+ {
+ if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ {
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("");
+ Archive->Push(libidoCode);
+ }
}
-
- // 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);
+}
+
+void File::RestoreWriteOfLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+ Archive->Restore(0x0008,0x0010);
+}
+
+ValEntry *File::CopyValEntry(uint16_t group,uint16_t element)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ ValEntry *newE;
+
+ if(oldE)
+ {
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
}
-
- // 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 = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
-
- } // ------------------------------------- endif (JPEG2000)
-
- else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
-
- JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
- (unsigned short *)destination,
- Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(),
- ln);
- res=1; // in order not to break the loop
-
- } // ------------------------------------- endif (JPEGLossless)
-
- else { // JPEG Lossy : call to IJG 6b
-
- if (Header->GetBitsStored() == 8) {
- res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
- }
- } // ------------------------------------- endif (JPEGLossy)
-
- if (!res) break;
-
- destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
-
- fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
-
- 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;
+ else
+ {
+ newE = GetHeader()->NewValEntryByNumber(group,element);
+ }
+
+ return(newE);
+}
+
+BinEntry *File::CopyBinEntry(uint16_t group,uint16_t element)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ BinEntry *newE;
+
+ if(oldE)
+ {
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntryByNumber(group,element);
+ }
+
+ return(newE);
}
+
//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
+{
+ WriteMode = WMODE_RAW;
+ WriteType = ExplicitVR;
+
+ PixelReadConverter = new PixelReadConvert;
+ PixelWriteConverter = new PixelWriteConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ }
+}
+
+uint8_t *File::GetRaw()
+{
+ uint8_t *raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ // The Raw image migth not be loaded yet:
+ std::ifstream *fp = HeaderInternal->OpenFile();
+ PixelReadConverter->ReadAndDecompressPixelData( fp );
+ if(fp)
+ HeaderInternal->CloseFile();
+
+ raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ dbg.Verbose(0, "File::GetRaw: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
+ }
+ }
+
+ return raw;
+}
+
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
+} // end namespace gdcm
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff