Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/06/25 17:48:45 $
- Version: $Revision: 1.110 $
+ Date: $Date: 2004/06/26 04:09:33 $
+ Version: $Revision: 1.111 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* @param header file to be opened for reading datas
* @return
*/
-gdcmFile::gdcmFile(gdcmHeader *header) {
- Header=header;
- SelfHeader=false;
- PixelRead=-1; // no ImageData read yet.
+gdcmFile::gdcmFile(gdcmHeader *header)
+{
+ Header = header;
+ SelfHeader = false;
+ PixelRead = -1; // no ImageData read yet.
if (Header->IsReadable())
+ {
SetPixelDataSizeFromHeader();
+ }
}
/**
gdcmFile::gdcmFile(std::string const & 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())
+ 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();
+ }
}
/**
* \note If the gdcmHeader is created by the gdcmFile, it is destroyed
* by the gdcmFile
*/
-gdcmFile::~gdcmFile() {
- if(SelfHeader)
+gdcmFile::~gdcmFile()
+{
+ if( SelfHeader )
+ {
delete Header;
- Header=NULL;
+ }
+ Header = 0;
}
//-----------------------------------------------------------------------------
* (no interest for compressed images).
* @return length to allocate
*/
-void gdcmFile::SetPixelDataSizeFromHeader() {
+void gdcmFile::SetPixelDataSizeFromHeader()
+{
// see PS 3.3-2003 : C.7.6.3.2.1
//
// MONOCHROME1
// 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;
- str_nb=Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
+ 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;
+ }
+ else
+ {
+ nb = atoi( str_nb.c_str() );
+ if (nb == 12)
+ {
+ nb =16;
+ }
}
- lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize()
- * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
+ 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()) {
- lgrTotale*=3;
+ if ( Header->HasLUT() )
+ {
+ ImageDataSize *= 3;
}
}
* the pixel data represented in this file.
* @return The size of pixel data in bytes.
*/
-size_t gdcmFile::GetImageDataSize() {
- return lgrTotale;
+size_t gdcmFile::GetImageDataSize()
+{
+ return ImageDataSize;
}
/**
* \warning to be used with GetImagePixelsRaw()
* @return The size of pixel data in bytes.
*/
-size_t gdcmFile::GetImageDataSizeRaw() {
- return lgrTotaleRaw;
+size_t gdcmFile::GetImageDataSizeRaw()
+{
+ return ImageDataSizeRaw;
}
/**
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-void * gdcmFile::GetImageData () {
- PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector
- if (PixelData) {
- GetImageDataIntoVector(PixelData, lgrTotale);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(),
- GetHeader()->GetNumPixel());
+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
+ PixelRead = 0; // no PixelRaw
return PixelData;
}
* @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;
+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
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *a = (unsigned char *)destination;
- unsigned char *lutRGBA = Header->GetLUTRGBA();
+ uint8_t *newDest = new uint8_t[ImageDataSize];
+ uint8_t *a = (uint8_t *)destination;
+ uint8_t *lutRGBA = Header->GetLUTRGBA();
- if (lutRGBA) {
- int l = lgrTotaleRaw;
- memmove(newDest, destination, l);// move Gray pixels to temp area
+ if ( lutRGBA )
+ {
int j;
- for (int i=0;i<l; i++) { // Build RGB Pixels
- j=newDest[i]*4;
- *a++ = lutRGBA[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];
}
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
+ }
+ else //why is there a 'else' when an allocation failed ?
+ {
+ // need to make RGB Pixels (?)
+ // from grey Pixels (?!)
+ // and Gray Lut (!?!)
+ // or Segmented xxx Palette Color Lookup Table Data and so on
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage such an image
- // It seems that *no Dicom Viewer* has any idea :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
+ // 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
+ std::string rgb = "MONOCHROME1 "; // Photometric Interpretation
Header->SetEntryByNumber(rgb,0x0028,0x0004);
}
+
/// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ return ImageDataSize;
}
/**
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-void * gdcmFile::GetImageDataRaw () {
- if (Header->HasLUT())
+void * gdcmFile::GetImageDataRaw ()
+{
+ size_t imgDataSize;
+ if ( Header->HasLUT() )
+ {
/// \todo Let gdcmHeader user a chance to get the right value
- /// Create a member lgrTotaleRaw ???
- lgrTotale /= 3;
- PixelData = new unsigned char[lgrTotale];
+ // ImageDataSize /= 3; //dangerous
+ imgDataSize = ImageDataSizeRaw;
+ }
- if (PixelData) {
- GetImageDataIntoVectorRaw(PixelData, lgrTotale);
+ // 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());
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
}
- PixelRead=1; // PixelRaw
+ PixelRead = 1; // PixelRaw
return PixelData;
}
* @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
+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;
+ return (size_t)0;
}
- ReadPixelData(destination);
+ ReadPixelData( destination );
// Number of Bits Allocated for storing a Pixel
- str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
+ std::string 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 ) {
+ }
+ 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() );
+ }
+ else
+ {
+ nbu = atoi( str_nbu.c_str() );
}
+
// High Bit Position
- str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
- if (str_highBit == GDCM_UNFOUND ) {
+ std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102);
+ if ( str_highBit == GDCM_UNFOUND )
+ {
highBit = nb - 1;
- } else {
- highBit = atoi(str_highBit.c_str() );
+ }
+ 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() );
+ std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103);
+ if ( str_sign == GDCM_UNFOUND )
+ {
+ sign = 0; // default is unsigned
+ }
+ else
+ {
+ sign = atoi( str_sign.c_str() );
}
// re arange bytes inside the integer (processor endianity)
- if (nb != 8)
- SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
+ if ( nb != 8 )
+ {
+ SwapZone(destination, Header->GetSwapCode(), ImageDataSize, 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++;
+ if ( nb == 16 && nbu < nb && sign == 0)
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ uint16_t *deb = (uint16_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
}
- }
+ deb++;
+ }
+ }
+
// re arange bits inside the bytes
- if (nbu != nb){
- int l = (int)lgrTotale / (nb/8);
- if (nb == 16) {
- guint16 mask = 0xffff;
+ if ( nbu != nb )
+ {
+ int l = (int)(ImageDataSize / (nb/8));
+ if ( nb == 16 )
+ {
+ uint16_t mask = 0xffff;
mask = mask >> (nb-nbu);
- guint16 *deb = (guint16 *)destination;
- for(int i = 0; i<l; i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
+ uint16_t *deb = (uint16_t *)destination;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ deb++;
}
- } else if (nb == 32 ) {
+ }
+ else if ( nb == 32 )
+ {
guint32 mask = 0xffffffff;
- mask = mask >> (nb-nbu);
+ mask = mask >> (nb - nbu);
guint32 *deb = (guint32 *)destination;
- for(int i = 0; i<l; i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ deb++;
}
- } else {
+ }
+ else
+ {
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
return 0;
}
- }
-// DO NOT remove this commented out code .
+ }
+// DO NOT remove this code commented out.
// Nobody knows what's expecting you ...
// Just to 'see' what was actually read on disk :-(
// FILE * f2;
// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,lgrTotale,1,f2);
+// fwrite(destination,ImageDataSize,1,f2);
// fclose(f2);
// Deal with the color
// -------------------
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
- return lgrTotale;
- }
+ if ( str_PhotometricInterpretation == "MONOCHROME1 "
+ || str_PhotometricInterpretation == "MONOCHROME2 " )
+ {
+ return ImageDataSize;
+ }
// Planar configuration = 0 : Pixels are already RGB
// Planar configuration = 1 : 3 planes : R, G, B
// PhotometricInterpretation=PALETTE COLOR
// and heuristic has to be found :-(
- int planConf=Header->GetPlanarConfiguration(); // 0028,0006
+ 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;
+ // Whatever Planar Configuration is,
+ // "PALETTE COLOR " implies that we deal with the palette.
+ if ( str_PhotometricInterpretation == "PALETTE COLOR ")
+ {
+ planConf = 2;
+ }
- switch (planConf) {
- case 0:
- // Pixels are already RGB
+ switch ( planConf )
+ {
+ case 0:
+ // Pixels are already RGB
break;
-
case 1:
-
+ if (str_PhotometricInterpretation == "YBR_FULL")
{
- 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();
+ // 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;
+ 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
/// 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;
+ for (int i = 0; i < nbFrames; i++)
+ {
+ for (int j = 0; j < l; j++)
+ {
+ R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R < 0.0) R = 0.0;
+ if (G < 0.0) G = 0.0;
+ if (B < 0.0) B = 0.0;
+ if (R > 255.0) R = 255.0;
+ if (G > 255.0) G = 255.0;
+ if (B > 255.0) B = 255.0;
+
+ *(x++) = (uint8_t)R;
+ *(x++) = (uint8_t)G;
+ *(x++) = (uint8_t)B;
a++; b++; c++;
}
- }
- memmove(destination,newDest,lgrTotale);
+ }
+ memmove(destination, newDest, ImageDataSize);
delete[] newDest;
+ }
+ else
+ {
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
- } 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();
+ 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;
+ 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++) {
+ for (int j = 0; j < l; j++)
+ {
*(x++) = *(a++);
*(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination,newDest,lgrTotale);
+ *(x++) = *(c++);
+ }
+ memmove(destination, newDest, ImageDataSize);
delete[] newDest;
- }
+ }
break;
- }
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return lgrTotale;
- }
+ case 2:
+ // Palettes were found
+ // Let the user deal with them !
+ return ImageDataSize;
+ }
// now, it's an RGB image
// Lets's write it in the Header
// CreateOrReplaceIfExist ?
std::string spp = "3"; // Samples Per Pixel
+ std::string rgb = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+
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);
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ /// \todo Drop Palette Color out of the Header?
+ return ImageDataSize;
}
/**
*
* @return boolean
*/
-bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) {
- Header->SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- PixelRead = 1;
+bool gdcmFile::SetImageData(void *inData, size_t expectedSize)
+{
+ Header->SetImageDataSize( expectedSize );
+ PixelData = inData;
+ ImageDataSize = expectedSize;
+ PixelRead = 1;
return true;
}
* @return false if write fails
*/
-bool gdcmFile::WriteRawData (std::string const & fileName) {
+bool gdcmFile::WriteRawData(std::string const & fileName)
+{
FILE *fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Fail to open (write) file [%s] \n",fileName.c_str());
+ 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);
+ fwrite (PixelData,ImageDataSize, 1, fp1);
fclose (fp1);
return true;
* @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string const & fileName) {
+bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+{
return WriteBase(fileName, gdcmImplicitVR);
}
* @return false if write fails
*/
-bool gdcmFile::WriteDcmExplVR (std::string const & fileName) {
+bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+{
return WriteBase(fileName, gdcmExplicitVR);
}
* @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string const & fileName) {
+bool gdcmFile::WriteAcr (std::string const & fileName)
+{
return WriteBase(fileName, gdcmACR);
}
* @param type file type (ExplicitVR, ImplicitVR, ...)
* @return false if write fails
*/
-bool gdcmFile::WriteBase (std::string const & fileName, FileType type) {
-
+bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+{
FILE *fp1;
-
- if (PixelRead==-1 && type != gdcmExplicitVR) {
+
+ 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);
+ 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;
+ if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ {
// writing Dicom File Preamble
- filePreamble=new char[128];
- memset(filePreamble,0,128);
- 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;
}
/// 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 ( Header->GetFileType() == gdcmACR_LIBIDO)
+ {
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
+
+ Header->SetEntryByNumber(columns, 0x0028, 0x0010);
+ Header->SetEntryByNumber(rows , 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
/// \todo get the grPixel, numPixel values (for some ACR-NEMA images only)
- guint16 grPixel =Header->GetGrPixel();
- guint16 numPixel=Header->GetNumPixel();;
+ uint16_t grPixel = Header->GetGrPixel();
+ uint16_t 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;
+ gdcmDocEntry* PixelElement;
- IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
+ IterHT it = Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
- if (Header->GetEntry().count(key) == 1) // only the first is significant
- p2=it.first; // iterator on the first (unique) synonym
+ 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
+ {
+ p2 = it.second;// iterator on the last synonym
+ }
- PixelElement=p2->second; // H Table target column (2-nd col)
+ 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);
+ if ( PixelRead == 1 )
+ {
+ PixelElement->SetLength( ImageDataSizeRaw );
+ }
+ else if ( PixelRead == 0 )
+ {
+ PixelElement->SetLength( ImageDataSize );
+ }
//PixelElement->SetPrintLevel(2);
//PixelElement->Print();
// ...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);
+ if ( Header->GetFileType() == gdcmACR_LIBIDO )
+ {
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
- // fwrite(PixelData, lgrTotale, 1, fp1); // should be useless, now
+ // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now
fclose (fp1);
return true;
* @param lgr Area Length
* @param nb Pixels Bit number
*/
-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:
- std::cout << "SWAP value (16 bits) not allowed :i" << swap << std::endl;
- }
-
- if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
-
- 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:
- std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl;
- }
+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;
+ }
+ }
}
/**
* @param destination where the pixel data should be stored.
*
*/
-bool gdcmFile::ReadPixelData(void *destination) {
+bool gdcmFile::ReadPixelData(void *destination)
+{
+ FILE *fp = Header->OpenFile();
- FILE *fp;
-
- if ( !(fp=Header->OpenFile()))
+ if ( !fp )
+ {
return false;
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+ }
+ 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] */
+ // unpack 12 Bits pixels into 16 Bits pixels
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
- if (Header->GetBitsAllocated()==12) {
+ if ( Header->GetBitsAllocated() == 12 )
+ {
int nbPixels = Header->GetXSize() * Header->GetYSize();
- unsigned char b0, b1, b2;
+ uint8_t b0, b1, b2;
- unsigned short int *pdestination = (unsigned short int*)destination;
- for(int p=0;p<nbPixels;p+=2) {
+ 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 */
+ // A B D
*pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- /* F */ /* C */ /* E */
+ // F C E
- // Troubles expected on Big-Endian processors ?
+ // Troubles expected on Big-Endian processors ?
}
Header->CloseFile();
return true;
- }
+ }
// ---------------------- Uncompressed File
if ( !Header->IsDicomV3() ||
Header->IsImplicitVRLittleEndianTransferSyntax() ||
Header->IsExplicitVRLittleEndianTransferSyntax() ||
Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ {
size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- if ( ItemRead != 1 ) {
- Header->CloseFile();
+ Header->CloseFile();
+ if ( ItemRead != 1 )
+ {
return false;
- } else {
- Header->CloseFile();
+ }
+ else
+ {
return true;
}
- }
+ }
// ---------------------- Run Length Encoding
- if (Header->IsRLELossLessTransferSyntax()) {
+ 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 ) {
+ 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 ?
+ }
+ 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();
+ * Header->GetSamplesPerPixel();
long fragmentBegining; // for ftell, fseek
- bool jpg2000 = Header->IsJPEG2000();
+ bool jpg2000 = Header->IsJPEG2000();
bool jpgLossless = Header->IsJPEGLossless();
bool res = true;
- guint16 ItemTagGr,ItemTagEl;
+ 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);
+ 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) {
+
+ 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);
+ 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);
+ if( Header->GetSwapCode() )
+ {
+ ItemTagGr = Header->SwapShort( ItemTagGr );
+ ItemTagEl = Header->SwapShort( ItemTagEl );
}
-
+
// parsing fragments until Sequence Delim. Tag found
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ 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 );
- 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
+ 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 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 = (bool)gdcm_read_JPEG_file (fp,destination);
+ }
+ else
+ {
+ // Reading Fragment pixels
+ res = (bool)gdcm_read_JPEG_file12 (fp,destination);
+ }
+ // ------------------------------------- endif (JPEGLossy)
+ }
+
+ if ( !res )
+ {
+ break;
+ }
- 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
+ // 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;
+ 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
-
+ 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 / commitdiff