Program: gdcm
Module: $RCSfile: RawToDicomStack.cxx,v $
Language: C++
- Date: $Date: 2008/06/12 13:26:39 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2009/01/19 17:05:13 $
+ Version: $Revision: 1.4 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <iostream>
#include <sstream>
-typedef char * PS8;
-typedef unsigned char * PU8;
-typedef short int * PS16;
+typedef char * PS8;
+typedef unsigned char * PU8;
+typedef short int * PS16;
typedef unsigned short int * PU16;
-typedef int * PS32;
-typedef unsigned int * PU32;
-
-#define CRR(t1,t2) { for(int i=0;i<nY;i++) \
- for(int j=0;j<nX;j++) \
- for(int k=0;k<samplesPerPixel;k++) \
- *((t2)planePixels + i*nX +j+k) = *(((t1)pixels)+ nbPlanes*nX*nY + i*nX +j+k);\
- }
+typedef int * PS32;
+typedef unsigned int * PU32;
+typedef float * PF32;
+typedef double * PD64;
+
+#define CRR(t1,t2) { for(int i=0;i<nY;i++) \
+ for(int j=0;j<nX;j++) \
+ for(int k=0;k<samplesPerPixel;k++) {\
+ *((t2)planePixelsOut + i*nX +j+k) = *(((t1)pixels)+ nbPlanes*nX*nY + i*nX +j+k);\
+ } \
+ }
#define CFR(PPt) switch ( pixelTypeOutCode ) { \
- case -8 : CRR(PPt,PS8); break; \
- case 8 : CRR(PPt,PU8); break; \
+ case -8 : CRR(PPt,PS8); break; \
+ case 8 : CRR(PPt,PU8); break; \
case -16 : CRR(PPt,PS16); break; \
case 16 : CRR(PPt,PU16); break; \
case -32 : CRR(PPt,PS32); break; \
case 32 : CRR(PPt,PU32); break; \
+ case 33 : CRR(PPt,PF32); break; \
+ case 64 : CRR(PPt,PD64); break; \
}
for( i = 0; i < RawSize / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
+ }
}
else if ( pixelSize == 4 )
{
" rows=nb of Rows ",
" lines=nb of Lines, ",
" [frames = nb of Frames] //defaulted to 1 ",
- " pixeltype={8U|8S|16U|16S|32U|32S} ",
- " pixeltypeout={8U|8S|16U|16S|32U|32S} ",
+ " pixeltype={8U|8S|16U|16S|32U|32S|32F|64D} ",
+ " pixeltypeout={8U|8S|16U|16S|32U|32S} ",
" [{b|l}] b:BigEndian,l:LittleEndian default : l ",
" [samples = {1|3}} //(1:Gray,3:RGB) defaulted to 1",
" [monochrome1] ",
" [studyid = ] [patientname = Patient's name] ",
" [debug] ",
" ",
- " monochrome1 = user wants MONOCHROME1 photom. interp. (0=white) ",
+ " monochrome1 = user wants MONOCHROME1 photom. interp. (0=white) ",
" studyUID : *aware* user wants to add the serie ",
" to an already existing study ",
" debug : developper wants to run the program in 'debug mode' ",
const char *inputFileName = am->ArgMgrGetString("filein");
const char *outputSkeletonFileName = am->ArgMgrGetString("fileout");
- const char *patientName = am->ArgMgrGetString("patientname", "g^Fantomas");
+ const char *patientName = am->ArgMgrGetString("patientname", "g^Fantomas");
int nX = am->ArgMgrWantInt("rows", usage);
int nY = am->ArgMgrWantInt("lines", usage);
int l = am->ArgMgrDefined("l");
char *pixelType = am->ArgMgrWantString("pixeltype", usage);
-
const char *pixelTypeOut = am->ArgMgrGetString("pixeltypeout", pixelType);
bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
// ----------- End Arguments Manager ---------
/// \TODO Deal with all the images of a directory
-
- // Read the Raw file
+
+ // Read the Raw file
std::ifstream *Fp = new std::ifstream(inputFileName, std::ios::in | std::ios::binary);
if ( ! *Fp )
- {
+ {
std::cout << "Cannot open file: " << inputFileName;
delete Fp;
Fp = 0;
return 0;
- }
+ }
bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
{
pixelSize = 1;
pixelSign = 0;
- pixelTypeCode = 8;
+ pixelTypeCode = 8;
}
else if (strPixelType == "16S")
{
{
pixelSize = 4;
pixelSign = 1;
- pixelTypeCode = -32;
+ pixelTypeCode = -32;
}
else if (strPixelType == "32U")
{
pixelSize = 4;
pixelSign = 0;
- pixelTypeCode = 32;
+ pixelTypeCode = 32;
+ }
+ else if (strPixelType == "32F")
+ {
+ pixelSize = 4;
+ pixelSign = 0;
+ pixelTypeCode = 33;
+ }
+
+ else if (strPixelType == "64D")
+ {
+ pixelSize = 8;
+ pixelSign = 0;
+ pixelTypeCode = 64;
}
else
{
std::string strPixelTypeOut(pixelTypeOut);
int pixelSignOut;
int pixelSizeOut;
- int pixelTypeOutCode; // for the swirch case
+ int pixelTypeOutCode; // for the switch case
if (strPixelTypeOut == "8S")
{
std::cout << "Wrong 'pixeltypeout' (" << strPixelTypeOut << ")" << std::endl;
return 1;
}
-
+
std::string strStudyUID;
std::string strSerieUID;
// Read the pixels
int singlePlaneDataSize = nX*nY*samplesPerPixel*pixelSizeOut;
- int dataSize = singlePlaneDataSize*nZ;
+ int dataSizeIn = nX*nY*samplesPerPixel*pixelSize*nZ;
+
+ uint8_t *pixels = new uint8_t[dataSizeIn];
+ uint8_t *planePixelsOut = new uint8_t[singlePlaneDataSize];
+
+ Fp->read((char*)pixels, (size_t)dataSizeIn);
- uint8_t *pixels = new uint8_t[dataSize];
- uint8_t *planePixels = new uint8_t[singlePlaneDataSize];
-
- Fp->read((char*)pixels, (size_t)dataSize);
-
if ( pixelSize !=1 && ( (l && bigEndian) || (b && ! bigEndian) ) )
{
- ConvertSwapZone(pixelSize, pixels, dataSize);
+ ConvertSwapZone(pixelSize, pixels, dataSizeIn);
}
// iterate on the planes.
char outputFileName[200];
-
-for(int nbPlanes=0; nbPlanes<nZ; nbPlanes++)
-{
-sprintf(outputFileName, "%s.%04d.dcm", outputSkeletonFileName,nbPlanes);
+ for(int nbPlanes=0; nbPlanes<nZ; nbPlanes++)
+ {
+
+ sprintf(outputFileName, "%s.%04d.dcm", outputSkeletonFileName,nbPlanes);
// Copy (and convert) pixels of a single plane
- switch ( pixelTypeCode ) {
- case 8 : CFR(PU8); break;
- case -8 : CFR(PS8); break;
- case -16 : CFR(PU16); break;
- case 16 : CFR(PS16); break;
- case -32 : CFR(PS32); break;
- case 32 : CFR(PU32); break;
- }
+ switch ( pixelTypeCode )
+ {
+ case 8 : CFR(PU8); break;
+ case -8 : CFR(PS8); break;
+ case -16 : CFR(PU16); break;
+ case 16 : CFR(PS16); break;
+ case -32 : CFR(PS32); break;
+ case 32 : CFR(PU32); break;
+ case 33 : CFR(PF32); break;
+ case 64 : CFR(PD64); break;
+ }
// Create an empty FileHelper
// Set the pixel type
str.str("");
- str << pixelSize*8;
+ str << pixelSizeOut*8;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0100, "US"); // Bits Allocated
str.str("");
- str << pixelSize*8;
+ str << pixelSizeOut*8;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "US"); // Bits Stored
str.str("");
- str << ( pixelSize*8 - 1 );
+ str << ( pixelSizeOut*8 - 1 );
fileToBuild->InsertEntryString(str.str(),0x0028,0x0102, "US"); // High Bit
str.str("");
str << pixelSign;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0103, "US"); // Pixel Representation
-
+
// If you deal with a Serie of images, as slices of a volume,
// it up to you to tell gdcm, for each image, what are the values of :
//
// 0020 0037 DS 6 Image Orientation (Patient)
str.str("");
- str << "0.0 \\ 0.0 \\" << nbPlanes;
+ str << "0.0 \\ 0.0 \\" << nbPlanes;
fileToBuild->InsertEntryString(str.str(),0x0020,0x0032, "DS");
str.str("");
fileH->SetPhotometricInterpretationToMonochrome1();
// Set the image Pixel Data (plane)
- fileH->SetImageData(planePixels,singlePlaneDataSize);
+ fileH->SetImageData(planePixelsOut,singlePlaneDataSize);
// Set the writting mode and write the image
fileH->SetWriteModeToRaw();
} // end iterate on the planes
delete[] pixels;
- delete[] planePixels;
+ delete[] planePixelsOut;
return 1;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff