# the following are utilities
#----------------------------
+ RawToInTagDicom
RawToDicomStack
PrintDicomDir
PrintFile
Program: gdcm
Module: $RCSfile: RawToDicom.cxx,v $
Language: C++
- Date: $Date: 2008/06/12 13:21:20 $
- Version: $Revision: 1.16 $
+ Date: $Date: 2009/01/19 17:05:13 $
+ Version: $Revision: 1.17 $
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 unsigned short int * PU16;
+typedef int * PS32;
+typedef unsigned int * PU32;
+typedef float * PF32;
+typedef double * PD64;
+
+#define CRR(t1,t2) { for(int l=0;l<nX*nY*nZ*samplesPerPixel;l++) \
+ *((t2)planePixelsOut + l) = *(((t1)pixels)+ l);\
+ }
+
+#define CFR(PPt) switch ( pixelTypeOutCode ) { \
+ 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; \
+ }
+
+
void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize);
void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize)
" rows=nb of Rows ",
" lines=nb of Lines, ",
" [frames = nb of Frames] //defaulted to 1 ",
- " pixeltype={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] ",
int l = am->ArgMgrDefined("l");
char *pixelType = am->ArgMgrWantString("pixeltype", usage);
+ const char *pixelTypeOut = am->ArgMgrGetString("pixeltypeout", pixelType);
bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
std::string strPixelType(pixelType);
int pixelSign;
int pixelSize;
+ int pixelTypeCode; // for the switch case
if (strPixelType == "8S")
{
pixelSize = 1;
pixelSign = 1;
+ pixelTypeCode = -8;
}
else if (strPixelType == "8U")
{
pixelSize = 1;
pixelSign = 0;
+ pixelTypeCode = 8;
}
else if (strPixelType == "16S")
{
pixelSize = 2;
pixelSign = 1;
+ pixelTypeCode = -16;
}
else if (strPixelType == "16U")
{
pixelSize = 2;
pixelSign = 0;
+ pixelTypeCode = 16;
}
else if (strPixelType == "32S")
{
pixelSize = 4;
pixelSign = 1;
+ pixelTypeCode = -32;
}
else if (strPixelType == "32U")
{
pixelSize = 4;
pixelSign = 0;
+ pixelTypeCode = 32;
+ }
+ else if (strPixelType == "32F")
+ {
+ pixelSize = 4;
+ pixelSign = 0;
+ pixelTypeCode = 33;
+ }
+
+ else if (strPixelType == "64D")
+ {
+ pixelSize = 8;
+ pixelSign = 0;
+ pixelTypeCode = 64;
}
else
{
return 1;
}
+ std::string strPixelTypeOut(pixelTypeOut);
+ int pixelSignOut;
+ int pixelSizeOut;
+ int pixelTypeOutCode; // for the switch case
+
+ if (strPixelTypeOut == "8S")
+ {
+ pixelSizeOut = 1;
+ pixelSignOut = 1;
+ pixelTypeOutCode = -8;
+ }
+ else if (strPixelTypeOut == "8U")
+ {
+ pixelSizeOut = 1;
+ pixelSignOut = 0;
+ pixelTypeOutCode = 8;
+ }
+ else if (strPixelTypeOut == "16S")
+ {
+ pixelSizeOut = 2;
+ pixelSignOut = 1;
+ pixelTypeOutCode = -16;
+ }
+ else if (strPixelTypeOut == "16U")
+ {
+ pixelSizeOut = 2;
+ pixelSignOut = 0;
+ pixelTypeOutCode = 16;
+ }
+ else if (strPixelTypeOut == "32S")
+ {
+ pixelSizeOut = 4;
+ pixelSignOut = 1;
+ pixelTypeOutCode = -32;
+ }
+ else if (strPixelTypeOut == "32U")
+ {
+ pixelSizeOut = 4;
+ pixelSignOut = 0;
+ pixelTypeOutCode = 32;
+ }
+ else
+ {
+ std::cout << "Wrong 'pixeltypeout' (" << strPixelTypeOut << ")" << std::endl;
+ return 1;
+ }
+
std::string strStudyUID;
std::string strSerieUID;
// Read the pixels
- int dataSize = nX*nY*nZ*samplesPerPixel*pixelSize;
+ int singlePlaneDataSize = nX*nY*samplesPerPixel*pixelSizeOut;
+ 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];
-
- Fp->read((char*)pixels, (size_t)dataSize);
-
if ( pixelSize !=1 && ( (l && bigEndian) || (b && ! bigEndian) ) )
{
- ConvertSwapZone(pixelSize, pixels, dataSize);
+ ConvertSwapZone(pixelSize, pixels, dataSizeIn);
}
+// 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;
+ case 33 : CFR(PF32); break;
+ case 64 : CFR(PD64); break;
+ }
+
// Create an empty FileHelper
GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New();
// 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
-
- str.str("");
- str << samplesPerPixel;
// 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 0032 DS 3 Image Position (Patient)
// 0020 0037 DS 6 Image Orientation (Patient)
+ str.str("");
+ str << "0.0 \\ 0.0 \\ 0.0";
+ fileToBuild->InsertEntryString(str.str(),0x0020,0x0032, "DS");
+
+ str.str("");
+ str << samplesPerPixel;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0002, "US"); // Samples per Pixel
if (strlen(patientName) != 0)
fileH->SetPhotometricInterpretationToMonochrome1();
// Set the image Pixel Data
- fileH->SetImageData(pixels,dataSize);
+ fileH->SetImageData(planePixelsOut,singlePlaneDataSize);
// Set the writting mode and write the image
fileH->SetWriteModeToRaw();
fileH->Delete();
delete[] pixels;
+ delete[] planePixelsOut;
return 1;
}
Program: gdcm
Module: $RCSfile: RawToDicomStack.cxx,v $
Language: C++
- Date: $Date: 2009/01/14 14:07:40 $
- Version: $Revision: 1.3 $
+ 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
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 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; \
for( i = 0; i < RawSize / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
+ }
}
else if ( pixelSize == 4 )
{
" lines=nb of Lines, ",
" [frames = nb of Frames] //defaulted to 1 ",
" pixeltype={8U|8S|16U|16S|32U|32S|32F|64D} ",
- " pixeltypeout={8U|8S|16U|16S|32U|32S} ",
+ " 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' ",
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;
- }
-
+ pixelTypeCode = 33;
+ }
+
else if (strPixelType == "64D")
{
pixelSize = 8;
pixelSign = 0;
- pixelTypeCode = 64;
+ pixelTypeCode = 64;
}
else
{
std::cout << "Wrong 'pixeltypeout' (" << strPixelTypeOut << ")" << std::endl;
return 1;
}
-
+
std::string strStudyUID;
std::string strSerieUID;
int dataSizeIn = nX*nY*samplesPerPixel*pixelSize*nZ;
uint8_t *pixels = new uint8_t[dataSizeIn];
- uint8_t *planePixelsOut = new uint8_t[singlePlaneDataSize];
-
+ uint8_t *planePixelsOut = new uint8_t[singlePlaneDataSize];
+
Fp->read((char*)pixels, (size_t)dataSizeIn);
if ( pixelSize !=1 && ( (l && bigEndian) || (b && ! bigEndian) ) )
{
- ConvertSwapZone(pixelSize, pixels, dataSizeIn);
+ ConvertSwapZone(pixelSize, pixels, dataSizeIn);
}
// iterate on the planes.
char outputFileName[200];
-
+
for(int nbPlanes=0; nbPlanes<nZ; nbPlanes++)
{
// Copy (and convert) pixels of a single plane
- switch ( pixelTypeCode )
+ switch ( pixelTypeCode )
{
case 8 : CFR(PU8); break;
case -8 : CFR(PS8); break;
case -32 : CFR(PS32); break;
case 32 : CFR(PU32); break;
case 33 : CFR(PF32); break;
- case 64 : CFR(PD64); break;
+ case 64 : CFR(PD64); break;
}
// Create an empty FileHelper
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("");
Program: gdcm
Module: $RCSfile: ToInTag.cxx,v $
Language: C++
- Date: $Date: 2007/10/24 08:03:10 $
- Version: $Revision: 1.20 $
+ Date: $Date: 2009/01/19 17:05:13 $
+ Version: $Revision: 1.21 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFileHelper.h"
#include "gdcmDirList.h"
#include "gdcmDebug.h"
-#include "gdcmArgMgr.h"
#include "gdcmUtil.h"
#include "gdcmSerieHelper.h"
+#include "gdcmArgMgr.h"
+
#include <iostream>
/**
}
const char *dirNamein;
- dirNamein = am->ArgMgrGetString("dirin",".");
+ dirNamein = am->ArgMgrGetString("dirin",".");
const char *dirNameout;
- dirNameout = am->ArgMgrGetString("dirout",".");
+ dirNameout = am->ArgMgrGetString("dirout",".");
int loadMode = GDCM_NAME_SPACE::LD_ALL;
if ( am->ArgMgrDefined("noshadowseq") )
{
std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
}
+
+
std::string strDirNamein(dirNamein);
GDCM_NAME_SPACE::DirList dirList(strDirNamein, true); // get recursively the list of files
s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
else
s->AddSeriesDetail(0x9999, 0x9999, false); // dirty trick to ignore 'Series Instance UID'
- s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
- s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order)
- s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
- s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
+ s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
+ s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order)
+ s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
+ s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
//uint8_t *imageData; // Useless : pixels will not be loaded
// (images are overwritten)
currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
}
- // Add a default ImagePositionPatient to avoid confusion at post processing time
+ // Add a default ImageOrientationPatient to avoid confusion at post processing time
if ( currentFile->GetEntryString(0x0020,0x0037) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
currentFile->GetEntryString(0x0020,0x0035) == GDCM_NAME_SPACE::GDCM_UNFOUND )
{
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff