Program: gdcm
Module: $RCSfile: RawToDicom.cxx,v $
Language: C++
- Date: $Date: 2005/12/16 16:38:24 $
- Version: $Revision: 1.4 $
+ 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
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 "gdcmFileHelper.h"
#include "gdcmDebug.h"
+#include "gdcmUtil.h"
#include "gdcmArgMgr.h"
#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; \
+ }
-int main(int argc, char *argv[])
+
+void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize);
+
+void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize)
{
+ unsigned int i;
+ if ( pixelSize == 2 )
+ {
+ uint16_t *im16 = (uint16_t*)Raw;
+ for( i = 0; i < RawSize / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ }
+ else if ( pixelSize == 4 )
+ {
+ uint32_t s32;
+ uint16_t high;
+ uint16_t low;
+ uint32_t *im32 = (uint32_t*)Raw;
+
+ for( i = 0; i < RawSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 3412
+ high = im32[i] >> 16;
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+
+ }
+}
+int main(int argc, char *argv[])
+{
START_USAGE(usage)
" \n RawToDicom : \n ",
" Writes a Dicom file from a Raw File ",
" fileout=outputFileName ",
" rows=nb of Rows ",
" lines=nb of Lines, ",
- " pixeltype={8U|8S|16U|16S} ",
" [frames = nb of Frames] //defaulted to 1 ",
- " [samples = {1|3}} //defaulted to 1(1:Gray,3:RGB) ",
- " [patientname = Patient's name] ",
+ " 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] ",
" ",
- " debug : user wants to run the program in 'debug mode' ",
+ " 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' ",
FINISH_USAGE
- // Initialize Arguments Manager
- gdcm::ArgMgr *am= new gdcm::ArgMgr(argc, argv);
+ // ------------ Initialize Arguments Manager ----------------
+ GDCM_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv);
if (argc == 1 || am->ArgMgrDefined("usage") )
{
return 1;
}
- char *inputFileName = am->ArgMgrGetString("filein",(char *)0);
- char *outputFileName = am->ArgMgrGetString("fileout",(char *)0);
- //char *dirName = am->ArgMgrGetString("dirin",(char *)0);
+ const char *inputFileName = am->ArgMgrGetString("filein");
+ const char *outputFileName = am->ArgMgrGetString("fileout");
- char *patientName = am->ArgMgrGetString("patientname",(char *)0);
+ const char *patientName = am->ArgMgrGetString("patientname", "g^Fantomas");
int nX = am->ArgMgrWantInt("rows", usage);
int nY = am->ArgMgrWantInt("lines", usage);
int nZ = am->ArgMgrGetInt("frames", 1);
int samplesPerPixel = am->ArgMgrGetInt("samples", 1);
-
+ int b = am->ArgMgrDefined("b");
+ int l = am->ArgMgrDefined("l");
+
char *pixelType = am->ArgMgrWantString("pixeltype", usage);
+ const char *pixelTypeOut = am->ArgMgrGetString("pixeltypeout", pixelType);
+
+ bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
if (am->ArgMgrDefined("debug"))
- gdcm::Debug::DebugOn();
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ bool userDefinedStudy = ( 0 != am->ArgMgrDefined("studyUID") );
+ const char *studyUID;
+ if (userDefinedStudy)
+ studyUID = am->ArgMgrGetString("studyUID");
+
+ // not described *on purpose* in the Usage !
+ bool userDefinedSerie = ( 0 != am->ArgMgrDefined("serieUID") );
+ const char *serieUID;
+ if(userDefinedSerie)
+ serieUID = am->ArgMgrGetString("serieUID");
/* if unused Param we give up */
if ( am->ArgMgrPrintUnusedLabels() )
// ----------- End Arguments Manager ---------
+ /// \TODO Deal with all the images of a directory
// Read the Raw file
std::ifstream *Fp = new std::ifstream(inputFileName, std::ios::in | std::ios::binary);
return 0;
}
+ bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
+
std::string strPixelType(pixelType);
int pixelSign;
int pixelSize;
+ int pixelTypeCode; // for the switch case
if (strPixelType == "8S")
{
pixelSize = 1;
- pixelSign = 0;
+ pixelSign = 1;
+ pixelTypeCode = -8;
}
- else if (strPixelType == "8U")
+ else if (strPixelType == "8U")
{
pixelSize = 1;
- pixelSign = 1;
+ pixelSign = 0;
+ pixelTypeCode = 8;
}
- else if (strPixelType == "16S")
+ else if (strPixelType == "16S")
{
pixelSize = 2;
- pixelSign = 0;
+ pixelSign = 1;
+ pixelTypeCode = -16;
}
- else if (strPixelType == "16U")
+ 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
+ {
+ std::cout << "Wrong 'pixeltype' (" << strPixelType << ")" << std::endl;
+ 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;
+ }
- int dataSize = nX*nY*nZ*pixelSize*samplesPerPixel;
- uint8_t *pixels = new uint8_t[dataSize];
+ std::string strStudyUID;
+ std::string strSerieUID;
+
+ if (userDefinedStudy)
+ strSerieUID = studyUID;
+ else
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- Fp->read((char*)pixels, (size_t)dataSize);
-
+ if (userDefinedSerie)
+ strSerieUID = serieUID;
+ else
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+ // Read the pixels
+
+ 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);
+
+ if ( pixelSize !=1 && ( (l && bigEndian) || (b && ! bigEndian) ) )
+ {
+ 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::FileHelper *fileH = gdcm::FileHelper::New();
+ GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New();
- // Get the (empty) image header.
- gdcm::File *fileToBuild = fileH->GetFile();
+ // Get the (empty) image header.
+ GDCM_NAME_SPACE::File *fileToBuild = fileH->GetFile();
+
+ // 'Study Instance UID'
+ // The user is allowed to create his own Study,
+ // keeping the same 'Study Instance UID' for various images
+ // The user may add images to a 'Manufacturer Study',
+ // adding new Series to an already existing Study
+
+ fileToBuild->InsertEntryString(strStudyUID,0x0020,0x000d,"UI"); // Study UID
+
+ // 'Serie Instance UID'
+ // The user is allowed to create his own Series,
+ // keeping the same 'Serie Instance UID' for various images
+ // The user shouldn't add any image to a 'Manufacturer Serie'
+ // but there is no way no to prevent him for doing that
+
+ fileToBuild->InsertEntryString(strSerieUID,0x0020,0x000e,"UI"); // Serie UID
+
std::ostringstream str;
// Set the image size
str.str("");
str << nX;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns
str.str("");
str << nY;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
str.str("");
str << nZ;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0008); // Number of Frames
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
// Set the pixel type
str.str("");
- str << pixelSize*8;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0100); // Bits Allocated
+ str << pixelSizeOut*8;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0100, "US"); // Bits Allocated
str.str("");
- str << pixelSize*8;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0101); // Bits Stored
+ str << pixelSizeOut*8;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "US"); // Bits Stored
str.str("");
- str << ( pixelSize*8 - 1 );
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0102); // High Bit
+ str << ( pixelSizeOut*8 - 1 );
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0102, "US"); // High Bit
str.str("");
str << pixelSign;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0103); // Pixel Representation
+ 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 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); // Samples per Pixel
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0002, "US"); // Samples per Pixel
if (strlen(patientName) != 0)
- fileToBuild->InsertEntryString(patientName,0x0010,0x0010); // Patient's Name
-
+ fileToBuild->InsertEntryString(patientName,0x0010,0x0010, "PN"); // Patient's Name
+
+ // 0=white
+ if(monochrome1)
+ 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;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff