X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FRawToDicom.cxx;h=0fdde49f023a453f6c475f953cd8eb27e8c290b8;hb=e7a642c06e4cdcfdbaf024090754283ccc564408;hp=f0c469aee6137dba578390505c8691825492ea03;hpb=bd456b7f5ed26e1c1de909c770e5d0d51db87ff4;p=gdcm.git diff --git a/Example/RawToDicom.cxx b/Example/RawToDicom.cxx index f0c469ae..0fdde49f 100755 --- a/Example/RawToDicom.cxx +++ b/Example/RawToDicom.cxx @@ -3,8 +3,8 @@ 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 @@ -13,7 +13,7 @@ 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. - + =========================================================================*/ /** @@ -24,16 +24,70 @@ #include "gdcmFile.h" #include "gdcmFileHelper.h" #include "gdcmDebug.h" +#include "gdcmUtil.h" #include "gdcmArgMgr.h" #include #include +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> 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 ", @@ -41,18 +95,24 @@ int main(int argc, char *argv[]) " 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") ) { @@ -61,22 +121,37 @@ int main(int argc, char *argv[]) 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() ) @@ -90,6 +165,7 @@ int main(int argc, char *argv[]) // ----------- 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); @@ -101,84 +177,235 @@ int main(int argc, char *argv[]) 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(); @@ -195,5 +422,6 @@ int main(int argc, char *argv[]) fileH->Delete(); delete[] pixels; + delete[] planePixelsOut; return 1; }