X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FRawToDicom.cxx;h=0fdde49f023a453f6c475f953cd8eb27e8c290b8;hb=e7a642c06e4cdcfdbaf024090754283ccc564408;hp=62710fc7e0f3670476fee4e4b02249f2a30906e2;hpb=8fd45dc6d321d1419854dc0e4fa6a37d6826b655;p=gdcm.git diff --git a/Example/RawToDicom.cxx b/Example/RawToDicom.cxx index 62710fc7..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: 2007/05/23 14:18:04 $ - Version: $Revision: 1.10 $ + 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 @@ -30,6 +30,31 @@ #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;lArgMgrDefined("usage") ) @@ -96,7 +124,7 @@ int main(int argc, char *argv[]) const char *inputFileName = am->ArgMgrGetString("filein"); const char *outputFileName = am->ArgMgrGetString("fileout"); - const char *patientName = am->ArgMgrGetString("patientname"); + const char *patientName = am->ArgMgrGetString("patientname", "g^Fantomas"); int nX = am->ArgMgrWantInt("rows", usage); int nY = am->ArgMgrWantInt("lines", usage); @@ -107,10 +135,24 @@ int main(int argc, char *argv[]) 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_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() ) { @@ -123,6 +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); @@ -139,83 +182,174 @@ int main(int argc, char *argv[]) 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; + 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 { 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; + } + + std::string strStudyUID; + std::string strSerieUID; + + if (userDefinedStudy) + strSerieUID = studyUID; + else + strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); - int dataSize = nX*nY*nZ*pixelSize*samplesPerPixel; - uint8_t *pixels = new uint8_t[dataSize]; - - 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, 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(); - // Get the (empty) image header. + // Get the (empty) image header. GDCM_NAME_SPACE::File *fileToBuild = fileH->GetFile(); - - - // If you want to use this program as a template to create - // a 'Single Study UID - Single Serie UID' file set - // keep the following lines out of the loop // '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 - std::string studyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); - fileToBuild->InsertEntryString(studyUID, 0x0020,0x000d,"UI"); + + 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 - std::string serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); - fileToBuild->InsertEntryString(serieUID, 0x0020,0x000e,"UI"); - - // end of 'keep out of loop lines + + fileToBuild->InsertEntryString(strSerieUID,0x0020,0x000e,"UI"); // Serie UID std::ostringstream str; @@ -234,37 +368,44 @@ int main(int argc, char *argv[]) // 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, it up to you to tell gdcm, -// for each image, what are the values of : +// 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) 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(); @@ -281,5 +422,6 @@ int main(int argc, char *argv[]) fileH->Delete(); delete[] pixels; + delete[] planePixelsOut; return 1; }