From: jpr Date: Thu, 12 Jun 2008 13:26:39 +0000 (+0000) Subject: Add RawToDicomStack, to convert multiframe to a stack of single frames X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=7408946e2adfd7422d281908ffc96b7a95b4cb52;p=gdcm.git Add RawToDicomStack, to convert multiframe to a stack of single frames --- diff --git a/Example/CMakeLists.txt b/Example/CMakeLists.txt index 09c24408..47bbf349 100644 --- a/Example/CMakeLists.txt +++ b/Example/CMakeLists.txt @@ -28,7 +28,8 @@ SET(EXAMPLE_SOURCES exMakeIcon # the following are utilities - #---------------------------- + #---------------------------- + RawToDicomStack PrintDicomDir PrintFile MakeDicomDir diff --git a/Example/RawToDicomStack.cxx b/Example/RawToDicomStack.cxx new file mode 100755 index 00000000..314debc8 --- /dev/null +++ b/Example/RawToDicomStack.cxx @@ -0,0 +1,417 @@ +/*========================================================================= + + Program: gdcm + Module: $RCSfile: RawToDicomStack.cxx,v $ + Language: C++ + Date: $Date: 2008/06/12 13:26:39 $ + Version: $Revision: 1.1 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + 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. + +=========================================================================*/ + +/** + * Writes a Dicom file from a Raw File + * User has to supply parameters. + * + */ +#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; + +#define CRR(t1,t2) { for(int i=0;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 ", + " usage: RawToDicom filein=inputFileName ", + " fileout=outputSkeletonName ", + " 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} ", + " [{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) ", + " 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_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv); + + if (argc == 1 || am->ArgMgrDefined("usage") ) + { + am->ArgMgrUsage(usage); // Display 'usage' + delete am; + return 1; + } + + const char *inputFileName = am->ArgMgrGetString("filein"); + const char *outputSkeletonFileName = am->ArgMgrGetString("fileout"); + + 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_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() ) + { + am->ArgMgrUsage(usage); + delete am; + return 1; + } + + delete am; // we don't need Argument Manager any longer + + // ----------- 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); + if ( ! *Fp ) + { + std::cout << "Cannot open file: " << inputFileName; + delete Fp; + Fp = 0; + 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 = 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 + { + std::cout << "Wrong 'pixeltype' (" << strPixelType << ")" << std::endl; + return 1; + } + + std::string strPixelTypeOut(pixelTypeOut); + int pixelSignOut; + int pixelSizeOut; + int pixelTypeOutCode; // for the swirch 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(); + + if (userDefinedSerie) + strSerieUID = serieUID; + else + strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); + + // Read the pixels + + int singlePlaneDataSize = nX*nY*samplesPerPixel*pixelSizeOut; + int dataSize = singlePlaneDataSize*nZ; + + 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); + } + +// iterate on the planes. + + char outputFileName[200]; + +for(int nbPlanes=0; nbPlanesGetFile(); + + // '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, "US"); // Columns + str.str(""); + str << nY; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows + + // Set the pixel type + + str.str(""); + str << pixelSize*8; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0100, "US"); // Bits Allocated + + str.str(""); + str << pixelSize*8; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "US"); // Bits Stored + + str.str(""); + str << ( pixelSize*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 0032 DS 3 Image Position (Patient) +// 0020 0037 DS 6 Image Orientation (Patient) + + str.str(""); + str << "0.0 \\ 0.0 \\" << nbPlanes; + 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 (plane) + fileH->SetImageData(planePixels,singlePlaneDataSize); + +// Set the writting mode and write the image + fileH->SetWriteModeToRaw(); + + // Write a DICOM Explicit VR file + fileH->SetWriteTypeToDcmExplVR(); + + if( !fileH->Write(outputFileName ) ) + { + std::cout << "Failed for [" << outputFileName << "]\n" + << " File is unwrittable\n"; + } + + fileH->Delete(); + +} // end iterate on the planes + + delete[] pixels; + delete[] planePixels; + return 1; +}