From: jpr Date: Mon, 19 Jan 2009 17:05:13 +0000 (+0000) Subject: Deal with any type on input + cosmetics X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?p=gdcm.git;a=commitdiff_plain;h=57c267fe1660d9198180f7d758c08113a5d73295 Deal with any type on input + cosmetics --- diff --git a/Example/CMakeLists.txt b/Example/CMakeLists.txt index dae79288..760f81f2 100644 --- a/Example/CMakeLists.txt +++ b/Example/CMakeLists.txt @@ -29,6 +29,7 @@ SET(EXAMPLE_SOURCES # the following are utilities #---------------------------- + RawToInTagDicom RawToDicomStack PrintDicomDir PrintFile diff --git a/Example/RawToDicom.cxx b/Example/RawToDicom.cxx index 4982554f..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: 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 @@ -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("l"); char *pixelType = am->ArgMgrWantString("pixeltype", usage); + const char *pixelTypeOut = am->ArgMgrGetString("pixeltypeout", pixelType); bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") ); @@ -155,36 +182,56 @@ 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; + 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 { @@ -192,6 +239,53 @@ int main(int argc, char *argv[]) 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; @@ -207,17 +301,33 @@ int main(int argc, char *argv[]) // 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(); @@ -258,23 +368,20 @@ 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, as slices of a volume, // it up to you to tell gdcm, for each image, what are the values of : @@ -282,6 +389,12 @@ int main(int argc, char *argv[]) // 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) @@ -292,7 +405,7 @@ int main(int argc, char *argv[]) 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(); @@ -309,5 +422,6 @@ int main(int argc, char *argv[]) fileH->Delete(); delete[] pixels; + delete[] planePixelsOut; return 1; } diff --git a/Example/RawToDicomStack.cxx b/Example/RawToDicomStack.cxx index 70e0212d..5c9976c4 100755 --- a/Example/RawToDicomStack.cxx +++ b/Example/RawToDicomStack.cxx @@ -3,8 +3,8 @@ 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 @@ -39,12 +39,12 @@ typedef unsigned int * PU32; typedef float * PF32; typedef double * PD64; -#define CRR(t1,t2) { for(int i=0;i> 8) | (im16[i] << 8 ); - } + } } else if ( pixelSize == 4 ) { @@ -100,14 +100,14 @@ int main(int argc, char *argv[]) " 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' ", @@ -138,7 +138,6 @@ 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") ); @@ -170,16 +169,16 @@ int main(int argc, char *argv[]) // ----------- 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(); @@ -198,7 +197,7 @@ int main(int argc, char *argv[]) { pixelSize = 1; pixelSign = 0; - pixelTypeCode = 8; + pixelTypeCode = 8; } else if (strPixelType == "16S") { @@ -216,26 +215,26 @@ int main(int argc, char *argv[]) { 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 { @@ -289,7 +288,7 @@ int main(int argc, char *argv[]) std::cout << "Wrong 'pixeltypeout' (" << strPixelTypeOut << ")" << std::endl; return 1; } - + std::string strStudyUID; std::string strSerieUID; @@ -309,19 +308,19 @@ int main(int argc, char *argv[]) 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; nbPlanesInsertEntryString(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 : // @@ -399,7 +398,7 @@ int main(int argc, char *argv[]) // 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(""); diff --git a/Example/ToInTag.cxx b/Example/ToInTag.cxx index 1b4f292d..05152877 100755 --- a/Example/ToInTag.cxx +++ b/Example/ToInTag.cxx @@ -3,8 +3,8 @@ 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 @@ -22,10 +22,11 @@ #include "gdcmFileHelper.h" #include "gdcmDirList.h" #include "gdcmDebug.h" -#include "gdcmArgMgr.h" #include "gdcmUtil.h" #include "gdcmSerieHelper.h" +#include "gdcmArgMgr.h" + #include /** @@ -139,10 +140,10 @@ int main(int argc, char *argv[]) } 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") ) @@ -234,6 +235,8 @@ int main(int argc, char *argv[]) { 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 @@ -308,10 +311,10 @@ int main(int argc, char *argv[]) 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) @@ -494,7 +497,7 @@ int main(int argc, char *argv[]) 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 ) {