From: jean-pierre roux Date: Mon, 12 Oct 2009 14:45:54 +0000 (+0000) Subject: Rectangular pixels X-Git-Tag: CREATOOLS.2-0-3~35 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?p=creaBruker.git;a=commitdiff_plain;h=4733eef5b89801ea0b0e799569677b1c4abc3203 Rectangular pixels --- diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index c2366e6..bdf1e4d 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -555,6 +555,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr double fovY = fov.GetDoubleValue()[1]; if (verbose) std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl; + + BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol"); + double spatResolX = spatResol.GetDoubleValue()[0]; + double spatResolY = spatResol.GetDoubleValue()[1]; + if (verbose) + std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl; + /// \TODO probabely a more sophisticated accessor will be necessary : /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) @@ -646,7 +653,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices ); fprintf(fp, "HeaderSize = %d\n", 0); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); + //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); + fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolX, sliceDistance ); fprintf(fp, "Position = 0 0 %d\n", 0 ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); @@ -682,7 +690,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr NY, nbFrames, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolX, sliceDistance, output2dseqSliceFileName, strPatientName, day, @@ -731,8 +740,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants); fprintf(fp, "HeaderSize = %d\n", 0); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie - fprintf(fp, "Position = 0 0 %d\n", sliceNb ); + //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // + fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolX, 1.0 ); //slice distance : no meaning for temporal serie + fprintf(fp, "Position = 0 0 %d\n", sliceNb ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); fprintf(fp, "ElementNumberOfChannels = 1\n" ); @@ -815,7 +825,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr NY, nbInstants, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, output2dseqSliceFileName, strPatientName, day, @@ -844,7 +855,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // deal with MatLab-generated Carto file. // ----------------------------------------------------- - dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance, + dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance, copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName); } @@ -852,7 +863,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // =========================================================================================== void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices, - double fovX, double fovY, double sliceDistance, + /*double fovX, double fovY, */ + double spatResolX, double spatResolY, double sliceDistance, char *copyFile, std::string ¤tOutputDirName, char *outputMhdFileName, char *output2dseqCartoName) { @@ -879,10 +891,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- [" << *it << "] is a file..." << std::endl; - icode = 0; - iseparator = 0; + icode = 0; while (code[icode][0] != 0) - { + { + iseparator = 0; while (separator[iseparator][0] != 0) { sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC" @@ -902,9 +914,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX } fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp); + // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() , std::cout << "Deal with Carto file :[" <<*it << "], computed length : " << NX*NY*sizeof(double)*nbSlices << std::endl; - std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); + std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); if (mhd) { // Copy the data file in the new directory @@ -912,7 +925,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str()); system(copyFile); sprintf(outputMhdFileName, "%s%c%s%s", - currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); + currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); if (verbose) std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl; @@ -929,9 +942,8 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX fprintf(fp, "BinaryData = True \n" ); fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); fprintf(fp, "HeaderSize = %d\n", 0 ); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); + fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance ); fprintf(fp, "Position = 0 0 0\n" ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); @@ -961,7 +973,8 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX NY, nbSlices, 8, // pixelSize - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqCartoName, strPatientName, day, @@ -979,14 +992,15 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl; break; // don't check for more ident on same file name! - } - iseparator ++; - } - icode++; - } - } - } // end iterate on files -} + + } // end deal with _ADC, -adc, etc + iseparator ++; + } // end iterate speparators + icode++; + } // end iterate code + } // end boost::filesystem::is_regular(*it) + } // end iterate on all objects (files, dir, etc) +} // end method // ========================================================================================================== @@ -1021,7 +1035,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName) else { if (verbose) - std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl; + std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl; } return 1; @@ -1361,8 +1375,8 @@ std::cout << "charImageOrientation " << fileH->Delete(); throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file ")); } - if (verbose) - file->Print(); + //if (verbose) + // file->Print(); file->Delete(); fileH->Delete();