--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: RawToInTagDicom.cxx,v $
+ Language: C++
+ Date: $Date: 2009/01/19 17:03:38 $
+ 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 an old style Bruker Dicom file, InTag compliant, from a Raw File
+ * User has to supply parameters.
+ *
+ */
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDebug.h"
+#include "gdcmUtil.h"
+#include "gdcmDirList.h"
+
+#include "gdcmArgMgr.h"
+
+#include <iostream>
+#include <sstream>
+
+
+/**
+ * \brief
+ * - explores the given directory
+ * - orders the Raw Files
+ * according to their names
+ * - fills a single level Directory with *all* the files,
+ * converted into a Brucker-like Dicom, Intags compliant
+ */
+
+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<nX*nY*/* nZ* */samplesPerPixel;l++) \
+ {*((t2)planePixelsOut + l) = *(((t1)pixels)+ l);}\
+ }
+
+#define CFR(PPt) switch ( pixelTypeOutCode ) { \
+ case -8 : CRR(PPt,PS8); break; \
+ case 8 : CRR(PPt,PU8); break; \
+ case -16 : CRR(PPt,PS16); break; \
+ case 16 : CRR(PPt,PU16); break; \
+ case -32 : CRR(PPt,PS32); break; \
+ case 32 : CRR(PPt,PU32); break; \
+ case 33 : CRR(PPt,PF32); break; \
+ case 64 : CRR(PPt,PD64); break; \
+ }
+
+
+void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize);
+
+void ConvertSwapZone(int pixelSize, void *Raw, size_t RawSize)
+{
+ unsigned int i;
+ if ( pixelSize == 2 )
+ {
+ uint16_t *im16 = (uint16_t*)Raw;
+ for( i = 0; i < RawSize / 2; i++ )
+ {
+ im16[i]= (im16[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 ",
+ " - explores recursively the given directory, ",
+ " - orders the Raw Files according to their names ",
+ " - fills a single level (*) Directory with *all* the files, ",
+ " converted into a Brucker-like Dicom, InTags compliant ",
+ " usage: RawToDicom dirin=rootDirectoryName ",
+ " dirout=outputDirectoryName ",
+ " rows=nb of Rows ",
+ " 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} ",
+ " [{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] [verbose] [listonly] ",
+ " ",
+ " 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 *dirNamein;
+ dirNamein = am->ArgMgrGetString("dirin",".");
+
+ const char *dirNameout;
+ dirNameout = am->ArgMgrGetString("dirout",".");
+
+ 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();
+
+ int verbose = am->ArgMgrDefined("verbose");
+ int listonly = am->ArgMgrDefined("listonly");
+
+ 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 ---------
+
+
+ // ----- Begin Processing -----
+
+
+ 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 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;
+ }
+
+
+
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) )
+ {
+ std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
+ }
+
+ std::string systemCommand;
+
+ std::cout << "Check for output directory :[" << dirNameout << "]."
+ <<std::endl;
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // dirout not found
+ {
+ std::string strDirNameout(dirNameout); // to please gcc 4
+ systemCommand = "mkdir " +strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ std::cout << "Directory [" << dirNameout << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
+ }
+
+ std::string strDirNamein(dirNamein);
+ GDCM_NAME_SPACE::DirList dirList(strDirNamein, false); // DON'T get recursively the list of files
+ std::string strDirNameout(dirNameout);
+
+ if (listonly)
+ {
+ std::cout << "------------List of found files ------------" << std::endl;
+ dirList.Print();
+ std::cout << 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();
+
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ GDCM_NAME_SPACE::File *f;
+ GDCM_NAME_SPACE::FileHelper *fh;
+
+ std::string outputFileName;
+
+ int sliceIndex = 1; // IMPORTANT : must start with non zero value
+ int frameIndex = 1; // IMPORTANT : must start with non zero value
+ std::string chSessionIndex("1");
+
+ // -----------------------------------------------------
+ // Iterate fo ALL the files found in the input directory
+ // -----------------------------------------------------
+
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+
+ // Open the Raw file
+ std::ifstream *Fp = new std::ifstream((*it).c_str(), std::ios::in | std::ios::binary);
+ if ( ! *Fp )
+ {
+ std::cout << "Cannot open file: [" << *it << "]" << std::endl;
+ delete Fp;
+ Fp = 0;
+ return 0;
+ }
+ if (verbose)
+ std::cout << "Success to open file: [" << *it << "]" << std::endl;
+
+ // 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);
+ }
+
+if (verbose)
+ std::cout << "After ConvertSwapZone" << std::endl;
+
+// 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;
+ }
+
+if (verbose)
+ std::cout << "After CFR" << std::endl;
+
+// Create an empty FileHelper
+
+ GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New();
+
+ // 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, "US"); // Columns
+ str.str("");
+ str << nY;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
+
+ if (verbose)
+ std::cout << "before debut des choses serieuses2"<< std::endl;
+
+// str.str("");
+// str << nZ;
+// fileToBuild->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
+
+ // Set the pixel type
+
+ str.str("");
+ str << pixelSizeOut*8;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0100, "US"); // Bits Allocated
+
+ str.str("");
+ str << pixelSizeOut*8;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "US"); // Bits Stored
+
+ str.str("");
+ 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
+
+// If you deal with a Serie of images, as slices of a volume,
+// it's 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";
+
+// take Frame Index as position (we don't know anything else) NO!
+
+ fileToBuild->InsertEntryString(str.str(),0x0020,0x0032, "DS");
+
+ fileToBuild->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial
+
+
+ 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();
+
+// Special InTag, now.
+
+ fileH->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
+
+ // Deal with 0x0021, 0x1020 : 'SLICE INDEX'
+ // will stay to 0, since the stuff deals with single slice directories
+ char chSliceIndex[5];
+ sprintf(chSliceIndex, "%04d", sliceIndex);
+ std::string strChSliceIndex(chSliceIndex);
+
+ // Deal with 0x0021, 0x1040 : 'FRAME INDEX'
+
+ str.str("");
+ str << frameIndex;
+ frameIndex++; // be ready for next one
+
+ fileH->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS");
+ fileH->InsertEntryString(str.str(), 0x0021, 0x1040, "IS");
+
+ // Pixel Size
+ /// \TODO Ask user to supply 'Pixel Size' value
+ float pxSzX = 1.0;
+ float pxSzY = 1.0;
+
+ // Field of view
+ char fov[64];
+ sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
+ fileH->InsertEntryString(fov, 0x0019, 0x1000, "DS");
+
+
+// Set the image Pixel Data
+ fileH->SetImageData(planePixelsOut,singlePlaneDataSize);
+
+// Set the writting mode and write the image
+ fileH->SetWriteModeToRaw();
+
+
+
+ // Write a DICOM Explicit VR file
+ fileH->SetWriteTypeToDcmExplVR();
+
+
+ outputFileName = strDirNameout + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + *it + "_ForInTag.dcm";
+ if( !fileH->Write(outputFileName ) )
+ {
+ std::cout << "Failed for [" << outputFileName << "]\n"
+ << " File is unwrittable\n";
+ }
+
+// End of : for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin() ...
+
+
+
+ fileH->Delete();
+
+ delete[] pixels;
+ delete[] planePixelsOut;
+
+ }
+ return 1;
+ } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
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