+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: PhilipsToBrucker2.cxx,v $
- Language: C++
- Date: $Date: 2006/03/17 14:36:37 $
- Version: $Revision: 1.20 $
-
- 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.
-
-=========================================================================*/
-#include "gdcmDocEntry.h"
-#include "gdcmDicomDir.h"
-#include "gdcmDicomDirPatient.h"
-#include "gdcmFile.h"
-#include "gdcmFileHelper.h"
-#include "gdcmDirList.h"
-#include "gdcmDebug.h"
-#include "gdcmArgMgr.h"
-#include "gdcmUtil.h"
-#include "gdcmSerieHelper.h"
-
-#include <iostream>
-
-/**
- * \brief
- * - explores recursively the given directory
- * - keeps the requested series
- * - orders the gdcm-readable found Files
- * according to their Patient/Study/Serie/Image characteristics
- * - fills a single level Directory with *all* the files,
- * converted into a Brucker-like Dicom, Intags compliant
- *
- */
-
-typedef std::map<std::string, gdcm::File*> SortedFiles;
-
-int main(int argc, char *argv[])
-{
- START_USAGE(usage)
- " \n PhilipsToBrucker :\n ",
- " - explores recursively the given directory, ",
- " - keeps the requested series/ drops the unrequested series ",
- " - orders the gdcm-readable found Files according to their ",
- " (0x0010, 0x0010) Patient's Name ",
- " (0x0020, 0x000e) Series Instance UID ",
- " (0x0020, 0x0032)PhilipsToBrucker2. Image Position (Patient) ",
- " (0x0018, 0x1060) Trigger Time ",
- " (0x0018, 0x1312) In-pl)ane Phase Encoding Direction ",
- " - fills a single level (*) Directory with *all* the files, ",
- " converted into a Brucker-like Dicom, InTags compliant ",
- " (*) actually : creates as many directories as Patients ",
- " -that shouldn't appear, but being carefull is better ! -",
- " or ",
- " - fills a tree-like structure of directories as : ",
- " - Patient ",
- " -- Serie ",
- " --- Position ",
- " Images are (sorted by Trigger Time / ",
- " Encoding Direction (Row, Column) ",
- " use : ",
- " 0x0021, 0x1020 : 'SLICE INDEX' ",
- " 0x0021, 0x1040 : 'FRAME INDEX' ",
- " 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) ",
- " usage: ",
- " PhilipsToBrucker dirin=rootDirectoryName ",
- " dirout=outputDirectoryName ",
- " { [keep= list of seriesNumber to process] ",
- " | [drop= list of seriesNumber to ignore] } ",
- " [taggrid] [skel] ",
- " [input = {ACR|DCM}] ",
- " [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ",
- " [listonly] [split] ",
- " [noshadowseq][noshadow][noseq] [verbose] [debug] ",
- " ",
- " dirout : will be created if doesn't exist ",
- " keep : if user wants to process a limited number of series ",
- " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
- " drop : if user wants to ignore a limited number of series ",
- " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
- " SeriesNumber are short enough to be human readable ",
- " e.g : 1030,1035,1043 ",
- " taggrid : user knows all the images are 'grid' -ie : not 'col', not 'raw'",
- " extent : DO NOT forget the leading '.' ! ",
- " skel: name skeleton eg : patName_1.nema -> skel=patName_ ",
- " split: creates a tree-like structure of directories as : ",
- " - Patient ",
- " -- Serie ",
- " --- Position ",
- " Images are (sorted by Trigger Time / ",
- " Encoding Direction (Row, Column) ",
- " noshadowseq: user doesn't want to load Private Sequences ",
- " noshadow : user doesn't want to load Private groups (odd number) ",
- " noseq : user doesn't want to load Sequences ",
- " verbose : user wants to run the program in 'verbose mode' ",
- " debug : *developer* wants to run the program in 'debug mode' ",
- FINISH_USAGE
-
- // ----- Initialize Arguments Manager ------
-
- gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
-
- if (argc == 1 || am->ArgMgrDefined("usage"))
- {
- am->ArgMgrUsage(usage); // Display 'usage'
- delete am;
- return 0;
- }
-
- const char *dirNamein;
- dirNamein = am->ArgMgrGetString("dirin",".");
-
- const char *dirNameout;
- dirNameout = am->ArgMgrGetString("dirout",".");
-
- int loadMode = gdcm::LD_ALL;
- if ( am->ArgMgrDefined("noshadowseq") )
- loadMode |= gdcm::LD_NOSHADOWSEQ;
- else
- {
- if ( am->ArgMgrDefined("noshadow") )
- loadMode |= gdcm::LD_NOSHADOW;
- if ( am->ArgMgrDefined("noseq") )
- loadMode |= gdcm::LD_NOSEQ;
- }
-
- if (am->ArgMgrDefined("debug"))
- gdcm::Debug::DebugOn();
-
- bool verbose = am->ArgMgrDefined("verbose");
- bool split = am->ArgMgrDefined("split");
- bool listonly = am->ArgMgrDefined("listonly");
-
- int nbSeriesToKeep;
- int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
- int nbSeriesToDrop;
- int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
-
- if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
- {
- std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
- delete am;
- return 0;
- }
-
- int taggrid = am->ArgMgrDefined("taggrid");
-
- int hasSkel = am->ArgMgrDefined("skel");
- const char *skel;
- if (hasSkel)
- skel = am->ArgMgrGetString("skel");
-
- const char *extent = am->ArgMgrGetString("extent",".DCM");
-
- // if unused Param we give up
- if ( am->ArgMgrPrintUnusedLabels() )
- {
- am->ArgMgrUsage(usage);
- delete am;
- return 0;
- }
- delete am; // we don't need Argument Manager any longer
-
- // ----- Begin Processing -----
-
- if ( ! gdcm::DirList::IsDirectory(dirNamein) )
- {
- std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
- exit(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::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::DirList::IsDirectory(dirNameout) ) // be sure it worked
- {
- std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
- exit(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::DirList dirList(strDirNamein, true); // get recursively the list of files
-
- if (listonly)
- {
- std::cout << "------------List of found files ------------" << std::endl;
- dirList.Print();
- }
-
- gdcm::DirListType fileNames;
- fileNames = dirList.GetFilenames();
- gdcm::SerieHelper *s; // Needed only to may use SerieHelper::AddSeriesDetail()
- s = gdcm::SerieHelper::New();
-
- std::string token = "%%%"; // Hope it's enough!
-/*
- std::cout << "---------------Print Serie--------------" << std::endl;
- s->SetDirectory(dirNamein, true); // true : recursive exploration
- s->SetUseSeriesDetails(true);
- s->AddSeriesDetail(0x0018, 0x1312);
- s->Print();
-*/
-
- gdcm::File *f;
- gdcm::FileHelper *fh;
- std::vector<std::string> tokens;
- std::vector<std::string> tokensForFileName;
-/*
- std::cout << "---------------Print Unique Series identifiers---------"
- << std::endl;
- std::string uniqueSeriesIdentifier;
-
- for (gdcm::DirListType::iterator it) = fileNames.begin();
- it != fileNames.end();
- ++it)
- {
- std::cout << "File Name : " << *it << std::endl;
- f = gdcm::File::New();
- f->SetLoadMode(gdcm::LD_ALL);
- f->SetFileName( *it );
- f->Load();
-
- uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
- std::cout << " [" <<
- uniqueSeriesIdentifier << "]" << std::endl;
- f->Delete();
- }
-*/
-
- if (verbose)
- std::cout << "------------------Print Break levels-----------------" << std::endl;
-
- std::string userFileIdentifier;
- SortedFiles sf;
-
- s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
- s->AddSeriesDetail(0x0020, 0x000e, false); // 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
-
- for (gdcm::DirListType::iterator it = fileNames.begin();
- it != fileNames.end();
- ++it)
- {
- f = gdcm::File::New();
- f->SetLoadMode(loadMode);
- f->SetFileName( *it );
- f->Load();
-
- // keep only requested Series
- std::string strSeriesNumber;
- int seriesNumber;
- int j;
-
- bool keep = false;
- if (nbSeriesToKeep != 0)
- {
- strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
- seriesNumber = atoi( strSeriesNumber.c_str() );
- for (j=0;j<nbSeriesToKeep; j++)
- {
- if(seriesNumber == seriesToKeep[j])
- {
- keep = true;
- break;
- }
- }
- if ( !keep)
- {
- f->Delete();
- continue;
- }
- }
- // drop all unrequested Series
- bool drop = false;
- if (nbSeriesToDrop != 0)
- {
- strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
- seriesNumber = atoi( strSeriesNumber.c_str() );
- for (j=0;j<nbSeriesToDrop; j++)
- {
- if(seriesNumber == seriesToDrop[j])
- {
- drop = true;
- break;
- }
- }
- if (drop)
- {
- f->Delete();
- continue;
- }
- }
-
- userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
- tokens.clear();
- gdcm::Util::Tokenize (userFileIdentifier, tokens, token);
-
- int imageNum; // Within FileName
- char newName[1024];
-
- if ( tokens[3] == "gdcmUnfound") // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
- {
- ///this is a trick to build up a lexicographical compliant name :
- /// eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
- std::string name = gdcm::Util::GetName( *it );
- if (hasSkel)
- {
- gdcm::Util::Tokenize (name, tokensForFileName, skel);
- imageNum = atoi ( tokensForFileName[0].c_str() );
- // probabely we could write something much more complicated using C++ !
- sprintf (newName, "%s%06d%s", skel, imageNum, extent);
- tokens[3] = newName;
- tokensForFileName.clear();
- }
- else
- tokens[3] = name;
-
-
- userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
- + tokens[3] + token + tokens[4] + token;
- }
- if (verbose)
- std::cout << "[" << userFileIdentifier << "]" << std::endl;
-
- // storing in a map ensures automatic sorting !
- sf[userFileIdentifier] = f;
- }
-
- std::string fullFilename, lastFilename;
- std::string previousPatientName, currentPatientName;
- std::string previousSerieInstanceUID, currentSerieInstanceUID;
- std::string previousImagePosition, currentImagePosition;
- std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
- std::string previousTriggerTime, currentTriggerTime;
-
- std::string writeDir, currentWriteDir;
- std::string currentPatientWriteDir, currentSerieWriteDir,
- currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
-
- std::string fullWriteFilename;
- std::string strExtent(extent);
-
- writeDir = gdcm::Util::NormalizePath(dirNameout);
- SortedFiles::iterator it2;
-
- previousPatientName = "";
- previousSerieInstanceUID = "";
- previousImagePosition = "";
- previousPhaseEncodingDirection = "";
- previousTriggerTime = "";
-
- int sliceIndex = 0; // Is incremented *at the beginning* of processing
- int frameIndex = 1;
- int flag = 0;
-
- gdcm::File *currentFile;
-
- for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
- {
- currentFile = it2->second;
-
- fullFilename = currentFile->GetFileName();
- lastFilename = gdcm::Util::GetName( fullFilename );
- std::cout << "Rewrite [" <<lastFilename << "]" << std::endl;
-
- tokens.clear();
- gdcm::Util::Tokenize (it2->first, tokens, token);
-
- currentPatientName = tokens[0];
- currentSerieInstanceUID = tokens[1];
- currentImagePosition = tokens[2];
- currentTriggerTime = tokens[3];
- currentPhaseEncodingDirection = tokens[4];
-
- if ( currentImagePosition[0] == '-')
- currentImagePosition[0] = 'M';
- if ( currentImagePosition[0] == '+')
- currentImagePosition[0] = 'P';
-
- if (previousPatientName != currentPatientName)
- {
- previousPatientName = currentPatientName;
- if (verbose)
- std::cout << "==== new Patient [" << currentPatientName << "]" << std::endl;
-
- previousPatientName = currentPatientName;
- previousSerieInstanceUID = ""; //currentSerieInstanceUID;
- previousImagePosition = ""; //currentImagePosition;
- previousTriggerTime = "";
- previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
-
- currentPatientWriteDir = writeDir + currentPatientName;
- //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
- {
- systemCommand = "mkdir " + currentPatientWriteDir;
- if (verbose)
- std::cout << systemCommand << std::endl;
- system ( systemCommand.c_str() );
- }
- }
-
- if (previousSerieInstanceUID != currentSerieInstanceUID)
- {
- if (verbose)
- std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
- << std::endl;
- if (split)
- {
- currentSerieWriteDir = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
- + currentSerieInstanceUID;
- systemCommand = "mkdir " + currentSerieWriteDir;
- system (systemCommand.c_str());
- }
- previousSerieInstanceUID = currentSerieInstanceUID;
- previousImagePosition = ""; //currentImagePosition;
- previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
- }
-
- if (previousImagePosition != currentImagePosition)
- {
- frameIndex = 1;
- flag = 0;
- if (verbose)
- std::cout << "=== === === new Position [" << currentImagePosition << "]"
- << std::endl;
- if (split)
- {
- currentPositionWriteDir = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
- + currentImagePosition;
- systemCommand = "mkdir " + currentPositionWriteDir;
- system (systemCommand.c_str());
- }
- previousImagePosition = currentImagePosition;
- previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
- if (split)
- sliceIndex = 1; // only *one* slice in a given directory
- else
- sliceIndex += 1;
- }
-
-// We don't split on Row/Column!
-/*
- if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
- {
- if (verbose)
- std::cout << "==== === === === new PhaseEncodingDirection ["
- << currentPhaseEncodingDirection << "]" << std::endl;
-
- if (split)
- {
- currentPhaseEncodingDirectionWriteDir = currentPositionWriteDir
- + gdcm::GDCM_FILESEPARATOR
- + currentPhaseEncodingDirection;
- systemCommand = "mkdir " + currentPhaseEncodingDirectionWriteDir;
- system (systemCommand.c_str());
- }
-
- previousPhaseEncodingDirection = currentPhaseEncodingDirection;
- }
-*/
-
- if (verbose)
- std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
- << std::endl;
-
- if ( gdcm::Debug::GetDebugFlag())
- std::cout << "--- --- --- --- --- " << it2->first << " "
- << (it2->second)->GetFileName() << " "
- << gdcm::Util::GetName( fullFilename ) << std::endl;
-
- // Transform the image to be 'Brucker-Like'
- // ----------------------------------------
-
- // Deal with 0x0019, 0x1000 : 'FOV'
- int nX = currentFile->GetXSize();
- int nY = currentFile->GetYSize();
- float pxSzX = currentFile->GetXSpacing();
- float pxSzY = currentFile->GetYSpacing();
- char fov[64];
- sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
- if (currentFile->IsVRCoherent(0x0019) == 1 )
- currentFile->InsertEntryString(fov, 0x0019, 0x1000, " ");
- else
- currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
-
-
- // Deal with 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number)
- std::string chSessionIndex;
- // CLEANME
- if (taggrid)
- chSessionIndex = "1";
- else
- {
- if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
- chSessionIndex = "1";
- else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
- chSessionIndex = "2";
- else
- {
- std::cout << "====================== PhaseEncodingDirection "
- << " neither COL nor ROW (?!?) : [ "
- << currentPhaseEncodingDirection << "]" << std::endl;
- chSessionIndex = "1";
- }
- }
- if (currentFile->IsVRCoherent(0x0020) == 1 )
- currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, " ");
- else
- currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
-
- // Deal with 0x0021, 0x1020 : 'SLICE INDEX'
- char chSliceIndex[5];
- sprintf(chSliceIndex, "%04d", sliceIndex);
- std::string strChSliceIndex(chSliceIndex);
-
- // Deal with 0x0021, 0x1040 : 'FRAME INDEX'
- char chFrameIndex[5];
- sprintf(chFrameIndex, "%04d", frameIndex);
-
- std::string stringVR;
- if (currentFile->IsVRCoherent(0x0021) == 1 )
- stringVR = " ";
- else
- stringVR = "IS";
-
- currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
- currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR);
-
- if (taggrid)
- frameIndex++;
- else
- {
- if (flag == 0)
- {
- flag = 1;
- }
- else
- {
- frameIndex++;
- flag = 0;
- }
- }
-
- if (split)
-
- //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
- // + lastFilename + strExtent;
- fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
- + lastFilename + strExtent;
- else
- fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
- + lastFilename + strExtent;
-
- /*
- systemCommand = "cp " + fullFilename + " " + fullWriteFilename;
- std::cout << systemCommand << std::endl;
- system ( systemCommand.c_str() );
- */
-
- // Load the pixels in RAM.
-
- fh = gdcm::FileHelper::New(currentFile);
- fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
- fh->SetWriteTypeToDcmExplVR();
- // We didn't modify pixels -> keep unchanged the following :
- // 'Media Storage SOP Class UID' (0x0002,0x0002)
- // 'SOP Class UID' (0x0008,0x0016)
- // 'Image Type' (0x0008,0x0008)
- // 'Conversion Type' (0x0008,0x0064)
- fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
- if (!fh->Write(fullWriteFilename))
- {
- std::cout << "Fail to write :[" << fullWriteFilename << "]"
- << std::endl;
- }
- fh->Delete();
- }
- }
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