From 1d72babed2631bf4c953b43164d6088149bc3e4e Mon Sep 17 00:00:00 2001 From: jean-pierre roux Date: Mon, 14 Dec 2009 14:08:04 +0000 Subject: [PATCH] Perform a desperate try when incomplete exam is supplied --- appli/CMakeLists.txt | 2 +- appli/testBruker2Dicom/testBruker2Dicom.cxx | 11 ++- lib/src1/bruker2dicom.cxx | 103 +++++++++++++------- 3 files changed, 76 insertions(+), 40 deletions(-) diff --git a/appli/CMakeLists.txt b/appli/CMakeLists.txt index 83cb90c..5c68369 100644 --- a/appli/CMakeLists.txt +++ b/appli/CMakeLists.txt @@ -10,7 +10,7 @@ SUBDIRS( # ==> Depending on the use or not of Wx, # ==> You will dupplicate WithWx or WithoutWx # - essaiDenis + #essaiDenis #SimpleBrukerToMhdDcm PrintParameterFile #exObjectVaryingProperties diff --git a/appli/testBruker2Dicom/testBruker2Dicom.cxx b/appli/testBruker2Dicom/testBruker2Dicom.cxx index ba04036..b815410 100644 --- a/appli/testBruker2Dicom/testBruker2Dicom.cxx +++ b/appli/testBruker2Dicom/testBruker2Dicom.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: testBruker2Dicom.cxx,v $ Language: C++ - Date: $Date: 2009/06/19 15:51:44 $ - Version: $Revision: 1.5 $ + Date: $Date: 2009/12/14 14:08:08 $ + Version: $Revision: 1.6 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -88,7 +88,7 @@ int main(int argc, char *argv[]) { START_USAGE(usage) " \n testBruker2Dicom : \n ", - " - explores the given directory, at the 3 levels, ", + " - explores the given directory (holding a FULL Bruker exam), at the 3 levels,", " - fills an equivalent Directory with the MHD files or the DICOM files ", " usage: testBruker2Dicom dirin=rootDirectoryName ", " dirout=outputDirectoryName ", @@ -99,6 +99,11 @@ int main(int argc, char *argv[]) " D : user wants to export as DICOM ", " M : user wants to export as MHD ", " debug : developper wants to run the program in 'debug mode' ", + " ", + " REMARK : ", + " If you were supplied an *incomplete* Bruker exam ", + " (e.g. only the '2' serie) put it a 'root' directory, ", + " and run this test using this 'root' directory as 'dirin' ", FINISH_USAGE // ------------ Initialize Arguments Manager ---------------- diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 813fdc5..6e97c5b 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -28,7 +28,7 @@ bool Bruker2Dicom::Execute() } // ----- Check output directory name ----- - + std::string strDirNameOut(OutputDirName); bool res=CreateDirectory(strDirNameOut); if (!res) { @@ -70,26 +70,35 @@ bool Bruker2Dicom::Execute() "subject"; if (verbose) std::cout << " Subject : [" << subject << "]" << std::endl; - canOpen =br_subject.LoadFile(subject); - + + bool subjectFound; + canOpen =br_subject.LoadFile(subject); if (!canOpen) { - std::cout << "Hopeless! no 'subject' found" << std::endl; - throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); - //exit(0); /// \TODO throw an exception ! + //std::cout << "Hopeless! no 'subject' found" << std::endl; + //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); + + std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl; + subjectFound = false; } else { - br_subject.FillMap(); + br_subject.FillMap(); + subjectFound = true; } //br_subject.PrintSelf(); // get info for 'Study Description' - BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); - subject_name = b_name.GetStringValue()[0]; - strPatientName = subject_name; - cleanString(subject_name); + if (subjectFound) + { + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + } + else + subject_name ="defaultPatName"; // creation directory : 'nom du patient' std::string tempStringPatDir(OutputDirName); @@ -101,26 +110,41 @@ bool Bruker2Dicom::Execute() throw ( BrukerHopelessException ("Patient directory creation failure ")); } - BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); - std::string subject_entry = b_entry.GetStringValue()[0]; - //cleanString(subject_entry); - subject_entry = subject_entry.substr(11, subject_entry.size()-11); + std::string subject_entry; + std::string subject_position; + std::string subject_date; + std::string subject_study_name; - BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position"); - std::string subject_position = b_position.GetStringValue()[0]; - //cleanString(subject_position); - subject_position = subject_position.substr(9, subject_position.size()-9); + if (subjectFound) + { + BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); + subject_entry = b_entry.GetStringValue()[0]; + //cleanString(subject_entry); + subject_entry = subject_entry.substr(11, subject_entry.size()-11); + + BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position"); + subject_position = b_position.GetStringValue()[0]; + //cleanString(subject_position); + subject_position = subject_position.substr(9, subject_position.size()-9); - BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date"); - std::string subject_date = b_date.GetStringValue()[0]; - strStudyTimeDate = subject_date; - cleanString(subject_date); + BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date"); + subject_date = b_date.GetStringValue()[0]; + strStudyTimeDate = subject_date; + cleanString(subject_date); - BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name"); - std::string subject_study_name = b_study_name.GetStringValue()[0]; - subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); - cleanString(subject_study_name); - + BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name"); + subject_study_name = b_study_name.GetStringValue()[0]; + subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); + cleanString(subject_study_name); + } + else // Desperate trick when file 'subject' is missing + { + subject_entry = "HeadFirst"; // Why not? + subject_position = "Supine"; // Why not? + strStudyTimeDate = "06_06_06_6_June_1666"; // Why not? + subject_date = "6_June_1666"; // Why not? + subject_study_name = "defStudyName"; // Why not? + } // subject_name is already in 'Patient Name' strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; @@ -140,6 +164,7 @@ bool Bruker2Dicom::Execute() strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); serieNumber = 0; instanceNumber = 0; + // ----------------------------------------------------- // Iterate to ALL the objets(files/directories) found in the input directory // (this is level ZERO) @@ -166,6 +191,7 @@ bool Bruker2Dicom::Execute() br_acqp.LoadFile(strAcqp); br_acqp.FillMap(); +//std::cout << "out of br_acqp.FillMap " << std::endl; std::string acqp_scan_name; std::string acqp_method; std::string acqp_protocol_location; @@ -173,20 +199,26 @@ bool Bruker2Dicom::Execute() BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location"); acqp_protocol_location = b_protocol_location.GetStringValue()[0]; cleanString(acqp_protocol_location); - + +//std::cout << "out of br_acqp.FillMap 1" << std::endl; BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name"); +//std::cout << "out of br_acqp.FillMap 11" << std::endl; acqp_scan_name = b_scan_name.GetStringValue()[0]; +//std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl; cleanString(acqp_scan_name); +//std::cout << "out of br_acqp.FillMap 2" << std::endl; + BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); + b_method.PrintSelf(); + acqp_method = b_method.GetStringValue()[0]; - BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); - acqp_method = b_method.GetStringValue()[0]; cleanString(acqp_method); - +//std::cout << "out of br_acqp.FillMap 3" << std::endl; BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size"); - //b_list_size.PrintSelf(); //JP +//std::cout << "out of br_acqp.FillMap 4" << std::endl; + //b_list_size.PrintSelf(); //JP nbSlices = b_list_size.GetIntValue()[0]; - +//std::cout << "out of br_acqp.FillMap 5" << std::endl; strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it) /* + "." + acqp_protocol_location */ // always the same (in each acquisition) + "." + acqp_scan_name @@ -216,7 +248,6 @@ bool Bruker2Dicom::Execute() } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it } - // ===================================================================== void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) { @@ -320,7 +351,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr 7 1 */ try { - DealWithNiveau2(*it,outputDirName ); + DealWithNiveau2(*it, outputDirName); } catch (BrukerHopelessException &e) { -- 2.47.1