API

Simplified API.

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Core

In the following code, we omit the namespace, use:

    using namespace syd;

Database manager

Get instance:

    DatabaseManager * m = DatabaseManager::GetInstance();
    auto & list = m->GetDatabaseSchemas();

Create a database:

    Database * db = m->Create("StandardDatabase", dbname, folder);

Read a database:

    Database * db = m->Read(dbname);
    StandardDatabase * db = m->Read<StandardDatabase>(dbname);

Functions common to all databases

Get information:

    std::string s = db->GetDatabaseSchema();   // Name of the sql schema, i.e. "StandardDatabase"
    std::string s = db->GetFilename();         // Filename i.e. test.db
    std::string s = db->GetDBFolder();         // Image folder of the db, relative to the test.db folder
    std::string s = db->GetAbsoluteDBFolder(); // Image folder (absolute path)

Basics operations are 'CRUD': Create, Read, Update and Delete.

Create: insert an element (with table Patient as example but could be other tables):

    db->Insert<Patient>(patient);
    db->Insert<Patient>(vector_of_patients); // vector of elements
    TableElement * e = db->InsertFromArg("Patient", string_vector); //FIXME

Query:

    // First, define a query
    typedef odb::query<Patient> QueryType;
    QueryType q = (QueryType::name == "toto" and QueryType::age < 20)

    db->Query<Patient>(vector_of_patients); // Get all patients
    db->Query<Patient>(q, vector_of_patients); // Get all patients matching the query
    patient = db->QueryOne(q);  // Get only one patient matching the query
    patient = db->QueryOne(id); // Get only one patient with id

    int n = db->Count(q);
    if (db->IfExist<Patient>(id)) { ... }

Update:

    db->Update<Patient>(patient);
    db->Update<Patient>(vector_of_patients);

Delete:

    // Delete by knowing the type of the table
    db->Delete<Patient>(patient);
    db->Delete<Patient>(vector_of_patients);
    // Delete with the name of the table and id
    db->Delete("Patient", id);
    db->Delete("Patient", vector_of_ids);

Exceptions. Every access to a database can fail for one reason, you can test the result with a try/catch. See here:

    try {
        // Here, access to the database (insert, query etc)
    }
    catch (const Exception & e) {
        std::cout << e->what(); // Go here if something wrong
    }

For debug, you can access to the last SQL query with:

    std::string s = db->GetLastSQLQuery();

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StandardDatabase

List of tables: TODO

Main class

Direct access to retrieve a patient, an injection:

    patient = db->FindPatientByNameOrStudyId("toto");
    injection = db->FindInjectionByNameOrId(patient, "Indium111");
    db->FindDicom(patient, patterns, series);

Records deletion

When records are delete, a mecanism takes care about dependencies.

DicomSerieBuilder

Create an object DicomSerieBuilder and set the basics informations:

    DicomSerieBuilder b(db);
    b.SetInjection(injection);
    b.SetForcePatientFlag(true);
    b.SearchForFilesInFolder(folder, files);

Main function to create a DicomSerie from a file. Checks if the file is not already in the db, guess if the file should be added to an existing DicomSerie or if a new DicomSerie. The DicomSerie is not yet inserted into the db. See next function.

    for(auto f:files) b.CreateDicomSerieFromFile(f.c_str());

Once the files have been created (previous function), insert all created series in the db.

    b.InsertDicomSeries();

TimepointBuilder

Create an object TimepointBuilder and set the basics informations:

    TimepointBuilder b(db);
    b.SetTag(tag);
    b.SetIntraTimepointMaxHourDiff(1); // 1 hour max difference between

Consider some DicomSerie and create the corresponding Timepoints. Guess that two dicoms with more than 1 hour acquisition time difference are not in the same Timepoint.

    for(auto d:dicom_series) b.InsertDicomSerie(d);

Other functions:

    GuessState s = b.GuessTimepointForThisDicomSerie(dicom_serie, vector_of_timepoints);
    GuessState s = b.GuessIfDicomCanBeInThisTimepoint(dicom_serie, timepoint);
    timepoint = b.CreateTimepoint(dicom_serie);
    b.AddDicom(timepoint, dicom_serie);

ImageBuilder

Create object Image and the associated mhd/raw image (with itk):

    ImageBuilder b(db);
    b.SetImageTag(tag);
    syd::Image image = b.InsertImageFromDicomSerie(dicom_serie);