API

Initialization (db manager)
Read a db
StandardDatabase tables
CRUD operations (Create/Read/Update/Delete) ; pointer/vector
Dicom: insert
Image: insert, tags
Processing:

1. Open a database

To be able to use syd and load a database, the following line must be use prior to anything else.

    syd::PluginManager::GetInstance()->Load();

The PluginManager looks for available database types that can be found in the SYD_PLUGIN environment variable.

To open a database, just call Open from the database manager (singleton):

    syd::DatabaseManager* m = syd::DatabaseManager::GetInstance();
    // If you know the db type :
    syd::StandardDatabase * db = m->Open<syd::StandardDatabase>(filename);
    // If you don't know:
    syd::Database * gdb = m->Open(filename);

2. Basics operations

CRUD operations (Create/Read/Update/Delete) are:

Create and insert new records

    syd::Patient::pointer p; // declare a pointer
    db->New(p); // Allocate

    // Allocate with table name
    syd::Record::pointer im = db->New("Image");

Warning: when the record is allocated by New, it is not yet in the database (we say it is not persistent), and will be lost once the program ends. To insert in the database (to make it persistent), use the Insert function: db->Insert(p).

Every record inherit from the syd::Record class and has an id field.

The id of an record is only valid when the record is inserted.

Every record has a pointer type and a vector type. The first is a std::shared_ptr and the second std::vector.

Read some records

3. Dicom insertion

To insert dicom files in the db, use the class syd::DicomSerieBuilder.

  syd::StandardDatabase * db = ...     // get a db
  std::vector<std::string> files = ... // get some files
  syd::Patient::pointer patient = ...  // get a patient

  syd::DicomSerieBuilder builder(db);
  builder.SetPatient(patient); // patient is a syd::Patient::pointer
  builder.SetForcePatientFlag(true);
  for(auto file:files) builder.SearchDicomInFile(file);
  builder.InsertDicomSeries();

4. Image insertion

syd::Image is maybe the most important class. It contains information about an image and is linked to a file in the db. The image file format is mhd/raw (ascii header and raw binary).

There are several ways to insert syd::Image into the db, from a (mhd) file or from a dicom that has been inserted in the db.

To insert from a file, syd::ImageHelper::InsertMhdFiles. Other useful functions are available in syd::ImageHelper as simple static functions.

    syd::Image::pointer output;
    db->New(output); // empty image
    output->patient = patient; // required
    syd::ImageHelper::InsertMhdFiles(output, filename);

To insert from a syd::DicomSerie, use a syd::ImageFromDicomBuilder. The builder has options.

    syd::DicomSerie::pointer dicom_serie = ... // get a dicom serie
    syd::ImageFromDicomBuilder builder;
    builder.SetInputDicomSerie(dicom_serie, "float");
    builder.Update();
    syd::Image::pointer image = builder.GetOutput();

5. Image processing

Common Database

Record
RecordWithHistory
RecordWithTags
RecordWithMD5Signature
File should be with MD5 ?
Tag

Standard Database

Patient
Injection
Radionuclide
Dicom tables
- DicomFile should inherit from File ?
- DicomSerie
Image tables
- Image
- PixelValueUnit
- Calibration
- ImageTransform
Roi tables
- RoiMaskImage [<-- Image]
- RoiType
- RoiStatistic
TAC tables
- TimePoints
- FitResult

Policy for empty field

When a field is not set, if it is a string, it must be set to empty_value. When the field is a NULL pointer, it is also printed with empty_value. Defined in syd::Record and syd::PrintTable.

By default all string in the db are set to empty_value with the pragam in syd::Record..

API

API