Table Tiers

To define a DataJoint table in Matlab:

1. Define the table via multi-line comment.
2. Define a class inheriting from the appropriate DataJoint class: dj.Lookup, dj.Manual, dj.Imported or dj.Computed.

Manual Tables

The following code defines two manual tables, Animal and Session:

File +experiment/Animal.m

%{
  # information about animal
  animal_id : int  # animal id assigned by the lab
  ---
  -> experiment.Species
  date_of_birth=null : date  # YYYY-MM-DD optional
  sex='' : enum('M', 'F', '')   # leave empty if unspecified
%}
classdef Animal < dj.Manual
end

File +experiment/Session.m

%{
  # Experiment Session
  -> experiment.Animal
  session  : smallint  # session number for the animal
  ---
  session_date : date  # YYYY-MM-DD
  session_start_time  : float     # seconds relative to session_datetime
  session_end_time    : float     # seconds relative to session_datetime
  -> [nullable] experiment.User
%}
classdef Session < dj.Manual
end

Note that the notation to permit null entries differs for attributes versus foreign key references.

Lookup Tables

Lookup tables are commonly populated from their contents property.

The table below is declared as a lookup table with its contents property provided to generate entities.

File +lab/User.m

%{
    # users in the lab
    username : varchar(20)   # user in the lab
    ---
    first_name  : varchar(20)   # user first name
    last_name   : varchar(20)   # user last name
%}
classdef User < dj.Lookup
    properties
        contents = {
            'cajal'  'Santiago' 'Cajal'
            'hubel'  'David'    'Hubel'
            'wiesel' 'Torsten'  'Wiesel'
        }
    end
end

Imported and Computed Tables

Imported and Computed tables provide make methods to determine how they are populated, either from files or other tables.

Imagine that there is a table test.Image that contains 2D grayscale images in its image attribute. We can define the Computed table, test.FilteredImage that filters the image in some way and saves the result in its filtered_image attribute.

%{ Filtered image
-> test.Image
---
filtered_image : longblob
%}

classdef FilteredImage < dj.Computed
    methods(Access=protected)
        function makeTuples(self, key)
            img = fetch1(test.Image & key, 'image');
            key.filtered_image = my_filter(img);
            self.insert(key)
        end
    end
end

makeTuples vs. make

Currently matlab uses makeTuples rather than make. This will be fixed in an upcoming release. You can monitor the discussion here

Part Tables

The following code defines a Imported table with an associated part table. In MATLAB, the master and part tables are declared in a separate classdef file. The name of the part table must begin with the name of the master table. The part table must declare the property master containing an object of the master.

+image/Scan.m

%{
    # Two-photon imaging scan
    -> Session
    scan : smallint  # scan number within the session
    ---
    -> Lens
    laser_wavelength : decimal(5,1)  # um
    laser_power      : decimal(4,1)  # mW
%}
classdef Scan < dj.Computed
    methods(Access=protected)
        function make(self, key)
            self.insert(key)
            make(image.ScanField, key)
        end
    end
end

+image/ScanField.m

%{
# Region of interest resulting from segmentation
-> image.Scan
mask            : smallint
---
ROI             : longblob  # Region of interest
%}

classdef ScanField < dj.Part
    properties(SetAccess=protected)
        master = image.Scan
    end
    methods
        function make(self, key)
            ...
            self.insert(entity)
        end
    end
end