Geometric Data

The database can be used to store simple geometric structures, which are usually used as regions of interests. This structures must be defined in a concrete coordinates system. There is one main table which stores general information about the structure (roi), and a table for each roi type which stores its concrete data for each subject.

ROIs

roi_name_exists(name)

Check if a ROI with the given name exists

Parameters:name (str) – ROI name Returns:True if a ROI with the given name exists in the database, False otherwise.

get_roi_id(roi_name)

Find the id of a ROI

Parameters:roi_name (str) – ROI Name Returns:ROI id in the database

get_roi_name(roi_id)

Find the name of a ROI

Parameters:roi_id (int) – ROI id Returns:ROI name

get_roi_type(name=None, roi_id=None)

Get the type of a ROI

Only one of the two arguments is required, roi_id is preferred

Parameters:

• name (str) – ROI name
• roi_id (int) – ROI id

Returns:

ROI type as a string, see create_roi() for options

get_roi_space(name=None, roi_id=None)

Retrieve the coordinate systems of a ROI

Only one of the two arguments is required, roi_id is preferred

Parameters:

• name (str) – ROI name
• roi_id (int) – ROI id

Returns:

coordinate system as a string, see create_roi() for options

create_roi(*args, **kwargs)

Creates a new ROI

Parameters:

• name (str) – ROI Name
• roi_type (str) –

  ROI type, current options are

  • sphere
  • line_sagital
  • line_coronal
  • line_axial
  • line_free
• coords (str) –

  coordinate system, options are

  • subject
  • talairach
  • dartel
• desc (str) – ROI description

Returns:

Id of ROI in the database

recursive_delete_roi(*args, **kwargs)

Removes a ROI from the database, including all its values.

Warning

This may delete large amounts of information and can’t be reversed

Parameters:roi_id (int) – ROI id

Spheres

Spheres are saved as a center (x,y,z) and a radius.

load_sphere(sphere_id, subject)

Loads a sphere for a subject

Parameters:

• sphere_id (int) – ROI id
• subject – subject id

Returns:

(r,x,y,z) where r is the radius of the sphere and (x,y,z) is its center.

get_available_spheres_df(space=None)

Get available spheres

Parameters:space (str) – Optional, filter to only rois in a certain space Returns:DataFrame with columns for sphere id, and number of subjects with the ROI defined; indexed by name

get_all_spheres(sphere_id)

Get a DataFrame of all the subjects spheres with a given id

Parameters:sphere_id (int) – ROI id Returns:pandas.DataFrame with columns for radius, center x, center y and center z; indexed by subject

subjects_with_sphere(sphere_id)

Get subjects who have a certain sphere defined

Parameters:sphere_id (int) – ROI id Returns:A set of subjects with the sphere defined

save_sphere(*args, **kwargs)

Save a sphere for a given subject into the database

Parameters:

• sphere_id (int) – ROI id
• subject – subject id
• radius (float) – sphere radius in mm.
• center (tuple) – The three coordinates for the sphere center in mm.

copy_spheres(*args, **kwargs)

Copies spheres from one ROI to another

Copies the definitions of spheres for each subject from one ROI to another ROI

Parameters:

• origi_id (int) – ROI id of the source spheres
• dest_id (int) – ROI id into which the spheres will be copied

Lines

Lines are saved as a starting point (xo,yo,zo) and an end point (xf,yf,zf)

load_line(line_id, subject)

Retrieves a line for a given subject

Parameters:

• line_id (int) – ROI id
• subject – subject id

Returns

(xo,yo,zo,xf,yf,zf) where (xo,yo,zo) is the line origin and (xf,yf,zf) is the end.

get_available_lines_df()

Get available lines

Returns:DataFrame with columns for line id, and number of subjects with the ROI defined; indexed by name

subjects_with_line(line_id)

Get subjects who have a certain line defined

Parameters:sphere_id (int) – ROI id Returns:A set of subjects with the line defined

save_line(*args, **kwargs)

Save a line from a given subject into the database

Parameters:

• line_id (int) – ROI id
• subject – subject id
• point1 (tuple) – coordinates (xo,yo,zo) of the line origin
• point2 (tuple) – coordinates (xf,yf,zf) of the line end