Welcome to PyBpod GUI API’s documentation!¶

This API makes available a set of functions and properties to allow the manipulation of a PyBpod GUI project using code.

Check the Examples section to learn how to use the API.

Examples¶

Create a new project¶

Create a new project programmatically. The resulting project can be opened with the PyBpod GUI.

from pybpodgui_api.models.project import Project

# create the project
proj = Project()
proj.name = 'First project'

# add an experiment to the project
exp  = proj.create_experiment()
exp.name = 'First experiment'

# add a setup to the project
stp  = exp.create_setup()
stp.name = 'First setup'

# add a board to the project
board = proj.create_board()
board.name = 'First board'
board.serial_port = 'COM3'

# add a subject to the project
subj  = proj.create_subject()
subj.name = 'First animal'

# add a new task\protocol to the project
task  = proj.create_task()
task.name = 'First task'

exp.task  = task # set the task\protocol to the experiment
stp.board = board # set the board to the setup
stp += subj # add a subject to the setup

proj.save('my-project-folder')

task.code = 'print("My first protocol")'

proj.save(proj.path)

Access to data from a session¶

The next examples shows how to access the messages in a pybpod session.

from pybpodgui_api.models.project import Project

# create the project
proj = Project()
proj.load('my-project-folder')

exp = proj.experiments[0]
stp = exp.setups[0]

for session in stp.sessions:

   for msg in session.messages_history:

      if msg.check_type('INFO'):
         pass
         #Do somehting

      elif msg.check_type('stderr'):
         pass
         #Do something

`API Models`¶

`models.board`¶

Overview¶

Enumerates Bpod board supported operations.

Implementation¶

class pybpodgui_api.models.board.Board(project)[source]¶

end_run_task_handler()¶

freegui()¶: Function used to release the processing to update the GUI events

kill_task()¶

load(path)¶

Load board data from filesystem

Variables:	board_path (str) – Path of the board data (dict) – data object that contains all board info

log2board(data)¶: Function used to update the board log

pause_trial()¶

remove()¶

resume_trial()¶

run_task_handler(flag=True)¶

save()¶

Save experiment data on filesystem.

Variables:	parent_path (dict) – Project path.
Returns:	Dictionary containing the board info to save. If None is returned, it means that ther was a failure.
Return type:	dict

start_run_task_handler()¶

stop_task()¶

stop_thread()¶

stop_trial()¶

INFO_BOARD_NAME = 'BOARD-NAME'¶

INFO_BPODGUI_VERSION = 'BPOD-GUI-VERSION'¶

INFO_CREATOR_NAME = 'CREATOR-NAME'¶

INFO_EXPERIMENT_NAME = 'EXPERIMENT-NAME'¶

INFO_PROJECT_NAME = 'PROJECT-NAME'¶

INFO_SETUP_NAME = 'SETUP-NAME'¶

INFO_SUBJECT_NAME = 'SUBJECT-NAME'¶

enabled_behaviorports¶

Get and set the experiment name

Return type:	list(Boolean)

enabled_bncports¶

Get and set enabled bncports

Return type:	list(Boolean)

enabled_wiredports¶

Get and set the enabled wired ports

Return type:	list(Boolean)

name¶

Get and set the board name

Return type:	str

net_port¶

Get and set the experiment name

Return type:	list(Boolean)

path¶

Get and set the board path

Return type:	str

project¶

Get and set the board project

Return type:	str

serial_port¶

Get and set the board serial port

Return type:	str

status¶

Get and set the board status

Return type:	str

`models.experiment`¶

Overview¶

Enumerates Bpod experiment supported operations.

Implementation¶

class pybpodgui_api.models.experiment.Experiment(project)[source]¶

create_setup()¶

Create new instance of setup

Return type:	Setup

load(path)¶

Load experiment data from filesystem

Variables:	experiment_path (str) – Path of the experiment data (dict) – data object that contains all experiment info
Returns:	Dictionary with loaded experiment info.

remove()¶: Remove experiment

save()¶

Save experiment data on filesystem.

Variables:	parent_path (dict) – Project path.
Returns:	Dictionary containing the experiment info to save.
Return type:	dict

name¶

Get and set the experiment name

Return type:	str

path¶

Get and set the experiment files path

Return type:	str

project¶

Get and set the experiment project

Return type:	Project

setups¶

Get the experiment setups

Return type:	list(Setup)

task¶

Get and set the experiment task

Return type:	Task

`models.project`¶

Overview¶

Enumerates Bpod project supported operations.

Implementation¶

class pybpodgui_api.models.project.Project[source]¶

create_board()¶

Add an board to the project, and return it.

Return type:	Board

create_experiment()¶

Add an experiment to the project, and return it.

Return type:	Experiment

create_subject()¶

Add an subject to the project, and return it.

Return type:	Subject

create_task()¶

Add an task to the project, and return it.

Return type:	Task

create_user()¶

Add a user bject to the project, and return it.

Return type:	User

find_board(name)¶

Find a board by the name

Variables:	name (str) – Name of the board to find.
Return type:	Board

find_session(uuid4)¶

find_setup_by_id(uuid4)¶

Find a setup by the id

Variables:	uuid4 (str) – UUID4 of the setup to find.
Return type:	Setup

find_subject(name)¶

Find a subject by the name

Variables:	name (str) – Name of the subject to find.
Return type:	Subject

find_subject_by_id(uuid4)¶

Find a subject by the name

Variables:	name (str) – Name of the subject to find.
Return type:	Subject

find_task(name)¶

Find a task by the name

Variables:	name (str) – Name of the task to find.
Return type:	Task

find_user(username)¶

import_task(filepath, importdir=False)¶

is_saved()¶

Verifies if project has changes by doing a recursive checksum on all entities

Return type:	bool

load(project_path)¶

Load project from a folder.

Variables:	project_path (str) – Full path of the project to load.

remove_non_existing_repositories(path, names)¶

save(project_path)¶: Save project data on file :param str project_path: path to project :return: project data saved on settings file

boards¶

Get the list of boards in the project

Return type:	list(Board)

experiments¶

Get the list of experiments in the project

Return type:	list(Experiment)

name¶

Get and set the project name

Return type:	str

path¶

Get and set the project path

Return type:	str

subjects¶

Get the list of subjects in the project

Return type:	list(Subject)

tasks¶

Get the list of tasks in the project

Return type:	list(Task)

users¶

Get the list of users in the project

Return type:	list(User)

`models.session`¶

Overview¶

Enumerates Bpod session supported operations.

Implementation¶

class pybpodgui_api.models.session.Session(setup)[source]¶

load(path)¶

Parameters:	session_path – data –
Returns:

load_contents(init_func=None, update_func=None, end_func=None)¶: Parses session history file, line by line and populates the history message on memory.

load_info()¶

remove()¶: Remove the session from the project

save()¶

Parameters:	parent_path –
Returns:

STATUS_READY = 0¶

STATUS_SESSION_RUNNING = 1¶

board_name¶

Get and set board name

Return type:	str

board_serial_port¶

Get and set board serial port

Return type:	str

ended¶

Get and set the end datetime of the session

Return type:	datetime.datetime

filepath¶

is_running¶

messages_history¶

Get and set the history of messages

Return type:	list(BaseMessage)

name¶

Get and set session name

Return type:	str

path¶

Get and set path name

Return type:	str

project¶

Get the session Project

Return type:	Project

setup¶

Get and set the setup

Return type:	Setup

setup_name¶

Get and set setup name

Return type:	str

started¶

Get and set the start datetime of the session

Return type:	datetime.datetime

status¶

Get and set the session status

Return type:	str

subjects¶

Get and set session name

Return type:

task¶

Get the session Task

Return type:	Task

task_name¶

Get and set the task name

Return type:	str

variables¶

`models.setup`¶

`models.board.board_task`¶

Overview¶

Enumerates Bpod BoardTask supported operations.

Implementation¶

class pybpodgui_api.models.setup.board_task.BoardTask(setup)[source]¶

Represents the association between one board and one task

Variables:	setup (Setup) – Setup to which the BoardTask belongs to

create_variable(name=None, value=None, datatype='string')[source]¶

Create a variable

Return type:	TaskVariable

load(data)[source]¶

Load setup data from filesystem

Variables:	setup_path (str) – Path of the setup data (dict) – data object that contains all setup info

save()[source]¶

Save board task data on filesystem.

Variables:	setup_path (str) – Setup path.
Returns:	Dictionary containing the board task info to save.
Return type:	dict

board¶

Get and set the board

Return type:	Board

task¶

Get and set the Task

Return type:	Task

update_variables¶

Get and set a flag that indicates if the variables should be updated at the end of the session

Return type:	bool

variables¶

Get and set list of variables

Return type:	list(TaskVariable)

`models.board.taskvariable`¶

Overview¶

Enumerates Bpod task variable supported operations.

Implementation¶

class pybpodgui_api.models.setup.task_variable.TaskVariable(board_task, name=None, value=None, datatype='string')[source]¶

load(data)[source]¶

Load variable data from filesystem

Variables:	data (dict) – data object that contains all task variable info

save()[source]¶

Save variable data on filesystem.

Variables:	setup_path (str) – Setup path.
Returns:	Dictionary containing the variable info to save.
Return type:	dict

datatype¶

Get and set variable data type. It can be from type ‘number’ or ‘string’

Return type:	str

name¶

Get and set variable name

Return type:	str

Overview¶

Enumerates Bpod setup supported operations.

Implementation¶

class pybpodgui_api.models.setup.Setup(experiment)[source]¶

can_run_task()¶

clear_subjects()¶

create_board_task()¶

Create a new BoardTask object

Return type:	BoardTask

create_session()¶

Create a new Session object

Return type:	Session

kill_task()¶

load(path)¶

Load setup data from filesystem

Variables:	setup_path (str) – Path of the setup data (dict) – data object that contains all setup info

pause_trial()¶

remove()¶: Remove the setup from the project

resume_trial()¶

save()¶

Save setup data on filesystem.

Variables:	parent_path (str) – Experiment path.
Returns:	Dictionary containing the setup info to save.
Return type:	dict

stop_task()¶

stop_trial()¶

board¶

Get and set setup board

Return type:	Board

detached¶

experiment¶

Get and set the experiment

Return type:	Experiment

last_session¶

Get last created session

Return type:	Session

name¶

Get and set setup name

Return type:	str

net_port¶

path¶

Get and set setup path

Return type:	str

project¶

Get project

Return type:	Project

sessions¶

Get the list of sessions

Return type:	list(Session)

status¶

subjects¶

Get list of subjects

Return type:	list(Subject)

task¶

Get and set task

Return type:	Task

update_variables¶

`models.subject`¶

Overview¶

Enumerates Bpod Subject supported operations.

Implementation¶

class pybpodgui_api.models.subject.Subject(project)[source]¶

can_run_task()¶

get_sessions()¶

Get all subject sessions

Return type:	list(Session)

load(path)¶

Load subject data from filesystem

Variables:	subject_path (str) – Path of the subject data (dict) – data object that contains all subject info

post_load()¶

remove()¶: Remove the subject from the project

run_task()¶

save()¶

Save subject data on filesystem.

Variables:	project_path (str) – Project path.
Returns:	Dictionary containing the setup info to save.
Return type:	dict

toJSON()¶

name¶

Get and set setup name

Return type:	str

path¶

Get and set the path

Return type:	str

project¶

Get and set project

Return type:	str

setup¶

Get and set project

Return type:	str

`models.task`¶

Overview¶

Enumerates Bpod Task supported operations.

Implementation¶

class pybpodgui_api.models.task.Task(project=None)[source]¶

create_execcmd()¶

create_scriptcmd()¶

load(path)¶

Load setup data from filesystem

Variables:	task_path (str) – Path of the task data (dict) – data object that contains all task info

make_emptyfile()¶: Creates the task folder if does not exists and an empty code file

make_path()¶: Creates the task folder

remove()¶: Remove the task from the project.

save()¶

Save setup data on filesystem.

Variables:	project_path (str) – Project path. data (dict) – Dictionary where to save the data to.
Returns:	Dictionary containing the task info to save.
Return type:	dict

commands¶

Get commands

Return type:	list(TaskCommand)

filepath¶

Get and set task file path

Return type:	str

name¶

Get and set task name

Return type:	str

path¶

Get and set task path

Return type:	str

project¶

Get and set project

Return type:	Project

trigger_softcodes¶

Get net port

Return type:	int

Project Info¶

The SWP Team¶

Scientific Software Platform (Champalimaud Foundation)

The Scientific Software Platform (SWP) from the Champalimaud Foundation provides technical know-how in software engineering and high quality software support for the Neuroscience and Cancer research community at the Champalimaud Foundation.

We typical work on computer vision / tracking, behavioral experiments, image registration and database management.

PyBpod project¶

PyBpod is a python port of the Bpod Matlab project.

All examples and Bpod’s state machine and communication logic were based on the original version made available by Josh Sanders (Sanworks).

License¶

This is Open Source software with a MIT license.

Maintenance team¶

The current and past members of the pybpodgui-api team.

@cajomferro Carlos Mão de Ferro
@JBauto João Baúto
@UmSenhorQualquer Ricardo Ribeiro
@MicBoucinha Luís Teixeira

Welcome to PyBpod GUI API’s documentation!¶

Examples¶

Create a new project¶

Access to data from a session¶

API Models¶

models.board¶

Overview¶

Implementation¶

models.experiment¶

Overview¶

Implementation¶

models.project¶

Overview¶

Implementation¶

models.session¶

Overview¶

Implementation¶

models.setup¶

models.board.board_task¶

Overview¶

Implementation¶

models.board.taskvariable¶

Overview¶

Implementation¶

Overview¶

Implementation¶

models.subject¶

Overview¶

Implementation¶

models.task¶

Overview¶

Implementation¶

Project Info¶

The SWP Team¶

PyBpod project¶

License¶

Maintenance team¶

`API Models`¶

`models.board`¶

`models.experiment`¶

`models.project`¶

`models.session`¶

`models.setup`¶

`models.board.board_task`¶

`models.board.taskvariable`¶

`models.subject`¶

`models.task`¶