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Update examples in docs
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Added inline examples
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@MicBoucinha
MicBoucinha committed Aug 6, 2019
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141 changes: 101 additions & 40 deletions docs/source/getting_started/running.rst
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
.. pybpodapi documentation master file, created by
sphinx-quickstart on Wed Jan 18 09:35:10 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
sphinx-quickstart on Wed Jan 18 09:35:10 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. _running-label:

Expand All @@ -13,23 +13,24 @@ Running examples
Configure settings
==================

In order to run protocols you need to specify bpod *'user_settings.py'* file that should be located at the execution directory.
In order to run protocols you need to specify a bpod *'user_settings.py'*
file that should be located at the execution folder.

Example of *'examples/user_settings.py'* file:
Example of *'examples/user_settings.py'* file:

::

# -*- coding: utf-8 -*-
# -*- coding: utf-8-*-

PYBPOD_API_LOG_LEVEL = None
PYBPOD_SESSION_PATH = 'SESSION-WORKSPACE'
PYBPOD_API_LOG_LEVEL = None

# if you do not define the next variable, the PYBPOD_SESSION
# will assume the current datetime value.
PYBPOD_SESSION = 'SESSION-NAME'
PYBPOD_SESSION_PATH = 'SESSION-WORKSPACE'

SERIAL_PORT = '/dev/ttyACM0'
# if you do not define the next variable, the PYBPOD_SESSION
# will assume the current datetime value.
PYBPOD_SESSION = 'SESSION-NAME'

SERIAL_PORT = '/dev/ttyACM0'



Expand All @@ -40,32 +41,39 @@ Example for running the *'add_trial_events.py'*:

::

cd PROJECT_FOLDER/examples
python3 -m function_examples.add_trial_events



cd PROJECT_FOLDER/examples
python -m function_examples.add_trial_events


Available examples
==================

Obtain Bpod Info
----------------
Basic example demonstrating how to initialize Bpod and read version, firmware version and machine type version.
Basic example demonstrating how to initialize Bpod and read version,
firmware version and machine type version.

.. literalinclude:: ../../../examples/function_examples/bpod_info.py

Run the example with:

::

python3 -m function_examples.bpod_info
python -m function_examples.bpod_info

One state example
-----------------

Simple example of adding a state to the state machine and run it. A timer is used to change state.
Simple example of adding a state to the state machine and run it.
A timer is used to change state.

.. literalinclude:: ../../../examples/state_machine_examples/one_state.py

Run the example with:

::

python3 -m state_machine_examples.one_state
python -m state_machine_examples.one_state

Light chasing example (3 pokes)
-------------------------------
Expand All @@ -74,9 +82,13 @@ Simulation of a light chasing scenario. Follow the light on 3 pokes.

Connect noseports to ports 1-3.

.. literalinclude:: ../../../examples/state_machine_examples/light_chasing.py

Run the example with:

::

python3 -m state_machine_examples.light_chasing
python -m state_machine_examples.light_chasing

Light chasing example (2 pokes)
-------------------------------
Expand All @@ -85,89 +97,138 @@ Simulation of a light chasing scenario. Follow the light on 2 pokes.

Connect noseports to ports 1-2.

.. literalinclude:: ../../../examples/state_machine_examples/light_chasing_2_pokes.py

Run the example with:

::

python3 -m state_machine_examples.light_chasing_2_pokes
python -m state_machine_examples.light_chasing_2_pokes

Add trial events
----------------
Demonstration of AddTrialEvents used in a simple visual 2AFC session.

AddTrialEvents formats each trial's data in a human-readable struct, and adds to myBpod.data (to save to disk later)
AddTrialEvents formats each trial's data in a human-readable struct,
and adds to myBpod.data (to save to disk later)

Connect noseports to ports 1-3.

.. literalinclude:: ../../../examples/function_examples/add_trial_events.py

Run the example with:

::

python3 -m function_examples.add_trial_events
python -m function_examples.add_trial_events

Add trial events 2
------------------
Similiar to previous example but using a global timer and adding more states.

Connect noseports to ports 1-3.

.. literalinclude:: ../../../examples/function_examples/add_trial_events2.py

Run the example with:

::

python3 -m function_examples.add_trial_events2
python -m function_examples.add_trial_events2


Manual override
---------------
Manually interact with Bpod hardware. For a detailed explanation, please refer to :ref:`Manual control of Bpod <manual-label>`.
Manually interact with Bpod hardware. For a detailed explanation,
please refer to :ref:`Manual control of Bpod <manual-label>`.

.. literalinclude:: ../../../examples/function_examples/manual_override.py

Run the example with:

::

python3 -m function_examples.manual_override
python -m function_examples.manual_override

Serial messages
---------------
Example on how to use serial capabilities of Bpod.

.. literalinclude:: ../../../examples/function_examples/serial_messages.py

Run the example with:
::

python3 -m function_examples.serial_message
python -m function_examples.serial_messages

Global timers examples
----------------------
Several examples demonstrating how to interact with Bpod timers.

.. literalinclude:: ../../../examples/state_machine_examples/global_timer_example.py

Run the example with:

::

python3 -m state_machine_examples.global_timer_example
python3 -m state_machine_examples.global_timer_example_digital
python3 -m state_machine_examples.global_timer_start_and_end_events
python -m state_machine_examples.global_timer_example

.. literalinclude:: ../../../examples/state_machine_examples/global_timer_example_digital.py

Run the example with:

::

python -m state_machine_examples.global_timer_example_digital

.. literalinclude:: ../../../examples/state_machine_examples/global_timer_start_and_end_events.py

Run the example with:

::

python -m state_machine_examples.global_timer_start_and_end_events

Global counter example
----------------------
After poke2 (PWM2) LED turns off, one will have an infinite loop between LED of poke1 (PWM1) and LED of poke3 (PWM1).
After poke2 (PWM2) LED turns off, one will have an infinite loop between LED
of poke1 (PWM1) and LED of poke3 (PWM1).

To interrupt the infinite loop one have to interrupt poke1 or poke3 a number
of times equal to threshold (in this case is 5 times).

To interrupt the infinite loop one have to interrupt poke1 or poke3 a number of times equal to threshold (in this case is 5 times).
.. literalinclude:: ../../../examples/state_machine_examples/global_counter_example.py

Run the example with:

::

python3 -m state_machine_examples.global_counter_example
python -m state_machine_examples.global_counter_example

Setting a condition example
---------------------------

Example on how to set a condition.

.. literalinclude:: ../../../examples/state_machine_examples/condition_example.py

Run the example with:

::

python3 -m state_machine_examples.condition_example
python -m state_machine_examples.condition_example


UART triggered state example
----------------------------

Example on how a UART event can trigger a state change.

::

python3 -m state_machine_examples.uart_triggered_state_change
.. literalinclude:: ../../../examples/state_machine_examples/uart_triggered_state_change.py

Run the example with:

::

python -m state_machine_examples.uart_triggered_state_change

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