Facilitate pybpod GUI for running protocol #7

ckarageorgkaneen · 2023-05-17T08:08:22Z

TODO:

git clone --recursive https://github.com/ckarageorgkaneen/pybpod.git chris-pybpod
Get emulator plugin up and running
Test it out on an example protocol in emulator mode, verify it works as expected
Integrate our mouse2afc protocol in the plugin, so we can select it
Run our protocol, simulate real mouse pokes and verify it works as expected
Mess with settings to see if each state, input and output work properly

The text was updated successfully, but these errors were encountered:

HenryJFlynn · 2023-05-25T09:14:35Z

Trying to clone repo and sub modules doesn't work

henry@henry-Vostro-270:~/Documents$ git clone --recursive https://github.com/ckarageorgkaneen/pybpod.git  chris-pybpod
Cloning into 'chris-pybpod'...
remote: Enumerating objects: 1273, done.
remote: Counting objects: 100% (12/12), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 1273 (delta 5), reused 7 (delta 2), pack-reused 1261
Receiving objects: 100% (1273/1273), 8.85 MiB | 834.00 KiB/s, done.
Resolving deltas: 100% (733/733), done.
Submodule 'base - pybpod-api' (ssh://[email protected]/ckarageorgkaneen/pybpod-api.git) registered for path 'base/pybpod-api'
Submodule 'base - pybpod-gui-api' (https://github.com/pybpod/pybpod-gui-api.git) registered for path 'base/pybpod-gui-api'
Submodule 'base - pybpod-gui-plugin' (ssh://[email protected]/ckarageorgkaneen/pybpod-gui-plugin.git) registered for path 'base/pybpod-gui-plugin'
Submodule 'libs - logging-bootstrap' (https://bitbucket.org/fchampalimaud/logging-bootstrap.git) registered for path 'libraries/logging-bootstrap'
Submodule 'libs - pyforms-generic-editor' (https://bitbucket.org/fchampalimaud/pyforms-generic-editor.git) registered for path 'libraries/pyforms-generic-editor'
Submodule 'libs - pyforms-gui' (https://github.com/UmSenhorQualquer/pyforms-gui.git) registered for path 'libraries/pyforms-gui'
Submodule 'libs - safe-collaborative-architecture' (https://bitbucket.org/fchampalimaud/safe-collaborative-architecture.git) registered for path 'libraries/safe-collaborative-architecture'
Submodule 'plugins - pge-terminal' (https://bitbucket.org/fchampalimaud/pge-plugin-terminal.git) registered for path 'plugins/pge-plugin-terminal'
Submodule 'plugins - pybpod-gui-plugin-alyx' (https://github.com/pybpod/pybpod-gui-plugin-alyx) registered for path 'plugins/pybpod-gui-plugin-alyx'
Submodule 'plugins - pybpod-gui-plugin-emulator' (ssh://[email protected]/ckarageorgkaneen/pybpod-gui-plugin-emulator.git) registered for path 'plugins/pybpod-gui-plugin-emulator'
Submodule 'plugins - pybpod-gui-plugin-rotaryencoder' (https://github.com/pybpod/pybpod-gui-plugin-rotaryencoder.git) registered for path 'plugins/pybpod-gui-plugin-rotaryencoder'
Submodule 'plugins - pybpod-gui-plugin-session-history' (https://github.com/pybpod/pybpod-gui-plugin-session-history.git) registered for path 'plugins/pybpod-gui-plugin-session-history'
Submodule 'plugins - pybpod-gui-plugin-soundcard' (https://github.com/pybpod/pybpod-gui-plugin-soundcard.git) registered for path 'plugins/pybpod-gui-plugin-soundcard'
Submodule 'plugins - pybpod-gui-plugin-stmdiagram' (https://github.com/pybpod/pybpod-gui-plugin-stmdiagram.git) registered for path 'plugins/pybpod-gui-plugin-stmdiagram'
Submodule 'plugins - pybpod-gui-plugin-timeline' (https://github.com/pybpod/pybpod-gui-plugin-timeline.git) registered for path 'plugins/pybpod-gui-plugin-timeline'
Submodule 'plugins - pybpod-gui-plugin-trial-timeline' (https://github.com/pybpod/pybpod-gui-plugin-trial-timeline) registered for path 'plugins/pybpod-gui-plugin-trial-timeline'
Submodule 'plugins - pybpod-gui-plugin-waveplayer' (https://github.com/pybpod/pybpod-gui-plugin-waveplayer) registered for path 'plugins/pybpod-gui-plugin-waveplayer'
Cloning into '/home/henry/Documents/chris-pybpod/base/pybpod-api'...
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'ssh://[email protected]/ckarageorgkaneen/pybpod-api.git' into submodule path '/home/henry/Documents/chris-pybpod/base/pybpod-api' failed
Failed to clone 'base/pybpod-api'. Retry scheduled
Cloning into '/home/henry/Documents/chris-pybpod/base/pybpod-gui-api'...
remote: Enumerating objects: 1566, done.        
remote: Counting objects: 100% (16/16), done.        
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remote: Total 1566 (delta 5), reused 9 (delta 3), pack-reused 1550        
Receiving objects: 100% (1566/1566), 250.80 KiB | 1.57 MiB/s, done.
Resolving deltas: 100% (1077/1077), done.
Cloning into '/home/henry/Documents/chris-pybpod/base/pybpod-gui-plugin'...
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'ssh://[email protected]/ckarageorgkaneen/pybpod-gui-plugin.git' into submodule path '/home/henry/Documents/chris-pybpod/base/pybpod-gui-plugin' failed
Failed to clone 'base/pybpod-gui-plugin'. Retry scheduled
Cloning into '/home/henry/Documents/chris-pybpod/libraries/logging-bootstrap'...
Cloning into '/home/henry/Documents/chris-pybpod/libraries/pyforms-generic-editor'...
Receiving objects: 100% (1060/1060), 690.53 KiB | 1.70 MiB/s, done.
Resolving deltas: 100% (578/578), done.
Cloning into '/home/henry/Documents/chris-pybpod/libraries/pyforms-gui'...
remote: Enumerating objects: 1426, done.        
remote: Counting objects: 100% (66/66), done.        
remote: Compressing objects: 100% (23/23), done.        
remote: Total 1426 (delta 26), reused 62 (delta 25), pack-reused 1360        
Receiving objects: 100% (1426/1426), 3.53 MiB | 1.52 MiB/s, done.
Resolving deltas: 100% (928/928), done.
Cloning into '/home/henry/Documents/chris-pybpod/libraries/safe-collaborative-architecture'...
Receiving objects: 100% (120/120), 19.26 KiB | 6.42 MiB/s, done.
Resolving deltas: 100% (51/51), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pge-plugin-terminal'...
Receiving objects: 100% (125/125), 102.58 KiB | 729.00 KiB/s, done.
Resolving deltas: 100% (56/56), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-alyx'...
remote: Enumerating objects: 410, done.        
remote: Counting objects: 100% (17/17), done.        
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Resolving deltas: 100% (242/242), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-emulator'...
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'ssh://[email protected]/ckarageorgkaneen/pybpod-gui-plugin-emulator.git' into submodule path '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-emulator' failed
Failed to clone 'plugins/pybpod-gui-plugin-emulator'. Retry scheduled
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-rotaryencoder'...
remote: Enumerating objects: 350, done.        
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Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-session-history'...
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Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-soundcard'...
remote: Enumerating objects: 421, done.        
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Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-stmdiagram'...
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Resolving deltas: 100% (17/17), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-timeline'...
remote: Enumerating objects: 137, done.        
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Receiving objects: 100% (137/137), 18.85 KiB | 371.00 KiB/s, done.
Resolving deltas: 100% (71/71), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-trial-timeline'...
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Resolving deltas: 100% (43/43), done.
Cloning into '/home/henry/Documents/chris-pybpod/plugins/pybpod-gui-plugin-waveplayer'...
remote: Enumerating objects: 121, done.        
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Receiving objects: 100% (121/121), 37.63 KiB | 786.00 KiB/s, done.
Resolving deltas: 100% (48/48), done.
Cloning into '/home/henry/Documents/chris-pybpod/base/pybpod-api'...
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'ssh://[email protected]/ckarageorgkaneen/pybpod-api.git' into submodule path '/home/henry/Documents/chris-pybpod/base/pybpod-api' failed
Failed to clone 'base/pybpod-api' a second time, aborting

HenryJFlynn · 2023-05-25T09:15:44Z

desktop/desktop#2344

HenryJFlynn · 2023-05-25T09:34:55Z

The sub modules could only be clonedwith ssh permission see pybpod/pybpod@98c03e6

ckarageorgkaneen · 2023-05-25T09:36:37Z

My bad. Fixed by amending pybpod/pybpod@98c03e6.

ckarageorgkaneen · 2023-05-25T11:14:26Z

For start-pybpod, see pybpod/pybpod#91.

HenryJFlynn · 2023-05-25T12:44:17Z

Must update pip in the environment for any pip install ... to work properly

HenryJFlynn · 2023-05-26T09:36:09Z

trying to get the pybod gui ti successfully run the examples protocol 10_state_example

When my_bpod = Bpod(emulator_mode=...) is
True nothing happens. Hit start, it runs for a few seconds then the gui resets. No output. No error. No nothing
False or gibberish or gbf or instantly runs and resets. no output. no error.
nothing, so Bpod() nothing happens

With clear errors in the protocol such as deleting half of the protocol, there is no error. In some of my proding i got it to pop this error but i haven't been able to reproduce it.

Traceback (most recent call last):
  File "/home/henry/Documents/pybpod-testing/Untitled project 7/tasks/10_state_example/10_state_example.py", line 2, in <module>
    my_bpod = Bpod(emulator_mode = dg98)
NameError: name 'dg98' is not defined
Traceback (most recent call last):
  File "/home/henry/Documents/pybpod-testing/Untitled project 7/tasks/10_state_example/10_state_example.py", line 3, in <module>
    sma = StateMachine(my_bpod)
  File "/home/henry/Documents/chris-pybpod/base/pybpod-api/pybpodapi/state_machine/state_machine_runner.py", line 20, in __init__
    StateMachineBuilder.__init__(self, bpod)
  File "/home/henry/Documents/chris-pybpod/base/pybpod-api/pybpodapi/state_machine/state_machine_base.py", line 52, in __init__
    self.state_timers = [0] * self.hardware.max_states  # list(float)
TypeError: can't multiply sequence by non-int of type 'NoneType'

This is with emulator mode enabled in the gui. Without, the protocol IO fails to open and crashes the program.

HenryJFlynn · 2023-05-26T11:45:54Z

when i first start the program

(pybpod-environment) henry@henry-Vostro-270:~/Documents/chris-pybpod/base/pybpod$ start-pybpod
/lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
ControlWeb will not work
QtWebEngine may be missing
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
libpng warning: iCCP: known incorrect sRGB profile
26/05/2023 02:44:40 | WARNING | 8756 | pyforms_generic_editor.plugins.loader | install_plugins | Plugins path was not defined by user
libGL error: MESA-LOADER: failed to open crocus: /usr/lib/dri/crocus_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: crocus
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast

HenryJFlynn · 2023-05-26T12:47:26Z

after trying: helloSystem/LinuxRuntime#11

ERROR: ld.so: object '/usr/lib64/libfreetype.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib64/libfreetype.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
/lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
ControlWeb will not work
QtWebEngine may be missing
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
libpng warning: iCCP: known incorrect sRGB profile
26/05/2023 03:46:40 | WARNING | 11250 | pyforms_generic_editor.plugins.loader | install_plugins | Plugins path was not defined by user
libGL error: MESA-LOADER: failed to open crocus: /usr/lib/dri/crocus_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: crocus
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast

HenryJFlynn · 2023-05-26T14:11:51Z

just gonna ignore that error ^.

Current problems:

Can run protocols but ones which require inputs such as poking in do not prompt the user. The protocol IO does not light up any behavior ports.
Do not know how to change user_settings

HenryJFlynn · 2023-05-26T14:15:23Z

also sometimes this happens

the task editor is blank. There should be code there

HenryJFlynn · 2023-05-26T14:22:27Z

just got the error e ignored in the board log. idk what is going on

HenryJFlynn · 2023-05-29T07:21:52Z

Steps start up and pybpod

open pybpod folder inside terminal
start-pybpod
File --> Open Project --> select your project
Go to boards --> Select Board --> select Emulator mode + click Console
Go to Users --> Double click on desired user for this experiment
Go to Project ->Experiment->ExperimentName->SetupName select board, protocol, and add subjects
Click Test Protocol IO button
run the protocol

HenryJFlynn · 2023-05-29T07:40:33Z

gui plugin must be at the end

HenryJFlynn · 2023-05-29T07:43:33Z

after changing user settings, protocols opened in the task editor are empty. Blank. There is no code.

ckarageorgkaneen · 2023-05-29T07:45:17Z

after changing user settings, protocols opened in the task editor are empty. Blank. There is no code.

If you revert the changes, does the code re-appear?

HenryJFlynn · 2023-05-29T07:45:46Z

going from ~/Documents/chris-pybpod/base/pybpod$ user_settings.py is created in Home, outside of Documents.

HenryJFlynn · 2023-05-29T08:36:51Z

pybpod gets its firmware and version from the api settings file. There is no way to easily change them as a user. To do this, we would like to add a snippet of code in board_com.py which takes the firmware and version type from a user_settings files which we specifiy

HenryJFlynn · 2023-05-29T08:38:31Z

another problem is that running the protocol light_chasing_examples... doesn't work properly. It requires a poke input which it never receives yet it runs.

HenryJFlynn · 2023-05-29T08:57:22Z

another problem is that running the protocol light_chasing_examples... doesn't work properly. It requires a poke input which it never receives yet it runs.

Once the proper firmware and version with correct number of ports are implemented in the gui, this protocol runs fine

ckarageorgkaneen · 2023-05-29T09:01:57Z

another problem is that running the protocol light_chasing_examples... doesn't work properly. It requires a poke input which it never receives yet it runs.

Once the proper firmware and version with correct number of ports are implemented in the gui, this protocol runs fine

awesome

HenryJFlynn · 2023-05-29T09:02:05Z

pybpod gets its firmware and version from the api settings file. There is no way to easily change them as a user. To do this, we would like to add a snippet of code in board_com.py which takes the firmware and version type from a user_settings files which we specifiy

I was wrong. We don't need to do this. Copy and pasting the desired settings into the user settings you can set in the gui works fine.

My setting look like this

SETTINGS_PRIORITY = 0

GENERIC_EDITOR_PLUGINS_LIST = ['pybpodgui_plugin', 'pybpod_gui_plugin_emulator']

TARGET_BPOD_FIRMWARE_VERSION = "8"
EMULATOR_BPOD_MACHINE_TYPE = 1

BPOD_BNC_PORTS_ENABLED = [True, True]
BPOD_WIRED_PORTS_ENABLED = [True, True, True, True]
BPOD_BEHAVIOR_PORTS_ENABLED = [True, True, True, False, False, False, False, False]

and I get this this

HenryJFlynn · 2023-05-29T09:24:06Z

problems with with the gui

if you poke in or out too fast, it crashes
if emulator mode isn't enables, it crashes
if buttons are checked when the protocol ends, they remain checked.
if you press Run Protocol and you can't run because you didn't save for examples, the button doesn't reset. It still looks pressed

HenryJFlynn · 2023-05-29T09:53:15Z

all the examples run fine except emulator_10_state_w_pwm_outputs_examples due to firmware requirements. I am looking past this as it is irrelevant and moving on to mouse2afc.

running emulator_mouse2afc_example, this is my complete output:

['__UUID4__', '8b305563-5c36-420b-9d10-4f4000850049']
['__CREATED-ON__', '2023-05-29 12:50:51.205583']
['__DEF-URL__', 'http://pybpod-api.readthedocs.org']
['__DEF-TEXT__', 'This file contains data recorded during a session from the PyBpod system']
['__SOFTWARE__', 'PyBpod API v1.8.2']
['__HAS-HEADER__']
['TYPE', 'PC-TIME', 'BPOD-INITIAL-TIME', 'BPOD-FINAL-TIME', 'MSG', '+INFO']
['INFO', '2023-05-29 12:50:51.206482', '', '', 'SERIAL-PORT', '']
['INFO', '2023-05-29 12:50:51.206549', '', '', 'PROTOCOL-NAME', 'emulator_mouse2afc_example']
['INFO', '2023-05-29 12:50:51.206575', '', '', 'CREATOR-NAME', '["csk", "9c98433a-110b-47a7-a0c8-80572324d10e", "local"]']
['INFO', '2023-05-29 12:50:51.206598', '', '', 'PROJECT-NAME', 'pybpod-project']
['INFO', '2023-05-29 12:50:51.206619', '', '', 'EXPERIMENT-NAME', 'Experiment_1']
['INFO', '2023-05-29 12:50:51.206640', '', '', 'BOARD-NAME', 'Board_1']
['INFO', '2023-05-29 12:50:51.206661', '', '', 'SETUP-NAME', 'Setup_1']
['INFO', '2023-05-29 12:50:51.206683', '', '', 'BPOD-GUI-VERSION', '']
['INFO', '2023-05-29 12:50:51.206702', '', '', 'NET-PORT', '36000']
['INFO', '2023-05-29 12:50:51.206725', '', '', 'SUBJECT-NAME', "['Mickey', 'f2ab9be6-1b0f-4c52-b78f-567f7dd06006']"]
['INFO', '2023-05-29 12:50:51.206761', '', '', 'This is a PYBPOD file. Find more info at http://pybpod.readthedocs.io', '']
['INFO', '2023-05-29 12:50:51.206784', '', '', 'BPOD-API-VERSION', '1.8.2']
['INFO', '2023-05-29 12:50:51.206803', '', '', 'SESSION-NAME', '20230529-125050']
['INFO', '2023-05-29 12:50:51.206822', '', '', 'SESSION-STARTED', '2023-05-29 12:50:51.205421']

b'Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.\n'
b'libGL error: MESA-LOADER: failed to open crocus: /usr/lib/dri/crocus_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n'
b'libGL error: failed to load driver: crocus\n'
b'libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n'
b'libGL error: failed to load driver: swrast\n'
['stderr', '2023-05-29 12:50:54.117685', '', 'Before StateMatrix()', '', '']
['stderr', '2023-05-29 12:50:54.117934', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.119799', '', 'Traceback (most recent call last):\n', '', '']
['stderr', '2023-05-29 12:50:54.119942', '', '  File "/home/henry/Documents/chris-pybpod/base/pybpod-api/pybpodapi/state_machine/state_machine_base.py", line 221, in add_state\n', '', '']
['stderr', '2023-05-29 12:50:54.120295', '', '    ', '', '']
['stderr', '2023-05-29 12:50:54.120343', '', 'action_name', '', '']
['stderr', '2023-05-29 12:50:54.120378', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.120418', '', 'ValueError', '', '']
['stderr', '2023-05-29 12:50:54.120452', '', ': ', '', '']
['stderr', '2023-05-29 12:50:54.120483', '', "'Wire1' is not in list", '', '']
['stderr', '2023-05-29 12:50:54.120516', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.120546', '', '\nDuring handling of the above exception, another exception occurred:\n\n', '', '']
['stderr', '2023-05-29 12:50:54.120581', '', 'Traceback (most recent call last):\n', '', '']
['stderr', '2023-05-29 12:50:54.120616', '', '  File "/home/henry/Documents/pybpod-project/tasks/emulator_mouse2afc_example/emulator_mouse2afc_example.py", line 8, in <module>\n', '', '']
['stderr', '2023-05-29 12:50:54.120752', '', '    ', '', '']
['stderr', '2023-05-29 12:50:54.120791', '', 'Mouse2AFC(bpod).run()', '', '']
['stderr', '2023-05-29 12:50:54.120823', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.120855', '', '  File "/home/henry/Documents/mouse2afc/mouse2afc.py", line 99, in run\n', '', '']
['stderr', '2023-05-29 12:50:54.120998', '', '    ', '', '']
['stderr', '2023-05-29 12:50:54.121036', '', 'self._bpod, self._task_parameters, self._data, i_trial)', '', '']
['stderr', '2023-05-29 12:50:54.121070', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.121102', '', '  File "/home/henry/Documents/mouse2afc/state_matrix.py", line 537, in __init__\n', '', '']
['stderr', '2023-05-29 12:50:54.121381', '', '    ', '', '']
['stderr', '2023-05-29 12:50:54.121420', '', 'output_actions=(IncorrectChoice_Signal + WaitFeedbackStim))', '', '']
['stderr', '2023-05-29 12:50:54.121453', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.121485', '', '  File "/home/henry/Documents/chris-pybpod/base/pybpod-api/pybpodapi/state_machine/state_machine_base.py", line 229, in add_state\n', '', '']
['stderr', '2023-05-29 12:50:54.121670', '', '    ', '', '']
['stderr', '2023-05-29 12:50:54.121708', '', '+ " is an invalid output name."', '', '']
['stderr', '2023-05-29 12:50:54.121740', '', '\n', '', '']
['stderr', '2023-05-29 12:50:54.121775', '', 'pybpodapi.state_machine.state_machine_base', '', '']
['stderr', '2023-05-29 12:50:54.121808', '', '.', '', '']
['stderr', '2023-05-29 12:50:54.121839', '', 'SMAError', '', '']
['stderr', '2023-05-29 12:50:54.121871', '', ': ', '', '']
['stderr', '2023-05-29 12:50:54.121901', '', 'Error creating state: Punishment. Wire1 is an invalid output name.', '', '']
['stderr', '2023-05-29 12:50:54.121934', '', '\n', '', '']

HenryJFlynn · 2023-05-29T12:27:34Z

Found another work around for ^^. In the task parameter gui, don't select BeepOnWire_1

Similarly, this error can happens with the state WaitForPunishStart due to its output of Wire1OutError :

# Wire1 settings
        Wire1OutError = iff(task_parameters.Wire1VideoTrigger, [(
                            'Wire2', 2)], [])
        Wire1OutCorrectCondition = task_parameters.Wire1VideoTrigger and \
            data.Custom.CatchTrial[i_trial]
        Wire1OutCorrect = iff(Wire1OutCorrectCondition,
                              [('Wire2', 2)], [])

If these two options are not selected to avoid ('WireX','Y') as an output, the protocol runs fun. There issue is with the wire outputs

HenryJFlynn · 2023-05-29T13:46:06Z

pybpod gets its firmware and version from the api settings file. There is no way to easily change them as a user. To do this, we would like to add a snippet of code in board_com.py which takes the firmware and version type from a user_settings files which we specifiy

I was wrong. We don't need to do this. Copy and pasting the desired settings into the user settings you can set in the gui works fine.

My setting look like this
SETTINGS_PRIORITY = 0

GENERIC_EDITOR_PLUGINS_LIST = ['pybpodgui_plugin', 'pybpod_gui_plugin_emulator']

TARGET_BPOD_FIRMWARE_VERSION = "8"
EMULATOR_BPOD_MACHINE_TYPE = 1

BPOD_BNC_PORTS_ENABLED = [True, True]
BPOD_WIRED_PORTS_ENABLED = [True, True, True, True]
BPOD_BEHAVIOR_PORTS_ENABLED = [True, True, True, False, False, False, False, False]
and I get this this

I was wrong about being wrong. I got the protocol to run without Wire1 is an invalid output name by 1. Changing the api settings files firmware and machine type and 2. Keeping

> BPOD_BNC_PORTS_ENABLED = [True, True]
> BPOD_WIRED_PORTS_ENABLED = [True, True, True, True]
> BPOD_BEHAVIOR_PORTS_ENABLED = [True, True, True, False, False, False, False, False]

in user settings. For some reason without it, pybpod crashes. Specifcally the file inside /home/henry/Documents/chris-pybpod/base/pybpod-api/pybpodapi/settings.py

HenryJFlynn · 2023-05-29T13:51:03Z

I do not understand why it works or doesn't work.

HenryJFlynn · 2023-05-30T08:34:44Z

I would like to do the first idea of inputting a line or two to check for user settings which would then overwrite the current settings as to add the current firmware and number of ports etc. My problem is finding where the program gets its settings to begin with

HenryJFlynn · 2023-05-30T09:23:28Z

in board_com.py

# load bpod configuration template
        template = os.path.join(os.path.dirname(__file__), 'run_settings_template.py')
        bpod_settings = open(template, 'r').read().format(
            serialport=board.serial_port,
            bnp_ports=('BPOD_BNC_PORTS_ENABLED = {0}'.format(board.enabled_bncports) if board.enabled_bncports else ''),
            wired_ports=('BPOD_WIRED_PORTS_ENABLED = {0}'.format(board.enabled_wiredports) if board.enabled_wiredports else ''),
            behavior_ports=('BPOD_BEHAVIOR_PORTS_ENABLED = {0}'.format(board.enabled_behaviorports) if board.enabled_behaviorports else ''),
            session_name=session.name,
            netport=board_task.board.net_port,
            stream2stdout=not detached,
            project=session.project.name,
            experiment=session.setup.experiment.name,
            board=board_task.board.name,
            setup=session.setup.name,
            session=session.name,
            protocolname=board_task.task.name,
            session_path=os.path.abspath(session.path).encode('unicode_escape').decode(),
            subjects=','.join(list(map(lambda x: '"'+str(x)+'"', session.subjects))),
            user=json.dumps([session.user.name, str(session.user.uuid4), session.user.connection] if session.user.uuid4 else None),
            subject_extra=','.join(list(map(lambda x: '"'+str(x)+'"', xt_subject))),
            user_extra=xt_user,
            variables_names=','.join(["'"+var.name+"'" for var in board_task.variables]),
            bpod_firmware_version=conf.TARGET_BPOD_FIRMWARE_VERSION
        )

The bpod_firmware_version=conf.TARGET_BPOD_FIRMWARE_VERSION is read from the gui user settings

ckarageorgkaneen · 2023-05-30T09:26:17Z

in board_com.py

# load bpod configuration template
        template = os.path.join(os.path.dirname(__file__), 'run_settings_template.py')
        bpod_settings = open(template, 'r').read().format(
            serialport=board.serial_port,
            bnp_ports=('BPOD_BNC_PORTS_ENABLED = {0}'.format(board.enabled_bncports) if board.enabled_bncports else ''),
            wired_ports=('BPOD_WIRED_PORTS_ENABLED = {0}'.format(board.enabled_wiredports) if board.enabled_wiredports else ''),
            behavior_ports=('BPOD_BEHAVIOR_PORTS_ENABLED = {0}'.format(board.enabled_behaviorports) if board.enabled_behaviorports else ''),
            session_name=session.name,
            netport=board_task.board.net_port,
            stream2stdout=not detached,
            project=session.project.name,
            experiment=session.setup.experiment.name,
            board=board_task.board.name,
            setup=session.setup.name,
            session=session.name,
            protocolname=board_task.task.name,
            session_path=os.path.abspath(session.path).encode('unicode_escape').decode(),
            subjects=','.join(list(map(lambda x: '"'+str(x)+'"', session.subjects))),
            user=json.dumps([session.user.name, str(session.user.uuid4), session.user.connection] if session.user.uuid4 else None),
            subject_extra=','.join(list(map(lambda x: '"'+str(x)+'"', xt_subject))),
            user_extra=xt_user,
            variables_names=','.join(["'"+var.name+"'" for var in board_task.variables]),
            bpod_firmware_version=conf.TARGET_BPOD_FIRMWARE_VERSION
        )

The bpod_firmware_version=conf.TARGET_BPOD_FIRMWARE_VERSION is read from the gui user settings

Put more custom settings in the GUI user settings. Then put a breakpoint after this statement and run a protocol. When the breakpoint is reached, print the contents of conf. If all the custom settings that you added are in there, then they are in fact picked up.

HenryJFlynn · 2023-05-31T08:01:00Z

See HenryJFlynn/pybpod-gui-api#1 for the fix to Error creating state: Punishment. Wire1 is an invalid output name

HenryJFlynn · 2023-05-31T08:33:16Z

Currently the pybpod task parameters settings are so that there is little to no time to make a choice. You centerpoke and before you can pokeout the trial is over. Gonna try to fix this by updating the config.py to reflect the settings in the matlab gui.

HenryJFlynn · 2023-05-31T08:35:40Z

Differences between matlab task parameter gui and pybpod

pybpod has no settings for a second experiment
location of certain values
pybpod has no isOptoTrial visible in gui

HenryJFlynn · 2023-05-31T08:44:31Z

Currently the pybpod task parameters settings are so that there is little to no time to make a choice. You centerpoke and before you can pokeout the trial is over. Gonna try to fix this by updating the config.py to reflect the settings in the matlab gui.

This didn't help and made things worse

HenryJFlynn · 2023-05-31T08:46:21Z

['stderr', '2023-05-31 11:43:40.798847', '', 'Before StateMatrix()', '', '']
['stderr', '2023-05-31 11:43:40.798933', '', '\n', '', '']
['stderr', '2023-05-31 11:43:40.800174', '', 'Before send_state_machine()', '', '']
['stderr', '2023-05-31 11:43:40.800325', '', '\n', '', '']
['stderr', '2023-05-31 11:43:40.805836', '', 'Before run_state_machine()', '', '']
['stderr', '2023-05-31 11:43:40.805992', '', '\n', '', '']
['TRIAL', '2023-05-31 11:43:40.806068', '', '', 'New trial', '']
['EVENT', '2023-05-31 11:43:40.816268', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:40.816771', '', '', 'WaitForCenterPoke', '']

['EVENT', '2023-05-31 11:43:44.730820', '', '', '44', 'Port2In']
['TRANSITION', '2023-05-31 11:43:44.730986', '', '', 'PreStimReward', '']
['EVENT', '2023-05-31 11:43:44.740809', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.740978', '', '', 'TriggerWaitForStimulus', '']
['EVENT', '2023-05-31 11:43:44.760811', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.760895', '', '', 'WaitForStimulus', '']
['EVENT', '2023-05-31 11:43:44.760977', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.761256', '', '', 'stimulus_delivery', '']
['EVENT', '2023-05-31 11:43:44.928123', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.928477', '', '', 'BeepMinSampling', '']
['EVENT', '2023-05-31 11:43:44.928582', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.928836', '', '', 'CenterPortRewardDelivery', '']
['EVENT', '2023-05-31 11:43:44.961520', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:44.961872', '', '', 'StimulusTime', '']
['EVENT', '2023-05-31 11:43:45.028618', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:45.029074', '', '', 'WaitCenterPortOut', '']
['EVENT', '2023-05-31 11:43:45.029174', '', '', '63', 'GlobalTimer1_End']
['TRANSITION', '2023-05-31 11:43:45.029250', '', '', 'timeOut_missed_choice', '']
['EVENT', '2023-05-31 11:43:45.039190', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:45.039560', '', '', 'ITI', '']
['EVENT', '2023-05-31 11:43:45.039650', '', '', '67', 'GlobalTimer5_End']
['EVENT', '2023-05-31 11:43:45.059208', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:45.059393', '', '', 'ext_ITI', '']
['EVENT', '2023-05-31 11:43:45.059489', '', '', '77', 'Condition5']
['END-TRIAL', '2023-05-31 11:43:45.059623', '', '', 'The trial ended', '']
['INFO', '2023-05-31 11:43:45.059668', '1685522620.806183', '1685522625.0594468', 'TRIAL-BPOD-TIME', '4.253263711929321']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059704', '0.010018348693847656', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059736', '3.924581289291382', '', '44', 'Port2In']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059764', '3.9345827102661133', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059790', '3.9545962810516357', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059819', '3.9547641277313232', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059845', '4.1218860149383545', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059873', '4.122363567352295', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059899', '4.1552817821502686', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059926', '4.222383260726929', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059952', '4.222947359085083', '', '63', 'GlobalTimer1_End']
['EVENT-SUMMARY', '2023-05-31 11:43:45.059980', '4.232963800430298', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.060006', '4.233433723449707', '', '67', 'GlobalTimer5_End']
['EVENT-SUMMARY', '2023-05-31 11:43:45.060033', '4.2529661655426025', '', '78', 'Tup']
['EVENT-SUMMARY', '2023-05-31 11:43:45.060059', '4.253263711929321', '', '77', 'Condition5']
['STATE', '2023-05-31 11:43:45.060113', '0', '0.010018348693847656', 'ITI_Signal', '0.010018348693847656']
['STATE', '2023-05-31 11:43:45.060164', '0.010018348693847656', '3.924581289291382', 'WaitForCenterPoke', '3.914562940597534']
['STATE', '2023-05-31 11:43:45.060196', '3.924581289291382', '3.9345827102661133', 'PreStimReward', '0.010001420974731445']
['STATE', '2023-05-31 11:43:45.060226', '3.9345827102661133', '3.9545962810516357', 'TriggerWaitForStimulus', '0.02001357078552246']
['STATE', '2023-05-31 11:43:45.060268', '3.9545962810516357', '3.9547641277313232', 'WaitForStimulus', '0.0001678466796875']
['STATE', '2023-05-31 11:43:45.060298', '3.9547641277313232', '4.1218860149383545', 'stimulus_delivery', '0.16712188720703125']
['STATE', '2023-05-31 11:43:45.060340', '4.1218860149383545', '4.122363567352295', 'BeepMinSampling', '0.0004775524139404297']
['STATE', '2023-05-31 11:43:45.060370', '4.122363567352295', '4.1552817821502686', 'CenterPortRewardDelivery', '0.03291821479797363']
['STATE', '2023-05-31 11:43:45.060399', '4.1552817821502686', '4.222383260726929', 'StimulusTime', '0.06710147857666016']
['STATE', '2023-05-31 11:43:45.060428', '4.222383260726929', '4.222947359085083', 'WaitCenterPortOut', '0.0005640983581542969']
['STATE', '2023-05-31 11:43:45.060458', '4.222947359085083', '4.232963800430298', 'timeOut_missed_choice', '0.010016441345214844']
['STATE', '2023-05-31 11:43:45.060488', '4.232963800430298', '4.2529661655426025', 'ITI', '0.020002365112304688']
['STATE', '2023-05-31 11:43:45.060517', '4.2529661655426025', '4.253263711929321', 'ext_ITI', '0.00029754638671875']
['STATE', '2023-05-31 11:43:45.060553', 'nan', 'nan', 'StimDelayGrace', 'nan']
['STATE', '2023-05-31 11:43:45.060581', 'nan', 'nan', 'broke_fixation', 'nan']
['STATE', '2023-05-31 11:43:45.060608', 'nan', 'nan', 'early_withdrawal', 'nan']
['STATE', '2023-05-31 11:43:45.060635', 'nan', 'nan', 'TriggerWaitChoiceTimer', 'nan']
['STATE', '2023-05-31 11:43:45.060662', 'nan', 'nan', 'WaitForChoice', 'nan']
['STATE', '2023-05-31 11:43:45.060689', 'nan', 'nan', 'WaitForRewardStart', 'nan']
['STATE', '2023-05-31 11:43:45.060716', 'nan', 'nan', 'WaitForReward', 'nan']
['STATE', '2023-05-31 11:43:45.060742', 'nan', 'nan', 'RewardGrace', 'nan']
['STATE', '2023-05-31 11:43:45.060768', 'nan', 'nan', 'Reward', 'nan']
['STATE', '2023-05-31 11:43:45.060797', 'nan', 'nan', 'WaitRewardOut', 'nan']
['STATE', '2023-05-31 11:43:45.060824', 'nan', 'nan', 'RegisterWrongWaitCorrect', 'nan']
['STATE', '2023-05-31 11:43:45.060851', 'nan', 'nan', 'WaitForPunishStart', 'nan']
['STATE', '2023-05-31 11:43:45.060877', 'nan', 'nan', 'WaitForPunish', 'nan']
['STATE', '2023-05-31 11:43:45.060906', 'nan', 'nan', 'PunishGrace', 'nan']
['STATE', '2023-05-31 11:43:45.060932', 'nan', 'nan', 'Punishment', 'nan']
['STATE', '2023-05-31 11:43:45.060958', 'nan', 'nan', 'WaitPunishOut', 'nan']
['STATE', '2023-05-31 11:43:45.060984', 'nan', 'nan', 'timeOut_EarlyWithdrawal', 'nan']
['STATE', '2023-05-31 11:43:45.061011', 'nan', 'nan', 'timeOut_EarlyWithdrawalFlashOn', 'nan']
['STATE', '2023-05-31 11:43:45.061037', 'nan', 'nan', 'timeOut_IncorrectChoice', 'nan']
['STATE', '2023-05-31 11:43:45.061063', 'nan', 'nan', 'timeOut_SkippedFeedback', 'nan']
['stderr', '2023-05-31 11:43:45.061852', '', 'Before StateMatrix()', '', '']
['stderr', '2023-05-31 11:43:45.061888', '', '\n', '', '']
['stderr', '2023-05-31 11:43:45.062968', '', 'Before send_state_machine()', '', '']
['stderr', '2023-05-31 11:43:45.063002', '', '\n', '', '']
['stderr', '2023-05-31 11:43:45.067969', '', 'Before run_state_machine()', '', '']
['stderr', '2023-05-31 11:43:45.068011', '', '\n', '', '']
['TRIAL', '2023-05-31 11:43:45.068041', '', '', 'New trial', '']
['EVENT', '2023-05-31 11:43:45.078167', '', '', '78', 'Tup']
['TRANSITION', '2023-05-31 11:43:45.078398', '', '', 'WaitForCenterPoke', '']

['EVENT', '2023-05-31 11:43:45.528845', '', '', '45', 'Port2Out']

as you can all every state transition is a timer which hits immediately. I did Port2In and before i even clicked out the trial ended and restarted which is why you can Port2Out as the last output.

HenryJFlynn · 2023-05-31T08:50:45Z

^^ WaitForChoice and ChoiceDeadline

Currently the pybpod task parameters settings are so that there is little to no time to make a choice. You centerpoke and before you can pokeout the trial is over. Gonna try to fix this by updating the config.py to reflect the settings in the matlab gui.

This didn't help and made things worse

Not all the changes made to config.py are seen in the gui. For exmaples. I changed ITI to =1 which can be seen but ChoiceDeadline I changed to =10 but in the gui it is still =0

HenryJFlynn · 2023-05-31T09:12:10Z

^^ ChoiceDeadline isn't the only problem. If you manually change its value in the gui, the same thing happens. I believe the problem is with the value of GlobalTimer1 which controls this transition

['TRANSITION', '2023-05-31 11:43:45.029074', '', '', 'WaitCenterPortOut', '']
['EVENT', '2023-05-31 11:43:45.029174', '', '', '63', 'GlobalTimer1_End']
['TRANSITION', '2023-05-31 11:43:45.029250', '', '', 'timeOut_missed_choice', '']

While in WaitCenterPortOut the timer ends so fast that a choice can't be made

HenryJFlynn · 2023-05-31T09:56:32Z

next steps: set break points in task_parameters and run protocol to trackd wo how ITI is set and then overwirteen with config data and compare that to choicedeadline which isn't being over writtne with config

HenryJFlynn · 2023-05-31T12:11:03Z

stepping through emulator_run_manual_override,py the variable task_parameters has the changes to ChoceDeadline and ITI which I made in the config file but only ITI is changes in the gui. The variable task_parameters which is using to create the GUI seen here:

class TaskParameters:

    _default_file = fullpath('config.py')

    def __init__(self, file_=None, open_gui=True):
        self._file = file_ or self._default_file
        self.task_parameters = None
        self._load()
        if open_gui:
            app = QApplication(sys.argv)
            self.GUI = TaskParametersGUI(self.task_parameters)
            app.exec_()
        self.task_parameters = AttrDict(**self.task_parameters)

the self.GUI = TaskParametersGUI(self.task_parameters) this self.task_parameters has the changes

HenryJFlynn · 2023-05-31T12:16:42Z

.ui file portion for ITI

</item>
                 <item row="1" column="0">
                  <widget class="QLabel" name="iTILabel">
                   <property name="text">
                    <string>ITI</string>
                   </property>
                  </widget>
                 </item>
                 <item row="1" column="1">
                  <widget class="QSpinBox" name="ITI"/>
                 </item>

vs portion related to ChoiceDeadline

  <item row="3" column="0">
                  <widget class="QLabel" name="choiceDeadlineLabel">
                   <property name="text">
                    <string>ChoiceDeadline</string>
                   </property>
                  </widget>
                 </item>
                 <item row="3" column="1">
                  <widget class="QSpinBox" name="ChoiceDeadline"/>
                 </item>

they're the same so it is not something to do with how the gui was created. I went into Qt Designer and verified this

HenryJFlynn · 2023-05-31T12:34:00Z

Variables which config isn't working with:

ChoiceDeadline ( = 0 )
Ports_LMAir ( = 0 )
PreStimDelayCntrReward ( = 0 )
Left,Cent,Right PokeAttenPct ( = 0 )
PCTimeout ( = False)

Each default to zero or false even tho they are non-zero or true in config

HenryJFlynn · 2023-05-31T13:36:09Z

the error are caused by spelling errors/discrepancies. Must edit .ui with Qt Designer and edit config to match.

In doing this I somehow broke it and am getting a calibration error so i am gonna restart

See #17

HenryJFlynn · 2023-05-31T14:10:19Z

Two problems:

No time to make a choice, likely GlobalTimer1 is set very small
When Ports_LMRAir config settings are picked up by the gui (like they should be) it pops an error. See Fix config and Gui spelling errors #17

HenryJFlynn · 2023-06-01T07:22:11Z

Global timer issue:
In pybpod, the timer is set by this

self.set_global_timer(1, FeedbackDelayCorrect)
...
 FeedbackDelayCorrect = iff(data.Custom.CatchTrial[
            i_trial], Const.FEEDBACK_CATCH_CORRECT_SEC,
            task_parameters.FeedbackDelay)

in matlab

sma = SetGlobalTimer(sma,TimerIDChoiceDeadLine,TaskParameters.GUI.ChoiceDeadLine);

I think the values of all the globaltimer has been jumbled. Globaltimer1 shouldn't be defined by FeedbackDelayCorrect but globaltimer2 should be

HenryJFlynn · 2023-06-01T09:11:14Z

Two problems:

No time to make a choice, likely GlobalTimer1 is set very small

When Ports_LMRAir config settings are picked up by the gui (like they should be) it pops an error. See Fix config and Gui spelling errors #17

For the global timer fix see Correct global timers #19 and 13d7973
For Ports_LMRAir Fix see Fix Ports_LMRAir #20

HenryJFlynn · 2023-06-01T11:36:53Z

Now am trying to get every state triggered, essentially stress testing the protocol

HenryJFlynn · 2023-06-01T11:38:11Z

After CenterPokeIn, a choice is presented that light (left or right) stays on in matlab for the entirety of WaitForChoice but it does not in python.

['EVENT', '2023-06-01 14:39:02.669515', '', '', '44', 'Port2In']
['TRANSITION', '2023-06-01 14:39:02.669700', '', '', 'PreStimReward', '']
['EVENT', '2023-06-01 14:39:02.679525', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.679735', '', '', 'TriggerWaitForStimulus', '']
['EVENT', '2023-06-01 14:39:02.699564', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.699698', '', '', 'WaitForStimulus', '']
['EVENT', '2023-06-01 14:39:02.699796', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.700116', '', '', 'stimulus_delivery', '']
['EVENT', '2023-06-01 14:39:02.866920', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.867315', '', '', 'BeepMinSampling', '']
['EVENT', '2023-06-01 14:39:02.867419', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.867688', '', '', 'CenterPortRewardDelivery', '']
['EVENT', '2023-06-01 14:39:02.900338', '', '', '78', 'Tup']
['TRANSITION', '2023-06-01 14:39:02.900690', '', '', 'StimulusTime', '']

Turning off the light is set somewhere in this, i think

HenryJFlynn · 2023-06-01T11:49:09Z

python the correct answer is always right

HenryJFlynn · 2023-06-01T12:11:35Z

Now am trying to get every state triggered, essentially stress testing the protocol

This is a general goal and not really an issue. Gonna use this idea to find problems which will become issues.

With that I am gonna close this issue

Correct errors

HenryJFlynn added this to Mouse2AFC Protocol May 16, 2023

ckarageorgkaneen assigned HenryJFlynn May 17, 2023

ckarageorgkaneen converted this from a draft issue May 17, 2023

ckarageorgkaneen moved this to Todo in Mouse2AFC Protocol May 17, 2023

ckarageorgkaneen added the enhancement New feature or request label May 25, 2023

ckarageorgkaneen moved this from Todo to In Progress in Mouse2AFC Protocol May 25, 2023

HenryJFlynn mentioned this issue Jun 1, 2023

Fix Ports_LMRAir #20

Closed

HenryJFlynn closed this as completed Jun 1, 2023

github-project-automation bot moved this from In Progress to Done in Mouse2AFC Protocol Jun 1, 2023

HenryJFlynn mentioned this issue Jun 1, 2023

Run protocol on pybpod GUI #9

Closed

HenryJFlynn pushed a commit that referenced this issue Jul 6, 2023

Merge pull request #7 from HenryJFlynn/master

1ed575c

Correct errors

Facilitate pybpod GUI for running protocol #7

Facilitate pybpod GUI for running protocol #7

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