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Report artifact enhancements, README, Python 3.10.6 support #357

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merged 17 commits into from
Oct 29, 2024
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Report artifact enhancements, README, Python 3.10.6 support #357

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a95499a
upgrade mne and wip artifact changes
tab-cmd Oct 24, 2024
66f7f8f
all a prompt in ask directory
tab-cmd Oct 25, 2024
786d7c8
Add demo, update tests and lint
tab-cmd Oct 25, 2024
4ab2938
update coverage config
tab-cmd Oct 25, 2024
d65c694
Update READMEs
tab-cmd Oct 25, 2024
e38d1c8
use the last version compatible with 3.8
tab-cmd Oct 25, 2024
bb089a0
Remove wishlist
tab-cmd Oct 25, 2024
563aceb
try adding python 3.10
tab-cmd Oct 25, 2024
ccb36c8
specify the version of 3.10
tab-cmd Oct 25, 2024
7ebeb8f
upgrade psychopy
tab-cmd Oct 28, 2024
740af67
add text on how artifact defaults were determined
tab-cmd Oct 28, 2024
8afd91d
Add default preview font, add preview text size parameters, add previ…
tab-cmd Oct 28, 2024
e62dd17
update tests
tab-cmd Oct 28, 2024
e5ed717
add missing init files
tab-cmd Oct 28, 2024
402391b
fix wheel install error on simulator
tab-cmd Oct 28, 2024
f5c981a
Add Task metadata needed for the SimulatorCopyPhraseTask
tab-cmd Oct 29, 2024
6fa1dca
lint
tab-cmd Oct 29, 2024
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5 changes: 4 additions & 1 deletion .coveragerc
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,15 @@
[run]
omit =
*__init__*
*__main__*
*/usr/local/lib*
*tests*
*test*
*demo*
*exceptions.py
*/gui/*
*/gui/experiments/*
*/gui/viewer/*
*/gui/BCInterface.py

[report]
exclude_lines =
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6 changes: 3 additions & 3 deletions .github/workflows/main.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [3.8, 3.9]
python-version: [3.8, 3.9, 3.10.6]

steps:
- uses: actions/checkout@v2
Expand Down Expand Up @@ -68,7 +68,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [3.8, 3.9]
python-version: [3.8, 3.9, 3.10.6]

steps:
- uses: actions/checkout@v2
Expand Down Expand Up @@ -103,7 +103,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [3.8, 3.9]
python-version: [3.8, 3.9, 3.10.6]

steps:
- uses: actions/checkout@v4
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -3,7 +3,7 @@ install:

dev-install:
pip install -r dev_requirements.txt
pip install psychopy==2023.2.1 --no-deps
pip install psychopy==2024.2.1 --no-deps
pip install kenlm==0.1 --global-option="--max_order=12"
make install

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105 changes: 78 additions & 27 deletions README.md
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Expand Up @@ -40,7 +40,8 @@ If using zsh, instead of bash, you may encounter a segementation fault when runn
## Installation
---------------

#### BciPy Setup
### BciPy Setup
----------------

In order to run BciPy on your computer, after following the dependencies above, you will need to install the BciPy package.

Expand All @@ -62,26 +63,86 @@ Alternately, if [Make](http://www.mingw.org/) is installed, you may run the foll
make dev-install
```

#### Client Usage
Invoke an experiment protocol or task directly using command line utility `bcipy`.
- You can pass it attributes with flags, if desired.
Running with a User ID and Task: `bcipy --user "bci_user" --task "RSVP Calibration"`
Running with a User ID and Tasks with a registered Protocol: `bcipy --user "bci_user" --experiment "default"`
Running with fake data: `bcipy --fake`
Running without visualizations: `bcipy --noviz`
Running with alerts after each Task execution: `bcipy --alert`
Running with custom parameters: `bcipy --parameters "path/to/valid/parameters.json"`
### Client Usage
----------------

##### Run an experiment protocol or task

Invoke an experiment protocol or task directly using command line utility `bcipy`.

- Use the help flag to see other available input options: `bcipy --help`
- You can pass it attributes with flags, if desired.
- Running with a User ID and Task:
- `bcipy --user "bci_user" --task "RSVP Calibration"`
- Running with a User ID and Tasks with a registered Protocol:
- `bcipy --user "bci_user" --experiment "default"`
- Running with fake data:
- `bcipy --fake`
- Running without visualizations:
- `bcipy --noviz`
- Running with alerts after each Task execution:
- `bcipy --alert`
- Running with custom parameters:
- `bcipy --parameters "path/to/valid/parameters.json"`

##### Train a signal model with registered BciPy models

To train a signal model (currently `PCARDAKDE`), run the following command after installing BciPy:

`bcipy-train`

- Use the help flag to see other available input options: `bcipy-train --help`
- You can pass it attributes with flags, if desired.
- Running without a window prompting for data session folder:
- `bcipy-train -d path/to/data`
- Running with data visualizations (ERPs, etc.):
- `bcipy-train -v`
- Running with data visualizations that do not show, but save to file:
- `bcipy-train -s`
- Running with balanced accuracy:
- `bcipy-train --balanced-acc`
- Running with alerts after each Task execution:
- `bcipy-train --alert`
- Running with custom parameters:
- `bcipy-train -p "path/to/valid/parameters.json"`

##### Visualize ERP data from a session with Target / Non-Target labels

To generate plots that can be shown or saved after collection of data, run the following command after installing BciPy:

`bcipy-erp-viz`

- Use the help flag to see other available input options: `bcipy-erp-viz --help`
- You can pass it attributes with flags, if desired.
- Running without a window prompting for data session folder:
- `bcipy-erp-viz -s path/to/data`
- Running with data visualizations (ERPs, etc.):
- `bcipy-erp-viz --show`
- Running with data visualizations that do not show, but save to file:
- `bcipy-erp-viz --save`
- Running with custom parameters (default is in bcipy/parameters/parameters.json):
- `bcipy-erp-viz -p "path/to/valid/parameters.json"`

##### BciPy Simulator Usage

The simulator can be run using the command line utility `bcipy-sim`.

Ex.
`bcipy-sim -d my_data_folder/ -p my_parameters.json -m my_models/ -n 5`

Run `bcipy-sim --help` for documentation or see the README in the simulator module.

- Use the help flag to see other available input options: `bcipy --help`

##### Example Usage as a Package
### Package Usage
-------------------

```python
from bcipy.helpers import system_utils
system_utils.get_system_info()
```

#### Example Usage through the GUI
### GUI Usage
-------------

Run the following command in your terminal to start the BciPy GUI:
```sh
Expand All @@ -95,16 +156,6 @@ make bci-gui
```


#### Simulator Usage

The simulator can be run using the command line utility `bcipy-sim`.

Ex.
`bcipy-sim -d my_data_folder/ -p my_parameters.json -m my_models/ -n 5`

Run `bcipy-sim --help` for documentation or see the README in the simulator module.


## Glossary
-----------

Expand Down Expand Up @@ -150,7 +201,7 @@ This a list of the major modules and their functionality. Each module will conta
## Paradigms
------------

See `bcipy/task/README.md` for more information on all supported paradigms and modes. The following are the supported and validated paradigms:
See `bcipy/task/README.md` for more information on all supported paradigms, tasks, actions and modes. The following are the supported and validated paradigms:


> RSVPKeyboard
Expand Down Expand Up @@ -213,7 +264,6 @@ After running the above command, the recommended offset correction value will be
```bash
# Let's say the recommneded offset value is 0.1
python bcipy/helpers/offset.py --offset "0.1" -p

```

Alternately, if Make is installed, you may run the follow command to run offset determination and display the results:
Expand Down Expand Up @@ -306,10 +356,11 @@ make type


### Contributions Welcome!
--------------------------

If you want to be added to the development team slack or have additional questions, please reach out to us at [email protected]!

### Contribution Guidelines
#### Contribution Guidelines

We follow and will enforce the contributor's covenant to foster a safe and inclusive environment for this open source software, please reference this link for more information: https://www.contributor-covenant.org/

Expand All @@ -325,7 +376,7 @@ Other guidelines:

See this resource for examples: http://docs.python-guide.org/en/latest/writing/style/

## Contributors
### Contributors
---------------

All contributions are greatly appreciated!
Expand Down
1 change: 1 addition & 0 deletions bcipy/display/main.py
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Expand Up @@ -293,6 +293,7 @@ class PreviewParams(NamedTuple):
preview_inquiry_key_input: str
preview_inquiry_progress_method: int
preview_inquiry_isi: float
preview_box_text_size: float

@property
def button_press_mode(self):
Expand Down
13 changes: 8 additions & 5 deletions bcipy/display/paradigm/rsvp/display.py
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Expand Up @@ -73,6 +73,8 @@ def __init__(
self.stimuli_colors = stimuli.stim_colors
self.stimuli_timing = stimuli.stim_timing
self.stimuli_font = stimuli.stim_font
# Note: there is a bug in TextBox2 that prevents certain custom fonts from being used. This is to avoid that.
self.textbox_font = 'Consolas'
self.stimuli_height = stimuli.stim_height
self.stimuli_pos = stimuli.stim_pos
self.is_txt_stim = stimuli.is_txt_stim
Expand Down Expand Up @@ -271,13 +273,12 @@ def _generate_inquiry_preview(self) -> visual.TextBox2:
text = ' '.join(self.stimuli_inquiry).split('+ ')[1]

return self._create_stimulus(
0.12,
self.preview_params.preview_box_text_size,
stimulus=text,
units='height',
stimuli_position=self.stimuli_pos,
mode='textbox',
align_text='left',
wrap_width=0.025)
align_text='left')

def _generate_inquiry(self) -> list:
"""Generate inquiry.
Expand Down Expand Up @@ -439,9 +440,11 @@ def _create_stimulus(
borderWidth=2,
borderColor='white',
units=units,
font=self.stimuli_font,
padding=0.05,
font=self.textbox_font,
letterHeight=height,
size=[.5, .5],
size=[.55, .55],
pos=stimuli_position,
alignment=align_text,
editable=False,
)
6 changes: 4 additions & 2 deletions bcipy/display/tests/paradigm/matrix/test_matrix_display.py
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Expand Up @@ -143,7 +143,8 @@ def test_do_inquiry_with_preview_accepted(self):
preview_inquiry_length=2,
preview_inquiry_key_input='return',
preview_inquiry_progress_method=2,
preview_inquiry_isi=1)
preview_inquiry_isi=1,
preview_box_text_size=0.1)
matrix = MatrixDisplay(window=self.window,
experiment_clock=self.experiment_clock,
stimuli=self.stimuli,
Expand Down Expand Up @@ -181,7 +182,8 @@ def test_do_inquiry_with_preview_rejected(self):
preview_inquiry_length=2,
preview_inquiry_key_input='return',
preview_inquiry_progress_method=2,
preview_inquiry_isi=1)
preview_inquiry_isi=1,
preview_box_text_size=0.1)
matrix = MatrixDisplay(window=self.window,
experiment_clock=self.experiment_clock,
stimuli=self.stimuli,
Expand Down
21 changes: 14 additions & 7 deletions bcipy/display/tests/paradigm/rsvp/test_rsvp_display.py
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Expand Up @@ -134,7 +134,8 @@ def test_preview_enabled_is_false(self):
preview_inquiry_length=2,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=1,
preview_inquiry_isi=1)
preview_inquiry_isi=1,
preview_box_text_size=0.1)
rsvp = RSVPDisplay(self.window,
self.static_clock,
self.experiment_clock,
Expand All @@ -151,7 +152,8 @@ def test_preview_enabled_is_true(self):
preview_inquiry_length=2,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=1,
preview_inquiry_isi=1)
preview_inquiry_isi=1,
preview_box_text_size=0.1)
rsvp = RSVPDisplay(self.window,
self.static_clock,
self.experiment_clock,
Expand All @@ -173,7 +175,8 @@ def test_preview_inquiry_evoked_press_to_accept_pressed(
preview_inquiry_length=0.01,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=1,
preview_inquiry_isi=0.01)
preview_inquiry_isi=0.01,
preview_box_text_size=0.1)
self.init_display(preview_config)

button_press_handler_mock.has_response.return_value = True
Expand Down Expand Up @@ -209,7 +212,8 @@ def test_preview_inquiry_evoked_press_to_skip_pressed(
preview_inquiry_length=0.01,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=2,
preview_inquiry_isi=0.01)
preview_inquiry_isi=0.01,
preview_box_text_size=0.1)
self.init_display(preview_config)

button_press_handler_mock.has_response.return_value = True
Expand Down Expand Up @@ -238,7 +242,8 @@ def test_preview_inquiry_evoked_press_to_accept_not_pressed(
preview_inquiry_length=0.01,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=1,
preview_inquiry_isi=0.01)
preview_inquiry_isi=0.01,
preview_box_text_size=0.1)
self.init_display(preview_config)

button_press_handler_mock.has_response.return_value = False
Expand All @@ -264,7 +269,8 @@ def test_preview_inquiry_evoked_press_to_skip_not_pressed(
preview_inquiry_length=0.01,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=2,
preview_inquiry_isi=0.01)
preview_inquiry_isi=0.01,
preview_box_text_size=0.1)
self.init_display(preview_config)

button_press_handler_mock.has_response.return_value = False
Expand All @@ -290,7 +296,8 @@ def test_preview_inquiry_preview_only_response_registered(
preview_inquiry_length=0.01,
preview_inquiry_key_input='space',
preview_inquiry_progress_method=0,
preview_inquiry_isi=0.01)
preview_inquiry_isi=0.01,
preview_box_text_size=0.1)
self.init_display(preview_config)

button_press_handler_mock.has_response.return_value = False
Expand Down
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