Bcipy

Contributions

Small patch release to fix a missing import in helpers/parameters.py

Our final release candidate before the official 2.0 release!

Contributions

- Multimodal Acquisition and Querying
- Support for multiple devices in online querying 286
- Support for trigger handling relative to a given device 293
- Support multiple device static offests 331
- Support for Device Status (passive or active) 310
- Session Orchestrator 339
- New task protocol for orchestrating tasks in a session. This refactors several Task and Cli functionality 339, 343
- Parameter guardrails 340
- Allow multiple phrases in a single protocol to be defined in a phrase.json and randomized 352
- BciPy Client Additions 346
- Other commands added for offline analysis, visualization and simulation.
- Artifact Module 336
- Simulator 350
- Task
- Calibration Task Refactor: pulls out common elements from RSVP and Matrix calibration tasks 330
- Registry Refactor 332
- Inquiry Preview
- Surface button error probability 347
- Add to Matrix 353
- Bugfixes/Refactor 348
- Add more stoppage criteria 351 (max_incorrect)
- Matrix
- Layout Support 349
- Grid always on 313
- Output stimuli position, screen capture and monitor information after Matrix tasks 303
- Row/Column spacing support 298
- VEP Calibration 304/296
- session data to VEP calibration 322
- Model
- Offline analysis to support multimodal fusion. Initial release of GazeModel, GazeReshaper, and Gaze Visualization 294
- Updates to ensure seamless offline analysis for both EEG and Gaze data 305
- Offline analysis support for EEG and (multiple) gaze models. Updates to support Eye Tracker Evidence class 360
- Language Model
- Add Oracle model 316
- Random Uniform model 311
- Stimuli
- Updates to ensure stimuli are presented at the same frequency 287
- Output stimuli position, screen capture and monitor information after Matrix tasks 303
- Dynamic Selection Window
- Updated trial_length to trial_window to allow for greater control of window used after stimulus presentations 291
- Report
- Functionality to generate a report in the form of a PDF 325
- Add a BciPy Calbiraiton Report Action 357
- Offset Support
- Add support for determining offsets between timing verification Tasks (Ex. RSVPTimingVerificationCalibration) and RawData with a photodiode trigger column. This is useful for setting up new systems and preventing errors before an experiment begins. 327
- Parameters
- Add a Range type parameter 285 Add editable fields 340 Update parameters.json to seperate relevant parameters by task
- Housekeeping
- Add mypy typing to the codebase 301
- Change default log level to INFO to prevent too many messages in the experiment logs 288
- Upgrade requirements for m1/2 chips 299/300
- Fix GitHub actions build issues with macOS 324
- Tests Improvements
- Fix occasionally failing test in `test_stimuli` 326
- Reshaper tests 302
- Fix parameter save as 323
- Pause error 321
- Fix data buffer issue 308
- GUI Refactor 337
- Create new `BCIUI` class for simpler more straightforward UI creation.
- Create dedicated external stylesheet for global styling
- Rewrite Experiment Registry to use new GUI code
- Create intertask action UI
- Task Return Object 334
- Create `TaskData` dataclass to be returned from tasks
- updates task `execute` methods to return an instance of `TaskData`
- Allows for optional storage of a save path and task dictionary in `TaskData`
-Experiment Refactor 333 329
- Refactors the Experiment Field Collection GUI to be an action
- Allows task protocol to be defined in the orchestrator

Contributions

- GUIs
- Parameter GUI `save as` functionality 255
- Parameter GUI user editable parameters defined in `bcipy/parameters.json` 256
- GUI history using a `.bcipy_cache` file 257
- Acquisition
- Set channel spec information in devices.json. Removed aliases. 266 Updated default analysis channels for Wearable Sensing devices 279
- Refactor to allow multiple devices to be configured for multimodal acquisition. 277
- Refinements to LSL server to use the device ChannelSpec information for generating metadata. 282
- Updated data consumers to explicitly set a chunk size. Refinements to LSL server to simulate different chunk sizes. 292
- Matrix
- Matrix calibration refinements 262
- Matrix Copy Phrase Task 261
- Matrix displays can be parameterized with a given number of rows and columns. 289
- RSVP
- RSVP Calibration pulls out inquiry preview parameters and calls the display with them if enabled
- RSVP Display `do_inquiry` accepts a preview_calibration argument that will present the full inquiry to come if True after the prompt and before the fixation
- RSVP Calibration now support Inquiry Preview 267
- Signal Processing
- update from `sosfilt` to `sosfiltfilt` 269 add prestimulus to trial reshaping in the InquiryReshaper 279
- add continuous wavelet transform to signal processing 279
- MNE
- convert to mne can now handle conversion to Volts from microvolts, and no channel map 259
- Dependencies
- Upgrade PsychoPy, transformers (268) and pandas, add support for python3.9, deprecate python3.7 272 upgrade scikit-learn and add pywavelets 279
- BciPy client
- Add `-nv` (no visualizations) and `-f` (fake data) client options 272
- Session
- After each session run using `bci_main` an ERP visualization is generated by default using new function `visualize_session_data` 260 add screen_resolution to logs and an alert if the screen resolution is too low 283
- Language Model
- removed previous `gpt2.py` implementation, replaced with generic Causal model `causal.py` 268
- added KenLM model `kenlm.py` 268
- added mixture model `mixture.py` and script to tune weights `mixture_tuning.py` 268
- added script to evaluate language model performance `lm_eval.py` 268
- Signal Model
- added `RdaKdeModel` and restructured to pull out common elements from the PcaRdaKdeModel 279
- Bug Fixes
- Missing inits and lock some dependencies 258 Fix Windows Builds (pin pygame version) 265 Fix Mac Os Builds (pin pyo version) 432
- Update cross_validation.py 271
- Add jitter to matrix and time tests 281
- Documentation
- Update README.md with correct installation instructions for development requirements 263 and new language model installation instructions 268
- Misc Features!
- Add `tobii_to_norm` and `norm_to_tobii` methods to `helpers/convert.py` 278
- Add a GUI TaskBar display component for Psychopy windows 270

Contributions

- New Display Paradigm: VEP Display 237
- New BciPy Session Features:
- Write session summary after Copy Phrase task 222
- Better Fake Data Handling 219
- Alerting for conditions that may affect system performance 227, 219, 238
- Logging improvements 244
- Device configuration moved to bcipy/parameters 242
- New MNE based plotting for EEG data 220
- New file export features for BciPy data, including .bdf format and prefiltering 246
- New Supported Devices: Tobii-Nano 234
- Bug fixes 218, 225, 228, 235, 240, 246
- Documentation for Matrix Speller and AUC calculation 253

Added

- `display/paradigm/vep`: added create_vep_codes for generating random flicker patterns, VEPBox to encapsulate each flickering box stimuli, and a working VEPDisplay for later task development. 237
- `helpers/visualization.py`: added methods for visualized MNE Epochs and better visualizing EEG data in BciPy. 220 `visualize_joint_average` and `visualize_evokeds`.
- `helpers/stimuli.py`: added a method for converting MNE RawArray to Epochs. 220 Added stimuli flash time jitter to calibration and inq_generation methods 233 Added ssvep_to_code method 232
- `helpers/convert.py`: added a convert to mne method that returns an MNE RawArray. Assumes standard_1020 eeg montage by default.220 Refactored the convert to edf method. Add convert to bdf method for better export resolution. Ensured the static offset output in the parameters file is accounted for. Add a pre-filter option. Fix annotations. 246
- Better handling of the `fake_data` parameter to avoid erroneous recordings. Added a confirmation dialog when the `fake_data` parameter is set to `True` to alert users that they are in a system test mode. 219
- `task/data.py`: session data contains more contextual data for interpreting the results, including the `symbol_set` and the `decision_threshold` used.
- `parameters/parameters.json`: Added `summarize_session` parameter is used to output richer session summaries after a Copy Phrase task. Added the `signal_model_path` parameter. When set this can be used for loading the pre-trained signal model during typing sessions.
- `config.py`: Added a config file for static paths and other constants 241 enabling bcipy to be called as a package outside of root 242


Updated

- `helpers/visualization.py`: `visualize_erp` updated to use MNE for average ERP plots + topomaps. 220 fix to demo 240
- `helpers/raw_data.py`: updated channel methods to accept transformation argument and return sampling rate. Add by_channel map method to call by_channel and remove channels by map ([0, 1, 1]). 220
- `gui.main.py`--> `gui/main.py`: refactor to follow rest of codebase convention. 218
- `bcipy/gui/BCInterface.py`: to include timeouts on buttons creating subprocess- this prevents multiple unintended windows or functionality from occurring after double clicks. 218 added alert to let experimenter know when a session has completed. Allow for custom paramter setting in GUI for offline_analysis (defaults to same as current, `bcipy/parameters.json`) 235

Removed

- `task/paradigm/rsvp/copy_phrase.py`: removed await_start to prevent two space hits for the task to start 225
- TCP-based data acquisition modules were removed 249

Contributions

This version contains major refactoring efforts and features. We anticipate a few additional refactor efforts in the near term based on feature requests from the community and (CAMBI)[cambi.tech]. These will support multi-modality, data sharing, and more complex language modeling. We are utilizing a release candidate to make features and bugfixes available sooner despite the full second version being in-progress. Thank you for your understanding and continued support! All pull requests in Github from 123 until 217 represent the 2.0.0-rc.1 work.

The highlights:

- `Acquisition Enhancements`: multi-modal support and better performance overall! 171, 174
- `Language Model Refactor`: deprecation of docker base models. Addition of `LanguageModel` base class, `UniformLanguageModel` and a hugggingface model `GPT2LanguageModel`. 207
- `Signal Model Refactor`: Refactor with base class definitions and general cleanup. PcaRdaKde model updates to decrease training time and limit the magnitude of likelihood responses. 132, 140, 141, 147, 208
- `Matrix Display: SCP`: A single character flash Matrix speller is now integrated. A `MatrixDisplay` and accompanying `MatrixCalibration` + `Matrix Time Test Calibration`. 192, 205, 213
- `Inquiry Preview`: a mode in RSVP spelling that allows a user to see an inquiry before it is presented in a serial fashion. The user may also engage with the preview using a key press; either to confirm or skip an inquiry. See below for more details.
- `GUI updates`: all BciPy core GUIs and methods are converted to PyQt5 for better cross-platform availability and tooling. See below for more details.
- `Linux compatibility`: with the upgrading of dependencies and a helpful shell script (see `scripts/shell/linux_requirements.sh`) for setting up new machines, we are linux compatible. See below for more details.
- `Prestimulus buffer and Inquiry Based Training` - support to add prestimulus data to reshaping and data queries to permit better filter application. Additionally, use this buffer and the inquiry reshaper to mimic data experienced in real time during training in offline_analysis.py 208

The details (incomplete, our apologies!):

Added

- `Makefile`: `run-with-defaults` make command for running `bcipy` and `viewer` command for running the data viewer 149
- `.bcipy/README.md`: describes experiments and fields in greater detail 156
- `signal/process/filter.py`: add `Notch` and `Bandpass` as classes 147
- `signal/process/transform.py`: add `Composition`, `Downsample`, and `get_default_transform` 147
- `helpers/visualization.py`: moved plot_edf function from demo to this module 126
- `helpers/raw_data.py`: module for raw data format support in BciPy 160
- `helpers/load.py`: add `load_users` method for extracting user names from data save location 125 add extract_mode method for determining the mode 126
- `helpers/task/`: add `Reshaper`, refactor trial reshaper and add inquiry reshaper 147 add `get_key_press` method with custom stamp argument. 129
- `helpers/stimuli.StimuliOrder`: defined ordering of inquiry stimuli. The current approach is to randomize. This adds an alphabetical option. 153
- `helpers/stimuli.alphabetize`: method for taking a list of strings and returning them in alphabetical order with characters last in the list. 153
- `helpers/validate`: `_validate_experiment_fields` and `validate_experiments`: validates experiments and fields in the correct format 156
- `bcipy/helpers/system_utils`: add report execution decorator 163
- `scripts/shell/linux_requirements.sh`: add script for installing necessary dependencies on linux systems 167
- `.github/workflows/main.yml`: adds support for CI in BciPy 166
- `bcipy/gui/file_dialog.py`: PyQt5 window for prompting for file locations 168
- `display/paradigm/matrix`: added MatrixDisplay class with single-character presentation (SCP). 180

Updated

- `LICENSE.md`: to used the Hippocratic license 2.1
- `CODE_OF_CONDUCT.md`: to latest version of the Contributor Covenant
- `README.md`: Add new glossary terms: mode, session and task 126 127 and cleanup 129
- `bcipy/main.py`: formally, `bci_main.py`. To give a better console entry point and infrastructure for integration testing. In the terminal, you can now run `bcipy` instead of `python bci_main.py`
- `parameters.json`: add stim_order 153 add max selections 175 remove max_inq_per_trial in favor of max_inq_per_series 176 add inquiry preview 177 with relevant stimuli units in help text, better starting stim_height, and inquiry preview keys 216
- `demo_stimuli_generation.py`: update imports and add a case showing the new ordering functionality. 153
- `copy_phrase_wrapper`: update logging and exception handling. add stim order. 153 BUGFIX: return transformed sampling rate 159
- `random_rsvp_calibration_inq_gen`: rename to `calibration_inquiry_generator` 153
- `ExperimentField.py`: updated to use new alert types with timeouts 156
- `ExperimentRegistry.py`: add the ability to toggle anonymization of field data and use new alert types with timeouts 156
- `FieldRegistry.py`: updated to use new alert types with timeout 156
- `gui/BCInterface.py`: use `load_users` method to populate user dropdown and remove internal BCInterface load method 125
- `gui/gui_main.py`: update to return a value in FormInput, set a value for IntegerInput only if provided 156
- `gui/viewer/data_viewer.py`: Replaced the original WxPython version of the signal data viewer with the new PyQt version 157. Use signal process filters instead of duplicating logic 147.
- `gui/viewer/file_viewer.py`: to use new raw data format 160
- `bcipy/acquisition`: refactored acquisition to support multi-modal acquisition and more performant real-time acquisition. These changes were significant and across multiple PRs. Support for new raw data format 160
- `ring_buffer_test.py` -> `test_ring_buffer.py`: to comply with naming conventions 156
- `signal/model/base_model.py`: add reshaper to base model class, requiring it to be defined in all models and return a `Reshaper`. Fix return types. 147
- `signal/model/offline_analysis.py`: updated to use new reshapers and transforms. 147 updated to report execution time and logging levels 163
- `bcipy/language_model/` --> `bcipy/language/` refactor for clarity and add base class `LanguageModel` 164
- `bcipy/tasks` --> `bcipy/task`: refactor for clarity, add README, organize tasks under paradigm 162 organize tasks operation objects into `control` module 162 178
- `task/paradigm/rsvp/copy_phrase.py`: refactored overall 146 to use new Session classes 127 and updated to use new reshapers and transforms 147 implements current state of inquiry preview 129 177 to account for max selection parameter 175 fix targetness 179
- `bcipy/task/data.py`: to track number of decisions made 175
- `task/control/handler.py`: added the ability to set constants in defined stimuli agent 178
- `task/control/query.py`: remove redundant best_selection in favor of one with constants. Implemented constants in return_stimuli methods. 178
- `display/rsvp/display.py`: refactored to use new trigger pulse and ensure it occurs only on first display call (whether that be `do_inquiry` or `preview_inquiry`) 149 Overall refactoring of properties into `StimuliProperties`, `InformationProperties`, `TaskDisplayProperties`. Added `PreviewInquiryProperties` and `preview_inquiry` kwarg. Add full-screen parameter to help with scaling stimuli. Add textbox to self.`_create_stimulus`. Add `preview_inquiry` and `_generate_inquiry_preview` methods. 129
- `static/images/gui_images`: updated to `gui` and refactored where defined 149
- `bcipy/display/main.py`: move `StimuliProperties`, `InformationProperties`, `TaskDisplayProperties` and `PreviewInquiryProperties` to higher level 180


- `helpers/stimuli.py `: refactored for clarity and add `get_fixation` method 149 glossary updates and remove unneeded code 178 fix targetness in copy phrase 179
- `helpers/triggers.py`: refactored `_calibration_trigger for clarity` and add `CalibrationType`(deprecating sound and adding text) 149 add an offset correction method 126
- `helpers/load.py`: updated to use new raw data format 160
- `helpers/convert.py`: mode, write_targetness, and annotation_channels keyword arguments 126 add compression/decompression support for experiments and BciPy session data 173
- `helpers/session.py`: refactored session helpers to use the new Session data structures. 127
- `helpers/exceptions`: refactored Field and Experiment exceptions to corresponding base exception 156
- `feedback/auditory_feedback`: to allow for easier setting of relevant parameters and testing 128
- `feedback/visual_feedback`: deprecate shape feedback type, line_color (in the administer method), and compare assertion as both were unused and added unneeded complexity. Set hard-coded values on the class instance for easier changing later. 128

Removed

- `target_rsvp_inquiry_generator`: 153 unused
- `rsvp_copy_phrase_inq_generator`: 153 unused
- `tasks/rsvp/icon_to_icon.py`: 129 unused
- `tasks/rsvp/calibration/inter_inquiry_feedback_calibration.py`: unused
- `generate_icon_match_images`: 153 deprecated task
- `signal/process/demo/text_filter_demo.py`: 147 removes old matlab generated filter
- `signal/process/filter/resources/filters.txt`: 147 in favor of new filters and transforms
- `signal/process/filter/notch.py`: 147 in favor of new filters and transforms
- `signal/process/filter/downsample.py`: 147 in favor of new filters and transforms
- `signal/process/filter/bandpass.py`: 147 in favor of new filters and transforms

Contributions

This version contains major refactoring and tooling improvements across the codebase. In addition, it introduces the concept of BciPy Experiments and Fields. Below we describe the major changes along with a PR in github where applicable.

Added
- Language model histogram 91
- BciPy official glossary (Sequence -> Inquiry & Epoch -> Series) 121
- System information to `system_utils` (cpu, platform, etc) 98
- BciPy Experiments and Fields: See PRs 113 111, 114 for more information on the additions!
- `.bcipy` system directory to support experiment and fields 100
- support for python 3.7
- `rsvp/query_mechanisms`: to model the way we build inquiries 108
- `Makefile`: contains useful install and development commands
- `convert`: a module for data conversions that will be useful for data sharing. Implemented a conversion function to the EDF format. 104
- `exceptions`: a module for BciPy core exceptions

Updated
- `acquisition`: refactored the acquisition module to separate the concept of a device (ex. DSI-24 headset) and a connection method to that device (TCP or LSL). 122
- `setup.py`: with new repo location and CAMBI official support email
- `offline_analysis`: to pull parameters from session file 90
- `requirements.txt`: to the latest available 99 107
- `Parameters` (added help text, removed redundant parameters). Refactored to make them immutable. 101
- `gui_main `: to use PyQt5. We will refactor all GUI code to use this in the future. After this PR, the signal viewer (WxPython) and a couple of loading functions will remain (Tk). 102
- `BCInterface` : updated to use new gui_main methods. Added user if validations. 102 120
- `params_form`: moved into a parameters modules within GUI and updated to use PyQt5. 109
- `dev_requirements`: used to be called test_requirements. It contains more than that, so we updated the name! 99
- `README`: with relevant updates and contributors

Removed
- `RSVPKeyboard.py`