Python Brain-Computer Interface Software
Patch for missing inits and static assets, catch sessions with no data, and move experiment and field assets to parameters location #284
save as functionality #255bcipy/parameters.json #256.bcipy_cache file #257do_inquiry accepts a preview_calibration argument that will present the full inquiry to come if True after the prompt and before the fixationsosfilt to sosfiltfilt #269 add prestimulus to trial reshaping in the InquiryReshaper #279-nv (no visualizations) and -f (fake data) client options #272bci_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 #283gpt2.py implementation, replaced with generic Causal model causal.py #268kenlm.py #268mixture.py and script to tune weights mixture_tuning.py #268lm_eval.py #268RdaKdeModel and restructured to pull out common elements from the PcaRdaKdeModel #279tobii_to_norm and norm_to_tobii methods to helpers/convert.py #278Small patch to rc2. This fixes a missing import in helpers/parameters.py
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. #237helpers/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 #232helpers/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. #246fake_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. #219task/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 #242helpers/visualization.py: visualize_erp updated to use MNE for average ERP plots + topomaps. #220 fix to demo #240helpers/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]). #220gui.main.py--> gui/main.py: refactor to follow rest of codebase convention. #218bcipy/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) #235task/paradigm/rsvp/copy_phrase.py: removed await_start to prevent two space hits for the task to start #225This 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. 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, #174Language Model Refactor: deprecation of docker base models. Addition of LanguageModel base class, UniformLanguageModel and a hugggingface model GPT2LanguageModel. #207Signal 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, #208Matrix Display: SCP: A single character flash Matrix speller is now integrated. A MatrixDisplay and accompanying MatrixCalibration + Matrix Time Test Calibration. #192, #205, #213Inquiry 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 #208The details (incomplete, our apologies!):
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 #156signal/process/filter.py: add Notch and Bandpass as classes #147signal/process/transform.py: add Composition, Downsample, and get_default_transform #147helpers/visualization.py: moved plot_edf function from demo to this module #126helpers/raw_data.py: module for raw data format support in BciPy #160helpers/load.py: add load_users method for extracting user names from data save location #125 add extract_mode method for determining the mode #126helpers/task/: add Reshaper, refactor trial reshaper and add inquiry reshaper #147 add get_key_press method with custom stamp argument. #129helpers/stimuli.StimuliOrder: defined ordering of inquiry stimuli. The current approach is to randomize. This adds an alphabetical option. #153helpers/stimuli.alphabetize: method for taking a list of strings and returning them in alphabetical order with characters last in the list. #153helpers/validate: _validate_experiment_fields and validate_experiments: validates experiments and fields in the correct format #156bcipy/helpers/system_utils: add report execution decorator #163scripts/shell/linux_requirements.sh: add script for installing necessary dependencies on linux systems #167.github/workflows/main.yml: adds support for CI in BciPy #166bcipy/gui/file_dialog.py: PyQt5 window for prompting for file locations #168display/paradigm/matrix: added MatrixDisplay class with single-character presentation (SCP). #180LICENSE.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
target_rsvp_inquiry_generator: #153 unusedrsvp_copy_phrase_inq_generator: #153 unusedtasks/rsvp/icon_to_icon.py: #129 unusedtasks/rsvp/calibration/inter_inquiry_feedback_calibration.py: unusedgenerate_icon_match_images: #153 deprecated tasksignal/process/demo/text_filter_demo.py: #147 removes old matlab generated filtersignal/process/filter/resources/filters.txt: #147 in favor of new filters and transformssignal/process/filter/notch.py: #147 in favor of new filters and transformssignal/process/filter/downsample.py: #147 in favor of new filters and transformssignal/process/filter/bandpass.py: #147 in favor of new filters and transformsThis version contains major refactoring and tooling improvements across the codebase. In addition, it indtrocudes the concept of BciPy Experiments and Fields. Below we describe the major changes along with a PR# in github where applicable.
system_utils (cpu, platform, etc) #98.bcipy system directory to support experiment and fields #100rsvp/query_mechanisms: to model the way we build inquiries #108Makefile: contains useful install and development commandsconvert: a module for data conversions that will be useful for data sharing. Implemented a conversion function to the EDF format. #104exceptions: a module for BciPy core exceptionsacquisition: 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). #122setup.py: with new repo location and CAMBI official support emailoffline_analysis: to pull parameters from session file #90requirements.txt: to the latest available #99 #107Parameters (added help text, removed redundant parameters). Refactored to make them immutable. #101gui_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). #102BCInterface : updated to use new gui_main methods. Added user if validations. #102 #120params_form: moved into a parameters modules within GUI and updated to use PyQt5. #109dev_requirements: used to be called test_requirements. It contains more than that, so we updated the name! #99README: with relevant updates and contributorsRSVPKeyboard.py
Patch for gui.viewer module. Missing init file.
This release focused on bug fixes, exposing parameters, and refactoring. Further dual screen configuration and testing were done to allow for simultaneous signal viewing and task operation.
- Dual screen configuration / updated support
- Parameters:
- Copy phrase decision thresholds
- Inter-sequence Feedback level thresholds
- RSVP Display: refactor
- Decision Maker / Evidence Fusion: refactor
- Signal Viewer: more distinct channel names
- bci_main: shutdown handling and bug fix
- Language Model Helper: bug fix for negative probabilities
- Multicolor Text
- Old LSL viewer
This release focused on the addition of a new Alert Tone Task, integration of the Language Model, and other fixes to make Copy Phrase work better.
- Alert Tone Task: a new calibration task that plays an alert tone prior to displaying the presentation letter. Adds parameters for the directory in which sounds (.wav files) are located as well as the length of the delay.
- SPACE symbol customization: allows users to customize the display of the SPACE character.
- New Language Model: experimental; adds a new oclm Language Model and allows users to select between this and the standard prelm model. Note that this functionality is still incomplete.
- Language Model integration: the Language Model now correctly starts up a Docker container on both Windows and Mac machines.
- Fixes to the CopyPhraseWrapper in its usage of the Language Model, including converting its output to the probability domain for integration, and correctly handling space characters.
- Fix for Copy Phrase backspace selection.
- Fixed issue loading EEG Classifier pkl files.
- General code cleanup in the acquisition module.
- Simplified code for starting a new task.
- There is now a task_registry which lists all available tasks and allows code to enumerate them.
- More obvious feedback when a CopyPhrase letter has been typed.
- Users can now override configuration for parameters with a drop-down menu. The previous behavior was to restrict users to the suggested values.