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2.0.0-rc.4

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

2.0.0-rc.3

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

2.0.1-rc.2

Contributions

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

2.0.0-rc.2

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

2.0.0-rc.1

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

1.5.0

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

1.4.2

Contributions

Added

  • Artifact Rejection
    • signal.evaluate.Evaluator
      • Evaluates sequences and flags sequences that break rules
    • signal.evaluate.Rule
      • Defines rules that sequences should follow
  • Re-added progress indicator for offline analysis
  • Scripts
    • timing_tools.py to help test display timing before experiments
  • Tests
  • Linting
  • Documentation improvements

Updated

  • DAQ file writing. Instead of writing to raw_data.csv during task executions, optionally write raw_data.csv on call to stop_acquisition, and only write to SQLite database during task.
  • get_data queries in buffer_server to increase speed on Windows machines.
  • RSVP sequence stimuli presentation. Reduces reported timing slips on Windows and Linux machines.
    • List of stimuli to be presented is now generated before each sequence is presented, rather than generating stimuli during the sequence.
    • The screen is now only drawn once per stimulus, rather than redrawing the screen every frame.
  • Signal viewer to shut down when data is no longer streaming
  • main_frame and copy_phrase to fix bug that prevents copy phrase tasks from completing in fake data mode
  • Target generation for icon-matching tasks has been changed to minimize instances of duplicate target stimuli over the course of an experiment
  • Fixed issue with icon-matching tasks flashing to desktop on Windows machines
  • params_form.py is now launched by creating another wxPython frame, rather than launching a subprocess

Removed

  • Module additions via __init__

1.4.1

Patch for gui.viewer module. Missing init file.

1.4.0

This release focused on bug fixes, exposing parameters, and refactoring. Further dual screen configuration and testing was done to allow for simultaneous signal viewing and task operation.

Added

- Dual screen configuration / updated support
- Parameters:
        - Copy phrase decision thresholds
        - Inter-sequence Feedback level thresholds

Updated

- 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

Removed

- Multicolor Text
- Old LSL viewer

1.3.0

This release focused on the addition of a Signal Viewer, Inter-sequence Feedback Task, Signal Processing / Decomposition Methods, and miscellaneous cleanup.

Added

- PSD: Power spectral density methods
- DSI VR-300 integration
- Logging session configuration and setup
- Version and git commit extraction
- Inter-sequence feedback task
- Backspace frequency parameterization and implementation
- Bandpass and Notch Filter implementation
- Custom Exceptions

Updated

- Refactor RSVP Task: Icon-to-Icon (WIP)
- Refactored Signal Module
- Dependencies (PsychoPy, pylsl, numpy, pandas, WxPython)
- Tests
- Documentation

Removed

- Bar Graph implementation

1.2.0

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.

New Features

- 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.

Updates

- 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.

1.1.0

This is a working version for use with LSL on Calibration and Copy phrase tasks. It will break implementation from previous release. Future minor versions should not do this.

Updated:

  • Structure of Signal Module
  • Signal Model and Trial Reshaper Refactored
  • Documentation
  • Data acquisition client naming

Added:

  • Image scaling
  • Initial Icon Word matching task
  • Task breaks
  • LSL offset correction
  • Unittests
  • AUC printing to filename
  • logging
  • Initial signal viewer
  • Initial average ERP generation plots
  • GUI enhancements

Removed

  • Duplicate dependencies