Releases: CAMBI-tech/BciPy
2.0.1rc3
2.0.0rc3
2.0.0-rc.3
Contributions
- GUIs
- 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
- Matrix
- 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
- MNE
- convert to mne can now handle conversion to Volts from microvolts, and no channel map #259
- Dependencies
- BciPy client
- Add
-nv
(no visualizations) and-f
(fake data) client options #272
- Add
- Session
- Language Model
- Signal Model
- added
RdaKdeModel
and restructured to pull out common elements from the PcaRdaKdeModel #279
- added
- Bug Fixes
- Documentation
- Misc Features!
2.0.1rc2
2.0.0-rc.2
2.0.0-rc.2
Contributions
- New Display Paradigm: VEP Display #237
- New BciPy Session Features:
- 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. #237helpers/visualization.py
: added methods for visualized MNE Epochs and better visualizing EEG data in BciPy. #220visualize_joint_average
andvisualize_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. #246- Better handling of the
fake_data
parameter to avoid erroneous recordings. Added a confirmation dialog when thefake_data
parameter is set toTrue
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 thesymbol_set
and thedecision_threshold
used.parameters/parameters.json
: Addedsummarize_session
parameter is used to output richer session summaries after a Copy Phrase task. Added thesignal_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 #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
) #235
Removed
2.0.0-rc.1
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. 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 ofLanguageModel
base class,UniformLanguageModel
and a hugggingface modelGPT2LanguageModel
. #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. AMatrixDisplay
and accompanyingMatrixCalibration
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 (seescripts/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 runningbcipy
andviewer
command for running the data viewer #149.bcipy/README.md
: describes experiments and fields in greater detail #156signal/process/filter.py
: addNotch
andBandpass
as classes #147signal/process/transform.py
: addComposition
,Downsample
, andget_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
: addload_users
method for extracting user names from data save location #125 add extract_mode method for determining the mode #126helpers/task/
: addReshaper
, refactor trial reshaper and add inquiry reshaper #147 addget_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
andvalidate_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). #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 runbcipy
instead ofpython 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 tocalibration_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
: useload_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 aReshaper
. 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 classLanguageModel
#164 -
bcipy/tasks
-->bcipy/task
: refactor for clarity, add README, organize tasks under paradigm #162 organize tasks operation objects intocontrol
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 bedo_inquiry
orpreview_inquiry
) #149 Overall refactoring of properties intoStimuliProperties
,InformationProperties
,TaskDisplayProperties
. AddedPreviewInquiryProperties
andpreview_inquiry
kwarg. Add full-screen parameter to help with scaling stimuli. Add textbox to self._create_stimulus
. Addpreview_inquiry
and_generate_inquiry_preview
methods. #129 -
static/images/gui_images
: updated togui
and refactored where defined #149 -
bcipy/display/main.py
: moveStimuliProperties
,InformationProperties
,TaskDisplayProperties
andPreviewInquiryProperties
to higher level #180 -
helpers/stimuli.py
: refactored for clarity and addget_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 addCalibrationType
(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 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 transforms
Version 1.5.0
1.5.0
Contributions
This 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.
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 and #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 #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 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). #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 contributors
Removed
RSVPKeyboard.py
v.1.4.1
v1.4.0
1.4.0
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.
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
v1.2.0
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.