Simulator fix and orchestrator saving updates (#358)

CHANGELOG.md

@@ -7,36 +7,68 @@ Our final release candidate before the official 2.0 release!
 - Multimodal Acquisition and Querying
     - Support for multiple devices in online querying #286
     - Support for trigger handling relative to a given device #293
-- Session Orchestrator
-    - New task protocol for orchestrating tasks in a session. This refactors several Task and Cli functionality #339
+    - 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
+- 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
+    - Updates to ensure stimuli are presented at the same frequency #287 
 - 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. #TODO
+  - 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
-    - Fix occasionally failing test in `test_stimuli` #326
-- GUI Refactor
+    - 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
+- 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
+-Experiment Refactor #333 #329
   - Refactors the Experiment Field Collection GUI to be an action
   - Allows task protocol to be defined in the orchestrator
 
@@ -77,7 +109,6 @@ Our final release candidate before the official 2.0 release!
     - 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
-    - added Oracle model #316
 - Signal Model
     - added `RdaKdeModel` and restructured to pull out common elements from the PcaRdaKdeModel #279
 - Bug Fixes

bcipy/config.py

@@ -27,9 +27,9 @@
 DEFAULT_USER_ID = 'test_user'
 TASK_SEPERATOR = '->'
 
-DEFAULT_PARAMETER_FILENAME = 'parameters.json'
+DEFAULT_PARAMETERS_FILENAME = 'parameters.json'
 DEFAULT_DEVICES_PATH = f"{BCIPY_ROOT}/parameters"
-DEFAULT_PARAMETERS_PATH = f'{BCIPY_ROOT}/parameters/{DEFAULT_PARAMETER_FILENAME}'
+DEFAULT_PARAMETERS_PATH = f'{BCIPY_ROOT}/parameters/{DEFAULT_PARAMETERS_FILENAME}'
 DEFAULT_DEVICE_SPEC_FILENAME = 'devices.json'
 DEVICE_SPEC_PATH = f'{BCIPY_ROOT}/parameters/{DEFAULT_DEVICE_SPEC_FILENAME}'
 DEFAULT_LM_PARAMETERS_FILENAME = 'lm_params.json'

bcipy/display/__init__.py

@@ -8,7 +8,6 @@
     Display,
     InformationProperties,
     init_display_window,
-    PreviewInquiryProperties,
     StimuliProperties,
     VEPStimuliProperties
 )
@@ -20,5 +19,4 @@
     'StimuliProperties',
     'VEPStimuliProperties',
     'InformationProperties',
-    'PreviewInquiryProperties'
 ]

bcipy/display/main.py

@@ -251,37 +251,6 @@ class ButtonPressMode(Enum):
     REJECT = 2
 
 
-class PreviewInquiryProperties:
-    """"Preview Inquiry Properties.
-    An encapsulation of properties relevant to preview_inquiry() operation.
-    """
-
-    def __init__(
-            self,
-            preview_on: bool,
-            preview_only: bool,
-            preview_inquiry_length: float,
-            preview_inquiry_progress_method: int,
-            preview_inquiry_key_input: str,
-            preview_inquiry_isi: float):
-        """Initialize Inquiry Preview Parameters.
-
-        preview_on(bool): If True, display an inquiry preview before the main inquiry.
-        preview_only(bool): If True, only preview the inquiry and do not probe for response
-        preview_inquiry_length(float): Length of time in seconds to present the inquiry preview
-        preview_inquiry_progress_method(int): Method of progression for inquiry preview.
-            0 == preview only; 1 == press to accept inquiry; 2 == press to skip inquiry.
-        preview_inquiry_key_input(str): Defines which key should be listened to for progressing
-        preview_inquiry_isi(float): Length of time after displaying the inquiry preview to display a blank screen
-        """
-        self.preview_on = preview_on
-        self.preview_inquiry_length = preview_inquiry_length
-        self.preview_inquiry_key_input = preview_inquiry_key_input
-        self.press_to_accept = True if preview_inquiry_progress_method == 1 else False
-        self.preview_only = preview_only
-        self.preview_inquiry_isi = preview_inquiry_isi
-
-
 class PreviewParams(NamedTuple):
     """Parameters relevant for the Inquiry Preview functionality.
 

bcipy/display/tests/components/test_button_press_handler.py

@@ -189,3 +189,7 @@ def test_press_to_reject_with_keypress(self, get_key_press_mock):
         self.assertTrue(handler.has_response())
         self.assertEqual('bcipy_key_press_space', handler.response_label)
         self.assertEqual(1.5, handler.response_timestamp)
+
+
+if __name__ == '__main__':
+    unittest.main()

bcipy/helpers/convert.py

@@ -13,7 +13,7 @@
 from tqdm import tqdm
 
 from bcipy.acquisition.devices import preconfigured_device
-from bcipy.config import (DEFAULT_PARAMETER_FILENAME, RAW_DATA_FILENAME,
+from bcipy.config import (DEFAULT_PARAMETERS_FILENAME, RAW_DATA_FILENAME,
                           TRIGGER_FILENAME, SESSION_LOG_FILENAME)
 from bcipy.helpers.load import load_json_parameters, load_raw_data
 from bcipy.helpers.raw_data import RawData
@@ -174,7 +174,7 @@ def pyedf_convert(data_dir: str,
             otherwise a string of the filter parameters used to filter the data
     """
 
-    params = load_json_parameters(str(Path(data_dir, DEFAULT_PARAMETER_FILENAME)),
+    params = load_json_parameters(str(Path(data_dir, DEFAULT_PARAMETERS_FILENAME)),
                                   value_cast=True)
     data = load_raw_data(str(Path(data_dir, f'{RAW_DATA_FILENAME}.csv')))
     fs = data.sample_rate

bcipy/helpers/demo/demo_report.py

@@ -3,7 +3,7 @@
 from bcipy.helpers.triggers import trigger_decoder, TriggerType
 from bcipy.config import (
     BCIPY_ROOT,
-    DEFAULT_PARAMETER_FILENAME,
+    DEFAULT_PARAMETERS_FILENAME,
     RAW_DATA_FILENAME,
     TRIGGER_FILENAME,
     DEFAULT_DEVICE_SPEC_FILENAME)
@@ -44,7 +44,7 @@
             if prompt != 'skip':
                 # load the parameters from the data directory
                 parameters = load_json_parameters(
-                    f'{session}/{DEFAULT_PARAMETER_FILENAME}', value_cast=True)
+                    f'{session}/{DEFAULT_PARAMETERS_FILENAME}', value_cast=True)
 
                 # load the raw data from the data directory
                 raw_data = load_raw_data(Path(session, f'{RAW_DATA_FILENAME}.csv'))

bcipy/helpers/demo/demo_visualization.py

@@ -15,7 +15,7 @@
 """
 import bcipy.acquisition.devices as devices
 from bcipy.config import (DEFAULT_DEVICE_SPEC_FILENAME,
-                          DEFAULT_PARAMETER_FILENAME, RAW_DATA_FILENAME,
+                          DEFAULT_PARAMETERS_FILENAME, RAW_DATA_FILENAME,
                           TRIGGER_FILENAME)
 from bcipy.helpers.acquisition import analysis_channels
 from bcipy.helpers.load import (load_experimental_data, load_json_parameters,
@@ -44,7 +44,7 @@
     if not path:
         path = load_experimental_data()
 
-    parameters = load_json_parameters(f'{path}/{DEFAULT_PARAMETER_FILENAME}',
+    parameters = load_json_parameters(f'{path}/{DEFAULT_PARAMETERS_FILENAME}',
                                       value_cast=True)
 
     # extract all relevant parameters

bcipy/helpers/offset.py

@@ -16,7 +16,7 @@
     DIODE_TRIGGER,
     RAW_DATA_FILENAME,
     DEFAULT_TRIGGER_CHANNEL_NAME,
-    DEFAULT_PARAMETER_FILENAME
+    DEFAULT_PARAMETERS_FILENAME
 )
 
 
@@ -343,7 +343,7 @@ def extract_data_latency_calculation(
         data_path = ask_directory()
 
     # grab the stim length from the data directory parameters
-    stim_length = load_json_parameters(f'{data_path}/{DEFAULT_PARAMETER_FILENAME}', value_cast=True)['stim_length']
+    stim_length = load_json_parameters(f'{data_path}/{DEFAULT_PARAMETERS_FILENAME}', value_cast=True)['stim_length']
 
     raw_data, triggers, static_offset = extract_data_latency_calculation(
         data_path,

bcipy/helpers/save.py

@@ -13,7 +13,7 @@
                           DEFAULT_EXPERIMENT_ID,
                           DEFAULT_LM_PARAMETERS_FILENAME,
                           DEFAULT_LM_PARAMETERS_PATH,
-                          DEFAULT_PARAMETER_FILENAME,
+                          DEFAULT_PARAMETERS_FILENAME,
                           SIGNAL_MODEL_FILE_SUFFIX,
                           STIMULI_POSITIONS_FILENAME)
 from bcipy.signal.model.base_model import SignalModel
@@ -95,7 +95,7 @@ def init_save_data_structure(data_save_path: str,
         os.makedirs(save_directory)
         os.makedirs(os.path.join(save_directory, 'logs'), exist_ok=True)
 
-    copyfile(parameters, Path(save_directory, DEFAULT_PARAMETER_FILENAME))
+    copyfile(parameters, Path(save_directory, DEFAULT_PARAMETERS_FILENAME))
 
     copyfile(DEFAULT_LM_PARAMETERS_PATH, Path(save_directory, DEFAULT_LM_PARAMETERS_FILENAME))
 

bcipy/helpers/session.py

@@ -17,7 +17,7 @@
 WHITE = COLOR_INDEX[1]
 YELLOW = COLOR_INDEX[5]
 from bcipy.config import (BCIPY_ROOT, DEFAULT_ENCODING,
-                          DEFAULT_PARAMETER_FILENAME, EXPERIMENT_DATA_FILENAME,
+                          DEFAULT_PARAMETERS_FILENAME, EXPERIMENT_DATA_FILENAME,
                           SESSION_DATA_FILENAME, SESSION_SUMMARY_FILENAME)
 from bcipy.helpers.load import (load_experiment_fields, load_experiments,
                                 load_json_parameters)
@@ -37,7 +37,7 @@ def session_data(data_dir: str) -> Dict:
     not useful for debugging."""
 
     parameters = load_json_parameters(os.path.join(data_dir,
-                                                   DEFAULT_PARAMETER_FILENAME),
+                                                   DEFAULT_PARAMETERS_FILENAME),
                                       value_cast=True)
     session = read_session(os.path.join(data_dir, SESSION_DATA_FILENAME))
     data = session.as_dict(evidence_only=True)

bcipy/helpers/tests/test_convert.py

@@ -12,7 +12,7 @@
 from mockito import mock, unstub, verify, verifyNoMoreInteractions, when
 
 import bcipy.acquisition.devices as devices
-from bcipy.config import (DEFAULT_ENCODING, DEFAULT_PARAMETER_FILENAME,
+from bcipy.config import (DEFAULT_ENCODING, DEFAULT_PARAMETERS_FILENAME,
                           RAW_DATA_FILENAME, TRIGGER_FILENAME)
 from bcipy.helpers import convert
 from bcipy.helpers.convert import (archive_list, compress, convert_to_bdf,
@@ -64,7 +64,7 @@ def create_bcipy_session_artifacts(
                                          filter_high=filter_settings['filter_high'],
                                          filter_low=filter_settings['filter_low'],
                                          filter_order=filter_settings['filter_order'])
-    params.save(write_dir, DEFAULT_PARAMETER_FILENAME)
+    params.save(write_dir, DEFAULT_PARAMETERS_FILENAME)
     return trg_data, data, params
 
 

bcipy/helpers/tests/test_save.py

@@ -6,7 +6,7 @@
 
 from bcipy.config import (
     DEFAULT_PARAMETERS_PATH,
-    DEFAULT_PARAMETER_FILENAME,
+    DEFAULT_PARAMETERS_FILENAME,
     DEFAULT_EXPERIMENT_ID,
     STIMULI_POSITIONS_FILENAME)
 from bcipy.helpers import save
@@ -50,7 +50,7 @@ def test_init_save_data_structure_creates_correct_save_folder(self):
     def test_parameter_file_copies(self):
 
         # construct the path of the parameters
-        param_path = self.save_folder_name + f'/{DEFAULT_PARAMETER_FILENAME}'
+        param_path = self.save_folder_name + f'/{DEFAULT_PARAMETERS_FILENAME}'
 
         # assert that the params file was created in the correct location
         self.assertTrue(os.path.isfile(param_path))

bcipy/signal/evaluate/artifact.py

@@ -7,7 +7,7 @@
 import logging
 
 from bcipy.config import (
-    DEFAULT_PARAMETER_FILENAME,
+    DEFAULT_PARAMETERS_FILENAME,
     RAW_DATA_FILENAME,
     TRIGGER_FILENAME,
     DEFAULT_DEVICE_SPEC_FILENAME,
@@ -577,7 +577,7 @@ def write_mne_annotations(
             if prompt != 'skip':
                 # load the parameters from the data directory
                 parameters = load_json_parameters(
-                    f'{session}/{DEFAULT_PARAMETER_FILENAME}', value_cast=True)
+                    f'{session}/{DEFAULT_PARAMETERS_FILENAME}', value_cast=True)
 
                 # load the raw data from the data directory
                 raw_data = load_raw_data(str(Path(session, f'{RAW_DATA_FILENAME}.csv')))

bcipy/signal/tests/model/test_offline_analysis.py

@@ -9,7 +9,7 @@
 import random
 import gzip
 
-from bcipy.config import RAW_DATA_FILENAME, DEFAULT_PARAMETER_FILENAME, TRIGGER_FILENAME, DEFAULT_DEVICE_SPEC_FILENAME
+from bcipy.config import RAW_DATA_FILENAME, DEFAULT_PARAMETERS_FILENAME, TRIGGER_FILENAME, DEFAULT_DEVICE_SPEC_FILENAME
 from bcipy.helpers.load import load_json_parameters
 from bcipy.signal.model.offline_analysis import offline_analysis
 
@@ -48,7 +48,7 @@ def setUpClass(cls):
         shutil.copyfile(input_folder / TRIGGER_FILENAME, cls.tmp_dir / TRIGGER_FILENAME)
         shutil.copyfile(input_folder / DEFAULT_DEVICE_SPEC_FILENAME, cls.tmp_dir / DEFAULT_DEVICE_SPEC_FILENAME)
 
-        params_path = pwd.parent.parent.parent / "parameters" / DEFAULT_PARAMETER_FILENAME
+        params_path = pwd.parent.parent.parent / "parameters" / DEFAULT_PARAMETERS_FILENAME
         cls.parameters = load_json_parameters(params_path, value_cast=True)
         models = offline_analysis(
             str(cls.tmp_dir),

bcipy/simulator/data/data_process.py

@@ -14,7 +14,7 @@
 from bcipy.acquisition.devices import DeviceSpec
 from bcipy.acquisition.multimodal import ContentType
 from bcipy.config import (DEFAULT_DEVICE_SPEC_FILENAME,
-                          DEFAULT_PARAMETER_FILENAME, TRIGGER_FILENAME)
+                          DEFAULT_PARAMETERS_FILENAME, TRIGGER_FILENAME)
 from bcipy.helpers.acquisition import analysis_channels, raw_data_filename
 from bcipy.helpers.list import grouper
 from bcipy.helpers.load import load_json_parameters, load_raw_data
@@ -270,7 +270,7 @@ def process(self, data_folder: str,
         raw_data, device_spec = load_device_data(data_folder,
                                                  self.content_type.name)
         data_parameters = load_json_parameters(
-            f"{data_folder}/{DEFAULT_PARAMETER_FILENAME}", value_cast=True)
+            f"{data_folder}/{DEFAULT_PARAMETERS_FILENAME}", value_cast=True)
 
         timing_params = parameters.instantiate(TimingParams)