Merge pull request #7 from int-brain-lab/neuromodulatorsExtraction

Several fixes

README.md

@@ -13,4 +13,4 @@ pip install -e .
 - `projects/task_extractor_map.json` - Map custom task protocols to Bpod trials extractor class
 - `projects/task_type_procedures.json` - Associate Alyx procedures to a custom task protocol
 - `projects/_template.py` - Example for creating a custom Bpod extractor, QC or DAQ sync task
-- `projects/_extraction_tasks.py` - Where to import pipeline tasks so they are readable by ibllib
+- `projects/extraction_tasks.py` - Where to import pipeline tasks so they are readable by ibllib

iblrig_custom_tasks/_sp_passiveVideo/task.py

@@ -7,6 +7,7 @@
 from pathlib import Path
 from collections import defaultdict
 import logging
+import warnings
 
 import pandas as pd
 from pybpodapi.protocol import Bpod
@@ -19,8 +20,11 @@
 # this allows the CI and automated tests to import the file and make sure it is valid without having vlc
 try:
     import vlc
-except (ModuleNotFoundError, FileNotFoundError):
-    _logger.error(f'VLC not installed. Please install VLC to use this task. {__file__}')
+except ModuleNotFoundError:
+    warnings.warn(
+        'Please install extra dependencies for _sp_passiveVideo: '
+        'pip install "project_extraction[passiveVideo] @ '
+        'git+https://github.com/int-brain-lab/project_extraction.git"', RuntimeWarning)
 
 
 class Player:

iblrig_custom_tasks/samuel_cuedBiasedChoiceWorld/task.py

@@ -3,7 +3,6 @@
 from pybpodapi.protocol import StateMachine
 
 import iblrig.misc
-from iblrig.path_helper import load_pydantic_yaml, HardwareSettings
 from iblrig.base_choice_world import BiasedChoiceWorldSession
 from iblrig.hardware import SOFTCODE
 from iblutil.util import setup_logger
@@ -19,15 +18,13 @@ class Session(BiasedChoiceWorldSession):
     protocol_name = 'samuel_cuedBiasedChoiceWorld'
 
     def __init__(self, *args, delay_secs=0, **kwargs):  #SP _init_ should be the same as biasedChoiceWorld, so should it be specified?
+        super().__init__(**kwargs)
+
         # loads in the settings in order to determine the main sync and thus the pipeline extractor tasks
-        hardware_settings = load_pydantic_yaml(HardwareSettings, kwargs.get('file_hardware_settings'))
-        hardware_settings.update(kwargs.get('hardware_settings', {}))
-        is_main_sync = hardware_settings.get('MAIN_SYNC', False)
+        is_main_sync = self.hardware_settings.get('MAIN_SYNC', False)
         trials_task = 'CuedBiasedTrials' if is_main_sync else 'CuedBiasedTrialsTimeline'
         self.extractor_tasks = ['TrialRegisterRaw', trials_task, 'TrainingStatus']
 
-        super().__init__(**kwargs)
-
         self.task_params["SESSION_DELAY_START"] = delay_secs
         # init behaviour data
         self.movement_left = self.device_rotary_encoder.THRESHOLD_EVENTS[

projects/_template.py

@@ -1,3 +1,8 @@
+"""Template boilerplate code for custom task protocol data extraction.
+
+For an example of how to modify Bpod trials extraction (with either Bpod only or unchanged DAQ time alignment) check out
+'projects.neuromodulators'.  For an example of custom task QC, see 'projects.samuel_cuedBiasedChoiceWorld'.
+"""
 from collections import OrderedDict
 
 from ibllib.pipes.tasks import Pipeline

projects/extraction_tasks.py

@@ -1,10 +1,9 @@
 """
 Custom behaviour extractor tasks for personal projects.
 
-The task class name(s) should be added to the
+The task class name(s) should be added to the imports
 
 NB: This may need changing in the future if one of these modules requires optional dependencies.
 """
-from projects.neuromodulators import ChoiceWorldNeuromodulators
 from projects.samuel_cuedBiasedChoiceWorld import CuedBiasedTrials, CuedBiasedTrialsTimeline
 from projects.nate_optoBiasedChoiceWorld import OptoTrialsNidq, OptoTrialsBpod

projects/neuromodulators.py

@@ -1,23 +1,24 @@
 import numpy as np
 from ibllib.io.extractors.biased_trials import BiasedTrials
-from ibllib.pipes.behavior_tasks import ChoiceWorldTrialsBpod
+from ibllib.io.extractors.base import BaseBpodTrialsExtractor, run_extractor_classes
 
 
-class ChoiceWorldNeuromodulators(ChoiceWorldTrialsBpod):
-    def _run(self, update=True):
-        """
-        Extracts an iblrig training session
-        """
-        save_path = self.session_path.joinpath(self.output_collection)
-        extractor = TrialsTableNeuromodulator(session_path=self.session_path, task_collection=self.task_collection, save_path=save_path)
-        out, fil = extractor.extract()
-        return fil
+class TrialsTableNeuromodulator(BaseBpodTrialsExtractor):
+    """Extract neuromodulator task events.
 
+    Include a couple custom trial variables in `var_names` property.
 
-class TrialsTableNeuromodulator(BiasedTrials):
+    NB: In order to save to file and register these variables, we would need a custom ibllib.pipes.tasks.Task with
+    the correct output file names.
+    """
+    save_names = BiasedTrials.save_names + (None, None)
+    var_names = BiasedTrials.var_names + ('omit_feedback', 'exit_state')
 
     def _extract(self, *args, **kwargs):
-        out = super(TrialsTableNeuromodulator, self)._extract(*args, **kwargs)
+        # Extract common biased choice world datasets
+        out, _ = run_extractor_classes(
+            [BiasedTrials], session_path=self.session_path, bpod_trials=self.bpod_trials,
+            settings=self.settings, save=False, task_collection=self.task_collection)
         out[0]['omit_feedback'] = np.array([t['omit_feedback'] for t in self.bpod_trials])
         out[0]['exit_state'] = np.array([t['behavior_data']['States timestamps']['exit_state'][0][0] for t in self.bpod_trials])
-        return out
+        return {k: out[k] for k in self.var_names}  # Ensures all datasets present and ordered

projects/samuel_cuedBiasedChoiceWorld.py

@@ -64,7 +64,7 @@ def check_stimOn_goCue_delays(self, data, audio_output='harp', **_):
 class CuedBiasedTrialsTimeline(ChoiceWorldTrialsTimeline):
     """Behaviour task for aligning cuedBiased task to Timeline."""
 
-    def _run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
+    def run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
         """
         Run task QC.
 
@@ -82,13 +82,13 @@ def _run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
         ibllib.qc.base.QC
             The QC object.
         """
-        return super()._run_qc(trials_data=trials_data, update=update, QC=QC)
+        return super().run_qc(trials_data=trials_data, update=update, QC=QC)
 
 
 class CuedBiasedTrials(ChoiceWorldTrialsBpod):
     """Behaviour task for extracting Bpod-only cuedBiased task."""
 
-    def _run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
+    def run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
         """
         Run task QC.
 
@@ -106,4 +106,4 @@ def _run_qc(self, trials_data=None, update=True, QC=TaskQC, **kwargs):
         ibllib.qc.base.QC
             The QC object.
         """
-        return super()._run_qc(trials_data=trials_data, update=update, QC=QC)
+        return super().run_qc(trials_data=trials_data, update=update, QC=QC)

projects/task_extractor_map.json

@@ -1,4 +1,5 @@
 {
   "samuel_cuedBiasedChoiceWorld": "BiasedTrials",
+  "_iblrig_tasks_neuromodulatorChoiceWorld": "projects.neuromodulators.TrialsTableNeuromodulator",
   "nate_optoBiasedChoiceWorld": "projects.nate_optoBiasedChoiceWorld.TrialsOpto"
 }

pyproject.toml

@@ -4,13 +4,15 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name            = "project_extraction"
-version         = "0.2.2"
+version         = "0.2.3"
 description     = "Custom extractors for satellite tasks"
 dynamic         = [ "readme" ]
 keywords        = [ "IBL", "neuro-science" ]
 requires-python = "~=3.10"
 license         = { file = "LICENSE" }
-dependencies    = [ "python-vlc" ]
+
+[project.optional-dependencies]
+passiveVideo    = [ "python-vlc" ]
 
 [tool.setuptools]
 include-package-data = true