diff --git a/docs/trials_table_mapping.md b/docs/trials_table_mapping.md index d53a059..7e1d457 100644 --- a/docs/trials_table_mapping.md +++ b/docs/trials_table_mapping.md @@ -42,21 +42,6 @@ Columns are grouped by the raw source they map from. | `block_beta`, `block_duration`, `block_min`, `block_max` | `block_length` | | `delay_beta`, `delay_duration`, `delay_min`, `delay_max` | `quiescent_duration_key` (scalar distribution, so no beta/min/max) | -### From `task_logic_input` (under `task_parameters`) - -| Trials column | Source field | -| --- | --- | -| `reward_size_left` | `task_parameters.reward_size.left_value_volume` — the reward volume (uL) at the left port. | -| `reward_size_right` | `task_parameters.reward_size.right_value_volume` — the reward volume (uL) at the right port. | - -> **Note:** `reward_size` is read from the task parameters, not the trial -> generator, so it is populated even when no summarising generator is resolved. -> The acquisition system can in principle vary reward size per trial, but the -> current data format only exposes a single session-level value, so these -> columns are constant across trials. They are **required** (non-nullable): a -> missing `TaskLogic` stream raises rather than silently producing null reward -> sizes when there are trials to build. - ### From `TrialMetrics.json` (`SoftwareEvents` stream) | Trials column | Mapping | @@ -81,6 +66,8 @@ Columns are grouped by the raw source they map from. | `response_duration` | `response_deadline_duration`. | | `reward_consumption_duration` | `Trial -> reward_consumption_duration`. | | `reward_probabilityL` / `reward_probabilityR` | The **block** probability from `Trial -> metadata -> p_reward_left` / `p_reward_right`. The top-level `trial.p_reward_left` / `p_reward_right` is the per-trial probability, not the block probability, so it is not used here. `None` when the trial or its metadata is missing. | +| `reward_size_left` | `Trial -> reward_size.left` — the reward volume (uL) at the left port. Defaults to `2.0` when not set on the trial. `None` when the trial is missing. | +| `reward_size_right` | `Trial -> reward_size.right` — the reward volume (uL) at the right port. Defaults to `2.0` when not set on the trial. `None` when the trial is missing. | | `rewarded_historyL` / `rewarded_historyR` | Filter `is_rewarded == True`, then on `is_right_choice`. | ### From `TrialGeneratorSpec.json` (`SoftwareEvents` stream) @@ -88,7 +75,7 @@ Columns are grouped by the raw source they map from. | Trials column | Mapping | | --- | --- | | `base_reward_probability_sum` | If `type == "CoupledTrialGenerator"`, look at `reward_probability_parameters`. | -| `min_reward_each_block` | Present when `type == "CoupledTrialGenerator"`; otherwise `None`. | +| `min_reward_each_block` | Present when `type == "CoupledWarmupTrialGenerator"` (has `min_block_reward`); otherwise `None`. | ### From `QuiescentPeriod.json` (`SoftwareEvents` stream) @@ -123,11 +110,11 @@ seconds, far too coarse for the ~tens-of-ms valve pulse. | --- | --- | | `goCue_start_time` | `PlaySoundOrFrequency` `WRITE` message. | -### From `InitialManipulatorPosition` (software event) +### From `HarpManipulator` `AccumulatedSteps` (+ `InputSchemas.Rig`) | Trials column | Mapping | | --- | --- | -| `lickspout_positions` | `data` field. | +| `lickspout_position_x` / `y1` / `y2` / `z` | Per-motor cumulative microstep count from the `AccumulatedSteps` stream, converted to millimetres via the rig manipulator calibration (`full_step_to_mm / microstep_resolution`) and re-referenced to the session-start position (displacement **relative to session start**, mm). The manipulator is a continuously-sampled hardware value, so — like the go cue — each trial takes the sample within its `[start_time, stop_time)` window nearest the start. `Motor{i}` drives `Axis(i + 1)` (X, Y1, Y2, Z). `None` when no sample falls in the trial window. The rig and `AccumulatedSteps` streams are required inputs (`build` raises if either is missing with trials present). | ### From `trainer_state.json` and `acquisition.json` (autoTrain — can be disregarded) @@ -155,3 +142,5 @@ These were mapped during exploration but are no longer in scope: | 2026-06-17 | `auto_waterL` / `auto_waterR` now encode no auto-response (`is_auto_reward_right` is `None`) and missing trials as `0` instead of `NULL`. The columns are non-nullable (`int`, default `0`). | | 2026-06-20 | Added `reward_size_left` / `reward_size_right` (reward volume in uL) from `task_parameters.reward_size`, and `side_bias` from the per-trial `TrialMetrics` event (`bias` field). | | 2026-06-20 | `reward_probabilityL` / `reward_probabilityR` now read the block probability from `trial.metadata.p_reward_left` / `p_reward_right` instead of the top-level per-trial `trial.p_reward_left` / `p_reward_right`. | +| 2026-07-22 | `lickspout_position_x` / `y1` / `y2` / `z` now derive from the `HarpManipulator` `AccumulatedSteps` stream (microsteps → mm via the `InputSchemas.Rig` manipulator calibration, `full_step_to_mm / microstep_resolution`), sampled per trial via the closest sample in the `[start_time, stop_time)` window and re-referenced to the session-start position (displacement relative to session start, mm), replacing the static `InitialManipulatorPosition` software event. `Motor{i}` maps to `Axis(i + 1)` (X, Y1, Y2, Z). The rig and `AccumulatedSteps` streams are required when there are trials (`build` raises if either is missing). Column descriptions corrected from `um` to `mm`. | +| 2026-07-24 | `reward_size_left` / `reward_size_right` moved from session-level `task_parameters.reward_size` to per-trial `Trial.reward_size` (fields `.left` / `.right`). The columns are now nullable — `None` when the trial is missing. A missing `TaskLogic` stream no longer raises; session distribution columns are simply null. `min_reward_each_block` moved from `CoupledTrialGenerator` to `CoupledWarmupTrialGenerator`. | diff --git a/pyproject.toml b/pyproject.toml index b57ebc2..ddf7ef1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,7 @@ readme = "README.md" version = "0.1.0" dependencies = [ - "aind-behavior-dynamic-foraging[data] @ git+https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging.git@baab12133b22f599c1ba0583260eca9eca216cc0", + "aind-behavior-dynamic-foraging[data] @ git+https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging.git@ac5ddbf909c9375b9e8875d6a5f90796cfa98653", "ipykernel", ] @@ -37,7 +37,7 @@ full = [ [dependency-groups] dev = [ - 'ruff', + 'ruff<0.16', 'coverage', 'interrogate', 'pytest', diff --git a/src/dynamic_foraging_processing/nwb/acquisition/acquisition_builder.py b/src/dynamic_foraging_processing/nwb/acquisition/acquisition_builder.py index 047bd48..a63fda2 100644 --- a/src/dynamic_foraging_processing/nwb/acquisition/acquisition_builder.py +++ b/src/dynamic_foraging_processing/nwb/acquisition/acquisition_builder.py @@ -106,8 +106,7 @@ def get_lick_times(self, device: str, stream_name: str, port: str) -> np.ndarray ``HarpBehavior``/``DigitalInputState``, with left licks on ``DIPort0`` and right licks on ``DIPort1``. The lickometer board exposes each side as its own device (``HarpLickometerLeft`` / ``HarpLickometerRight``) - with a ``LickState`` stream and a ``Channel0`` column. A lick time is a - timestamp at which the selected column's digital input is high. + with a ``LickState`` stream and a ``Channel0`` column. Parameters ---------- @@ -131,6 +130,7 @@ def get_lick_times(self, device: str, stream_name: str, port: str) -> np.ndarray data = self.loader.dataset.at("Behavior").at(device).at(stream_name).load().data except (KeyError, FileNotFoundError): return np.array([]) + data = data[data["MessageType"] == "EVENT"] licks = data[data[port].fillna(False).astype(bool)] return licks.index.to_numpy() diff --git a/src/dynamic_foraging_processing/pipeline/_pipeline.py b/src/dynamic_foraging_processing/pipeline/_pipeline.py index 0796cdc..dfa2d6f 100644 --- a/src/dynamic_foraging_processing/pipeline/_pipeline.py +++ b/src/dynamic_foraging_processing/pipeline/_pipeline.py @@ -26,6 +26,7 @@ import numpy as np import pandas as pd import pynwb +from aind_data_schema.components.identifiers import DataAsset from aind_data_schema.core.processing import ( Code, DataProcess, @@ -279,8 +280,17 @@ def _write_processing( experimenters=["Alex Piet", "Micah Woodard", "Bruno Cruz", "Arjun Sridhar"], start_date_time=start_date_time, end_date_time=end_date_time, + pipeline_name="dynamic-foraging-processing-pipeline", ) - ] + ], + pipelines=[ + Code( + url=_CODE_URL, + version=_PACKAGE_VERSION, + name="dynamic-foraging-processing-pipeline", + input_data=[DataAsset(name=Path(self.loader.path).stem)], + ) + ], ) processing.write_standard_file(output_directory=Path(output_path)) diff --git a/src/dynamic_foraging_processing/processing/_trial_table.py b/src/dynamic_foraging_processing/processing/_trial_table.py index b83fb63..73963ac 100644 --- a/src/dynamic_foraging_processing/processing/_trial_table.py +++ b/src/dynamic_foraging_processing/processing/_trial_table.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd +from aind_behavior_dynamic_foraging.rig import AindDynamicForagingRig from aind_behavior_dynamic_foraging.task_logic import AindDynamicForagingTaskLogic from aind_behavior_dynamic_foraging.task_logic.trial_generators import TrialGeneratorSpec from aind_behavior_dynamic_foraging.task_logic.trial_models import ( @@ -24,6 +25,12 @@ logger = logging.getLogger(__name__) +# The four manipulator axes, ordered so that index ``i`` is the axis driven +# by ``Motor{i}`` in the ``AccumulatedSteps`` stream: ``Motor{i}`` maps to +# ``Axis(i + 1)`` (Axis.X=1, Y1=2, Y2=3, Z=4), whose names match the +# ``lickspout_position_*`` suffixes and the ``full_step_to_mm`` attributes. +_MANIPULATOR_AXES = ("x", "y1", "y2", "z") + class TrialTableBuilder: """Builds the NWB ``trials`` table from a dynamic foraging ``Dataset``. @@ -236,7 +243,7 @@ def _animal_response(payload: t.Any) -> int: return 1 if bool(choice) else 0 @staticmethod - def _parse_outcome(payload: t.Any) -> t.Optional[TrialOutcome]: + def _parse_outcome(payload: t.Any) -> TrialOutcome: """Parse a ``TrialOutcome`` software-event payload into its domain model. Parameters @@ -247,11 +254,16 @@ def _parse_outcome(payload: t.Any) -> t.Optional[TrialOutcome]: Returns ------- - TrialOutcome or None - The parsed model, or ``None`` if ``payload`` is empty. + TrialOutcome + The parsed model. + + Raises + ------ + ValueError + If ``payload`` is ``None``. """ if payload is None: - return None + raise ValueError("TrialOutcome payload is required but received None.") if isinstance(payload, TrialOutcome): return payload if isinstance(payload, str): @@ -320,7 +332,7 @@ def _rewarded_history( return is_rewarded and (is_right_choice is is_right) @staticmethod - def _is_baited(trial: t.Optional[Trial], *, is_right: bool) -> bool: + def _is_baited(trial: Trial, *, is_right: bool) -> bool: """Return whether the requested lickport is baited on this trial. A port is "baited" when reward is guaranteed there (its reward @@ -343,16 +355,15 @@ def _is_baited(trial: t.Optional[Trial], *, is_right: bool) -> bool: Parameters ---------- - trial : Trial or None - The per-trial task-logic model, or ``None`` when unavailable. + trial : Trial + The per-trial task-logic model. is_right : bool ``True`` for the right port, ``False`` for the left port. Returns ------- bool - Whether the requested side is baited. A missing ``trial`` is treated - as not baited (``False``). + Whether the requested side is baited. Examples -------- @@ -374,8 +385,6 @@ def _is_baited(trial: t.Optional[Trial], *, is_right: bool) -> bool: >>> TrialTableBuilder._is_baited(trial, is_right=False) False """ - if trial is None: - return False auto = trial.is_auto_reward_right if is_right: # Right stays baited unless the animal was auto-responded right. @@ -384,20 +393,19 @@ def _is_baited(trial: t.Optional[Trial], *, is_right: bool) -> bool: return trial.p_reward_left == 1 and auto in (None, True) @staticmethod - def _auto_water(trial: t.Optional[Trial], *, is_right: bool) -> int: + def _auto_water(trial: Trial, *, is_right: bool) -> int: """Encode autowater for a side from ``is_auto_reward_right``. Returns ``1`` if the auto response was to the requested side, else ``0``. - A missing trial or no auto-response (``is_auto_reward_right`` is - ``None``) counts as no autowater (``0``). ``is_right`` is ``True`` for - right. + No auto-response (``is_auto_reward_right`` is ``None``) counts as no + autowater (``0``). ``is_right`` is ``True`` for right. """ - if trial is None or trial.is_auto_reward_right is None: + if trial.is_auto_reward_right is None: return 0 return int(trial.is_auto_reward_right is is_right) @staticmethod - def _block_reward_probability(trial: t.Optional[Trial], *, is_right: bool) -> t.Optional[float]: + def _block_reward_probability(trial: Trial, *, is_right: bool) -> t.Optional[float]: """Return the block reward probability for a side from the trial metadata. The top-level ``trial.p_reward_left/right`` is the *per-trial* probability; @@ -406,18 +414,17 @@ def _block_reward_probability(trial: t.Optional[Trial], *, is_right: bool) -> t. Parameters ---------- - trial : Trial or None - The per-trial task-logic model, or ``None`` when unavailable. + trial : Trial + The per-trial task-logic model. is_right : bool ``True`` for the right port, ``False`` for the left port. Returns ------- float or None - The block reward probability, or ``None`` when the trial or its - metadata is unavailable. + The block reward probability, or ``None`` when metadata is unavailable. """ - if trial is None or trial.metadata is None: + if trial.metadata is None: return None return trial.metadata.p_reward_right if is_right else trial.metadata.p_reward_left @@ -483,14 +490,6 @@ def _session_columns(self, task_logic: AindDynamicForagingTaskLogic) -> t.Dict[s if task_logic is None: return columns - # Reward volumes live on the task parameters, not the trial generator, so - # populate them before the generator resolution (which may bail out). - # Known limitation: the acquisition system can vary reward size per trial, - # but the current data format only exposes a single session-level value. - reward_size = task_logic.task_parameters.reward_size - columns["reward_size_left"] = reward_size.left_value_volume - columns["reward_size_right"] = reward_size.right_value_volume - generator = self._summary_generator(task_logic.task_parameters.trial_generator) if generator is None: return columns @@ -519,46 +518,145 @@ def _session_columns(self, task_logic: AindDynamicForagingTaskLogic) -> t.Dict[s delay_max=delay_max, base_reward_probability_sum=base_reward_sum, ) - # ``min_block_reward`` is coupled-only; uncoupled generators omit it. + # ``min_block_reward`` is warmup-generator-only; main coupled generators omit it. if hasattr(generator, "min_block_reward"): columns["min_reward_each_block"] = generator.min_block_reward return columns - def _lickspout_columns( - self, manipulator: t.Optional[pd.DataFrame] + def _manipulator_mm_per_step(self, rig: AindDynamicForagingRig) -> t.Dict[str, float]: + """Return millimetres travelled per accumulated step, keyed by axis. + + ``AccumulatedSteps`` counts *microsteps*. The physical distance per + microstep is the full-step-to-mm calibration divided by the microstep + resolution (e.g. ``MICROSTEP8`` → 8 microsteps per full step), both read + from the rig's manipulator calibration. + + Parameters + ---------- + rig : AindDynamicForagingRig + The ``InputSchemas.Rig`` stream data. The rig is a required input + schema, so ``build`` guarantees it is present before this is called. + + Returns + ------- + dict of str to float + ``{axis: mm_per_step}`` for ``x`` / ``y1`` / ``y2`` / ``z``. + + Raises + ------ + ValueError + If the manipulator calibration is missing one of the four axes. + """ + calibration = rig.manipulator.calibration + resolution_by_axis = { + config.axis.name.lower(): config.microstep_resolution + for config in calibration.axis_configuration + } + mm_per_step: t.Dict[str, float] = {} + for axis in _MANIPULATOR_AXES: + resolution = resolution_by_axis.get(axis) + if resolution is None: + raise ValueError( + f"Manipulator calibration is missing axis {axis!r}; " + "cannot derive lickspout position." + ) + # Resolution enum names encode the divisor (MICROSTEP8 -> 8); the + # enum *value* (0..3) does not, so parse from the name. + microsteps = int(resolution.name.replace("MICROSTEP", "")) + mm_per_step[axis] = getattr(calibration.full_step_to_mm, axis) / microsteps + return mm_per_step + + def _manipulator_positions( + self, + accumulated_steps: pd.DataFrame, + rig: AindDynamicForagingRig, + ) -> pd.DataFrame: + """Return a time-indexed frame of lickspout position (mm) over the session. + + Built from the ``HarpManipulator`` ``AccumulatedSteps`` stream: each + ``EVENT`` row's per-motor microstep count is converted to millimetres via + the rig calibration. ``AccumulatedSteps`` is absolute (zero-referenced at + the homing position), so the count maps directly to position with no + offset. The frame is then re-referenced to the session start (the first + sample subtracted from every row), so the stored values are displacement + *relative to session start* — the units the QC plot expects. + + Parameters + ---------- + accumulated_steps : pandas.DataFrame + The ``AccumulatedSteps`` stream data (``Motor0``..``Motor3`` columns). + Required; guaranteed present by ``build``. + rig : AindDynamicForagingRig + The ``InputSchemas.Rig`` stream data (required; guaranteed present by + ``build``). + + Returns + ------- + pandas.DataFrame + Columns ``lickspout_position_x`` / ``y1`` / ``y2`` / ``z`` indexed by + time (sorted ascending), relative to the session-start position. + + Raises + ------ + ValueError + If the stream has no ``EVENT`` rows, is missing a motor column, or the + rig calibration is missing an axis. + """ + mm_per_step = self._manipulator_mm_per_step(rig) + events = accumulated_steps + if "MessageType" in events.columns: + events = events[events["MessageType"] == "EVENT"] + if len(events) == 0: + raise ValueError( + "AccumulatedSteps stream has no EVENT rows; cannot derive lickspout position." + ) + events = events.sort_index() + columns: t.Dict[str, np.ndarray] = {} + for index, axis in enumerate(_MANIPULATOR_AXES): + motor = f"Motor{index}" + if motor not in events.columns: + raise ValueError( + f"AccumulatedSteps stream is missing column {motor}; " + "cannot derive lickspout position." + ) + columns[f"lickspout_position_{axis}"] = ( + events[motor].to_numpy(dtype=float) * mm_per_step[axis] + ) + positions = pd.DataFrame(columns, index=events.index) + # Re-reference to session start so the stored values are displacement + # from the first sample (previously done in the plot as ``values[0]``). + return positions - positions.iloc[0] + + def _sample_lickspout( + self, positions: pd.DataFrame, start: float, stop: float ) -> t.Dict[str, t.Optional[float]]: - """Return lickspout position columns from ``InitialManipulatorPosition``. + """Return the lickspout position sampled within a trial's window. - The event's ``data`` payload carries the x / y1 / y2 / z positions. These - are the *initial* manipulator coordinates recorded once at experiment - start, so the columns are currently constant across trials. + The manipulator position is a continuously-sampled hardware value, so — + like the go cue — each trial takes the sample within its ``[start, stop)`` + window nearest the start (see :meth:`_closest_time_in_window`). - Known limitation: the manipulator can move within a session (e.g. the - anti-bias intervention shifts the lickspouts horizontally), which this - static initial position does not capture. + Parameters + ---------- + positions : pandas.DataFrame + The time-indexed position frame from :meth:`_manipulator_positions`. + start, stop : float + The trial window bounds (seconds); ``start`` inclusive, ``stop`` + exclusive. May be ``NaN`` when unaligned. - TODO: think about how to represent - this if it becomes relevant. The ideal solution would be to use the harp files - to track the manipulator position over time + Returns + ------- + dict of str to (float or None) + The four ``lickspout_position_*`` values, all ``None`` for a trial + whose window contains no manipulator sample. """ - keys = ( - "lickspout_position_x", - "lickspout_position_y1", - "lickspout_position_y2", - "lickspout_position_z", - ) - empty = {key: None for key in keys} - payloads = self._event_payloads(manipulator) - if not payloads: - return empty - payload = payloads[0] - components = ("x", "y1", "y2", "z") - if isinstance(payload, dict): - return {key: payload.get(comp) for key, comp in zip(keys, components)} - if isinstance(payload, (list, tuple)) and len(payload) == len(keys): - return {key: payload[idx] for idx, key in enumerate(keys)} - logger.warning("Unrecognized InitialManipulatorPosition payload; leaving lickspout null.") - return empty + keys = tuple(f"lickspout_position_{axis}" for axis in _MANIPULATOR_AXES) + times = positions.index.to_numpy(dtype=float) + sample_time = self._closest_time_in_window(times, start, stop) + if sample_time is None: + return {key: None for key in keys} + row = positions.loc[sample_time] + return {key: (None if pd.isna(row[key]) else float(row[key])) for key in keys} # ------------------------------------------------------------------ # # Per-trial assembly @@ -566,7 +664,7 @@ def _lickspout_columns( def _build_row( self, *, - outcome: t.Optional[TrialOutcome], + outcome: TrialOutcome, start: float, stop: float, response: t.Any, @@ -578,9 +676,9 @@ def _build_row( lickspout: t.Dict[str, t.Optional[float]], ) -> TrialConfig: """Assemble a single ``TrialConfig`` from aligned per-trial inputs.""" - trial = outcome.trial if outcome is not None else None - is_right_choice = outcome.is_right_choice if outcome is not None else None - is_rewarded = bool(outcome.is_rewarded) if outcome is not None else False + trial = outcome.trial + is_right_choice = outcome.is_right_choice + is_rewarded = bool(outcome.is_rewarded) return TrialConfig( start_time=start, @@ -596,13 +694,13 @@ def _build_row( bait_right=self._is_baited(trial, is_right=True), reward_probabilityL=self._block_reward_probability(trial, is_right=False), reward_probabilityR=self._block_reward_probability(trial, is_right=True), + reward_size_left=trial.reward_size.left, + reward_size_right=trial.reward_size.right, side_bias=side_bias, - response_duration=trial.response_deadline_duration if trial is not None else None, - reward_consumption_duration=( - trial.reward_consumption_duration if trial is not None else None - ), - ITI_duration=trial.inter_trial_interval_duration if trial is not None else None, - delay_duration=trial.quiescence_period_duration if trial is not None else None, + response_duration=trial.response_deadline_duration, + reward_consumption_duration=trial.reward_consumption_duration, + ITI_duration=trial.inter_trial_interval_duration, + delay_duration=trial.quiescence_period_duration, auto_waterL=self._auto_water(trial, is_right=False), auto_waterR=self._auto_water(trial, is_right=True), **session, @@ -669,9 +767,7 @@ def build(self) -> pd.DataFrame: Raises ------ ValueError - If the ``TaskLogic`` stream is missing while there are trials to - build (the required reward-size columns are sourced from it), or if - ``raise_on_error`` is ``True`` and a per-trial stream length + If ``raise_on_error`` is ``True`` and a per-trial stream length disagrees with the ``TrialOutcome`` trial count. """ outcomes = self._load("Behavior", "SoftwareEvents", "TrialOutcome") @@ -683,7 +779,8 @@ def build(self) -> pd.DataFrame: pulse_supply_left = self._load("Behavior", "HarpBehavior", "PulseSupplyPort0") pulse_supply_right = self._load("Behavior", "HarpBehavior", "PulseSupplyPort1") go_cue = self._load("Behavior", "HarpSoundCard", "PlaySoundOrFrequency") - manipulator = self._load("Behavior", "SoftwareEvents", "InitialManipulatorPosition") + accumulated_steps = self._load("Behavior", "HarpManipulator", "AccumulatedSteps") + rig = self._load("Behavior", "InputSchemas", "Rig") task_logic = self._load("Behavior", "InputSchemas", "TaskLogic") # Per-trial streams: one payload/timestamp per trial, aligned by index. @@ -696,16 +793,6 @@ def build(self) -> pd.DataFrame: # Guard the positional alignment before we pair streams by index. n_trials = len(outcome_payloads) - # Reward size is sourced from the task logic and is a required column, so - # a missing TaskLogic stream cannot yield a valid table when there are - # trials to build. Surface that clearly rather than failing later with a - # cryptic per-row validation error. - if n_trials > 0 and task_logic is None: - raise ValueError( - "TaskLogic stream is required to build the trials table " - f"(reward sizes are sourced from it) but it failed to load for {n_trials} trials." - ) - warnings = self._check_aligned( n_trials, { @@ -732,7 +819,15 @@ def build(self) -> pd.DataFrame: go_cue_times = self._write_times(go_cue) session = self._session_columns(task_logic) - lickspout = self._lickspout_columns(manipulator) + if n_trials: + if rig is None: + raise ValueError("Rig stream is required when there are trials.") + if accumulated_steps is None: + raise ValueError("AccumulatedSteps stream is required when there are trials.") + # With no trials the frame goes unused (the loop does not run). + lickspout_positions = ( + self._manipulator_positions(accumulated_steps, rig) if n_trials else None + ) rows: t.List[TrialConfig] = [] for i, outcome_payload in enumerate(outcome_payloads): @@ -743,6 +838,7 @@ def build(self) -> pd.DataFrame: stop = float(stop_times[i]) if i < stop_times.size else np.nan response = response_payloads[i] if i < len(response_payloads) else None side_bias = self._side_bias(metric_payloads[i] if i < len(metric_payloads) else None) + lickspout = self._sample_lickspout(lickspout_positions, start, stop) rows.append( self._build_row( diff --git a/src/dynamic_foraging_processing/processing/models/trial_config.py b/src/dynamic_foraging_processing/processing/models/trial_config.py index 8c20bcc..ed3425b 100644 --- a/src/dynamic_foraging_processing/processing/models/trial_config.py +++ b/src/dynamic_foraging_processing/processing/models/trial_config.py @@ -142,18 +142,20 @@ class TrialConfig(BaseModel): # --- lickspout_position (mapping's `lickspout_positions` -> these four components) --- lickspout_position_x: Optional[float] = Field( - default=None, description="x position (um) of the lickspout position (left-right)" + default=None, + description="x lickspout position (mm), relative to session start (left-right)", ) lickspout_position_y1: Optional[float] = Field( default=None, - description="y1 position (um) of the left lickspout position (forward-backward)", + description="y1 left lickspout position (mm), relative to session start (forward-backward)", ) lickspout_position_y2: Optional[float] = Field( default=None, - description="y2 position (um) of the right lickspout position (forward-backward)", + description="y2 right lickspout position (mm), relative to session start (forward-backward)", ) lickspout_position_z: Optional[float] = Field( - default=None, description="z position (um) of the lickspout position (up-down)" + default=None, + description="z lickspout position (mm), relative to session start (up-down)", ) @classmethod diff --git a/src/dynamic_foraging_processing/qc/_core/builder.py b/src/dynamic_foraging_processing/qc/_core/builder.py index d9b590f..a7ee77f 100644 --- a/src/dynamic_foraging_processing/qc/_core/builder.py +++ b/src/dynamic_foraging_processing/qc/_core/builder.py @@ -1,8 +1,8 @@ """Assemble the dynamic foraging ``QualityControl`` object. -Collects a flat list of metrics (behavior + contract QA) into a single -``QualityControl``, wiring up ``default_grouping`` so the QC portal lays out -``behavior`` and ``test_suite`` as sibling top-level groups. +Collects a flat list of metrics (behavior + contract QC) into a single +``QualityControl``, wiring up ``default_grouping`` so the QC portal groups +metrics by their ``type`` and ``test_suite`` tags. """ import typing as t @@ -10,7 +10,7 @@ from aind_data_schema.core.quality_control import QCMetric, QualityControl #: Tag keys laid out as siblings at the top level of the QC portal. -DEFAULT_GROUPING = ["behavior", "test_suite"] +DEFAULT_GROUPING = [("type", "test_suite")] def build_quality_control( @@ -26,9 +26,9 @@ def build_quality_control( Parameters ---------- metrics : list of QCMetric - All metrics (behavior + contract QA). + All metrics (behavior + contract QC). default_grouping : list of str, optional - Tag keys the portal groups by. Defaults to ``["behavior", "test_suite"]``. + Tag keys the portal groups by. Defaults to ``[("type", "test_suite")]``. allow_tag_failures : list of str, optional Tag values whose metric failures should not fail the overall QC. key_experimenters : list of str, optional diff --git a/src/dynamic_foraging_processing/qc/processed/behavior.py b/src/dynamic_foraging_processing/qc/processed/behavior.py index ffc6e9e..b9e019e 100644 --- a/src/dynamic_foraging_processing/qc/processed/behavior.py +++ b/src/dynamic_foraging_processing/qc/processed/behavior.py @@ -146,8 +146,8 @@ def side_bias_result(side_bias: np.ndarray, results_folder: t.Optional[str] = No ------- QCResult Passes when ``abs(mean_bias) < 0.5``. Fails when the column is empty or - all ``nan`` (``mean_bias`` is ``nan``). Tagged ``{"behavior": ...}`` and - referencing the side-bias plot. + all ``nan`` (``mean_bias`` is ``nan``). Tagged + ``{"type": "Average_Side_Bias"}`` and referencing the side-bias plot. """ values = np.asarray(side_bias, dtype=float) if values.size == 0 or np.all(np.isnan(values)): @@ -159,9 +159,9 @@ def side_bias_result(side_bias: np.ndarray, results_folder: t.Optional[str] = No name=name, value=mean_bias, passed=bool(abs(mean_bias) < 0.5), # nan comparisons are False -> fails - description="Average side bias across the session (right is positive).", + description="Average side bias should be less than 0.5", reference=_plot_reference(SIDE_BIAS_PLOT, results_folder), - tags={"behavior": name}, + tags={"type": "Average_Side_Bias"}, ) @@ -203,7 +203,7 @@ def lick_interval_results( passed=value < limit, description=f"{name} of inter-lick intervals; passes when < {limit}.", reference=_plot_reference(LICK_INTERVALS_PLOT, results_folder), - tags={"behavior": name}, + tags={"metric": name, "type": "Lick_Interval"}, ) for name, value, limit in specs ] diff --git a/src/dynamic_foraging_processing/qc/processed/plots.py b/src/dynamic_foraging_processing/qc/processed/plots.py index d04c941..e46e335 100644 --- a/src/dynamic_foraging_processing/qc/processed/plots.py +++ b/src/dynamic_foraging_processing/qc/processed/plots.py @@ -122,7 +122,9 @@ def _add_lickspout_position_plot( if position is None or len(position) == 0: continue values = np.asarray(position, dtype=float) - ax.plot(values - values[0], color, label=label) + # Values already come in relative to session start (normalized by the + # trial-table builder), so plot them directly. + ax.plot(values, color, label=label) plotted = True if plotted: ax.legend() @@ -303,6 +305,14 @@ def plot_side_bias( ) _add_reward_probabilities(ax[3], reward_probability_left, reward_probability_right) + # Align the x-axis across every panel so trials line up vertically. The + # panels are all indexed by trial, but some auto-scale (adding margins) while + # others set [0, N]; pin them all to a common [0, n_trials]. + n_trials = max(len(np.asarray(side_bias)), len(np.asarray(animal_response))) + if n_trials: + for axis in ax: + axis.set_xlim([0, n_trials]) + fig.savefig(Path(results_folder) / SIDE_BIAS_PLOT, dpi=300, bbox_inches="tight") plt.close(fig) return SIDE_BIAS_PLOT diff --git a/src/dynamic_foraging_processing/qc/processed/results.py b/src/dynamic_foraging_processing/qc/processed/results.py index 762890f..a263f1a 100644 --- a/src/dynamic_foraging_processing/qc/processed/results.py +++ b/src/dynamic_foraging_processing/qc/processed/results.py @@ -22,15 +22,15 @@ from dynamic_foraging_processing.qc.processed.plots import plot_lick_intervals, plot_side_bias # Logical input -> trials-table column name. Centralized so the mapping is easy -# to correct against the trial-table builder; ``side_bias`` and the -# ``lickspout_*`` arrays are not yet pinned down in trials_table_mapping.md. +# to correct against the trial-table builder. The lickspout columns are the +# ``lickspout_position_*`` fields documented in trials_table_mapping.md. _COLUMNS = { "animal_response": "animal_response", "side_bias": "side_bias", - "lickspout_x": "lickspout_x", - "lickspout_y1": "lickspout_y1", - "lickspout_y2": "lickspout_y2", - "lickspout_z": "lickspout_z", + "lickspout_x": "lickspout_position_x", + "lickspout_y1": "lickspout_position_y1", + "lickspout_y2": "lickspout_position_y2", + "lickspout_z": "lickspout_position_z", "rewarded_left": "rewarded_historyL", "rewarded_right": "rewarded_historyR", "reward_probability_left": "reward_probabilityL", diff --git a/tests/test_nwb/test_acquisition/test_acquisition_builder.py b/tests/test_nwb/test_acquisition/test_acquisition_builder.py index 3ee8c05..4b1f91f 100644 --- a/tests/test_nwb/test_acquisition/test_acquisition_builder.py +++ b/tests/test_nwb/test_acquisition/test_acquisition_builder.py @@ -88,13 +88,18 @@ def _empty_manual_water_frame() -> pd.DataFrame: def _make_digital_input_frame() -> pd.DataFrame: - """Build a DigitalInputState frame: left licks high at 1.0, right at 2.0/2.5.""" + """Build a DigitalInputState frame: left licks high at 1.0, right at 2.0/2.5. + + Includes a non-EVENT ``READ`` row at 0.5 with ``DIPort0`` latched high; it + reports register state rather than a lick and must be filtered out. + """ return pd.DataFrame( { - "DIPort0": [True, False, False], - "DIPort1": [False, True, True], + "MessageType": ["READ", "EVENT", "EVENT", "EVENT"], + "DIPort0": [True, True, False, False], + "DIPort1": [False, False, True, True], }, - index=pd.Index([1.0, 2.0, 2.5], name="time"), + index=pd.Index([0.5, 1.0, 2.0, 2.5], name="time"), ) @@ -196,6 +201,17 @@ def test_get_lick_times_selects_di_port_by_side(): ) +def test_get_lick_times_ignores_non_event_rows(): + """Only EVENT rows are licks; latched-high READ/WRITE rows are ignored.""" + builder = AcquisitionBuilder(loader=_make_loader()) + + # DIPort0 is high in the READ row at 0.5 and the EVENT row at 1.0; only the + # EVENT-row timestamp is returned. + np.testing.assert_array_equal( + builder.get_lick_times("HarpBehavior", "DigitalInputState", "DIPort0"), np.array([1.0]) + ) + + def test_get_lick_times_returns_empty_when_absent(): """A missing DigitalInputState stream yields an empty array.""" dataset = _FakeNode( diff --git a/tests/test_pipeline/test_pipeline.py b/tests/test_pipeline/test_pipeline.py index cef052f..24fe4f1 100644 --- a/tests/test_pipeline/test_pipeline.py +++ b/tests/test_pipeline/test_pipeline.py @@ -1,5 +1,6 @@ """Tests for ``dynamic_foraging_processing.pipeline._pipeline``.""" +from datetime import datetime, timezone from pathlib import Path from unittest.mock import MagicMock @@ -371,6 +372,25 @@ def test_run_nwb_writes_nwb_and_processing(tmp_path): assert processing_json.exists() loaded = Processing.model_validate_json(processing_json.read_text()) assert loaded.data_processes[0].process_type == ProcessName.PIPELINE + # The data process and the top-level pipeline are linked by name. + assert loaded.data_processes[0].pipeline_name == "dynamic-foraging-processing-pipeline" + assert [p.name for p in loaded.pipelines] == ["dynamic-foraging-processing-pipeline"] + assert loaded.pipelines[0].version == _pipeline._PACKAGE_VERSION + assert loaded.pipelines[0].url == _pipeline._CODE_URL + + +def test_write_processing_records_input_data_from_loader_path(tmp_path): + """``_write_processing`` records the loader file stem as the pipeline ``input_data``.""" + pipeline = _make_pipeline() + pipeline.loader.path = Path("some/dir/my_session.json") + start = datetime(2024, 1, 1, tzinfo=timezone.utc) + end = datetime(2024, 1, 2, tzinfo=timezone.utc) + + pipeline._write_processing(str(tmp_path), start, end) + + loaded = Processing.model_validate_json((tmp_path / "processing.json").read_text()) + input_data = loaded.pipelines[0].input_data + assert [asset.name for asset in input_data] == ["my_session"] def test_run_qc_writes_quality_control(tmp_path): diff --git a/tests/test_processing/test_trial_table.py b/tests/test_processing/test_trial_table.py index e4b91a6..65c0eb1 100644 --- a/tests/test_processing/test_trial_table.py +++ b/tests/test_processing/test_trial_table.py @@ -1,12 +1,13 @@ """Tests for ``dynamic_foraging_processing.processing._trial_table``.""" +from types import SimpleNamespace + import numpy as np import pandas as pd import pytest from aind_behavior_dynamic_foraging.task_logic import ( AindDynamicForagingTaskLogic, AindDynamicForagingTaskParameters, - RewardSize, ) from aind_behavior_dynamic_foraging.task_logic.trial_generators import ( CoupledTrialGeneratorSpec, @@ -15,6 +16,7 @@ UncoupledTrialGeneratorSpec, ) from aind_behavior_dynamic_foraging.task_logic.trial_models import TrialOutcome +from aind_behavior_services.rig.aind_manipulator import Axis, MicrostepResolution from aind_behavior_services.task.distributions import ( ExponentialDistribution, ExponentialDistributionParameters, @@ -89,13 +91,16 @@ def _outcome( auto=None, block_p_left=None, block_p_right=None, + reward_size_left=None, + reward_size_right=None, ): """Build a serialized ``TrialOutcome`` payload (dict, as delivered by the reader). ``p_left`` / ``p_right`` are the per-trial probabilities (top-level ``trial`` fields); ``block_p_left`` / ``block_p_right``, when given, are the block probabilities stored under ``trial.metadata`` (the source of the - ``reward_probability`` columns). + ``reward_probability`` columns). ``reward_size_left`` / ``reward_size_right`` + override the default per-trial reward volumes (uL). """ trial = { "p_reward_left": p_left, @@ -106,6 +111,11 @@ def _outcome( "inter_trial_interval_duration": 4.0, "is_auto_reward_right": auto, } + if reward_size_left is not None or reward_size_right is not None: + trial["reward_size"] = { + "left": reward_size_left if reward_size_left is not None else 2.0, + "right": reward_size_right if reward_size_right is not None else 2.0, + } if block_p_left is not None or block_p_right is not None: trial["metadata"] = {"p_reward_left": block_p_left, "p_reward_right": block_p_right} return { @@ -138,10 +148,7 @@ def _task_logic(quiescent_scalar=True): min_block_reward=2, ) return AindDynamicForagingTaskLogic( - task_parameters=AindDynamicForagingTaskParameters( - trial_generator=spec, - reward_size=RewardSize(left_value_volume=2.0, right_value_volume=4.0), - ) + task_parameters=AindDynamicForagingTaskParameters(trial_generator=spec) ) @@ -157,6 +164,35 @@ def _pulse_supply(column, value_ms): ) +def _rig(step_mm=0.01, resolution=MicrostepResolution.MICROSTEP8): + """Build a rig stub exposing the manipulator calibration the builder reads. + + A ``SimpleNamespace`` mirrors the ``AindDynamicForagingRig`` attribute path + (``manipulator.calibration.full_step_to_mm`` / ``axis_configuration``) used by + the builder, with real ``Axis`` / ``MicrostepResolution`` enums. + """ + full_step_to_mm = SimpleNamespace(x=step_mm, y1=step_mm, y2=step_mm, z=step_mm) + axis_configuration = [ + SimpleNamespace(axis=axis, microstep_resolution=resolution) + for axis in (Axis.X, Axis.Y1, Axis.Y2, Axis.Z) + ] + calibration = SimpleNamespace( + full_step_to_mm=full_step_to_mm, axis_configuration=axis_configuration + ) + return SimpleNamespace(manipulator=SimpleNamespace(calibration=calibration)) + + +def _accumulated_steps(times, motor_steps): + """Build an ``AccumulatedSteps`` frame (Motor0..Motor3 microstep counts). + + ``motor_steps`` is a sequence of ``(m0, m1, m2, m3)`` per timestamp; all rows + are ``EVENT`` messages, mirroring the HarpManipulator stream. + """ + columns = {f"Motor{i}": [row[i] for row in motor_steps] for i in range(4)} + columns["MessageType"] = ["EVENT"] * len(times) + return pd.DataFrame(columns, index=pd.Index(times, name="Time")) + + def _full_dataset(): """Assemble a two-trial fake dataset covering the common path.""" software_events = _Node( @@ -172,6 +208,8 @@ def _full_dataset(): is_rewarded=True, block_p_left=0.7, block_p_right=0.1, + reward_size_left=2.0, + reward_size_right=4.0, ), _outcome(0.5, 0.5, is_right_choice=None, is_rewarded=False), ], @@ -184,9 +222,6 @@ def _full_dataset(): [10.5, 20.5], [{"Item1": 10.5, "Item2": True}, {"Item1": 20.5, "Item2": None}] ) ), - "InitialManipulatorPosition": _Stream( - _events([5.0], [{"x": 1.0, "y1": 2.0, "y2": 3.0, "z": 4.0}]) - ), "TrialMetrics": _Stream(_events([10.2, 20.2], [{"bias": 0.3}, {"bias": None}])), } ) @@ -209,7 +244,20 @@ def _full_dataset(): ) } ), - "InputSchemas": _Node({"TaskLogic": _Stream(_task_logic())}), + "HarpManipulator": _Node( + { + # 0.00125 mm/microstep (0.01 / MICROSTEP8). One sample falls + # inside each trial window ([10, 20) and [20, 30)); x moves + # 10.0 -> 15.0 between the two trials. + "AccumulatedSteps": _Stream( + _accumulated_steps( + [10.5, 20.5], + [(8000, 1600, 2400, 4000), (12000, 1600, 2400, 4000)], + ) + ) + } + ), + "InputSchemas": _Node({"TaskLogic": _Stream(_task_logic()), "Rig": _Stream(_rig())}), } ) return _Node({"Behavior": behavior}) @@ -275,29 +323,55 @@ def test_build_full_dataset(): assert first["ITI_min"] == 1.0 and first["ITI_max"] == 10.0 assert first["block_beta"] == pytest.approx(20.0) assert pd.isna(first["delay_beta"]) # scalar quiescent distribution - assert first["min_reward_each_block"] == 2 + assert pd.isna(first["min_reward_each_block"]) # removed from generator schema assert first["base_reward_probability_sum"] == pytest.approx(0.8) - # Lickspout positions from InitialManipulatorPosition. - assert first["lickspout_position_x"] == 1.0 - assert first["lickspout_position_z"] == 4.0 + # Lickspout positions from AccumulatedSteps (microsteps * 0.00125 mm), + # sampled at each trial start and re-referenced to session start. The first + # sample is the baseline (all zero); x then moves +5.0 mm for the second trial. + assert first["lickspout_position_x"] == 0.0 + assert first["lickspout_position_y1"] == 0.0 + assert first["lickspout_position_y2"] == 0.0 + assert first["lickspout_position_z"] == 0.0 + assert second["lickspout_position_x"] == 5.0 - # Session-level reward volumes (uL) from task_parameters.reward_size. + # Per-trial reward volumes (uL) from trial.reward_size; second trial uses the default. assert first["reward_size_left"] == 2.0 assert first["reward_size_right"] == 4.0 assert second["reward_size_left"] == 2.0 + assert second["reward_size_right"] == 2.0 # Per-trial side bias from the TrialMetrics event; null when not recorded. assert first["side_bias"] == pytest.approx(0.3) assert pd.isna(second["side_bias"]) -def test_build_raises_when_task_logic_missing_with_trials(): - """A missing TaskLogic stream is an error when there are trials (reward size is required).""" +def test_build_missing_task_logic_leaves_session_columns_null(): + """A missing TaskLogic stream still builds; session distribution columns are null.""" dataset = _full_dataset() input_schemas = dataset.children["Behavior"].children["InputSchemas"] input_schemas.children["TaskLogic"] = _FailedStream() - with pytest.raises(ValueError, match="TaskLogic stream is required"): + table = TrialTableBuilder(dataset).build() + assert len(table) == 2 + assert table["ITI_beta"].isna().all() + assert table["block_beta"].isna().all() + + +def test_build_raises_when_rig_missing_with_trials(): + """A missing Rig stream is an error when there are trials (lickspout position needs it).""" + dataset = _full_dataset() + input_schemas = dataset.children["Behavior"].children["InputSchemas"] + input_schemas.children["Rig"] = _FailedStream() + with pytest.raises(ValueError, match="Rig stream is required"): + TrialTableBuilder(dataset).build() + + +def test_build_raises_when_accumulated_steps_missing_with_trials(): + """A missing AccumulatedSteps stream is an error when there are trials.""" + dataset = _full_dataset() + harp_manipulator = dataset.children["Behavior"].children["HarpManipulator"] + harp_manipulator.children["AccumulatedSteps"] = _FailedStream() + with pytest.raises(ValueError, match="AccumulatedSteps stream is required"): TrialTableBuilder(dataset).build() @@ -348,7 +422,7 @@ def test_summary_generator_prefers_coupled_over_uncoupled(): composite = TrialGeneratorCompositeSpec(generators=[UncoupledTrialGeneratorSpec(), coupled]) resolved = TrialTableBuilder._summary_generator(composite) assert resolved.type == "CoupledTrialGenerator" - assert resolved.min_block_reward == coupled.min_block_reward + assert resolved is coupled def test_summary_generator_falls_back_to_uncoupled(): @@ -367,29 +441,16 @@ def test_summary_generator_none_when_no_coupled_or_uncoupled(caplog): assert "No coupled or uncoupled generator" in caplog.text -def test_session_columns_only_reward_size_when_no_summary_generator(): - """With no coupled/uncoupled generator, only the generator-independent reward size remains.""" +def test_session_columns_empty_when_no_summary_generator(): + """With no coupled/uncoupled generator, the session columns dict is empty.""" task_logic = AindDynamicForagingTaskLogic( task_parameters=AindDynamicForagingTaskParameters( trial_generator=TrialGeneratorCompositeSpec( generators=[CoupledWarmupTrialGeneratorSpec()] ), - reward_size=RewardSize(left_value_volume=2.0, right_value_volume=4.0), ) ) - # Reward size lives on the task parameters, not the generator, so it is the - # only column populated when no summarising generator is found. - assert TrialTableBuilder(_Node({}))._session_columns(task_logic) == { - "reward_size_left": 2.0, - "reward_size_right": 4.0, - } - - -def test_session_columns_include_reward_size(): - """Reward volumes are read from ``task_parameters.reward_size``.""" - columns = TrialTableBuilder(_Node({}))._session_columns(_task_logic()) - assert columns["reward_size_left"] == 2.0 - assert columns["reward_size_right"] == 4.0 + assert TrialTableBuilder(_Node({}))._session_columns(task_logic) == {} def test_side_bias_parses_dict_model_json_and_none(): @@ -414,6 +475,17 @@ def test_build_missing_trial_metrics_leaves_side_bias_null(): assert table["side_bias"].isna().all() +def test_session_columns_warmup_generator_populates_min_reward_each_block(): + """A warmup generator exposes ``min_block_reward``, populating ``min_reward_each_block``.""" + task_logic = AindDynamicForagingTaskLogic( + task_parameters=AindDynamicForagingTaskParameters( + trial_generator=CoupledWarmupTrialGeneratorSpec() + ) + ) + columns = TrialTableBuilder(_Node({}))._session_columns(task_logic) + assert columns["min_reward_each_block"] == CoupledWarmupTrialGeneratorSpec().min_block_reward + + def test_session_columns_uncoupled_has_null_reward_sum(): """An uncoupled generator populates distribution columns but no coupled-only fields.""" task_logic = AindDynamicForagingTaskLogic( @@ -516,12 +588,6 @@ def test_animal_response_encoding(): assert TrialTableBuilder._animal_response({"Item1": 1.0}) == 2 -def test_is_baited_none_trial_returns_false(): - """A missing trial yields ``False`` bait for both sides.""" - assert TrialTableBuilder._is_baited(None, is_right=True) is False - assert TrialTableBuilder._is_baited(None, is_right=False) is False - - def test_is_baited_forfeited_by_auto_response_on_same_side(): """A side with guaranteed reward stays baited unless auto-responded to that side.""" trial = TrialOutcome.model_validate( @@ -538,8 +604,7 @@ def test_auto_water_encodes_side_from_auto_response(): ).trial assert TrialTableBuilder._auto_water(trial, is_right=True) == 1 assert TrialTableBuilder._auto_water(trial, is_right=False) == 0 - # A missing trial or no auto-response counts as no autowater (0). - assert TrialTableBuilder._auto_water(None, is_right=True) == 0 + # No auto-response counts as no autowater (0). no_auto = TrialOutcome.model_validate( _outcome(1.0, 1.0, is_right_choice=True, is_rewarded=True, auto=None) ).trial @@ -557,9 +622,8 @@ def test_block_reward_probability_reads_metadata_not_trial(): assert TrialTableBuilder._block_reward_probability(trial, is_right=True) == pytest.approx(0.1) -def test_block_reward_probability_none_without_metadata_or_trial(): - """A missing trial or absent metadata yields ``None``.""" - assert TrialTableBuilder._block_reward_probability(None, is_right=True) is None +def test_block_reward_probability_none_without_metadata(): + """Absent metadata yields ``None``.""" no_meta = TrialOutcome.model_validate( _outcome(1.0, 0.2, is_right_choice=True, is_rewarded=True) ).trial @@ -570,15 +634,19 @@ def test_block_reward_probability_none_without_metadata_or_trial(): @pytest.mark.parametrize( "payload", [ - None, _outcome(1.0, 1.0, is_right_choice=True, is_rewarded=True), TrialOutcome.model_validate(_outcome(1.0, 1.0, is_right_choice=False, is_rewarded=False)), ], ) -def test_parse_outcome_accepts_dict_model_and_none(payload): - """``_parse_outcome`` accepts dicts, model instances, and ``None``.""" - result = TrialTableBuilder._parse_outcome(payload) - assert result is None or isinstance(result, TrialOutcome) +def test_parse_outcome_accepts_dict_and_model(payload): + """``_parse_outcome`` accepts dicts and model instances.""" + assert isinstance(TrialTableBuilder._parse_outcome(payload), TrialOutcome) + + +def test_parse_outcome_raises_on_none(): + """``_parse_outcome`` raises ``ValueError`` for a ``None`` payload.""" + with pytest.raises(ValueError, match="required"): + TrialTableBuilder._parse_outcome(None) def test_parse_outcome_accepts_json_string(): @@ -589,23 +657,109 @@ def test_parse_outcome_accepts_json_string(): assert isinstance(TrialTableBuilder._parse_outcome(payload), TrialOutcome) -def test_lickspout_columns_from_list_payload(): - """A list payload is mapped positionally to x/y1/y2/z.""" +def test_manipulator_mm_per_step_from_calibration(): + """mm-per-microstep is full_step_to_mm / microstep resolution, per axis.""" builder = TrialTableBuilder(_Node({})) - columns = builder._lickspout_columns(_events([1.0], [[10.0, 20.0, 30.0, 40.0]])) - assert columns["lickspout_position_x"] == 10.0 - assert columns["lickspout_position_y2"] == 30.0 + mm_per_step = builder._manipulator_mm_per_step(_rig()) + assert mm_per_step == {"x": 0.00125, "y1": 0.00125, "y2": 0.00125, "z": 0.00125} -def test_lickspout_columns_unrecognized_payload_is_null(): - """An unrecognized payload leaves all lickspout positions ``None``.""" +def test_manipulator_mm_per_step_respects_resolution(): + """A finer microstep resolution shrinks the distance per step.""" builder = TrialTableBuilder(_Node({})) - columns = builder._lickspout_columns(_events([1.0], ["unexpected"])) - assert all(value is None for value in columns.values()) + mm_per_step = builder._manipulator_mm_per_step( + _rig(step_mm=0.01, resolution=MicrostepResolution.MICROSTEP16) + ) + assert mm_per_step["x"] == pytest.approx(0.01 / 16) + + +def test_manipulator_mm_per_step_missing_axis_raises(): + """A calibration lacking one of the four axes raises ``ValueError``.""" + builder = TrialTableBuilder(_Node({})) + rig = _rig() + # Drop the Z axis configuration. + rig.manipulator.calibration.axis_configuration = [ + config + for config in rig.manipulator.calibration.axis_configuration + if config.axis is not Axis.Z + ] + with pytest.raises(ValueError, match="missing axis 'z'"): + builder._manipulator_mm_per_step(rig) + + +def test_manipulator_positions_converts_steps_to_mm_relative_to_start(): + """EVENT rows convert to mm and are re-referenced to the session-start sample.""" + builder = TrialTableBuilder(_Node({})) + steps = _accumulated_steps([8.0, 15.0], [(8000, 1600, 2400, 4000), (12000, 1600, 2400, 4000)]) + positions = builder._manipulator_positions(steps, _rig()) + assert list(positions.index) == [8.0, 15.0] + # First sample is the baseline (zeroed); x then moves +5.0 mm (4000 steps). + assert positions.loc[8.0, "lickspout_position_x"] == 0.0 + assert positions.loc[15.0, "lickspout_position_x"] == 5.0 + assert positions.loc[8.0, "lickspout_position_z"] == 0.0 + + +def test_manipulator_positions_filters_non_event_rows(): + """Only ``EVENT`` rows contribute to the position frame.""" + builder = TrialTableBuilder(_Node({})) + steps = _accumulated_steps([8.0, 15.0], [(8000, 1600, 2400, 4000), (12000, 1600, 2400, 4000)]) + steps.loc[15.0, "MessageType"] = "WRITE" + positions = builder._manipulator_positions(steps, _rig()) + assert list(positions.index) == [8.0] + + +def test_manipulator_positions_all_non_event_raises(): + """A stream with no ``EVENT`` rows raises ``ValueError``.""" + builder = TrialTableBuilder(_Node({})) + steps = _accumulated_steps([8.0], [(8000, 1600, 2400, 4000)]) + steps["MessageType"] = "WRITE" + with pytest.raises(ValueError, match="no EVENT rows"): + builder._manipulator_positions(steps, _rig()) + + +def test_manipulator_positions_missing_motor_column_raises(): + """A stream missing a Motor column raises ``ValueError``.""" + builder = TrialTableBuilder(_Node({})) + steps = _accumulated_steps([8.0], [(8000, 1600, 2400, 4000)]).drop(columns=["Motor3"]) + with pytest.raises(ValueError, match="missing column Motor3"): + builder._manipulator_positions(steps, _rig()) + + +def test_manipulator_positions_incomplete_calibration_raises(): + """Steps present but a calibration axis missing raises ``ValueError``.""" + builder = TrialTableBuilder(_Node({})) + steps = _accumulated_steps([8.0], [(8000, 1600, 2400, 4000)]) + rig = _rig() + rig.manipulator.calibration.axis_configuration = [ + config + for config in rig.manipulator.calibration.axis_configuration + if config.axis is not Axis.Z + ] + with pytest.raises(ValueError, match="missing axis 'z'"): + builder._manipulator_positions(steps, rig) + + +def _two_sample_positions(builder): + """Build a position frame relative to session start: t=8.0 (x=0.0), t=15.0 (x=5.0).""" + return builder._manipulator_positions( + _accumulated_steps([8.0, 15.0], [(8000, 1600, 2400, 4000), (12000, 1600, 2400, 4000)]), + _rig(), + ) + + +def test_sample_lickspout_picks_sample_nearest_start_in_window(): + """A trial takes the in-window sample nearest its start.""" + builder = TrialTableBuilder(_Node({})) + positions = _two_sample_positions(builder) + # Window [7.0, 12.0) contains only the t=8.0 baseline sample (0.0). + assert builder._sample_lickspout(positions, 7.0, 12.0)["lickspout_position_x"] == 0.0 + # Window [14.0, 20.0) contains only the t=15.0 sample (+5.0 mm). + assert builder._sample_lickspout(positions, 14.0, 20.0)["lickspout_position_x"] == 5.0 -def test_lickspout_columns_missing_stream_is_null(): - """A missing manipulator stream leaves all lickspout positions ``None``.""" +def test_sample_lickspout_no_sample_in_window_is_null(): + """A trial whose window contains no sample yields ``None`` columns.""" builder = TrialTableBuilder(_Node({})) - columns = builder._lickspout_columns(None) + positions = _two_sample_positions(builder) + columns = builder._sample_lickspout(positions, 20.0, 30.0) assert all(value is None for value in columns.values()) diff --git a/tests/test_qc/test_behavior.py b/tests/test_qc/test_behavior.py index 8fff460..d366034 100644 --- a/tests/test_qc/test_behavior.py +++ b/tests/test_qc/test_behavior.py @@ -49,7 +49,7 @@ def test_side_bias_result_pass_and_fail(): assert passing.passed is True assert passing.value == pytest.approx(0.0) assert passing.reference == _behavior.SIDE_BIAS_PLOT - assert passing.tags == {"behavior": "average side bias"} + assert passing.tags == {"type": "Average_Side_Bias"} failing = _behavior.side_bias_result(np.array([0.8, 0.9, 1.0])) assert failing.passed is False @@ -75,7 +75,7 @@ def test_lick_interval_results_names_and_count(): "Artifact Percent (%)", ] assert all(r.reference == _behavior.LICK_INTERVALS_PLOT for r in results) - assert all(r.tags == {"behavior": r.name} for r in results) + assert all(r.tags == {"metric": r.name, "type": "Lick_Interval"} for r in results) def test_reference_includes_results_folder_name(): diff --git a/tests/test_qc/test_builder.py b/tests/test_qc/test_builder.py index 69507e8..bbf97e5 100644 --- a/tests/test_qc/test_builder.py +++ b/tests/test_qc/test_builder.py @@ -29,6 +29,22 @@ def test_behavior_qc_results_without_plots(): assert results[0].name == "average side bias" +def test_lickspout_columns_map_to_trial_table_names(): + """The lickspout mapping resolves to the ``lickspout_position_*`` trial columns.""" + trials = pd.DataFrame( + { + "lickspout_position_x": [16.0, 16.0], + "lickspout_position_y1": [9.6, 9.6], + "lickspout_position_y2": [9.7, 9.7], + "lickspout_position_z": [17.25, 17.25], + } + ) + for key in ("lickspout_x", "lickspout_y1", "lickspout_y2", "lickspout_z"): + column = _results._column(trials, key) + assert column is not None, key + assert column[0] == trials[_results._COLUMNS[key]][0] + + def test_behavior_qc_results_writes_plots(tmp_path): """Supplying a results folder writes both behavior plots.""" trials = pd.DataFrame( diff --git a/uv.lock b/uv.lock index 798d492..7f499f5 100644 --- a/uv.lock +++ b/uv.lock @@ -39,7 +39,7 @@ wheels = [ [[package]] name = "aind-behavior-dynamic-foraging" version = "0.0.2" -source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging.git?rev=baab12133b22f599c1ba0583260eca9eca216cc0#baab12133b22f599c1ba0583260eca9eca216cc0" } +source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.DynamicForaging.git?rev=ac5ddbf909c9375b9e8875d6a5f90796cfa98653#ac5ddbf909c9375b9e8875d6a5f90796cfa98653" } dependencies = [ { name = "aind-behavior-services" }, { name = "pydantic-settings" }, @@ -53,7 +53,7 @@ data = [ [[package]] name = "aind-behavior-services" -version = "0.13.7" +version = "0.13.8" source = { registry = "https://pypi.org/simple" } dependencies = 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