twopy 0.1.0__py3-none-any.whl

twopy/__init__.py

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+"""Top-level package for the twopy two-photon imaging analysis tool.
+
+The package exposes project metadata and script-friendly public APIs.
+Inputs: none.
+Outputs: package constants and helper functions imported by users and scripts.
+"""
+
+from twopy.analysis import (
+    DEFAULT_RESPONSE_POST_WINDOW_SECONDS,
+    DEFAULT_RESPONSE_PRE_WINDOW_SECONDS,
+    AnalysisResponseComputation,
+    AnalysisResponseRun,
+    BackgroundCorrectedRoiTraces,
+    BackgroundCorrectionMethod,
+    DeltaFOverFFitMode,
+    EpochFrameWindow,
+    FrameWindow,
+    GroupedRoiResponses,
+    GroupedRoiResponseSummary,
+    InterpolatedEpochMapping,
+    LoadedAnalysisOutputs,
+    RoiDeltaFOverF,
+    RoiResponseSummary,
+    RoiResponseTrial,
+    WindowedRoiResponse,
+    analyze_recording_responses,
+    apply_motion_artifact_mask_to_delta_f_over_f,
+    compute_recording_responses,
+    compute_roi_delta_f_over_f,
+    extract_background_corrected_roi_traces,
+    frame_windows_from_photodiode_alignment,
+    group_delta_f_over_f_by_epoch,
+    interpolate_stimulus_epochs_to_frame_windows,
+    is_gray_epoch_name,
+    load_analysis_outputs,
+    make_frame_windows,
+    map_stimulus_epochs_to_frame_windows,
+    save_analysis_outputs,
+    select_epoch_frame_windows,
+    split_traces_by_frame_windows,
+    summarize_epoch_roi_responses,
+    summarize_grouped_responses,
+    write_response_summary_grouped_csv,
+    write_response_summary_trials_csv,
+)
+from twopy.api import find_recordings
+from twopy.conversion import convert_recording_to_twopy, load_source_conversion_inputs
+from twopy.converted import load_converted_recording
+from twopy.napari import (
+    NapariControlDocks,
+    NapariRecordingView,
+    add_twopy_magicgui_controls,
+    launch_napari,
+    open_recording_in_napari,
+    roi_label_image_from_layer,
+    save_napari_label_rois,
+)
+from twopy.photodiode_classification import (
+    ClassifiedPhotodiodeEvent,
+    ClassifiedStimulusTiming,
+    ClassifiedStimulusWindow,
+    PhotodiodeDurationClass,
+    PhotodiodeEventType,
+    classify_recording_photodiode_events,
+)
+from twopy.roi import (
+    RoiSet,
+    RoiTraces,
+    extract_roi_traces,
+    load_roi_set,
+    make_roi_set,
+    make_roi_set_from_label_image,
+    roi_set_to_label_image,
+    save_roi_set,
+)
+from twopy.spatial import SpatialCrop, SpatialDomain, full_frame_crop
+from twopy.stimulus import (
+    StimulusSpecificColumnMapping,
+    map_stimulus_specific_column,
+)
+from twopy.synchronization import (
+    AlignedPhotodiodeEvent,
+    PhotodiodeAlignment,
+    PhotodiodeEvent,
+    PhotodiodeEventSet,
+    detect_photodiode_events,
+    detect_recording_photodiode_events,
+    pair_photodiode_events_to_imaging_frames,
+)
+
+__all__ = [
+    "__version__",
+    "AlignedPhotodiodeEvent",
+    "AnalysisResponseRun",
+    "AnalysisResponseComputation",
+    "analyze_recording_responses",
+    "add_twopy_magicgui_controls",
+    "apply_motion_artifact_mask_to_delta_f_over_f",
+    "BackgroundCorrectedRoiTraces",
+    "BackgroundCorrectionMethod",
+    "ClassifiedPhotodiodeEvent",
+    "ClassifiedStimulusTiming",
+    "ClassifiedStimulusWindow",
+    "classify_recording_photodiode_events",
+    "compute_roi_delta_f_over_f",
+    "compute_recording_responses",
+    "convert_recording_to_twopy",
+    "DEFAULT_RESPONSE_POST_WINDOW_SECONDS",
+    "DEFAULT_RESPONSE_PRE_WINDOW_SECONDS",
+    "detect_photodiode_events",
+    "detect_recording_photodiode_events",
+    "DeltaFOverFFitMode",
+    "EpochFrameWindow",
+    "extract_background_corrected_roi_traces",
+    "extract_roi_traces",
+    "find_recordings",
+    "frame_windows_from_photodiode_alignment",
+    "FrameWindow",
+    "full_frame_crop",
+    "group_delta_f_over_f_by_epoch",
+    "GroupedRoiResponseSummary",
+    "GroupedRoiResponses",
+    "InterpolatedEpochMapping",
+    "interpolate_stimulus_epochs_to_frame_windows",
+    "is_gray_epoch_name",
+    "launch_napari",
+    "load_analysis_outputs",
+    "load_converted_recording",
+    "load_roi_set",
+    "load_source_conversion_inputs",
+    "LoadedAnalysisOutputs",
+    "make_roi_set_from_label_image",
+    "make_frame_windows",
+    "make_roi_set",
+    "map_stimulus_epochs_to_frame_windows",
+    "map_stimulus_specific_column",
+    "NapariControlDocks",
+    "NapariRecordingView",
+    "open_recording_in_napari",
+    "pair_photodiode_events_to_imaging_frames",
+    "PhotodiodeAlignment",
+    "PhotodiodeDurationClass",
+    "PhotodiodeEvent",
+    "PhotodiodeEventType",
+    "PhotodiodeEventSet",
+    "RoiDeltaFOverF",
+    "RoiResponseSummary",
+    "RoiResponseTrial",
+    "RoiSet",
+    "RoiTraces",
+    "roi_label_image_from_layer",
+    "roi_set_to_label_image",
+    "save_analysis_outputs",
+    "save_napari_label_rois",
+    "save_roi_set",
+    "select_epoch_frame_windows",
+    "split_traces_by_frame_windows",
+    "SpatialCrop",
+    "SpatialDomain",
+    "StimulusSpecificColumnMapping",
+    "summarize_epoch_roi_responses",
+    "summarize_grouped_responses",
+    "WindowedRoiResponse",
+    "write_response_summary_grouped_csv",
+    "write_response_summary_trials_csv",
+]
+
+__version__ = "0.1.0"

twopy/_segments.py

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+"""Small helpers for finding contiguous runs in one-dimensional arrays.
+
+Inputs: boolean or integer NumPy vectors.
+Outputs: inclusive-start, exclusive-stop index pairs for contiguous runs.
+
+Timing code uses these helpers to turn threshold masks and epoch vectors into
+auditable windows without duplicating low-level indexing logic.
+"""
+
+import numpy as np
+import numpy.typing as npt
+
+__all__ = ["constant_segments", "true_segments"]
+
+
+def true_segments(active: npt.NDArray[np.bool_]) -> tuple[tuple[int, int], ...]:
+    """Find contiguous true runs in a Boolean vector.
+
+    Args:
+        active: Boolean vector.
+
+    Returns:
+        Tuple of inclusive-start, exclusive-stop index pairs.
+    """
+    if active.size == 0:
+        return ()
+
+    padded = np.concatenate(([False], active, [False]))
+    changes = np.flatnonzero(padded[1:] != padded[:-1])
+    return tuple(
+        (int(changes[index]), int(changes[index + 1]))
+        for index in range(0, len(changes), 2)
+    )
+
+
+def constant_segments(values: npt.NDArray[np.int64]) -> tuple[tuple[int, int], ...]:
+    """Find contiguous runs with the same integer value.
+
+    Args:
+        values: One-dimensional integer vector.
+
+    Returns:
+        Tuple of inclusive-start, exclusive-stop index pairs.
+    """
+    if values.size == 0:
+        return ()
+
+    changes = np.flatnonzero(values[1:] != values[:-1]) + 1
+    starts = np.r_[0, changes]
+    stops = np.r_[changes, values.size]
+    return tuple(
+        (int(start), int(stop)) for start, stop in zip(starts, stops, strict=True)
+    )

twopy/analysis/__init__.py

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+"""Analysis helpers for converted two-photon recordings.
+
+Inputs: converted twopy recordings, ROI traces, photodiode-aligned windows, and
+analysis parameters.
+Outputs: background-corrected traces and trial/frame-window response objects.
+
+This package is GUI-independent and operates only on twopy-owned converted
+files or in-memory objects derived from them.
+"""
+
+from twopy.analysis.background_subtraction import (
+    BackgroundCorrectedRoiTraces,
+    BackgroundCorrectionMethod,
+    extract_background_corrected_roi_traces,
+)
+from twopy.analysis.dff import (
+    DeltaFOverFFitMode,
+    RoiDeltaFOverF,
+    compute_roi_delta_f_over_f,
+)
+from twopy.analysis.epoch_mapping import (
+    InterpolatedEpochMapping,
+    interpolate_stimulus_epochs_to_frame_windows,
+)
+from twopy.analysis.motion import apply_motion_artifact_mask_to_delta_f_over_f
+from twopy.analysis.persistence import (
+    ANALYSIS_OUTPUT_FILE_FORMAT,
+    LoadedAnalysisOutputs,
+    load_analysis_outputs,
+    save_analysis_outputs,
+    write_response_summary_grouped_csv,
+    write_response_summary_trials_csv,
+)
+from twopy.analysis.responses import (
+    GroupedRoiResponses,
+    GroupedRoiResponseSummary,
+    RoiResponseSummary,
+    RoiResponseTrial,
+    group_delta_f_over_f_by_epoch,
+    is_gray_epoch_name,
+    summarize_epoch_roi_responses,
+    summarize_grouped_responses,
+)
+from twopy.analysis.trials import (
+    EpochFrameWindow,
+    FrameWindow,
+    WindowedRoiResponse,
+    frame_windows_from_photodiode_alignment,
+    make_frame_windows,
+    map_stimulus_epochs_to_frame_windows,
+    select_epoch_frame_windows,
+    split_traces_by_frame_windows,
+)
+from twopy.analysis.workflow import (
+    DEFAULT_RESPONSE_POST_WINDOW_SECONDS,
+    DEFAULT_RESPONSE_PRE_WINDOW_SECONDS,
+    AnalysisResponseComputation,
+    AnalysisResponseRun,
+    analyze_recording_responses,
+    compute_recording_responses,
+)
+
+__all__ = [
+    "analyze_recording_responses",
+    "AnalysisResponseComputation",
+    "AnalysisResponseRun",
+    "DEFAULT_RESPONSE_POST_WINDOW_SECONDS",
+    "DEFAULT_RESPONSE_PRE_WINDOW_SECONDS",
+    "apply_motion_artifact_mask_to_delta_f_over_f",
+    "ANALYSIS_OUTPUT_FILE_FORMAT",
+    "BackgroundCorrectedRoiTraces",
+    "BackgroundCorrectionMethod",
+    "compute_roi_delta_f_over_f",
+    "compute_recording_responses",
+    "DeltaFOverFFitMode",
+    "EpochFrameWindow",
+    "extract_background_corrected_roi_traces",
+    "frame_windows_from_photodiode_alignment",
+    "FrameWindow",
+    "group_delta_f_over_f_by_epoch",
+    "GroupedRoiResponseSummary",
+    "GroupedRoiResponses",
+    "InterpolatedEpochMapping",
+    "interpolate_stimulus_epochs_to_frame_windows",
+    "is_gray_epoch_name",
+    "load_analysis_outputs",
+    "LoadedAnalysisOutputs",
+    "make_frame_windows",
+    "map_stimulus_epochs_to_frame_windows",
+    "RoiDeltaFOverF",
+    "RoiResponseSummary",
+    "RoiResponseTrial",
+    "save_analysis_outputs",
+    "select_epoch_frame_windows",
+    "split_traces_by_frame_windows",
+    "summarize_epoch_roi_responses",
+    "summarize_grouped_responses",
+    "WindowedRoiResponse",
+    "write_response_summary_grouped_csv",
+    "write_response_summary_trials_csv",
+]