TwoPy 0.3.3__tar.gz → 0.3.5__tar.gz

{twopy-0.3.3 → twopy-0.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.3.3
+Version: 0.3.5
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT

{twopy-0.3.3 → twopy-0.3.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.3.3"
+version = "0.3.5"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"
@@ -38,7 +38,7 @@ Repository = "https://github.com/gumadeiras/twopy"
 where = ["src"]
 
 [tool.setuptools.package-data]
-twopy = ["calibrations/*.csv", "config.example.yml", "napari/assets/*.png"]
+twopy = ["calibrations/*.csv", "config.example.yml", "napari/assets/*.icns", "napari/assets/*.png"]
 
 [tool.ruff]
 line-length = 88

twopy-0.3.5/src/twopy/__init__.py

@@ -0,0 +1,328 @@
+"""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 importlib import import_module
+
+_LAZY_EXPORTS = {
+    "__version__": ("twopy._version", "__version__"),
+    "DEFAULT_RESPONSE_POST_WINDOW_SECONDS": (
+        "twopy.analysis",
+        "DEFAULT_RESPONSE_POST_WINDOW_SECONDS",
+    ),
+    "DEFAULT_RESPONSE_PRE_WINDOW_SECONDS": (
+        "twopy.analysis",
+        "DEFAULT_RESPONSE_PRE_WINDOW_SECONDS",
+    ),
+    "AnalysisResponseComputation": ("twopy.analysis", "AnalysisResponseComputation"),
+    "AnalysisResponseRun": ("twopy.analysis", "AnalysisResponseRun"),
+    "BackgroundCorrectedRoiTraces": ("twopy.analysis", "BackgroundCorrectedRoiTraces"),
+    "BackgroundCorrectionMethod": ("twopy.analysis", "BackgroundCorrectionMethod"),
+    "CorrelationFilterOptions": ("twopy.analysis", "CorrelationFilterOptions"),
+    "DeltaFOverFBaselineMode": ("twopy.analysis", "DeltaFOverFBaselineMode"),
+    "DeltaFOverFFitMode": ("twopy.analysis", "DeltaFOverFFitMode"),
+    "DeltaFOverFOptions": ("twopy.analysis", "DeltaFOverFOptions"),
+    "EpochFrameWindow": ("twopy.analysis", "EpochFrameWindow"),
+    "EpochResponseMap": ("twopy.analysis", "EpochResponseMap"),
+    "FrameWindow": ("twopy.analysis", "FrameWindow"),
+    "GroupedRoiResponses": ("twopy.analysis", "GroupedRoiResponses"),
+    "GroupedRoiResponseSummary": ("twopy.analysis", "GroupedRoiResponseSummary"),
+    "Hemisphere": ("twopy.analysis", "Hemisphere"),
+    "KernelFitMethod": ("twopy.analysis", "KernelFitMethod"),
+    "KernelStimulusModality": ("twopy.analysis", "KernelStimulusModality"),
+    "LoadedAnalysisOutputs": ("twopy.analysis", "LoadedAnalysisOutputs"),
+    "LowPassFilterOptions": ("twopy.analysis", "LowPassFilterOptions"),
+    "ManualFovGroupRow": ("twopy.analysis", "ManualFovGroupRow"),
+    "ManualRoiMatchGroup": ("twopy.analysis", "ManualRoiMatchGroup"),
+    "ManualRoiMatchRow": ("twopy.analysis", "ManualRoiMatchRow"),
+    "ManualRoiMatchStatus": ("twopy.analysis", "ManualRoiMatchStatus"),
+    "RecordingKernelFit": ("twopy.analysis", "RecordingKernelFit"),
+    "RecordingTiming": ("twopy.analysis", "RecordingTiming"),
+    "ResponseMapData": ("twopy.analysis", "ResponseMapData"),
+    "ResponseMapMode": ("twopy.analysis", "ResponseMapMode"),
+    "ResponseMapOptions": ("twopy.analysis", "ResponseMapOptions"),
+    "ResponseProcessingOptions": ("twopy.analysis", "ResponseProcessingOptions"),
+    "RoiCorrelationScores": ("twopy.analysis", "RoiCorrelationScores"),
+    "RoiDeltaFOverF": ("twopy.analysis", "RoiDeltaFOverF"),
+    "RoiResponseSummary": ("twopy.analysis", "RoiResponseSummary"),
+    "RoiResponseTrial": ("twopy.analysis", "RoiResponseTrial"),
+    "SmoothingOptions": ("twopy.analysis", "SmoothingOptions"),
+    "StimulusKernelOptions": ("twopy.analysis", "StimulusKernelOptions"),
+    "TimingSource": ("twopy.analysis", "TimingSource"),
+    "WindowedRoiResponse": ("twopy.analysis", "WindowedRoiResponse"),
+    "add_manual_roi_match_group": ("twopy.analysis", "add_manual_roi_match_group"),
+    "analyze_recording_responses": ("twopy.analysis", "analyze_recording_responses"),
+    "append_manual_roi_match_rows": ("twopy.analysis", "append_manual_roi_match_rows"),
+    "apply_motion_artifact_mask_to_delta_f_over_f": (
+        "twopy.analysis",
+        "apply_motion_artifact_mask_to_delta_f_over_f",
+    ),
+    "compute_recording_response_maps": (
+        "twopy.analysis",
+        "compute_recording_response_maps",
+    ),
+    "compute_recording_responses": ("twopy.analysis", "compute_recording_responses"),
+    "compute_roi_delta_f_over_f": ("twopy.analysis", "compute_roi_delta_f_over_f"),
+    "default_baseline_epoch_number": (
+        "twopy.analysis",
+        "default_baseline_epoch_number",
+    ),
+    "default_kernel_stimulus_column": (
+        "twopy.analysis",
+        "default_kernel_stimulus_column",
+    ),
+    "default_recording_baseline_epoch_number": (
+        "twopy.analysis",
+        "default_recording_baseline_epoch_number",
+    ),
+    "extract_background_corrected_roi_traces": (
+        "twopy.analysis",
+        "extract_background_corrected_roi_traces",
+    ),
+    "finite_mean_and_sem": ("twopy.analysis", "finite_mean_and_sem"),
+    "fit_recording_stimulus_kernels": (
+        "twopy.analysis",
+        "fit_recording_stimulus_kernels",
+    ),
+    "fit_stimulus_kernel": ("twopy.analysis", "fit_stimulus_kernel"),
+    "group_delta_f_over_f_by_epoch": (
+        "twopy.analysis",
+        "group_delta_f_over_f_by_epoch",
+    ),
+    "is_baseline_epoch_name": ("twopy.analysis", "is_baseline_epoch_name"),
+    "load_analysis_outputs": ("twopy.analysis", "load_analysis_outputs"),
+    "load_manual_fov_group_rows": ("twopy.analysis", "load_manual_fov_group_rows"),
+    "load_manual_roi_match_rows": ("twopy.analysis", "load_manual_roi_match_rows"),
+    "load_response_map_data": ("twopy.analysis", "load_response_map_data"),
+    "make_frame_windows": ("twopy.analysis", "make_frame_windows"),
+    "make_manual_fov_group_rows": ("twopy.analysis", "make_manual_fov_group_rows"),
+    "make_manual_roi_match_rows": ("twopy.analysis", "make_manual_roi_match_rows"),
+    "matched_manual_roi_groups": ("twopy.analysis", "matched_manual_roi_groups"),
+    "next_group_cell_id": ("twopy.analysis", "next_group_cell_id"),
+    "no_baseline_epoch_frame_windows": (
+        "twopy.analysis",
+        "no_baseline_epoch_frame_windows",
+    ),
+    "remove_manual_roi_match_group": (
+        "twopy.analysis",
+        "remove_manual_roi_match_group",
+    ),
+    "replace_manual_roi_match_group": (
+        "twopy.analysis",
+        "replace_manual_roi_match_group",
+    ),
+    "resolve_baseline_frame_windows": (
+        "twopy.analysis",
+        "resolve_baseline_frame_windows",
+    ),
+    "resolve_recording_timing": ("twopy.analysis", "resolve_recording_timing"),
+    "save_analysis_outputs": ("twopy.analysis", "save_analysis_outputs"),
+    "save_manual_fov_group_rows": ("twopy.analysis", "save_manual_fov_group_rows"),
+    "save_manual_roi_match_rows": ("twopy.analysis", "save_manual_roi_match_rows"),
+    "save_response_map_data": ("twopy.analysis", "save_response_map_data"),
+    "select_baseline_frame_windows": (
+        "twopy.analysis",
+        "select_baseline_frame_windows",
+    ),
+    "split_traces_by_frame_windows": (
+        "twopy.analysis",
+        "split_traces_by_frame_windows",
+    ),
+    "summarize_epoch_roi_responses": (
+        "twopy.analysis",
+        "summarize_epoch_roi_responses",
+    ),
+    "summarize_grouped_responses": ("twopy.analysis", "summarize_grouped_responses"),
+    "validate_grouped_roi_responses": (
+        "twopy.analysis",
+        "validate_grouped_roi_responses",
+    ),
+    "write_response_summary_grouped_csv": (
+        "twopy.analysis",
+        "write_response_summary_grouped_csv",
+    ),
+    "write_response_summary_trials_csv": (
+        "twopy.analysis",
+        "write_response_summary_trials_csv",
+    ),
+    "find_recordings": ("twopy.api", "find_recordings"),
+    "convert_recording_to_twopy": ("twopy.conversion", "convert_recording_to_twopy"),
+    "load_source_conversion_inputs": (
+        "twopy.conversion",
+        "load_source_conversion_inputs",
+    ),
+    "load_converted_recording": ("twopy.converted", "load_converted_recording"),
+    "recording_frame_rate_hz": ("twopy.converted", "recording_frame_rate_hz"),
+    "recording_hemisphere": ("twopy.converted", "recording_hemisphere"),
+    "ClassifiedPhotodiodeEvent": (
+        "twopy.photodiode_classification",
+        "ClassifiedPhotodiodeEvent",
+    ),
+    "ClassifiedStimulusTiming": (
+        "twopy.photodiode_classification",
+        "ClassifiedStimulusTiming",
+    ),
+    "ClassifiedStimulusWindow": (
+        "twopy.photodiode_classification",
+        "ClassifiedStimulusWindow",
+    ),
+    "PhotodiodeDurationClass": (
+        "twopy.photodiode_classification",
+        "PhotodiodeDurationClass",
+    ),
+    "PhotodiodeEventType": ("twopy.photodiode_classification", "PhotodiodeEventType"),
+    "classify_recording_photodiode_events": (
+        "twopy.photodiode_classification",
+        "classify_recording_photodiode_events",
+    ),
+    "DEFAULT_PIXEL_CALIBRATION_PATH": (
+        "twopy.pixel_calibration",
+        "DEFAULT_PIXEL_CALIBRATION_PATH",
+    ),
+    "PixelCalibrationResolution": (
+        "twopy.pixel_calibration",
+        "PixelCalibrationResolution",
+    ),
+    "PixelCalibrationResolutionMethod": (
+        "twopy.pixel_calibration",
+        "PixelCalibrationResolutionMethod",
+    ),
+    "PixelCalibrationRow": ("twopy.pixel_calibration", "PixelCalibrationRow"),
+    "load_pixel_calibrations": ("twopy.pixel_calibration", "load_pixel_calibrations"),
+    "resolve_pixel_size_um": ("twopy.pixel_calibration", "resolve_pixel_size_um"),
+    "DEFAULT_PIXEL_CALIBRATION_PROFILE_PATH": (
+        "twopy.pixel_calibration_profiles",
+        "DEFAULT_PIXEL_CALIBRATION_PROFILE_PATH",
+    ),
+    "PixelCalibrationGroup": (
+        "twopy.pixel_calibration_profiles",
+        "PixelCalibrationGroup",
+    ),
+    "PixelCalibrationProfile": (
+        "twopy.pixel_calibration_profiles",
+        "PixelCalibrationProfile",
+    ),
+    "PixelCalibrationProfileMapping": (
+        "twopy.pixel_calibration_profiles",
+        "PixelCalibrationProfileMapping",
+    ),
+    "PixelCalibrationProfileSource": (
+        "twopy.pixel_calibration_profiles",
+        "PixelCalibrationProfileSource",
+    ),
+    "load_pixel_calibration_profile_mappings": (
+        "twopy.pixel_calibration_profiles",
+        "load_pixel_calibration_profile_mappings",
+    ),
+    "resolve_pixel_calibration_profile": (
+        "twopy.pixel_calibration_profiles",
+        "resolve_pixel_calibration_profile",
+    ),
+    "select_pixel_calibration_group": (
+        "twopy.pixel_calibration_profiles",
+        "select_pixel_calibration_group",
+    ),
+    "ResponseNormalization": ("twopy.response_roi_extraction", "ResponseNormalization"),
+    "ResponsePolarity": ("twopy.response_roi_extraction", "ResponsePolarity"),
+    "ResponseStatistic": ("twopy.response_roi_extraction", "ResponseStatistic"),
+    "ResponseWatershedExtraction": (
+        "twopy.response_roi_extraction",
+        "ResponseWatershedExtraction",
+    ),
+    "ResponseWatershedScoreImages": (
+        "twopy.response_roi_extraction",
+        "ResponseWatershedScoreImages",
+    ),
+    "extract_response_watershed_rois": (
+        "twopy.response_roi_extraction",
+        "extract_response_watershed_rois",
+    ),
+    "response_watershed_roi_set": (
+        "twopy.response_roi_extraction",
+        "response_watershed_roi_set",
+    ),
+    "RoiSet": ("twopy.roi", "RoiSet"),
+    "RoiTraces": ("twopy.roi", "RoiTraces"),
+    "extract_roi_traces": ("twopy.roi", "extract_roi_traces"),
+    "load_roi_set": ("twopy.roi", "load_roi_set"),
+    "make_roi_set": ("twopy.roi", "make_roi_set"),
+    "make_roi_set_from_label_image": ("twopy.roi", "make_roi_set_from_label_image"),
+    "roi_set_to_label_image": ("twopy.roi", "roi_set_to_label_image"),
+    "save_roi_set": ("twopy.roi", "save_roi_set"),
+    "RoiExtractionConfig": ("twopy.roi_extraction", "RoiExtractionConfig"),
+    "RoiExtractionMethod": ("twopy.roi_extraction", "RoiExtractionMethod"),
+    "extract_rois_from_image": ("twopy.roi_extraction", "extract_rois_from_image"),
+    "grid_roi_set": ("twopy.roi_extraction", "grid_roi_set"),
+    "grid_roi_set_microns": ("twopy.roi_extraction", "grid_roi_set_microns"),
+    "grid_size_pixels_from_microns": (
+        "twopy.roi_extraction",
+        "grid_size_pixels_from_microns",
+    ),
+    "watershed_roi_set": ("twopy.roi_extraction", "watershed_roi_set"),
+    "SpatialCrop": ("twopy.spatial", "SpatialCrop"),
+    "SpatialDomain": ("twopy.spatial", "SpatialDomain"),
+    "full_frame_crop": ("twopy.spatial", "full_frame_crop"),
+    "StimulusSpecificColumnMapping": (
+        "twopy.stimulus",
+        "StimulusSpecificColumnMapping",
+    ),
+    "map_stimulus_specific_column": ("twopy.stimulus", "map_stimulus_specific_column"),
+    "stimulus_epoch_names_by_number": (
+        "twopy.stimulus",
+        "stimulus_epoch_names_by_number",
+    ),
+    "AlignedPhotodiodeEvent": ("twopy.synchronization", "AlignedPhotodiodeEvent"),
+    "PhotodiodeAlignment": ("twopy.synchronization", "PhotodiodeAlignment"),
+    "PhotodiodeEvent": ("twopy.synchronization", "PhotodiodeEvent"),
+    "PhotodiodeEventSet": ("twopy.synchronization", "PhotodiodeEventSet"),
+    "detect_photodiode_events": ("twopy.synchronization", "detect_photodiode_events"),
+    "detect_recording_photodiode_events": (
+        "twopy.synchronization",
+        "detect_recording_photodiode_events",
+    ),
+    "pair_photodiode_events_to_imaging_frames": (
+        "twopy.synchronization",
+        "pair_photodiode_events_to_imaging_frames",
+    ),
+}
+
+__all__ = list(_LAZY_EXPORTS)
+
+
+def __getattr__(name: str) -> object:
+    """Load public API names only when callers ask for them.
+
+    Args:
+        name: Public attribute requested from ``twopy``.
+
+    Returns:
+        The exported object from its owning module.
+
+    The napari launcher imports this package before it can import
+    ``twopy.napari``. Delaying the scientific API imports keeps application
+    startup from paying for SciPy and HDF5 modules before the GUI needs them.
+    """
+    try:
+        module_name, attribute_name = _LAZY_EXPORTS[name]
+    except KeyError as error:
+        msg = f"module {__name__!r} has no attribute {name!r}"
+        raise AttributeError(msg) from error
+    module = import_module(module_name)
+    value = getattr(module, attribute_name)
+    globals()[name] = value
+    return value
+
+
+def __dir__() -> list[str]:
+    """Return module attributes plus lazy public API names.
+
+    Args:
+        None.
+
+    Returns:
+        Sorted module names for notebooks, shells, and documentation tools.
+    """
+    return sorted(set(globals()) | set(__all__))