TwoPy 0.1.8__tar.gz → 0.2.0__tar.gz

{twopy-0.1.8 → twopy-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.1.8
+Version: 0.2.0
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT
@@ -75,6 +75,7 @@ When a source recording has not been converted yet, twopy converts it first. Con
 
 - [GUI guide](docs/gui.md): napari loading, ROI editing, plotting, and saved outputs.
 - [Python API guide](docs/python_api.md): find recordings, convert data, run analysis, and open napari from scripts.
+- [Custom workflow guide](docs/custom_workflows.md): add versioned local analyses to the napari Custom tab.
 - [Development guide](docs/development.md): source setup and local checks.
 - [Input data spec](docs/input_data_spec.md): short recording folder contract.
 - [Recording file reference](docs/recording_file_schema.md): detailed source and converted file schema.

{twopy-0.1.8 → twopy-0.2.0}/README.md

@@ -55,6 +55,7 @@ When a source recording has not been converted yet, twopy converts it first. Con
 
 - [GUI guide](docs/gui.md): napari loading, ROI editing, plotting, and saved outputs.
 - [Python API guide](docs/python_api.md): find recordings, convert data, run analysis, and open napari from scripts.
+- [Custom workflow guide](docs/custom_workflows.md): add versioned local analyses to the napari Custom tab.
 - [Development guide](docs/development.md): source setup and local checks.
 - [Input data spec](docs/input_data_spec.md): short recording folder contract.
 - [Recording file reference](docs/recording_file_schema.md): detailed source and converted file schema.

{twopy-0.1.8 → twopy-0.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.1.8"
+version = "0.2.0"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"

{twopy-0.1.8 → twopy-0.2.0}/src/twopy/__init__.py

@@ -18,36 +18,67 @@ from twopy.analysis import (
     DeltaFOverFFitMode,
     DeltaFOverFOptions,
     EpochFrameWindow,
+    EpochResponseMap,
     FrameWindow,
     GroupedRoiResponses,
     GroupedRoiResponseSummary,
-    InterpolatedEpochMapping,
+    Hemisphere,
+    KernelFitMethod,
+    KernelStimulusModality,
     LoadedAnalysisOutputs,
     LowPassFilterOptions,
+    ManualFovGroupRow,
+    ManualRoiMatchGroup,
+    ManualRoiMatchRow,
+    ManualRoiMatchStatus,
+    RecordingKernelFit,
+    RecordingTiming,
+    ResponseMapData,
+    ResponseMapMode,
+    ResponseMapOptions,
     ResponseProcessingOptions,
     RoiCorrelationScores,
     RoiDeltaFOverF,
     RoiResponseSummary,
     RoiResponseTrial,
     SmoothingOptions,
+    StimulusKernelOptions,
+    TimingSource,
     WindowedRoiResponse,
+    add_manual_roi_match_group,
     analyze_recording_responses,
+    append_manual_roi_match_rows,
     apply_motion_artifact_mask_to_delta_f_over_f,
+    compute_recording_response_maps,
     compute_recording_responses,
     compute_roi_delta_f_over_f,
     default_baseline_epoch_number,
+    default_kernel_stimulus_column,
     default_recording_baseline_epoch_number,
     extract_background_corrected_roi_traces,
-    frame_windows_from_photodiode_alignment,
+    finite_mean_and_sem,
+    fit_recording_stimulus_kernels,
+    fit_stimulus_kernel,
     group_delta_f_over_f_by_epoch,
-    interpolate_stimulus_epochs_to_frame_windows,
     is_baseline_epoch_name,
     load_analysis_outputs,
+    load_manual_fov_group_rows,
+    load_manual_roi_match_rows,
+    load_response_map_data,
     make_frame_windows,
-    map_stimulus_epochs_to_frame_windows,
+    make_manual_fov_group_rows,
+    make_manual_roi_match_rows,
+    matched_manual_roi_groups,
+    next_group_cell_id,
     no_baseline_epoch_frame_windows,
+    remove_manual_roi_match_group,
+    replace_manual_roi_match_group,
     resolve_baseline_frame_windows,
+    resolve_recording_timing,
     save_analysis_outputs,
+    save_manual_fov_group_rows,
+    save_manual_roi_match_rows,
+    save_response_map_data,
     select_baseline_frame_windows,
     split_traces_by_frame_windows,
     summarize_epoch_roi_responses,
@@ -58,7 +89,11 @@ from twopy.analysis import (
 )
 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, recording_frame_rate_hz
+from twopy.converted import (
+    load_converted_recording,
+    recording_frame_rate_hz,
+    recording_hemisphere,
+)
 from twopy.napari import (
     NapariRecordingView,
     NapariSidebarWidgets,
@@ -143,8 +178,10 @@ __all__ = [
     "AlignedPhotodiodeEvent",
     "AnalysisResponseRun",
     "AnalysisResponseComputation",
+    "add_manual_roi_match_group",
     "analyze_recording_responses",
     "add_twopy_magicgui_controls",
+    "append_manual_roi_match_rows",
     "apply_motion_artifact_mask_to_delta_f_over_f",
     "BackgroundCorrectedRoiTraces",
     "BackgroundCorrectionMethod",
@@ -153,6 +190,7 @@ __all__ = [
     "ClassifiedStimulusWindow",
     "classify_recording_photodiode_events",
     "compute_roi_delta_f_over_f",
+    "compute_recording_response_maps",
     "compute_recording_responses",
     "CorrelationFilterOptions",
     "convert_recording_to_twopy",
@@ -161,32 +199,39 @@ __all__ = [
     "DEFAULT_PIXEL_CALIBRATION_PATH",
     "DEFAULT_PIXEL_CALIBRATION_PROFILE_PATH",
     "default_baseline_epoch_number",
+    "default_kernel_stimulus_column",
     "default_recording_baseline_epoch_number",
     "detect_photodiode_events",
     "detect_recording_photodiode_events",
     "DeltaFOverFBaselineMode",
     "DeltaFOverFFitMode",
     "DeltaFOverFOptions",
+    "EpochResponseMap",
     "EpochFrameWindow",
     "extract_background_corrected_roi_traces",
     "extract_response_watershed_rois",
     "extract_rois_from_image",
     "extract_roi_traces",
     "find_recordings",
-    "frame_windows_from_photodiode_alignment",
+    "fit_recording_stimulus_kernels",
+    "fit_stimulus_kernel",
     "FrameWindow",
     "full_frame_crop",
     "group_delta_f_over_f_by_epoch",
     "GroupedRoiResponseSummary",
     "GroupedRoiResponses",
+    "Hemisphere",
     "grid_roi_set",
     "grid_roi_set_microns",
     "grid_size_pixels_from_microns",
-    "InterpolatedEpochMapping",
-    "interpolate_stimulus_epochs_to_frame_windows",
     "is_baseline_epoch_name",
+    "KernelFitMethod",
+    "KernelStimulusModality",
     "launch_napari",
     "load_analysis_outputs",
+    "load_response_map_data",
+    "load_manual_fov_group_rows",
+    "load_manual_roi_match_rows",
     "load_converted_recording",
     "load_pixel_calibrations",
     "load_pixel_calibration_profile_mappings",
@@ -194,11 +239,20 @@ __all__ = [
     "load_source_conversion_inputs",
     "LoadedAnalysisOutputs",
     "LowPassFilterOptions",
+    "ManualFovGroupRow",
+    "ManualRoiMatchGroup",
+    "ManualRoiMatchRow",
+    "ManualRoiMatchStatus",
+    "matched_manual_roi_groups",
     "make_roi_set_from_label_image",
     "make_frame_windows",
+    "make_manual_fov_group_rows",
+    "make_manual_roi_match_rows",
     "make_roi_set",
-    "map_stimulus_epochs_to_frame_windows",
+    "next_group_cell_id",
     "no_baseline_epoch_frame_windows",
+    "remove_manual_roi_match_group",
+    "replace_manual_roi_match_group",
     "map_stimulus_specific_column",
     "NapariRecordingView",
     "NapariSidebarWidgets",
@@ -218,14 +272,21 @@ __all__ = [
     "PixelCalibrationRow",
     "ResponseNormalization",
     "ResponsePolarity",
+    "ResponseMapData",
+    "ResponseMapMode",
+    "ResponseMapOptions",
     "ResponseProcessingOptions",
     "ResponseStatistic",
     "ResponseWatershedExtraction",
     "ResponseWatershedScoreImages",
+    "RecordingKernelFit",
+    "RecordingTiming",
     "recording_frame_rate_hz",
+    "recording_hemisphere",
     "resolve_pixel_size_um",
     "resolve_pixel_calibration_profile",
     "resolve_baseline_frame_windows",
+    "resolve_recording_timing",
     "response_watershed_roi_set",
     "RoiExtractionConfig",
     "RoiExtractionMethod",
@@ -238,6 +299,9 @@ __all__ = [
     "roi_label_image_from_layer",
     "roi_set_to_label_image",
     "save_analysis_outputs",
+    "save_response_map_data",
+    "save_manual_fov_group_rows",
+    "save_manual_roi_match_rows",
     "save_napari_label_rois",
     "save_roi_set",
     "select_baseline_frame_windows",
@@ -246,10 +310,13 @@ __all__ = [
     "SmoothingOptions",
     "SpatialCrop",
     "SpatialDomain",
+    "StimulusKernelOptions",
     "StimulusSpecificColumnMapping",
     "stimulus_epoch_names_by_number",
+    "finite_mean_and_sem",
     "summarize_epoch_roi_responses",
     "summarize_grouped_responses",
+    "TimingSource",
     "validate_grouped_roi_responses",
     "watershed_roi_set",
     "WindowedRoiResponse",

{twopy-0.1.8 → twopy-0.2.0}/src/twopy/analysis/__init__.py

@@ -19,9 +19,33 @@ from twopy.analysis.dff import (
     compute_roi_delta_f_over_f,
 )
 from twopy.analysis.dff_options import DeltaFOverFBaselineMode, DeltaFOverFOptions
-from twopy.analysis.epoch_mapping import (
-    InterpolatedEpochMapping,
-    interpolate_stimulus_epochs_to_frame_windows,
+from twopy.analysis.group_matching import (
+    ManualFovGroupRow,
+    ManualRoiMatchGroup,
+    ManualRoiMatchRow,
+    ManualRoiMatchStatus,
+    add_manual_roi_match_group,
+    append_manual_roi_match_rows,
+    load_manual_fov_group_rows,
+    load_manual_roi_match_rows,
+    make_manual_fov_group_rows,
+    make_manual_roi_match_rows,
+    matched_manual_roi_groups,
+    next_group_cell_id,
+    remove_manual_roi_match_group,
+    replace_manual_roi_match_group,
+    save_manual_fov_group_rows,
+    save_manual_roi_match_rows,
+)
+from twopy.analysis.kernels import (
+    Hemisphere,
+    KernelFitMethod,
+    KernelStimulusModality,
+    RecordingKernelFit,
+    StimulusKernelOptions,
+    default_kernel_stimulus_column,
+    fit_recording_stimulus_kernels,
+    fit_stimulus_kernel,
 )
 from twopy.analysis.motion import apply_motion_artifact_mask_to_delta_f_over_f
 from twopy.analysis.persistence import (
@@ -33,6 +57,15 @@ from twopy.analysis.persistence import (
     write_response_summary_trials_csv,
 )
 from twopy.analysis.response_context import default_recording_baseline_epoch_number
+from twopy.analysis.response_maps import (
+    EpochResponseMap,
+    ResponseMapData,
+    ResponseMapMode,
+    ResponseMapOptions,
+    compute_recording_response_maps,
+    load_response_map_data,
+    save_response_map_data,
+)
 from twopy.analysis.response_processing import (
     CorrelationFilterOptions,
     LowPassFilterOptions,
@@ -45,20 +78,24 @@ from twopy.analysis.responses import (
     GroupedRoiResponseSummary,
     RoiResponseSummary,
     RoiResponseTrial,
+    finite_mean_and_sem,
     group_delta_f_over_f_by_epoch,
     summarize_epoch_roi_responses,
     summarize_grouped_responses,
     validate_grouped_roi_responses,
 )
+from twopy.analysis.timing import (
+    RecordingTiming,
+    TimingSource,
+    resolve_recording_timing,
+)
 from twopy.analysis.trials import (
     EpochFrameWindow,
     FrameWindow,
     WindowedRoiResponse,
     default_baseline_epoch_number,
-    frame_windows_from_photodiode_alignment,
     is_baseline_epoch_name,
     make_frame_windows,
-    map_stimulus_epochs_to_frame_windows,
     no_baseline_epoch_frame_windows,
     resolve_baseline_frame_windows,
     select_baseline_frame_windows,
@@ -85,40 +122,71 @@ __all__ = [
     "BackgroundCorrectionMethod",
     "compute_roi_delta_f_over_f",
     "compute_recording_responses",
+    "compute_recording_response_maps",
     "CorrelationFilterOptions",
     "default_baseline_epoch_number",
     "default_recording_baseline_epoch_number",
     "DeltaFOverFBaselineMode",
     "DeltaFOverFOptions",
     "DeltaFOverFFitMode",
+    "EpochResponseMap",
     "EpochFrameWindow",
     "extract_background_corrected_roi_traces",
-    "frame_windows_from_photodiode_alignment",
+    "fit_recording_stimulus_kernels",
+    "fit_stimulus_kernel",
+    "default_kernel_stimulus_column",
+    "Hemisphere",
     "FrameWindow",
     "group_delta_f_over_f_by_epoch",
     "GroupedRoiResponseSummary",
     "GroupedRoiResponses",
-    "InterpolatedEpochMapping",
-    "interpolate_stimulus_epochs_to_frame_windows",
     "is_baseline_epoch_name",
+    "KernelFitMethod",
+    "KernelStimulusModality",
     "load_analysis_outputs",
+    "load_response_map_data",
     "LoadedAnalysisOutputs",
     "LowPassFilterOptions",
+    "ManualFovGroupRow",
+    "ManualRoiMatchGroup",
+    "ManualRoiMatchRow",
+    "ManualRoiMatchStatus",
+    "matched_manual_roi_groups",
     "make_frame_windows",
-    "map_stimulus_epochs_to_frame_windows",
+    "make_manual_fov_group_rows",
+    "make_manual_roi_match_rows",
     "no_baseline_epoch_frame_windows",
+    "next_group_cell_id",
+    "RecordingKernelFit",
+    "RecordingTiming",
     "RoiDeltaFOverF",
+    "ResponseMapData",
+    "ResponseMapMode",
+    "ResponseMapOptions",
     "ResponseProcessingOptions",
     "RoiCorrelationScores",
     "RoiResponseSummary",
     "RoiResponseTrial",
     "resolve_baseline_frame_windows",
+    "resolve_recording_timing",
+    "add_manual_roi_match_group",
+    "append_manual_roi_match_rows",
+    "load_manual_fov_group_rows",
+    "load_manual_roi_match_rows",
+    "remove_manual_roi_match_group",
+    "replace_manual_roi_match_group",
     "save_analysis_outputs",
+    "save_response_map_data",
+    "save_manual_fov_group_rows",
+    "save_manual_roi_match_rows",
     "select_baseline_frame_windows",
+    "finite_mean_and_sem",
     "split_traces_by_frame_windows",
+    "StimulusKernelOptions",
     "SmoothingOptions",
     "summarize_epoch_roi_responses",
     "summarize_grouped_responses",
+    "TimingSource",
     "validate_grouped_roi_responses",
     "WindowedRoiResponse",
     "write_response_summary_grouped_csv",