TwoPy 0.1.2__tar.gz → 0.1.4__tar.gz

twopy-0.1.4/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: twopy
+Version: 0.1.4
+Summary: Two-photon imaging analysis tool with a napari interface.
+Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
+License-Expression: MIT
+Requires-Python: <3.14,>=3.13
+Description-Content-Type: text/markdown
+Requires-Dist: h5py<4,>=3.16
+Requires-Dist: matplotlib<4,>=3.10
+Requires-Dist: napari[all]<0.8,>=0.7
+Requires-Dist: numpy<3,>=2.3
+Requires-Dist: pre-commit<5,>=4.6
+Requires-Dist: qtpy<3,>=2.4
+Requires-Dist: pyyaml<7,>=6.0.3
+Requires-Dist: ruff>=0.15
+Requires-Dist: scipy<2,>=1.17
+Requires-Dist: tifffile<2027,>=2026.3
+Requires-Dist: ty<0.1,>=0.0.34
+
+# twopy
+
+Two-photon imaging analysis tool for the Clark Lab output format.
+
+![twopy napari interface](https://raw.githubusercontent.com/gumadeiras/twopy/main/docs/assets/twopy-napari.png)
+
+## Getting Started
+
+twopy lets you open two-photon recordings, draw ROIs, plot responses in real time, process and analyze them, and save them.
+
+When you first load a recording, twopy converts it to a standardized HDF5 format. The converted format includes the aligned movie, mean image, stimulus tables, photodiode signals, and  recording metadata. Analysis and the GUI both work from the converted files, so the original source files remain separate from twopy's outputs.
+
+## Install
+
+Examples use micromamba, but any conda-compatible environment manager should work.
+
+
+```sh
+micromamba create -n twopy -c conda-forge python=3.13 pip -y
+micromamba run -n twopy python -m pip install twopy
+```
+
+Verify the install:
+
+```sh
+micromamba run -n twopy python -c 'import twopy; print(twopy.__name__)'
+```
+
+For a source checkout, copy `config.example.yml` to `config.yml` and edit the paths for your computer. `config.yml` stays local and is not tracked by git.
+
+## Start
+
+```sh
+micromamba activate twopy
+twopy
+```
+
+Open a source recording or converted recording directly:
+
+```sh
+twopy /path/to/source/recording
+twopy /path/to/recording_data.h5
+```
+
+Basic GUI flow:
+
+1. Choose a recording.
+2. Draw or edit ROIs in the `rois` Labels layer.
+3. Click Save ROIs.
+4. Update response plots from the current ROIs.
+5. Save analysis outputs.
+
+When a source recording has not been converted yet, twopy converts it first. Converted data includes the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata.
+
+## Docs
+
+- [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.
+- [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.
+
+## Check
+
+```sh
+micromamba run -n twopy pre-commit run --all-files
+```

twopy-0.1.4/README.md

@@ -0,0 +1,67 @@
+# twopy
+
+Two-photon imaging analysis tool for the Clark Lab output format.
+
+![twopy napari interface](https://raw.githubusercontent.com/gumadeiras/twopy/main/docs/assets/twopy-napari.png)
+
+## Getting Started
+
+twopy lets you open two-photon recordings, draw ROIs, plot responses in real time, process and analyze them, and save them.
+
+When you first load a recording, twopy converts it to a standardized HDF5 format. The converted format includes the aligned movie, mean image, stimulus tables, photodiode signals, and  recording metadata. Analysis and the GUI both work from the converted files, so the original source files remain separate from twopy's outputs.
+
+## Install
+
+Examples use micromamba, but any conda-compatible environment manager should work.
+
+
+```sh
+micromamba create -n twopy -c conda-forge python=3.13 pip -y
+micromamba run -n twopy python -m pip install twopy
+```
+
+Verify the install:
+
+```sh
+micromamba run -n twopy python -c 'import twopy; print(twopy.__name__)'
+```
+
+For a source checkout, copy `config.example.yml` to `config.yml` and edit the paths for your computer. `config.yml` stays local and is not tracked by git.
+
+## Start
+
+```sh
+micromamba activate twopy
+twopy
+```
+
+Open a source recording or converted recording directly:
+
+```sh
+twopy /path/to/source/recording
+twopy /path/to/recording_data.h5
+```
+
+Basic GUI flow:
+
+1. Choose a recording.
+2. Draw or edit ROIs in the `rois` Labels layer.
+3. Click Save ROIs.
+4. Update response plots from the current ROIs.
+5. Save analysis outputs.
+
+When a source recording has not been converted yet, twopy converts it first. Converted data includes the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata.
+
+## Docs
+
+- [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.
+- [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.
+
+## Check
+
+```sh
+micromamba run -n twopy pre-commit run --all-files
+```

{twopy-0.1.2 → twopy-0.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.1.2"
+version = "0.1.4"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"

{twopy-0.1.2 → twopy-0.1.4}/src/twopy/__init__.py

@@ -15,6 +15,7 @@ from twopy.analysis import (
     BackgroundCorrectionMethod,
     CorrelationFilterOptions,
     DeltaFOverFFitMode,
+    DeltaFOverFOptions,
     EpochFrameWindow,
     FrameWindow,
     GroupedRoiResponses,
@@ -33,25 +34,28 @@ from twopy.analysis import (
     apply_motion_artifact_mask_to_delta_f_over_f,
     compute_recording_responses,
     compute_roi_delta_f_over_f,
+    default_baseline_epoch_number,
     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,
+    is_baseline_epoch_name,
     load_analysis_outputs,
     make_frame_windows,
     map_stimulus_epochs_to_frame_windows,
+    resolve_baseline_frame_windows,
     save_analysis_outputs,
-    select_epoch_frame_windows,
+    select_baseline_frame_windows,
     split_traces_by_frame_windows,
     summarize_epoch_roi_responses,
     summarize_grouped_responses,
+    validate_grouped_roi_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.converted import load_converted_recording, recording_frame_rate_hz
 from twopy.napari import (
     NapariControlDocks,
     NapariRecordingView,
@@ -83,6 +87,7 @@ from twopy.spatial import SpatialCrop, SpatialDomain, full_frame_crop
 from twopy.stimulus import (
     StimulusSpecificColumnMapping,
     map_stimulus_specific_column,
+    stimulus_epoch_names_by_number,
 )
 from twopy.synchronization import (
     AlignedPhotodiodeEvent,
@@ -114,9 +119,11 @@ __all__ = [
     "convert_recording_to_twopy",
     "DEFAULT_RESPONSE_POST_WINDOW_SECONDS",
     "DEFAULT_RESPONSE_PRE_WINDOW_SECONDS",
+    "default_baseline_epoch_number",
     "detect_photodiode_events",
     "detect_recording_photodiode_events",
     "DeltaFOverFFitMode",
+    "DeltaFOverFOptions",
     "EpochFrameWindow",
     "extract_background_corrected_roi_traces",
     "extract_roi_traces",
@@ -129,7 +136,7 @@ __all__ = [
     "GroupedRoiResponses",
     "InterpolatedEpochMapping",
     "interpolate_stimulus_epochs_to_frame_windows",
-    "is_gray_epoch_name",
+    "is_baseline_epoch_name",
     "launch_napari",
     "load_analysis_outputs",
     "load_converted_recording",
@@ -152,6 +159,8 @@ __all__ = [
     "PhotodiodeEventType",
     "PhotodiodeEventSet",
     "ResponseProcessingOptions",
+    "recording_frame_rate_hz",
+    "resolve_baseline_frame_windows",
     "RoiDeltaFOverF",
     "RoiCorrelationScores",
     "RoiResponseSummary",
@@ -163,14 +172,16 @@ __all__ = [
     "save_analysis_outputs",
     "save_napari_label_rois",
     "save_roi_set",
-    "select_epoch_frame_windows",
+    "select_baseline_frame_windows",
     "split_traces_by_frame_windows",
     "SmoothingOptions",
     "SpatialCrop",
     "SpatialDomain",
     "StimulusSpecificColumnMapping",
+    "stimulus_epoch_names_by_number",
     "summarize_epoch_roi_responses",
     "summarize_grouped_responses",
+    "validate_grouped_roi_responses",
     "WindowedRoiResponse",
     "write_response_summary_grouped_csv",
     "write_response_summary_trials_csv",

{twopy-0.1.2 → twopy-0.1.4}/src/twopy/analysis/__init__.py

@@ -18,6 +18,7 @@ from twopy.analysis.dff import (
     RoiDeltaFOverF,
     compute_roi_delta_f_over_f,
 )
+from twopy.analysis.dff_options import DeltaFOverFOptions
 from twopy.analysis.epoch_mapping import (
     InterpolatedEpochMapping,
     interpolate_stimulus_epochs_to_frame_windows,
@@ -44,18 +45,21 @@ from twopy.analysis.responses import (
     RoiResponseSummary,
     RoiResponseTrial,
     group_delta_f_over_f_by_epoch,
-    is_gray_epoch_name,
     summarize_epoch_roi_responses,
     summarize_grouped_responses,
+    validate_grouped_roi_responses,
 )
 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,
-    select_epoch_frame_windows,
+    resolve_baseline_frame_windows,
+    select_baseline_frame_windows,
     split_traces_by_frame_windows,
 )
 from twopy.analysis.workflow import (
@@ -80,6 +84,8 @@ __all__ = [
     "compute_roi_delta_f_over_f",
     "compute_recording_responses",
     "CorrelationFilterOptions",
+    "default_baseline_epoch_number",
+    "DeltaFOverFOptions",
     "DeltaFOverFFitMode",
     "EpochFrameWindow",
     "extract_background_corrected_roi_traces",
@@ -90,7 +96,7 @@ __all__ = [
     "GroupedRoiResponses",
     "InterpolatedEpochMapping",
     "interpolate_stimulus_epochs_to_frame_windows",
-    "is_gray_epoch_name",
+    "is_baseline_epoch_name",
     "load_analysis_outputs",
     "LoadedAnalysisOutputs",
     "LowPassFilterOptions",
@@ -101,12 +107,14 @@ __all__ = [
     "RoiCorrelationScores",
     "RoiResponseSummary",
     "RoiResponseTrial",
+    "resolve_baseline_frame_windows",
     "save_analysis_outputs",
-    "select_epoch_frame_windows",
+    "select_baseline_frame_windows",
     "split_traces_by_frame_windows",
     "SmoothingOptions",
     "summarize_epoch_roi_responses",
     "summarize_grouped_responses",
+    "validate_grouped_roi_responses",
     "WindowedRoiResponse",
     "write_response_summary_grouped_csv",
     "write_response_summary_trials_csv",