TwoPy 0.2.0__tar.gz → 0.3.0__tar.gz

{twopy-0.2.0 → twopy-0.3.0}/PKG-INFO

@@ -1,9 +1,11 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.2.0
+Version: 0.3.0
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT
+Project-URL: Homepage, https://twopy.gumadeiras.com
+Project-URL: Repository, https://github.com/gumadeiras/twopy
 Requires-Python: <3.14,>=3.13
 Description-Content-Type: text/markdown
 Requires-Dist: h5py<4,>=3.16
@@ -73,9 +75,11 @@ When a source recording has not been converted yet, twopy converts it first. Con
 
 ## 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.
-- [Custom workflow guide](docs/custom_workflows.md): add versioned local analyses to the napari Custom tab.
+- [Full documentation](https://twopy.gumadeiras.com)
+- [Getting started](docs/getting_started.md): install, configure, launch, and save your first analysis.
+- [GUI guide](docs/gui/index.md): one page per task — loading, ROIs, plots, custom workflows, group matching, saving.
+- [Python API guide](docs/python_api.md): find recordings, convert data, extract traces, fit kernels, and open napari from scripts.
+- [Writing custom workflows](docs/writing_custom_workflows.md): add your own analysis 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-0.2.0 → twopy-0.3.0}/README.md

@@ -53,9 +53,11 @@ When a source recording has not been converted yet, twopy converts it first. Con
 
 ## 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.
-- [Custom workflow guide](docs/custom_workflows.md): add versioned local analyses to the napari Custom tab.
+- [Full documentation](https://twopy.gumadeiras.com)
+- [Getting started](docs/getting_started.md): install, configure, launch, and save your first analysis.
+- [GUI guide](docs/gui/index.md): one page per task — loading, ROIs, plots, custom workflows, group matching, saving.
+- [Python API guide](docs/python_api.md): find recordings, convert data, extract traces, fit kernels, and open napari from scripts.
+- [Writing custom workflows](docs/writing_custom_workflows.md): add your own analysis 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-0.2.0 → twopy-0.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.2.0"
+version = "0.3.0"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"
@@ -29,6 +29,10 @@ dependencies = [
 [project.scripts]
 twopy = "twopy.napari:main"
 
+[project.urls]
+Homepage = "https://twopy.gumadeiras.com"
+Repository = "https://github.com/gumadeiras/twopy"
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
@@ -43,11 +47,15 @@ target-version = "py313"
 [tool.ruff.lint]
 select = [
   "ANN",
+  "ARG",
   "B",
+  "C4",
   "D",
   "E",
   "F",
   "I",
+  "NPY",
+  "PTH",
   "SIM",
   "UP",
   "W",

{twopy-0.2.0 → twopy-0.3.0}/src/twopy/analysis/background_subtraction.py

@@ -15,6 +15,7 @@ from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
+from scipy import sparse
 
 from twopy.converted import RecordingData
 from twopy.frame_ranges import normalize_frame_range
@@ -278,6 +279,7 @@ def _extract_mean_traces_from_indices(
     rather than total recording length.
     """
     traces = np.empty((frame_stop - frame_start, len(pixel_indices_by_trace)))
+    projection = _mean_projection(pixel_indices_by_trace)
     _check_cancelled(check_cancelled)
     for chunk_start, chunk_stop, frames in recording.movie.iter_frame_batches(
         chunk_frames=chunk_frames,
@@ -289,10 +291,7 @@ def _extract_mean_traces_from_indices(
         chunk_offset = chunk_start - frame_start
         chunk_slice = slice(chunk_offset, chunk_offset + (chunk_stop - chunk_start))
         chunk_flat = frames.reshape(frames.shape[0], -1)
-        for trace_index, pixel_indices in enumerate(pixel_indices_by_trace):
-            traces[chunk_slice, trace_index] = chunk_flat[:, pixel_indices].mean(
-                axis=1,
-            )
+        traces[chunk_slice, :] = _project_trace_pixels(chunk_flat, projection)
         _check_cancelled(check_cancelled)
 
     return traces
@@ -344,6 +343,7 @@ def _extract_movie_global_percentile_corrected_traces(
     )
     frame_count = frame_stop - frame_start
     roi_count = len(roi_pixel_indices)
+    projection = _mean_projection(roi_pixel_indices)
     raw_values = np.empty((frame_count, roi_count), dtype=np.float64)
     background_values = np.empty((frame_count, roi_count), dtype=np.float64)
     corrected_values = np.empty((frame_count, roi_count), dtype=np.float64)
@@ -359,14 +359,19 @@ def _extract_movie_global_percentile_corrected_traces(
         chunk_slice = slice(chunk_offset, chunk_offset + (chunk_stop - chunk_start))
         chunk_flat = frames.reshape(frames.shape[0], -1)
         background_trace = chunk_flat[:, background_indices].mean(axis=1)
-        for roi_index, pixel_indices in enumerate(roi_pixel_indices):
-            roi_pixels = chunk_flat[:, pixel_indices]
-            raw_values[chunk_slice, roi_index] = roi_pixels.mean(axis=1)
-            background_values[chunk_slice, roi_index] = background_trace
-            # Clamp pixels before averaging so dim pixels cannot pull the
-            # corrected ROI trace below zero.
-            corrected_pixels = np.maximum(roi_pixels - background_trace[:, None], 0.0)
-            corrected_values[chunk_slice, roi_index] = corrected_pixels.mean(axis=1)
+        roi_pixels = chunk_flat[:, projection.pixel_indices]
+        raw_values[chunk_slice, :] = _project_selected_pixels(roi_pixels, projection)
+        background_values[chunk_slice, :] = background_trace[:, np.newaxis]
+        # Clamp pixels before averaging so dim pixels cannot pull the
+        # corrected ROI trace below zero.
+        corrected_pixels = np.maximum(
+            roi_pixels - background_trace[:, np.newaxis],
+            0.0,
+        )
+        corrected_values[chunk_slice, :] = _project_selected_pixels(
+            corrected_pixels,
+            projection,
+        )
         _check_cancelled(check_cancelled)
 
     metadata: dict[str, BackgroundMetadataValue] = {
@@ -440,6 +445,7 @@ def _extract_movie_y_stripe_percentile_corrected_traces(
     )
     frame_count = frame_stop - frame_start
     roi_count = len(roi_pixel_indices)
+    projection = _mean_projection(roi_pixel_indices)
     raw_values = np.empty((frame_count, roi_count), dtype=np.float64)
     background_values = np.empty((frame_count, roi_count), dtype=np.float64)
     corrected_values = np.empty((frame_count, roi_count), dtype=np.float64)
@@ -460,15 +466,21 @@ def _extract_movie_y_stripe_percentile_corrected_traces(
         )
         chunk_flat = frames.reshape(frames.shape[0], -1)
         background_flat = background_field.reshape(background_field.shape[0], -1)
-        for roi_index, pixel_indices in enumerate(roi_pixel_indices):
-            roi_pixels = chunk_flat[:, pixel_indices]
-            roi_background_pixels = background_flat[:, pixel_indices]
-            raw_values[chunk_slice, roi_index] = roi_pixels.mean(axis=1)
-            background_values[chunk_slice, roi_index] = roi_background_pixels.mean(
-                axis=1,
-            )
-            corrected_pixels = np.maximum(roi_pixels - roi_background_pixels, 0.0)
-            corrected_values[chunk_slice, roi_index] = corrected_pixels.mean(axis=1)
+        roi_pixels = chunk_flat[:, projection.pixel_indices]
+        roi_background_pixels = background_flat[:, projection.pixel_indices]
+        raw_values[chunk_slice, :] = _project_selected_pixels(roi_pixels, projection)
+        background_values[chunk_slice, :] = _project_selected_pixels(
+            roi_background_pixels,
+            projection,
+        )
+        corrected_pixels = np.maximum(
+            roi_pixels - roi_background_pixels,
+            0.0,
+        )
+        corrected_values[chunk_slice, :] = _project_selected_pixels(
+            corrected_pixels,
+            projection,
+        )
         _check_cancelled(check_cancelled)
 
     metadata: dict[str, BackgroundMetadataValue] = {
@@ -593,6 +605,93 @@ def _roi_pixel_indices_from_masks(
     return tuple(np.flatnonzero(mask).astype(np.int64) for mask in flat_masks)
 
 
+@dataclass(frozen=True)
+class _MeanProjection:
+    """Sparse averaging matrix plus selected flattened pixel indices."""
+
+    pixel_indices: npt.NDArray[np.int64]
+    matrix: sparse.csc_matrix
+
+
+def _mean_projection(
+    pixel_indices_by_trace: tuple[npt.NDArray[np.int64], ...],
+) -> _MeanProjection:
+    """Return selected pixels and a sparse pixel-to-trace averaging matrix.
+
+    Args:
+        pixel_indices_by_trace: One flattened pixel-index array per trace.
+
+    Returns:
+        Selected flattened pixel indices plus a sparse matrix shaped
+        ``(selected_pixels, traces)`` whose columns average each trace.
+
+    Pixel indices are concatenated per trace instead of deduplicated. That
+    preserves the existing behavior for overlapping ROIs, where the same movie
+    pixel can contribute independently to more than one ROI mean.
+    """
+    selected_pixel_indices: list[npt.NDArray[np.int64]] = []
+    rows: list[npt.NDArray[np.int64]] = []
+    columns: list[npt.NDArray[np.int64]] = []
+    values: list[npt.NDArray[np.float64]] = []
+    row_start = 0
+    for trace_index, pixel_indices in enumerate(pixel_indices_by_trace):
+        if pixel_indices.size == 0:
+            continue
+        selected_pixel_indices.append(pixel_indices)
+        rows.append(
+            np.arange(
+                row_start,
+                row_start + pixel_indices.size,
+                dtype=np.int64,
+            ),
+        )
+        row_start += pixel_indices.size
+        columns.append(
+            np.full(pixel_indices.shape, trace_index, dtype=np.int64),
+        )
+        values.append(
+            np.full(
+                pixel_indices.shape,
+                1.0 / float(pixel_indices.size),
+                dtype=np.float64,
+            ),
+        )
+    if len(selected_pixel_indices) == 0:
+        return _MeanProjection(
+            pixel_indices=np.array([], dtype=np.int64),
+            matrix=sparse.csc_matrix((0, len(pixel_indices_by_trace))),
+        )
+    return _MeanProjection(
+        pixel_indices=np.concatenate(selected_pixel_indices),
+        matrix=sparse.csc_matrix(
+            (
+                np.concatenate(values),
+                (np.concatenate(rows), np.concatenate(columns)),
+            ),
+            shape=(row_start, len(pixel_indices_by_trace)),
+        ),
+    )
+
+
+def _project_trace_pixels(
+    chunk_flat: npt.NDArray[np.float64],
+    projection: _MeanProjection,
+) -> npt.NDArray[np.float64]:
+    """Return trace means from a flattened movie chunk and projection."""
+    return _project_selected_pixels(chunk_flat[:, projection.pixel_indices], projection)
+
+
+def _project_selected_pixels(
+    selected_pixels: npt.NDArray[np.float64],
+    projection: _MeanProjection,
+) -> npt.NDArray[np.float64]:
+    """Return trace means from selected pixel columns."""
+    return np.asarray(
+        selected_pixels @ projection.matrix,
+        dtype=np.float64,
+    )
+
+
 def _check_cancelled(check_cancelled: Callable[[], None] | None) -> None:
     """Raise ``CancelledError`` when an interactive caller superseded this work."""
     if check_cancelled is None:

{twopy-0.2.0 → twopy-0.3.0}/src/twopy/analysis/dff.py

@@ -115,6 +115,10 @@ def compute_roi_delta_f_over_f(
         data_rate_hz=data_rate_hz,
         baseline_sample_seconds=baseline_sample_seconds,
     )
+    _validate_baseline_samples_for_background_method(
+        traces=traces,
+        baseline_samples=baseline_samples,
+    )
     tau = _fit_shared_tau(
         frame_numbers=baseline_samples.frame_numbers,
         mean_fluorescence=baseline_samples.values.mean(axis=1),
@@ -274,6 +278,35 @@ def _baseline_samples(
     )
 
 
+def _validate_baseline_samples_for_background_method(
+    *,
+    traces: BackgroundCorrectedRoiTraces,
+    baseline_samples: _BaselineSamples,
+) -> None:
+    """Reject background-corrected baselines that cannot support dF/F."""
+    if traces.method != "roi_y_stripe_percentile":
+        return
+
+    invalid = ~np.isfinite(baseline_samples.values) | (baseline_samples.values <= 0.0)
+    if not np.any(invalid):
+        return
+
+    roi_indices = np.flatnonzero(np.any(invalid, axis=0))
+    labels = ", ".join(traces.labels[index] for index in roi_indices[:5])
+    if roi_indices.size > 5:
+        labels = f"{labels}, ..."
+    minimum = float(np.nanmin(baseline_samples.values[:, roi_indices]))
+    msg = (
+        "ROI y-stripe P% background subtraction over-subtracted baseline "
+        f"fluorescence for {labels}; minimum corrected baseline sample is "
+        f"{minimum:.6g}. dF/F needs positive baseline fluorescence, so the "
+        "local y-stripe pixels are not a valid additive background for those "
+        "ROIs. Use shared y-stripe P%, global percentile, or revise the ROIs "
+        "to leave dim local background pixels."
+    )
+    raise ValueError(msg)
+
+
 def _validate_baseline_local_range(
     *,
     window: FrameWindow,

{twopy-0.2.0 → twopy-0.3.0}/src/twopy/analysis/kernels/__init__.py

@@ -80,8 +80,8 @@ class StimulusKernelOptions:
     baseline_epoch_number: int = 1
     discard_first_stimulus_epoch: bool = True
     selected_epoch_numbers: tuple[int, ...] | None = None
-    num_stim_past: int = 150
-    num_stim_future: int = 25
+    num_stim_past: int = 100
+    num_stim_future: int = 10
     method: KernelFitMethod = "ols"
     hemisphere: Hemisphere | None = None
 

{twopy-0.2.0 → twopy-0.3.0}/src/twopy/analysis/persistence.py

@@ -48,6 +48,10 @@ from twopy.hdf5_utils import (
     write_string_dataset as _write_string_dataset,
 )
 from twopy.roi import RoiSet, TraceStatistic, make_roi_set
+from twopy.spatial_orientation import (
+    require_twopy_spatial_orientation,
+    write_twopy_spatial_orientation,
+)
 from twopy.typing_guards import (
     require_bool_array,
     require_float64_array,
@@ -238,7 +242,9 @@ def load_analysis_outputs(path: Path) -> LoadedAnalysisOutputs:
         return LoadedAnalysisOutputs(
             path=input_path,
             roi_set=(
-                _read_roi_set(h5_file["roi_set"]) if "roi_set" in h5_file else None
+                _read_roi_set(h5_file["roi_set"], path=input_path)
+                if "roi_set" in h5_file
+                else None
             ),
             traces=(
                 _read_background_traces(h5_file["traces"])
@@ -347,19 +353,28 @@ def _write_roi_set(group: h5py.Group, roi_set: RoiSet) -> None:
     Returns:
         None.
     """
-    group.create_dataset("masks", data=roi_set.masks, compression="gzip")
+    write_twopy_spatial_orientation(group)
+    masks = group.create_dataset("masks", data=roi_set.masks, compression="gzip")
+    write_twopy_spatial_orientation(masks)
     _write_string_dataset(group, "labels", roi_set.labels)
 
 
-def _read_roi_set(group: h5py.Group) -> RoiSet:
+def _read_roi_set(group: h5py.Group, *, path: Path) -> RoiSet:
     """Read a persisted ROI set.
 
     Args:
         group: HDF5 ``roi_set`` group.
+        path: Analysis output path used in validation errors.
 
     Returns:
         ``RoiSet`` with validated masks and labels.
     """
+    require_twopy_spatial_orientation(group, path=path, label="roi_set")
+    require_twopy_spatial_orientation(
+        group["masks"],
+        path=path,
+        label="roi_set/masks",
+    )
     return make_roi_set(
         require_bool_array(group["masks"][()], name="roi_set/masks", ndim=3),
         labels=_read_string_dataset(group, "labels"),
@@ -869,7 +884,7 @@ def _trial_response_row(
         "stop_frame": trial.stop_frame,
         "frame_count": trial.stop_frame - trial.start_frame,
     }
-    row.update({column: "" for column in time_columns})
+    row.update(dict.fromkeys(time_columns, ""))
     for time_seconds, value in zip(
         trial.time_seconds,
         trial.values[:, roi_index],

{twopy-0.2.0 → twopy-0.3.0}/src/twopy/analysis/response_maps.py

@@ -43,6 +43,10 @@ from twopy.analysis.timing import resolve_recording_timing
 from twopy.analysis.trials import EpochFrameWindow, is_baseline_epoch_name
 from twopy.converted import RecordingData, recording_frame_rate_hz
 from twopy.spatial import SpatialCrop
+from twopy.spatial_orientation import (
+    require_twopy_spatial_orientation,
+    write_twopy_spatial_orientation,
+)
 
 __all__ = [
     "EpochResponseMap",
@@ -247,29 +251,33 @@ def save_response_map_data(path: Path, map_data: ResponseMapData) -> None:
     recording-level movie products. Values are stored as normalized signed maps
     with the original dF/F scale in ``response_scale`` for audit.
     """
+    _require_response_map_shapes(map_data)
     output_path = path.expanduser()
     output_path.parent.mkdir(parents=True, exist_ok=True)
     with h5py.File(output_path, "w") as h5_file:
         h5_file.attrs["twopy_format"] = RESPONSE_MAP_FILE_FORMAT
         h5_file.attrs["response_scale"] = map_data.response_scale
+        write_twopy_spatial_orientation(h5_file)
         _write_response_map_options(h5_file.create_group("options"), map_data.options)
         _write_spatial_crop(h5_file.create_group("spatial_crop"), map_data.spatial_crop)
-        h5_file.create_dataset(
+        mean_image = h5_file.create_dataset(
             "mean_image",
             data=map_data.mean_image,
             compression="gzip",
         )
+        write_twopy_spatial_orientation(mean_image)
         epochs_group = h5_file.create_group("epochs")
         for index, epoch in enumerate(map_data.epochs):
             epoch_group = epochs_group.create_group(f"{index:04d}")
             epoch_group.attrs["epoch_name"] = epoch.epoch_name
             epoch_group.attrs["epoch_number"] = epoch.epoch_number
             epoch_group.attrs["trial_count"] = epoch.trial_count
-            epoch_group.create_dataset(
+            response_values = epoch_group.create_dataset(
                 "response_values",
                 data=epoch.response_values,
                 compression="gzip",
             )
+            write_twopy_spatial_orientation(response_values)
 
 
 def load_response_map_data(path: Path) -> ResponseMapData:
@@ -287,21 +295,34 @@ def load_response_map_data(path: Path) -> ResponseMapData:
     input_path = path.expanduser()
     with h5py.File(input_path, "r") as h5_file:
         _require_response_map_format(h5_file, input_path)
+        require_twopy_spatial_orientation(
+            h5_file,
+            path=input_path,
+            label="response heatmap file",
+        )
         options = _read_response_map_options(h5_file["options"])
         spatial_crop = _read_spatial_crop(h5_file["spatial_crop"])
-        mean_image = np.asarray(h5_file["mean_image"], dtype=np.float64)
+        mean_image_dataset = h5_file["mean_image"]
+        require_twopy_spatial_orientation(
+            mean_image_dataset,
+            path=input_path,
+            label="mean_image",
+        )
+        mean_image = np.asarray(mean_image_dataset, dtype=np.float64)
         epochs_group = h5_file["epochs"]
         epochs = tuple(
-            _read_epoch_response_map(epochs_group[name])
+            _read_epoch_response_map(epochs_group[name], path=input_path)
             for name in sorted(epochs_group.keys())
         )
-        return ResponseMapData(
+        map_data = ResponseMapData(
             mean_image=mean_image,
             epochs=epochs,
             options=options,
             spatial_crop=spatial_crop,
             response_scale=float(h5_file.attrs["response_scale"]),
         )
+        _require_response_map_shapes(map_data)
+        return map_data
 
 
 def _write_response_map_options(
@@ -357,16 +378,45 @@ def _read_spatial_crop(group: h5py.Group) -> SpatialCrop:
     )
 
 
-def _read_epoch_response_map(group: h5py.Group) -> EpochResponseMap:
+def _read_epoch_response_map(group: h5py.Group, *, path: Path) -> EpochResponseMap:
     """Read one persisted epoch response map."""
+    response_values = group["response_values"]
+    require_twopy_spatial_orientation(
+        response_values,
+        path=path,
+        label=f"{group.name}/response_values",
+    )
     return EpochResponseMap(
         epoch_name=_string_attr(group, "epoch_name"),
         epoch_number=int(group.attrs["epoch_number"]),
-        response_values=np.asarray(group["response_values"], dtype=np.float64),
+        response_values=np.asarray(response_values, dtype=np.float64),
         trial_count=int(group.attrs["trial_count"]),
     )
 
 
+def _require_response_map_shapes(map_data: ResponseMapData) -> None:
+    """Require heatmap spatial arrays to match their recorded crop."""
+    if map_data.mean_image.ndim != 2:
+        msg = (
+            f"response heatmap mean_image must be 2-D; got {map_data.mean_image.shape}"
+        )
+        raise ValueError(msg)
+    if map_data.mean_image.shape != map_data.spatial_crop.shape:
+        msg = (
+            "response heatmap mean_image shape must match spatial_crop shape; "
+            f"got {map_data.mean_image.shape} and {map_data.spatial_crop.shape}"
+        )
+        raise ValueError(msg)
+    for epoch in map_data.epochs:
+        if epoch.response_values.shape != map_data.mean_image.shape:
+            msg = (
+                "response heatmap response_values shape must match mean_image "
+                f"shape; got {epoch.response_values.shape} for "
+                f"{epoch.epoch_name!r} and {map_data.mean_image.shape}"
+            )
+            raise ValueError(msg)
+
+
 def _require_response_map_format(h5_file: h5py.File, path: Path) -> None:
     """Raise when an HDF5 file is not a twopy response heatmap file."""
     actual = _string_attr(h5_file, "twopy_format")