phenotypic.sdk_.napari_ package#

Napari-based interactive tools for PhenoTypic.

Developer utilities for visual point picking and coordinate selection using napari viewers. These are dev-time tools, not user-facing GUI components.

class phenotypic.sdk_.napari_.LabelEditorWidget[source]#

Bases: object

Open a napari viewer to edit an image’s object labels and save them back.

The viewer shows rgb (when present), gray, and detect_mat as image layers plus one editable labels layer seeded from the called accessor (objmap or objmask). A dock panel provides “Save to Image” and “Discard & Close” buttons. run blocks until the viewer is closed.

run(image, accessor_name: str, *, viewer: napari.Viewer | None = None) → np.ndarray | None[source]#

Open the editor and block until closed.

Parameters:

  • image – A PhenoTypic Image whose layers are displayed and whose objmap/objmask is edited.

  • accessor_name (str) – "objmap" or "objmask" — selects which accessor the editable layer is seeded from and saved back to.

  • viewer (napari.Viewer | None) – Optional existing napari viewer to reuse. When None a new napari.Viewer(title="Label Editor") is created.

Returns:

The array written back to the image on save, or None if the user discarded or closed the viewer without saving.

Raises:

ImportError – If napari is not installed.

Return type:

np.ndarray | None

class phenotypic.sdk_.napari_.PointPickerWidget(max_points: int | None = None)[source]#

Bases: object

Interactive point picker that opens a napari viewer for coordinate selection.

Parameters:

max_points (int | None) – Maximum number of points allowed. None means unlimited.

run(image) → numpy.ndarray[source]#

Open a napari viewer for interactive point selection and block until closed.

Parameters:

image – A PhenoTypic Image instance whose layers will be displayed.

Returns:

An (N, 2) array of confirmed (y, x) coordinates. Returns an empty (0, 2) array if the viewer is closed without confirming.

Raises:

ImportError – If napari is not installed.

Return type:

numpy.ndarray

phenotypic.sdk_.napari_.add_image_layer(viewer, array, *, name: str, visible: bool = True, gamma: float = 1.0)[source]#

Add (or replace) an image layer with non-stretched contrast limits.

Mirrors the contrast convention of the detect-mode preview tool (DetectMat.preview_modes): integer layers use the full dtype range and single-channel normalized float intensities use a fixed (0.0, 1.0) range. This renders each layer at its true brightness instead of letting napari auto-stretch the display to the data’s own (min, max) — which exaggerates contrast and makes layers look washed out when several are shown together. Three-dimensional arrays are treated as RGB.

Parameters:

  • viewer – A napari Viewer (or any object exposing layers and add_image).

  • array – The image array — 2-D intensity or 3-D RGB.

  • name (str) – Layer name. An existing layer with this name is updated in place rather than duplicated.

  • visible (bool) – Initial layer visibility. Defaults to True.

  • gamma (float) – Display gamma. Defaults to 1.0 (no gamma adjustment).

Returns:

The created or updated napari image layer.