Module curlew.utils.napari_viewer

2D and 3D visualisation using Napari, with an add-layer API similar in spirit to curlew.utils.datascreen.DataScreen (real-world coordinates).

Requires napari (and a Qt backend) to be installed separately.

The affine helpers image_affine_from_grid and image_affine_napari_row_column_image_2d are implemented here. :func:image_affine_from_grid etc. (now implemented directly here.)

Classes

class NapariViewer (title: str = 'curlew', *, ndisplay: int = None, viewer=None, **viewer_kwds)

Expand source code

class NapariViewer:
    """
    Open a Napari viewer (2D or 3D) and add meshes, point clouds, images / volumes, and shapes.

    **Coordinate conventions (Curlew → Napari)**

    Napari uses dimension order **(z, y, x)** in layer data: slice/depth first, then row,
    then column. Curlew 2D points are **(x, y)** (first model axis, second). They are mapped
    to ``(0, y, x)``. Curlew 3D positions **(x, y, z)** map to ``(z, y, x)``. The padded
    slice coordinate is **always the first component**, not the last.

    **2D images:** Curlew rasters from :meth:`~curlew.geometry.Grid.reshape` are indexed
    ``(i₀, i₁)`` like **(x-axis, y-axis)**. Napari ``Image`` arrays are **row-major**
    ``(row, col)`` with ``row = i₁``, ``col = i₀``; pass ``volume.T`` and use
    :func:`~curlew.utils.grid_napari_affine.image_affine_napari_row_column_image_2d` — this
    is applied automatically when you call :meth:`addVolume` with a 2D ``grid``.

    Parameters
    ----------
    title : str, optional
        Viewer window title.
    ndisplay : int, optional
        ``2`` or ``3`` (default). Use ``2`` for planar models and ``matplotlib``-style sections.
    **viewer_kwds
        Extra keyword arguments passed to `napari.Viewer()`.
    """

    def __init__(
        self,
        title: str = "curlew",
        *,
        ndisplay: int = None,
        viewer=None,
        **viewer_kwds,
    ):
        if ndisplay is None:
            ndisplay = curlew.default_dim
        if ndisplay not in (2, 3):
            raise ValueError("ndisplay must be 2 or 3")

        # Configure Napari's 3D axis orientation preferences (when supported) so that
        # Curlew's convention matches the viewer defaults:
        # - depth axis: towards
        # - vertical axis: up
        # - horizontal axis: right
        try: # can differ between versions....
            from napari.settings import get_settings
            _settings = get_settings()
            _app = getattr(_settings, "application", None)
            if _app is not None:
                # Newer napari versions may expose a single tuple-valued field.
                if hasattr(_app, "camera_orientation"):
                    _app.camera_orientation = ("towards", "up", "right")
                # Fallbacks for split fields (name variants differ across releases).
                if hasattr(_app, "depth_axis_orientation"):
                    _app.depth_axis_orientation = "towards"
                if hasattr(_app, "vertical_axis_orientation"):
                    _app.vertical_axis_orientation = "up"
                if hasattr(_app, "horizontal_axis_orientation"):
                    _app.horizontal_axis_orientation = "right"
        except Exception:
            pass

        self.viewer = viewer if viewer is not None else napari.Viewer(title=title, **viewer_kwds)
        self._ndisplay = int(ndisplay)
        self.viewer.dims.ndisplay = self._ndisplay

        # Ensure the active viewer matches the requested orientation, independent of
        # whether global settings took effect.
        try:  # can differ between versions...
            if hasattr(self.viewer, "camera") and hasattr(self.viewer.camera, "orientation"):
                self.viewer.camera.orientation = ("towards", "up", "right")
        except Exception:
            pass

        # Match Curlew's axis convention in the Napari GUI.
        # Napari's displayed axes are controlled by `viewer.axes`, while `dims.axis_labels`
        # controls the text shown next to the sliders.
        if hasattr(self.viewer, "axes"):
            self.viewer.axes.visible = True
        if hasattr(self.viewer, "scale_bar"):
            self.viewer.scale_bar.visible = True
        self._layers: dict[str, napari.layers.Layer] = {}
        self.viewer.dims.axis_labels = ("z", "y", "x") if self._ndisplay == 3 else ("y", "x")
        self._cnt = 0

    def _remove_layer_if_present(self, name: str) -> None:
        # hack; but put this here as axis labels are not properly set in the constructor for some reason. 
        self.viewer.dims.axis_labels = ("z", "y", "x") if self._ndisplay == 3 else ("y", "x")
        
        # now check if the layer exists and remove if need be. 
        if name in self._layers:
            try:
                self.viewer.layers.remove(self._layers[name])
            except ValueError:
                pass
            del self._layers[name]

    def _to_napari_xyz(self, arr) -> np.ndarray:
        """
        Curlew positions or directions ``(x, y)`` / ``(x, y, z)`` → napari **(z, y, x)**.
        """
        a = np.asarray(arr, dtype=np.float64)
        if a.size == 0:
            return a.reshape(0, 3)
        if a.ndim == 1:
            a = a.reshape(1, -1)
        if a.shape[1] == 2:
            # Pad to (z, y, x) with z=0 for 2D inputs.
            # n.b. napari defaults to y-axis-down, we want y-axis-up.
            return np.column_stack([np.zeros(a.shape[0]), a[:, 1], a[:, 0]])
        if a.shape[1] == 3:
            return np.column_stack([a[:, 2], a[:, 1], a[:, 0]])
        raise ValueError(
            f"Expected 2 or 3 columns (Curlew x,y or x,y,z); got shape {a.shape}"
        )

    def addMesh(
        self,
        name: str,
        verts: np.ndarray,
        faces: np.ndarray,
        normals: np.ndarray | None = None,
        rgb: str | np.ndarray = "green",
        shading: str = "smooth",
        *,
        curlew_coords: bool = True,
        **kwargs,
    ):
        """
        Add a triangular surface mesh.

        Parameters
        ----------
        name : str
            Layer name (replaces an existing layer with the same name).
        verts : array, shape (N, 3)
        faces : array, shape (M, 3)
            Triangle vertex indices.
        normals : array, optional
            Per-vertex normals (N, 3). Not passed to napari when incompatible with the
            installed napari version; use ``vertex_colors`` / shading only.
        rgb : str or array, optional
            Matplotlib colour name if `str`. If array, per-vertex colours with shape (N, 3) RGB
            or (N, 4) RGBA in [0, 1].
        shading : str, optional
            Passed to `viewer.add_surface` (e.g. ``'smooth'``, ``'flat'``).
        curlew_coords : bool, optional
            If True (default), treat ``verts`` / ``normals`` as Curlew **(x, y, z)** and map to
            napari **(z, y, x)**. If False, vertices are already in napari order.
        **kwargs
            Additional arguments for `viewer.viewer.add_surface`.
        """
        verts = np.asarray(verts, dtype=np.float64)
        faces = np.asarray(faces)
        if verts.ndim != 2 or verts.shape[1] != 3:
            raise ValueError("verts must have shape (N, 3)")
        if curlew_coords:
            verts = np.column_stack([verts[:, 2], verts[:, 1], verts[:, 0]])

        if normals is not None:
            normals = np.asarray(normals, dtype=np.float64)
            if normals.ndim != 2 or normals.shape[1] != 3:
                raise ValueError("normals must have shape (N, 3)")
            if normals.shape[0] != verts.shape[0]:
                raise ValueError(
                    "normals shape mismatch: expected per-vertex normals with the same "
                    f"length as verts (got normals.shape[0]={normals.shape[0]} vs verts.shape[0]={verts.shape[0]})"
                )
            if curlew_coords:
                normals = np.column_stack(
                    [normals[:, 2], normals[:, 1], normals[:, 0]]
                )

        if isinstance(rgb, str):
            from matplotlib.colors import to_rgba

            rgba = np.asarray(to_rgba(rgb), dtype=np.float64)
            vertex_colors = np.tile(rgba, (len(verts), 1))
        else:
            vc = np.asarray(rgb, dtype=np.float64)
            if vc.shape[0] != len(verts):
                raise ValueError("rgb array must have one row per vertex")
            if vc.shape[1] == 3:
                vertex_colors = np.c_[vc, np.ones(len(verts))]
            elif vc.shape[1] == 4:
                vertex_colors = vc
            else:
                raise ValueError("rgb must be (N, 3) or (N, 4)")

        self._remove_layer_if_present(name)
        
        kwargs = dict(kwargs)
        kwargs.pop("normals", None)
        layer = self.viewer.add_surface(
            (verts, faces),
            name=name,
            vertex_colors=vertex_colors,
            shading=shading,
            **kwargs,
        )
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addPoints(
        self,
        name: str,
        xyz: np.ndarray,
        rgb: str | np.ndarray | None = None,
        scalar: np.ndarray | None = None,
        colormap=None,
        size: float = 10.0,
        border_color: str | None = None,
        symbol: str = "o",
        *,
        curlew_coords: bool = True,
        **kwargs,
    ):
        """
        Add a point cloud.

        By default ``xyz`` uses Curlew **(x, y)** or **(x, y, z)** — same as :class:`~curlew.core.Geode`
        ``x`` / constraint positions. Set ``curlew_coords=False`` only if you already permuted to
        napari **(z, y, x)**.
        """
        xyz = np.asarray(xyz, dtype=np.float64)
        if xyz.ndim != 2 or xyz.shape[1] not in (2, 3):
            raise ValueError("xyz must have shape (N, 2) or (N, 3)")
        if curlew_coords:
            xyz = self._to_napari_xyz(xyz)
        elif xyz.shape[1] != 3:
            raise ValueError("xyz must have shape (N, 3) when curlew_coords=False")

        if scalar is not None and rgb is not None:
            raise ValueError("Pass either scalar= or rgb=, not both.")

        self._remove_layer_if_present(name)

        n = xyz.shape[0]

        layer_opts: dict = {
            "out_of_slice_display": True,
            "symbol": symbol,
        }
        if border_color is None:
            if "border_width" not in kwargs:
                layer_opts["border_width"] = 0
        else:
            layer_opts["border_color"] = border_color
            if "border_width" not in kwargs:
                layer_opts["border_width"] = 0.05

        if scalar is not None:
            v = np.asarray(scalar)
            if v.ndim != 1 or v.shape[0] != n:
                raise ValueError("scalar must be a 1D array of length N")
            feat_key = "_curlew_scalar_points"
            cmap = resolve_cmap(colormap)
            layer = self.viewer.add_points(
                xyz,
                name=name,
                features={feat_key: v},
                face_color=feat_key,
                face_colormap=cmap,
                size=size,
                **layer_opts,
                **kwargs,
            )
        elif rgb is None:
            layer = self.viewer.add_points(
                xyz,
                name=name,
                face_color="red",
                size=size,
                **layer_opts,
                **kwargs,
            )
        elif isinstance(rgb, str):
            layer = self.viewer.add_points(
                xyz,
                name=name,
                face_color=rgb,
                size=size,
                **layer_opts,
                **kwargs,
            )
        else:
            v = np.asarray(rgb)
            if v.ndim == 2 and v.shape[0] == n and v.shape[1] in (3, 4):
                layer = self.viewer.add_points(
                    xyz,
                    name=name,
                    face_color=v,
                    size=size,
                    **layer_opts,
                    **kwargs,
                )
            else:
                raise ValueError(
                    "rgb must be str or an array of shape (N,3)/(N,4) for per-point colours"
                )

        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addVolume(
        self,
        name: str,
        volume: np.ndarray,
        *,
        grid=None,
        scale=None,
        translate=None,
        affine=None,
        rendering: str = "iso",
        colormap=None,
        blending: str = "opaque",
        interpolation2d: str = "nearest",
        interpolation3d: str = "nearest",
        **kwargs,
    ):
        """
        Add a 2D image or 3D volume (scalar field on a regular grid).

        When ``grid`` is **2D**, ``volume`` must have shape ``grid.shape`` (Curlew
        ``(i₀, i₁)``). It is passed to napari as ``flipud(transpose(volume))`` so the
        vertical axis matches :func:`curlew.visualise.plot2D` (matplotlib
        ``imshow(..., origin='lower')``). Napari's default row order would otherwise flip
        the section upside down relative to drillholes and constraints. When ``grid`` is
        **3D**, ``volume`` must match ``grid.shape`` (Curlew ``(x, y, z)``); it is
        internally transposed to Napari axes ``(z, y, x)`` when an affine is inferred.

        For 2D map views, set ``ndisplay=2`` on the viewer.
        """
        volume = np.asarray(volume)
        if volume.ndim not in (2, 3):
            raise ValueError("volume must be a 2D or 3D array")

        if grid is not None and (scale is not None or translate is not None):
            raise ValueError(
                "addVolume: use grid=... for affine, or scale=/translate=, not both."
            )
        if grid is not None and grid.ndim != volume.ndim:
            raise ValueError(
                f"grid.ndim ({grid.ndim}) must match volume.ndim ({volume.ndim})"
            )

        colormap = resolve_cmap(colormap)

        affine_use = affine
        if affine_use is None and grid is not None:
            if grid.ndim == 2:
                volume = np.flipud(np.transpose(volume))
                affine_use = image_affine_napari_row_column_image_2d(grid)
            else:
                # Curlew grids are sampled in (x, y, z) order, while Napari image
                # axes (and the viewer coordinate convention we use for points/surfaces)
                # are (z, y, x). Transpose the volume data accordingly, and permute the
                # affine so voxel indices (z, y, x) map to world coordinates (z, y, x).
                volume = np.transpose(volume, (2, 1, 0))
                A_cur = image_affine_from_grid(grid)  # maps (x,y,z indices) -> (x,y,z world)
                # Swap axes 0 and 2 (x <-> z) in both input indices and output world coords.
                P = np.array(
                    [
                        [0.0, 0.0, 1.0, 0.0],
                        [0.0, 1.0, 0.0, 0.0],
                        [1.0, 0.0, 0.0, 0.0],
                        [0.0, 0.0, 0.0, 1.0],
                    ],
                    dtype=np.float64,
                )
                affine_use = P @ A_cur @ P

        legacy_interp = kwargs.pop("interpolation", None)
        if legacy_interp is not None:
            import warnings

            warnings.warn(
                "napari add_image does not accept `interpolation=`; use "
                "`interpolation2d=` and `interpolation3d=` on addVolume instead. "
                f"Applying {legacy_interp!r} to both.",
                UserWarning,
                stacklevel=2,
            )
            interpolation2d = interpolation3d = legacy_interp

        opts: dict = {
            "name": name,
            "rendering": rendering,
            "colormap": colormap,
            "blending": blending,
            "interpolation2d": interpolation2d,
            "interpolation3d": interpolation3d,
        }
        if scale is not None:
            opts["scale"] = scale
        if translate is not None:
            opts["translate"] = translate
        if affine_use is not None:
            opts["affine"] = affine_use
        opts.update(kwargs)

        self._remove_layer_if_present(name)
        layer = self.viewer.add_image(volume, **opts)
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addVectors(
        self,
        name: str,
        origins: np.ndarray,
        directions: np.ndarray,
        *,
        rgb: str | np.ndarray | None = None,
        length: float = 1.0,
        width: float = 1,
        colormap=None,
        curlew_coords: bool = True,
        **kwargs,
    ):
        """
        Add a vector field as napari ``Vectors`` (2D and 3D viewers).

        By default ``origins`` and ``directions`` use Curlew **(x, y)** / **(x, y, z)**. Pass
        ``curlew_coords=False`` if they are already in napari **(z, y, x)**.
        """
        origins = np.asarray(origins, dtype=np.float64)
        directions = np.asarray(directions, dtype=np.float64)
        if origins.ndim != 2 or origins.shape[1] not in (2, 3):
            raise ValueError("origins must have shape (N, 2) or (N, 3)")
        if directions.shape != origins.shape:
            raise ValueError("directions must have the same shape as origins")
        if curlew_coords:
            origins = self._to_napari_xyz(origins)
            directions = self._to_napari_xyz(directions)
        elif origins.shape[1] != 3:
            raise ValueError("origins must have shape (N, 3) when curlew_coords=False")
        n = origins.shape[0]
        data = np.stack([origins, directions], axis=1)

        opts: dict = {
            "name": name,
            "length": length,
            "edge_width": width,
            "vector_style": kwargs.get("vector_style", "arrow"),
            "out_of_slice_display": kwargs.get("out_of_slice_display", True),
        }
        if isinstance(rgb, str):
            opts["edge_color"] = rgb
        elif rgb is not None:
            v = np.asarray(rgb)
            if v.ndim != 1 or v.shape[0] != n:
                raise ValueError(
                    "rgb must be str or a 1D array of length N (scalar per vector)"
                )
            feat_key = "_curlew_scalar"
            opts["features"] = {feat_key: v}
            opts["edge_color"] = feat_key
            opts["edge_colormap"] = resolve_cmap(colormap)
        else:
            opts["edge_color"] = "red"

        opts.update(kwargs)

        self._remove_layer_if_present(name)
        layer = self.viewer.add_vectors(data, **opts)
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addPaths(
        self,
        name: str,
        paths: list[np.ndarray],
        *,
        edge_color: str | np.ndarray = "white",
        edge_width: float = 2.0,
        curlew_coords: bool = True,
        **kwargs,
    ):
        """
        Add open polylines as a ``Shapes`` layer. Vertex rows use Curlew **(x, y)** / **(x, y, z)**
        by default (same as contour / model world coordinates). Use ``curlew_coords=False`` for
        napari **(z, y, x)**.
        """
        if not paths:
            return None
        if curlew_coords:
            paths = [self._to_napari_xyz(p) for p in paths]
        shape_type = ["path"] * len(paths)
        self._remove_layer_if_present(name)
        layer = self.viewer.add_shapes(
            paths,
            shape_type=shape_type,
            name=name,
            edge_width=edge_width,
            edge_color=edge_color,
            face_color=_get_colors(len(paths)),
            **kwargs,
        )
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addDrillHole(
        self,
        name: str,
        hole,
        *,
        vmn: float = 0.0,
        vmx: float = 20.0,
        cmap: str | MplColormap | None = None,
        linewidth: float = 4.0,
        **kwargs,
    ):
        """
        Draw a drillhole trace as napari ``Shapes`` **line** segments (cf. ``plotDrill2D``).

        Works with ``ndisplay=2`` or ``3``. Uses transparent faces so GUI **edge width**
        controls line thickness.

        ``hole`` may be a :class:`~curlew.core.Geode` (or any object with ``.numpy()``);
        positions **(x, y)** or **(x, y, z)** are mapped to napari **(z, y, x)**.

        Each segment ``x[i]``→``x[i+1]`` is coloured by ``lithoID[i]``.

        Parameters
        ----------
        cmap
            Matplotlib **name**, :class:`matplotlib.colors.Colormap`, or ``None`` (uses
            :attr:`curlew.ccramp` if set, else ``tab20b``) for the segment colours.
        """
        from matplotlib.colors import Normalize
        from matplotlib import colormaps as mpl_colormaps
        from matplotlib.colors import Colormap as MplColormap

        if hasattr(hole, "numpy") and callable(hole.numpy):
            hole = hole.numpy()
        x = np.asarray(hole.x, dtype=np.float64)
        lid = np.asarray(hole.lithoID).ravel()
        if x.shape[0] < 2:
            return None
        if x.shape[1] not in (2, 3):
            raise ValueError("hole.x must have shape (N, 2) or (N, 3)")
        x = self._to_napari_xyz(x)

        # Use a matplotlib colormap to compute per-segment RGBA.
        if cmap is None:
            mpl_c = curlew.ccramp if curlew.ccramp is not None else mpl_colormaps["tab20b"]
        elif isinstance(cmap, str):
            mpl_c = mpl_colormaps[cmap]
        elif isinstance(cmap, MplColormap):
            mpl_c = cmap
        else:
            raise TypeError("cmap must be None, str, or matplotlib.colors.Colormap")
        norm = Normalize(vmin=vmn, vmax=vmx)

        lines: list[np.ndarray] = []
        colors: list[np.ndarray] = []
        for i in range(len(x) - 1):
            seg = np.asarray([x[i], x[i + 1]], dtype=np.float64)
            lines.append(seg)
            rgba = np.asarray(mpl_c(norm(float(lid[i]))), dtype=np.float64)
            colors.append(rgba)

        edge_rgba = np.stack(colors, axis=0).astype(np.float32)
        return self.addLines(
            name,
            lines,
            edge_color=edge_rgba,
            edge_width=linewidth,
            curlew_coords=False,
            **kwargs,
        )

    def addLines(
        self,
        name: str,
        segments: list[np.ndarray],
        *,
        edge_color: str | np.ndarray = "white",
        edge_width: float = 2.0,
        curlew_coords: bool = True,
        **kwargs,
    ):
        """
        Add 2-point **line** segments (``shape_type='line'``) with transparent faces so the
        GUI **edge width** controls line thickness. Vertex rows use Curlew coordinates by default.
        """
        if not segments:
            return None
        if curlew_coords:
            segments = [self._to_napari_xyz(s) for s in segments]
        shape_type = ["line"] * len(segments)
        self._remove_layer_if_present(name)
        layer = self.viewer.add_shapes(
            segments,
            shape_type=shape_type,
            name=name,
            edge_width=edge_width,
            edge_color=edge_color,
            face_color=_get_colors(len(segments)),
            **kwargs,
        )
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def addGeode(
        self,
        geode: Geode,
        *,
        lithoID: bool = True,
        scalar: bool = True,
        surfaces: bool = True,
        displacement: bool = True,
        offset_length: float = 1.0,
        offset_width: float = 20.0,
    ) -> dict[str, napari.layers.Layer]:
        """
        Visualise a :class:`curlew.core.Geode` (model prediction) in the viewer.

        For a 2D :class:`~curlew.geometry.Grid`, scalar fields are 2D images; isosurfaces are
        drawn as contour polylines (``Shapes``). For 3D grids, behaviour matches the previous
        ``Napari3D`` implementation (volumes + triangle meshes).
        """
        from curlew.core import Geode as GeodeType

        if not isinstance(geode, GeodeType):
            raise TypeError("geode must be a curlew.core.Geode instance")

        geode = geode.numpy()
        cmap = resolve_cmap()
        layers: dict[str, napari.layers.Layer] = {}
        grid = geode.grid

        def add_scalar_field(
            suffix: str,
            data,
            *,
            opacity=0.8,
            visible: bool,
        ) -> None:
            if data is None:
                return
            nm = f"{suffix}"
            flat = _geode_ravel_values(data)
            if grid is not None:
                vol = np.asarray(grid.reshape(flat), dtype=np.float64)
                if vol.ndim not in (2, 3):
                    raise ValueError(
                        f"{suffix}: grid.reshape produced shape {vol.shape}; expected 2D or 3D"
                    )
                layers[nm] = self.addVolume(
                    nm,
                    vol,
                    grid=grid,
                    colormap=cmap,
                    blending="additive" if suffix == "lithoID" else "opaque",
                    rendering="additive" if suffix == "lithoID" else "iso",
                    visible=visible,
                    opacity=opacity,
                )
            else:
                if geode.x is None:
                    raise ValueError(
                        f"Cannot add {suffix}: geode has no grid and no x coordinates"
                    )
                gx = np.asarray(geode.x, dtype=np.float64)
                if flat.shape[0] != gx.shape[0]:
                    raise ValueError(
                        f"{suffix}: length {flat.shape[0]} does not match x rows {gx.shape[0]}"
                    )
                layers[nm] = self.addPoints(
                    nm,
                    gx,
                    scalar=flat.astype(np.float64),
                    colormap=cmap,
                    visible=visible,
                    opacity=opacity,
                )

        if lithoID and geode.lithoID is not None:
            add_scalar_field("lithoID", geode.lithoID, visible=True, opacity=0.35)

        if scalar and geode.scalar is not None:
            add_scalar_field("scalar", geode.scalar, visible=False)

        if scalar and geode.fields:
            for key, arr in geode.fields.items():
                add_scalar_field(f"field_{key}", arr, visible=False)

        if surfaces and geode.isosurfaces and geode.grid is not None:
            if geode.grid.ndim == 2:
                path_specs: list[tuple[str, np.ndarray]] = []
                path_idx = 0
                for field in geode.fields:
                    for surf_name in geode.isosurfaces[field]:
                        polylines = geode.getSurface(field, surf_name, normals=False)
                        if not isinstance(polylines, list):
                            continue
                        for poly in polylines:
                            if poly is None or len(poly) < 2:
                                continue
                            n = f"{field}_{surf_name}_c{path_idx}"
                            path_idx += 1
                            path_specs.append((n, poly))
                n_paths = max(1, len(path_specs))
                for i, (n, poly) in enumerate(path_specs):
                    col = np.asarray(curlew.ccramp(i / n_paths), dtype=np.float32)
                    edge_rgba = np.tile(col, (1, 1))
                    layers[n] = self.addPaths(
                        n,
                        [poly],
                        edge_color=edge_rgba,
                        edge_width=2.0,
                    )
            else:
                names = []
                for field in geode.fields:
                    for surf_name in geode.isosurfaces[field]:
                        n = f"{field}_{surf_name}"
                        verts, faces, normals = geode.getSurface(
                            field, surf_name, normals=True
                        )
                        layers[n] = self.addMesh(
                            n,
                            verts,
                            faces,
                            normals=normals,
                            rgb="white",
                            shading="smooth",
                        )
                        names.append(n)

                for i, n in enumerate(names):
                    verts = layers[n].data[0]
                    col = curlew.ccramp(i / len(names))
                    vertex_colors = np.tile(col, (len(verts), 1))
                    layers[n].vertex_colors = vertex_colors

        if displacement and geode.offsets:
            if geode.x is None:
                raise ValueError("geode.offsets requires geode.x for vector origins")
            x0 = np.asarray(geode.x, dtype=np.float64)
            for key, disp in geode.offsets.items():
                nm = f"offset_{key}"
                d = np.asarray(disp, dtype=np.float64)
                if d.shape != x0.shape:
                    raise ValueError(
                        f"offsets[{key!r}] shape {d.shape} does not match x shape {x0.shape}"
                    )
                if x0.shape[0] == 0:
                    continue
                mag = np.linalg.norm(d, axis=1)
                layers[nm] = self.addVectors(
                    nm,
                    x0,
                    d,
                    rgb=mag,
                    length=offset_length,
                    width=offset_width,
                    vector_style="arrow",
                    visible=False,
                )

        return layers

    def addCSet(
        self,
        name: str,
        C: CSet,
        *,
        lithoID: bool = True,
        scalar: bool = True,
        displacement: bool = True,
        H=None,
        grad_length: float = 50.0,
        grad_width: float = 20.0,
        orient_length: float = 50.0,
        orient_width: float = 10.0,
        bedding_length: float = 0.0,
        bedding_width: float = 4.0,
        bedding_edge_color: str = "black",
        value_size: float = 30.0,
        value_border_color: str | None = "black",
        iq_size: float = 10.0,
    ) -> dict[str, napari.layers.Layer]:
        """
        Visualise a :class:`curlew.core.CSet` in the viewer.

        Optional ``H`` (e.g. :class:`~curlew.core.HSet`) gates layers like
        :func:`curlew.visualise.plotConstraints2D`. When ``bedding_length > 0`` and gradient
        constraints are shown, adds perpendicular "bedding" tick lines (2D-style).
        """
        from curlew.core import CSet as CSetType

        if not isinstance(C, CSetType):
            raise TypeError("C must be a curlew.core.CSet instance")

        C = C.numpy()
        _ = (lithoID, displacement)

        layers: dict[str, napari.layers.Layer] = {}
        cmap_pts = resolve_cmap()

        if C.gp is not None and C.gv is not None:
            gp = np.asarray(C.gp, dtype=np.float64)
            gv = np.asarray(C.gv, dtype=np.float64)
            if gp.shape[0] > 0:
                nm = f"{name}_gradient"
                layers[nm] = self.addVectors(
                    nm,
                    gp,
                    gv,
                    rgb="red",
                    length=grad_length,
                    width=grad_width,
                    vector_style="arrow",
                )
                if bedding_length > 0 and self._ndisplay == 2:
                    gv_n = self._to_napari_xyz(C.gv)
                    gvn = np.linalg.norm(gv_n, axis=1, keepdims=True)
                    gu = gv_n / (gvn + 1e-8)
                    # In napari (z,y,x), gradient in the display plane uses axes 1 and 2.
                    perp = np.column_stack(
                        [np.zeros(len(gu)), -gu[:, 2], gu[:, 1]]
                    )
                    gp_n = self._to_napari_xyz(C.gp)
                    nm_b = f"{name}_gradient_bedding"
                    layers[nm_b] = self.addVectors(
                        nm_b,
                        gp_n,
                        perp,
                        rgb=bedding_edge_color,
                        length=bedding_length,
                        width=bedding_width,
                        vector_style="line",
                        curlew_coords=False,
                    )

        if C.gop is not None and C.gov is not None:
            gop = np.asarray(C.gop, dtype=np.float64)
            gov = np.asarray(C.gov, dtype=np.float64)
            if gop.shape[0] > 0:
                nm = f"{name}_orientation"
                layers[nm] = self.addVectors(
                    nm,
                    gop,
                    gov,
                    rgb="green",
                    length=orient_length,
                    width=orient_width,
                    vector_style="line",
                )

        if scalar and C.vp is not None and C.vv is not None and C.pp is None:
            vp = np.asarray(C.vp, dtype=np.float64)
            vv = np.asarray(C.vv, dtype=np.float64)
            if vp.shape[0] > 0:
                scalars = vv.squeeze()
                if scalars.shape[0] != vp.shape[0]:
                    raise ValueError(
                        "vp and vv must have the same number of rows for value constraints"
                    )
                nm = f"{name}_value"
                pt_kw: dict = {}
                if value_border_color is not None:
                    pt_kw["border_color"] = value_border_color
                    pt_kw["border_width"] = 0.05
                layers[nm] = self.addPoints(
                    nm,
                    vp,
                    scalar=scalars,
                    colormap=cmap_pts,
                    size=value_size,
                    symbol="clobber",
                    **pt_kw,
                )

        if C.pp is not None and C.pv is not None:
            pp = np.asarray(C.pp, dtype=np.float64)
            pv = np.asarray(C.pv, dtype=np.float64)
            if pp.shape[0] > 0:
                nm = f"{name}_property"
                if pv.shape[-1] == 1:
                    layers[nm] = self.addPoints(
                        nm,
                        pp,
                        scalar=pv[:, 0],
                        colormap=cmap_pts,
                        size=value_size * 0.5,
                    )
                elif pv.shape[-1] >= 3:
                    rgb = pv[:, [0, 1, 2]].astype(float)
                    rgb -= np.min(rgb, axis=0)[None, :]
                    denom = np.max(rgb, axis=0)[None, :] - np.min(rgb, axis=0)[None, :]
                    denom = np.where(denom < 1e-12, 1.0, denom)
                    rgb = rgb / denom
                    rgba = np.c_[rgb, np.ones(len(rgb))]
                    layers[nm] = self.addPoints(
                        nm,
                        pp,
                        rgb=rgba.astype(np.float64),
                        size=value_size * 0.5,
                    )

        if C.iq is not None:
            iq_list = C.iq[1]
            from matplotlib import colormaps as mpl_colormaps

            cmap_lhs = mpl_colormaps["Reds"]
            cmap_rhs = mpl_colormaps["Blues"]
            cmap_eq = mpl_colormaps["viridis"]

            eq_pts_parts: list[np.ndarray] = []
            eq_rgba_parts: list[np.ndarray] = []
            eq_sym_parts: list[str] = []
            n_iq = max(1, len(iq_list))
            for i, entry in enumerate(iq_list):
                P1, P2, rel = entry
                rel_s = (rel if isinstance(rel, str) else str(rel)).strip()
                p1 = np.asarray(P1, dtype=np.float64)
                p2 = np.asarray(P2, dtype=np.float64)

                t = 0.0 if n_iq <= 1 else (i / (n_iq - 1))
                col_lhs = np.asarray(cmap_lhs(t), dtype=np.float32)
                col_rhs = np.asarray(cmap_rhs(t), dtype=np.float32)
                col_eq = np.asarray(cmap_eq(t), dtype=np.float32)

                if rel_s == "=":
                    if p1.shape[0] > 0:
                        p1n = self._to_napari_xyz(p1)
                        eq_pts_parts.append(p1n)
                        eq_rgba_parts.append(np.tile(col_eq, (p1n.shape[0], 1)))
                        eq_sym_parts.extend(["diamond"] * p1n.shape[0])
                    continue

                # inequality: choose symbols by relationship and side
                # '>' : LHS cross, RHS hbar; '<' : LHS hbar, RHS cross
                if rel_s == ">":
                    lhs_sym, rhs_sym = ("cross", "hbar")
                elif rel_s == "<":
                    lhs_sym, rhs_sym = ("hbar", "cross")
                else:
                    raise ValueError(
                        f"Unsupported inequality relation {rel_s!r}; expected '=', '<', or '>'"
                    )

                pts_parts: list[np.ndarray] = []
                sym_parts: list[str] = []
                rgba_parts: list[np.ndarray] = []
                n_pts = 0

                if p1.shape[0] > 0:
                    p1n = self._to_napari_xyz(p1)
                    pts_parts.append(p1n)
                    sym_parts.extend([lhs_sym] * p1n.shape[0])
                    rgba_parts.append(np.tile(col_lhs, (p1n.shape[0], 1)))
                    n_pts += p1n.shape[0]

                if p2.shape[0] > 0:
                    p2n = self._to_napari_xyz(p2)
                    pts_parts.append(p2n)
                    sym_parts.extend([rhs_sym] * p2n.shape[0])
                    rgba_parts.append(np.tile(col_rhs, (p2n.shape[0], 1)))
                    n_pts += p2n.shape[0]

                if pts_parts:
                    nm = f"{name}_iq{i}"
                    self._remove_layer_if_present(nm)
                    xyz = np.concatenate(pts_parts, axis=0)
                    rgba = np.concatenate(rgba_parts, axis=0)
                    layer = self.viewer.add_points(
                        xyz,
                        name=nm,
                        face_color=rgba,
                        symbol=np.asarray(sym_parts, dtype=object),
                        size=iq_size,
                        out_of_slice_display=True,
                    )
                    layer.visible = False # hidden by default.
                    self._layers[nm] = layer
                    self._cnt += 1
                    layers[nm] = layer

            if eq_pts_parts:
                nm_eq = f"{name}_eq"
                self._remove_layer_if_present(nm_eq)
                eq_xyz = np.concatenate(eq_pts_parts, axis=0)
                eq_rgba = np.concatenate(eq_rgba_parts, axis=0)
                eq_layer = self.viewer.add_points(
                    eq_xyz,
                    name=nm_eq,
                    face_color=eq_rgba,
                    symbol=np.asarray(eq_sym_parts, dtype=object),
                    size=iq_size,
                    out_of_slice_display=True,
                )
                eq_layer.visible = False # hidden by default.
                self._layers[nm_eq] = eq_layer
                self._cnt += 1
                layers[nm_eq] = eq_layer

        return layers
    
    def addTracks(
        self,
        name: str,
        tracks,
        *,
        features: dict | None = None,
        colormap=None,
        tail_width: float = 2.0,
        tail_length: int = 30,
        head_length: int = 0,
        **kwargs,
    ):
        """
        Add 3D particle trajectories as a napari ``Tracks`` layer.

        Parameters
        ----------
        name : str
            Layer name (replaces an existing layer with the same name).
        tracks : array-like
            One of three formats:

            - **Napari format** ``(N, 5)`` — columns are ``[track_id, t, x0, x1, x2]``
                (passed through directly).
            - **Stacked trajectories** ``(N_tracks, T, 3)`` — ``N_tracks`` particle paths,
                each sampled at ``T`` equally-spaced time steps, coordinates ``(x, y, z)``.
                Track IDs are assigned as ``0 … N_tracks-1`` and time as ``0 … T-1``.
            - **List of arrays** — each element is ``(T_i, 3)`` for variable-length paths.
                Track IDs and per-track time indices are assigned automatically.

        features : dict, optional
            Per-point scalar attributes (length ``N``), passed to napari as ``features``.
            Example: ``{'speed': speed_array}``. Can be used for colour-by-feature.
        colormap : optional
            Napari colormap (or name) for ``color_by`` features. Defaults to Curlew
            ``ccramp`` when available.
        tail_width : float, optional
            Track tail line width.
        tail_length : int, optional
            Number of previous time-steps to render as a tail.
        head_length : int, optional
            Number of future time-steps to render ahead of the current frame.
        **kwargs
            Additional arguments passed to ``viewer.add_tracks`` (e.g. ``color_by``,
            ``blending``, ``opacity``).

        Returns
        -------
        napari.layers.Tracks
        """
        _require_napari()

        tracks_arr = np.asarray(tracks, dtype=np.float64) if not isinstance(tracks, list) else None

        if tracks_arr is not None and tracks_arr.ndim == 2 and tracks_arr.shape[1] == 5:
            # Already in napari format [track_id, t, x0, x1, x2]
            data = tracks_arr
        elif tracks_arr is not None and tracks_arr.ndim == 3 and tracks_arr.shape[2] == 3:
            # (N_tracks, T, 3) → (N_tracks*T, 5)
            n_tracks, T, _ = tracks_arr.shape
            ids = np.repeat(np.arange(n_tracks, dtype=np.float64), T)
            times = np.tile(np.arange(T, dtype=np.float64), n_tracks)
            coords = tracks_arr.reshape(-1, 3)
            data = np.column_stack([ids, times, coords])
        elif isinstance(tracks, list) or (tracks_arr is not None and tracks_arr.ndim == 1):
            # List of variable-length (T_i, 3) arrays
            rows = []
            for track_id, traj in enumerate(tracks):
                t = np.asarray(traj, dtype=np.float64)
                if t.ndim != 2 or t.shape[1] != 3:
                    raise ValueError(
                        f"Track {track_id}: expected shape (T, 3), got {t.shape}"
                    )
                ids = np.full(len(t), track_id, dtype=np.float64)
                times = np.arange(len(t), dtype=np.float64)
                rows.append(np.column_stack([ids, times, t]))
            data = np.vstack(rows)
        else:
            raise ValueError(
                "tracks must be (N, 5) napari format, (N_tracks, T, 3), or a list of (T_i, 3) arrays"
            )

        opts: dict = {
            "name": name,
            "tail_width": tail_width,
            "tail_length": tail_length,
            "head_length": head_length,
        }
        if features is not None:
            opts["features"] = features
        if colormap is not None:
            opts["colormap"] = colormap
        elif features:
            opts["colormap"] = _curlew_napari_colormap()
        opts.update(kwargs)

        self._remove_layer_if_present(name)
        layer = self.viewer.add_tracks(data, **opts)
        self._layers[name] = layer
        self._cnt += 1
        return layer

    def show(self, *, block: bool = False):
        """
        Show the viewer window (Qt). In a script you may need ``napari.run()`` afterwards
        unless ``block=True``.
        """
        self.viewer.show(block=block)
        return self.viewer

Open a Napari viewer (2D or 3D) and add meshes, point clouds, images / volumes, and shapes.

Coordinate conventions (Curlew → Napari)

Napari uses dimension order (z, y, x) in layer data: slice/depth first, then row, then column. Curlew 2D points are (x, y) (first model axis, second). They are mapped to (0, y, x). Curlew 3D positions (x, y, z) map to (z, y, x). The padded slice coordinate is always the first component, not the last.

2D images: Curlew rasters from :meth:~curlew.geometry.Grid.reshape are indexed (i₀, i₁) like (x-axis, y-axis). Napari Image arrays are row-major (row, col) with row = i₁, col = i₀; pass volume.T and use :func:~curlew.utils.grid_napari_affine.image_affine_napari_row_column_image_2d — this is applied automatically when you call :meth:addVolume with a 2D grid.

Parameters

title : str, optional

Viewer window title.

ndisplay : int, optional

2 or 3 (default). Use 2 for planar models and matplotlib-style sections.

**viewer_kwds

Extra keyword arguments passed to napari.Viewer().

Methods

def addCSet(self,
name: str,
C: CSet,
*,
lithoID: bool = True,
scalar: bool = True,
displacement: bool = True,
H=None,
grad_length: float = 50.0,
grad_width: float = 20.0,
orient_length: float = 50.0,
orient_width: float = 10.0,
bedding_length: float = 0.0,
bedding_width: float = 4.0,
bedding_edge_color: str = 'black',
value_size: float = 30.0,
value_border_color: str | None = 'black',
iq_size: float = 10.0) ‑> dict[str, napari.layers.Layer]

Expand source code

def addCSet(
    self,
    name: str,
    C: CSet,
    *,
    lithoID: bool = True,
    scalar: bool = True,
    displacement: bool = True,
    H=None,
    grad_length: float = 50.0,
    grad_width: float = 20.0,
    orient_length: float = 50.0,
    orient_width: float = 10.0,
    bedding_length: float = 0.0,
    bedding_width: float = 4.0,
    bedding_edge_color: str = "black",
    value_size: float = 30.0,
    value_border_color: str | None = "black",
    iq_size: float = 10.0,
) -> dict[str, napari.layers.Layer]:
    """
    Visualise a :class:`curlew.core.CSet` in the viewer.

    Optional ``H`` (e.g. :class:`~curlew.core.HSet`) gates layers like
    :func:`curlew.visualise.plotConstraints2D`. When ``bedding_length > 0`` and gradient
    constraints are shown, adds perpendicular "bedding" tick lines (2D-style).
    """
    from curlew.core import CSet as CSetType

    if not isinstance(C, CSetType):
        raise TypeError("C must be a curlew.core.CSet instance")

    C = C.numpy()
    _ = (lithoID, displacement)

    layers: dict[str, napari.layers.Layer] = {}
    cmap_pts = resolve_cmap()

    if C.gp is not None and C.gv is not None:
        gp = np.asarray(C.gp, dtype=np.float64)
        gv = np.asarray(C.gv, dtype=np.float64)
        if gp.shape[0] > 0:
            nm = f"{name}_gradient"
            layers[nm] = self.addVectors(
                nm,
                gp,
                gv,
                rgb="red",
                length=grad_length,
                width=grad_width,
                vector_style="arrow",
            )
            if bedding_length > 0 and self._ndisplay == 2:
                gv_n = self._to_napari_xyz(C.gv)
                gvn = np.linalg.norm(gv_n, axis=1, keepdims=True)
                gu = gv_n / (gvn + 1e-8)
                # In napari (z,y,x), gradient in the display plane uses axes 1 and 2.
                perp = np.column_stack(
                    [np.zeros(len(gu)), -gu[:, 2], gu[:, 1]]
                )
                gp_n = self._to_napari_xyz(C.gp)
                nm_b = f"{name}_gradient_bedding"
                layers[nm_b] = self.addVectors(
                    nm_b,
                    gp_n,
                    perp,
                    rgb=bedding_edge_color,
                    length=bedding_length,
                    width=bedding_width,
                    vector_style="line",
                    curlew_coords=False,
                )

    if C.gop is not None and C.gov is not None:
        gop = np.asarray(C.gop, dtype=np.float64)
        gov = np.asarray(C.gov, dtype=np.float64)
        if gop.shape[0] > 0:
            nm = f"{name}_orientation"
            layers[nm] = self.addVectors(
                nm,
                gop,
                gov,
                rgb="green",
                length=orient_length,
                width=orient_width,
                vector_style="line",
            )

    if scalar and C.vp is not None and C.vv is not None and C.pp is None:
        vp = np.asarray(C.vp, dtype=np.float64)
        vv = np.asarray(C.vv, dtype=np.float64)
        if vp.shape[0] > 0:
            scalars = vv.squeeze()
            if scalars.shape[0] != vp.shape[0]:
                raise ValueError(
                    "vp and vv must have the same number of rows for value constraints"
                )
            nm = f"{name}_value"
            pt_kw: dict = {}
            if value_border_color is not None:
                pt_kw["border_color"] = value_border_color
                pt_kw["border_width"] = 0.05
            layers[nm] = self.addPoints(
                nm,
                vp,
                scalar=scalars,
                colormap=cmap_pts,
                size=value_size,
                symbol="clobber",
                **pt_kw,
            )

    if C.pp is not None and C.pv is not None:
        pp = np.asarray(C.pp, dtype=np.float64)
        pv = np.asarray(C.pv, dtype=np.float64)
        if pp.shape[0] > 0:
            nm = f"{name}_property"
            if pv.shape[-1] == 1:
                layers[nm] = self.addPoints(
                    nm,
                    pp,
                    scalar=pv[:, 0],
                    colormap=cmap_pts,
                    size=value_size * 0.5,
                )
            elif pv.shape[-1] >= 3:
                rgb = pv[:, [0, 1, 2]].astype(float)
                rgb -= np.min(rgb, axis=0)[None, :]
                denom = np.max(rgb, axis=0)[None, :] - np.min(rgb, axis=0)[None, :]
                denom = np.where(denom < 1e-12, 1.0, denom)
                rgb = rgb / denom
                rgba = np.c_[rgb, np.ones(len(rgb))]
                layers[nm] = self.addPoints(
                    nm,
                    pp,
                    rgb=rgba.astype(np.float64),
                    size=value_size * 0.5,
                )

    if C.iq is not None:
        iq_list = C.iq[1]
        from matplotlib import colormaps as mpl_colormaps

        cmap_lhs = mpl_colormaps["Reds"]
        cmap_rhs = mpl_colormaps["Blues"]
        cmap_eq = mpl_colormaps["viridis"]

        eq_pts_parts: list[np.ndarray] = []
        eq_rgba_parts: list[np.ndarray] = []
        eq_sym_parts: list[str] = []
        n_iq = max(1, len(iq_list))
        for i, entry in enumerate(iq_list):
            P1, P2, rel = entry
            rel_s = (rel if isinstance(rel, str) else str(rel)).strip()
            p1 = np.asarray(P1, dtype=np.float64)
            p2 = np.asarray(P2, dtype=np.float64)

            t = 0.0 if n_iq <= 1 else (i / (n_iq - 1))
            col_lhs = np.asarray(cmap_lhs(t), dtype=np.float32)
            col_rhs = np.asarray(cmap_rhs(t), dtype=np.float32)
            col_eq = np.asarray(cmap_eq(t), dtype=np.float32)

            if rel_s == "=":
                if p1.shape[0] > 0:
                    p1n = self._to_napari_xyz(p1)
                    eq_pts_parts.append(p1n)
                    eq_rgba_parts.append(np.tile(col_eq, (p1n.shape[0], 1)))
                    eq_sym_parts.extend(["diamond"] * p1n.shape[0])
                continue

            # inequality: choose symbols by relationship and side
            # '>' : LHS cross, RHS hbar; '<' : LHS hbar, RHS cross
            if rel_s == ">":
                lhs_sym, rhs_sym = ("cross", "hbar")
            elif rel_s == "<":
                lhs_sym, rhs_sym = ("hbar", "cross")
            else:
                raise ValueError(
                    f"Unsupported inequality relation {rel_s!r}; expected '=', '<', or '>'"
                )

            pts_parts: list[np.ndarray] = []
            sym_parts: list[str] = []
            rgba_parts: list[np.ndarray] = []
            n_pts = 0

            if p1.shape[0] > 0:
                p1n = self._to_napari_xyz(p1)
                pts_parts.append(p1n)
                sym_parts.extend([lhs_sym] * p1n.shape[0])
                rgba_parts.append(np.tile(col_lhs, (p1n.shape[0], 1)))
                n_pts += p1n.shape[0]

            if p2.shape[0] > 0:
                p2n = self._to_napari_xyz(p2)
                pts_parts.append(p2n)
                sym_parts.extend([rhs_sym] * p2n.shape[0])
                rgba_parts.append(np.tile(col_rhs, (p2n.shape[0], 1)))
                n_pts += p2n.shape[0]

            if pts_parts:
                nm = f"{name}_iq{i}"
                self._remove_layer_if_present(nm)
                xyz = np.concatenate(pts_parts, axis=0)
                rgba = np.concatenate(rgba_parts, axis=0)
                layer = self.viewer.add_points(
                    xyz,
                    name=nm,
                    face_color=rgba,
                    symbol=np.asarray(sym_parts, dtype=object),
                    size=iq_size,
                    out_of_slice_display=True,
                )
                layer.visible = False # hidden by default.
                self._layers[nm] = layer
                self._cnt += 1
                layers[nm] = layer

        if eq_pts_parts:
            nm_eq = f"{name}_eq"
            self._remove_layer_if_present(nm_eq)
            eq_xyz = np.concatenate(eq_pts_parts, axis=0)
            eq_rgba = np.concatenate(eq_rgba_parts, axis=0)
            eq_layer = self.viewer.add_points(
                eq_xyz,
                name=nm_eq,
                face_color=eq_rgba,
                symbol=np.asarray(eq_sym_parts, dtype=object),
                size=iq_size,
                out_of_slice_display=True,
            )
            eq_layer.visible = False # hidden by default.
            self._layers[nm_eq] = eq_layer
            self._cnt += 1
            layers[nm_eq] = eq_layer

    return layers

Visualise a :class:CSet in the viewer.

Optional H (e.g. :class:~curlew.core.HSet) gates layers like :func:plotConstraints2D(). When bedding_length > 0 and gradient constraints are shown, adds perpendicular "bedding" tick lines (2D-style).

def addDrillHole(self,
name: str,
hole,
*,
vmn: float = 0.0,
vmx: float = 20.0,
cmap: str | MplColormap | None = None,
linewidth: float = 4.0,
**kwargs)

Expand source code

def addDrillHole(
    self,
    name: str,
    hole,
    *,
    vmn: float = 0.0,
    vmx: float = 20.0,
    cmap: str | MplColormap | None = None,
    linewidth: float = 4.0,
    **kwargs,
):
    """
    Draw a drillhole trace as napari ``Shapes`` **line** segments (cf. ``plotDrill2D``).

    Works with ``ndisplay=2`` or ``3``. Uses transparent faces so GUI **edge width**
    controls line thickness.

    ``hole`` may be a :class:`~curlew.core.Geode` (or any object with ``.numpy()``);
    positions **(x, y)** or **(x, y, z)** are mapped to napari **(z, y, x)**.

    Each segment ``x[i]``→``x[i+1]`` is coloured by ``lithoID[i]``.

    Parameters
    ----------
    cmap
        Matplotlib **name**, :class:`matplotlib.colors.Colormap`, or ``None`` (uses
        :attr:`curlew.ccramp` if set, else ``tab20b``) for the segment colours.
    """
    from matplotlib.colors import Normalize
    from matplotlib import colormaps as mpl_colormaps
    from matplotlib.colors import Colormap as MplColormap

    if hasattr(hole, "numpy") and callable(hole.numpy):
        hole = hole.numpy()
    x = np.asarray(hole.x, dtype=np.float64)
    lid = np.asarray(hole.lithoID).ravel()
    if x.shape[0] < 2:
        return None
    if x.shape[1] not in (2, 3):
        raise ValueError("hole.x must have shape (N, 2) or (N, 3)")
    x = self._to_napari_xyz(x)

    # Use a matplotlib colormap to compute per-segment RGBA.
    if cmap is None:
        mpl_c = curlew.ccramp if curlew.ccramp is not None else mpl_colormaps["tab20b"]
    elif isinstance(cmap, str):
        mpl_c = mpl_colormaps[cmap]
    elif isinstance(cmap, MplColormap):
        mpl_c = cmap
    else:
        raise TypeError("cmap must be None, str, or matplotlib.colors.Colormap")
    norm = Normalize(vmin=vmn, vmax=vmx)

    lines: list[np.ndarray] = []
    colors: list[np.ndarray] = []
    for i in range(len(x) - 1):
        seg = np.asarray([x[i], x[i + 1]], dtype=np.float64)
        lines.append(seg)
        rgba = np.asarray(mpl_c(norm(float(lid[i]))), dtype=np.float64)
        colors.append(rgba)

    edge_rgba = np.stack(colors, axis=0).astype(np.float32)
    return self.addLines(
        name,
        lines,
        edge_color=edge_rgba,
        edge_width=linewidth,
        curlew_coords=False,
        **kwargs,
    )

Draw a drillhole trace as napari Shapes line segments (cf. plotDrill2D).

Works with ndisplay=2 or 3. Uses transparent faces so GUI edge width controls line thickness.

hole may be a :class:~curlew.core.Geode (or any object with .numpy()); positions (x, y) or (x, y, z) are mapped to napari (z, y, x).

Each segment x[i]→x[i+1] is coloured by lithoID[i].

Parameters

cmap

Matplotlib name, :class:matplotlib.colors.Colormap, or None (uses :attr:ccramp if set, else tab20b) for the segment colours.

def addGeode(self,
geode: Geode,
*,
lithoID: bool = True,
scalar: bool = True,
surfaces: bool = True,
displacement: bool = True,
offset_length: float = 1.0,
offset_width: float = 20.0) ‑> dict[str, napari.layers.Layer]

Expand source code

def addGeode(
    self,
    geode: Geode,
    *,
    lithoID: bool = True,
    scalar: bool = True,
    surfaces: bool = True,
    displacement: bool = True,
    offset_length: float = 1.0,
    offset_width: float = 20.0,
) -> dict[str, napari.layers.Layer]:
    """
    Visualise a :class:`curlew.core.Geode` (model prediction) in the viewer.

    For a 2D :class:`~curlew.geometry.Grid`, scalar fields are 2D images; isosurfaces are
    drawn as contour polylines (``Shapes``). For 3D grids, behaviour matches the previous
    ``Napari3D`` implementation (volumes + triangle meshes).
    """
    from curlew.core import Geode as GeodeType

    if not isinstance(geode, GeodeType):
        raise TypeError("geode must be a curlew.core.Geode instance")

    geode = geode.numpy()
    cmap = resolve_cmap()
    layers: dict[str, napari.layers.Layer] = {}
    grid = geode.grid

    def add_scalar_field(
        suffix: str,
        data,
        *,
        opacity=0.8,
        visible: bool,
    ) -> None:
        if data is None:
            return
        nm = f"{suffix}"
        flat = _geode_ravel_values(data)
        if grid is not None:
            vol = np.asarray(grid.reshape(flat), dtype=np.float64)
            if vol.ndim not in (2, 3):
                raise ValueError(
                    f"{suffix}: grid.reshape produced shape {vol.shape}; expected 2D or 3D"
                )
            layers[nm] = self.addVolume(
                nm,
                vol,
                grid=grid,
                colormap=cmap,
                blending="additive" if suffix == "lithoID" else "opaque",
                rendering="additive" if suffix == "lithoID" else "iso",
                visible=visible,
                opacity=opacity,
            )
        else:
            if geode.x is None:
                raise ValueError(
                    f"Cannot add {suffix}: geode has no grid and no x coordinates"
                )
            gx = np.asarray(geode.x, dtype=np.float64)
            if flat.shape[0] != gx.shape[0]:
                raise ValueError(
                    f"{suffix}: length {flat.shape[0]} does not match x rows {gx.shape[0]}"
                )
            layers[nm] = self.addPoints(
                nm,
                gx,
                scalar=flat.astype(np.float64),
                colormap=cmap,
                visible=visible,
                opacity=opacity,
            )

    if lithoID and geode.lithoID is not None:
        add_scalar_field("lithoID", geode.lithoID, visible=True, opacity=0.35)

    if scalar and geode.scalar is not None:
        add_scalar_field("scalar", geode.scalar, visible=False)

    if scalar and geode.fields:
        for key, arr in geode.fields.items():
            add_scalar_field(f"field_{key}", arr, visible=False)

    if surfaces and geode.isosurfaces and geode.grid is not None:
        if geode.grid.ndim == 2:
            path_specs: list[tuple[str, np.ndarray]] = []
            path_idx = 0
            for field in geode.fields:
                for surf_name in geode.isosurfaces[field]:
                    polylines = geode.getSurface(field, surf_name, normals=False)
                    if not isinstance(polylines, list):
                        continue
                    for poly in polylines:
                        if poly is None or len(poly) < 2:
                            continue
                        n = f"{field}_{surf_name}_c{path_idx}"
                        path_idx += 1
                        path_specs.append((n, poly))
            n_paths = max(1, len(path_specs))
            for i, (n, poly) in enumerate(path_specs):
                col = np.asarray(curlew.ccramp(i / n_paths), dtype=np.float32)
                edge_rgba = np.tile(col, (1, 1))
                layers[n] = self.addPaths(
                    n,
                    [poly],
                    edge_color=edge_rgba,
                    edge_width=2.0,
                )
        else:
            names = []
            for field in geode.fields:
                for surf_name in geode.isosurfaces[field]:
                    n = f"{field}_{surf_name}"
                    verts, faces, normals = geode.getSurface(
                        field, surf_name, normals=True
                    )
                    layers[n] = self.addMesh(
                        n,
                        verts,
                        faces,
                        normals=normals,
                        rgb="white",
                        shading="smooth",
                    )
                    names.append(n)

            for i, n in enumerate(names):
                verts = layers[n].data[0]
                col = curlew.ccramp(i / len(names))
                vertex_colors = np.tile(col, (len(verts), 1))
                layers[n].vertex_colors = vertex_colors

    if displacement and geode.offsets:
        if geode.x is None:
            raise ValueError("geode.offsets requires geode.x for vector origins")
        x0 = np.asarray(geode.x, dtype=np.float64)
        for key, disp in geode.offsets.items():
            nm = f"offset_{key}"
            d = np.asarray(disp, dtype=np.float64)
            if d.shape != x0.shape:
                raise ValueError(
                    f"offsets[{key!r}] shape {d.shape} does not match x shape {x0.shape}"
                )
            if x0.shape[0] == 0:
                continue
            mag = np.linalg.norm(d, axis=1)
            layers[nm] = self.addVectors(
                nm,
                x0,
                d,
                rgb=mag,
                length=offset_length,
                width=offset_width,
                vector_style="arrow",
                visible=False,
            )

    return layers

Visualise a :class:Geode (model prediction) in the viewer.

For a 2D :class:~curlew.geometry.Grid, scalar fields are 2D images; isosurfaces are drawn as contour polylines (Shapes). For 3D grids, behaviour matches the previous Napari3D implementation (volumes + triangle meshes).

def addLines(self,
name: str,
segments: list[np.ndarray],
*,
edge_color: str | np.ndarray = 'white',
edge_width: float = 2.0,
curlew_coords: bool = True,
**kwargs)

Expand source code

def addLines(
    self,
    name: str,
    segments: list[np.ndarray],
    *,
    edge_color: str | np.ndarray = "white",
    edge_width: float = 2.0,
    curlew_coords: bool = True,
    **kwargs,
):
    """
    Add 2-point **line** segments (``shape_type='line'``) with transparent faces so the
    GUI **edge width** controls line thickness. Vertex rows use Curlew coordinates by default.
    """
    if not segments:
        return None
    if curlew_coords:
        segments = [self._to_napari_xyz(s) for s in segments]
    shape_type = ["line"] * len(segments)
    self._remove_layer_if_present(name)
    layer = self.viewer.add_shapes(
        segments,
        shape_type=shape_type,
        name=name,
        edge_width=edge_width,
        edge_color=edge_color,
        face_color=_get_colors(len(segments)),
        **kwargs,
    )
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add 2-point line segments (shape_type='line') with transparent faces so the GUI edge width controls line thickness. Vertex rows use Curlew coordinates by default.

def addMesh(self,
name: str,
verts: np.ndarray,
faces: np.ndarray,
normals: np.ndarray | None = None,
rgb: str | np.ndarray = 'green',
shading: str = 'smooth',
*,
curlew_coords: bool = True,
**kwargs)

Expand source code

def addMesh(
    self,
    name: str,
    verts: np.ndarray,
    faces: np.ndarray,
    normals: np.ndarray | None = None,
    rgb: str | np.ndarray = "green",
    shading: str = "smooth",
    *,
    curlew_coords: bool = True,
    **kwargs,
):
    """
    Add a triangular surface mesh.

    Parameters
    ----------
    name : str
        Layer name (replaces an existing layer with the same name).
    verts : array, shape (N, 3)
    faces : array, shape (M, 3)
        Triangle vertex indices.
    normals : array, optional
        Per-vertex normals (N, 3). Not passed to napari when incompatible with the
        installed napari version; use ``vertex_colors`` / shading only.
    rgb : str or array, optional
        Matplotlib colour name if `str`. If array, per-vertex colours with shape (N, 3) RGB
        or (N, 4) RGBA in [0, 1].
    shading : str, optional
        Passed to `viewer.add_surface` (e.g. ``'smooth'``, ``'flat'``).
    curlew_coords : bool, optional
        If True (default), treat ``verts`` / ``normals`` as Curlew **(x, y, z)** and map to
        napari **(z, y, x)**. If False, vertices are already in napari order.
    **kwargs
        Additional arguments for `viewer.viewer.add_surface`.
    """
    verts = np.asarray(verts, dtype=np.float64)
    faces = np.asarray(faces)
    if verts.ndim != 2 or verts.shape[1] != 3:
        raise ValueError("verts must have shape (N, 3)")
    if curlew_coords:
        verts = np.column_stack([verts[:, 2], verts[:, 1], verts[:, 0]])

    if normals is not None:
        normals = np.asarray(normals, dtype=np.float64)
        if normals.ndim != 2 or normals.shape[1] != 3:
            raise ValueError("normals must have shape (N, 3)")
        if normals.shape[0] != verts.shape[0]:
            raise ValueError(
                "normals shape mismatch: expected per-vertex normals with the same "
                f"length as verts (got normals.shape[0]={normals.shape[0]} vs verts.shape[0]={verts.shape[0]})"
            )
        if curlew_coords:
            normals = np.column_stack(
                [normals[:, 2], normals[:, 1], normals[:, 0]]
            )

    if isinstance(rgb, str):
        from matplotlib.colors import to_rgba

        rgba = np.asarray(to_rgba(rgb), dtype=np.float64)
        vertex_colors = np.tile(rgba, (len(verts), 1))
    else:
        vc = np.asarray(rgb, dtype=np.float64)
        if vc.shape[0] != len(verts):
            raise ValueError("rgb array must have one row per vertex")
        if vc.shape[1] == 3:
            vertex_colors = np.c_[vc, np.ones(len(verts))]
        elif vc.shape[1] == 4:
            vertex_colors = vc
        else:
            raise ValueError("rgb must be (N, 3) or (N, 4)")

    self._remove_layer_if_present(name)
    
    kwargs = dict(kwargs)
    kwargs.pop("normals", None)
    layer = self.viewer.add_surface(
        (verts, faces),
        name=name,
        vertex_colors=vertex_colors,
        shading=shading,
        **kwargs,
    )
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add a triangular surface mesh.

Parameters

name : str

Layer name (replaces an existing layer with the same name).

verts : array, shape (N, 3)

 

faces : array, shape (M, 3)

Triangle vertex indices.

normals : array, optional

Per-vertex normals (N, 3). Not passed to napari when incompatible with the installed napari version; use vertex_colors / shading only.

rgb : str or array, optional

Matplotlib colour name if str. If array, per-vertex colours with shape (N, 3) RGB or (N, 4) RGBA in [0, 1].

shading : str, optional

Passed to viewer.add_surface (e.g. 'smooth', 'flat').

curlew_coords : bool, optional

If True (default), treat verts / normals as Curlew (x, y, z) and map to napari (z, y, x). If False, vertices are already in napari order.

**kwargs

Additional arguments for viewer.viewer.add_surface.

def addPaths(self,
name: str,
paths: list[np.ndarray],
*,
edge_color: str | np.ndarray = 'white',
edge_width: float = 2.0,
curlew_coords: bool = True,
**kwargs)

Expand source code

def addPaths(
    self,
    name: str,
    paths: list[np.ndarray],
    *,
    edge_color: str | np.ndarray = "white",
    edge_width: float = 2.0,
    curlew_coords: bool = True,
    **kwargs,
):
    """
    Add open polylines as a ``Shapes`` layer. Vertex rows use Curlew **(x, y)** / **(x, y, z)**
    by default (same as contour / model world coordinates). Use ``curlew_coords=False`` for
    napari **(z, y, x)**.
    """
    if not paths:
        return None
    if curlew_coords:
        paths = [self._to_napari_xyz(p) for p in paths]
    shape_type = ["path"] * len(paths)
    self._remove_layer_if_present(name)
    layer = self.viewer.add_shapes(
        paths,
        shape_type=shape_type,
        name=name,
        edge_width=edge_width,
        edge_color=edge_color,
        face_color=_get_colors(len(paths)),
        **kwargs,
    )
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add open polylines as a Shapes layer. Vertex rows use Curlew (x, y) / (x, y, z) by default (same as contour / model world coordinates). Use curlew_coords=False for napari (z, y, x).

def addPoints(self,
name: str,
xyz: np.ndarray,
rgb: str | np.ndarray | None = None,
scalar: np.ndarray | None = None,
colormap=None,
size: float = 10.0,
border_color: str | None = None,
symbol: str = 'o',
*,
curlew_coords: bool = True,
**kwargs)

Expand source code

def addPoints(
    self,
    name: str,
    xyz: np.ndarray,
    rgb: str | np.ndarray | None = None,
    scalar: np.ndarray | None = None,
    colormap=None,
    size: float = 10.0,
    border_color: str | None = None,
    symbol: str = "o",
    *,
    curlew_coords: bool = True,
    **kwargs,
):
    """
    Add a point cloud.

    By default ``xyz`` uses Curlew **(x, y)** or **(x, y, z)** — same as :class:`~curlew.core.Geode`
    ``x`` / constraint positions. Set ``curlew_coords=False`` only if you already permuted to
    napari **(z, y, x)**.
    """
    xyz = np.asarray(xyz, dtype=np.float64)
    if xyz.ndim != 2 or xyz.shape[1] not in (2, 3):
        raise ValueError("xyz must have shape (N, 2) or (N, 3)")
    if curlew_coords:
        xyz = self._to_napari_xyz(xyz)
    elif xyz.shape[1] != 3:
        raise ValueError("xyz must have shape (N, 3) when curlew_coords=False")

    if scalar is not None and rgb is not None:
        raise ValueError("Pass either scalar= or rgb=, not both.")

    self._remove_layer_if_present(name)

    n = xyz.shape[0]

    layer_opts: dict = {
        "out_of_slice_display": True,
        "symbol": symbol,
    }
    if border_color is None:
        if "border_width" not in kwargs:
            layer_opts["border_width"] = 0
    else:
        layer_opts["border_color"] = border_color
        if "border_width" not in kwargs:
            layer_opts["border_width"] = 0.05

    if scalar is not None:
        v = np.asarray(scalar)
        if v.ndim != 1 or v.shape[0] != n:
            raise ValueError("scalar must be a 1D array of length N")
        feat_key = "_curlew_scalar_points"
        cmap = resolve_cmap(colormap)
        layer = self.viewer.add_points(
            xyz,
            name=name,
            features={feat_key: v},
            face_color=feat_key,
            face_colormap=cmap,
            size=size,
            **layer_opts,
            **kwargs,
        )
    elif rgb is None:
        layer = self.viewer.add_points(
            xyz,
            name=name,
            face_color="red",
            size=size,
            **layer_opts,
            **kwargs,
        )
    elif isinstance(rgb, str):
        layer = self.viewer.add_points(
            xyz,
            name=name,
            face_color=rgb,
            size=size,
            **layer_opts,
            **kwargs,
        )
    else:
        v = np.asarray(rgb)
        if v.ndim == 2 and v.shape[0] == n and v.shape[1] in (3, 4):
            layer = self.viewer.add_points(
                xyz,
                name=name,
                face_color=v,
                size=size,
                **layer_opts,
                **kwargs,
            )
        else:
            raise ValueError(
                "rgb must be str or an array of shape (N,3)/(N,4) for per-point colours"
            )

    self._layers[name] = layer
    self._cnt += 1
    return layer

Add a point cloud.

By default xyz uses Curlew (x, y) or (x, y, z) — same as :class:~curlew.core.Geode x / constraint positions. Set curlew_coords=False only if you already permuted to napari (z, y, x).

def addTracks(self,
name: str,
tracks,
*,
features: dict | None = None,
colormap=None,
tail_width: float = 2.0,
tail_length: int = 30,
head_length: int = 0,
**kwargs)

Expand source code

def addTracks(
    self,
    name: str,
    tracks,
    *,
    features: dict | None = None,
    colormap=None,
    tail_width: float = 2.0,
    tail_length: int = 30,
    head_length: int = 0,
    **kwargs,
):
    """
    Add 3D particle trajectories as a napari ``Tracks`` layer.

    Parameters
    ----------
    name : str
        Layer name (replaces an existing layer with the same name).
    tracks : array-like
        One of three formats:

        - **Napari format** ``(N, 5)`` — columns are ``[track_id, t, x0, x1, x2]``
            (passed through directly).
        - **Stacked trajectories** ``(N_tracks, T, 3)`` — ``N_tracks`` particle paths,
            each sampled at ``T`` equally-spaced time steps, coordinates ``(x, y, z)``.
            Track IDs are assigned as ``0 … N_tracks-1`` and time as ``0 … T-1``.
        - **List of arrays** — each element is ``(T_i, 3)`` for variable-length paths.
            Track IDs and per-track time indices are assigned automatically.

    features : dict, optional
        Per-point scalar attributes (length ``N``), passed to napari as ``features``.
        Example: ``{'speed': speed_array}``. Can be used for colour-by-feature.
    colormap : optional
        Napari colormap (or name) for ``color_by`` features. Defaults to Curlew
        ``ccramp`` when available.
    tail_width : float, optional
        Track tail line width.
    tail_length : int, optional
        Number of previous time-steps to render as a tail.
    head_length : int, optional
        Number of future time-steps to render ahead of the current frame.
    **kwargs
        Additional arguments passed to ``viewer.add_tracks`` (e.g. ``color_by``,
        ``blending``, ``opacity``).

    Returns
    -------
    napari.layers.Tracks
    """
    _require_napari()

    tracks_arr = np.asarray(tracks, dtype=np.float64) if not isinstance(tracks, list) else None

    if tracks_arr is not None and tracks_arr.ndim == 2 and tracks_arr.shape[1] == 5:
        # Already in napari format [track_id, t, x0, x1, x2]
        data = tracks_arr
    elif tracks_arr is not None and tracks_arr.ndim == 3 and tracks_arr.shape[2] == 3:
        # (N_tracks, T, 3) → (N_tracks*T, 5)
        n_tracks, T, _ = tracks_arr.shape
        ids = np.repeat(np.arange(n_tracks, dtype=np.float64), T)
        times = np.tile(np.arange(T, dtype=np.float64), n_tracks)
        coords = tracks_arr.reshape(-1, 3)
        data = np.column_stack([ids, times, coords])
    elif isinstance(tracks, list) or (tracks_arr is not None and tracks_arr.ndim == 1):
        # List of variable-length (T_i, 3) arrays
        rows = []
        for track_id, traj in enumerate(tracks):
            t = np.asarray(traj, dtype=np.float64)
            if t.ndim != 2 or t.shape[1] != 3:
                raise ValueError(
                    f"Track {track_id}: expected shape (T, 3), got {t.shape}"
                )
            ids = np.full(len(t), track_id, dtype=np.float64)
            times = np.arange(len(t), dtype=np.float64)
            rows.append(np.column_stack([ids, times, t]))
        data = np.vstack(rows)
    else:
        raise ValueError(
            "tracks must be (N, 5) napari format, (N_tracks, T, 3), or a list of (T_i, 3) arrays"
        )

    opts: dict = {
        "name": name,
        "tail_width": tail_width,
        "tail_length": tail_length,
        "head_length": head_length,
    }
    if features is not None:
        opts["features"] = features
    if colormap is not None:
        opts["colormap"] = colormap
    elif features:
        opts["colormap"] = _curlew_napari_colormap()
    opts.update(kwargs)

    self._remove_layer_if_present(name)
    layer = self.viewer.add_tracks(data, **opts)
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add 3D particle trajectories as a napari Tracks layer.

Parameters

name : str

Layer name (replaces an existing layer with the same name).

tracks : array-like

One of three formats:

• Napari format (N, 5) — columns are [track_id, t, x0, x1, x2] (passed through directly).
• Stacked trajectories (N_tracks, T, 3) — N_tracks particle paths, each sampled at T equally-spaced time steps, coordinates (x, y, z). Track IDs are assigned as 0 … N_tracks-1 and time as 0 … T-1.
• List of arrays — each element is (T_i, 3) for variable-length paths. Track IDs and per-track time indices are assigned automatically.

features : dict, optional

Per-point scalar attributes (length N), passed to napari as features. Example: {'speed': speed_array}. Can be used for colour-by-feature.

colormap : optional

Napari colormap (or name) for color_by features. Defaults to Curlew ccramp when available.

tail_width : float, optional

Track tail line width.

tail_length : int, optional

Number of previous time-steps to render as a tail.

head_length : int, optional

Number of future time-steps to render ahead of the current frame.

**kwargs

Additional arguments passed to viewer.add_tracks (e.g. color_by, blending, opacity).

Returns

napari.layers.Tracks

 

def addVectors(self,
name: str,
origins: np.ndarray,
directions: np.ndarray,
*,
rgb: str | np.ndarray | None = None,
length: float = 1.0,
width: float = 1,
colormap=None,
curlew_coords: bool = True,
**kwargs)

Expand source code

def addVectors(
    self,
    name: str,
    origins: np.ndarray,
    directions: np.ndarray,
    *,
    rgb: str | np.ndarray | None = None,
    length: float = 1.0,
    width: float = 1,
    colormap=None,
    curlew_coords: bool = True,
    **kwargs,
):
    """
    Add a vector field as napari ``Vectors`` (2D and 3D viewers).

    By default ``origins`` and ``directions`` use Curlew **(x, y)** / **(x, y, z)**. Pass
    ``curlew_coords=False`` if they are already in napari **(z, y, x)**.
    """
    origins = np.asarray(origins, dtype=np.float64)
    directions = np.asarray(directions, dtype=np.float64)
    if origins.ndim != 2 or origins.shape[1] not in (2, 3):
        raise ValueError("origins must have shape (N, 2) or (N, 3)")
    if directions.shape != origins.shape:
        raise ValueError("directions must have the same shape as origins")
    if curlew_coords:
        origins = self._to_napari_xyz(origins)
        directions = self._to_napari_xyz(directions)
    elif origins.shape[1] != 3:
        raise ValueError("origins must have shape (N, 3) when curlew_coords=False")
    n = origins.shape[0]
    data = np.stack([origins, directions], axis=1)

    opts: dict = {
        "name": name,
        "length": length,
        "edge_width": width,
        "vector_style": kwargs.get("vector_style", "arrow"),
        "out_of_slice_display": kwargs.get("out_of_slice_display", True),
    }
    if isinstance(rgb, str):
        opts["edge_color"] = rgb
    elif rgb is not None:
        v = np.asarray(rgb)
        if v.ndim != 1 or v.shape[0] != n:
            raise ValueError(
                "rgb must be str or a 1D array of length N (scalar per vector)"
            )
        feat_key = "_curlew_scalar"
        opts["features"] = {feat_key: v}
        opts["edge_color"] = feat_key
        opts["edge_colormap"] = resolve_cmap(colormap)
    else:
        opts["edge_color"] = "red"

    opts.update(kwargs)

    self._remove_layer_if_present(name)
    layer = self.viewer.add_vectors(data, **opts)
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add a vector field as napari Vectors (2D and 3D viewers).

By default origins and directions use Curlew (x, y) / (x, y, z). Pass curlew_coords=False if they are already in napari (z, y, x).

def addVolume(self,
name: str,
volume: np.ndarray,
*,
grid=None,
scale=None,
translate=None,
affine=None,
rendering: str = 'iso',
colormap=None,
blending: str = 'opaque',
interpolation2d: str = 'nearest',
interpolation3d: str = 'nearest',
**kwargs)

Expand source code

def addVolume(
    self,
    name: str,
    volume: np.ndarray,
    *,
    grid=None,
    scale=None,
    translate=None,
    affine=None,
    rendering: str = "iso",
    colormap=None,
    blending: str = "opaque",
    interpolation2d: str = "nearest",
    interpolation3d: str = "nearest",
    **kwargs,
):
    """
    Add a 2D image or 3D volume (scalar field on a regular grid).

    When ``grid`` is **2D**, ``volume`` must have shape ``grid.shape`` (Curlew
    ``(i₀, i₁)``). It is passed to napari as ``flipud(transpose(volume))`` so the
    vertical axis matches :func:`curlew.visualise.plot2D` (matplotlib
    ``imshow(..., origin='lower')``). Napari's default row order would otherwise flip
    the section upside down relative to drillholes and constraints. When ``grid`` is
    **3D**, ``volume`` must match ``grid.shape`` (Curlew ``(x, y, z)``); it is
    internally transposed to Napari axes ``(z, y, x)`` when an affine is inferred.

    For 2D map views, set ``ndisplay=2`` on the viewer.
    """
    volume = np.asarray(volume)
    if volume.ndim not in (2, 3):
        raise ValueError("volume must be a 2D or 3D array")

    if grid is not None and (scale is not None or translate is not None):
        raise ValueError(
            "addVolume: use grid=... for affine, or scale=/translate=, not both."
        )
    if grid is not None and grid.ndim != volume.ndim:
        raise ValueError(
            f"grid.ndim ({grid.ndim}) must match volume.ndim ({volume.ndim})"
        )

    colormap = resolve_cmap(colormap)

    affine_use = affine
    if affine_use is None and grid is not None:
        if grid.ndim == 2:
            volume = np.flipud(np.transpose(volume))
            affine_use = image_affine_napari_row_column_image_2d(grid)
        else:
            # Curlew grids are sampled in (x, y, z) order, while Napari image
            # axes (and the viewer coordinate convention we use for points/surfaces)
            # are (z, y, x). Transpose the volume data accordingly, and permute the
            # affine so voxel indices (z, y, x) map to world coordinates (z, y, x).
            volume = np.transpose(volume, (2, 1, 0))
            A_cur = image_affine_from_grid(grid)  # maps (x,y,z indices) -> (x,y,z world)
            # Swap axes 0 and 2 (x <-> z) in both input indices and output world coords.
            P = np.array(
                [
                    [0.0, 0.0, 1.0, 0.0],
                    [0.0, 1.0, 0.0, 0.0],
                    [1.0, 0.0, 0.0, 0.0],
                    [0.0, 0.0, 0.0, 1.0],
                ],
                dtype=np.float64,
            )
            affine_use = P @ A_cur @ P

    legacy_interp = kwargs.pop("interpolation", None)
    if legacy_interp is not None:
        import warnings

        warnings.warn(
            "napari add_image does not accept `interpolation=`; use "
            "`interpolation2d=` and `interpolation3d=` on addVolume instead. "
            f"Applying {legacy_interp!r} to both.",
            UserWarning,
            stacklevel=2,
        )
        interpolation2d = interpolation3d = legacy_interp

    opts: dict = {
        "name": name,
        "rendering": rendering,
        "colormap": colormap,
        "blending": blending,
        "interpolation2d": interpolation2d,
        "interpolation3d": interpolation3d,
    }
    if scale is not None:
        opts["scale"] = scale
    if translate is not None:
        opts["translate"] = translate
    if affine_use is not None:
        opts["affine"] = affine_use
    opts.update(kwargs)

    self._remove_layer_if_present(name)
    layer = self.viewer.add_image(volume, **opts)
    self._layers[name] = layer
    self._cnt += 1
    return layer

Add a 2D image or 3D volume (scalar field on a regular grid).

When grid is 2D, volume must have shape grid.shape (Curlew (i₀, i₁)). It is passed to napari as flipud(transpose(volume)) so the vertical axis matches :func:plot2D() (matplotlib imshow(..., origin='lower')). Napari's default row order would otherwise flip the section upside down relative to drillholes and constraints. When grid is 3D, volume must match grid.shape (Curlew (x, y, z)); it is internally transposed to Napari axes (z, y, x) when an affine is inferred.

For 2D map views, set ndisplay=2 on the viewer.

def show(self, *, block: bool = False)

Expand source code

def show(self, *, block: bool = False):
    """
    Show the viewer window (Qt). In a script you may need ``napari.run()`` afterwards
    unless ``block=True``.
    """
    self.viewer.show(block=block)
    return self.viewer

Show the viewer window (Qt). In a script you may need napari.run() afterwards unless block=True.