import warnings
from collections import deque
from collections.abc import Sequence
from contextlib import contextmanager
from typing import (
Callable,
ClassVar,
Optional,
Union,
cast,
)
import numpy as np
import numpy.typing as npt
import pandas as pd
from scipy import ndimage as ndi
from skimage.draw import polygon2mask
from napari.layers._data_protocols import LayerDataProtocol
from napari.layers._multiscale_data import MultiScaleData
from napari.layers._scalar_field.scalar_field import ScalarFieldBase
from napari.layers.base import Layer, no_op
from napari.layers.base._base_mouse_bindings import (
highlight_box_handles,
transform_with_box,
)
from napari.layers.image._image_utils import guess_multiscale
from napari.layers.image._slice import _ImageSliceResponse
from napari.layers.labels._labels_constants import (
LabelColorMode,
LabelsRendering,
Mode,
)
from napari.layers.labels._labels_mouse_bindings import (
BrushSizeOnMouseMove,
draw,
pick,
)
from napari.layers.labels._labels_utils import (
expand_slice,
get_contours,
indices_in_shape,
interpolate_coordinates,
sphere_indices,
)
from napari.layers.utils.layer_utils import _FeatureTable
from napari.utils._dtype import normalize_dtype, vispy_texture_dtype
from napari.utils._indexing import elements_in_slice, index_in_slice
from napari.utils.colormaps import (
direct_colormap,
label_colormap,
)
from napari.utils.colormaps.colormap import (
CyclicLabelColormap,
LabelColormapBase,
)
from napari.utils.colormaps.colormap_utils import shuffle_and_extend_colormap
from napari.utils.events import EmitterGroup, Event
from napari.utils.events.custom_types import Array
from napari.utils.geometry import clamp_point_to_bounding_box
from napari.utils.misc import StringEnum, _is_array_type
from napari.utils.naming import magic_name
from napari.utils.status_messages import generate_layer_coords_status
from napari.utils.translations import trans
__all__ = ('Labels',)
[docs]
class Labels(ScalarFieldBase):
"""Labels (or segmentation) layer.
An image-like layer where every pixel contains an integer ID
corresponding to the region it belongs to.
Parameters
----------
data : array or list of array
Labels data as an array or multiscale. Must be integer type or bools.
Please note multiscale rendering is only supported in 2D. In 3D, only
the lowest resolution scale is displayed.
affine : n-D array or napari.utils.transforms.Affine
(N+1, N+1) affine transformation matrix in homogeneous coordinates.
The first (N, N) entries correspond to a linear transform and
the final column is a length N translation vector and a 1 or a napari
`Affine` transform object. Applied as an extra transform on top of the
provided scale, rotate, and shear values.
blending : str
One of a list of preset blending modes that determines how RGB and
alpha values of the layer visual get mixed. Allowed values are
{'opaque', 'translucent', and 'additive'}.
cache : bool
Whether slices of out-of-core datasets should be cached upon retrieval.
Currently, this only applies to dask arrays.
colormap : CyclicLabelColormap or DirectLabelColormap or None
Colormap to use for the labels. If None, a random colormap will be
used.
depiction : str
3D Depiction mode. Must be one of {'volume', 'plane'}.
The default value is 'volume'.
experimental_clipping_planes : list of dicts, list of ClippingPlane, or ClippingPlaneList
Each dict defines a clipping plane in 3D in data coordinates.
Valid dictionary keys are {'position', 'normal', and 'enabled'}.
Values on the negative side of the normal are discarded if the plane is enabled.
features : dict[str, array-like] or DataFrame
Features table where each row corresponds to a label and each column
is a feature. The first row corresponds to the background label.
metadata : dict
Layer metadata.
multiscale : bool
Whether the data is a multiscale image or not. Multiscale data is
represented by a list of array like image data. If not specified by
the user and if the data is a list of arrays that decrease in shape
then it will be taken to be multiscale. The first image in the list
should be the largest. Please note multiscale rendering is only
supported in 2D. In 3D, only the lowest resolution scale is
displayed.
name : str
Name of the layer.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
plane : dict or SlicingPlane
Properties defining plane rendering in 3D. Properties are defined in
data coordinates. Valid dictionary keys are
{'position', 'normal', 'thickness', and 'enabled'}.
projection_mode : str
How data outside the viewed dimensions but inside the thick Dims slice will
be projected onto the viewed dimensions
properties : dict {str: array (N,)} or DataFrame
Properties for each label. Each property should be an array of length
N, where N is the number of labels, and the first property corresponds
to background.
rendering : str
3D Rendering mode used by vispy. Must be one {'translucent', 'iso_categorical'}.
'translucent' renders without lighting. 'iso_categorical' uses isosurface
rendering to calculate lighting effects on labeled surfaces.
The default value is 'iso_categorical'.
rotate : float, 3-tuple of float, or n-D array.
If a float convert into a 2D rotation matrix using that value as an
angle. If 3-tuple convert into a 3D rotation matrix, using a yaw,
pitch, roll convention. Otherwise assume an nD rotation. Angles are
assumed to be in degrees. They can be converted from radians with
np.degrees if needed.
scale : tuple of float
Scale factors for the layer.
shear : 1-D array or n-D array
Either a vector of upper triangular values, or an nD shear matrix with
ones along the main diagonal.
translate : tuple of float
Translation values for the layer.
visible : bool
Whether the layer visual is currently being displayed.
Attributes
----------
data : array or list of array
Integer label data as an array or multiscale. Can be N dimensional.
Every pixel contains an integer ID corresponding to the region it
belongs to. The label 0 is rendered as transparent. Please note
multiscale rendering is only supported in 2D. In 3D, only
the lowest resolution scale is displayed.
multiscale : bool
Whether the data is a multiscale image or not. Multiscale data is
represented by a list of array like image data. The first image in the
list should be the largest. Please note multiscale rendering is only
supported in 2D. In 3D, only the lowest resolution scale is
displayed.
metadata : dict
Labels metadata.
num_colors : int
Number of unique colors to use in colormap. DEPRECATED: set
``colormap`` directly, using `napari.utils.colormaps.label_colormap`.
features : Dataframe-like
Features table where each row corresponds to a label and each column
is a feature. The first row corresponds to the background label.
properties : dict {str: array (N,)}, DataFrame
Properties for each label. Each property should be an array of length
N, where N is the number of labels, and the first property corresponds
to background.
color : dict of int to str or array
Custom label to color mapping. Values must be valid color names or RGBA
arrays. While there is no limit to the number of custom labels, the
the layer will render incorrectly if they map to more than 1024 distinct
colors. DEPRECATED: set ``colormap`` directly, using
`napari.utils.colormaps.DirectLabelColormap`.
seed : float
Seed for colormap random generator. DEPRECATED: set ``colormap``
directly, using `napari.utils.colormaps.label_colormap`.
opacity : float
Opacity of the labels, must be between 0 and 1.
contiguous : bool
If `True`, the fill bucket changes only connected pixels of same label.
n_edit_dimensions : int
The number of dimensions across which labels will be edited.
contour : int
If greater than 0, displays contours of labels instead of shaded regions
with a thickness equal to its value. Must be >= 0.
brush_size : float
Size of the paint brush in data coordinates.
selected_label : int
Index of selected label. Can be greater than the current maximum label.
mode : str
Interactive mode. The normal, default mode is PAN_ZOOM, which
allows for normal interactivity with the canvas.
In PICK mode the cursor functions like a color picker, setting the
clicked on label to be the current label. If the background is picked it
will select the background label `0`.
In PAINT mode the cursor functions like a paint brush changing any
pixels it brushes over to the current label. If the background label
`0` is selected than any pixels will be changed to background and this
tool functions like an eraser. The size and shape of the cursor can be
adjusted in the properties widget.
In FILL mode the cursor functions like a fill bucket replacing pixels
of the label clicked on with the current label. It can either replace
all pixels of that label or just those that are contiguous with the
clicked on pixel. If the background label `0` is selected than any
pixels will be changed to background and this tool functions like an
eraser.
In ERASE mode the cursor functions similarly to PAINT mode, but to
paint with background label, which effectively removes the label.
plane : SlicingPlane
Properties defining plane rendering in 3D.
experimental_clipping_planes : ClippingPlaneList
Clipping planes defined in data coordinates, used to clip the volume.
Notes
-----
_selected_color : 4-tuple or None
RGBA tuple of the color of the selected label, or None if the
background label `0` is selected.
"""
events: EmitterGroup
_colormap: LabelColormapBase
_modeclass = Mode
_drag_modes: ClassVar[dict[Mode, Callable[['Labels', Event], None]]] = { # type: ignore[assignment]
Mode.PAN_ZOOM: no_op,
Mode.TRANSFORM: transform_with_box,
Mode.PICK: pick,
Mode.PAINT: draw,
Mode.FILL: draw,
Mode.ERASE: draw,
Mode.POLYGON: no_op, # the overlay handles mouse events in this mode
}
brush_size_on_mouse_move = BrushSizeOnMouseMove(min_brush_size=1)
_move_modes: ClassVar[
dict[StringEnum, Callable[['Labels', Event], None]]
] = { # type: ignore[assignment]
Mode.PAN_ZOOM: no_op,
Mode.TRANSFORM: highlight_box_handles,
Mode.PICK: no_op,
Mode.PAINT: brush_size_on_mouse_move,
Mode.FILL: no_op,
Mode.ERASE: brush_size_on_mouse_move,
Mode.POLYGON: no_op, # the overlay handles mouse events in this mode
}
_cursor_modes: ClassVar[dict[Mode, str]] = { # type: ignore[assignment]
Mode.PAN_ZOOM: 'standard',
Mode.TRANSFORM: 'standard',
Mode.PICK: 'cross',
Mode.PAINT: 'circle',
Mode.FILL: 'cross',
Mode.ERASE: 'circle',
Mode.POLYGON: 'cross',
}
_history_limit = 100
def __init__(
self,
data,
*,
affine=None,
blending='translucent',
cache=True,
colormap=None,
depiction='volume',
experimental_clipping_planes=None,
features=None,
metadata=None,
multiscale=None,
name=None,
opacity=0.7,
plane=None,
projection_mode='none',
properties=None,
rendering='iso_categorical',
rotate=None,
scale=None,
shear=None,
translate=None,
visible=True,
) -> None:
if name is None and data is not None:
name = magic_name(data)
self._seed = 0.5
# We use 50 colors (49 + transparency) by default for historical
# consistency. This may change in future versions.
self._random_colormap = label_colormap(
49, self._seed, background_value=0
)
self._original_random_colormap = self._random_colormap
self._direct_colormap = direct_colormap(
{0: 'transparent', None: 'black'}
)
self._colormap = self._random_colormap
self._color_mode = LabelColorMode.AUTO
self._show_selected_label = False
self._contour = 0
data = self._ensure_int_labels(data)
super().__init__(
data,
rendering=rendering,
depiction=depiction,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
rotate=rotate,
shear=shear,
affine=affine,
opacity=opacity,
blending=blending,
visible=visible,
multiscale=multiscale,
cache=cache,
plane=plane,
experimental_clipping_planes=experimental_clipping_planes,
projection_mode=projection_mode,
)
self.events.add(
brush_shape=Event,
brush_size=Event,
colormap=Event,
contiguous=Event,
contour=Event,
features=Event,
labels_update=Event,
n_edit_dimensions=Event,
paint=Event,
preserve_labels=Event,
properties=Event,
selected_label=Event,
show_selected_label=Event,
)
from napari.components.overlays.labels_polygon import (
LabelsPolygonOverlay,
)
self._overlays.update({'polygon': LabelsPolygonOverlay()})
self._feature_table = _FeatureTable.from_layer(
features=features, properties=properties
)
self._label_index = self._make_label_index()
self._n_edit_dimensions = 2
self._contiguous = True
self._brush_size = 10
self._selected_label = 1
self.colormap.selection = self._selected_label
self.colormap.use_selection = self._show_selected_label
self._prev_selected_label = None
self._selected_color = self.get_color(self._selected_label)
self._updated_slice = None
if colormap is not None:
self._set_colormap(colormap)
self._status = self.mode
self._preserve_labels = False
def _post_init(self):
self._reset_history()
# Trigger generation of view slice and thumbnail
self.refresh()
self._reset_editable()
@property
def rendering(self):
"""Return current rendering mode.
Selects a preset rendering mode in vispy that determines how
lablels are displayed. Options include:
* ``translucent``: voxel colors are blended along the view ray until
the result is opaque.
* ``iso_categorical``: isosurface for categorical data.
Cast a ray until a non-background value is encountered. At that
location, lighning calculations are performed to give the visual
appearance of a surface.
Returns
-------
str
The current rendering mode
"""
return str(self._rendering)
@rendering.setter
def rendering(self, rendering):
self._rendering = LabelsRendering(rendering)
self.events.rendering()
@property
def contiguous(self):
"""bool: fill bucket changes only connected pixels of same label."""
return self._contiguous
@contiguous.setter
def contiguous(self, contiguous):
self._contiguous = contiguous
self.events.contiguous()
@property
def n_edit_dimensions(self):
return self._n_edit_dimensions
@n_edit_dimensions.setter
def n_edit_dimensions(self, n_edit_dimensions):
self._n_edit_dimensions = n_edit_dimensions
self.events.n_edit_dimensions()
@property
def contour(self) -> int:
"""int: displays contours of labels instead of shaded regions."""
return self._contour
@contour.setter
def contour(self, contour: int) -> None:
if contour < 0:
raise ValueError('contour value must be >= 0')
self._contour = int(contour)
self.events.contour()
self.refresh()
@property
def brush_size(self):
"""float: Size of the paint in world coordinates."""
return self._brush_size
@brush_size.setter
def brush_size(self, brush_size):
self._brush_size = int(brush_size)
self.cursor_size = self._calculate_cursor_size()
self.events.brush_size()
def _calculate_cursor_size(self):
# Convert from brush size in data coordinates to
# cursor size in world coordinates
scale = self._data_to_world.scale
min_scale = np.min(
[abs(scale[d]) for d in self._slice_input.displayed]
)
return abs(self.brush_size * min_scale)
def new_colormap(self, seed: Optional[int] = None):
if seed is None:
seed = np.random.default_rng().integers(2**32 - 1)
orig = self._original_random_colormap
self.colormap = shuffle_and_extend_colormap(
self._original_random_colormap, seed
)
self._original_random_colormap = orig
@property
def colormap(self) -> LabelColormapBase:
return self._colormap
@colormap.setter
def colormap(self, colormap: LabelColormapBase):
self._set_colormap(colormap)
def _set_colormap(self, colormap):
if isinstance(colormap, CyclicLabelColormap):
self._random_colormap = colormap
self._original_random_colormap = colormap
self._colormap = self._random_colormap
color_mode = LabelColorMode.AUTO
else:
self._direct_colormap = colormap
# `self._direct_colormap.color_dict` may contain just the default None and background label
# colors, in which case we need to be in AUTO color mode. Otherwise,
# `self._direct_colormap.color_dict` contains colors for all labels, and we should be in DIRECT
# mode.
# For more information
# - https://github.com/napari/napari/issues/2479
# - https://github.com/napari/napari/issues/2953
if self._is_default_colors(self._direct_colormap.color_dict):
color_mode = LabelColorMode.AUTO
self._colormap = self._random_colormap
else:
color_mode = LabelColorMode.DIRECT
self._colormap = self._direct_colormap
self._cached_labels = None # invalidate the cached color mapping
self._selected_color = self.get_color(self.selected_label)
self._color_mode = color_mode
self.events.colormap() # Will update the LabelVispyColormap shader
self.events.selected_label()
self.refresh()
@property
def data(self) -> Union[LayerDataProtocol, MultiScaleData]:
"""array: Image data."""
return self._data
@data.setter
def data(self, data: Union[LayerDataProtocol, MultiScaleData]):
data = self._ensure_int_labels(data)
self._data = data
self._ndim = len(self._data.shape)
self._update_dims()
self.events.data(value=self.data)
self._reset_editable()
@property
def features(self):
"""Dataframe-like features table.
It is an implementation detail that this is a `pandas.DataFrame`. In the future,
we will target the currently-in-development Data API dataframe protocol [1]_.
This will enable us to use alternate libraries such as xarray or cuDF for
additional features without breaking existing usage of this.
If you need to specifically rely on the pandas API, please coerce this to a
`pandas.DataFrame` using `features_to_pandas_dataframe`.
References
----------
.. [1] https://data-apis.org/dataframe-protocol/latest/API.html
"""
return self._feature_table.values
@features.setter
def features(
self,
features: Union[dict[str, np.ndarray], pd.DataFrame],
) -> None:
self._feature_table.set_values(features)
self._label_index = self._make_label_index()
self.events.properties()
self.events.features()
@property
def properties(self) -> dict[str, np.ndarray]:
"""dict {str: array (N,)}, DataFrame: Properties for each label."""
return self._feature_table.properties()
@properties.setter
def properties(self, properties: dict[str, Array]):
self.features = properties
def _make_label_index(self) -> dict[int, int]:
features = self._feature_table.values
label_index = {}
if 'index' in features:
label_index = {i: k for k, i in enumerate(features['index'])}
elif features.shape[1] > 0:
label_index = {i: i for i in range(features.shape[0])}
return label_index
def _is_default_colors(self, color):
"""Returns True if color contains only default colors, otherwise False.
Default colors are black for `None` and transparent for
`self.colormap.background_value`.
Parameters
----------
color : Dict
Dictionary of label value to color array
Returns
-------
bool
True if color contains only default colors, otherwise False.
"""
if {None, self.colormap.background_value} != set(color.keys()):
return False
if not np.allclose(color[None], [0, 0, 0, 1]):
return False
if not np.allclose(
color[self.colormap.background_value], [0, 0, 0, 0]
):
return False
return True
def _ensure_int_labels(self, data):
"""Ensure data is integer by converting from bool if required, raising an error otherwise."""
looks_multiscale, data = guess_multiscale(data)
if not looks_multiscale:
data = [data]
int_data = []
for data_level in data:
# normalize_dtype turns e.g. tensorstore or torch dtypes into
# numpy dtypes
if np.issubdtype(normalize_dtype(data_level.dtype), np.floating):
raise TypeError(
trans._(
'Only integer types are supported for Labels layers, but data contains {data_level_type}.',
data_level_type=data_level.dtype,
)
)
if data_level.dtype == bool:
int_data.append(data_level.astype(np.int8))
else:
int_data.append(data_level)
data = int_data
if not looks_multiscale:
data = data[0]
return data
def _get_state(self):
"""Get dictionary of layer state.
Returns
-------
state : dict
Dictionary of layer state.
"""
state = self._get_base_state()
state.update(
{
'multiscale': self.multiscale,
'properties': self.properties,
'rendering': self.rendering,
'depiction': self.depiction,
'plane': self.plane.dict(),
'experimental_clipping_planes': [
plane.dict() for plane in self.experimental_clipping_planes
],
'data': self.data,
'features': self.features,
'colormap': self.colormap,
}
)
return state
@property
def selected_label(self):
"""int: Index of selected label."""
return self._selected_label
@selected_label.setter
def selected_label(self, selected_label):
if selected_label == self.selected_label:
return
self._prev_selected_label = self.selected_label
self.colormap.selection = selected_label
self._selected_label = selected_label
self._selected_color = self.get_color(selected_label)
self.events.selected_label()
if self.show_selected_label:
self.refresh()
[docs]
def swap_selected_and_background_labels(self):
"""Swap between the selected label and the background label."""
if self.selected_label != self.colormap.background_value:
self.selected_label = self.colormap.background_value
else:
self.selected_label = self._prev_selected_label
@property
def show_selected_label(self):
"""Whether to filter displayed labels to only the selected label or not"""
return self._show_selected_label
@show_selected_label.setter
def show_selected_label(self, show_selected):
self._show_selected_label = show_selected
self.colormap.use_selection = show_selected
self.colormap.selection = self.selected_label
self.events.show_selected_label(show_selected_label=show_selected)
self.refresh()
# Only overriding to change the docstring
@property
def mode(self):
"""MODE: Interactive mode. The normal, default mode is PAN_ZOOM, which
allows for normal interactivity with the canvas.
In PICK mode the cursor functions like a color picker, setting the
clicked on label to be the current label. If the background is picked it
will select the background label `0`.
In PAINT mode the cursor functions like a paint brush changing any
pixels it brushes over to the current label. If the background label
`0` is selected than any pixels will be changed to background and this
tool functions like an eraser. The size and shape of the cursor can be
adjusted in the properties widget.
In FILL mode the cursor functions like a fill bucket replacing pixels
of the label clicked on with the current label. It can either replace
all pixels of that label or just those that are contiguous with the
clicked on pixel. If the background label `0` is selected than any
pixels will be changed to background and this tool functions like an
eraser.
In ERASE mode the cursor functions similarly to PAINT mode, but to
paint with background label, which effectively removes the label.
"""
return Layer.mode.fget(self)
# Only overriding to change the docstring of the setter above
@mode.setter
def mode(self, mode):
Layer.mode.fset(self, mode)
def _mode_setter_helper(self, mode):
mode = super()._mode_setter_helper(mode)
if mode == self._mode:
return mode
self._overlays['polygon'].enabled = mode == Mode.POLYGON
if mode in {Mode.PAINT, Mode.ERASE}:
self.cursor_size = self._calculate_cursor_size()
return mode
@property
def preserve_labels(self):
"""Defines if painting should preserve existing labels.
Default to false to allow paint on existing labels. When
set to true, existing labels will be preserved during painting.
"""
return self._preserve_labels
@preserve_labels.setter
def preserve_labels(self, preserve_labels: bool):
self._preserve_labels = preserve_labels
self.events.preserve_labels(preserve_labels=preserve_labels)
def _reset_editable(self) -> None:
self.editable = not self.multiscale
def _on_editable_changed(self) -> None:
if not self.editable:
self.mode = Mode.PAN_ZOOM
self._reset_history()
@staticmethod
def _to_vispy_texture_dtype(data):
"""Convert data to a dtype that can be used as a VisPy texture.
Labels layers allow all integer dtypes for data, but only a subset
are supported by VisPy textures. For now, we convert all data to
float32 as it can represent all input values (though not losslessly,
see https://github.com/napari/napari/issues/6084).
"""
return vispy_texture_dtype(data)
def _update_slice_response(self, response: _ImageSliceResponse) -> None:
"""Override to convert raw slice data to displayed label colors."""
response = response.to_displayed(self._raw_to_displayed)
super()._update_slice_response(response)
def _partial_labels_refresh(self):
"""Prepares and displays only an updated part of the labels."""
if self._updated_slice is None or not self.loaded:
return
dims_displayed = self._slice_input.displayed
raw_displayed = self._slice.image.raw
# Keep only the dimensions that correspond to the current view
updated_slice = tuple(
self._updated_slice[index] for index in dims_displayed
)
offset = [axis_slice.start for axis_slice in updated_slice]
if self.contour > 0:
colors_sliced = self._raw_to_displayed(
raw_displayed, data_slice=updated_slice
)
else:
colors_sliced = self._slice.image.view[updated_slice]
# The next line is needed to make the following tests pass in
# napari/_vispy/_tests/:
# - test_vispy_labels_layer.py::test_labels_painting
# - test_vispy_labels_layer.py::test_labels_fill_slice
# See https://github.com/napari/napari/pull/6112/files#r1291613760
# and https://github.com/napari/napari/issues/6185
self._slice.image.view[updated_slice] = colors_sliced
self.events.labels_update(data=colors_sliced, offset=offset)
self._updated_slice = None
def _calculate_contour(
self, labels: np.ndarray, data_slice: tuple[slice, ...]
) -> Optional[np.ndarray]:
"""Calculate the contour of a given label array within the specified data slice.
Parameters
----------
labels : np.ndarray
The label array.
data_slice : Tuple[slice, ...]
The slice of the label array on which to calculate the contour.
Returns
-------
Optional[np.ndarray]
The calculated contour as a boolean mask array.
Returns None if the contour parameter is less than 1,
or if the label array has more than 2 dimensions.
"""
if self.contour < 1:
return None
if labels.ndim > 2:
warnings.warn(
trans._(
'Contours are not displayed during 3D rendering',
deferred=True,
)
)
return None
expanded_slice = expand_slice(data_slice, labels.shape, 1)
sliced_labels = get_contours(
labels[expanded_slice],
self.contour,
self.colormap.background_value,
)
# Remove the latest one-pixel border from the result
delta_slice = tuple(
slice(s1.start - s2.start, s1.stop - s2.start)
for s1, s2 in zip(data_slice, expanded_slice)
)
return sliced_labels[delta_slice]
def _raw_to_displayed(
self, raw, data_slice: Optional[tuple[slice, ...]] = None
) -> np.ndarray:
"""Determine displayed image from a saved raw image and a saved seed.
This function ensures that the 0 label gets mapped to the 0 displayed
pixel.
Parameters
----------
raw : array or int
Raw integer input image.
data_slice : numpy array slice
Slice that specifies the portion of the input image that
should be computed and displayed.
If None, the whole input image will be processed.
Returns
-------
mapped_labels : array
Encoded colors mapped between 0 and 1 to be displayed.
"""
if data_slice is None:
data_slice = tuple(slice(0, size) for size in raw.shape)
labels = raw # for readability
sliced_labels = self._calculate_contour(labels, data_slice)
# lookup function -> self._as_type
if sliced_labels is None:
sliced_labels = labels[data_slice]
return self.colormap._data_to_texture(sliced_labels)
def _update_thumbnail(self):
"""Update the thumbnail with current data and colormap.
This is overridden from _ImageBase because we don't need to do things
like adjusting gamma or changing the data based on the contrast
limits.
"""
if not self.loaded:
# ASYNC_TODO: Do not compute the thumbnail until we are loaded.
# Is there a nicer way to prevent this from getting called?
return
image = self._slice.thumbnail.raw
if self._slice_input.ndisplay == 3 and self.ndim > 2:
# we are only using the current slice so `image` will never be
# bigger than 3. If we are in this clause, it is exactly 3, so we
# use max projection. For labels, ideally we would use "first
# nonzero projection", but we leave that for a future PR. (TODO)
image = np.max(image, axis=0)
imshape = np.array(image.shape[:2])
thumbshape = np.array(self._thumbnail_shape[:2])
raw_zoom_factor = np.min(thumbshape / imshape)
new_shape = np.clip(
raw_zoom_factor * imshape, a_min=1, a_max=thumbshape
)
zoom_factor = tuple(new_shape / imshape)
downsampled = ndi.zoom(image, zoom_factor, prefilter=False, order=0)
color_array = self.colormap.map(downsampled)
color_array[..., 3] *= self.opacity
self.thumbnail = color_array
[docs]
def get_color(self, label):
"""Return the color corresponding to a specific label."""
if label == self.colormap.background_value:
col = None
elif label is None or (
self.show_selected_label and label != self.selected_label
):
col = self.colormap.map(self.colormap.background_value)
else:
col = self.colormap.map(label)
return col
def _get_value_ray(
self,
start_point: Optional[np.ndarray],
end_point: Optional[np.ndarray],
dims_displayed: list[int],
) -> Optional[int]:
"""Get the first non-background value encountered along a ray.
Parameters
----------
start_point : np.ndarray
(n,) array containing the start point of the ray in data coordinates.
end_point : np.ndarray
(n,) array containing the end point of the ray in data coordinates.
dims_displayed : List[int]
The indices of the dimensions currently displayed in the viewer.
Returns
-------
value : Optional[int]
The first non-zero value encountered along the ray. If none
was encountered or the viewer is in 2D mode, None is returned.
"""
if start_point is None or end_point is None:
return None
if len(dims_displayed) == 3:
# only use get_value_ray on 3D for now
# we use dims_displayed because the image slice
# has its dimensions in th same order as the vispy
# Volume
# Account for downsampling in the case of multiscale
# -1 means lowest resolution here.
start_point = (
start_point[dims_displayed]
/ self.downsample_factors[-1][dims_displayed]
)
end_point = (
end_point[dims_displayed]
/ self.downsample_factors[-1][dims_displayed]
)
start_point = cast(np.ndarray, start_point)
end_point = cast(np.ndarray, end_point)
sample_ray = end_point - start_point
length_sample_vector = np.linalg.norm(sample_ray)
n_points = int(2 * length_sample_vector)
sample_points = np.linspace(
start_point, end_point, n_points, endpoint=True
)
im_slice = self._slice.image.raw
# ensure the bounding box is for the proper multiscale level
bounding_box = self._display_bounding_box_at_level(
dims_displayed, self.data_level
)
# the display bounding box is returned as a closed interval
# (i.e. the endpoint is included) by the method, but we need
# open intervals in the code that follows, so we add 1.
bounding_box[:, 1] += 1
clamped = clamp_point_to_bounding_box(
sample_points,
bounding_box,
).astype(int)
values = im_slice[tuple(clamped.T)]
nonzero_indices = np.flatnonzero(values)
if len(nonzero_indices > 0):
# if a nonzer0 value was found, return the first one
return values[nonzero_indices[0]]
return None
def _get_value_3d(
self,
start_point: Optional[np.ndarray],
end_point: Optional[np.ndarray],
dims_displayed: list[int],
) -> Optional[int]:
"""Get the first non-background value encountered along a ray.
Parameters
----------
start_point : np.ndarray
(n,) array containing the start point of the ray in data coordinates.
end_point : np.ndarray
(n,) array containing the end point of the ray in data coordinates.
dims_displayed : List[int]
The indices of the dimensions currently displayed in the viewer.
Returns
-------
value : int
The first non-zero value encountered along the ray. If a
non-zero value is not encountered, returns 0 (the background value).
"""
return (
self._get_value_ray(
start_point=start_point,
end_point=end_point,
dims_displayed=dims_displayed,
)
or 0
)
def _reset_history(self, event=None):
self._undo_history = deque(maxlen=self._history_limit)
self._redo_history = deque(maxlen=self._history_limit)
self._staged_history = []
self._block_history = False
[docs]
@contextmanager
def block_history(self):
"""Context manager to group history-editing operations together.
While in the context, history atoms are grouped together into a
"staged" history. When exiting the context, that staged history is
committed to the undo history queue, and an event is emitted
containing the change.
"""
prev = self._block_history
self._block_history = True
try:
yield
self._commit_staged_history()
finally:
self._block_history = prev
def _commit_staged_history(self):
"""Save staged history to undo history and clear it."""
if self._staged_history:
self._append_to_undo_history(self._staged_history)
self._staged_history = []
def _append_to_undo_history(self, item):
"""Append item to history and emit paint event.
Parameters
----------
item : List[Tuple[ndarray, ndarray, int]]
list of history atoms to append to undo history.
"""
self._undo_history.append(item)
self.events.paint(value=item)
def _save_history(self, value):
"""Save a history "atom" to the undo history.
A history "atom" is a single change operation to the array. A history
*item* is a collection of atoms that were applied together to make a
single change. For example, when dragging and painting, at each mouse
callback we create a history "atom", but we save all those atoms in
a single history item, since we would want to undo one drag in one
undo operation.
Parameters
----------
value : 3-tuple of arrays
The value is a 3-tuple containing:
- a numpy multi-index, pointing to the array elements that were
changed
- the values corresponding to those elements before the change
- the value(s) after the change
"""
self._redo_history.clear()
if self._block_history:
self._staged_history.append(value)
else:
self._append_to_undo_history([value])
def _load_history(self, before, after, undoing=True):
"""Load a history item and apply it to the array.
Parameters
----------
before : list of history items
The list of elements from which we want to load.
after : list of history items
The list of element to which to append the loaded element. In the
case of an undo operation, this is the redo queue, and vice versa.
undoing : bool
Whether we are undoing (default) or redoing. In the case of
redoing, we apply the "after change" element of a history element
(the third element of the history "atom").
See Also
--------
Labels._save_history
"""
if len(before) == 0:
return
history_item = before.pop()
after.append(list(reversed(history_item)))
for prev_indices, prev_values, next_values in reversed(history_item):
values = prev_values if undoing else next_values
self.data[prev_indices] = values
self.refresh()
def undo(self):
self._load_history(
self._undo_history, self._redo_history, undoing=True
)
def redo(self):
self._load_history(
self._redo_history, self._undo_history, undoing=False
)
[docs]
def fill(self, coord, new_label, refresh=True):
"""Replace an existing label with a new label, either just at the
connected component if the `contiguous` flag is `True` or everywhere
if it is `False`, working in the number of dimensions specified by
the `n_edit_dimensions` flag.
Parameters
----------
coord : sequence of float
Position of mouse cursor in image coordinates.
new_label : int
Value of the new label to be filled in.
refresh : bool
Whether to refresh view slice or not. Set to False to batch paint
calls.
"""
int_coord = tuple(np.round(coord).astype(int))
# If requested fill location is outside data shape then return
if np.any(np.less(int_coord, 0)) or np.any(
np.greater_equal(int_coord, self.data.shape)
):
return
# If requested new label doesn't change old label then return
old_label = np.asarray(self.data[int_coord]).item()
if old_label == new_label or (
self.preserve_labels
and old_label != self.colormap.background_value
):
return
dims_to_fill = sorted(
self._slice_input.order[-self.n_edit_dimensions :]
)
data_slice_list = list(int_coord)
for dim in dims_to_fill:
data_slice_list[dim] = slice(None)
data_slice = tuple(data_slice_list)
labels = np.asarray(self.data[data_slice])
slice_coord = tuple(int_coord[d] for d in dims_to_fill)
matches = labels == old_label
if self.contiguous:
# if contiguous replace only selected connected component
labeled_matches, num_features = ndi.label(matches)
if num_features != 1:
match_label = labeled_matches[slice_coord]
matches = np.logical_and(
matches, labeled_matches == match_label
)
match_indices_local = np.nonzero(matches)
if self.ndim not in {2, self.n_edit_dimensions}:
n_idx = len(match_indices_local[0])
match_indices = []
j = 0
for d in data_slice:
if isinstance(d, slice):
match_indices.append(match_indices_local[j])
j += 1
else:
match_indices.append(np.full(n_idx, d, dtype=np.intp))
else:
match_indices = match_indices_local
match_indices = _coerce_indices_for_vectorization(
self.data, match_indices
)
self.data_setitem(match_indices, new_label, refresh)
def _draw(self, new_label, last_cursor_coord, coordinates):
"""Paint into coordinates, accounting for mode and cursor movement.
The draw operation depends on the current mode of the layer.
Parameters
----------
new_label : int
value of label to paint
last_cursor_coord : sequence
last painted cursor coordinates
coordinates : sequence
new cursor coordinates
"""
if coordinates is None:
return
interp_coord = interpolate_coordinates(
last_cursor_coord, coordinates, self.brush_size
)
for c in interp_coord:
if (
self._slice_input.ndisplay == 3
and self.data[tuple(np.round(c).astype(int))] == 0
):
continue
if self._mode in [Mode.PAINT, Mode.ERASE]:
self.paint(c, new_label, refresh=False)
elif self._mode == Mode.FILL:
self.fill(c, new_label, refresh=False)
self._partial_labels_refresh()
[docs]
def paint(self, coord, new_label, refresh=True):
"""Paint over existing labels with a new label, using the selected
brush shape and size, either only on the visible slice or in all
n dimensions.
Parameters
----------
coord : sequence of int
Position of mouse cursor in image coordinates.
new_label : int
Value of the new label to be filled in.
refresh : bool
Whether to refresh view slice or not. Set to False to batch paint
calls.
"""
shape, dims_to_paint = self._get_shape_and_dims_to_paint()
paint_scale = np.array(
[self.scale[i] for i in dims_to_paint], dtype=float
)
slice_coord = [int(np.round(c)) for c in coord]
if self.n_edit_dimensions < self.ndim:
coord_paint = [coord[i] for i in dims_to_paint]
else:
coord_paint = coord
# Ensure circle doesn't have spurious point
# on edge by keeping radius as ##.5
radius = np.floor(self.brush_size / 2) + 0.5
mask_indices = sphere_indices(radius, tuple(paint_scale))
mask_indices = mask_indices + np.round(np.array(coord_paint)).astype(
int
)
self._paint_indices(
mask_indices, new_label, shape, dims_to_paint, slice_coord, refresh
)
[docs]
def paint_polygon(self, points, new_label):
"""Paint a polygon over existing labels with a new label.
Parameters
----------
points : list of coordinates
List of coordinates of the vertices of a polygon.
new_label : int
Value of the new label to be filled in.
"""
shape, dims_to_paint = self._get_shape_and_dims_to_paint()
if len(dims_to_paint) != 2:
raise NotImplementedError(
'Polygon painting is implemented only in 2D.'
)
points = np.array(points, dtype=int)
slice_coord = points[0].tolist()
points2d = points[:, dims_to_paint]
polygon_mask = polygon2mask(shape, points2d)
mask_indices = np.argwhere(polygon_mask)
self._paint_indices(
mask_indices,
new_label,
shape,
dims_to_paint,
slice_coord,
refresh=True,
)
def _paint_indices(
self,
mask_indices,
new_label,
shape,
dims_to_paint,
slice_coord=None,
refresh=True,
):
"""Paint over existing labels with a new label, using the selected
mask indices, either only on the visible slice or in all n dimensions.
Parameters
----------
mask_indices : numpy array of integer coordinates
Mask to paint represented by an array of its coordinates.
new_label : int
Value of the new label to be filled in.
shape : list
The label data shape upon which painting is performed.
dims_to_paint : list
List of dimensions of the label data that are used for painting.
refresh : bool
Whether to refresh view slice or not. Set to False to batch paint
calls.
"""
dims_not_painted = sorted(
self._slice_input.order[: -self.n_edit_dimensions]
)
# discard candidate coordinates that are out of bounds
mask_indices = indices_in_shape(mask_indices, shape)
# Transfer valid coordinates to slice_coord,
# or expand coordinate if 3rd dim in 2D image
slice_coord_temp = list(mask_indices.T)
if self.n_edit_dimensions < self.ndim:
for j, i in enumerate(dims_to_paint):
slice_coord[i] = slice_coord_temp[j]
for i in dims_not_painted:
slice_coord[i] = slice_coord[i] * np.ones(
mask_indices.shape[0], dtype=int
)
else:
slice_coord = slice_coord_temp
slice_coord = _coerce_indices_for_vectorization(self.data, slice_coord)
# slice coord is a tuple of coordinate arrays per dimension
# subset it if we want to only paint into background/only erase
# current label
if self.preserve_labels:
if new_label == self.colormap.background_value:
keep_coords = self.data[slice_coord] == self.selected_label
else:
keep_coords = (
self.data[slice_coord] == self.colormap.background_value
)
slice_coord = tuple(sc[keep_coords] for sc in slice_coord)
self.data_setitem(slice_coord, new_label, refresh)
def _get_shape_and_dims_to_paint(self) -> tuple[list, list]:
dims_to_paint = sorted(self._get_dims_to_paint())
shape = list(self.data.shape)
if self.n_edit_dimensions < self.ndim:
shape = [shape[i] for i in dims_to_paint]
return shape, dims_to_paint
def _get_dims_to_paint(self) -> list:
return list(self._slice_input.order[-self.n_edit_dimensions :])
def _get_pt_not_disp(self) -> dict[int, int]:
"""
Get indices of current visible slice.
"""
slice_input = self._slice.slice_input
point = np.round(
self.world_to_data(slice_input.world_slice.point)
).astype(int)
return {dim: point[dim] for dim in slice_input.not_displayed}
[docs]
def data_setitem(self, indices, value, refresh=True):
"""Set `indices` in `data` to `value`, while writing to edit history.
Parameters
----------
indices : tuple of arrays of int
Indices in data to overwrite. Must be a tuple of arrays of length
equal to the number of data dimensions. (Fancy indexing in [2]_).
value : int or array of int
New label value(s). If more than one value, must match or
broadcast with the given indices.
refresh : bool, default True
whether to refresh the view, by default True
References
----------
.. [2] https://numpy.org/doc/stable/user/basics.indexing.html
"""
changed_indices = self.data[indices] != value
indices = tuple(x[changed_indices] for x in indices)
if isinstance(value, Sequence):
value = np.asarray(value, dtype=self._slice.image.raw.dtype)
else:
value = self._slice.image.raw.dtype.type(value)
# Resize value array to remove unchanged elements
if isinstance(value, np.ndarray):
value = value[changed_indices]
if not indices or indices[0].size == 0:
return
self._save_history(
(
indices,
np.array(self.data[indices], copy=True),
value,
)
)
# update the labels image
self.data[indices] = value
pt_not_disp = self._get_pt_not_disp()
displayed_indices = index_in_slice(
indices, pt_not_disp, self._slice.slice_input.order
)
if isinstance(value, np.ndarray):
visible_values = value[elements_in_slice(indices, pt_not_disp)]
else:
visible_values = value
if not ( # if not a numpy array or numpy-backed xarray
isinstance(self.data, np.ndarray)
or isinstance(getattr(self.data, 'data', None), np.ndarray)
):
# In the absence of slicing, the current slice becomes
# invalidated by data_setitem; only in the special case of a NumPy
# array, or a NumPy-array-backed Xarray, is the slice a view and
# therefore updated automatically.
# For other types, we update it manually here.
self._slice.image.raw[displayed_indices] = visible_values
# tensorstore and xarray do not return their indices in
# np.ndarray format, so they need to be converted explicitly
if not isinstance(self.data, np.ndarray):
indices = [np.array(x).flatten() for x in indices]
updated_slice = tuple(
[
slice(min(axis_indices), max(axis_indices) + 1)
for axis_indices in indices
]
)
if self.contour > 0:
# Expand the slice by 1 pixel as the changes can go beyond
# the original slice because of the morphological dilation
# (1 pixel because get_countours always applies 1 pixel dilation)
updated_slice = expand_slice(updated_slice, self.data.shape, 1)
else:
# update data view
self._slice.image.view[displayed_indices] = (
self.colormap._data_to_texture(visible_values)
)
if self._updated_slice is None:
self._updated_slice = updated_slice
else:
self._updated_slice = tuple(
[
slice(min(s1.start, s2.start), max(s1.stop, s2.stop))
for s1, s2 in zip(updated_slice, self._updated_slice)
]
)
if refresh is True:
self._partial_labels_refresh()
[docs]
def get_status(
self,
position: Optional[npt.ArrayLike] = None,
*,
view_direction: Optional[npt.ArrayLike] = None,
dims_displayed: Optional[list[int]] = None,
world: bool = False,
) -> dict:
"""Status message information of the data at a coordinate position.
Parameters
----------
position : tuple
Position in either data or world coordinates.
view_direction : Optional[np.ndarray]
A unit vector giving the direction of the ray in nD world coordinates.
The default value is None.
dims_displayed : Optional[List[int]]
A list of the dimensions currently being displayed in the viewer.
The default value is None.
world : bool
If True the position is taken to be in world coordinates
and converted into data coordinates. False by default.
Returns
-------
source_info : dict
Dict containing a information that can be used in a status update.
"""
if position is not None:
value = self.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
else:
value = None
source_info = self._get_source_info()
pos = position
if pos is not None:
pos = np.asarray(pos)[-self.ndim :]
source_info['coordinates'] = generate_layer_coords_status(pos, value)
# if this labels layer has properties
properties = self._get_properties(
position,
view_direction=np.asarray(view_direction),
dims_displayed=dims_displayed,
world=world,
)
if properties:
source_info['coordinates'] += '; ' + ', '.join(properties)
return source_info
def _get_tooltip_text(
self,
position,
*,
view_direction: Optional[np.ndarray] = None,
dims_displayed: Optional[list[int]] = None,
world: bool = False,
):
"""
tooltip message of the data at a coordinate position.
Parameters
----------
position : tuple
Position in either data or world coordinates.
view_direction : Optional[np.ndarray]
A unit vector giving the direction of the ray in nD world coordinates.
The default value is None.
dims_displayed : Optional[List[int]]
A list of the dimensions currently being displayed in the viewer.
The default value is None.
world : bool
If True the position is taken to be in world coordinates
and converted into data coordinates. False by default.
Returns
-------
msg : string
String containing a message that can be used as a tooltip.
"""
return '\n'.join(
self._get_properties(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
)
def _get_properties(
self,
position,
*,
view_direction: Optional[np.ndarray] = None,
dims_displayed: Optional[list[int]] = None,
world: bool = False,
) -> list:
if len(self._label_index) == 0 or self.features.shape[1] == 0:
return []
value = self.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
# if the cursor is not outside the image or on the background
if value is None:
return []
label_value = value[1] if self.multiscale else value
if label_value not in self._label_index:
return [trans._('[No Properties]')]
idx = self._label_index[label_value]
return [
f'{k}: {v[idx]}'
for k, v in self.features.items()
if k != 'index'
and len(v) > idx
and v[idx] is not None
and not (isinstance(v[idx], float) and np.isnan(v[idx]))
]
def _coerce_indices_for_vectorization(array, indices: list) -> tuple:
"""Coerces indices so that they can be used for vectorized indexing in the given data array."""
if _is_array_type(array, 'xarray.DataArray'):
# Fix indexing for xarray if necessary
# See http://xarray.pydata.org/en/stable/indexing.html#vectorized-indexing
# for difference from indexing numpy
try:
import xarray as xr
except ModuleNotFoundError:
pass
else:
return tuple(xr.DataArray(i) for i in indices)
return tuple(indices)