from __future__ import annotations
import contextlib
import itertools
import typing
import warnings
from collections.abc import Iterable
from functools import cached_property
from typing import TYPE_CHECKING, Literal
import numpy as np
import pint
from napari.components.dims import RangeTuple
from napari.layers import Layer
from napari.layers.utils.layer_utils import Extent, LayerListExtent
from napari.utils.events import Event
from napari.utils.events.containers import SelectableEventedList
from napari.utils.naming import inc_name_count
from napari.utils.transforms._units import get_units_from_name
from napari.utils.translations import trans
if TYPE_CHECKING:
from npe2.manifest.io import WriterContribution
from typing_extensions import Self
__all__ = ('LayerList',)
def get_name(layer: Layer) -> str:
"""Return the name of a layer."""
return layer.name
[docs]
class LayerList(SelectableEventedList[Layer]):
"""List-like layer collection with built-in reordering and callback hooks.
Parameters
----------
data : iterable
Iterable of napari.layer.Layer
Events
~~~~~~
inserting : (index: int)
emitted before an item is inserted at ``index``
inserted : (index: int, value: T)
emitted after ``value`` is inserted at ``index``
removing : (index: int)
emitted before an item is removed at ``index``
removed : (index: int, value: T)
emitted after ``value`` is removed at ``index``
moving : (index: int, new_index: int)
emitted before an item is moved from ``index`` to ``new_index``
moved : (index: int, new_index: int, value: T)
emitted after ``value`` is moved from ``index`` to ``new_index``
changed : (index: int, old_value: T, value: T)
emitted when item at ``index`` is changed from ``old_value`` to
``value``
changed <OVERLOAD> : (index: slice, old_value: List[_T], value: List[_T])
emitted when items at ``index``es are changed from ``old_value`` to
``value``
reordered : (value: self)
emitted when the list is reordered (eg. moved/reversed).
renamed : (index: int)
emitted when a layer in the list is renamed, providing the index
of the layer.
selection.events.changed : (added: Set[_T], removed: Set[_T])
emitted when the set changes, includes item(s) that have been added
and/or removed from the set.
selection.events.active : (value: _T)
emitted when the current item has changed.
selection.events._current : (value: _T)
emitted when the current item has changed. (Private event)
units: (value: tuple[pint.Unit, ...] | None)
emitted when the global overriding units for the layer list is changed.
Notes
-----
Note that ``changed`` events are only emitted when an element of the
list changes, *not* when the list itself changes (for example when items
are added or removed). For example, ``layerlist.append(layer)`` will emit
an ``inserted`` event. ``layerlist[idx] = layer`` *will* emit a ``changed``
event.
However, the layerlist does not have a way of detecting when an object in
the list is modified in-place. Therefore, although
``layerlist[idx].scale = [2, 1, 1]`` changes the *value* of the layer at
position ``idx``, a ``changed`` event will not be emitted.
Examples
--------
>>> import napari
>>> from skimage.data import astronaut
>>> viewer = napari.Viewer()
>>> event_list = []
Connect to the event list:
>>> viewer.layers.events.connect(event_list.append)
<built-in method append of list object at 0x7fc225764780>
>>> viewer.add_image(astronaut())
<Image layer 'Image' at 0x7f0fe7fa9e90>
>>> viewer.add_points()
<Points layer 'Points' at 0x7f102f962350>
>>> viewer.layers
[<Image layer 'Image' at 0x7f0fe7fa9e90>, <Points layer 'Points' at 0x7f102f962350>]
Inspecting the list of events, we see:
>>> event_list[0].type
'inserting'
>>> viewer.layers.pop(1)
<Points layer 'Points' at 0x7f102f962350>
>>> event_list[-1].type
'removed'
"""
def __init__(self, data=()) -> None:
self._units = None
super().__init__(
data=data,
basetype=Layer,
lookup={str: get_name},
)
self.events.add(
begin_batch=Event, end_batch=Event, renamed=Event, units=Event
)
self.events.inserted.connect(self._on_layer_inserted)
self.events.removed.connect(self._on_layer_removed)
self._create_contexts()
def _on_layer_inserted(self, event: Event):
"""Connect to layer events when a new layer is inserted."""
layer = event.value
layer.events.name.connect(self._on_layer_renamed)
def _on_layer_removed(self, event: Event):
"""Disconnect from layer events when a layer is removed."""
layer = event.value
layer.events.name.disconnect(self._on_layer_renamed)
def _on_layer_renamed(self, event: Event):
"""Re-emit layer name changes from a layer as a LayerList event."""
layer = event.source
index = self.index(layer)
self.events.renamed(index=index)
def _create_contexts(self):
"""Create contexts to manage enabled/visible action/menu states.
Connects LayerList and Selection[Layer] to their context keys to allow
actions and menu items (in the GUI) to be dynamically enabled/disabled
and visible/hidden based on the state of layers in the list.
"""
# TODO: figure out how to move this context creation bit.
# Ideally, the app should be aware of the layerlist, but not vice versa.
# This could probably be done by having the layerlist emit events that
# the app connects to, then the `_ctx` object would live on the app,
# (not here)
from napari._app_model.context import create_context
from napari._app_model.context._layerlist_context import (
LayerListContextKeys,
LayerListSelectionContextKeys,
)
self._ctx = create_context(self)
if self._ctx is not None: # happens during Viewer type creation
self._ctx_keys = LayerListContextKeys(self._ctx)
self.events.inserted.connect(self._ctx_keys.update)
self.events.removed.connect(self._ctx_keys.update)
self._selection_ctx_keys = LayerListSelectionContextKeys(self._ctx)
self.selection.events.changed.connect(
self._selection_ctx_keys.update
)
def _process_delete_item(self, item: Layer):
super()._process_delete_item(item)
item.events.extent.disconnect(self._clean_cache)
item.events._extent_augmented.disconnect(self._clean_cache)
self._clean_cache()
def _clean_cache(self):
cached_properties = (
'extent',
'_extent_world',
'_extent_world_augmented',
'_step_size',
)
[self.__dict__.pop(p, None) for p in cached_properties]
def __newlike__(self, data):
return LayerList(data)
def _coerce_name(self, name, layer=None):
"""Coerce a name into a unique equivalent.
Parameters
----------
name : str
Original name.
layer : napari.layers.Layer, optional
Layer for which name is generated.
Returns
-------
new_name : str
Coerced, unique name.
"""
existing_layers = {x.name for x in self if x is not layer}
for _ in range(len(self)):
if name in existing_layers:
name = inc_name_count(name)
return name
def _update_name(self, event):
"""Coerce name of the layer in `event.layer`."""
layer = event.source
layer.name = self._coerce_name(layer.name, layer)
def _ensure_unique(self, values, allow=()):
bad = set(self._list) - set(allow)
values = tuple(values) if isinstance(values, Iterable) else (values,)
for v in values:
if v in bad:
raise ValueError(
trans._(
"Layer '{v}' is already present in layer list",
deferred=True,
v=v,
)
)
return values
@typing.overload
def __getitem__(self, item: int | str) -> Layer: ...
@typing.overload
def __getitem__(self, item: slice) -> Self: ...
def __getitem__(self, item):
return super().__getitem__(item)
def __setitem__(self, key, value):
old = self._list[key]
if isinstance(key, slice):
value = self._ensure_unique(value, old)
elif isinstance(key, int):
(value,) = self._ensure_unique((value,), (old,))
super().__setitem__(key, value)
[docs]
def insert(self, index: int, value: Layer):
"""Insert ``value`` before index."""
(value,) = self._ensure_unique((value,))
new_layer = self._type_check(value)
new_layer.name = self._coerce_name(new_layer.name)
self._clean_cache()
new_layer.events.extent.connect(self._clean_cache)
new_layer.events._extent_augmented.connect(self._clean_cache)
new_layer.events.data.connect(
self._trigger_check_ndim_and_maybe_clean_units
)
super().insert(index, new_layer)
self._check_ndim_and_maybe_clean_units(new_layer.ndim)
[docs]
def remove_selected(self):
"""Remove selected layers from LayerList, but first unlink them."""
if not self.selection:
return
self.unlink_layers(self.selection)
with self.batched_update():
super().remove_selected()
[docs]
def toggle_selected_visibility(self):
"""Toggle visibility of selected layers"""
for layer in self.selection:
layer.visible = not layer.visible
@cached_property
def _extent_world(
self,
) -> np.ndarray[tuple[Literal[2], int], np.dtype[np.float64]]:
"""Extent of layers in world coordinates.
Default to 2D with (-0.5, 511.5) min/ max values if no data is present.
Corresponds to pixels centered at [0, ..., 511].
Returns
-------
extent_world : array, shape (2, D)
"""
return self._get_extent_world(
[layer.extent for layer in self], units=self.units
)
@cached_property
def _extent_world_augmented(
self,
) -> np.ndarray[tuple[Literal[2], int], np.dtype[np.float64]]:
"""Extent of layers in world coordinates.
Default to 2D with (-0.5, 511.5) min/ max values if no data is present.
Corresponds to pixels centered at [0, ..., 511].
Returns
-------
extent_world : array, shape (2, D)
"""
return self._get_extent_world(
[layer._extent_augmented for layer in self],
augmented=True,
units=self.units,
)
def _get_min_and_max(self, mins_list, maxes_list):
# Reverse dimensions since it is the last dimensions that are
# displayed.
mins_list = [mins[::-1] for mins in mins_list]
maxes_list = [maxes[::-1] for maxes in maxes_list]
with warnings.catch_warnings():
# Taking the nanmin and nanmax of an axis of all nan
# raises a warning and returns nan for that axis
# as we have do an explicit nan_to_num below this
# behaviour is acceptable and we can filter the
# warning
warnings.filterwarnings(
'ignore',
message=str(
trans._('All-NaN axis encountered', deferred=True)
),
)
min_v = np.nanmin(
list(itertools.zip_longest(*mins_list, fillvalue=np.nan)),
axis=1,
)
max_v = np.nanmax(
list(itertools.zip_longest(*maxes_list, fillvalue=np.nan)),
axis=1,
)
# 512 element default extent as documented in `_get_extent_world`
min_v = np.nan_to_num(min_v, nan=-0.5)
max_v = np.nan_to_num(max_v, nan=511.5)
# switch back to original order
return min_v[::-1], max_v[::-1]
def _get_extent_world(
self,
layer_extent_list,
augmented: bool = False,
units: tuple[pint.Unit, ...] | None = None,
) -> np.ndarray[tuple[Literal[2], int], np.dtype[np.float32]]:
"""Extent of layers in world coordinates.
Default to 2D image-like with (0, 511) min/ max values if no data is present.
Corresponds to image with 512 pixels in each dimension.
Returns
-------
extent_world : array, shape (2, D)
"""
if len(self) == 0:
min_v = np.zeros(self.ndim)
max_v = np.full(self.ndim, 511.0)
# image-like augmented extent is actually expanded by 0.5
if augmented:
min_v -= 0.5
max_v += 0.5
else:
if units is None:
extrema = [extent.world for extent in layer_extent_list]
else:
extrema = [
self._convert_scale_between_units(
extent.world.T, extent.units, units
).T
for extent in layer_extent_list
]
mins = [e[0] for e in extrema]
maxs = [e[1] for e in extrema]
min_v, max_v = self._get_min_and_max(mins, maxs)
return np.vstack([min_v, max_v])
@cached_property
def _step_size(self) -> np.ndarray:
"""Ideal step size between planes in world coordinates.
Computes the best step size that allows all data planes to be
sampled if moving through the full range of world coordinates.
The current implementation just takes the minimum scale.
Returns
-------
step_size : array, shape (D,)
"""
return self._get_step_size([layer.extent for layer in self])
def _step_size_from_scales(self, scales):
# Reverse order so last axes of scale with different ndim are aligned
scales = [scale[::-1] for scale in scales]
full_scales = list(
np.array(list(itertools.zip_longest(*scales, fillvalue=np.nan)))
)
# restore original order
return np.nanmin(full_scales, axis=1)[::-1]
@staticmethod
def _convert_scale_between_units(
scale: np.ndarray[tuple[int], np.dtype[np.float32]],
from_units: tuple[pint.Unit, ...],
to_units: tuple[pint.Unit, ...],
) -> np.ndarray:
"""Convert units of scale to target units.
Parameters
----------
scale : np.ndarray
Scale to convert.
from_units : tuple[pint.Unit, ...]
Units of the scale.
to_units : tuple[pint.Unit, ...]
Target units.
Returns
-------
np.ndarray
Converted scale.
"""
clipped_target_units = to_units[-len(from_units) :]
return np.array(
[
(s * u).to(cu).magnitude
for s, u, cu in zip(
scale, from_units, clipped_target_units, strict=False
)
]
)
def _get_step_size(
self,
layer_extent_list: list[Extent],
units: tuple[pint.Unit, ...] | None = None,
):
if len(layer_extent_list) == 0:
return np.ones(self.ndim)
if units is None:
scales = [extent.step for extent in layer_extent_list]
else:
scales = [
self._convert_scale_between_units(
extent.step, extent.units, units
)
for extent in layer_extent_list
]
return self._step_size_from_scales(scales)
[docs]
def get_extent(self, layers: Iterable[Layer]) -> LayerListExtent:
"""
Return extent for a given layer list.
Extent bounds are inclusive. This function is useful for calculating the extent
of a subset of layers when preparing and updating some supplementary layers.
For example see the cross Vectors layer in the `multiple_viewer_widget` example.
Parameters
----------
layers : list of Layer
list of layers for which extent should be calculated
Returns
-------
extent : LayerListExtent
extent for selected layers
"""
extent_list = [layer.extent for layer in layers]
units = self._units or self._get_units(extent_list)
return LayerListExtent(
data=None,
world=self._get_extent_world(extent_list, units=units),
step=self._get_step_size(extent_list, units=units),
units=units,
)
@staticmethod
def _get_units(
layers_extent: list[Extent],
) -> tuple[pint.Unit, ...] | None:
"""Get units for a given list of layer extents.
Given extents could be of all layers in the `LayerList` or only a subset.
Parameters
----------
layers_extent : list of layer Extent
list of layer extents for which units should be calculated
Returns
-------
units : list of pint.Unit or None
consistent units for given layer extents.
If cannot be determined, returns None.
"""
if not layers_extent:
return None
reg = pint.get_application_registry()
units = ()
dimensionality_to_unit: dict[pint.util.UnitsContainer, pint.Unit] = {}
# for each dimensionality of units (time, length, mass, etc.)
# we will store the 'smallest' unit (e.g for nm and um, we will choose nm)
for extent in layers_extent:
update_u_dkt(extent.units, dimensionality_to_unit, reg)
for u1_, u2_ in zip(extent.units[::-1], units[::-1], strict=False):
if u1_.dimensionality != u2_.dimensionality:
return None
if len(extent.units) > len(units):
units = extent.units
if not units:
return None # pragma: no cover
return tuple(dimensionality_to_unit[u.dimensionality] for u in units)
@cached_property
def extent(self) -> LayerListExtent:
"""
Extent of layers in data and world coordinates.
Extent bounds are inclusive. See Layer.extent for a detailed explanation
of how extents are calculated.
"""
return self.get_extent(list(self))
@property
def _ranges(self) -> tuple[RangeTuple, ...]:
"""Get ranges for Dims.range in world coordinates."""
ext = self.extent
return tuple(
RangeTuple(*x)
for x in zip(ext.world[0], ext.world[1], ext.step, strict=False)
)
@property
def units(self) -> tuple[pint.Unit, ...] | None:
"""Units of layers in world coordinates.
Returns
-------
units : tuple[pint.Unit, ...] or None
Units of layers in world coordinates.
"""
if self.extent.units is None:
return None
return self._units or self.extent.units
@units.setter
def units(self, units: tuple[pint.Unit, ...] | None):
"""Set override of units of layers in world coordinates.
Parameters
----------
units : tuple[pint.Unit, ...] or None
Units to set for layers in world coordinates. If None, units are not changed.
"""
if units is None:
self._units = None
self._clean_cache()
self.events.units(value=self.units)
return
if self.extent.units is None:
raise ValueError(
'Cannot set units when layers have inconsistent dimensionality.'
)
if len(units) < self.ndim:
raise ValueError(
'Number of units must be at least the number of dimensions.'
)
units = get_units_from_name(units)
for i, (new_unit, old_unit) in enumerate(
zip(units[::-1], self.units[::-1], strict=False), start=1
):
if new_unit.dimensionality != old_unit.dimensionality:
text = (
f'On axis -{i} units must be consistent across all dimensions.'
f'The new dimensionality is {new_unit.dimensionality} '
f'while the previous dimensionality was {old_unit.dimensionality}.'
)
raise ValueError(text)
self._units = units
self._clean_cache()
self.events.units(value=self.units)
def _trigger_check_ndim_and_maybe_clean_units(self, event: Event):
"""Trigger check of new layer's ndim and maybe clean units."""
self._check_ndim_and_maybe_clean_units(event.source.ndim)
def _check_ndim_and_maybe_clean_units(self, ndim: int):
if self._units is not None and ndim > len(self._units):
warnings.warn(
'New layer has more dimensions than the current units, dropping units override.',
stacklevel=2,
)
self.units = None
@property
def ndim(self) -> int:
"""Maximum dimensionality of layers.
Defaults to 2 if no data is present.
Returns
-------
ndim : int
"""
return max((layer.ndim for layer in self), default=2)
def _link_layers(
self,
method: str,
layers: Iterable[str | Layer] | None = None,
attributes: Iterable[str] = (),
):
# adding this method here allows us to emit an event when
# layers in this group are linked/unlinked. Which is necessary
# for updating context
from napari.layers.utils import _link_layers
if layers is not None:
layers = [self[x] if isinstance(x, str) else x for x in layers] # type: ignore
else:
layers = self
getattr(_link_layers, method)(layers, attributes)
self.selection.events.changed(added={}, removed={})
[docs]
def link_layers(
self,
layers: Iterable[str | Layer] | None = None,
attributes: Iterable[str] = (),
):
"""
Links the selected layers.
Once layers are linked, any action performed on one layer will be
performed on all linked layers at the same time.
"""
return self._link_layers('link_layers', layers, attributes)
[docs]
def unlink_layers(
self,
layers: Iterable[str | Layer] | None = None,
attributes: Iterable[str] = (),
):
"""Unlinks previously linked layers.
Changes to one of the layer's properties no longer result in the same
changes to the previously linked layers.
"""
return self._link_layers('unlink_layers', layers, attributes)
[docs]
def save(
self,
path: str,
*,
selected: bool = False,
plugin: str | None = None,
_writer: WriterContribution | None = None,
) -> list[str]:
"""Save all or only selected layers to a path using writer plugins.
If ``plugin`` is provided, we attempt to write with that plugin.
If ``plugin`` is not provided, we call the first compatible writer for
the given layer(s) and path.
If any errors occur during writing, they are raised. If the given ``plugin``
does not provide a compatible writer or does not write any files, or
if there are no compatible writers available, a warning will be issued.
Parameters
----------
path : str
A filepath, directory, or URL to open. Extensions may be used to
specify output format (provided a plugin is available for the
requested format).
selected : bool
Optional flag to only save selected layers. False by default.
plugin : str, optional
Name of the plugin to use for saving. If None then the first compatible
writer (if one exists), will be used.
_writer : WriterContribution, optional
private: npe2 specific writer override.
Returns
-------
list of str
File paths of any files that were written.
"""
from napari.plugins.io import save_layers
layers = (
[x for x in self if x in self.selection]
if selected
else list(self)
)
if selected:
msg = trans._('No layers selected', deferred=True)
else:
msg = trans._('No layers to save', deferred=True)
if not layers:
warnings.warn(msg)
return []
return save_layers(path, layers, plugin=plugin, _writer=_writer)
[docs]
def clear(self):
"""Remove all layers from viewer."""
with self.batched_update():
super().clear()
@contextlib.contextmanager
def batched_update(self):
try:
self.events.begin_batch()
yield
finally:
self.events.end_batch()
def cmp(u1: pint.Unit, u2: pint.Unit, registry: pint.UnitRegistry) -> bool:
"""
Compare two units using pint register
Parameters
----------
u1: pint.Unit
first unit to compare
u2: pint.Unit
second unit to compare
registry: pint.UnitRegistry
unit registry used for unit comparison
Returns
-------
bool
True if u1 is smaller than u2, False otherwise
"""
return registry.get_base_units(u1)[0] < registry.get_base_units(u2)[0]
def update_u_dkt(
units_l: Iterable[pint.Unit],
dimensionality_to_unit: dict[pint.util.UnitsContainer, pint.Unit],
registry: pint.UnitRegistry,
) -> None:
"""Update the dimensionality_to_unit dictionary with the smallest units.
Iterate over the units in units_t and for each dimensionality,
check if it is already in the dimensionality_to_unit dictionary.
If it is not, or if the current unit is 'smaller' than the existing
unit (as determined by the cmp function), update the dictionary
Parameters
----------
units_l : iterable of pint.Unit
sequence of units to be checked and possibly updated
dimensionality_to_unit : dict
dictionary mapping dimensionality to the smallest unit
registry : pint.UnitRegistry
unit registry used for unit comparison
"""
for u in units_l:
dim = u.dimensionality
if not (
dim in dimensionality_to_unit
and cmp(dimensionality_to_unit[dim], u, registry)
):
dimensionality_to_unit[dim] = u
