scatter.py

from typing import List, Optional, Tuple

import matplotlib.colors as mcolor
import napari
import numpy as np
from magicgui import magicgui
from magicgui.widgets import ComboBox

from .base import NapariMPLWidget
from .util import Interval

__all__ = ["ScatterWidget", "FeaturesScatterWidget", "FeaturesHistogramWidget"]


class ScatterBaseWidget(NapariMPLWidget):
    # opacity value for the markers
    _marker_alpha = 0.5

    # flag set to True if histogram should be used
    # for plotting large points
    _histogram_for_large_data = True

    # if the number of points is greater than this value,
    # the scatter is plotted as a 2dhist
    _threshold_to_switch_to_histogram = 500

    def __init__(self, napari_viewer: napari.viewer.Viewer):
        super().__init__(napari_viewer)

        self.axes = self.canvas.figure.subplots()
        self.update_layers(None)

    def clear(self) -> None:
        """
        Clear the axes.
        """
        self.axes.clear()

    def draw(self) -> None:
        """
        Scatter the currently selected layers.
        """
        data, x_axis_name, y_axis_name = self._get_data()

        if len(data) == 0:
            # don't plot if there isn't data
            return

        if self._histogram_for_large_data and (
            data[0].size > self._threshold_to_switch_to_histogram
        ):
            self.axes.hist2d(
                data[0].ravel(),
                data[1].ravel(),
                bins=100,
                norm=mcolor.LogNorm(),
            )
        else:
            self.axes.scatter(data[0], data[1], alpha=self._marker_alpha)

        self.axes.set_xlabel(x_axis_name)
        self.axes.set_ylabel(y_axis_name)

    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
        """Get the plot data.

        This must be implemented on the subclass.

        Returns
        -------
        data : np.ndarray
            The list containing the scatter plot data.
        x_axis_name : str
            The label to display on the x axis
        y_axis_name: str
            The label to display on the y axis
        """
        raise NotImplementedError


class ScatterWidget(ScatterBaseWidget):
    """
    Widget to display scatter plot of two similarly shaped image layers.

    If there are more than 500 data points, a 2D histogram is displayed instead
    of a scatter plot, to avoid too many scatter points.
    """

    n_layers_input = Interval(2, 2)
    input_layer_types = (napari.layers.Image,)

    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
        """Get the plot data.

        Returns
        -------
        data : List[np.ndarray]
            List contains the in view slice of X and Y axis images.
        x_axis_name : str
            The title to display on the x axis
        y_axis_name: str
            The title to display on the y axis
        """
        data = [layer.data[self.current_z] for layer in self.layers]
        x_axis_name = self.layers[0].name
        y_axis_name = self.layers[1].name

        return data, x_axis_name, y_axis_name


class FeaturesScatterWidget(ScatterBaseWidget):
    n_layers_input = Interval(1, 1)
    # All layers that have a .features attributes
    input_layer_types = (
        napari.layers.Labels,
        napari.layers.Points,
        napari.layers.Shapes,
        napari.layers.Tracks,
        napari.layers.Vectors,
    )

    def __init__(self, napari_viewer: napari.viewer.Viewer):
        super().__init__(napari_viewer)
        self._key_selection_widget = magicgui(
            self._set_axis_keys,
            x_axis_key={"choices": self._get_valid_axis_keys},
            y_axis_key={"choices": self._get_valid_axis_keys},
            call_button="plot",
        )

        self.layout().addWidget(self._key_selection_widget.native)

    @property
    def x_axis_key(self) -> Optional[str]:
        """Key to access x axis data from the FeaturesTable"""
        return self._x_axis_key

    @x_axis_key.setter
    def x_axis_key(self, key: Optional[str]) -> None:
        self._x_axis_key = key
        self._draw()

    @property
    def y_axis_key(self) -> Optional[str]:
        """Key to access y axis data from the FeaturesTable"""
        return self._y_axis_key

    @y_axis_key.setter
    def y_axis_key(self, key: Optional[str]) -> None:
        self._y_axis_key = key
        self._draw()

    def _set_axis_keys(self, x_axis_key: str, y_axis_key: str) -> None:
        """Set both axis keys and then redraw the plot"""
        self._x_axis_key = x_axis_key
        self._y_axis_key = y_axis_key
        self._draw()

    def _get_valid_axis_keys(
        self, combo_widget: Optional[ComboBox] = None
    ) -> List[str]:
        """
        Get the valid axis keys from the layer FeatureTable.

        Returns
        -------
        axis_keys : List[str]
            The valid axis keys in the FeatureTable. If the table is empty
            or there isn't a table, returns an empty list.
        """
        if len(self.layers) == 0 or not (hasattr(self.layers[0], "features")):
            return []
        else:
            return self.layers[0].features.keys()

    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
        """Get the plot data.

        Returns
        -------
        data : List[np.ndarray]
            List contains X and Y columns from the FeatureTable. Returns
            an empty array if nothing to plot.
        x_axis_name : str
            The title to display on the x axis. Returns
            an empty string if nothing to plot.
        y_axis_name: str
            The title to display on the y axis. Returns
            an empty string if nothing to plot.
        """
        if not hasattr(self.layers[0], "features"):
            # if the selected layer doesn't have a featuretable,
            # skip draw
            return [], "", ""

        feature_table = self.layers[0].features

        if (
            (len(feature_table) == 0)
            or (self.x_axis_key is None)
            or (self.y_axis_key is None)
        ):
            return [], "", ""

        data_x = feature_table[self.x_axis_key]
        data_y = feature_table[self.y_axis_key]
        data = [data_x, data_y]

        x_axis_name = self.x_axis_key.replace("_", " ")
        y_axis_name = self.y_axis_key.replace("_", " ")

        return data, x_axis_name, y_axis_name

    def _on_update_layers(self) -> None:
        """
        This is called when the layer selection changes by
        ``self.update_layers()``.
        """
        if hasattr(self, "_key_selection_widget"):
            self._key_selection_widget.reset_choices()

        # reset the axis keys
        self._x_axis_key = None
        self._y_axis_key = None


class FeaturesHistogramWidget(NapariMPLWidget):
    n_layers_input = Interval(1, 1)
    # All layers that have a .features attributes
    input_layer_types = (
        napari.layers.Labels,
        napari.layers.Points,
        napari.layers.Shapes,
        napari.layers.Tracks,
        napari.layers.Vectors,
    )

    def __init__(self, napari_viewer: napari.viewer.Viewer):
        super().__init__(napari_viewer)
        self.axes = self.canvas.figure.subplots()

        self._key_selection_widget = magicgui(
            self._set_axis_keys,
            x_axis_key={"choices": self._get_valid_axis_keys},
            call_button="plot",
        )
        self.layout().addWidget(self._key_selection_widget.native)

        self.update_layers(None)

    def clear(self) -> None:
        """
        Clear the axes.
        """
        self.axes.clear()

        self.layout().addWidget(self._key_selection_widget.native)

    @property
    def x_axis_key(self) -> Optional[str]:
        """Key to access x axis data from the FeaturesTable"""
        return self._x_axis_key

    @x_axis_key.setter
    def x_axis_key(self, key: Optional[str]) -> None:
        self._x_axis_key = key
        self._draw()

    def _set_axis_keys(self, x_axis_key: str) -> None:
        """Set both axis keys and then redraw the plot"""
        self._x_axis_key = x_axis_key
        self._draw()

    def _get_valid_axis_keys(
        self, combo_widget: Optional[ComboBox] = None
    ) -> List[str]:
        """
        Get the valid axis keys from the layer FeatureTable.

        Returns
        -------
        axis_keys : List[str]
            The valid axis keys in the FeatureTable. If the table is empty
            or there isn't a table, returns an empty list.
        """
        if len(self.layers) == 0 or not (hasattr(self.layers[0], "features")):
            return []
        else:
            return self.layers[0].features.keys()

    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
        """Get the plot data.

        Returns
        -------
        data : List[np.ndarray]
            List contains X and Y columns from the FeatureTable. Returns
            an empty array if nothing to plot.
        x_axis_name : str
            The title to display on the x axis. Returns
            an empty string if nothing to plot.
        """
        if not hasattr(self.layers[0], "features"):
            # if the selected layer doesn't have a featuretable,
            # skip draw
            return [], ""

        feature_table = self.layers[0].features

        if (
            (len(feature_table) == 0)
            or (self.x_axis_key is None)
        ):
            return [], ""

        data = feature_table[self.x_axis_key]
        x_axis_name = self.x_axis_key.replace("_", " ")

        return data, x_axis_name

    def _on_update_layers(self) -> None:
        """
        This is called when the layer selection changes by
        ``self.update_layers()``.
        """
        if hasattr(self, "_key_selection_widget"):
            self._key_selection_widget.reset_choices()

        # reset the axis keys
        self._x_axis_key = None

    def draw(self) -> None:
        """Clear the axes and histogram the currently selected layer/slice."""

        data, x_axis_name = self._get_data()

        if len(data) == 0:
            return

        _, _, _ = self.axes.hist(data, bins=50, edgecolor='white',
                                 linewidth=0.3)

        # # set ax labels
        self.axes.set_xlabel(x_axis_name)
        self.axes.set_ylabel('Counts [#]')