scikit-image/skimage/viewer/plugins/lineprofile.py

import warnings

import numpy as np
from skimage.util.dtype import dtype_range
from skimage import draw
from skimage import measure

from .plotplugin import PlotPlugin
from ..canvastools import ThickLineTool


__all__ = ['LineProfile']


class LineProfile(PlotPlugin):
    """Plugin to compute interpolated intensity under a scan line on an image.

    See PlotPlugin and Plugin classes for additional details.

    Parameters
    ----------
    maxdist : float
        Maximum pixel distance allowed when selecting end point of scan line.
    epsilon : float
        Deprecated. Use `maxdist` instead.
    limits : tuple or {None, 'image', 'dtype'}
        (minimum, maximum) intensity limits for plotted profile. The following
        special values are defined:

            None : rescale based on min/max intensity along selected scan line.
            'image' : fixed scale based on min/max intensity in image.
            'dtype' : fixed scale based on min/max intensity of image dtype.
    """
    name = 'Line Profile'

    def __init__(self, maxdist=10, epsilon='deprecated',
                 limits='image', **kwargs):
        super(LineProfile, self).__init__(**kwargs)

        if not epsilon == 'deprecated':
            warnings.warn("Parameter `epsilon` deprecated; use `maxdist`.")
            maxdist = epsilon
        self.maxdist = maxdist
        self._limit_type = limits
        print(self.help())

    def attach(self, image_viewer):
        super(LineProfile, self).attach(image_viewer)

        image = image_viewer.original_image

        if self._limit_type == 'image':
            self.limits = (np.min(image), np.max(image))
        elif self._limit_type == 'dtype':
            self._limit_type = dtype_range[image.dtype.type]
        elif self._limit_type is None or len(self._limit_type) == 2:
            self.limits = self._limit_type
        else:
            raise ValueError("Unrecognized `limits`: %s" % self._limit_type)

        if not self._limit_type is None:
            self.ax.set_ylim(self.limits)

        h, w = image.shape[0:2]
        x = [w / 3, 2 * w / 3]
        y = [h / 2] * 2

        self.line_tool = ThickLineTool(self.image_viewer.ax,
                                       maxdist=self.maxdist,
                                       on_move=self.line_changed,
                                       on_change=self.line_changed)
        self.line_tool.end_points = np.transpose([x, y])

        scan_data = measure.profile_line(image, 
                                         *self.line_tool.end_points[:, ::-1])
        self.scan_data = scan_data
        if scan_data.ndim == 1:
            scan_data = scan_data[:, np.newaxis]

        self.reset_axes(scan_data)

        self._autoscale_view()

    def help(self):
        helpstr = ("Line profile tool",
                   "+ and - keys or mouse scroll changes width of scan line.",
                   "Select and drag ends of the scan line to adjust it.")
        return '\n'.join(helpstr)

    def get_profiles(self):
        """Return intensity profile of the selected line.

        Returns
        -------
        end_points: (2, 2) array
            The positions ((x1, y1), (x2, y2)) of the line ends.
        profile: list of 1d arrays
            Profile of intensity values. Length 1 (grayscale) or 3 (rgb).
        """
        profiles = [data.get_ydata() for data in self.profile]
        return self.line_tool.end_points, profiles

    def _autoscale_view(self):
        if self.limits is None:
            self.ax.autoscale_view(tight=True)
        else:
            self.ax.autoscale_view(scaley=False, tight=True)

    def line_changed(self, end_points):
        x, y = np.transpose(end_points)
        self.line_tool.end_points = end_points
        scan = measure.profile_line(self.image_viewer.original_image,
                                    *end_points[:, ::-1],
                                    linewidth=self.line_tool.linewidth)
        self.scan_data = scan
        if scan.ndim == 1:
            scan = scan[:, np.newaxis]

        if scan.shape[1] != len(self.profile):
            self.reset_axes(scan)

        for i in range(len(scan[0])):
            self.profile[i].set_xdata(np.arange(scan.shape[0]))
            self.profile[i].set_ydata(scan[:, i])

        self.ax.relim()

        self._autoscale_view()
        self.redraw()

    def reset_axes(self, scan_data):
        # Clear lines out
        for line in self.ax.lines:
            self.ax.lines = []

        if scan_data.shape[1] == 1:
            self.profile = self.ax.plot(scan_data, 'k-')
        else:
            self.profile = self.ax.plot(scan_data[:, 0], 'r-',
                                        scan_data[:, 1], 'g-',
                                        scan_data[:, 2], 'b-')

    def output(self):
        """Return the drawn line and the resulting scan.

        Returns
        -------
        line_image : (M, N) uint8 array, same shape as image
            An array of 0s with the scanned line set to 255.
        scan : (P,) or (P, 3) array of int or float
            The line scan values across the image.
        """
        (x1, y1), (x2, y2) = self.line_tool.end_points
        line_image = np.zeros(self.image_viewer.original_image.shape[:2],
                              np.uint8)
        rr, cc = draw.line(y1, x1, y2, x2)
        line_image[rr, cc] = 255
        return line_image, self.scan_data