import numpy as np from ...util.dtype import dtype_range from ... import draw, 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. 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) 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.limits = 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, 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], mode='reflect') 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). """ self._update_data() 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 self._update_data() self.ax.relim() self._autoscale_view() self.redraw() def _update_data(self): scan = measure.profile_line(self.image_viewer.image, *self.line_tool.end_points[:, ::-1], linewidth=self.line_tool.linewidth, mode='reflect') 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]) 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. If the linewidth of the line tool is greater than 1, sets the values within the profiled polygon to 128. scan : (P,) or (P, 3) array of int or float The line scan values across the image. """ end_points = self.line_tool.end_points line_image = np.zeros(self.image_viewer.image.shape[:2], np.uint8) width = self.line_tool.linewidth if width > 1: rp, cp = measure.profile._line_profile_coordinates( *end_points[:, ::-1], linewidth=width) # the points are aliased, so create a polygon using the corners yp = np.rint(rp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int) xp = np.rint(cp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int) rp, cp = draw.polygon(yp, xp, line_image.shape) line_image[rp, cp] = 128 (x1, y1), (x2, y2) = end_points.astype(int) rr, cc = draw.line(y1, x1, y2, x2) line_image[rr, cc] = 255 return line_image, self.scan_data