166 lines
5.8 KiB
Python
166 lines
5.8 KiB
Python
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import numpy as np
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from ...util.dtype import dtype_range
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from ... import draw, measure
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from .plotplugin import PlotPlugin
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from ..canvastools import ThickLineTool
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__all__ = ['LineProfile']
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class LineProfile(PlotPlugin):
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"""Plugin to compute interpolated intensity under a scan line on an image.
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See PlotPlugin and Plugin classes for additional details.
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Parameters
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----------
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maxdist : float
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Maximum pixel distance allowed when selecting end point of scan line.
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limits : tuple or {None, 'image', 'dtype'}
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(minimum, maximum) intensity limits for plotted profile. The following
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special values are defined:
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None : rescale based on min/max intensity along selected scan line.
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'image' : fixed scale based on min/max intensity in image.
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'dtype' : fixed scale based on min/max intensity of image dtype.
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"""
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name = 'Line Profile'
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def __init__(self, maxdist=10, epsilon='deprecated',
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limits='image', **kwargs):
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super(LineProfile, self).__init__(**kwargs)
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self.maxdist = maxdist
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self._limit_type = limits
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print(self.help())
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def attach(self, image_viewer):
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super(LineProfile, self).attach(image_viewer)
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image = image_viewer.original_image
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if self._limit_type == 'image':
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self.limits = (np.min(image), np.max(image))
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elif self._limit_type == 'dtype':
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self.limits = dtype_range[image.dtype.type]
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elif self._limit_type is None or len(self._limit_type) == 2:
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self.limits = self._limit_type
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else:
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raise ValueError("Unrecognized `limits`: %s" % self._limit_type)
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if not self._limit_type is None:
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self.ax.set_ylim(self.limits)
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h, w = image.shape[0:2]
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x = [w / 3, 2 * w / 3]
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y = [h / 2] * 2
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self.line_tool = ThickLineTool(self.image_viewer,
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maxdist=self.maxdist,
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on_move=self.line_changed,
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on_change=self.line_changed)
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self.line_tool.end_points = np.transpose([x, y])
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scan_data = measure.profile_line(image,
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*self.line_tool.end_points[:, ::-1])
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self.scan_data = scan_data
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if scan_data.ndim == 1:
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scan_data = scan_data[:, np.newaxis]
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self.reset_axes(scan_data)
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self._autoscale_view()
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def help(self):
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helpstr = ("Line profile tool",
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"+ and - keys or mouse scroll changes width of scan line.",
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"Select and drag ends of the scan line to adjust it.")
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return '\n'.join(helpstr)
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def get_profiles(self):
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"""Return intensity profile of the selected line.
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Returns
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-------
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end_points: (2, 2) array
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The positions ((x1, y1), (x2, y2)) of the line ends.
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profile: list of 1d arrays
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Profile of intensity values. Length 1 (grayscale) or 3 (rgb).
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"""
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self._update_data()
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profiles = [data.get_ydata() for data in self.profile]
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return self.line_tool.end_points, profiles
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def _autoscale_view(self):
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if self.limits is None:
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self.ax.autoscale_view(tight=True)
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else:
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self.ax.autoscale_view(scaley=False, tight=True)
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def line_changed(self, end_points):
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x, y = np.transpose(end_points)
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self.line_tool.end_points = end_points
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self._update_data()
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self.ax.relim()
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self._autoscale_view()
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self.redraw()
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def _update_data(self):
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scan = measure.profile_line(self.image_viewer.image,
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*self.line_tool.end_points[:, ::-1],
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linewidth=self.line_tool.linewidth)
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self.scan_data = scan
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if scan.ndim == 1:
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scan = scan[:, np.newaxis]
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if scan.shape[1] != len(self.profile):
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self.reset_axes(scan)
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for i in range(len(scan[0])):
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self.profile[i].set_xdata(np.arange(scan.shape[0]))
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self.profile[i].set_ydata(scan[:, i])
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def reset_axes(self, scan_data):
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# Clear lines out
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for line in self.ax.lines:
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self.ax.lines = []
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if scan_data.shape[1] == 1:
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self.profile = self.ax.plot(scan_data, 'k-')
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else:
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self.profile = self.ax.plot(scan_data[:, 0], 'r-',
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scan_data[:, 1], 'g-',
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scan_data[:, 2], 'b-')
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def output(self):
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"""Return the drawn line and the resulting scan.
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Returns
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-------
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line_image : (M, N) uint8 array, same shape as image
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An array of 0s with the scanned line set to 255.
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If the linewidth of the line tool is greater than 1,
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sets the values within the profiled polygon to 128.
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scan : (P,) or (P, 3) array of int or float
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The line scan values across the image.
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"""
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end_points = self.line_tool.end_points
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line_image = np.zeros(self.image_viewer.image.shape[:2],
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np.uint8)
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width = self.line_tool.linewidth
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if width > 1:
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rp, cp = measure.profile._line_profile_coordinates(
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*end_points[:, ::-1], linewidth=width)
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# the points are aliased, so create a polygon using the corners
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yp = np.rint(rp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int)
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xp = np.rint(cp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int)
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rp, cp = draw.polygon(yp, xp, line_image.shape)
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line_image[rp, cp] = 128
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(x1, y1), (x2, y2) = end_points.astype(int)
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rr, cc = draw.line(y1, x1, y2, x2)
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line_image[rr, cc] = 255
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return line_image, self.scan_data
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