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https://github.com/wassname/scikit-image.git
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Add LineProfile plugin.
This commit is contained in:
Tony S Yu
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import numpy as np
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import scipy.ndimage as ndi
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from skimage.util.dtype import dtype_range
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from .base import PlotPlugin
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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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Parameters
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----------
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image_viewer : ImageViewer instance.
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Window containing image used in measurement.
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useblit : bool
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If True, use blitting to speed up animation. Only available on some
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backends. If None, set to True when using Agg backend, otherwise False.
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linewidth : float
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Line width for interpolation. Wider lines average over more pixels.
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epsilon : 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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def __init__(self, image_viewer, useblit=None,
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linewidth=1, epsilon=5, limits='image'):
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super(LineProfile, self).__init__(image_viewer, height=200, width=600,
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useblit=useblit)
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self.linewidth = linewidth
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self.epsilon = epsilon
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if limits == 'image':
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self.limits = (np.min(self.image), np.max(self.image))
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elif limits == 'dtype':
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self.limits = dtype_range[self.image.dtype.type]
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elif limits is None or len(limits) == 2:
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self.limits = limits
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else:
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raise ValueError("Unrecognized `limits`: %s" % limits)
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if not limits is None:
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self.ax.set_ylim(self.limits)
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h, w = self.image.shape
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self._init_end_pts = np.array([[w/3, h/2], [2*w/3, h/2]])
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self.end_pts = self._init_end_pts.copy()
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x, y = np.transpose(self.end_pts)
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self.scan_line = self.image_viewer.ax.plot(x, y, 'y-s', markersize=5,
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lw=linewidth, alpha=0.5,
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solid_capstyle='butt')[0]
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self.artists.append(self.scan_line)
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scan_data = profile_line(self.image, self.end_pts)
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self.profile = self.ax.plot(scan_data, 'k-')[0]
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self._autoscale_view()
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self._active_pt = None
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self.connect_event('key_press_event', self.on_key_press)
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self.connect_event('button_press_event', self.on_mouse_press)
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self.connect_event('button_release_event', self.on_mouse_release)
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self.connect_event('motion_notify_event', self.on_move)
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self.connect_event('scroll_event', self.on_scroll)
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self.image_viewer.redraw()
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print self.help()
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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_profile(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_pts: (2, 2) array
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The positions ((x1, y1), (x2, y2)) of the line ends.
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profile: 1d array
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Profile of intensity values.
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"""
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end_pts = self.scan_line.get_xydata()
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profile = self.profile.get_ydata()
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return end_pts, profile
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def on_scroll(self, event):
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if not event.inaxes: return
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if event.button == 'up':
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self._thicken_scan_line()
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elif event.button == 'down':
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self._shrink_scan_line()
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def on_key_press(self, event):
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if not event.inaxes: return
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elif event.key == '+':
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self._thicken_scan_line()
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elif event.key == '-':
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self._shrink_scan_line()
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elif event.key == 'r':
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self.reset()
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def _thicken_scan_line(self):
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self.linewidth += 1
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self.line_changed(None, None)
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def _shrink_scan_line(self):
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if self.linewidth > 1:
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self.linewidth -= 1
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self.line_changed(None, None)
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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 get_pt_under_cursor(self, event):
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"""Return index of the end point under cursor, if sufficiently close"""
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xy = np.asarray(self.scan_line.get_xydata())
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xyt = self.scan_line.get_transform().transform(xy)
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xt, yt = xyt[:, 0], xyt[:, 1]
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d = np.sqrt((xt - event.x)**2 + (yt - event.y)**2)
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indseq = np.nonzero(np.equal(d, np.amin(d)))[0]
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ind = indseq[0]
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if d[ind] >= self.epsilon:
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ind = None
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return ind
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def on_mouse_press(self, event):
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if event.button != 1: return
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if event.inaxes==None: return
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self._active_pt = self.get_pt_under_cursor(event)
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def on_mouse_release(self, event):
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if event.button != 1: return
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self._active_pt = None
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def on_move(self, event):
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if event.button != 1: return
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if self._active_pt is None: return
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if not self.image_viewer.ax.in_axes(event): return
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x,y = event.xdata, event.ydata
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self.line_changed(x, y)
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def reset(self):
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self.end_pts = self._init_end_pts.copy()
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self.scan_line.set_data(np.transpose(self.end_pts))
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self.line_changed(None, None)
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def line_changed(self, x, y):
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if x is not None:
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self.end_pts[self._active_pt, :] = x, y
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self.scan_line.set_data(np.transpose(self.end_pts))
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self.scan_line.set_linewidth(self.linewidth)
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scan = profile_line(self.image, self.end_pts, linewidth=self.linewidth)
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self.profile.set_xdata(np.arange(scan.shape[0]))
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self.profile.set_ydata(scan)
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self.ax.relim()
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if self.useblit:
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self.image_viewer.canvas.restore_region(self.img_background)
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self.ax.draw_artist(self.scan_line)
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self.ax.draw_artist(self.profile)
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self.image_viewer.canvas.blit(self.image_viewer.ax.bbox)
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self._autoscale_view()
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self.image_viewer.redraw()
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self.redraw()
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def profile_line(img, end_pts, linewidth=1):
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"""Return the intensity profile of an image measured along a scan line.
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Parameters
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----------
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img : 2d array
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The image.
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end_pts: (2, 2) list
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End points ((x1, y1), (x2, y2)) of scan line.
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linewidth: int
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Width of the scan, perpendicular to the line
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Returns
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-------
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return_value : array
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The intensity profile along the scan line. The length of the profile
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is the ceil of the computed length of the scan line.
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"""
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point1, point2 = end_pts
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x1, y1 = point1 = np.asarray(point1, dtype = float)
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x2, y2 = point2 = np.asarray(point2, dtype = float)
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dx, dy = point2 - point1
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# Quick calculation if perfectly horizontal or vertical (remove?)
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if x1 == x2:
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pixels = img[min(y1, y2) : max(y1, y2)+1,
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x1 - linewidth / 2 : x1 + linewidth / 2 + 1]
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intensities = pixels.mean(axis = 1)
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return intensities
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elif y1 == y2:
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pixels = img[y1 - linewidth / 2 : y1 + linewidth / 2 + 1,
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min(x1, x2) : max(x1, x2)+1]
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intensities = pixels.mean(axis = 0)
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return intensities
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theta = np.arctan2(dy,dx)
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a = dy/dx
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b = y1 - a * x1
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length = np.hypot(dx, dy)
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line_x = np.linspace(min(x1, x2), max(x1, x2), np.ceil(length))
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line_y = line_x * a + b
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y_width = abs(linewidth * np.cos(theta)/2)
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perp_ys = np.array([np.linspace(yi - y_width,
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yi + y_width, linewidth) for yi in line_y])
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perp_xs = - a * perp_ys + (line_x + a * line_y)[:, np.newaxis]
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perp_lines = np.array([perp_ys, perp_xs])
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pixels = ndi.map_coordinates(img, perp_lines)
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intensities = pixels.mean(axis=1)
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return intensities
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@@ -0,0 +1,10 @@
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from skimage import data
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from skimage.viewer import ImageViewer
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from skimage.viewer.plugins.lineprofile import LineProfile
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image = data.camera()
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viewer = ImageViewer(image)
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p = LineProfile(viewer)
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p.show()
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viewer.show()
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