168 lines
5.9 KiB
Python
168 lines
5.9 KiB
Python
|
|
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
|