def worm_image_coords_in_lab_frame(lab_image_shape, worm_image_shape, center_tck, width_tck,
standard_width=None, zoom=1, reflect_centerline=False):
"""Produce a map in the lab frame noting the coordinates of each worm pixel in the
frame of reference of an image as generated by to_worm_frame().
The output coordinates are relative to a worm frame-of-reference image, as
produced by to_worm_frame(). All parameters must be the same as those passed
to to_worm_frame() for the coordinate transform to be correct. In particular,
if a standard_width and/or a zoom factor were used to produce the image,
those values must be used here as well.
Areas outside of the worm will be nan.
Parameters:
lab_image_shape: shape of output image in lab frame
worm_image_shape: shape of worm image in which the coordinates are defined
center_tck: centerline spline of the worm in the lab frame.
width_tck: spline width profile of the worm.
standard_width: a width spline specifying the "standardized" width
profile for the output image.
zoom: zoom factor.
reflect_centerline: reflect worm coordinates over the centerline
Returns: (x_coords, y_coords), each of shape lab_image_shape
"""
triangle_strip = spline_geometry.triangle_strip(center_tck, width_tck)
wtck = width_tck if standard_width is None else standard_width
widths = interpolate.spline_interpolate(wtck, num_points=len(triangle_strip)//2)
right = worm_image_shape[1]/2 - widths*zoom # worm_image_shape[1]/2 is the position of the centerline
left = worm_image_shape[1]/2 + widths*zoom # worm_image_shape[1]/2 is the position of the centerline
return _worm_coords(lab_image_shape, triangle_strip, x_max=worm_image_shape[0], right=right, left=left, reflect_centerline=reflect_centerline)
def abs_worm_coords_in_lab_frame(lab_image_shape,
center_tck,
width_tck,
reflect_centerline=False):
"""Produce a map of the pixel-wise worm coordinates in the lab frame.
Output x-coords run from 0 to the length of the worm, and y-coords from
-width (right side) to width, which varies along the worm.
Areas outside of the worm will be nan.
Parameters:
lab_image_shape: shape of output image in lab frame
center_tck: centerline spline of the worm in the lab frame.
width_tck: spline width profile of the worm.
reflect_centerline: reflect worm coordinates over the centerline
Returns: (x_coords, y_coords), each of shape lab_image_shape
"""
triangle_strip = spline_geometry.triangle_strip(center_tck, width_tck)
x_max = spline_geometry.arc_length(center_tck)
widths = interpolate.spline_interpolate(width_tck,
num_points=len(triangle_strip) //
2)
return _worm_coords(lab_image_shape,
triangle_strip,
x_max,
right=-widths,
left=widths,
reflect_centerline=reflect_centerline)
def rel_worm_coords_in_lab_frame(lab_image_shape, center_tck, width_tck, reflect_centerline=False):
"""Produce a map of the relative worm coordinates in the lab frame.
Output x-coords run from 0 to 1, and y-coords from -1 (right side) to 1.
Areas outside of the worm will be nan.
Parameters:
lab_image_shape: shape of output image in lab frame
center_tck: centerline spline of the worm in the lab frame.
width_tck: spline width profile of the worm.
reflect_centerline: reflect worm coordinates over the centerline
Returns: (x_coords, y_coords), each of shape lab_image_shape
"""
triangle_strip = spline_geometry.triangle_strip(center_tck, width_tck)
return _worm_coords(lab_image_shape, triangle_strip, x_max=1, right=-1, left=1, reflect_centerline=reflect_centerline)
def worm_coords_lab_frame_mask(lab_image_shape, center_tck, width_tck):
"""Produce a boolean image mask that is pixel accurate for lab-frame worm coordinate images.
NB: lab_frame_mask() uses a different algorithm to draw an (optionally antialiased)
mask that is not guaranteed to be in perfect pixel alignment with the worm
coordinate images generated by the [abs|rel]_worm_coords[...] functions. Use
this instead if such guarantees are needed but antialiasing is not.
Parameters:
lab_image_shape: shape of output image in lab frame
center_tck: centerline spline of the worm in the lab frame.
width_tck: spline width profile of the worm.
Returns: boolean mask of shape lab_image_shape
"""
triangle_strip = spline_geometry.triangle_strip(center_tck, width_tck)
return draw.mask_triangle_strip(triangle_strip, lab_image_shape)
def worm_self_intersection_map(lab_image_shape, center_tck, width_tck):
"""Produce a self-intersection map in the lab frame.
The returned image contains a count of the number of worm pixels occupied by
each lab-frame image pixel. Positions of self-intersection will have pixel
values >1 indicating that the worm mask passes over that pixel multiple times.
Parameters:
lab_image_shape: shape of output image in lab frame
center_tck: centerline spline of the worm in the lab frame.
width_tck: spline width profile of the worm.
Returns: intersection_map, intersection_fraction
intersection_map: image of shape lab_image_shape with count of pixel occupancies
intersection_fraction: fraction of worm pixels that are self-occluded
"""
triangle_strip = spline_geometry.triangle_strip(center_tck, width_tck)
vertex_vals = numpy.ones(len(triangle_strip))
intersection_map = draw.gouraud_triangle_strip(triangle_strip, vertex_vals, lab_image_shape, accumulate=True)
intersection_fraction = (intersection_map > 1).sum() / (intersection_map > 0).sum()
return intersection_map, intersection_fraction