def raster(poly, use_convex_hull=False,
offset=0,
step=1,
find_min=False, theta=None):
poly = np.array(poly)
poly = sort_clockwise(poly, poly)
if use_convex_hull:
poly = convex_hull(poly)
poly = np.array(poly)
if offset:
opoly = polygon_offset(poly, offset)
opoly = np.array(opoly, dtype=int)
opoly = opoly[:, (0, 1)]
else:
opoly = poly
lens = []
rtheta = 0
if find_min:
lines, rtheta, lens = find_minimum_orientation(opoly, step)
else:
lines = make_raster_polygon(opoly, step)
if theta is not None:
cx, cy = get_center(opoly)
P_prime = rotate_poly(opoly.T, theta, loc=(cx, cy))
lines = make_raster_polygon(P_prime.T, step)
lines = rotate_lines(lines, theta, cx, cy)
return lines, lens, rtheta
def raster(poly, use_convex_hull=False, offset=0, step=1, find_min=False, theta=None):
poly = np.array(poly)
poly = sort_clockwise(poly, poly)
if use_convex_hull:
poly = convex_hull(poly)
poly = np.array(poly)
if offset:
opoly = polygon_offset(poly, offset)
opoly = np.array(opoly, dtype=int)
opoly = opoly[:, (0, 1)]
else:
opoly = poly
lens = []
rtheta = 0
if find_min:
lines, rtheta, lens = find_minimum_orientation(opoly, step)
else:
lines = make_raster_polygon(opoly, step)
if theta is not None:
cx, cy = get_center(opoly)
P_prime = rotate_poly(opoly.T, theta, loc=(cx, cy))
lines = make_raster_polygon(P_prime.T, step)
lines = rotate_lines(lines, theta, cx, cy)
return lines, lens, rtheta
def _replot_polygon(self, poly):
pts = [(pi.x, pi.y) for pi in poly.points]
pts = sort_clockwise(pts, pts)
# pts = pts + pts[:1]
pts = array(pts)
scale = 1000
pts *= scale
use_convex_hull = False
find_min = poly.find_min
npoints, lens, theta = raster(
pts,
step=poly.scan_size,
offset=-poly.offset if poly.use_outline else 0,
use_convex_hull=use_convex_hull,
find_min=find_min,
theta=poly.theta)
poly._set_theta(theta)
# poly.trait_set(theta=theta)
g = self.graph
g.clear()
g.plotcontainer.padding = 5
g.new_plot(
padding=[60, 30, 30, 50],
# bounds=[400, 400],
# resizable='h',
xtitle='X (microns)',
ytitle='Y (microns)')
g.new_plot(
padding=[50, 30, 30, 30],
xtitle='Theta (degrees)',
ytitle='Num. Scan Lines',
# bounds=[400, 100],
# resizable='h'
)
if find_min:
ts, ls = zip(*lens)
g.new_series(ts, ls, plotid=1)
# plot original
pts = vstack((pts, pts[:1]))
xs, ys = pts.T
self.graph.new_series(xs, ys, plotid=0)
self.graph.set_x_limits(min(xs), max(xs), pad='0.1')
self.graph.set_y_limits(min(ys), max(ys), pad='0.1')
for ps in npoints:
for i in range(0, len(ps), 2):
p1, p2 = ps[i], ps[i + 1]
g.new_series((p1[0], p2[0]), (p1[1], p2[1]),
color='black',
plotid=0)
if poly.use_outline:
from pychron.core.geometry.polygon_offset import polygon_offset
opoly = polygon_offset(pts, -1 * poly.offset)
opoly = array(opoly)
xs, ys, _ = opoly.T
self.graph.new_series(xs, ys, plotid=0)
def _replot_polygon(self, poly):
pts = [(pi.x, pi.y) for pi in poly.points]
pts = sort_clockwise(pts, pts)
# pts = pts + pts[:1]
pts = array(pts)
scale = 1000
pts *= scale
use_convex_hull = False
find_min = poly.find_min
npoints, lens, theta = raster(pts,
step=poly.scan_size,
offset=-poly.offset if poly.use_outline else 0,
use_convex_hull=use_convex_hull,
find_min=find_min,
theta=poly.theta
)
poly._set_theta(theta)
# poly.trait_set(theta=theta)
g = self.graph
g.clear()
g.plotcontainer.padding = 5
g.new_plot(padding=[60, 30, 30, 50],
# bounds=[400, 400],
# resizable='h',
xtitle='X (microns)',
ytitle='Y (microns)')
g.new_plot(padding=[50, 30, 30, 30],
xtitle='Theta (degrees)',
ytitle='Num. Scan Lines',
# bounds=[400, 100],
# resizable='h'
)
if find_min:
ts, ls = zip(*lens)
g.new_series(ts, ls, plotid=1)
# plot original
pts = vstack((pts, pts[:1]))
xs, ys = pts.T
self.graph.new_series(xs, ys, plotid=0)
self.graph.set_x_limits(min(xs), max(xs), pad='0.1')
self.graph.set_y_limits(min(ys), max(ys), pad='0.1')
for ps in npoints:
for i in range(0, len(ps), 2):
p1, p2 = ps[i], ps[i + 1]
g.new_series((p1[0], p2[0]),
(p1[1], p2[1]), color='black', plotid=0)
if poly.use_outline:
from pychron.core.geometry.polygon_offset import polygon_offset
opoly = polygon_offset(pts, -1 * poly.offset)
opoly = array(opoly)
xs, ys, _ = opoly.T
self.graph.new_series(xs, ys, plotid=0)
def _move_polygon(self, pts, velocity=5,
offset=50,
use_outline=True,
find_min=False,
scan_size=None,
use_move=True,
use_convex_hull=True,
motors=None,
verbose=True,
start_callback=None, end_callback=None):
"""
motors is a dict of motor_name:value pairs
"""
if pts is None:
return
if not isinstance(pts, list):
velocity = pts.velocity
use_convex_hull = pts.use_convex_hull
if scan_size is None:
scan_size = pts.scan_size
use_outline = pts.use_outline
offset = pts.offset
find_min = pts.find_min
pts = [dict(xy=(pi.x, pi.y), z=pi.z, ) for pi in pts.points]
# set motors
if motors is not None:
for k, v in motors.values():
'''
motor will not set if it has been locked using set_motor_lock or
remotely using SetMotorLock
'''
if use_move:
self.parent.set_motor(k, v, block=True)
xy = [pi['xy'] for pi in pts]
n = 1000
if scan_size is None:
scan_size = n / 2
# convert points to um
pts = array(xy)
pts *= n
pts = asarray(pts, dtype=int)
'''
sort clockwise ensures consistent offset behavior
a polygon gain have a inner or outer sense depending on order of vertices
always use sort_clockwise prior to any polygon manipulation
'''
pts = sort_clockwise(pts, pts)
sc = self.stage_controller
sc.set_program_mode('absolute')
# do smooth transitions between points
sc.set_smooth_transitions(True)
if use_convex_hull:
pts = convex_hull(pts)
if use_outline:
# calculate new polygon
offset_pts = polygon_offset(pts, -offset)
offset_pts = array(offset_pts, dtype=int)
# polygon offset used 3D vectors.
# trim to only x,y
pts = offset_pts[:, (0, 1)]
# trace perimeter
if use_move:
p0 = xy[0]
self.linear_move(p0[0], p0[1], mode='absolute', block=True)
sc.timer = sc.timer_factory()
if start_callback is not None:
start_callback()
# buf=[]
for pi in xy[1:]:
self.linear_move(pi[0], pi[1],
velocity=velocity,
mode='absolute', set_stage=False)
# finish at first point
self.linear_move(p0[0], p0[1],
velocity=velocity,
mode='absolute', set_stage=False)
sc.block()
self.info('polygon perimeter trace complete')
'''
have the oppurtunity here to turn off laser and change parameters i.e mask
'''
if use_move:
# calculate and step thru scan lines
self._raster(pts, velocity,
step=scan_size,
scale=n,
find_min=find_min,
start_callback=start_callback, end_callback=end_callback,
verbose=verbose)
sc.set_program_mode('relative')
if end_callback is not None:
end_callback()
self.info('polygon raster complete')
cx, cy = xs.mean(), ys.mean()
# plot original
g.new_series(xs, ys)
g.set_x_limits(min(xs), max(xs), pad='0.1')
g.set_y_limits(min(ys), max(ys), pad='0.1')
for ps in npoints:
for i in range(0, len(ps), 2):
p1, p2 = ps[i], ps[i + 1]
g.new_series((p1[0], p2[0]),
(p1[1], p2[1]), color='black')
# plot offset polygon
# poly = sort_clockwise(poly, poly)
opoly = polygon_offset(poly, -500)
if use_convex_hull:
opoly = convex_hull(opoly)
xs, ys, _ = opoly.T
xs = np.hstack((xs, xs[0]))
ys = np.hstack((ys, ys[0]))
else:
opoly = np.array(opoly, dtype=int)
xs, ys, _ = opoly.T
# opoly = opoly[:, (0, 1)]
# rpoly = rotate_poly(opoly.T, 145, loc=(cx, cy))
# xs, ys = rpoly[0], rpoly[1]
g.new_series(xs, ys)
g.new_plot(padding=[50, 30, 30, 30],
cx, cy = xs.mean(), ys.mean()
# plot original
g.new_series(xs, ys)
g.set_x_limits(min(xs), max(xs), pad="0.1")
g.set_y_limits(min(ys), max(ys), pad="0.1")
for ps in npoints:
for i in range(0, len(ps), 2):
p1, p2 = ps[i], ps[i + 1]
g.new_series((p1[0], p2[0]), (p1[1], p2[1]), color="black")
# plot offset polygon
# poly = sort_clockwise(poly, poly)
opoly = polygon_offset(poly, -500)
if use_convex_hull:
opoly = convex_hull(opoly)
xs, ys, _ = opoly.T
xs = np.hstack((xs, xs[0]))
ys = np.hstack((ys, ys[0]))
else:
opoly = np.array(opoly, dtype=int)
xs, ys, _ = opoly.T
# opoly = opoly[:, (0, 1)]
# rpoly = rotate_poly(opoly.T, 145, loc=(cx, cy))
# xs, ys = rpoly[0], rpoly[1]
g.new_series(xs, ys)
g.new_plot(
def _move_polygon(self, pts, velocity=5,
offset=50,
use_outline=True,
find_min=False,
scan_size=None,
use_move=True,
use_convex_hull=True,
motors=None,
verbose=True,
start_callback=None, end_callback=None):
"""
motors is a dict of motor_name:value pairs
"""
if pts is None:
return
if not isinstance(pts, list):
velocity = pts.velocity
use_convex_hull = pts.use_convex_hull
if scan_size is None:
scan_size = pts.scan_size
use_outline = pts.use_outline
offset = pts.offset
find_min = pts.find_min
pts = [dict(xy=(pi.x, pi.y), z=pi.z, ) for pi in pts.points]
# set motors
if motors is not None:
for k, v in motors.values():
'''
motor will not set if it has been locked using set_motor_lock or
remotely using SetMotorLock
'''
if use_move:
self.parent.set_motor(k, v, block=True)
xy = [pi['xy'] for pi in pts]
n = 1000
if scan_size is None:
scan_size = n / 2
# convert points to um
pts = array(xy)
pts *= n
pts = asarray(pts, dtype=int)
'''
sort clockwise ensures consistent offset behavior
a polygon gain have a inner or outer sense depending on order of vertices
always use sort_clockwise prior to any polygon manipulation
'''
pts = sort_clockwise(pts, pts)
sc = self.stage_controller
sc.set_program_mode('absolute')
# do smooth transitions between points
sc.set_smooth_transitions(True)
if use_convex_hull:
pts = convex_hull(pts)
if use_outline:
# calculate new polygon
offset_pts = polygon_offset(pts, -offset)
offset_pts = array(offset_pts, dtype=int)
# polygon offset used 3D vectors.
# trim to only x,y
pts = offset_pts[:, (0, 1)]
# trace perimeter
if use_move:
p0 = xy[0]
self.linear_move(p0[0], p0[1], mode='absolute', block=True)
sc.timer = sc.timer_factory()
if start_callback is not None:
start_callback()
# buf=[]
for pi in xy[1:]:
self.linear_move(pi[0], pi[1],
velocity=velocity,
mode='absolute', set_stage=False)
# finish at first point
self.linear_move(p0[0], p0[1],
velocity=velocity,
mode='absolute', set_stage=False)
sc.block()
self.info('polygon perimeter trace complete')
'''
have the oppurtunity here to turn off laser and change parameters i.e mask
'''
if use_move:
# calculate and step thru scan lines
self._raster(pts, velocity,
step=scan_size,
scale=n,
find_min=find_min,
start_callback=start_callback, end_callback=end_callback,
verbose=verbose)
sc.set_program_mode('relative')
if end_callback is not None:
end_callback()
self.info('polygon raster complete')
