def do_scan(S,
K,
max_ai_clock_rate,
ai_task,
ao_task,
do_task,
N,
M,
pixel_time,
scan_speed,
pixel_size_x,
alpha,
roi,
cache=None):
key = (S, K, N, M, pixel_time, scan_speed, alpha, roi)
flyback_ratio = K / N
flystart_ratio = S / K
sample_clock = SampleClock(pixel_time=pixel_time * 1e-6,
pixel_size=pixel_size_x * 1e-6)
T, clock_rate, min_clock_rate = sample_clock.get_optimal_scanning_parameters(
verbose=False)
mirror = MirrorDriver(image_size=(N, M),
T=T,
flyback_ratio=flyback_ratio,
flystart_ratio=flystart_ratio,
alpha=alpha,
roi=roi,
clock_rate=clock_rate,
verbose=False)
output_input_clock_ratio = min(int(clock_rate / max_ai_clock_rate) + 1, T)
while mirror.T % output_input_clock_ratio:
output_input_clock_ratio += 1
ai_clock_rate = clock_rate // output_input_clock_ratio
result = None
if cache is not None:
result = cache.data.get(key)
if result is None:
vx_target = mirror.vx_t_array()
vy_target = mirror.vy_t_array()
i_target = mirror.i_t_array()
j_target = mirror.j_t_array()
ai_task.configure_timing_sample_clock(
rate=ai_clock_rate,
active_edge='rising',
sample_mode='finite',
samples_per_channel=vx_target.size)
ao_task.configure_timing_sample_clock(
rate=clock_rate,
active_edge='rising',
sample_mode='finite',
samples_per_channel=vx_target.size)
# first iteration
vx_input = vx_target
vy_input = vy_target
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input,
output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(
i_target, j_target, i_pos, j_pos)
# second iteration
mirror.set_params(t_offset=toffset + mirror.t_offset)
vx_input = mirror.vx_t_array()
vy_input = mirror.vy_t_array()
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input,
output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(
i_target, j_target, i_pos, j_pos)
# third iteration
mirror.set_params(
i_offset=ioffset + mirror.i_offset,
j_offset=joffset + mirror.j_offset,
)
vx_input = mirror.vx_t_array()
vy_input = mirror.vy_t_array()
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input,
output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
i_input = mirror.i_v(vx_input, vy_input)
j_input = mirror.j_v(vx_input, vy_input)
result = vx_target, vy_target, i_target, j_target, vx_input, vy_input, i_input, j_input, vx_pos, vy_pos, i_pos, j_pos, vx_err, vy_err
if cache is not None:
cache.data[key] = result
cache.dump()
else:
print 'Using cache for key=', key
vx_target, vy_target, i_target, j_target, vx_input, vy_input, i_input, j_input, vx_pos, vy_pos, i_pos, j_pos, vx_err, vy_err = result
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(
i_target, j_target, i_pos, j_pos)
print 'XXX:', pixel_time, scan_speed, N, M, K, T, '->', toffset, ioffset, joffset, ioffset_std, joffset_std
from ioc.microscope.regress import regress
regress_scale = min(1, 20 / N)
i_pos, i_pos_grad = regress(i_pos, (regress_scale, ), method='average')
j_pos, j_pos_grad = regress(j_pos, (regress_scale, ), method='average')
vx_pos, vx_pos_grad = regress(vx_pos, (regress_scale, ), method='average')
vy_pos, vy_pos_grad = regress(vy_pos, (regress_scale, ), method='average')
plt = mk_figure(vx_target, vy_target, i_target, j_target, vx_input,
vy_input, i_input, j_input, vx_pos, vy_pos, i_pos, j_pos,
vx_err, vy_err, mirror, sample_clock,
output_input_clock_ratio)
plt.xlabel('ioffset=%s(%.3f,%.3f), joffset=%s(%.3f,%.3f), toffset=%s' %
(ioffset, ioffset_std, ioffset_max, joffset, joffset_std,
joffset_max, toffset))
plt.draw()
plt.show()
return ioffset_max
def do_scan(S, K, max_ai_clock_rate, ai_task, ao_task, do_task, N, M, pixel_time, scan_speed, pixel_size_x, alpha, roi,
cache = None):
key = (S, K, N, M, pixel_time, scan_speed, alpha, roi)
flyback_ratio = K/N
flystart_ratio = S/K
sample_clock = SampleClock(pixel_time = pixel_time * 1e-6,
pixel_size = pixel_size_x * 1e-6)
T, clock_rate, min_clock_rate = sample_clock.get_optimal_scanning_parameters(verbose=False)
mirror = MirrorDriver(image_size = (N,M),
T=T, flyback_ratio = flyback_ratio,
flystart_ratio = flystart_ratio,
alpha = alpha,
roi = roi,
clock_rate = clock_rate,
verbose=False)
output_input_clock_ratio = min(int(clock_rate / max_ai_clock_rate)+1, T)
while mirror.T % output_input_clock_ratio:
output_input_clock_ratio += 1
ai_clock_rate = clock_rate // output_input_clock_ratio
result = None
if cache is not None:
result = cache.data.get(key)
if result is None:
vx_target = mirror.vx_t_array()
vy_target = mirror.vy_t_array()
i_target = mirror.i_t_array()
j_target = mirror.j_t_array()
ai_task.configure_timing_sample_clock(rate = ai_clock_rate,
active_edge = 'rising',
sample_mode = 'finite',
samples_per_channel = vx_target.size
)
ao_task.configure_timing_sample_clock(rate = clock_rate,
active_edge = 'rising',
sample_mode = 'finite',
samples_per_channel = vx_target.size
)
# first iteration
vx_input = vx_target
vy_input = vy_target
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input, output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(i_target, j_target, i_pos, j_pos)
# second iteration
mirror.set_params(t_offset=toffset + mirror.t_offset)
vx_input = mirror.vx_t_array()
vy_input = mirror.vy_t_array()
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input, output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(i_target, j_target, i_pos, j_pos)
# third iteration
mirror.set_params(i_offset=ioffset + mirror.i_offset,
j_offset=joffset + mirror.j_offset,
)
vx_input = mirror.vx_t_array()
vy_input = mirror.vy_t_array()
vx_pos, vy_pos, vx_err, vy_err = run_mirrors(ao_task, ai_task, do_task,
vx_input, vy_input, output_input_clock_ratio)
i_pos = mirror.i_v(vx_pos, vy_pos)
j_pos = mirror.j_v(vx_pos, vy_pos)
i_input = mirror.i_v(vx_input, vy_input)
j_input = mirror.j_v(vx_input, vy_input)
result = vx_target, vy_target, i_target, j_target, vx_input, vy_input, i_input, j_input, vx_pos, vy_pos, i_pos, j_pos, vx_err, vy_err
if cache is not None:
cache.data[key] = result
cache.dump()
else:
print 'Using cache for key=', key
vx_target, vy_target, i_target, j_target, vx_input, vy_input, i_input, j_input, vx_pos, vy_pos, i_pos, j_pos, vx_err, vy_err = result
toffset, ioffset, joffset, ioffset_std, joffset_std, ioffset_max, joffset_max = mirror.estimate_offsets(i_target, j_target, i_pos, j_pos)
print 'XXX:', pixel_time, scan_speed, N,M,K,T,'->',toffset, ioffset, joffset, ioffset_std, joffset_std
from ioc.microscope.regress import regress
regress_scale = min(1, 20/N)
i_pos, i_pos_grad = regress(i_pos, (regress_scale,), method='average')
j_pos, j_pos_grad = regress(j_pos, (regress_scale,), method='average')
vx_pos, vx_pos_grad = regress(vx_pos, (regress_scale,), method='average')
vy_pos, vy_pos_grad = regress(vy_pos, (regress_scale,), method='average')
plt = mk_figure(vx_target, vy_target, i_target, j_target, vx_input, vy_input,
i_input, j_input,
vx_pos, vy_pos, i_pos, j_pos, vx_err, vy_err,
mirror, sample_clock, output_input_clock_ratio
)
plt.xlabel('ioffset=%s(%.3f,%.3f), joffset=%s(%.3f,%.3f), toffset=%s' % (ioffset, ioffset_std, ioffset_max, joffset, joffset_std, joffset_max, toffset))
plt.draw()
plt.show()
return ioffset_max
scan_speed = pixel_size / pixel_time
if options.flyback is None:
flyback = min(2, pixel_size / pixel_time / pixel_flyback_rate)
else:
flyback = options.flyback
assert flyback >= 0, ` flyback `
mirror_params = {}
for k, v in options.__dict__.items():
if k.startswith('param_'):
mirror_params[k[6:]] = v
if options.task != 'scan':
sample_clock = SampleClock(pixel_time=pixel_time,
pixel_size=pixel_size)
samples_per_pixel, clock_rate, min_clock_rate = sample_clock.get_optimal_scanning_parameters(
)
mirror = MirrorDriver(
image_size=(image_width, options.image_height),
T=samples_per_pixel,
flyback_ratio=flyback,
flystart_ratio=0.05,
alpha=options.orientation_angle,
roi=(options.roi_x0, options.roi_y0, options.roi_x1,
options.roi_y1),
clock_rate=clock_rate,
#params = mirror_params
)
if options.task == 'initialize':
if options.flyback is None:
flyback = min(2, pixel_size / pixel_time / pixel_flyback_rate)
else:
flyback = options.flyback
assert flyback>=0, `flyback`
mirror_params = {}
for k,v in options.__dict__.items():
if k.startswith ('param_'):
mirror_params[k[6:]] = v
if options.task!='scan':
sample_clock = SampleClock(pixel_time = pixel_time,
pixel_size = pixel_size)
samples_per_pixel, clock_rate, min_clock_rate = sample_clock.get_optimal_scanning_parameters()
mirror = MirrorDriver(image_size = (image_width, options.image_height),
T=samples_per_pixel,
flyback_ratio = flyback,
flystart_ratio = 0.05,
alpha = options.orientation_angle,
roi = (options.roi_x0, options.roi_y0, options.roi_x1, options.roi_y1),
clock_rate = clock_rate,
#params = mirror_params
)
if options.task=='initialize':
return