def _home_fired(self):
"""
"""
t = Thread(name='stage.home', target=self._home)
t.start()
# need to store a reference to thread so it is not garbage collected
self.move_thread = t
def _do_execute(self):
mapper = self.mapper
mapper.laser_manager = self._laser_manager
editor = self.editor
padding = editor.padding
# if editor.discrete_scan:
# mapper.canvas = self.canvas
# self.component = self.canvas
# else:
c = mapper.make_component(padding)
self.component = c
bd = editor.beam_diameter
rp = editor.request_power
cx = editor.center_x
cy = editor.center_y
step_len = editor.step_length
t = Thread(target=mapper.do_power_mapping,
args=(bd, rp, cx, cy, padding, step_len))
t.start()
self._execute_thread = t
return True
def _do_execute(self):
mapper = self.mapper
mapper.laser_manager = self._laser_manager
editor = self.editor
padding = editor.padding
# if editor.discrete_scan:
# mapper.canvas = self.canvas
# self.component = self.canvas
# else:
c = mapper.make_component(padding)
self.component = c
bd = editor.beam_diameter
rp = editor.request_power
cx = editor.center_x
cy = editor.center_y
step_len = editor.step_length
t = Thread(target=mapper.do_power_mapping,
args=(bd, rp, cx, cy, padding, step_len))
t.start()
self._execute_thread = t
return True
def _test1(self):
print('test1')
ld = LumenDetector()
def func():
src = copy(self.manager.video.get_cached_frame())
# dim = self.stage_map.g_dimension
ld.pxpermm = 31
dim = 1.5
mask_dim = dim * 1.05
offx, offy = 0, 0
cropdim = dim * 2.5
src = ld.crop(src, cropdim, cropdim, offx, offy, verbose=False)
ld.find_targets(
self.display_image,
src,
dim,
mask=mask_dim,
search={
'start_offset_scalar': 1,
# 'width': 2
})
# self.manager.calculate_new_center(0, 0, 0, 0, dim=1.25)
t = Thread(target=func)
t.start()
self.t = t
def _home_fired(self):
"""
"""
t = Thread(name='stage.home', target=self._home)
t.start()
# need to store a reference to thread so it is not garbage collected
self.move_thread = t
def _test1(self):
self.test_image.setup_images(
3,
# (475, 613)
(640, 480))
t = Thread(target=self._test)
t.start()
self._t = t
def _test1(self):
self.test_image.setup_images(3,
# (475, 613)
(640, 480)
)
t = Thread(target=self._test)
t.start()
self._t = t
def _test_fired(self):
from pychron.globals import globalv
p = '/Users/ross/Sandbox/test_target.jpg'
# p = '/Users/ross/Sandbox/pos_err/pos_err_200_0-002.jpg'
p = '/Users/ross/Sandbox/poserror/pos_err_221_0-007.jpg'
# p = '/Users/ross/Sandbox/poserror/snapshot009.jpg'
# force video to reload test image
self.video.source_frame = None
globalv.video_test_path = p
im = self.setup_image()
# self._test2(im)
from pychron.core.ui.thread import Thread
t = Thread(target=self._test2, args=(im,))
t.start()
self._t = t
def _test_fired(self):
from pychron.globals import globalv
p = '/Users/ross/Sandbox/test_target.jpg'
# p = '/Users/ross/Sandbox/pos_err/pos_err_200_0-002.jpg'
p = '/Users/ross/Sandbox/poserror/pos_err_221_0-007.jpg'
# p = '/Users/ross/Sandbox/poserror/snapshot009.jpg'
# force video to reload test image
self.video.source_frame = None
globalv.video_test_path = p
im = self.setup_image()
# self._test2(im)
from pychron.core.ui.thread import Thread
t = Thread(target=self._test2, args=(im, ))
t.start()
self._t = t
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True):
self.debug('doing pc')
self.canceled = False
self.alive = True
args = (save, confirm_save, warn)
if new_thread:
t = Thread(name='ion_optics.peak_center', target=self._peak_center,
args=args)
t.start()
self._thread = t
return t
else:
self._peak_center(*args)
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True):
self.debug('doing pc')
self.canceled = False
self.alive = True
args = (save, confirm_save, warn)
if new_thread:
t = Thread(name='ion_optics.peak_center',
target=self._peak_center,
args=args)
t.start()
self._thread = t
return t
else:
self._peak_center(*args)
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True,
message='',
on_end=None,
timeout=None):
self.debug('doing pc')
self.canceled = False
self.alive = True
self.peak_center_result = None
args = (save, confirm_save, warn, message, on_end, timeout)
if new_thread:
t = Thread(name='ion_optics.peak_center', target=self._peak_center,
args=args)
t.start()
self._centering_thread = t
return t
else:
self._peak_center(*args)
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True,
message='',
on_end=None,
timeout=None):
self.debug('doing pc')
self.canceled = False
self.alive = True
self.peak_center_result = None
args = (save, confirm_save, warn, message, on_end, timeout)
if new_thread:
t = Thread(name='ion_optics.peak_center',
target=self._peak_center,
args=args)
t.start()
self._centering_thread = t
return t
else:
self._peak_center(*args)
class PatternExecutor(Patternable):
"""
a pattern is only good for one execution.
self.pattern needs to be reset after stop or finish using load_pattern(name_or_pickle)
"""
controller = Any
laser_manager = Any
show_patterning = Bool(False)
_alive = Bool(False)
def __init__(self, *args, **kw):
super(PatternExecutor, self).__init__(*args, **kw)
self._next_point = None
self.pattern = None
self._xy_thread = None
self._power_thread = None
self._z_thread = None
def start(self, show=False):
self._alive = True
if show:
self.show_pattern()
if self.pattern:
self.pattern.clear_graph()
def finish(self):
self._alive = False
self.close_pattern()
self.pattern = None
def set_stage_values(self, sm):
if self.pattern:
self.pattern.set_stage_values(sm)
def set_current_position(self, x, y, z):
if self.isPatterning():
graph = self.pattern.graph
graph.set_data([x], series=1, axis=0)
graph.set_data([y], series=1, axis=1)
graph.add_datum((x, y), series=2)
graph.redraw()
def load_pattern(self, name_or_pickle):
"""
look for name_or_pickle in local pattern dir
if not found try interpreting name_or_pickle is a pickled name_or_pickle
"""
if name_or_pickle is None:
path = self.open_file_dialog()
if path is None:
return
else:
path = self.is_local_pattern(name_or_pickle)
if path:
wfile = open(path, 'rb')
else:
# convert name_or_pickle into a file like obj
wfile = StringIO(name_or_pickle)
# self._load_pattern sets self.pattern
pattern = self._load_pattern(wfile, path)
self.on_trait_change(self.stop, 'canceled')
return pattern
def is_local_pattern(self, name):
def test_name(ni):
path = os.path.join(paths.pattern_dir, ni)
if os.path.isfile(path):
return path
for ni in (name, name + '.lp'):
p = test_name(ni)
if p:
return p
def stop(self):
self._alive = False
if self.controller:
self.info('User requested stop')
self.controller.stop()
if self.pattern is not None:
if self.controller:
self.controller.linear_move(self.pattern.cx, self.pattern.cy, source='pattern stop')
# self.pattern.close_ui()
self.info('Pattern {} stopped'.format(self.pattern_name))
# prevent future stops (AbortJogs from massspec) from executing
self.pattern = None
def isPatterning(self):
return self._alive
def close_pattern(self):
pass
def show_pattern(self):
self.pattern.window_x = 50
self.pattern.window_y = 50
open_view(self.pattern, view='graph_view')
def execute(self, block=False, duration=None, thread_safe=True):
"""
if block is true wait for patterning to finish
before returning
"""
if not self.pattern:
return
self.start(show=self.show_patterning)
evt = None
# if current_thread().name != 'MainThread':
if thread_safe:
evt = Event()
invoke_in_main_thread(self._pre_execute, evt)
while not evt.is_set():
time.sleep(0.05)
else:
self._pre_execute(evt)
self.debug('execute xy pattern')
xyp = self.pattern.xy_pattern_enabled
if duration:
self.pattern.external_duration = float(duration)
if xyp:
self._xy_thread = Thread(target=self._execute_xy_pattern)
self._xy_thread.start()
pp = self.pattern.power_pattern
if pp:
self.debug('execute power pattern')
self._power_thread = Thread(target=self._execute_power_pattern)
self._power_thread.start()
zp = self.pattern.z_pattern
if zp:
self.debug('execute z pattern')
self._z_thread = Thread(target=self._execute_z_pattern)
self._z_thread.start()
if block:
if self._xy_thread:
self._xy_thread.join()
if self._z_thread:
self._z_thread.join()
if self._power_thread:
self._power_thread.join()
self.finish()
def _pre_execute(self, evt):
self.debug('pre execute')
pattern = self.pattern
kind = pattern.kind
if kind in ('SeekPattern', 'DragonFlyPeakPattern'):
self._info = open_view(pattern, view='execution_graph_view')
if evt is not None:
evt.set()
self.debug('pre execute finished')
def _execute_power_pattern(self):
pat = self.pattern
self.info('starting power pattern {}'.format(pat.name))
def func(v):
self.laser_manager.set_laser_power(v)
self._execute_(func, pat.power_values(), pat.power_sample, 'power pattern setpoint={value}')
def _execute_z_pattern(self):
pat = self.pattern
self.info('starting power pattern {}'.format(pat.name))
def func(v):
self.controller.set_z(v)
self._execute_(func, pat.z_values(), pat.z_sample, 'z pattern z={value}')
def _execute_(self, func, vs, period, msg):
for v in vs:
st = time.time()
self.debug(msg.format(value=v))
func(v)
et = st - time.time()
p = period - et
time.sleep(p)
def _execute_xy_pattern(self):
pat = self.pattern
self.info('starting pattern {}'.format(pat.name))
st = time.time()
self.controller.update_position()
time.sleep(1)
pat.cx, pat.cy = self.controller.x, self.controller.y
try:
for ni in range(pat.niterations):
if not self.isPatterning():
break
self.info('doing pattern iteration {}'.format(ni))
self._execute_iteration()
self.controller.linear_move(pat.cx, pat.cy, block=True, source='execute_xy_pattern')
if pat.disable_at_end:
self.laser_manager.disable_device()
self.finish()
self.info('finished pattern: transit time={:0.1f}s'.format(time.time() - st))
except (TargetPositionError, PositionError) as e:
self.finish()
self.controller.stop()
self.laser_manager.emergency_shutoff(str(e))
def _execute_iteration(self):
controller = self.controller
pattern = self.pattern
if controller is not None:
kind = pattern.kind
if kind == 'ArcPattern':
self._execute_arc(controller, pattern)
elif kind == 'CircularContourPattern':
self._execute_contour(controller, pattern)
elif kind in ('SeekPattern', 'DragonFlyPeakPattern'):
self._execute_seek(controller, pattern)
else:
self._execute_points(controller, pattern, multipoint=False)
def _execute_points(self, controller, pattern, multipoint=False):
pts = pattern.points_factory()
if multipoint:
controller.multiple_point_move(pts, velocity=pattern.velocity)
else:
for x, y in pts:
if not self.isPatterning():
break
controller.linear_move(x, y, block=True,
velocity=pattern.velocity)
def _execute_contour(self, controller, pattern):
for ni in range(pattern.nsteps):
if not self.isPatterning():
break
r = pattern.radius * (1 + ni * pattern.percent_change)
self.info('doing circular contour {} {}'.format(ni + 1, r))
controller.single_axis_move('x', pattern.cx + r,
block=True)
controller.arc_move(pattern.cx, pattern.cy, 360,
block=True)
time.sleep(0.1)
def _execute_arc(self, controller, pattern):
controller.single_axis_move('x', pattern.radius, block=True)
controller.arc_move(pattern.cx, pattern.cy, pattern.degrees, block=True)
def _execute_seek(self, controller, pattern):
duration = pattern.duration
total_duration = pattern.total_duration
lm = self.laser_manager
sm = lm.stage_manager
ld = sm.lumen_detector
ld.mask_kind = pattern.mask_kind
ld.custom_mask = pattern.custom_mask_radius
osdp = sm.canvas.show_desired_position
sm.canvas.show_desired_position = False
st = time.time()
self.debug('Pre seek delay {}'.format(pattern.pre_seek_delay))
time.sleep(pattern.pre_seek_delay)
self.debug('starting seek')
self.debug('total duration {}'.format(total_duration))
self.debug('dwell duration {}'.format(duration))
if pattern.kind == 'DragonFlyPeakPattern':
try:
self._dragonfly_peak(st, pattern, lm, controller)
except BaseException as e:
self.critical('Dragonfly exception. {}'.format(e))
else:
self._hill_climber(st, controller, pattern)
sm.canvas.show_desired_position = osdp
from pyface.gui import GUI
GUI.invoke_later(self._info.dispose)
def _dragonfly_peak(self, st, pattern, lm, controller):
# imgplot, imgplot2, imgplot3 = pattern.setup_execution_graph()
# imgplot, imgplot2 = pattern.setup_execution_graph()
imgplot, imgplot2 = pattern.setup_execution_graph(nplots=2)
cx, cy = pattern.cx, pattern.cy
sm = lm.stage_manager
linear_move = controller.linear_move
in_motion = controller.in_motion
find_lum_peak = sm.find_lum_peak
set_data = imgplot.data.set_data
set_data2 = imgplot2.data.set_data
duration = pattern.duration
sat_threshold = pattern.saturation_threshold
total_duration = pattern.total_duration
min_distance = pattern.min_distance
aggressiveness = pattern.aggressiveness
update_period = pattern.update_period / 1000.
move_threshold = pattern.move_threshold
blur = pattern.blur
px, py = cx, cy
point_gen = None
cnt = 0
peak = None
while time.time() - st < total_duration:
if not self._alive:
break
sats = []
pts = []
ist = time.time()
npt = None
self.debug('starting iteration={}, in_motion={}'.format(cnt, in_motion()))
while time.time() - ist < duration or in_motion():
args = find_lum_peak(min_distance, blur)
if args is None:
continue
pt, peakcol, peakrow, peak_img, sat, src = args
sats.append(sat)
if peak is None:
peak = peak_img
else:
peak = ((peak.astype('int16') - 2) + peak_img).clip(0, 255)
img = gray2rgb(peak).astype(uint8)
src = gray2rgb(src).astype(uint8)
if pt:
pts.append(pt)
c = circle(peakrow, peakcol, min_distance / 2)
img[c] = (255, 0, 0)
src[c] = (255, 0, 0)
# set_data('imagedata', src)
set_data2('imagedata', src)
set_data('imagedata', img)
sleep(update_period)
self.debug('iteration {} finished, npts={}'.format(cnt, len(pts)))
pattern.position_str = '---'
if pts:
w = array(sats)
avg_sat_score = w.mean()
self.debug('Average Saturation: {} threshold={}'.format(avg_sat_score, sat_threshold))
pattern.average_saturation = avg_sat_score
if avg_sat_score < sat_threshold:
pts = array(pts)
x, y, w = pts.T
ws = w.sum()
nx = (x * w).sum() / ws
ny = (y * w).sum() / ws
self.debug('New point {},{}'.format(nx, ny))
npt = nx, ny, 1
else:
continue
# if npt is None:
# if not point_gen:
# point_gen = pattern.point_generator()
# # wait = False
# npt = next(point_gen)
# self.debug('generating new point={}'.format(npt))
#
# else:
# point_gen = None
# wait = True
if npt is None:
block = total_duration - (time.time() - st) < duration
linear_move(cx, cy, source='recenter_dragonfly{}'.format(cnt), block=block, velocity=pattern.velocity,
use_calibration=False)
pattern.position_str = 'Return to Center'
px, py = cx, cy
continue
try:
scalar = npt[2]
except IndexError:
scalar = 1
ascalar = scalar * aggressiveness
dx = npt[0] / sm.pxpermm * ascalar
dy = npt[1] / sm.pxpermm * ascalar
if abs(dx) < move_threshold or abs(dy) < move_threshold:
self.debug('Deviation too small dx={},dy={}'.format(dx, dy, move_threshold))
pattern.position_str = 'Deviation too small'
continue
px += dx
py -= dy
self.debug('i: {}. point={},{}. '
'Intensitiy Scalar={}, Modified Scalar={}'.format(cnt, px, py, scalar, ascalar))
if not pattern.validate(px, py):
self.debug('invalid position. {},{}'.format(px, py))
px, py = pattern.reduce_vector_magnitude(px, py, 0.85)
self.debug('reduced vector magnitude. new pos={},{}'.format(px, py))
pattern.position_str = '{:0.5f},{:0.5f}'.format(px, py)
# if there is less than 1 duration left then block is true
block = total_duration - (time.time() - st) < duration
self.debug('blocking ={}'.format(block))
linear_move(px, py, source='dragonfly{}'.format(cnt), block=block, velocity=pattern.velocity,
use_calibration=False)
# if wait:
# et = time.time() - ist
# d = duration - et
# if d > 0:
# time.sleep(d)
cnt += 1
# time.sleep(1)
self.debug('dragonfly complete')
controller.block()
def _hill_climber(self, st, controller, pattern):
g = pattern.execution_graph
imgplot, cp = pattern.setup_execution_graph()
cx, cy = pattern.cx, pattern.cy
sm = self.laser_manager.stage_manager
linear_move = controller.linear_move
get_scores = sm.get_scores
moving = sm.moving
update_axes = sm.update_axes
set_data = imgplot.data.set_data
sat_threshold = pattern.saturation_threshold
total_duration = pattern.total_duration
duration = pattern.duration
pattern.perimeter_radius *= sm.pxpermm
avg_sat_score = -1
# current_x, current_y =None, None
for i, pt in enumerate(pattern.point_generator()):
update_plot = True
x, y = pt.x, pt.y
ax, ay = cx + x, cy + y
if not self._alive:
break
if time.time() - st > total_duration:
break
# use_update_point = False
if avg_sat_score < sat_threshold:
# use_update_point = False
# current_x, current_y = x, y
linear_move(ax, ay, block=False, velocity=pattern.velocity,
use_calibration=False,
update=False,
immediate=True)
else:
self.debug('Saturation target reached. not moving')
update_plot = False
density_scores = []
ts = []
saturation_scores = []
positions = []
def measure_scores(update=False):
if update:
update_axes()
positions.append((controller.x, controller.y))
score_density, score_saturation, img = get_scores()
density_scores.append(score_density)
saturation_scores.append(score_saturation)
set_data('imagedata', img)
ts.append(time.time() - st)
time.sleep(0.1)
while moving(force_query=True):
measure_scores(update=True)
mt = time.time()
while time.time() - mt < duration:
measure_scores()
if density_scores:
n = len(density_scores)
density_scores = array(density_scores)
saturation_scores = array(saturation_scores)
weights = [1 / (max(0.0001, ((xi - ax) ** 2 + (yi - ay) ** 2)) ** 0.5) for xi, yi in positions]
avg_score = average(density_scores, weights=weights)
avg_sat_score = average(saturation_scores, weights=weights)
score = avg_score
m, b = polyfit(ts, density_scores, 1)
if m > 0:
score *= (1 + m)
pattern.set_point(score, pt)
self.debug('i:{} XY:({:0.5f},{:0.5f})'.format(i, x, y))
self.debug('Density. AVG:{:0.3f} N:{} Slope:{:0.3f}'.format(avg_score, n, m))
self.debug('Modified Density Score: {:0.3f}'.format(score))
self.debug('Saturation. AVG:{:0.3f}'.format(avg_sat_score))
if update_plot:
cp.add_point((x, y))
g.add_datum((x, y), plotid=0)
t = time.time() - st
g.add_datum((t, avg_score), plotid=1)
# g.add_bulk_data(ts, density_scores, plotid=1, series=1)
g.add_datum((t, score),
ypadding='0.1',
ymin_anchor=-0.1,
update_y_limits=True, plotid=1)
update_axes()
class Scanner(Loggable):
"""
Scanner is a base class for displaying a scan of device data
ScanableDevices has this ability built in but more complicated scans are
best done here. ScanableDevice scan is best used from continuous long term recording
of a single or multiple values
"""
_graph = Instance(StreamStackedGraph)
manager = Instance(ILaserManager)
data_manager = Instance(CSVDataManager, ())
'''
list of callables. should return a signal value for graphing
'''
functions = List
static_values = List
scan_period = Int # ms
stop_event = Event
setpoint = Float(enter_set=True, auto_set=False)
control_path = File
_warned = False
_scanning = Bool
_directory = None
_base_frame_name = None
def new_static_value(self, name, *args, **kw):
self.static_values.append((name, None))
if args:
self.set_static_value(name, *args, **kw)
def set_static_value(self, name_or_idx, value, plotid=None):
"""
if the plotid is not None add a horizontal guide at value
"""
if isinstance(name_or_idx, str):
name_or_idx = next(
(i for i, (e, a) in enumerate(self.static_values)), None)
if name_or_idx is not None:
name = self.static_values[name_or_idx][0]
self.static_values[name_or_idx] = (name, value)
if plotid is not None:
self._graph.add_horizontal_rule(value, plotid=plotid)
def setup(self, directory=None, base_frame_name=None):
self._directory = directory
self._base_frame_name = base_frame_name
def new_function(self, function, name=None):
if name is None:
name = function.func_name
# g = self.graph
# func = self.functions
# kw = dict(ytitle=name,)
# n = len(func)
# if n == 0:
# kw['xtitle'] = 'Time'
self.functions.append((function, name))
def make_graph(self):
g = StreamStackedGraph(window_x=50, window_y=100)
for i, (_, name) in enumerate(self.functions):
kw = dict(ytitle=name, )
if i == 0:
kw['xtitle'] = 'Time'
g.new_plot(data_limit=3000, **kw)
g.new_series(plotid=i)
self._graph = g
return g
def stop(self):
self._timer.Stop()
self._scanning = False
self.stop_event = True
self.info('scan stopped')
if self.manager:
self._stop_hook()
self.manager.disable_device()
def _stop_hook(self):
pass
def execute(self):
if self._scanning:
self.stop()
else:
self.data_manager.new_frame(directory=self._directory,
base_frame_name=self._base_frame_name)
# write metadata if available
self._write_metadata()
# make header row
header = ['t'] + self._make_func_names() + \
[n for n, _ in self.static_values]
self.data_manager.write_to_frame(header)
self._scanning = True
if self.manager:
if self.manager.enable_device():
self._scanning = True
return self._scanning
def do_scan(self):
self._starttime = time.time()
self._execute()
def _execute(self):
yd = self._read_control_path()
if yd is None:
sp = 1000
else:
sp = yd['period']
# starts automatically
self.debug('scan starting')
self._timer = Timer(sp, self._scan)
self.info('scan started')
# yd = self._read_control_path()
if yd is not None:
# start a control thread
self._control_thread = Thread(target=self._control, args=(yd, ))
self._control_thread.start()
self.info('control started')
# if self.manager:
# if self.manager.enable_device():
#
# # starts automatically
# self.debug('scan starting')
# self._timer = Timer(sp, self._scan)
#
# self.info('scan started')
# self._scanning = True
# # yd = self._read_control_path()
# if yd is not None:
# # start a control thread
# self._control_thread = Thread(target=self._control,
# args=(yd,)
# )
# self._control_thread.start()
# self.info('control started')
# else:
# self.warning('Could not enable device')
# else:
# self.warning('no manager available')
def _control(self, ydict):
self.start_control_hook(ydict)
# if self.manager:
# if self.manager.temperature_controller:
# self.manager.temperature_controller.enable_tru_tune = True
start_delay = ydict['start_delay']
end_delay = ydict['end_delay']
setpoints = ydict['setpoints']
print setpoints
self.set_static_value('Setpoint', 0)
time.sleep(start_delay)
for args in setpoints:
t = args[0]
if self._scanning:
self.setpoint = t
self._set_power_hook(t)
self.set_static_value('Setpoint', t, plotid=0)
self._maintain_setpoint(t, *args[1:])
if self._scanning:
self.setpoint = 0
self.set_static_value('Setpoint', 0)
self._set_power_hook(0)
# if self.manager:
# self.manager.set_laser_temperature(0)
time.sleep(end_delay)
self.stop()
self.end_control_hook(self._scanning)
def _set_power_hook(self, t):
if self.manager:
self.manager.set_laser_temperature(t)
def _maintain_setpoint(self, t, d, *args):
self.info('setting setpoint to {} for {}s'.format(t, d))
st = time.time()
while time.time() - st < d and self._scanning:
time.sleep(1)
def start_control_hook(self, *args, **kw):
pass
def end_control_hook(self, ok):
pass
def _make_func_names(self):
return [name for _, name in self.functions]
def _write_metadata(self):
pass
def _scan(self):
functions = self.functions
data = []
record = self._graph.record
# record = self.graph.record
x = time.time() - self._starttime
for i, (func, _) in enumerate(functions):
try:
if hasattr(func, 'next'):
func = func.next
v = float(func())
data.append(v)
# do_after no longer necessary with Qt
record(v, plotid=i, x=x, do_after=None)
except Exception, e:
print 'exception', e
sv = []
for _, v in self.static_values:
if v is None:
v = ''
sv.append(v)
data = [x] + data + sv
self.data_manager.write_to_frame(data)
class StageManager(BaseStageManager):
"""
"""
autocenter_button = Button
stage_controller_klass = String('Newport')
stage_controller = Instance(MotionController)
points_programmer = Instance(PointsProgrammer)
motion_controller_manager = Instance(MotionControllerManager)
# canvas = Instance(LaserTrayCanvas)
simulation = DelegatesTo('stage_controller')
# stage_map_klass = StageMap
# _stage_map = Instance(StageMap)
# stage_map = Property(depends_on='_stage_map')
# stage_maps = Property(depends_on='_stage_maps')
# _stage_maps = List
# ===========================================================================
# buttons
# ===========================================================================
home = Button('home')
home_option = String('Home All')
home_options = List
ejoystick = Event
joystick_label = String('Enable Joystick')
joystick = Bool(False)
joystick_timer = None
back_button = Button
stop_button = Button('Stop')
use_autocenter = Bool
keep_images_open = Bool(False)
_default_z = 0
_cached_position = None
_cached_current_hole = None
_homing = False
def __init__(self, *args, **kw):
"""
"""
super(StageManager, self).__init__(*args, **kw)
self.stage_controller = self._stage_controller_factory()
def measure_grain_polygon(self):
pass
def stop_measure_grain_polygon(self):
pass
def shutdown(self):
self._save_stage_map()
def create_device(self, *args, **kw):
dev = super(StageManager, self).create_device(*args, **kw)
dev.parent = self
return dev
def goto_position(self, v, **kw):
if XY_REGEX[0].match(v):
self._move_to_calibrated_position(v)
elif POINT_REGEX.match(v) or TRANSECT_REGEX[0].match(v):
self.move_to_point(v)
else:
self.move_to_hole(v, user_entry=True, **kw)
def get_current_position(self):
if self.stage_controller:
x = self.stage_controller.x
y = self.stage_controller.y
return x, y
def get_current_hole(self):
pos = self.get_current_position()
if self.stage_map:
if distance_threshold(pos, self._cached_position, self.stage_map.g_dimension / 4):
h = self.get_calibrated_hole(*pos, tol=self.stage_map.g_dimension / 2.)
if h is not None:
self._cached_current_hole = h
self._cached_position = pos
return self._cached_current_hole
def is_auto_correcting(self):
return False
def bind_preferences(self, pref_id):
bind_preference(self.canvas, 'show_grids', '{}.show_grids'.format(pref_id))
self.canvas.change_grid_visibility()
bind_preference(self.canvas, 'show_laser_position', '{}.show_laser_position'.format(pref_id))
bind_preference(self.canvas, 'show_desired_position', '{}.show_desired_position'.format(pref_id))
bind_preference(self.canvas, 'desired_position_color', '{}.desired_position_color'.format(pref_id),
factory=ColorPreferenceBinding)
# bind_preference(self.canvas, 'render_map', '{}.render_map'.format(pref_id))
#
bind_preference(self.canvas, 'crosshairs_kind', '{}.crosshairs_kind'.format(pref_id))
bind_preference(self.canvas, 'crosshairs_line_width', '{}.crosshairs_line_width'.format(pref_id))
bind_preference(self.canvas, 'crosshairs_color',
'{}.crosshairs_color'.format(pref_id),
factory=ColorPreferenceBinding)
bind_preference(self.canvas, 'crosshairs_radius', '{}.crosshairs_radius'.format(pref_id))
bind_preference(self.canvas, 'crosshairs_offsetx', '{}.crosshairs_offsetx'.format(pref_id))
bind_preference(self.canvas, 'crosshairs_offsety', '{}.crosshairs_offsety'.format(pref_id))
bind_preference(self.canvas, 'show_hole_label', '{}.show_hole_label'.format(pref_id))
bind_preference(self.canvas, 'hole_label_color', '{}.hole_label_color'.format(pref_id))
bind_preference(self.canvas, 'hole_label_size', '{}.hole_label_size'.format(pref_id))
self.canvas.handle_hole_label_size(self.canvas.hole_label_size)
bind_preference(self.canvas, 'scaling', '{}.scaling'.format(pref_id))
bind_preference(self.canvas, 'show_bounds_rect',
'{}.show_bounds_rect'.format(pref_id))
self.canvas.request_redraw()
def load(self):
super(StageManager, self).load()
config = self.get_configuration()
if config:
self._default_z = self.config_get(config, 'Defaults', 'z', default=13, cast='float')
self.points_programmer.load_stage_map(self.stage_map_name)
# load the calibration file
# should have calibration files for each stage map
self.tray_calibration_manager.load_calibration()
def finish_loading(self):
self.initialize_stage()
def initialize_stage(self):
self.update_axes()
axes = self.stage_controller.axes
self.home_options = ['Home All', 'XY'] + sorted([axes[a].name.upper() for a in axes])
self.canvas.parent = self
def save_calibration(self, name):
self.tray_calibration_manager.save_calibration(name=name)
# def add_stage_map(self, v):
# sm = self.stage_map_klass(file_path=v)
# psm = self._get_stage_map_by_name(sm.name)
# if psm:
# self._stage_maps.remove(psm)
# self._stage_maps.append(sm)
def accept_point(self):
self.points_programmer.accept_point()
def set_stage_map(self, v):
return self._set_stage_map(v)
def single_axis_move(self, *args, **kw):
return self.stage_controller.single_axis_move(*args, **kw)
def linear_move(self, x, y, use_calibration=True, check_moving=False, abort_if_moving=False, **kw):
if check_moving:
if self.moving():
self.warning('MotionController already in motion')
if abort_if_moving:
self.warning('Move to {},{} aborted'.format(x, y))
return
else:
self.stop()
self.debug('Motion stopped. moving to {},{}'.format(x, y))
pos = (x, y)
if use_calibration:
pos = self.get_calibrated_position(pos)
f = lambda x: '{:0.5f},{:0.5f}'.format(*x)
self.debug('%%%%%%%%%%%%%%%%% mapped {} to {}'.format(f((x, y)), f(pos)))
self.stage_controller.linear_move(*pos, **kw)
def move_to_hole(self, hole, **kw):
if self.stage_map.check_valid_hole(hole, **kw):
self._move(self._move_to_hole, hole, name='move_to_hole', **kw)
def move_to_point(self, pt):
self._move(self._move_to_point, pt, name='move_to_point')
def move_polyline(self, line):
self._move(self._move_to_line, line, name='move_to_line')
def move_polygon(self, poly):
self._move(self._move_polygon, poly, name='move_polygon')
def drill_point(self, pt):
self._move(self._drill_point, pt, name='drill_point')
def set_x(self, value, **kw):
return self.stage_controller.single_axis_move('x', value, **kw)
def set_y(self, value, **kw):
return self.stage_controller.single_axis_move('y', value, **kw)
def set_z(self, value, **kw):
return self.stage_controller.single_axis_move('z', value, **kw)
def set_xy(self, x, y, **kw):
hole = self._get_hole_by_position(x, y)
if hole:
self.move_to_hole(hole)
# self._set_hole(hole.id)
# self.move_to_hole(hole.id)
# self._set_hole(hole.id)
else:
return self.linear_move(x, y, **kw)
def get_hole(self, name):
if self.stage_map:
return self.stage_map.get_hole(name)
def move_to_load_position(self):
"""
"""
x, y, z = self.stage_controller.get_load_position()
self.info('moving to load position, x={}, y={}, z={}'.format(x, y, z))
self.stage_controller.linear_move(x, y, grouped_move=False, block=False)
self.stage_controller.set_z(z)
self.stage_controller.block()
def stop(self, ax_key=None, verbose=False):
self._stop(ax_key, verbose)
def relative_move(self, *args, **kw):
self.stage_controller.relative_move(*args, **kw)
def key_released(self):
sc = self.stage_controller
sc.add_consumable((sc.update_axes, tuple()))
def moving(self, force_query=False, **kw):
moving = False
if force_query:
moving = self.stage_controller.moving(**kw)
elif self.stage_controller.timer is not None:
moving = self.stage_controller.timer.isActive()
return moving
def get_brightness(self, **kw):
return 0
def get_scores(self, **kw):
return 0, 0
def define_home(self, **kw):
self.stage_controller.define_home(**kw)
def get_z(self):
return self.stage_controller._z_position
def get_uncalibrated_xy(self, pos=None):
if pos is None:
pos = (self.stage_controller.x, self.stage_controller.y)
if self.stage_controller.xy_swapped():
pos = pos[1], pos[0]
canvas = self.canvas
ca = canvas.calibration_item
if ca:
pos = self.stage_map.map_to_uncalibration(pos,
ca.center,
ca.rotation,
ca.scale)
return pos
def get_calibrated_xy(self):
pos = (self.stage_controller.x, self.stage_controller.y)
if self.stage_controller.xy_swapped():
pos = pos[1], pos[0]
pos = self.canvas.map_offset_position(pos)
return self.get_calibrated_position(pos)
def get_calibrated_hole(self, x, y, tol):
ca = self.canvas.calibration_item
if ca is not None:
smap = self.stage_map
xx, yy = smap.map_to_uncalibration((x, y), ca.center, ca.rotation)
return next((hole for hole in smap.sample_holes
if abs(hole.x - xx) < tol and abs(hole.y - yy) < tol), None)
def get_hole_xy(self, key):
pos = self.stage_map.get_hole_pos(key)
# map the position to calibrated space
pos = self.get_calibrated_position(pos)
return pos
def finish_move_to_hole(self, user_entry):
pass
# private
def _update_axes(self):
if self.stage_controller:
self.stage_controller.update_axes()
def _home(self):
"""
"""
if self._homing:
return
self._homing = True
if self.home_option == 'Home All':
msg = 'homing all motors'
homed = ['x', 'y', 'z']
home_kwargs = dict(x=-25, y=-25, z=50)
elif self.home_option == 'XY':
msg = 'homing x,y'
homed = ['x', 'y']
home_kwargs = dict(x=-25, y=-25)
else:
# define_home =
msg = 'homing {}'.format(self.home_option)
home_kwargs = {self.home_option: -25 if self.home_option in ['X', 'Y'] else 50}
homed = [self.home_option.lower().strip()]
self.info(msg)
# if define_home:
self.stage_controller.set_home_position(**home_kwargs)
self.stage_controller.home(homed)
# explicitly block
# self.stage_controller.block()
if 'z' in homed and 'z' in self.stage_controller.axes:
# will be a positive limit error in z
# self.stage_controller.read_error()
time.sleep(1)
self.info('setting z to nominal position. {} mm '.format(self._default_z))
self.stage_controller.single_axis_move('z', self._default_z, block=True)
self.stage_controller._z_position = self._default_z
if self.home_option in ['XY', 'Home All']:
time.sleep(0.25)
# the stage controller should think x and y are at -25,-25
self.stage_controller._x_position = -25
self.stage_controller._y_position = -25
self.info('moving to center')
try:
self.stage_controller.linear_move(0, 0, block=True, sign_correct=False)
except TargetPositionError as e:
self.warning_dialog('Move Failed. {}'.format(e))
self._homing = False
def _get_hole_by_position(self, x, y):
if self.stage_map:
return self.stage_map._get_hole_by_position(x, y)
def _get_hole_by_name(self, key):
sm = self.stage_map
return sm.get_hole(key)
# ===============================================================================
# special move
# ===============================================================================
def _stop(self, ax_key=None, verbose=False):
self.stage_controller.stop(ax_key=ax_key, verbose=verbose)
if self.parent.pattern_executor:
self.parent.pattern_executor.stop()
# def _move(self, func, pos, name=None, *args, **kw):
# if pos is None:
# return
#
# if self.move_thread and self.move_thread.isRunning():
# self.stage_controller.stop()
# if name is None:
# name = func.func_name
#
# self.move_thread = Thread(name='stage.{}'.format(name),
# target=func, args=(pos,) + args, kwargs=kw)
# self.move_thread.start()
def _drill_point(self, pt):
zend = pt.zend
vel = pt.velocity
# assume already at zstart
st = time.time()
self.info('start drilling. move to {}. velocity={}'.format(zend, vel))
self.set_z(zend, velocity=vel, block=True)
et = time.time() - st
self.info('drilling complete. drilled for {}s'.format(et))
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')
def _raster(self, points, velocity,
step=500,
scale=1000,
find_min=False,
start_callback=None, end_callback=None, verbose=False):
from pychron.core.geometry.scan_line import raster
lines = raster(points, step=step, find_min=find_min)
# initialize variables
cnt = 0
direction = 1
flip = False
lasing = False
sc = self.stage_controller
if verbose:
self.info('start raster')
# print lines
# loop thru each scan line
# for yi, xs in lines[::skip]:
for yi, xs in lines:
if direction == -1:
xs = list(reversed(xs))
# convert odd numbers lists to even
n = len(xs)
if n % 2 != 0:
xs = sorted(list(set(xs)))
# traverse each x-intersection pair
n = len(xs)
for i in range(0, n, 2):
if len(xs) <= 1:
continue
x1, x2, yy = xs[i] / scale, xs[i + 1] / scale, yi / scale
if abs(x1 - x2) > 1e-10:
if not lasing:
if verbose:
self.info('fast to {} {},{}'.format(cnt, x1, yy))
self.linear_move(x1, yy,
mode='absolute', set_stage=False,
block=True)
if start_callback is not None:
start_callback()
lasing = True
else:
if verbose:
self.info('slow to {} {},{}'.format(cnt, x1, yy))
sc.timer = sc.timer_factory()
self.linear_move(x1, yy,
mode='absolute', set_stage=False,
velocity=velocity)
if verbose:
self.info('move to {}a {},{}'.format(cnt, x2, yy))
# if n > 2 and not i * 2 >= n:
# line this scan line has more then 1 segment turn off laser at end of segment
if i + 2 < n and not xs[i + 1] == xs[i + 2]:
self.linear_move(x2, yy, velocity=velocity,
mode='absolute', set_stage=False,
block=True)
self.info('wait for move complete')
if end_callback is not None:
end_callback()
lasing = False
else:
self.linear_move(x2, yy, velocity=velocity,
mode='absolute', set_stage=False,
)
cnt += 1
flip = True
else:
flip = False
if flip:
direction *= -1
sc.block()
if verbose:
self.info('end raster')
def _move_polyline(self, pts, start_callback=None, end_callback=None):
if not isinstance(pts, list):
segs = pts.velocity_segments
segs = segs[:1] + segs
pts = [dict(xy=(pi.x, pi.y), z=pi.z, velocity=vi) for vi, pi in
zip(segs, pts.points)]
sc = self.stage_controller
self.linear_move(pts[0]['xy'][0], pts[0]['xy'][1],
update_hole=False,
use_calibration=False,
block=True)
sc.set_z(pts[0]['z'], block=True)
cpos = dict()
# set motors
for motor in ('mask', 'attenuator'):
if motor in pts[0]:
self.parent.set_motor(motor, pts[0][motor])
cpos[motor] = pts[0][motor]
sc.set_program_mode('absolute')
sc.timer = sc.timer_factory()
if start_callback:
start_callback()
npts = pts[1:]
setmotors = dict()
for i, di in enumerate(npts):
xi, yi, zi, vi = di['xy'][0], di['xy'][1], di['z'], di['velocity']
sc.set_z(zi)
block = False
for motor in ('mask', 'attenuator'):
# fix next step sets motor should block
if i + 1 < len(npts):
dii = npts[i + 1]
if motor in dii and dii[motor] != cpos[motor]:
m = self.parent.get_motor(motor)
if not m.locked:
block = True
setmotors[motor] = dii[motor]
self.linear_move(xi, yi, velocity=vi,
block=block,
mode='absolute', # use absolute mode because commands are queued
set_stage=False)
if block:
if end_callback:
end_callback()
for k, v in setmotors.items():
self.parent.set_motor(k, v, block=True)
if start_callback:
start_callback()
# wait until motion complete
sc.block()
if end_callback:
end_callback()
sc.set_program_mode('relative')
# if start and smooth:
# sc.execute_command_buffer()
# sc.end_command_buffer()
# def start_enqueued(self):
# sc = self.stage_controller
# sc.execute_command_buffer()
# sc.end_command_buffer()
def _move_to_point(self, pt):
self.debug('move to point={}'.format(pt))
if isinstance(pt, str):
pt = self.canvas.get_point(pt)
self.debug('move to point canvas pt={}'.format(pt))
if pt is not None:
pos = pt.x, pt.y
self.info('Move to point {}: {:0.5f},{:0.5f},{:0.5f}'.format(pt.identifier,
pt.x, pt.y, pt.z))
self.stage_controller.linear_move(block=True, *pos)
if hasattr(pt, 'z'):
self.stage_controller.set_z(pt.z, block=True)
self.debug('Not setting motors for pt')
# self.parent.set_motors_for_point(pt)
self._move_to_point_hook()
self.info('Move complete')
self.update_axes()
def _move_to_hole(self, key, correct_position=True, user_entry=False, autocenter_only=False):
self.info('Move to hole {} type={}'.format(key, str(type(key))))
autocentered_position = False
if not autocenter_only:
self.temp_hole = key
self.temp_position = self.stage_map.get_hole_pos(key)
pos = self.stage_map.get_corrected_hole_pos(key)
self.info('position {}'.format(pos))
if pos is not None:
if abs(pos[0]) < 1e-6:
pos = self.stage_map.get_hole_pos(key)
# map the position to calibrated space
pos = self.get_calibrated_position(pos, key=key)
else:
# check if this is an interpolated position
# if so probably want to do an autocentering routine
hole = self.stage_map.get_hole(key)
if hole.interpolated:
self.info('using an interpolated value')
else:
self.info('using previously calculated corrected position')
autocentered_position = True
try:
self.stage_controller.linear_move(block=True, source='move_to_hole {}'.format(pos),
raise_zero_displacement=True, *pos)
except TargetPositionError as e:
self.warning('(001) Move to {} failed'.format(pos))
self.parent.emergency_shutoff(str(e))
return
except ZeroDisplacementException:
correct_position = False
try:
self._move_to_hole_hook(key, correct_position,
autocentered_position)
except TargetPositionError as e:
self.warning('(002) Move failed. {}'.format(e))
self.parent.emergency_shutoff(str(e))
return
self.finish_move_to_hole(user_entry)
self.info('Move complete')
def _move_to_hole_hook(self, *args):
pass
def _move_to_point_hook(self):
pass
# ===============================================================================
# Property Get / Set
# ===============================================================================
def _set_stage_map(self, v):
if v in self.stage_map_names:
for root, ext in ((self.root, '.txt'), (paths.user_points_dir, '.yaml')):
p = os.path.join(root, add_extension(v, ext))
if os.path.isfile(p):
self.info('setting stage map to {}'.format(v))
sm = self.stage_map_klass(file_path=p)
self.canvas.set_map(sm)
self.tray_calibration_manager.load_calibration(stage_map=v)
self.points_programmer.load_stage_map(sm)
return True
else:
self.warning('No stage map named "{}"'.format(v))
return False
def _get_calibrate_stage_label(self):
if self._calibration_state == 'set_center':
r = 'Locate Center'
elif self._calibration_state == 'set_right':
r = 'Locate Right'
else:
r = 'Calibrate Stage'
return r
def _get_program_points_label(self):
return 'Program Points' if not self.canvas.markup else 'End Program'
def _validate_hole(self, v):
nv = None
try:
if v.strip():
nv = int(v)
except TypeError:
self.warning('invalid hole {}'.format(v))
return nv
# def _get_calibrated_position_entry(self):
# return self._calibrated_position
#
# def _set_calibrated_position_entry(self, v):
# self._calibrated_position = v
# if XY_REGEX.match(v):
# self._move_to_calibrated_position(v)
# else:
# self.move_to_hole(v)
def _move_to_calibrated_position(self, pos):
try:
args = csv_to_floats(pos)
except ValueError:
self.warning('invalid calibrated position "{}". Could not convert to floats'.format(pos))
return
if len(args) == 2:
x, y = args
self.linear_move(x, y, use_calibration=True, block=False)
else:
self.warning('invalid calibrated position. incorrect number of arguments "{}"'.format(args))
# def _set_hole(self, v):
# if v is None:
# return
#
# if self.canvas.calibrate:
# self.warning_dialog('Cannot move while calibrating')
# return
#
# if self.canvas.markup:
# self.warning_dialog('Cannot move while adding/editing points')
# return
#
# v = str(v)
#
# if self.move_thread is not None:
# self.stage_controller.stop()
#
# # if self.move_thread is None:
#
# pos = self._stage_map.get_hole_pos(v)
# if pos is not None:
# self.visualizer.set_current_hole(v)
# # self._hole = v
# self.move_thread = Thread(name='stage.move_to_hole',
# target=self._move_to_hole, args=(v,))
# self.move_thread.start()
# else:
# err = 'Invalid hole {}'.format(v)
# self.warning(err)
# return err
# def _get_hole(self):
# return self._hole
def _set_point(self, v):
if self.canvas.calibrate:
self.warning_dialog('Cannot move while calibrating')
return
if self.canvas.markup:
self.warning_dialog('Cannot move while adding/editing points')
return
if (self.move_thread is None or not self.move_thread.isRunning()) and v is not self._point:
pos = self.canvas.get_item('point', int(v) - 1)
if pos is not None:
self._point = v
self.move_thread = Thread(target=self._move_to_point, args=(pos,))
self.move_thread.start()
else:
err = 'Invalid point {}'.format(v)
self.warning(err)
return err
def _get_point(self):
return self._point
# ===============================================================================
# handlers
# ===============================================================================
def _stop_button_fired(self):
self._stop()
def _ejoystick_fired(self):
self.joystick = not self.joystick
if self.joystick:
self.stage_controller.enable_joystick()
self.joystick_label = 'Disable Joystick'
self.joystick_timer = self.timer_factory(func=self._joystick_inprogress_update)
else:
if self.joystick_timer is not None:
self.joystick_timer.Stop()
self.stage_controller.disable_joystick()
self.joystick_label = 'Enable Joystick'
def _home_fired(self):
"""
"""
t = Thread(name='stage.home', target=self._home)
t.start()
# need to store a reference to thread so it is not garbage collected
self.move_thread = t
# do_later(self._home)
def _test_fired(self):
# self.do_pattern('testpattern')
self.do_pattern('pattern003')
# ===============================================================================
# factories
# ===============================================================================
def _motion_configure_factory(self, **kw):
return MotionControllerManager(motion_controller=self.stage_controller,
application=self.application,
**kw)
def _stage_controller_factory(self):
if self.stage_controller_klass == 'Newport':
from pychron.hardware.newport.newport_motion_controller import NewportMotionController
factory = NewportMotionController
elif self.stage_controller_klass == 'Aerotech':
from pychron.hardware.aerotech.aerotech_motion_controller import AerotechMotionController
factory = AerotechMotionController
m = factory(name='{}controller'.format(self.name),
configuration_name='stage_controller',
configuration_dir_name=self.configuration_dir_name,
parent=self)
return m
def _canvas_factory(self):
"""
"""
w = 640 / 2.0 / 23.2
h = 0.75 * w
l = LaserTrayCanvas(stage_manager=self,
padding=[30, 5, 5, 30],
map=self.stage_map,
view_x_range=[-w, w],
view_y_range=[-h, h])
return l
# ===============================================================================
# defaults
# ===============================================================================
def _motion_controller_manager_default(self):
return self._motion_configure_factory()
def _title_default(self):
return '%s Stage Manager' % self.name[:-5].capitalize()
def _points_programmer_default(self):
pp = PointsProgrammer(canvas=self.canvas,
stage_map_klass=self.stage_map_klass,
stage_manager=self)
pp.on_trait_change(self.move_to_point, 'point')
pp.on_trait_change(self.move_polygon, 'polygon')
pp.on_trait_change(self.move_polyline, 'line')
return pp
def execute(self):
self.canceled = False
t = Thread(target=self._execute)
t.start()
self._t = t
class PatternExecutor(Patternable):
"""
a pattern is only good for one execution.
self.pattern needs to be reset after stop or finish using load_pattern(name_or_pickle)
"""
controller = Any
laser_manager = Any
show_patterning = Bool(False)
_alive = Bool(False)
def __init__(self, *args, **kw):
super(PatternExecutor, self).__init__(*args, **kw)
self._next_point = None
self.pattern = None
self._xy_thread = None
self._power_thread = None
self._z_thread = None
def start(self, show=False):
self._alive = True
if show:
self.show_pattern()
if self.pattern:
self.pattern.clear_graph()
def finish(self):
self._alive = False
self.close_pattern()
self.pattern = None
def set_stage_values(self, sm):
if self.pattern:
self.pattern.set_stage_values(sm)
def set_current_position(self, x, y, z):
if self.isPatterning():
graph = self.pattern.graph
graph.set_data([x], series=1, axis=0)
graph.set_data([y], series=1, axis=1)
graph.add_datum((x, y), series=2)
graph.redraw()
def load_pattern(self, name_or_pickle):
"""
look for name_or_pickle in local pattern dir
if not found try interpreting name_or_pickle is a pickled name_or_pickle
"""
if name_or_pickle is None:
path = self.open_file_dialog()
if path is None:
return
else:
path = self.is_local_pattern(name_or_pickle)
if path:
wfile = open(path, 'rb')
else:
# convert name_or_pickle into a file like obj
wfile = StringIO(name_or_pickle)
# self._load_pattern sets self.pattern
pattern = self._load_pattern(wfile, path)
self.on_trait_change(self.stop, 'canceled')
return pattern
def is_local_pattern(self, name):
def test_name(ni):
path = os.path.join(paths.pattern_dir, ni)
if os.path.isfile(path):
return path
for ni in (name, name + '.lp'):
p = test_name(ni)
if p:
return p
def stop(self):
self._alive = False
if self.controller:
self.info('User requested stop')
self.controller.stop()
if self.pattern is not None:
if self.controller:
self.controller.linear_move(self.pattern.cx,
self.pattern.cy,
source='pattern stop')
# self.pattern.close_ui()
self.info('Pattern {} stopped'.format(self.pattern_name))
# prevent future stops (AbortJogs from massspec) from executing
self.pattern = None
def isPatterning(self):
return self._alive
def close_pattern(self):
pass
def show_pattern(self):
self.pattern.window_x = 50
self.pattern.window_y = 50
open_view(self.pattern, view='graph_view')
def execute(self, block=False, duration=None, thread_safe=True):
"""
if block is true wait for patterning to finish
before returning
"""
if not self.pattern:
return
self.start(show=self.show_patterning)
evt = None
# if current_thread().name != 'MainThread':
if thread_safe:
evt = Event()
invoke_in_main_thread(self._pre_execute, evt)
while not evt.is_set():
time.sleep(0.05)
else:
self._pre_execute(evt)
self.debug('execute xy pattern')
xyp = self.pattern.xy_pattern_enabled
if duration:
self.pattern.external_duration = float(duration)
if xyp:
self._xy_thread = Thread(target=self._execute_xy_pattern)
self._xy_thread.start()
pp = self.pattern.power_pattern
if pp:
self.debug('execute power pattern')
self._power_thread = Thread(target=self._execute_power_pattern)
self._power_thread.start()
zp = self.pattern.z_pattern
if zp:
self.debug('execute z pattern')
self._z_thread = Thread(target=self._execute_z_pattern)
self._z_thread.start()
if block:
if self._xy_thread:
self._xy_thread.join()
if self._z_thread:
self._z_thread.join()
if self._power_thread:
self._power_thread.join()
self.finish()
def _pre_execute(self, evt):
self.debug('pre execute')
pattern = self.pattern
kind = pattern.kind
if kind in ('SeekPattern', 'DragonFlyPeakPattern'):
self._info = open_view(pattern, view='execution_graph_view')
if evt is not None:
evt.set()
self.debug('pre execute finished')
def _execute_power_pattern(self):
pat = self.pattern
self.info('starting power pattern {}'.format(pat.name))
def func(v):
self.laser_manager.set_laser_power(v)
self._execute_(func, pat.power_values(), pat.power_sample,
'power pattern setpoint={value}')
def _execute_z_pattern(self):
pat = self.pattern
self.info('starting power pattern {}'.format(pat.name))
def func(v):
self.controller.set_z(v)
self._execute_(func, pat.z_values(), pat.z_sample,
'z pattern z={value}')
def _execute_(self, func, vs, period, msg):
for v in vs:
st = time.time()
self.debug(msg.format(value=v))
func(v)
et = st - time.time()
p = period - et
time.sleep(p)
def _execute_xy_pattern(self):
pat = self.pattern
self.info('starting pattern {}'.format(pat.name))
st = time.time()
self.controller.update_position()
time.sleep(1)
pat.cx, pat.cy = self.controller.x, self.controller.y
try:
for ni in range(pat.niterations):
if not self.isPatterning():
break
self.info('doing pattern iteration {}'.format(ni))
self._execute_iteration(ni)
self.controller.linear_move(pat.cx,
pat.cy,
block=True,
source='execute_xy_pattern')
if pat.disable_at_end:
self.laser_manager.disable_device()
self.finish()
self.info(
'finished pattern: transit time={:0.1f}s'.format(time.time() -
st))
except (TargetPositionError, PositionError) as e:
self.finish()
self.controller.stop()
self.laser_manager.emergency_shutoff(str(e))
def _execute_iteration(self, iteration):
controller = self.controller
pattern = self.pattern
if controller is not None:
kind = pattern.kind
if kind == 'ArcPattern':
self._execute_arc(controller, pattern)
elif kind == 'CircularContourPattern':
self._execute_contour(controller, pattern)
elif kind in ('SeekPattern', 'DragonFlyPeakPattern'):
self._execute_seek(controller, pattern)
else:
self._execute_points(controller,
pattern,
iteration,
multipoint=False)
def _execute_points(self,
controller,
pattern,
iteration,
multipoint=False):
pts = pattern.points_factory()
if multipoint:
controller.multiple_point_move(pts, velocity=pattern.velocity)
else:
for i, (x, y) in enumerate(pts):
self.debug('Pattern Point. {},{}'.format(iteration, i))
if not self.isPatterning():
break
# skip first point after first iteration
if iteration and not i:
self.debug('skipping first point')
continue
self.debug('Pattern Point. {},{}: {},{}'.format(
iteration, i, x, y))
controller.linear_move(x,
y,
block=True,
velocity=pattern.velocity)
def _execute_contour(self, controller, pattern):
for ni in range(pattern.nsteps):
if not self.isPatterning():
break
r = pattern.radius * (1 + ni * pattern.percent_change)
self.info('doing circular contour {} {}'.format(ni + 1, r))
controller.single_axis_move('x', pattern.cx + r, block=True)
controller.arc_move(pattern.cx, pattern.cy, 360, block=True)
time.sleep(0.1)
def _execute_arc(self, controller, pattern):
controller.single_axis_move('x', pattern.radius, block=True)
controller.arc_move(pattern.cx,
pattern.cy,
pattern.degrees,
block=True)
def _execute_seek(self, controller, pattern):
duration = pattern.duration
total_duration = pattern.total_duration
lm = self.laser_manager
sm = lm.stage_manager
ld = sm.lumen_detector
ld.mask_kind = pattern.mask_kind
ld.custom_mask = pattern.custom_mask_radius
osdp = sm.canvas.show_desired_position
sm.canvas.show_desired_position = False
st = time.time()
self.debug('Pre seek delay {}'.format(pattern.pre_seek_delay))
time.sleep(pattern.pre_seek_delay)
self.debug('starting seek')
self.debug('total duration {}'.format(total_duration))
self.debug('dwell duration {}'.format(duration))
if pattern.kind == 'DragonFlyPeakPattern':
try:
self._dragonfly_peak(st, pattern, lm, controller)
except BaseException as e:
self.critical('Dragonfly exception. {}'.format(e))
self.debug_exception()
else:
self._hill_climber(st, controller, pattern)
sm.canvas.show_desired_position = osdp
from pyface.gui import GUI
GUI.invoke_later(self._info.dispose)
def _dragonfly_peak(self, st, pattern, lm, controller):
# imgplot, imgplot2, imgplot3 = pattern.setup_execution_graph()
# imgplot, imgplot2 = pattern.setup_execution_graph()
imgplot, imgplot2 = pattern.setup_execution_graph(nplots=2)
cx, cy = pattern.cx, pattern.cy
sm = lm.stage_manager
linear_move = controller.linear_move
in_motion = controller.in_motion
find_lum_peak = sm.find_lum_peak
pxpermm = sm.pxpermm
set_data = imgplot.data.set_data
set_data2 = imgplot2.data.set_data
# set_data3 = imgplot3.data.set_data
duration = pattern.duration
sat_threshold = pattern.saturation_threshold
total_duration = pattern.total_duration
min_distance = pattern.min_distance
aggressiveness = pattern.aggressiveness
update_period = pattern.update_period / 1000.
move_threshold = pattern.move_threshold
blur = pattern.blur
px, py = cx, cy
ncx, ncy = cx, cy
point_gen = None
cnt = 0
# peak = None
oimg = sm.get_preprocessed_src()
pos_img = zeros_like(oimg, dtype='int16')
per_img = zeros_like(oimg, dtype='int16')
img_h, img_w = pos_img.shape
perimeter_circle = circle(img_h / 2, img_w / 2,
pattern.perimeter_radius * pxpermm)
color = 2**15 - 1
per_img[perimeter_circle] = 50
set_data('imagedata', gray2rgb(per_img.astype(uint8)))
while time.time() - st < total_duration:
if not self._alive:
break
sats = []
pts = []
ist = time.time()
npt = None
self.debug('starting iteration={}, in_motion={}'.format(
cnt, in_motion()))
while time.time() - ist < duration or in_motion():
args = find_lum_peak(min_distance, blur)
if args is None:
sleep(update_period / 5)
continue
sleep(update_period)
pt, peakcol, peakrow, peak_img, sat, src = args
sats.append(sat)
# if peak is None:
# peak = peak_img
# else:
# peak = ((peak.astype('int16') - 2) + peak_img).clip(0, 255)
# img = gray2rgb(peak).astype(uint8)
src = gray2rgb(src).astype(uint8)
if pt:
pts.append(pt)
c = circle(peakrow, peakcol, 2)
# img[c] = (255, 0, 0)
src[c] = (255, 0, 0)
# set_data('imagedata', src)
set_data2('imagedata', src)
# set_data('imagedata', img)
self.debug('iteration {} finished, npts={}'.format(cnt, len(pts)))
pattern.position_str = NULL_STR
if pts:
w = array(sats)
avg_sat_score = w.mean()
self.debug('Average Saturation: {} threshold={}'.format(
avg_sat_score, sat_threshold))
pattern.average_saturation = avg_sat_score
if avg_sat_score < sat_threshold:
# pts = array(pts)
x, y, w = array(pts).T
ws = w.sum()
nx = (x * w).sum() / ws
ny = (y * w).sum() / ws
self.debug('New point {},{}'.format(nx, ny))
npt = nx, ny, 1
else:
continue
if npt is None:
if not point_gen:
point_gen = pattern.point_generator()
# wait = False
x, y = next(point_gen)
px, py = ncx + x, ncy + y
self.debug('generating new point={},{} ---- {},{}'.format(
x, y, px, py))
else:
point_gen = None
# wait = True
if npt is None:
block = total_duration - (time.time() - st) < duration
linear_move(cx,
cy,
source='recenter_dragonfly{}'.format(cnt),
block=block,
velocity=pattern.velocity,
use_calibration=False)
pattern.position_str = 'Return to Center'
px, py = cx, cy
continue
try:
scalar = npt[2]
except IndexError:
scalar = 1
ascalar = scalar * aggressiveness
dx = npt[0] / pxpermm * ascalar
dy = npt[1] / pxpermm * ascalar
if abs(dx) < move_threshold or abs(dy) < move_threshold:
self.debug('Deviation too small dx={},dy={}'.format(
dx, dy, move_threshold))
pattern.position_str = 'Deviation too small'
continue
px += dx
py -= dy
self.debug('i: {}. point={},{}. '
'Intensitiy Scalar={}, Modified Scalar={}'.format(
cnt, px, py, scalar, ascalar))
ncx, ncy = px, py
if not pattern.validate(px, py):
self.debug('invalid position. {},{}'.format(px, py))
curx = px - dx
cury = py + dy
vx = curx - cx
vy = cury - cy
px = vx * aggressiveness + cx
py = vy * aggressiveness + cy
self.debug('reduced vector magnitude. new pos={},{}'.format(
px, py))
# for safety validate this new position
# if above calculation is correct the new position should always be valid
if not pattern.validate(px, py):
self.debug(
'vector calculations incorrect. moving to center position'
)
px, py = cx, cy
ncx, ncy = px, py
pattern.position_str = '{:0.5f},{:0.5f}'.format(px, py)
# if there is less than 1 duration left then block is true
block = total_duration - (time.time() - st) < duration
self.debug('blocking ={}'.format(block))
linear_move(px,
py,
source='dragonfly{}'.format(cnt),
block=block,
velocity=pattern.velocity,
use_calibration=False)
ay, ax = py - cy, px - cx
# self.debug('position mm ax={},ay={}'.format(ax, ay))
ay, ax = int(-ay * pxpermm) + img_h / 2, int(
ax * pxpermm) + img_w / 2
# self.debug('position pixel ax={},ay={}'.format(ax, ay))
pos_img -= 5
pos_img = pos_img.clip(0, color)
c = circle(ay, ax, 2)
pos_img[c] = color - 60
nimg = ((pos_img + per_img).astype(uint8))
set_data('imagedata', gray2rgb(nimg))
cnt += 1
self.debug('dragonfly complete')
controller.block()
def _hill_climber(self, st, controller, pattern):
g = pattern.execution_graph
imgplot, cp = pattern.setup_execution_graph()
cx, cy = pattern.cx, pattern.cy
sm = self.laser_manager.stage_manager
linear_move = controller.linear_move
get_scores = sm.get_scores
moving = sm.moving
update_axes = sm.update_axes
set_data = imgplot.data.set_data
sat_threshold = pattern.saturation_threshold
total_duration = pattern.total_duration
duration = pattern.duration
pattern.perimeter_radius *= sm.pxpermm
avg_sat_score = -1
# current_x, current_y =None, None
for i, pt in enumerate(pattern.point_generator()):
update_plot = True
x, y = pt.x, pt.y
ax, ay = cx + x, cy + y
if not self._alive:
break
if time.time() - st > total_duration:
break
# use_update_point = False
if avg_sat_score < sat_threshold:
# use_update_point = False
# current_x, current_y = x, y
linear_move(ax,
ay,
block=False,
velocity=pattern.velocity,
use_calibration=False,
update=False,
immediate=True)
else:
self.debug('Saturation target reached. not moving')
update_plot = False
density_scores = []
ts = []
saturation_scores = []
positions = []
def measure_scores(update=False):
if update:
update_axes()
positions.append((controller.x, controller.y))
score_density, score_saturation, img = get_scores()
density_scores.append(score_density)
saturation_scores.append(score_saturation)
set_data('imagedata', img)
ts.append(time.time() - st)
time.sleep(0.1)
while moving(force_query=True):
measure_scores(update=True)
mt = time.time()
while time.time() - mt < duration:
measure_scores()
if density_scores:
n = len(density_scores)
density_scores = array(density_scores)
saturation_scores = array(saturation_scores)
weights = [
1 / (max(0.0001, ((xi - ax)**2 + (yi - ay)**2))**0.5)
for xi, yi in positions
]
avg_score = average(density_scores, weights=weights)
avg_sat_score = average(saturation_scores, weights=weights)
score = avg_score
m, b = polyfit(ts, density_scores, 1)
if m > 0:
score *= (1 + m)
pattern.set_point(score, pt)
self.debug('i:{} XY:({:0.5f},{:0.5f})'.format(i, x, y))
self.debug('Density. AVG:{:0.3f} N:{} Slope:{:0.3f}'.format(
avg_score, n, m))
self.debug('Modified Density Score: {:0.3f}'.format(score))
self.debug('Saturation. AVG:{:0.3f}'.format(avg_sat_score))
if update_plot:
cp.add_point((x, y))
g.add_datum((x, y), plotid=0)
t = time.time() - st
g.add_datum((t, avg_score), plotid=1)
# g.add_bulk_data(ts, density_scores, plotid=1, series=1)
g.add_datum((t, score),
ypadding='0.1',
ymin_anchor=-0.1,
update_y_limits=True,
plotid=1)
update_axes()
class AutoFocusManager(Manager):
"""
currently uses passive focus techniques
see
http://en.wikipedia.org/wiki/Autofocus
"""
video = Any
laser_manager = Any
stage_controller = Any
canvas = Any
parameters = Instance(FocusParameters)
configure_button = Button('configure')
autofocus_button = Event
autofocus_label = Property(depends_on='autofocusing')
autofocusing = Bool
# threading event for cancel signal
_evt_autofocusing = None
image = Instance(Image, ())
graph = None
def dump_parameters(self):
p = os.path.join(paths.hidden_dir, 'autofocus_configure')
self.info('dumping parameters to {}'.format(p))
with open(p, 'wb') as f:
pickle.dump(self.parameters, f)
def load_parameter(self):
p = os.path.join(paths.hidden_dir, 'autofocus_configure')
if os.path.isfile(p):
with open(p, 'rb') as f:
try:
params = pickle.load(f)
self.info('loading parameters from {}'.format(p))
if not isinstance(params, FocusParameters):
self.info('out of date parameters file. using default')
params = FocusParameters()
return params
except Exception as e:
print('autofocus load parameter', e)
return FocusParameters()
else:
return FocusParameters()
def passive_focus(self, block=False, **kw):
self._evt_autofocusing = TEvent()
self._evt_autofocusing.clear()
# manager = self.laser_manager
oper = self.parameters.operator
self.info('passive focus. operator = {}'.format(oper))
g = self.graph
if not g:
g = Graph(plotcontainer_dict=dict(padding=10),
window_x=0.70,
window_y=20,
window_width=325,
window_height=325,
window_title='Autofocus')
self.graph = g
g.clear()
g.new_plot(padding=[40, 10, 10, 40],
xtitle='Z (mm)',
ytitle='Focus Measure ({})'.format(oper))
g.new_series()
g.new_series()
invoke_in_main_thread(self._open_graph)
target = self._passive_focus
self._passive_focus_thread = Thread(name='autofocus',
target=target,
args=(self._evt_autofocusing, ),
kwargs=kw)
self._passive_focus_thread.start()
if block:
# while 1:
# if not self._passive_focus_thread.isRunning():
# break
# time.sleep(0.25)
self._passive_focus_thread.join()
def _open_graph(self):
ui = self.graph.edit_traits()
self.add_window(ui)
def stop_focus(self):
if self.stage_controller:
self.stage_controller.stop()
self.info('autofocusing stopped by user')
def _passive_focus(self, stop_signal, set_zoom=True):
'''
sweep z looking for max focus measure
FMgrad= roberts or sobel (sobel removes noise)
FMvar = intensity variance
'''
self.autofocusing = True
manager = self.laser_manager
fstart = self.parameters.fstart
fend = self.parameters.fend
step_scalar = self.parameters.step_scalar
zoom = self.parameters.zoom
operator = self.parameters.operator
steps = step_scalar * (max(fend, fstart) - min(fend, fstart)) + 1
prev_zoom = None
if set_zoom and \
manager is not None and \
zoom:
motor = manager.get_motor('zoom')
if motor:
prev_zoom = motor.data_position
self.info('setting zoom: {}'.format(zoom))
manager.set_motor('zoom', zoom, block=True)
time.sleep(1.5)
args = self._do_focusing(fstart, fend, steps, operator)
if manager is not None:
if prev_zoom is not None:
self.info('returning to previous zoom: {}'.format(prev_zoom))
manager.set_motor('zoom', prev_zoom, block=True)
if args:
mi, fmi, ma, fma = args
self.info('''passive focus results:Operator={}
ImageGradmin={} (z={})
ImageGradmax={}, (z={})'''.format(operator, mi, fmi, ma, fma))
focus_pos = fma
self.graph.add_vertical_rule(focus_pos)
self.graph.redraw()
# self.graph.add_vertical_rule(fma)
self.info('calculated focus z= {}'.format(focus_pos))
# if set_z:
controller = self.stage_controller
if controller is not None:
if not stop_signal.isSet():
controller.single_axis_move('z', focus_pos, block=True)
controller._z_position = focus_pos
controller.z_progress = focus_pos
self.autofocusing = False
def _cancel_sweep(self, vo):
if self._evt_autofocusing.isSet():
# return to original velocity
self.autofocusing = False
self._reset_velocity(vo)
return True
def _reset_velocity(self, vo):
if self.stage_controller:
pdict = dict(velocity=vo, key='z')
self.stage_controller.set_single_axis_motion_parameters(
pdict=pdict)
def _do_focusing(self, start, end, steps, operator):
screen_roi = self._get_roi()
self._add_focus_area_rect(*screen_roi)
src = self._load_source()
src = asarray(src)
h, w, _d = src.shape
cx = w / 2.
cy = h / 2.
cw = self.parameters.crop_width
ch = self.parameters.crop_height
roi = cx, cy, cw, ch
'''
start the z in motion and take pictures as you go
query stage_controller to get current z
'''
self.info('focus sweep start={} end={}'.format(start, end))
# move to start position
controller = self.stage_controller
if controller:
vo = controller.axes['z'].velocity
if self._cancel_sweep(vo):
return
self.graph.set_x_limits(min(start, end), max(start, end), pad=2)
# sweep 1 and velocity 1
self._do_sweep(start,
end,
velocity=self.parameters.velocity_scalar1)
fms, focussteps = self._collect_focus_measures(operator, roi)
if not (fms and focussteps):
return
# reached end of sweep
# calculate a nominal focal point
args = self._calculate_nominal_focal_point(fms, focussteps)
if not args:
return
nfocal = args[3]
nwin = self.parameters.negative_window
pwin = self.parameters.positive_window
if self._cancel_sweep(vo):
return
nstart, nend = max(0, nfocal - nwin), nfocal + pwin
# mi = min(min(nstart, nend), min(start, end))
# ma = max(max(nstart, nend), max(start, end))
# self.graph.set_x_limits(mi, ma, pad=2)
time.sleep(1)
# do a slow tight sweep around the nominal focal point
self._do_sweep(nstart,
nend,
velocity=self.parameters.velocity_scalar2)
fms, focussteps = self._collect_focus_measures(operator,
roi,
series=1)
self._reset_velocity(vo)
else:
focussteps = linspace(0, 10, 11)
fms = -(focussteps - 5)**2 + 10 + random.random(11)
self.info('frames analyzed {}'.format(len(fms)))
# self.canvas.markupcontainer.pop('croprect')
return self._calculate_nominal_focal_point(fms, focussteps)
def _do_sweep(self, start, end, velocity=None):
controller = self.stage_controller
controller.single_axis_move('z', start, block=True)
# time.sleep(0.1)
# explicitly check for motion
# controller.block(axis='z')
if velocity:
vo = controller.axes['z'].velocity
controller.set_single_axis_motion_parameters(
pdict=dict(velocity=vo * velocity, key='z'))
self.info('starting sweep from {}'.format(controller.z_progress))
# pause before moving to end
time.sleep(0.25)
controller.single_axis_move('z', end, update=100, immediate=True)
def _collect_focus_measures(self, operator, roi, series=0):
controller = self.stage_controller
focussteps = []
fms = []
if controller.timer:
p = controller.timer.get_interval()
self.debug('controller timer period {}'.format(p))
pz = controller.z_progress
while 1:
src = self._load_source()
x = controller.z_progress
if x != pz:
y = self._calculate_focus_measure(src, operator, roi)
self.graph.add_datum((x, y), series=series)
focussteps.append(x)
fms.append(y)
pz = x
if not (controller.timer.isActive() and \
not self._evt_autofocusing.isSet()):
break
time.sleep(p)
self.debug('sweep finished')
return fms, focussteps
def _calculate_nominal_focal_point(self, fms, focussteps):
if fms:
sfms = smooth(fms)
if sfms is not None:
self.graph.new_series(focussteps, sfms)
self.graph.redraw()
fmi = focussteps[argmin(sfms)]
fma = focussteps[argmax(sfms)]
mi = min(sfms)
ma = max(sfms)
return mi, fmi, ma, fma
def _calculate_focus_measure(self, src, operator, roi):
'''
see
IMPLEMENTATION OF A PASSIVE AUTOMATIC FOCUSING ALGORITHM
FOR DIGITAL STILL CAMERA
DOI 10.1109/30.468047
and
http://cybertron.cg.tu-berlin.de/pdci10/frankencam/#autofocus
'''
# need to resize to 640,480. this is the space the roi is in
# s = resize(grayspace(pychron), 640, 480)
src = grayspace(src)
v = crop(src, *roi)
di = dict(var=lambda x: variance(x),
laplace=lambda x: get_focus_measure(x, 'laplace'),
sobel=lambda x: ndsum(
generic_gradient_magnitude(x, sobel, mode='nearest')))
func = di[operator]
return func(v)
def image_view(self):
v = View(
Item('image',
show_label=False,
editor=ImageEditor(),
width=640,
height=480,
style='custom'))
return v
def traits_view(self):
v = View(
HGroup(self._button_factory('autofocus_button', 'autofocus_label'),
Item('configure_button', show_label=False),
show_border=True,
label='Autofocus'))
return v
def configure_view(self):
v = View(Item('parameters', style='custom', show_label=False),
handler=ConfigureHandler,
buttons=['OK', 'Cancel'],
kind='livemodal',
title='Configure Autofocus',
x=0.80,
y=0.05)
return v
def _load_source(self):
src = self.video.get_frame()
return src
# if pychron:
# return Image.new_frame(pychron)
# self.image.load(pychron)
# return self.image.source_frame
def _get_roi(self):
w = self.parameters.crop_width
h = self.parameters.crop_height
cx, cy = self.canvas.get_center_rect_position(w, h)
# cw, ch = self.canvas.outer_bounds
# print w, h, cw, ch
# cx = cw / 2. - w / 2.
# cy = ch / 2. - h / 2.
# cx = (cw - w) / 2.
# cy = (ch - h) / 2.
# cx = (640 * self.canvas.scaling - w) / 2
# cy = (480 * self.canvas.scaling - h) / 2
roi = cx, cy, w, h
return roi
def _add_focus_area_rect(self, cx, cy, w, h):
# pl = self.canvas.padding_left
# pb = self.canvas.padding_bottom
self.canvas.remove_item('croprect')
self.canvas.add_markup_rect(cx, cy, w, h, identifier='croprect')
def _autofocus_button_fired(self):
if not self.autofocusing:
self.autofocusing = True
self.passive_focus()
else:
self.autofocusing = False
self._evt_autofocusing.set()
self.stop_focus()
def _configure_button_fired(self):
self._crop_rect_update()
self.edit_traits(view='configure_view', kind='livemodal')
self.canvas.remove_item('croprect')
# try:
# self.canvas.markupcontainer.pop('croprect')
# except KeyError:
# pass
@on_trait_change('parameters:[_crop_width,_crop_height]')
def _crop_rect_update(self):
roi = self._get_roi()
self._add_focus_area_rect(*roi)
def _get_autofocus_label(self):
return 'Autofocus' if not self.autofocusing else 'Stop'
def _parameters_default(self):
return self.load_parameter()
def _autofocusing_changed(self, new):
if not new:
self.canvas.remove_item('croprect')
class StageManager(BaseStageManager):
"""
"""
stage_controller_klass = String('Newport')
stage_controller = Instance(MotionController)
points_programmer = Instance(PointsProgrammer)
motion_controller_manager = Instance(MotionControllerManager)
# canvas = Instance(LaserTrayCanvas)
simulation = DelegatesTo('stage_controller')
# stage_map_klass = StageMap
# _stage_map = Instance(StageMap)
# stage_map = Property(depends_on='_stage_map')
# stage_maps = Property(depends_on='_stage_maps')
# _stage_maps = List
# ===========================================================================
# buttons
# ===========================================================================
home = Button('home')
home_option = String('Home All')
home_options = List
manual_override_position_button = Event
ejoystick = Event
joystick_label = String('Enable Joystick')
joystick = Bool(False)
joystick_timer = None
back_button = Button
stop_button = Button('Stop')
_default_z = 0
_cached_position = None
_cached_current_hole = None
_homing = False
def __init__(self, *args, **kw):
"""
"""
super(StageManager, self).__init__(*args, **kw)
self.stage_controller = self._stage_controller_factory()
def measure_grain_polygon(self):
pass
def stop_measure_grain_polygon(self):
pass
def shutdown(self):
self._save_stage_map()
def create_device(self, *args, **kw):
dev = super(StageManager, self).create_device(*args, **kw)
dev.parent = self
return dev
def goto_position(self, v, **kw):
if XY_REGEX[0].match(v):
self._move_to_calibrated_position(v)
elif POINT_REGEX.match(v) or TRANSECT_REGEX[0].match(v):
self.move_to_point(v)
else:
self.move_to_hole(v, user_entry=True, **kw)
def get_current_position(self):
if self.stage_controller:
x = self.stage_controller.x
y = self.stage_controller.y
return x, y
def get_current_hole(self):
pos = self.get_current_position()
if self.stage_map:
if distance_threshold(pos, self._cached_position, self.stage_map.g_dimension / 4):
h = self.get_calibrated_hole(*pos, tol=self.stage_map.g_dimension / 2.)
if h is not None:
self._cached_current_hole = h
self._cached_position = pos
return self._cached_current_hole
def is_auto_correcting(self):
return False
def bind_preferences(self, pref_id):
bind_preference(self.canvas, 'show_grids', '{}.show_grids'.format(pref_id))
self.canvas.change_grid_visibility()
bind_preference(self.canvas, 'show_laser_position', '{}.show_laser_position'.format(pref_id))
bind_preference(self.canvas, 'show_desired_position', '{}.show_desired_position'.format(pref_id))
bind_preference(self.canvas, 'desired_position_color', '{}.desired_position_color'.format(pref_id),
factory=ColorPreferenceBinding)
# bind_preference(self.canvas, 'render_map', '{}.render_map'.format(pref_id))
#
bind_preference(self.canvas, 'crosshairs_kind', '{}.crosshairs_kind'.format(pref_id))
for tag in ('', 'aux_'):
for key in ('line_width', 'color', 'radius', 'offsetx', 'offsety'):
key = '{}crosshairs_{}'.format(tag, key)
factory = ColorPreferenceBinding if key.endswith('color') else None
pref = '{}.{}'.format(pref_id, key)
bind_preference(self.canvas, key, pref, factory=factory)
# bind_preference(self.canvas, '{}crosshairs_line_width', '{}.{}crosshairs_line_width'.format(pref_id))
# bind_preference(self.canvas, 'crosshairs_color',
# '{}.crosshairs_color'.format(pref_id),
# factory=ColorPreferenceBinding)
# bind_preference(self.canvas, 'crosshairs_radius', '{}.crosshairs_radius'.format(pref_id))
# bind_preference(self.canvas, 'crosshairs_offsetx', '{}.crosshairs_offsetx'.format(pref_id))
# bind_preference(self.canvas, 'crosshairs_offsety', '{}.crosshairs_offsety'.format(pref_id))
bind_preference(self.canvas, 'show_hole_label', '{}.show_hole_label'.format(pref_id))
bind_preference(self.canvas, 'hole_label_color', '{}.hole_label_color'.format(pref_id))
bind_preference(self.canvas, 'hole_label_size', '{}.hole_label_size'.format(pref_id))
self.canvas.handle_hole_label_size(self.canvas.hole_label_size)
bind_preference(self.canvas, 'scaling', '{}.scaling'.format(pref_id))
bind_preference(self.canvas, 'show_bounds_rect',
'{}.show_bounds_rect'.format(pref_id))
self.canvas.request_redraw()
def load(self):
super(StageManager, self).load()
config = self.get_configuration()
if config:
self._default_z = self.config_get(config, 'Defaults', 'z', default=13, cast='float')
self.points_programmer.load_stage_map(self.stage_map_name)
# load the calibration file
# should have calibration files for each stage map
self.tray_calibration_manager.load_calibration()
def finish_loading(self):
self.initialize_stage()
def initialize_stage(self):
self.update_axes()
axes = self.stage_controller.axes
self.home_options = ['Home All', 'XY'] + sorted([axes[a].name.upper() for a in axes])
self.canvas.parent = self
def save_calibration(self, name):
self.tray_calibration_manager.save_calibration(name=name)
# def add_stage_map(self, v):
# sm = self.stage_map_klass(file_path=v)
# psm = self._get_stage_map_by_name(sm.name)
# if psm:
# self._stage_maps.remove(psm)
# self._stage_maps.append(sm)
def accept_point(self):
self.points_programmer.accept_point()
def set_stage_map(self, v):
return self._set_stage_map(v)
def single_axis_move(self, *args, **kw):
return self.stage_controller.single_axis_move(*args, **kw)
def linear_move(self, x, y, use_calibration=True, check_moving=False, abort_if_moving=False, **kw):
if check_moving:
if self.moving():
self.warning('MotionController already in motion')
if abort_if_moving:
self.warning('Move to {},{} aborted'.format(x, y))
return
else:
self.stop()
self.debug('Motion stopped. moving to {},{}'.format(x, y))
pos = (x, y)
if use_calibration:
pos = self.get_calibrated_position(pos)
f = lambda x: '{:0.5f},{:0.5f}'.format(*x)
self.debug('%%%%%%%%%%%%%%%%% mapped {} to {}'.format(f((x, y)), f(pos)))
self.stage_controller.linear_move(*pos, **kw)
def move_to_hole(self, hole, **kw):
if self.stage_map.check_valid_hole(hole, **kw):
self._move(self._move_to_hole, hole, name='move_to_hole', **kw)
def move_to_point(self, pt):
self._move(self._move_to_point, pt, name='move_to_point')
def move_polyline(self, line):
self._move(self._move_to_line, line, name='move_to_line')
def move_polygon(self, poly):
self._move(self._move_polygon, poly, name='move_polygon')
def drill_point(self, pt):
self._move(self._drill_point, pt, name='drill_point')
def set_x(self, value, **kw):
return self.stage_controller.single_axis_move('x', value, **kw)
def set_y(self, value, **kw):
return self.stage_controller.single_axis_move('y', value, **kw)
def set_z(self, value, **kw):
return self.stage_controller.single_axis_move('z', value, **kw)
def set_xy(self, x, y, **kw):
hole = self._get_hole_by_position(x, y)
if hole:
self.move_to_hole(hole)
# self._set_hole(hole.id)
# self.move_to_hole(hole.id)
# self._set_hole(hole.id)
else:
return self.linear_move(x, y, **kw)
def get_hole(self, name):
if self.stage_map:
return self.stage_map.get_hole(name)
def move_to_load_position(self):
"""
"""
x, y, z = self.stage_controller.get_load_position()
self.info('moving to load position, x={}, y={}, z={}'.format(x, y, z))
self.stage_controller.linear_move(x, y, grouped_move=False, block=False)
self.stage_controller.set_z(z)
self.stage_controller.block()
def stop(self, ax_key=None, verbose=False):
self._stop(ax_key, verbose)
def relative_move(self, *args, **kw):
self.stage_controller.relative_move(*args, **kw)
def key_released(self):
sc = self.stage_controller
sc.add_consumable((sc.update_axes, tuple()))
def moving(self, force_query=False, **kw):
moving = False
if force_query:
moving = self.stage_controller.moving(**kw)
elif self.stage_controller.timer is not None:
moving = self.stage_controller.timer.isActive()
return moving
def get_brightness(self, **kw):
return 0
def get_scores(self, **kw):
return 0, 0
def define_home(self, **kw):
self.stage_controller.define_home(**kw)
def get_z(self):
return self.stage_controller._z_position
def get_uncalibrated_xy(self, pos=None):
if pos is None:
pos = (self.stage_controller.x, self.stage_controller.y)
if self.stage_controller.xy_swapped():
pos = pos[1], pos[0]
canvas = self.canvas
ca = canvas.calibration_item
if ca:
pos = self.stage_map.map_to_uncalibration(pos,
ca.center,
ca.rotation,
ca.scale)
return pos
def get_calibrated_xy(self):
pos = (self.stage_controller.x, self.stage_controller.y)
if self.stage_controller.xy_swapped():
pos = pos[1], pos[0]
pos = self.canvas.map_offset_position(pos)
return self.get_calibrated_position(pos)
def get_calibrated_hole(self, x, y, tol):
ca = self.canvas.calibration_item
if ca is not None:
smap = self.stage_map
xx, yy = smap.map_to_uncalibration((x, y), ca.center, ca.rotation)
return next((hole for hole in smap.sample_holes
if abs(hole.x - xx) < tol and abs(hole.y - yy) < tol), None)
def get_hole_xy(self, key):
pos = self.stage_map.get_hole_pos(key)
# map the position to calibrated space
pos = self.get_calibrated_position(pos)
return pos
def finish_move_to_hole(self, user_entry):
pass
# private
def _update_axes(self):
if self.stage_controller:
self.stage_controller.update_axes()
def _home(self):
"""
"""
if self._homing:
return
self._homing = True
if self.home_option == 'Home All':
msg = 'homing all motors'
homed = ['x', 'y', 'z']
home_kwargs = dict(x=-25, y=-25, z=50)
elif self.home_option == 'XY':
msg = 'homing x,y'
homed = ['x', 'y']
home_kwargs = dict(x=-25, y=-25)
else:
# define_home =
msg = 'homing {}'.format(self.home_option)
home_kwargs = {self.home_option: -25 if self.home_option in ['X', 'Y'] else 50}
homed = [self.home_option.lower().strip()]
self.info(msg)
# if define_home:
self.stage_controller.set_home_position(**home_kwargs)
self.stage_controller.home(homed)
# explicitly block
# self.stage_controller.block()
if 'z' in homed and 'z' in self.stage_controller.axes:
# will be a positive limit error in z
# self.stage_controller.read_error()
time.sleep(1)
self.info('setting z to nominal position. {} mm '.format(self._default_z))
self.stage_controller.single_axis_move('z', self._default_z, block=True)
self.stage_controller._z_position = self._default_z
if self.home_option in ['XY', 'Home All']:
time.sleep(0.25)
# the stage controller should think x and y are at -25,-25
self.stage_controller._x_position = -25
self.stage_controller._y_position = -25
self.info('moving to center')
try:
self.stage_controller.linear_move(0, 0, block=True, sign_correct=False)
except TargetPositionError as e:
self.warning_dialog('Move Failed. {}'.format(e))
self._homing = False
def _get_hole_by_position(self, x, y):
if self.stage_map:
return self.stage_map._get_hole_by_position(x, y)
def _get_hole_by_name(self, key):
sm = self.stage_map
return sm.get_hole(key)
# ===============================================================================
# special move
# ===============================================================================
def _stop(self, ax_key=None, verbose=False):
self.stage_controller.stop(ax_key=ax_key, verbose=verbose)
if self.parent.pattern_executor:
self.parent.pattern_executor.stop()
# def _move(self, func, pos, name=None, *args, **kw):
# if pos is None:
# return
#
# if self.move_thread and self.move_thread.isRunning():
# self.stage_controller.stop()
# if name is None:
# name = func.func_name
#
# self.move_thread = Thread(name='stage.{}'.format(name),
# target=func, args=(pos,) + args, kwargs=kw)
# self.move_thread.start()
def _drill_point(self, pt):
zend = pt.zend
vel = pt.velocity
# assume already at zstart
st = time.time()
self.info('start drilling. move to {}. velocity={}'.format(zend, vel))
self.set_z(zend, velocity=vel, block=True)
et = time.time() - st
self.info('drilling complete. drilled for {}s'.format(et))
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')
def _raster(self, points, velocity,
step=500,
scale=1000,
find_min=False,
start_callback=None, end_callback=None, verbose=False):
from pychron.core.geometry.scan_line import raster
lines = raster(points, step=step, find_min=find_min)
# initialize variables
cnt = 0
direction = 1
flip = False
lasing = False
sc = self.stage_controller
if verbose:
self.info('start raster')
# print lines
# loop thru each scan line
# for yi, xs in lines[::skip]:
for yi, xs in lines:
if direction == -1:
xs = list(reversed(xs))
# convert odd numbers lists to even
n = len(xs)
if n % 2 != 0:
xs = sorted(list(set(xs)))
# traverse each x-intersection pair
n = len(xs)
for i in range(0, n, 2):
if len(xs) <= 1:
continue
x1, x2, yy = xs[i] / scale, xs[i + 1] / scale, yi / scale
if abs(x1 - x2) > 1e-10:
if not lasing:
if verbose:
self.info('fast to {} {},{}'.format(cnt, x1, yy))
self.linear_move(x1, yy,
mode='absolute', set_stage=False,
block=True)
if start_callback is not None:
start_callback()
lasing = True
else:
if verbose:
self.info('slow to {} {},{}'.format(cnt, x1, yy))
sc.timer = sc.timer_factory()
self.linear_move(x1, yy,
mode='absolute', set_stage=False,
velocity=velocity)
if verbose:
self.info('move to {}a {},{}'.format(cnt, x2, yy))
# if n > 2 and not i * 2 >= n:
# line this scan line has more then 1 segment turn off laser at end of segment
if i + 2 < n and not xs[i + 1] == xs[i + 2]:
self.linear_move(x2, yy, velocity=velocity,
mode='absolute', set_stage=False,
block=True)
self.info('wait for move complete')
if end_callback is not None:
end_callback()
lasing = False
else:
self.linear_move(x2, yy, velocity=velocity,
mode='absolute', set_stage=False,
)
cnt += 1
flip = True
else:
flip = False
if flip:
direction *= -1
sc.block()
if verbose:
self.info('end raster')
def _move_polyline(self, pts, start_callback=None, end_callback=None):
if not isinstance(pts, list):
segs = pts.velocity_segments
segs = segs[:1] + segs
pts = [dict(xy=(pi.x, pi.y), z=pi.z, velocity=vi) for vi, pi in
zip(segs, pts.points)]
sc = self.stage_controller
self.linear_move(pts[0]['xy'][0], pts[0]['xy'][1],
update_hole=False,
use_calibration=False,
block=True)
sc.set_z(pts[0]['z'], block=True)
cpos = dict()
# set motors
for motor in ('mask', 'attenuator'):
if motor in pts[0]:
self.parent.set_motor(motor, pts[0][motor])
cpos[motor] = pts[0][motor]
sc.set_program_mode('absolute')
sc.timer = sc.timer_factory()
if start_callback:
start_callback()
npts = pts[1:]
setmotors = dict()
for i, di in enumerate(npts):
xi, yi, zi, vi = di['xy'][0], di['xy'][1], di['z'], di['velocity']
sc.set_z(zi)
block = False
for motor in ('mask', 'attenuator'):
# fix next step sets motor should block
if i + 1 < len(npts):
dii = npts[i + 1]
if motor in dii and dii[motor] != cpos[motor]:
m = self.parent.get_motor(motor)
if not m.locked:
block = True
setmotors[motor] = dii[motor]
self.linear_move(xi, yi, velocity=vi,
block=block,
mode='absolute', # use absolute mode because commands are queued
set_stage=False)
if block:
if end_callback:
end_callback()
for k, v in setmotors.items():
self.parent.set_motor(k, v, block=True)
if start_callback:
start_callback()
# wait until motion complete
sc.block()
if end_callback:
end_callback()
sc.set_program_mode('relative')
# if start and smooth:
# sc.execute_command_buffer()
# sc.end_command_buffer()
# def start_enqueued(self):
# sc = self.stage_controller
# sc.execute_command_buffer()
# sc.end_command_buffer()
def _move_to_point(self, pt):
self.debug('move to point={}'.format(pt))
if isinstance(pt, str):
pt = self.canvas.get_point(pt)
self.debug('move to point canvas pt={}'.format(pt))
if pt is not None:
pos = pt.x, pt.y
self.info('Move to point {}: {:0.5f},{:0.5f},{:0.5f}'.format(pt.identifier,
pt.x, pt.y, pt.z))
self.stage_controller.linear_move(block=True, *pos)
if hasattr(pt, 'z'):
self.stage_controller.set_z(pt.z, block=True)
self.debug('Not setting motors for pt')
# self.parent.set_motors_for_point(pt)
self._move_to_point_hook()
self.info('Move complete')
self.update_axes()
def _move_to_hole(self, key, correct_position=True, user_entry=False, autocenter_only=False):
self.info('Move to hole {} type={}'.format(key, str(type(key))))
autocentered_position = False
if not autocenter_only:
self.temp_hole = key
self.temp_position = self.stage_map.get_hole_pos(key)
pos = self.stage_map.get_corrected_hole_pos(key)
self.info('position {}'.format(pos))
if pos is not None:
if abs(pos[0]) < 1e-6:
pos = self.stage_map.get_hole_pos(key)
# map the position to calibrated space
pos = self.get_calibrated_position(pos, key=key)
else:
# check if this is an interpolated position
# if so probably want to do an autocentering routine
hole = self.stage_map.get_hole(key)
if hole.interpolated:
self.info('using an interpolated value')
else:
self.info('using previously calculated corrected position')
autocentered_position = True
try:
self.stage_controller.linear_move(block=True, source='move_to_hole {}'.format(pos),
raise_zero_displacement=True, *pos)
except TargetPositionError as e:
self.warning('(001) Move to {} failed'.format(pos))
self.parent.emergency_shutoff(str(e))
return
except ZeroDisplacementException:
correct_position = False
try:
self._move_to_hole_hook(key, correct_position,
autocentered_position)
except TargetPositionError as e:
self.warning('(002) Move failed. {}'.format(e))
self.parent.emergency_shutoff(str(e))
return
self.finish_move_to_hole(user_entry)
self.info('Move complete')
def _move_to_hole_hook(self, *args):
pass
def _move_to_point_hook(self):
pass
# ===============================================================================
# Property Get / Set
# ===============================================================================
def _set_stage_map(self, v):
if v in self.stage_map_names:
for root, ext in ((self.root, '.txt'), (paths.user_points_dir, '.yaml')):
p = os.path.join(root, add_extension(v, ext))
if os.path.isfile(p):
self.info('setting stage map to {}'.format(v))
sm = self.stage_map_klass(file_path=p)
self.canvas.set_map(sm)
self.tray_calibration_manager.load_calibration(stage_map=v)
self.points_programmer.load_stage_map(sm)
return True
else:
self.warning('No stage map named "{}"'.format(v))
return False
def _get_calibrate_stage_label(self):
if self._calibration_state == 'set_center':
r = 'Locate Center'
elif self._calibration_state == 'set_right':
r = 'Locate Right'
else:
r = 'Calibrate Stage'
return r
def _get_program_points_label(self):
return 'Program Points' if not self.canvas.markup else 'End Program'
def _validate_hole(self, v):
nv = None
try:
if v.strip():
nv = int(v)
except TypeError:
self.warning('invalid hole {}'.format(v))
return nv
# def _get_calibrated_position_entry(self):
# return self._calibrated_position
#
# def _set_calibrated_position_entry(self, v):
# self._calibrated_position = v
# if XY_REGEX.match(v):
# self._move_to_calibrated_position(v)
# else:
# self.move_to_hole(v)
def _move_to_calibrated_position(self, pos):
try:
args = csv_to_floats(pos)
except ValueError:
self.warning('invalid calibrated position "{}". Could not convert to floats'.format(pos))
return
if len(args) == 2:
x, y = args
self.linear_move(x, y, use_calibration=True, block=False)
else:
self.warning('invalid calibrated position. incorrect number of arguments "{}"'.format(args))
def _set_point(self, v):
if self.canvas.calibrate:
self.warning_dialog('Cannot move while calibrating')
return
if self.canvas.markup:
self.warning_dialog('Cannot move while adding/editing points')
return
if (self.move_thread is None or not self.move_thread.isRunning()) and v is not self._point:
pos = self.canvas.get_item('point', int(v) - 1)
if pos is not None:
self._point = v
self.move_thread = Thread(target=self._move_to_point, args=(pos,))
self.move_thread.start()
else:
err = 'Invalid point {}'.format(v)
self.warning(err)
return err
def _get_point(self):
return self._point
# ===============================================================================
# handlers
# ===============================================================================
def _manual_override_position_button_fired(self):
sm = self.stage_map
pos = self.calibrated_position_entry
hole = self.stage_map.get_hole(pos)
if hole is not None:
x, y = self.stage_controller.x, self.stage_controller.y
sm.set_hole_correction(pos, x, y)
sm.dump_correction_file()
self.info('updated {} correction file. Saved {}: {},{}'.format(sm.name, pos, x, y))
def _stop_button_fired(self):
self._stop()
def _ejoystick_fired(self):
self.joystick = not self.joystick
if self.joystick:
self.stage_controller.enable_joystick()
self.joystick_label = 'Disable Joystick'
self.joystick_timer = self.timer_factory(func=self._joystick_inprogress_update)
else:
if self.joystick_timer is not None:
self.joystick_timer.Stop()
self.stage_controller.disable_joystick()
self.joystick_label = 'Enable Joystick'
def _home_fired(self):
"""
"""
t = Thread(name='stage.home', target=self._home)
t.start()
# need to store a reference to thread so it is not garbage collected
self.move_thread = t
# do_later(self._home)
def _test_fired(self):
# self.do_pattern('testpattern')
self.do_pattern('pattern003')
# ===============================================================================
# factories
# ===============================================================================
def _motion_configure_factory(self, **kw):
return MotionControllerManager(motion_controller=self.stage_controller,
application=self.application,
**kw)
def _stage_controller_factory(self):
if self.stage_controller_klass == 'Newport':
from pychron.hardware.newport.newport_motion_controller import NewportMotionController
factory = NewportMotionController
elif self.stage_controller_klass == 'Aerotech':
from pychron.hardware.aerotech.aerotech_motion_controller import AerotechMotionController
factory = AerotechMotionController
m = factory(name='{}controller'.format(self.name),
configuration_name='stage_controller',
configuration_dir_name=self.configuration_dir_name,
parent=self)
return m
def _canvas_factory(self):
"""
"""
w = 640 / 2.0 / 23.2
h = 0.75 * w
l = LaserTrayCanvas(stage_manager=self,
padding=[30, 5, 5, 30],
map=self.stage_map,
view_x_range=[-w, w],
view_y_range=[-h, h])
return l
# ===============================================================================
# defaults
# ===============================================================================
def _motion_controller_manager_default(self):
return self._motion_configure_factory()
def _title_default(self):
return '%s Stage Manager' % self.name[:-5].capitalize()
def _points_programmer_default(self):
pp = PointsProgrammer(canvas=self.canvas,
stage_map_klass=self.stage_map_klass,
stage_manager=self)
pp.on_trait_change(self.move_to_point, 'point')
pp.on_trait_change(self.move_polygon, 'polygon')
pp.on_trait_change(self.move_polyline, 'line')
return pp
class AutoFocusManager(Manager):
"""
currently uses passive focus techniques
see
http://en.wikipedia.org/wiki/Autofocus
"""
video = Any
laser_manager = Any
stage_controller = Any
canvas = Any
parameters = Instance(FocusParameters)
configure_button = Button('configure')
autofocus_button = Event
autofocus_label = Property(depends_on='autofocusing')
autofocusing = Bool
# threading event for cancel signal
_evt_autofocusing = None
image = Instance(Image, ())
graph = None
def dump_parameters(self):
p = os.path.join(paths.hidden_dir, 'autofocus_configure')
self.info('dumping parameters to {}'.format(p))
with open(p, 'wb') as f:
pickle.dump(self.parameters, f)
def load_parameter(self):
p = os.path.join(paths.hidden_dir, 'autofocus_configure')
if os.path.isfile(p):
with open(p, 'rb') as f:
try:
params = pickle.load(f)
self.info('loading parameters from {}'.format(p))
if not isinstance(params, FocusParameters):
self.info('out of date parameters file. using default')
params = FocusParameters()
return params
except Exception as e:
print('autofocus load parameter', e)
return FocusParameters()
else:
return FocusParameters()
def passive_focus(self, block=False, **kw):
self._evt_autofocusing = TEvent()
self._evt_autofocusing.clear()
# manager = self.laser_manager
oper = self.parameters.operator
self.info('passive focus. operator = {}'.format(oper))
g = self.graph
if not g:
g = Graph(plotcontainer_dict=dict(padding=10),
window_x=0.70,
window_y=20,
window_width=325,
window_height=325,
window_title='Autofocus'
)
self.graph = g
g.clear()
g.new_plot(padding=[40, 10, 10, 40],
xtitle='Z (mm)',
ytitle='Focus Measure ({})'.format(oper)
)
g.new_series()
g.new_series()
invoke_in_main_thread(self._open_graph)
target = self._passive_focus
self._passive_focus_thread = Thread(name='autofocus', target=target,
args=(self._evt_autofocusing,
),
kwargs=kw
)
self._passive_focus_thread.start()
if block:
# while 1:
# if not self._passive_focus_thread.isRunning():
# break
# time.sleep(0.25)
self._passive_focus_thread.join()
def _open_graph(self):
ui = self.graph.edit_traits()
self.add_window(ui)
def stop_focus(self):
if self.stage_controller:
self.stage_controller.stop()
self.info('autofocusing stopped by user')
def _passive_focus(self, stop_signal, set_zoom=True):
'''
sweep z looking for max focus measure
FMgrad= roberts or sobel (sobel removes noise)
FMvar = intensity variance
'''
self.autofocusing = True
manager = self.laser_manager
fstart = self.parameters.fstart
fend = self.parameters.fend
step_scalar = self.parameters.step_scalar
zoom = self.parameters.zoom
operator = self.parameters.operator
steps = step_scalar * (max(fend, fstart) - min(fend, fstart)) + 1
prev_zoom = None
if set_zoom and \
manager is not None and \
zoom:
motor = manager.get_motor('zoom')
if motor:
prev_zoom = motor.data_position
self.info('setting zoom: {}'.format(zoom))
manager.set_motor('zoom', zoom, block=True)
time.sleep(1.5)
args = self._do_focusing(fstart, fend, steps, operator)
if manager is not None:
if prev_zoom is not None:
self.info('returning to previous zoom: {}'.format(prev_zoom))
manager.set_motor('zoom', prev_zoom, block=True)
if args:
mi, fmi, ma, fma = args
self.info('''passive focus results:Operator={}
ImageGradmin={} (z={})
ImageGradmax={}, (z={})'''.format(operator, mi, fmi, ma, fma))
focus_pos = fma
self.graph.add_vertical_rule(focus_pos)
self.graph.redraw()
# self.graph.add_vertical_rule(fma)
self.info('calculated focus z= {}'.format(focus_pos))
# if set_z:
controller = self.stage_controller
if controller is not None:
if not stop_signal.isSet():
controller.single_axis_move('z', focus_pos, block=True)
controller._z_position = focus_pos
controller.z_progress = focus_pos
self.autofocusing = False
def _cancel_sweep(self, vo):
if self._evt_autofocusing.isSet():
# return to original velocity
self.autofocusing = False
self._reset_velocity(vo)
return True
def _reset_velocity(self, vo):
if self.stage_controller:
pdict = dict(velocity=vo, key='z')
self.stage_controller.set_single_axis_motion_parameters(pdict=pdict)
def _do_focusing(self, start, end, steps, operator):
screen_roi = self._get_roi()
self._add_focus_area_rect(*screen_roi)
src = self._load_source()
src = asarray(src)
h, w, _d = src.shape
cx = w / 2.
cy = h / 2.
cw = self.parameters.crop_width
ch = self.parameters.crop_height
roi = cx, cy, cw, ch
'''
start the z in motion and take pictures as you go
query stage_controller to get current z
'''
self.info('focus sweep start={} end={}'.format(start, end))
# move to start position
controller = self.stage_controller
if controller:
vo = controller.axes['z'].velocity
if self._cancel_sweep(vo):
return
self.graph.set_x_limits(min(start, end), max(start, end), pad=2)
# sweep 1 and velocity 1
self._do_sweep(start, end, velocity=self.parameters.velocity_scalar1)
fms, focussteps = self._collect_focus_measures(operator, roi)
if not (fms and focussteps):
return
# reached end of sweep
# calculate a nominal focal point
args = self._calculate_nominal_focal_point(fms, focussteps)
if not args:
return
nfocal = args[3]
nwin = self.parameters.negative_window
pwin = self.parameters.positive_window
if self._cancel_sweep(vo):
return
nstart, nend = max(0, nfocal - nwin), nfocal + pwin
# mi = min(min(nstart, nend), min(start, end))
# ma = max(max(nstart, nend), max(start, end))
# self.graph.set_x_limits(mi, ma, pad=2)
time.sleep(1)
# do a slow tight sweep around the nominal focal point
self._do_sweep(nstart, nend, velocity=self.parameters.velocity_scalar2)
fms, focussteps = self._collect_focus_measures(operator, roi, series=1)
self._reset_velocity(vo)
else:
focussteps = linspace(0, 10, 11)
fms = -(focussteps - 5) ** 2 + 10 + random.random(11)
self.info('frames analyzed {}'.format(len(fms)))
# self.canvas.markupcontainer.pop('croprect')
return self._calculate_nominal_focal_point(fms, focussteps)
def _do_sweep(self, start, end, velocity=None):
controller = self.stage_controller
controller.single_axis_move('z', start, block=True)
# time.sleep(0.1)
# explicitly check for motion
# controller.block(axis='z')
if velocity:
vo = controller.axes['z'].velocity
controller.set_single_axis_motion_parameters(pdict=dict(velocity=vo * velocity,
key='z'))
self.info('starting sweep from {}'.format(controller.z_progress))
# pause before moving to end
time.sleep(0.25)
controller.single_axis_move('z', end, update=100, immediate=True)
def _collect_focus_measures(self, operator, roi, series=0):
controller = self.stage_controller
focussteps = []
fms = []
if controller.timer:
p = controller.timer.get_interval()
self.debug('controller timer period {}'.format(p))
pz = controller.z_progress
while 1:
src = self._load_source()
x = controller.z_progress
if x != pz:
y = self._calculate_focus_measure(src, operator, roi)
self.graph.add_datum((x, y), series=series)
focussteps.append(x)
fms.append(y)
pz = x
if not (controller.timer.isActive() and \
not self._evt_autofocusing.isSet()):
break
time.sleep(p)
self.debug('sweep finished')
return fms, focussteps
def _calculate_nominal_focal_point(self, fms, focussteps):
if fms:
sfms = smooth(fms)
if sfms is not None:
self.graph.new_series(focussteps, sfms)
self.graph.redraw()
fmi = focussteps[argmin(sfms)]
fma = focussteps[argmax(sfms)]
mi = min(sfms)
ma = max(sfms)
return mi, fmi, ma, fma
def _calculate_focus_measure(self, src, operator, roi):
'''
see
IMPLEMENTATION OF A PASSIVE AUTOMATIC FOCUSING ALGORITHM
FOR DIGITAL STILL CAMERA
DOI 10.1109/30.468047
and
http://cybertron.cg.tu-berlin.de/pdci10/frankencam/#autofocus
'''
# need to resize to 640,480. this is the space the roi is in
# s = resize(grayspace(pychron), 640, 480)
src = grayspace(src)
v = crop(src, *roi)
di = dict(var=lambda x:variance(x),
laplace=lambda x: get_focus_measure(x, 'laplace'),
sobel=lambda x: ndsum(generic_gradient_magnitude(x, sobel, mode='nearest'))
)
func = di[operator]
return func(v)
def image_view(self):
v = View(Item('image', show_label=False, editor=ImageEditor(),
width=640,
height=480,
style='custom'))
return v
def traits_view(self):
v = View(
HGroup(self._button_factory('autofocus_button', 'autofocus_label'),
Item('configure_button', show_label=False),
show_border=True,
label='Autofocus'
)
)
return v
def configure_view(self):
v = View(Item('parameters', style='custom', show_label=False),
handler=ConfigureHandler,
buttons=['OK', 'Cancel'],
kind='livemodal',
title='Configure Autofocus',
x=0.80,
y=0.05
)
return v
def _load_source(self):
src = self.video.get_frame()
return src
# if pychron:
# return Image.new_frame(pychron)
# self.image.load(pychron)
# return self.image.source_frame
def _get_roi(self):
w = self.parameters.crop_width
h = self.parameters.crop_height
cx, cy = self.canvas.get_center_rect_position(w, h)
# cw, ch = self.canvas.outer_bounds
# print w, h, cw, ch
# cx = cw / 2. - w / 2.
# cy = ch / 2. - h / 2.
# cx = (cw - w) / 2.
# cy = (ch - h) / 2.
# cx = (640 * self.canvas.scaling - w) / 2
# cy = (480 * self.canvas.scaling - h) / 2
roi = cx, cy, w, h
return roi
def _add_focus_area_rect(self, cx, cy, w, h):
# pl = self.canvas.padding_left
# pb = self.canvas.padding_bottom
self.canvas.remove_item('croprect')
self.canvas.add_markup_rect(cx, cy, w, h, identifier='croprect')
def _autofocus_button_fired(self):
if not self.autofocusing:
self.autofocusing = True
self.passive_focus()
else:
self.autofocusing = False
self._evt_autofocusing.set()
self.stop_focus()
def _configure_button_fired(self):
self._crop_rect_update()
self.edit_traits(view='configure_view', kind='livemodal')
self.canvas.remove_item('croprect')
# try:
# self.canvas.markupcontainer.pop('croprect')
# except KeyError:
# pass
@on_trait_change('parameters:[_crop_width,_crop_height]')
def _crop_rect_update(self):
roi = self._get_roi()
self._add_focus_area_rect(*roi)
def _get_autofocus_label(self):
return 'Autofocus' if not self.autofocusing else 'Stop'
def _parameters_default(self):
return self.load_parameter()
def _autofocusing_changed(self, new):
if not new:
self.canvas.remove_item('croprect')
class BaseStageManager(Manager):
keyboard_focus = Event
canvas_editor_klass = LaserComponentEditor
tray_calibration_manager = Instance(TrayCalibrationManager)
stage_map_klass = LaserStageMap
stage_map_name = Str
stage_map_names = List
stage_map = Instance(BaseStageMap)
canvas = Instance(MapCanvas)
# root = Str(paths.map_dir)
calibrated_position_entry = String(enter_set=True, auto_set=False)
move_thread = None
temp_position = None
temp_hole = None
root = Str
# use_modified = Bool(True) # set true to use modified affine calculation
def motor_event_hook(self, name, value, *args, **kw):
pass
def goto_position(self, pos):
raise NotImplementedError
def refresh_stage_map_names(self):
sms = get_stage_map_names(root=self.root)
self.stage_map_names = sms
def load(self):
self.refresh_stage_map_names()
psm = self._load_previous_stage_map()
sms = self.stage_map_names
sm = None
if psm in sms:
sm = psm
elif sms:
sm = sms[0]
if sm:
self.stage_map_name = ''
self.stage_map_name = sm
def kill(self):
r = super(BaseStageManager, self).kill()
self._save_stage_map()
return r
@property
def stage_map_path(self):
return os.path.join(paths.hidden_dir, '{}.stage_map'.format(self.id))
def canvas_editor_factory(self):
return self.canvas_editor_klass(keyboard_focus='keyboard_focus')
def move_to_hole(self, hole, **kw):
self._move(self._move_to_hole, hole, name='move_to_hole', **kw)
def get_calibrated_position(self, pos, key=None):
smap = self.stage_map
# use a affine transform object to map
canvas = self.canvas
ca = canvas.calibration_item
# check if a calibration applies to this hole
hole_calibration = get_hole_calibration(smap.name, key)
if hole_calibration:
self.debug('Using hole calibration')
ca = hole_calibration
if ca:
rot = ca.rotation
cpos = ca.center
scale = ca.scale
self.debug('Calibration parameters: '
'rot={:0.3f}, cpos={} scale={:0.3f}'.format(rot, cpos,
scale))
pos = smap.map_to_calibration(pos, cpos, rot,
scale=scale)
return pos
def update_axes(self):
"""
"""
self.info('querying axis positions')
self._update_axes()
# private
def _update_axes(self):
pass
def _move_to_hole(self, key, correct_position=True, **kw):
pass
def _stop(self):
pass
def _move(self, func, pos, name=None, *args, **kw):
if pos is None:
return
if self.move_thread and self.move_thread.isRunning():
self._stop()
if name is None:
name = func.__name__
self.move_thread = Thread(name='stage.{}'.format(name),
target=func, args=(pos,) + args, kwargs=kw)
self.move_thread.start()
def _canvas_factory(self):
raise NotImplementedError
def _stage_map_changed_hook(self):
pass
# handlers
def _calibrated_position_entry_changed(self, new):
self.debug('User entered calibrated position {}'.format(new))
self.goto_position(new)
def _stage_map_name_changed(self, new):
if new:
self.debug('setting stage map to {}'.format(new))
root = self.root
path = os.path.join(root, add_extension(new, '.txt'))
sm = self.stage_map_klass(file_path=path)
self.tray_calibration_manager.load_calibration(stage_map=new)
self.canvas.set_map(sm)
self.canvas.request_redraw()
self.stage_map = sm
self._stage_map_changed_hook()
# defaults
def _root_default(self):
return paths.map_dir
def _tray_calibration_manager_default(self):
t = TrayCalibrationManager(parent=self,
canvas=self.canvas)
return t
def _canvas_default(self):
return self._canvas_factory()
def _save_stage_map(self):
p = self.stage_map_path
self.info('saving stage_map {} to {}'.format(self.stage_map_name, p))
with open(p, 'wb') as f:
pickle.dump(self.stage_map_name, f)
def _load_previous_stage_map(self):
p = self.stage_map_path
if os.path.isfile(p):
self.info('loading previous stage map from {}'.format(p))
with open(p, 'rb') as f:
try:
sm = pickle.load(f)
if not sm.endswith('.center'):
return sm
except (pickle.PickleError, ValueError):
pass
class Scanner(Loggable):
"""
Scanner is a base class for displaying a scan of device data
ScanableDevices has this ability built in but more complicated scans are
best done here. ScanableDevice scan is best used from continuous long term recording
of a single or multiple values
"""
_graph = Instance(StreamStackedGraph)
manager = Instance(ILaserManager)
data_manager = Instance(CSVDataManager, ())
'''
list of callables. should return a signal value for graphing
'''
functions = List
static_values = List
scan_period = Int # ms
stop_event = Event
setpoint = Float(enter_set=True, auto_set=False)
control_path = File
_warned = False
_scanning = Bool
_directory = None
_base_frame_name = None
def new_static_value(self, name, *args, **kw):
self.static_values.append((name, None))
if args:
self.set_static_value(name, *args, **kw)
def set_static_value(self, name_or_idx, value, plotid=None):
"""
if the plotid is not None add a horizontal guide at value
"""
if isinstance(name_or_idx, str):
name_or_idx = next((i for i, (e, a) in enumerate(self.static_values)), None)
if name_or_idx is not None:
name = self.static_values[name_or_idx][0]
self.static_values[name_or_idx] = (name, value)
if plotid is not None:
self._graph.add_horizontal_rule(value, plotid=plotid)
def setup(self, directory=None, base_frame_name=None):
self._directory = directory
self._base_frame_name = base_frame_name
def new_function(self, function, name=None):
if name is None:
name = function.func_name
# g = self.graph
# func = self.functions
# kw = dict(ytitle=name,)
# n = len(func)
# if n == 0:
# kw['xtitle'] = 'Time'
self.functions.append((function, name))
def make_graph(self):
g = StreamStackedGraph(window_x=50,
window_y=100)
for i, (_, name) in enumerate(self.functions):
kw = dict(ytitle=name, )
if i == 0:
kw['xtitle'] = 'Time'
g.new_plot(
data_limit=3000,
**kw)
g.new_series(plotid=i)
self._graph = g
return g
def stop(self):
self._timer.Stop()
self._scanning = False
self.stop_event = True
self.info('scan stopped')
if self.manager:
self._stop_hook()
self.manager.disable_device()
def _stop_hook(self):
pass
def execute(self):
if self._scanning:
self.stop()
else:
self.data_manager.new_frame(directory=self._directory,
base_frame_name=self._base_frame_name)
# write metadata if available
self._write_metadata()
# make header row
header = ['t'] + \
self._make_func_names() + \
[n for n, _ in self.static_values]
self.data_manager.write_to_frame(header)
self._scanning = True
if self.manager:
if self.manager.enable_device():
self._scanning = True
return self._scanning
def do_scan(self):
self._starttime = time.time()
self._execute()
def _execute(self):
yd = self._read_control_path()
if yd is None:
sp = 1000
else:
sp = yd['period']
# starts automatically
self.debug('scan starting')
self._timer = Timer(sp, self._scan)
self.info('scan started')
# yd = self._read_control_path()
if yd is not None:
# start a control thread
self._control_thread = Thread(target=self._control,
args=(yd,)
)
self._control_thread.start()
self.info('control started')
# if self.manager:
# if self.manager.enable_device():
#
# # starts automatically
# self.debug('scan starting')
# self._timer = Timer(sp, self._scan)
#
# self.info('scan started')
# self._scanning = True
# # yd = self._read_control_path()
# if yd is not None:
# # start a control thread
# self._control_thread = Thread(target=self._control,
# args=(yd,)
# )
# self._control_thread.start()
# self.info('control started')
# else:
# self.warning('Could not enable device')
# else:
# self.warning('no manager available')
def _control(self, ydict):
self.start_control_hook(ydict)
# if self.manager:
# if self.manager.temperature_controller:
# self.manager.temperature_controller.enable_tru_tune = True
start_delay = ydict['start_delay']
end_delay = ydict['end_delay']
setpoints = ydict['setpoints']
print setpoints
self.set_static_value('Setpoint', 0)
time.sleep(start_delay)
for args in setpoints:
t=args[0]
if self._scanning:
self.setpoint = t
self._set_power_hook(t)
self.set_static_value('Setpoint', t, plotid=0)
self._maintain_setpoint(t, *args[1:])
if self._scanning:
self.setpoint = 0
self.set_static_value('Setpoint', 0)
self._set_power_hook(0)
# if self.manager:
# self.manager.set_laser_temperature(0)
time.sleep(end_delay)
self.stop()
self.end_control_hook(self._scanning)
def _set_power_hook(self, t):
if self.manager:
self.manager.set_laser_temperature(t)
def _maintain_setpoint(self, t, d, *args):
self.info('setting setpoint to {} for {}s'.format(t, d))
st = time.time()
while time.time() - st < d and self._scanning:
time.sleep(1)
def start_control_hook(self, *args, **kw):
pass
def end_control_hook(self, ok):
pass
def _make_func_names(self):
return [name for _, name in self.functions]
def _write_metadata(self):
pass
def _scan(self):
functions = self.functions
data = []
record = self._graph.record
# record = self.graph.record
x = time.time() - self._starttime
for i, (func, _) in enumerate(functions):
try:
if hasattr(func, 'next'):
func = func.next
v = float(func())
data.append(v)
# do_after no longer necessary with Qt
record(v, plotid=i, x=x, do_after=None)
except Exception, e:
print 'exception', e
sv = []
for _, v in self.static_values:
if v is None:
v = ''
sv.append(v)
data = [x] + data + sv
self.data_manager.write_to_frame(data)
class VideoStageManager(StageManager):
"""
"""
video = Instance(Video)
camera = Instance(BaseCamera)
canvas_editor_klass = VideoComponentEditor
camera_zoom_coefficients = Property(String(enter_set=True, auto_set=False),
depends_on='_camera_zoom_coefficients')
_camera_zoom_coefficients = String
use_auto_center_interpolation = Bool(False)
configure_camera_device_button = Button
autocenter_button = Button('AutoCenter')
configure_autocenter_button = Button('Configure')
autocenter_manager = Instance(
'pychron.mv.autocenter_manager.AutoCenterManager')
autofocus_manager = Instance(
'pychron.mv.focus.autofocus_manager.AutoFocusManager')
# zoom_calibration_manager = Instance(
# 'pychron.mv.zoom.zoom_calibration.ZoomCalibrationManager')
snapshot_button = Button('Snapshot')
snapshot_mode = Enum('Single', '3 Burst', '10 Burst')
auto_save_snapshot = Bool(True)
record = Event
record_label = Property(depends_on='is_recording')
is_recording = Bool
use_db = False
use_video_archiver = Bool(True)
video_archiver = Instance('pychron.core.helpers.archiver.Archiver')
video_identifier = Str
# use_video_server = Bool(False)
# video_server_port = Int
# video_server_quality = Int
# video_server = Instance('pychron.image.video_server.VideoServer')
use_media_storage = Bool(False)
auto_upload = Bool(False)
keep_local_copy = Bool(False)
lumen_detector = Instance(LumenDetector)
render_with_markup = Bool(False)
burst_delay = Int(250)
_auto_correcting = False
stop_timer = Event
pxpermm = Float(23)
_measure_grain_t = None
_measure_grain_evt = None
grain_polygons = None
# test_button = Button
# _test_state = False
# def _test_button_fired(self):
# if self._test_state:
# # self.stop_measure_grain_polygon()
# #
# # time.sleep(2)
# #
# # d = self.get_grain_polygon_blob()
# # print d
# self.parent.disable_laser()
# else:
# self.parent.luminosity_degas_test()
# # self.start_measure_grain_polygon()
# self._test_state = not self._test_state
def motor_event_hook(self, name, value, *args, **kw):
if name == 'zoom':
self._update_zoom(value)
def bind_preferences(self, pref_id):
self.debug('binding preferences')
super(VideoStageManager, self).bind_preferences(pref_id)
if self.autocenter_manager:
self.autocenter_manager.bind_preferences(pref_id)
# bind_preference(self.autocenter_manager, 'use_autocenter',
# '{}.use_autocenter'.format(pref_id))
bind_preference(self, 'render_with_markup',
'{}.render_with_markup'.format(pref_id))
bind_preference(self, 'burst_delay', '{}.burst_delay'.format(pref_id))
bind_preference(self, 'auto_upload', '{}.auto_upload'.format(pref_id))
bind_preference(self, 'use_media_storage',
'{}.use_media_storage'.format(pref_id))
bind_preference(self, 'keep_local_copy',
'{}.keep_local_copy'.format(pref_id))
bind_preference(self, 'use_video_archiver',
'{}.use_video_archiver'.format(pref_id))
bind_preference(self, 'video_identifier',
'{}.video_identifier'.format(pref_id))
bind_preference(self, 'use_video_server',
'{}.use_video_server'.format(pref_id))
bind_preference(self.video_archiver, 'archive_months',
'{}.video_archive_months'.format(pref_id))
bind_preference(self.video_archiver, 'archive_days',
'{}.video_archive_days'.format(pref_id))
bind_preference(self.video_archiver, 'archive_hours',
'{}.video_archive_hours'.format(pref_id))
bind_preference(self.video_archiver, 'root',
'{}.video_directory'.format(pref_id))
# bind_preference(self.video, 'output_mode',
# '{}.video_output_mode'.format(pref_id))
# bind_preference(self.video, 'ffmpeg_path',
# '{}.ffmpeg_path'.format(pref_id))
def get_grain_polygon(self):
ld = self.lumen_detector
l, m = ld.lum()
return m.tostring()
def get_grain_polygon_blob(self):
# self.debug('Get grain polygons n={}'.format(len(self.grain_polygons)))
try:
t, md, p = next(self.grain_polygons)
a = pack('ff', ((t, md), ))
b = pack('HH', p)
return encode_blob(a + b)
except (StopIteration, TypeError) as e:
self.debug('No more grain polygons. {}'.format(e))
def stop_measure_grain_polygon(self):
self.debug('Stop measure polygons {}'.format(self._measure_grain_evt))
if self._measure_grain_evt:
self._measure_grain_evt.set()
return True
def start_measure_grain_polygon(self):
self._measure_grain_evt = evt = TEvent()
def _measure_grain_polygon():
ld = self.lumen_detector
dim = self.stage_map.g_dimension
ld.pxpermm = self.pxpermm
self.debug('Starting measure grain polygon')
masks = []
display_image = self.autocenter_manager.display_image
mask_dim = dim * 1.05
mask_dim_mm = mask_dim * self.pxpermm
ld.grain_measuring = True
while not evt.is_set():
src = self._get_preprocessed_src()
if src is not None:
targets = ld.find_targets(
display_image,
src,
dim,
mask=mask_dim,
search={'start_offset_scalar': 1})
if targets:
t = time.time()
targets = [(t, mask_dim_mm, ti.poly_points.tolist())
for ti in targets]
masks.extend(targets)
sleep(0.1)
ld.grain_measuring = False
self.grain_polygons = (m for m in masks)
self.debug('exiting measure grain')
self._measure_grain_t = QThread(target=_measure_grain_polygon)
self._measure_grain_t.start()
return True
def start_recording(self,
path=None,
use_dialog=False,
basename='vm_recording',
**kw):
"""
"""
directory = None
if os.path.sep in basename:
args = os.path.split(basename)
directory, basename = os.path.sep.join(args[:-1]), args[-1]
if path is None:
if use_dialog:
path = self.save_file_dialog()
else:
vd = self.video_archiver.root
self.debug('video archiver root {}'.format(vd))
if not vd:
vd = paths.video_dir
if directory:
vd = os.path.join(vd, directory)
if not os.path.isdir(vd):
os.mkdir(vd)
path = unique_path_from_manifest(vd, basename, extension='avi')
kw['path'] = path
kw['basename'] = basename
self._start_recording(**kw)
self.is_recording = True
return path
def stop_recording(self, user='******', delay=None):
"""
"""
def close():
self.is_recording = False
self.info('stop video recording')
p = self.video.output_path
if self.video.stop_recording(wait=True):
if self.auto_upload:
try:
p = self._upload(p, inform=False)
except BaseException as e:
self.critical('Failed uploading {}. error={}'.format(
p, e))
return p
if self.video.is_recording():
if delay:
t = Timer(delay, close)
t.start()
else:
return close()
@property
def video_configuration_path(self):
if self.configuration_dir_path:
return os.path.join(self.configuration_dir_path, 'camera.yaml')
def initialize_video(self):
if self.video:
identifier = 0
p = self.video_configuration_path
if os.path.isfile(p):
with open(p, 'r') as rfile:
yd = yaml.load(rfile)
vid = yd['Device']
identifier = vid.get('identifier', 0)
self.video.open(identifier=identifier)
self.video.load_configuration(p)
self.lumen_detector.pixel_depth = self.video.pixel_depth
def initialize_stage(self):
super(VideoStageManager, self).initialize_stage()
self.initialize_video()
# s = self.stage_controller
# if s.axes:
# xa = s.axes['x'].drive_ratio
# ya = s.axes['y'].drive_ratio
# self._drive_xratio = xa
# self._drive_yratio = ya
self._update_zoom(0)
def autocenter(self, *args, **kw):
return self._autocenter(*args, **kw)
def snapshot(self,
path=None,
name=None,
auto=False,
inform=True,
return_blob=False,
pic_format='.jpg',
include_raw=True):
"""
path: abs path to use
name: base name to use if auto saving in default dir
auto: force auto save
returns:
path: local abs path
upath: remote abs path
"""
if path is None:
if self.auto_save_snapshot or auto:
if name is None:
name = 'snapshot'
path = unique_path_from_manifest(paths.snapshot_dir, name,
pic_format)
elif name is not None:
if not os.path.isdir(os.path.dirname(name)):
path = unique_path_from_manifest(paths.snapshot_dir, name,
pic_format)
else:
path = name
else:
path = self.save_file_dialog()
if path:
self.info('saving snapshot {}'.format(path))
# play camera shutter sound
# play_sound('shutter')
if include_raw:
frame = self.video.get_cached_frame()
head, _ = os.path.splitext(path)
raw_path = '{}.tif'.format(head)
pil_save(frame, raw_path)
self._render_snapshot(path)
if self.auto_upload:
if include_raw:
self._upload(raw_path)
upath = self._upload(path, inform=inform)
if upath is None:
upath = ''
if inform:
if self.keep_local_copy:
self.information_dialog(
'Snapshot saved: "{}".\nUploaded : "{}"'.format(
path, upath))
else:
self.information_dialog(
'Snapshot uploaded to "{}"'.format(upath))
else:
upath = None
if inform:
self.information_dialog(
'Snapshot saved to "{}"'.format(path))
if return_blob:
with open(path, 'rb') as rfile:
im = rfile.read()
return path, upath, im
else:
return path, upath
def kill(self):
"""
"""
super(VideoStageManager, self).kill()
if self.camera:
self.camera.save_calibration()
self.stop_timer = True
self.canvas.close_video()
if self.video:
self.video.close(force=True)
# if self.use_video_server:
# self.video_server.stop()
# if self._stage_maps:
# for s in self._stage_maps:
# s.dump_correction_file()
self.clean_video_archive()
def clean_video_archive(self):
if self.use_video_archiver:
self.info('Cleaning video directory')
self.video_archiver.clean(('manifest.yaml', ))
def is_auto_correcting(self):
return self._auto_correcting
crop_width = 5
crop_height = 5
def get_scores(self, **kw):
ld = self.lumen_detector
src = self._get_preprocessed_src()
return ld.get_scores(src, **kw)
def find_lum_peak(self, min_distance, blur, **kw):
ld = self.lumen_detector
src = self._get_preprocessed_src()
dim = self.stage_map.g_dimension
mask_dim = dim * 1.05
# mask_dim_mm = mask_dim * self.pxpermm
if src is not None and src.ndim >= 2:
return ld.find_lum_peak(src,
dim,
mask_dim,
blur=blur,
min_distance=min_distance,
**kw)
def get_brightness(self, **kw):
ld = self.lumen_detector
src = self._get_preprocessed_src()
dim = self.stage_map.g_dimension
return ld.get_value(src, dim, **kw)
# src = self.video.get_cached_frame()
# csrc = copy(src)
# src, v = ld.get_value(csrc, **kw)
# return csrc, src, v
def get_frame_size(self):
cw = 2 * self.crop_width * self.pxpermm
ch = 2 * self.crop_height * self.pxpermm
return cw, ch
def close_open_images(self):
if self.autocenter_manager:
self.autocenter_manager.close_open_images()
def finish_move_to_hole(self, user_entry):
self.debug('finish move to hole')
# if user_entry and not self.keep_images_open:
# self.close_open_images()
def get_preprocessed_src(self):
return self._get_preprocessed_src()
# private
def _get_preprocessed_src(self):
ld = self.lumen_detector
src = copy(self.video.get_cached_frame())
dim = self.stage_map.g_dimension
ld.pxpermm = self.pxpermm
offx, offy = self.canvas.get_screen_offset()
cropdim = dim * 2.5
if src is not None:
if len(src.shape):
src = ld.crop(src, cropdim, cropdim, offx, offy, verbose=False)
return src
def _stage_map_changed_hook(self):
self.lumen_detector.hole_radius = self.stage_map.g_dimension
def _upload(self, src, inform=True):
if not self.use_media_storage:
msg = 'Use Media Storage not enabled in Laser preferences'
if inform:
self.warning_dialog(msg)
else:
self.warning(msg)
else:
srv = 'pychron.media_storage.manager.MediaStorageManager'
msm = self.parent.application.get_service(srv)
if msm is not None:
d = os.path.split(os.path.dirname(src))[-1]
dest = os.path.join(self.parent.name, d, os.path.basename(src))
msm.put(src, dest)
if not self.keep_local_copy:
self.debug('removing {}'.format(src))
if src.endswith('.avi'):
head, ext = os.path.splitext(src)
vd = '{}-images'.format(head)
self.debug(
'removing video build directory {}'.format(vd))
shutil.rmtree(vd)
os.remove(src)
dest = '{}/{}'.format(msm.get_base_url(), dest)
return dest
else:
msg = 'Media Storage Plugin not enabled'
if inform:
self.warning_dialog(msg)
else:
self.warning(msg)
def _render_snapshot(self, path):
from chaco.plot_graphics_context import PlotGraphicsContext
c = self.canvas
p = None
was_visible = False
if not self.render_with_markup:
p = c.show_laser_position
c.show_laser_position = False
if self.points_programmer.is_visible:
c.hide_all()
was_visible = True
gc = PlotGraphicsContext((int(c.outer_width), int(c.outer_height)))
c.do_layout()
gc.render_component(c)
# gc.save(path)
from pychron.core.helpers import save_gc
save_gc.save(gc, path)
if p is not None:
c.show_laser_position = p
if was_visible:
c.show_all()
def _start_recording(self, path, basename):
self.info('start video recording {}'.format(path))
d = os.path.dirname(path)
if not os.path.isdir(d):
self.warning('invalid directory {}'.format(d))
self.warning('using default directory')
path, _ = unique_path(paths.video_dir, basename, extension='avi')
self.info('saving recording to path {}'.format(path))
# if self.use_db:
# db = self.get_video_database()
# db.connect()
#
# v = db.add_video_record(rid=basename)
# db.add_path(v, path)
# self.info('saving {} to database'.format(basename))
# db.commit()
video = self.video
crop_to_hole = True
dim = self.stage_map.g_dimension
cropdim = dim * 8 * self.pxpermm
color = self.canvas.crosshairs_color.getRgb()[:3]
r = int(self.canvas.get_crosshairs_radius() * self.pxpermm)
# offx, offy = self.canvas.get_screen_offset()
def renderer(p):
# cw, ch = self.get_frame_size()
frame = video.get_cached_frame()
if frame is not None:
if not len(frame.shape):
return
frame = copy(frame)
# ch, cw, _ = frame.shape
# ch, cw = int(ch), int(cw)
if crop_to_hole:
frame = video.crop(frame, 0, 0, cropdim, cropdim)
if self.render_with_markup:
# draw crosshairs
if len(frame.shape) == 2:
frame = gray2rgb(frame)
ch, cw, _ = frame.shape
ch, cw = int(ch), int(cw)
y = ch // 2
x = cw // 2
cp = circle_perimeter(y, x, r, shape=(ch, cw))
frame[cp] = color
frame[line(y, 0, y, x - r)] = color # left
frame[line(y, x + r, y, int(cw) - 1)] = color # right
frame[line(0, x, y - r, x)] = color # bottom
frame[line(y + r, x, int(ch) - 1, x)] = color # top
if frame is not None:
pil_save(frame, p)
self.video.start_recording(path, renderer)
def _move_to_hole_hook(self, holenum, correct, autocentered_position):
args = holenum, correct, autocentered_position
self.debug('move to hole hook holenum={}, '
'correct={}, autocentered_position={}'.format(*args))
if correct:
ntries = 1 if autocentered_position else 3
self._auto_correcting = True
try:
self._autocenter(holenum=holenum, ntries=ntries, save=True)
except BaseException as e:
self.critical('Autocentering failed. {}'.format(e))
self._auto_correcting = False
# def find_center(self):
# ox, oy = self.canvas.get_screen_offset()
# rpos, src = self.autocenter_manager.calculate_new_center(
# self.stage_controller.x,
# self.stage_controller.y,
# ox, oy,
# dim=self.stage_map.g_dimension, open_image=False)
#
# return rpos, src
# def find_target(self):
# if self.video:
# ox, oy = self.canvas.get_screen_offset()
# src = self.video.get_cached_frame()
#
# ch = cw = self.pxpermm * self.stage_map.g_dimension * 2.5
# src = self.video.crop(src, ox, oy, cw, ch)
# return self.lumen_detector.find_target(src)
#
# def find_best_target(self):
# if self.video:
# src = self.video.get_cached_frame()
# src = self.autocenter_manager.crop(src)
# return self.lumen_detector.find_best_target(src)
def _autocenter(self, holenum=None, ntries=3, save=False, inform=False):
self.debug('do autocenter')
rpos = None
interp = False
sm = self.stage_map
st = time.time()
if self.autocenter_manager.use_autocenter:
time.sleep(0.1)
dim = sm.g_dimension
shape = sm.g_shape
if holenum is not None:
hole = sm.get_hole(holenum)
if hole is not None:
dim = hole.dimension
shape = hole.shape
ox, oy = self.canvas.get_screen_offset()
for ti in range(max(1, ntries)):
# use machine vision to calculate positioning error
rpos = self.autocenter_manager.calculate_new_center(
self.stage_controller.x,
self.stage_controller.y,
ox,
oy,
dim=dim,
shape=shape)
if rpos is not None:
self.linear_move(*rpos,
block=True,
source='autocenter',
use_calibration=False,
update_hole=False,
velocity_scalar=0.1)
time.sleep(0.1)
else:
self.snapshot(auto=True,
name='pos_err_{}_{}'.format(holenum, ti),
inform=inform)
break
# if use_interpolation and rpos is None:
# self.info('trying to get interpolated position')
# rpos = sm.get_interpolated_position(holenum)
# if rpos:
# s = '{:0.3f},{:0.3f}'
# interp = True
# else:
# s = 'None'
# self.info('interpolated position= {}'.format(s))
if rpos:
corrected = True
# add an adjustment value to the stage map
if save and holenum is not None:
sm.set_hole_correction(holenum, *rpos)
sm.dump_correction_file()
# f = 'interpolation' if interp else 'correction'
else:
# f = 'uncorrected'
corrected = False
if holenum is not None:
hole = sm.get_hole(holenum)
if hole:
rpos = hole.nominal_position
self.debug('Autocenter duration ={}'.format(time.time() - st))
return rpos, corrected, interp
# ===============================================================================
# views
# ===============================================================================
# ===============================================================================
# view groups
# ===============================================================================
# ===============================================================================
# handlers
# ===============================================================================
def _configure_camera_device_button_fired(self):
if self.video:
self.video.load_configuration(self.video_configuration_path)
if hasattr(self.video.cap, 'reload_configuration'):
self.video.cap.reload_configuration(
self.video_configuration_path)
self.lumen_detector.pixel_depth = self.video.pixel_depth
def _update_zoom(self, v):
if self.camera:
self._update_xy_limits()
@on_trait_change('parent:motor_event')
def _update_motor(self, new):
print('motor event', new, self.canvas, self.canvas.camera)
# s = self.stage_controller
if self.camera:
if not isinstance(new, (int, float)):
args, _ = new
name, v = args[:2]
else:
name = 'zoom'
v = new
if name == 'zoom':
self._update_xy_limits()
# pxpermm = self.canvas.camera.set_limits_by_zoom(v, s.x, s.y)
# self.pxpermm = pxpermm
elif name == 'beam':
self.lumen_detector.beam_radius = v / 2.0
def _pxpermm_changed(self, new):
if self.autocenter_manager:
self.autocenter_manager.pxpermm = new
self.lumen_detector.pxpermm = new
# self.lumen_detector.mask_radius = new*self.stage_map.g_dimension
def _autocenter_button_fired(self):
self.goto_position(self.calibrated_position_entry,
autocenter_only=True)
# def _configure_autocenter_button_fired(self):
# info = self.autocenter_manager.edit_traits(view='configure_view',
# kind='livemodal')
# if info.result:
# self.autocenter_manager.dump_detector()
def _snapshot_button_fired(self):
n = 1
if self.snapshot_mode == '3 Burst':
n = 3
elif self.snapshot_mode == '10 Burst':
n = 10
bd = self.burst_delay * 0.001
delay = n > 1
for i in range(n):
st = time.time()
self.snapshot(inform=False)
if delay:
time.sleep(max(0, bd - time.time() + st))
def _record_fired(self):
# time.sleep(4)
# self.stop_recording()
if self.is_recording:
self.stop_recording()
else:
self.start_recording()
def _use_video_server_changed(self):
if self.use_video_server:
self.video_server.start()
else:
self.video_server.stop()
def _get_camera_zoom_coefficients(self):
return self.camera.zoom_coefficients
def _set_camera_zoom_coefficients(self, v):
self.camera.zoom_coefficients = ','.join(map(str, v))
self._update_xy_limits()
def _validate_camera_zoom_coefficients(self, v):
try:
return list(map(float, v.split(',')))
except ValueError:
pass
def _update_xy_limits(self):
z = 0
if self.parent is not None:
zoom = self.parent.get_motor('zoom')
if zoom is not None:
z = zoom.data_position
x = self.stage_controller.get_current_position('x')
y = self.stage_controller.get_current_position('y')
if self.camera:
pxpermm = self.camera.set_limits_by_zoom(z, x, y, self.canvas)
self.pxpermm = pxpermm
self.debug('updated xy limits zoom={}, pxpermm={}'.format(
z, pxpermm))
self.canvas.request_redraw()
def _get_record_label(self):
return 'Start Recording' if not self.is_recording else 'Stop'
# ===============================================================================
# factories
# ===============================================================================
def _canvas_factory(self):
"""
"""
v = VideoLaserTrayCanvas(stage_manager=self, padding=30)
return v
def _canvas_editor_factory(self):
e = super(VideoStageManager, self)._canvas_editor_factory()
e.stop_timer = 'stop_timer'
return e
# ===============================================================================
# defaults
# ===============================================================================
def _camera_default(self):
klass = YamlCamera
# p = os.path.join(self.configuration_dir_path, 'camera.yaml')
p = self.video_configuration_path
if p is not None:
if not os.path.isfile(p):
klass = Camera
pp = os.path.join(self.configuration_dir_path, 'camera.cfg')
if not os.path.isfile(pp):
self.warning_dialog(
'No Camera configuration file a {} or {}'.format(
p, pp))
p = pp
camera = klass()
camera.load(p)
else:
camera = Camera()
camera.set_limits_by_zoom(0, 0, 0, self.canvas)
self._camera_zoom_coefficients = camera.zoom_coefficients
return camera
def _lumen_detector_default(self):
ld = LumenDetector()
ld.pixel_depth = self.video.pixel_depth
return ld
def _video_default(self):
v = Video()
self.canvas.video = v
return v
def _video_server_default(self):
from pychron.image.video_server import VideoServer
return VideoServer(video=self.video)
def _video_archiver_default(self):
from pychron.core.helpers.archiver import Archiver
return Archiver()
def _autocenter_manager_default(self):
if self.parent.mode != 'client':
# from pychron.mv.autocenter_manager import AutoCenterManager
if 'co2' in self.parent.name.lower():
from pychron.mv.autocenter_manager import CO2AutocenterManager
klass = CO2AutocenterManager
else:
from pychron.mv.autocenter_manager import DiodeAutocenterManager
klass = DiodeAutocenterManager
return klass(video=self.video,
canvas=self.canvas,
application=self.application)
def _autofocus_manager_default(self):
if self.parent.mode != 'client':
from pychron.mv.focus.autofocus_manager import AutoFocusManager
return AutoFocusManager(video=self.video,
laser_manager=self.parent,
stage_controller=self.stage_controller,
canvas=self.canvas,
application=self.application)
class FusionsLaserManager(LaserManager):
"""
"""
laser_controller = Instance(FusionsLogicBoard)
fiber_light = Instance(FiberLight)
# optics_view = Instance(OpticsView)
# beam = DelegatesTo('laser_controller')
# beammin = DelegatesTo('laser_controller')
# beammax = DelegatesTo('laser_controller')
# update_beam = DelegatesTo('laser_controller')
# beam_enabled = DelegatesTo('laser_controller')
# # beam_enabled = Bool(True)
#
# zoom = DelegatesTo('laser_controller')
# zoommin = DelegatesTo('laser_controller')
# zoommax = DelegatesTo('laser_controller')
# update_zoom = DelegatesTo('laser_controller')
# execute_button = DelegatesTo('laser_script_executor')
# execute_label = DelegatesTo('laser_script_executor')
pointer = Event
pointer_state = Bool(False)
pointer_label = Property(depends_on='pointer_state')
step_heat_manager = None
lens_configuration = Str('gaussian')
lens_configuration_dict = Dict
lens_configuration_names = List
power_timer = None
brightness_timer = None
power_graph = None
_prev_power = 0
record_brightness = Bool
# recording_zoom = Float
# record = Event
# record_label = Property(depends_on='_recording_power_state')
_recording_power_state = Bool(False)
simulation = DelegatesTo('laser_controller')
data_manager = None
_data_manager_lock = None
_current_rid = None
# brightness_meter = Instance(BrightnessPIDManager)
chiller = Any
motor_event = Event
_degas_thread = None
@on_trait_change('laser_controller:refresh_canvas')
def refresh_canvas(self):
if self.stage_manager:
self.stage_manager.canvas.request_redraw()
# ===============================================================================
# IExtractionDevice interface
# ===============================================================================
def extract(self, power, **kw):
self.enable_laser()
self.set_laser_power(power, **kw)
def end_extract(self):
self.disable_laser()
self.stop_pattern()
def open_motor_configure(self):
self.laser_controller.open_motor_configure()
# def _record_fired(self):
# if self._recording_power_state:
# save = self.db_save_dialog()
# self.stop_power_recording(delay=0, save=save)
# else:
# t = Thread(name='fusions.power_record',
# target=self.start_power_recording, args=('Manual',))
# t.start()
# self._recording_power_state = not self._recording_power_state
def bind_preferences(self, pref_id):
self.debug('binding preferences')
super(FusionsLaserManager, self).bind_preferences(pref_id)
bind_preference(self, 'recording_zoom',
'{}.recording_zoom'.format(pref_id))
bind_preference(self, 'record_brightness',
'{}.record_brightness'.format(pref_id))
self.debug('preferences bound')
def set_light(self, value):
self.set_light_state(value > 0)
self.set_light_intensity(value)
def set_light_state(self, state):
if state:
self.fiber_light.power_off()
else:
self.fiber_light.power_on()
def set_light_intensity(self, v):
self.fiber_light.intensity = min(max(0, v), 100)
@on_trait_change('pointer')
def pointer_ononff(self):
"""
"""
self.pointer_state = not self.pointer_state
self.laser_controller.set_pointer_onoff(self.pointer_state)
def get_laser_watts(self):
return self._requested_power
def get_coolant_temperature(self, **kw):
"""
"""
chiller = self.chiller
if chiller is not None:
return chiller.get_coolant_out_temperature(**kw)
def get_coolant_status(self, **kw):
chiller = self.chiller
if chiller is not None:
return chiller.get_faults(**kw)
def do_motor_initialization(self, name):
if self.laser_controller:
motor = self.laser_controller.get_motor(name)
if motor is not None:
n = 4
from pychron.core.ui.progress_dialog import myProgressDialog
pd = myProgressDialog(max=n, size=(550, 15))
pd.open()
motor.initialize(progress=pd)
pd.close()
def set_beam_diameter(self, bd, force=False, **kw):
"""
"""
result = False
motor = self.get_motor('beam')
if motor is not None:
if motor.enabled or force:
self.set_motor('beam', bd, **kw)
result = True
else:
self.info('beam disabled by lens configuration {}'.format(self.lens_configuration))
return result
def set_zoom(self, z, **kw):
"""
"""
self.set_motor('zoom', z, **kw)
def set_motor_lock(self, name, value):
m = self.get_motor(name)
if m is not None:
m.locked = to_bool(value)
return True
def set_motor(self, *args, **kw):
self.motor_event = (args, kw)
return self.laser_controller.set_motor(*args, **kw)
def get_motor(self, name):
return next((mi for mi in self.laser_controller.motors if mi.name == name), None)
def do_autofocus(self, **kw):
if self.use_video:
am = self.stage_manager.autofocus_manager
am.passive_focus(block=True, **kw)
def take_snapshot(self, *args, **kw):
if self.use_video:
return self.stage_manager.snapshot(
auto=True,
inform=False,
*args, **kw)
def start_video_recording(self, name='video', *args, **kw):
if self.use_video:
self.stage_manager.start_recording(basename=name)
def stop_video_recording(self, *args, **kw):
if self.use_video:
self.stage_manager.stop_recording()
def degasser_factory(self):
from pychron.mv.degas.degasser import Degasser
dm = Degasser(
laser_manager=self,
video=self.stage_manager.video,
)
return dm
def do_machine_vision_degas(self, lumens, duration, new_thread=False):
if self.use_video:
dm = self.degasser_factory()
def func():
dm.degas(lumens, duration)
if new_thread:
self._degas_thread = Thread(target=func)
self._degas_thread.start()
else:
func()
def get_brightness(self):
if self.use_video:
return self.stage_manager.get_brightness()
else:
return super(FusionsLaserManager, self).get_brightness()
def is_degassing(self):
if self._degas_thread:
return self._degas_thread.isRunning()
# ===============================================================================
# pyscript interface
# ===============================================================================
def _move_to_position(self, position, autocenter):
if self.stage_manager is not None:
if isinstance(position, tuple):
if len(position) > 1:
x, y = position[:2]
self.stage_manager.linear_move(x, y)
if len(position) == 3:
self.stage_manager.set_z(position[2])
else:
self.stage_manager.move_to_hole(position)
return True
def set_stage_map(self, mapname):
if self.stage_manager is not None:
self.stage_manager.set_stage_map(mapname)
def _enable_hook(self, **kw):
resp = self.laser_controller._enable_laser(**kw)
if self.laser_controller.simulation:
resp = True
return resp
def _disable_hook(self):
resp = self.laser_controller._disable_laser()
if self.laser_controller.simulation:
resp = True
return resp
def show_motion_controller_manager(self):
"""
"""
stage_controller = self.stage_manager.stage_controller
package = 'pychron.managers.motion_controller_managers'
if 'Aerotech' in stage_controller.__class__.__name__:
klass = 'AerotechMotionControllerManager'
package += '.aerotech_motion_controller_manager'
else:
klass = 'NewportMotionControllerManager'
package += '.newport_motion_controller_manager'
module = __import__(package, globals(), locals(), [klass], -1)
factory = getattr(module, klass)
m = factory(motion_controller=stage_controller)
self.open_view(m)
# ========================= views =========================
def get_control_buttons(self):
"""
"""
return [('enable', 'enable_label', None), ]
# def get_control_items(self):
# '''
# '''
# # return Item('laser_controller', show_label=False,
# # editor=InstanceEditor(view='control_view'),
# # style='custom',
# # springy=False, height= -100)
#
# # return self.laser_controller.get_control_group()
# s = [('zoom', 'zoom', {}),
# ('beam', 'beam', {'enabled_when':'object.beam_enabled'})
# ]
# return self._update_slider_group_factory(s)
# def get_lens_configuration_group(self):
# return Item('lens_configuration',
# editor=EnumEditor(values=self.lens_configuration_names)
# )
# def get_optics_group(self):
# csliders = self.get_control_items()
# vg = HGroup(csliders,
# show_border=True,
# label='Optics', springy=False
# )
#
# lens_config = self.get_lens_configuration_group()
# if lens_config:
# vg.content.insert(0, lens_config)
#
# return vg
# def get_control_button_group(self):
# grp = HGroup(spring, Item('enabled_led', show_label=False, style='custom', editor=LEDEditor()),
# self._button_group_factory(self.get_control_buttons(), orientation='h'),
# # springy=True
# )
# return grp
def get_power_group(self):
power_grp = VGroup(
self.get_control_button_group(),
HGroup(
Item('requested_power', style='readonly',
format_str='%0.2f',
width=100),
spring,
Item('units', show_label=False, style='readonly'),
spring),
# Item('laser_script_executor', show_label=False, style='custom'),
# self._button_factory('execute_button', 'execute_label'),
show_border=True,
# springy=True,
label='Power')
ps = self.get_power_slider()
if ps:
# ps.springy = True
power_grp.content.append(ps)
return power_grp
# def get_additional_group(self):
# og = Group(Item('laser_controller', show_label=False,
# editor=InstanceEditor(view='control_view'),
# style='custom'),
# label='Optics',
# )
# ac = Group(
# og,
# show_border=True,
# label='Additional Controls',
# layout='tabbed')
#
# aclist = self.get_additional_controls()
# if aclist is None:
# og.label = 'Optics'
# og.show_border = True
# ac = og
# else:
# for ai in aclist:
# ac.content.append(ai)
# return ac
# def get_control_group(self):
# '''
# '''
# power_grp = self.get_power_group()
# pulse_grp = Group(Item('pulse', style='custom', show_label=False),
# label='Pulse', show_border=True
# )
# power_grp = HGroup(power_grp, pulse_grp)
# ac = self.get_additional_group()
# g = HGroup(power_grp, ac)
#
# return g
def _get_pointer_label(self):
"""
"""
return 'Pointer ON' if not self.pointer_state else 'Pointer OFF'
def _get_record_label(self):
return 'Record' if not self._recording_power_state else 'Stop'
def _get_record_brightness(self):
return self.record_brightness and self._get_machine_vision() is not None
# ========================= defaults =======================
# def get_power_database(self):
# from pychron.database.adapters.power_adapter import PowerAdapter
#
# db = PowerAdapter(name=self.dbname,
# kind='sqlite')
# return db
# def get_power_calibration_database(self):
# from pychron.database.adapters.power_calibration_adapter import PowerCalibrationAdapter
#
# db = PowerCalibrationAdapter(name=self.dbname,
# kind='sqlite')
# return db
# def _subsystem_default(self):
# '''
# '''
# return ArduinoSubsystem(name='arduino_subsystem_2')
# def _brightness_meter_default(self):
# if self.use_video:
# b = BrightnessPIDManager(parent=self)
# # b.brightness_manager.video = self.stage_manager.video
#
# return b
def _fiber_light_default(self):
"""
"""
return FiberLight(name='fiber_light')
def do_coincidence_scan(self, new_thread=True):
if new_thread:
t = Thread(name='ion_optics.coincidence', target=self._coincidence)
t.start()
self._centering_thread = t
class NMGRLFurnaceManager(BaseFurnaceManager):
funnel = Instance(NMGRLFunnel)
loader_logic = Instance(LoaderLogic)
magnets = Instance(NMGRLMagnetDumper)
setpoint_readback_min = Float(0)
setpoint_readback_max = Float(1600.0)
graph = Instance(StreamGraph)
update_period = Int(2)
dumper_canvas = Instance(DumperCanvas)
_alive = False
_guide_overlay = None
_dumper_thread = None
mode = 'normal'
def activate(self):
# pref_id = 'pychron.furnace'
# bind_preference(self, 'update_period', '{}.update_period'.format(pref_id))
self._start_update()
def prepare_destroy(self):
self._stop_update()
self.loader_logic.manager = None
def dump_sample(self):
self.debug('dump sample')
if self._dumper_thread is None:
self._dumper_thread = Thread(name='DumpSample',
target=self._dump_sample)
self._dumper_thread.start()
def is_dump_complete(self):
ret = self._dumper_thread is None
return ret
def actuate_magnets(self):
self.debug('actuate magnets')
if self.loader_logic.check('AM'):
self.magnet.open()
# wait for actuate magnets
pass
else:
self.warning('actuate magnets not enabled')
def lower_funnel(self):
self.debug('lower funnel')
if self.loader_logic.check('FD'):
self.funnel.set_value(self.funnel.down_position)
# todo: update canvas state
return True
else:
self.warning('lowering funnel not enabled')
def raise_funnel(self):
self.debug('raise funnel')
if self.loader_logic.check('FU'):
self.funnel.set_value(self.funnel.up_position)
# todo: update canvas state
return True
else:
self.warning('raising funnel not enabled')
def set_setpoint(self, v):
if self.controller:
# print self.controller, self.controller._cdevice
self.controller.set_setpoint(v)
if not self._guide_overlay:
self._guide_overlay = self.graph.add_horizontal_rule(v)
self._guide_overlay.visible = bool(v)
self._guide_overlay.value = v
# ymi, yma = self.graph.get_y_limits()
d = self.graph.get_data(axis=1)
self.graph.set_y_limits(min_=0, max_=max(d.max(), v * 1.1))
self.graph.redraw()
def read_setpoint(self, update=False):
v = 0
if self.controller:
force = update and not self.controller.is_scanning()
v = self.controller.read_setpoint(force=force)
try:
self.setpoint_readback = v
return v
except TraitError:
pass
# canvas
def set_software_lock(self, name, lock):
if self.switch_manager is not None:
if lock:
self.switch_manager.lock(name)
else:
self.switch_manager.unlock(name)
def open_valve(self, name, **kw):
if not self._open_logic(name):
self.debug('logic failed')
return False, False
if self.switch_manager:
return self.switch_manager.open_switch(name, **kw)
def close_valve(self, name, **kw):
if not self._close_logic(name):
self.debug('logic failed')
return False, False
if self.switch_manager:
return self.switch_manager.close_switch(name, **kw)
def set_selected_explanation_item(self, item):
pass
# logic
def get_switch_state(self, name):
if self.switch_manager:
return self.switch_manager.get_state_by_name(name, force=True)
def get_flag_state(self, flag):
self.debug('get_flag_state {}'.format(flag))
if flag in ('no_motion', 'no_dump', 'funnel_up', 'funnel_down'):
return getattr(self, flag)()
return False
def funnel_up(self):
return self.funnel.in_up_position()
def funnel_down(self):
return self.funnel.in_down_position()
def no_motion(self):
v = not self.stage_manager.in_motion()
self.debug('no motion {}'.format(v))
return v
def no_dump(self):
v = not self.magnets.dump_in_progress()
self.debug('no dump {}'.format(v))
return v
# private
def _open_logic(self, name):
"""
check the logic rules to see if its ok to open "name"
return True if ok
"""
return self.loader_logic.open(name)
def _close_logic(self, name):
"""
check the logic rules to see if its ok to close "name"
return True if ok
"""
return self.loader_logic.close(name)
def _stop_update(self):
self._alive = False
def _start_update(self):
self._alive = True
self.graph = g = StreamGraph()
# g.plotcontainer.padding_top = 5
# g.plotcontainer.padding_right = 5
g.new_plot(xtitle='Time (s)',
ytitle='Temp. (C)',
padding_top=5,
padding_right=5)
g.set_scan_width(600)
g.new_series()
self._update_readback()
def _update_readback(self):
v = self.read_setpoint(update=True)
self.graph.record(v, track_y=False)
if self._alive:
do_after(self.update_period * 1000, self._update_readback)
def _dump_sample(self):
"""
1. open gate valve
2. open shutters
3. lower funnel
4. actuate magnets
5. raise funnel
6. close shutters
7. close gate valve
:return:
"""
self.debug('dump sample started')
for line in self._load_dump_script():
self.debug(line)
self._execute_script_line(line)
self.stage_manager.set_sample_dumped()
self._dumper_thread = None
def _load_dump_script(self):
p = os.path.join(paths.device_dir, 'furnace', 'dump_sequence.txt')
return pathtolist(p)
def _execute_script_line(self, line):
if ' ' in line:
cmd, args = line.split(' ')
else:
cmd, args = line, None
if cmd == 'sleep':
time.sleep(float(args))
elif cmd == 'open':
self.switch_manager.open_switch(args)
self.dumper_canvas.set_item_state(args, True)
elif cmd == 'close':
self.switch_manager.close_switch(args)
self.dumper_canvas.set_item_state(args, False)
elif cmd == 'lower_funnel':
self.lower_funnel()
self.dumper_canvas.set_item_state(args, True)
elif cmd == 'raise_funnel':
self.raise_funnel()
self.dumper_canvas.set_item_state(args, False)
elif cmd == 'actuate_magnets':
self.actuate_magnets()
self.dumper_canvas.request_redraw()
# handlers
def _setpoint_changed(self, new):
self.set_setpoint(new)
def _stage_manager_default(self):
sm = NMGRLFurnaceStageManager(
stage_manager_id='nmgrl.furnace.stage_map')
return sm
def _switch_manager_default(self):
sm = SwitchManager()
return sm
def _dumper_canvas_default(self):
dc = DumperCanvas(manager=self)
pathname = os.path.join(paths.canvas2D_dir, 'dumper.xml')
configpath = os.path.join(paths.canvas2D_dir, 'dumper_config.xml')
valvepath = os.path.join(paths.extraction_line_dir, 'valves.xml')
dc.load_canvas_file(pathname, configpath, valvepath, dc)
return dc
def _funnel_default(self):
f = NMGRLFunnel(name='funnel', configuration_dir_name='furnace')
return f
def _loader_logic_default(self):
l = LoaderLogic(manager=self)
l.load_config()
return l
def _magnets_default(self):
m = NMGRLMagnetDumper(name='magnets', configuration_dir_name='furnace')
return m
class NMGRLFurnaceManager(BaseFurnaceManager):
funnel = Instance(NMGRLFunnel)
loader_logic = Instance(LoaderLogic)
magnets = Instance(NMGRLMagnetDumper)
setpoint_readback_min = Float(0)
setpoint_readback_max = Float(1600.0)
graph = Instance(StreamGraph)
update_period = Int(2)
dumper_canvas = Instance(DumperCanvas)
_alive = False
_guide_overlay = None
_dumper_thread = None
mode = 'normal'
def activate(self):
# pref_id = 'pychron.furnace'
# bind_preference(self, 'update_period', '{}.update_period'.format(pref_id))
self._start_update()
def prepare_destroy(self):
self._stop_update()
self.loader_logic.manager = None
def dump_sample(self):
self.debug('dump sample')
if self._dumper_thread is None:
self._dumper_thread = Thread(name='DumpSample', target=self._dump_sample)
self._dumper_thread.start()
def is_dump_complete(self):
ret = self._dumper_thread is None
return ret
def actuate_magnets(self):
self.debug('actuate magnets')
if self.loader_logic.check('AM'):
self.magnet.open()
# wait for actuate magnets
pass
else:
self.warning('actuate magnets not enabled')
def lower_funnel(self):
self.debug('lower funnel')
if self.loader_logic.check('FD'):
self.funnel.set_value(self.funnel.down_position)
# todo: update canvas state
return True
else:
self.warning('lowering funnel not enabled')
def raise_funnel(self):
self.debug('raise funnel')
if self.loader_logic.check('FU'):
self.funnel.set_value(self.funnel.up_position)
# todo: update canvas state
return True
else:
self.warning('raising funnel not enabled')
def set_setpoint(self, v):
if self.controller:
# print self.controller, self.controller._cdevice
self.controller.set_setpoint(v)
if not self._guide_overlay:
self._guide_overlay = self.graph.add_horizontal_rule(v)
self._guide_overlay.visible = bool(v)
self._guide_overlay.value = v
# ymi, yma = self.graph.get_y_limits()
d = self.graph.get_data(axis=1)
self.graph.set_y_limits(min_=0, max_=max(d.max(), v * 1.1))
self.graph.redraw()
def read_setpoint(self, update=False):
v = 0
if self.controller:
force = update and not self.controller.is_scanning()
v = self.controller.read_setpoint(force=force)
try:
self.setpoint_readback = v
return v
except TraitError:
pass
# canvas
def set_software_lock(self, name, lock):
if self.switch_manager is not None:
if lock:
self.switch_manager.lock(name)
else:
self.switch_manager.unlock(name)
def open_valve(self, name, **kw):
if not self._open_logic(name):
self.debug('logic failed')
return False, False
if self.switch_manager:
return self.switch_manager.open_switch(name, **kw)
def close_valve(self, name, **kw):
if not self._close_logic(name):
self.debug('logic failed')
return False, False
if self.switch_manager:
return self.switch_manager.close_switch(name, **kw)
def set_selected_explanation_item(self, item):
pass
# logic
def get_switch_state(self, name):
if self.switch_manager:
return self.switch_manager.get_state_by_name(name, force=True)
def get_flag_state(self, flag):
self.debug('get_flag_state {}'.format(flag))
if flag in ('no_motion', 'no_dump', 'funnel_up', 'funnel_down'):
return getattr(self, flag)()
return False
def funnel_up(self):
return self.funnel.in_up_position()
def funnel_down(self):
return self.funnel.in_down_position()
def no_motion(self):
v = not self.stage_manager.in_motion()
self.debug('no motion {}'.format(v))
return v
def no_dump(self):
v = not self.magnets.dump_in_progress()
self.debug('no dump {}'.format(v))
return v
# private
def _open_logic(self, name):
"""
check the logic rules to see if its ok to open "name"
return True if ok
"""
return self.loader_logic.open(name)
def _close_logic(self, name):
"""
check the logic rules to see if its ok to close "name"
return True if ok
"""
return self.loader_logic.close(name)
def _stop_update(self):
self._alive = False
def _start_update(self):
self._alive = True
self.graph = g = StreamGraph()
# g.plotcontainer.padding_top = 5
# g.plotcontainer.padding_right = 5
g.new_plot(xtitle='Time (s)', ytitle='Temp. (C)', padding_top=5, padding_right=5)
g.set_scan_width(600)
g.new_series()
self._update_readback()
def _update_readback(self):
v = self.read_setpoint(update=True)
self.graph.record(v, track_y=False)
if self._alive:
do_after(self.update_period * 1000, self._update_readback)
def _dump_sample(self):
"""
1. open gate valve
2. open shutters
3. lower funnel
4. actuate magnets
5. raise funnel
6. close shutters
7. close gate valve
:return:
"""
self.debug('dump sample started')
for line in self._load_dump_script():
self.debug(line)
self._execute_script_line(line)
self.stage_manager.set_sample_dumped()
self._dumper_thread = None
def _load_dump_script(self):
p = os.path.join(paths.device_dir, 'furnace', 'dump_sequence.txt')
return pathtolist(p)
def _execute_script_line(self, line):
if ' ' in line:
cmd, args = line.split(' ')
else:
cmd, args = line, None
if cmd == 'sleep':
time.sleep(float(args))
elif cmd == 'open':
self.switch_manager.open_switch(args)
self.dumper_canvas.set_item_state(args, True)
elif cmd == 'close':
self.switch_manager.close_switch(args)
self.dumper_canvas.set_item_state(args, False)
elif cmd == 'lower_funnel':
self.lower_funnel()
self.dumper_canvas.set_item_state(args, True)
elif cmd == 'raise_funnel':
self.raise_funnel()
self.dumper_canvas.set_item_state(args, False)
elif cmd == 'actuate_magnets':
self.actuate_magnets()
self.dumper_canvas.request_redraw()
# handlers
def _setpoint_changed(self, new):
self.set_setpoint(new)
def _stage_manager_default(self):
sm = NMGRLFurnaceStageManager(stage_manager_id='nmgrl.furnace.stage_map')
return sm
def _switch_manager_default(self):
sm = SwitchManager()
return sm
def _dumper_canvas_default(self):
dc = DumperCanvas(manager=self)
pathname = os.path.join(paths.canvas2D_dir, 'dumper.xml')
configpath = os.path.join(paths.canvas2D_dir, 'dumper_config.xml')
valvepath = os.path.join(paths.extraction_line_dir, 'valves.xml')
dc.load_canvas_file(pathname, configpath, valvepath, dc)
return dc
def _funnel_default(self):
f = NMGRLFunnel(name='funnel', configuration_dir_name='furnace')
return f
def _loader_logic_default(self):
l = LoaderLogic(manager=self)
l.load_config()
return l
def _magnets_default(self):
m = NMGRLMagnetDumper(name='magnets', configuration_dir_name='furnace')
return m
def do_coincidence_scan(self, new_thread=True):
if new_thread:
t = Thread(name='ion_optics.coincidence', target=self._coincidence)
t.start()
self._centering_thread = t
def _position_changed(self):
if self.position is not None:
t = Thread(target=self._move_to_position,
args=(self.position, self.use_autocenter))
t.start()
self._position_thread = t
class IonOpticsManager(Manager):
reference_detector = Instance(BaseDetector)
reference_isotope = Any
magnet_dac = Range(0.0, 6.0)
graph = Instance(Graph)
peak_center_button = Button('Peak Center')
stop_button = Button('Stop')
alive = Bool(False)
spectrometer = Any
peak_center = Instance(PeakCenter)
coincidence = Instance(Coincidence)
peak_center_config = Instance(PeakCenterConfigurer)
# coincidence_config = Instance(CoincidenceConfig)
canceled = False
peak_center_result = None
_centering_thread = None
def close(self):
self.cancel_peak_center()
def cancel_peak_center(self):
self.alive = False
self.canceled = True
self.peak_center.canceled = True
self.peak_center.stop()
self.info('peak center canceled')
def get_mass(self, isotope_key):
spec = self.spectrometer
molweights = spec.molecular_weights
return molweights[isotope_key]
def set_mftable(self, name=None):
"""
if mt is None set to the default mftable located at setupfiles/spectrometer/mftable.csv
:param mt:
:return:
"""
if name and name != os.path.splitext(os.path.basename(paths.mftable))[0]:
self.spectrometer.use_deflection_correction = False
else:
self.spectrometer.use_deflection_correction = True
self.spectrometer.magnet.set_mftable(name)
def get_position(self, *args, **kw):
kw['update_isotopes'] = False
return self._get_position(*args, **kw)
def position(self, pos, detector, *args, **kw):
dac = self._get_position(pos, detector, *args, **kw)
mag = self.spectrometer.magnet
self.info('positioning {} ({}) on {}'.format(pos, dac, detector))
return mag.set_dac(dac)
def do_coincidence_scan(self, new_thread=True):
if new_thread:
t = Thread(name='ion_optics.coincidence', target=self._coincidence)
t.start()
self._centering_thread = t
def setup_coincidence(self):
pcc = self.coincidence_config
pcc.dac = self.spectrometer.magnet.dac
info = pcc.edit_traits()
if not info.result:
return
detector = pcc.detector
isotope = pcc.isotope
detectors = [d for d in pcc.additional_detectors]
# integration_time = pcc.integration_time
if pcc.use_nominal_dac:
center_dac = self.get_position(isotope, detector)
elif pcc.use_current_dac:
center_dac = self.spectrometer.magnet.dac
else:
center_dac = pcc.dac
# self.spectrometer.save_integration()
# self.spectrometer.set_integration(integration_time)
cs = Coincidence(spectrometer=self.spectrometer,
center_dac=center_dac,
reference_detector=detector,
reference_isotope=isotope,
additional_detectors=detectors)
self.coincidence = cs
return cs
def get_center_dac(self, det, iso):
spec = self.spectrometer
det = spec.get_detector(det)
molweights = spec.molecular_weights
mass = molweights[iso]
dac = spec.magnet.map_mass_to_dac(mass, det.name)
# correct for deflection
return spec.correct_dac(det, dac)
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True,
message='',
on_end=None,
timeout=None):
self.debug('doing pc')
self.canceled = False
self.alive = True
self.peak_center_result = None
args = (save, confirm_save, warn, message, on_end, timeout)
if new_thread:
t = Thread(name='ion_optics.peak_center', target=self._peak_center,
args=args)
t.start()
self._centering_thread = t
return t
else:
self._peak_center(*args)
def setup_peak_center(self, detector=None, isotope=None,
integration_time=1.04,
directions='Increase',
center_dac=None, plot_panel=None, new=False,
standalone_graph=True, name='', show_label=False,
window=0.015, step_width=0.0005, min_peak_height=1.0, percent=80,
deconvolve=None,
use_interpolation=False,
interpolation_kind='linear',
dac_offset=None, calculate_all_peaks=False,
config_name=None,
use_configuration_dac=True):
if deconvolve is None:
n_peaks, select_peak = 1, 1
if dac_offset is not None:
use_dac_offset = True
spec = self.spectrometer
spec.save_integration()
self.debug('setup peak center. detector={}, isotope={}'.format(detector, isotope))
self._setup_config()
pcc = None
if detector is None or isotope is None:
self.debug('ask user for peak center configuration')
self.peak_center_config.load(dac=spec.magnet.dac)
if config_name:
self.peak_center_config.active_name = config_name
info = self.peak_center_config.edit_traits()
if not info.result:
return
else:
pcc = self.peak_center_config.active_item
elif config_name:
self.peak_center_config.load(dac=spec.magnet.dac)
self.peak_center_config.active_name = config_name
pcc = self.peak_center_config.active_item
if pcc:
if not detector:
detector = pcc.active_detectors
if not isotope:
isotope = pcc.isotope
directions = pcc.directions
integration_time = pcc.integration_time
window = pcc.window
min_peak_height = pcc.min_peak_height
step_width = pcc.step_width
percent = pcc.percent
use_interpolation = pcc.use_interpolation
interpolation_kind = pcc.interpolation_kind
n_peaks = pcc.n_peaks
select_peak = pcc.select_n_peak
use_dac_offset = pcc.use_dac_offset
dac_offset = pcc.dac_offset
calculate_all_peaks = pcc.calculate_all_peaks
if center_dac is None and use_configuration_dac:
center_dac = pcc.dac
spec.set_integration_time(integration_time)
period = int(integration_time * 1000 * 0.9)
if not isinstance(detector, (tuple, list)):
detector = (detector,)
ref = detector[0]
ref = self.spectrometer.get_detector(ref)
self.reference_detector = ref
self.reference_isotope = isotope
if center_dac is None:
center_dac = self.get_center_dac(ref, isotope)
if len(detector) > 1:
ad = detector[1:]
else:
ad = []
pc = self.peak_center
if not pc or new:
pc = PeakCenter()
pc.trait_set(center_dac=center_dac,
period=period,
window=window,
percent=percent,
min_peak_height=min_peak_height,
step_width=step_width,
directions=directions,
reference_detector=ref,
additional_detectors=ad,
reference_isotope=isotope,
spectrometer=spec,
show_label=show_label,
use_interpolation=use_interpolation,
interpolation_kind=interpolation_kind,
n_peaks=n_peaks,
select_peak=select_peak,
use_dac_offset=use_dac_offset,
dac_offset=dac_offset,
calculate_all_peaks=calculate_all_peaks)
self.peak_center = pc
graph = pc.graph
graph.name = name
if plot_panel:
plot_panel.set_peak_center_graph(graph)
else:
graph.close_func = self.close
if standalone_graph:
# set graph window attributes
graph.window_title = 'Peak Center {}({}) @ {:0.3f}'.format(ref, isotope, center_dac)
graph.window_width = 300
graph.window_height = 250
open_view(graph)
return self.peak_center
# private
def _setup_config(self):
config = self.peak_center_config
config.detectors = self.spectrometer.detector_names
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
def _get_peak_center_config(self, config_name):
if config_name is None:
config_name = 'default'
config = self.peak_center_config.get(config_name)
config.detectors = self.spectrometer.detectors_names
if config.detector_name:
config.detector = next((di for di in config.detectors if di == config.detector_name), None)
if not config.detector:
config.detector = config.detectors[0]
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
return config
def _timeout_func(self, timeout, evt):
st = time.time()
while not evt.is_set():
if not self.alive:
break
if time.time() - st > timeout:
self.warning('Peak Centering timed out after {}s'.format(timeout))
self.cancel_peak_center()
break
time.sleep(0.01)
def _peak_center(self, save, confirm_save, warn, message, on_end, timeout):
pc = self.peak_center
spec = self.spectrometer
ref = self.reference_detector
isotope = self.reference_isotope
if timeout:
evt = Event()
self.timeout_thread = Thread(target=self._timeout_func, args=(timeout, evt))
self.timeout_thread.start()
dac_d = pc.get_peak_center()
self.peak_center_result = dac_d
if dac_d:
args = ref, isotope, dac_d
self.info('new center pos {} ({}) @ {}'.format(*args))
det = spec.get_detector(ref)
dac_a = spec.uncorrect_dac(det, dac_d)
self.info('dac uncorrected for HV and deflection {}'.format(dac_a))
if save:
if confirm_save:
msg = 'Update Magnet Field Table with new peak center- {} ({}) @ RefDetUnits= {}'.format(*args)
save = self.confirmation_dialog(msg)
if save:
spec.magnet.update_field_table(det, isotope, dac_a, message)
spec.magnet.set_dac(dac_d)
elif not self.canceled:
msg = 'centering failed'
if warn:
self.warning_dialog(msg)
self.warning(msg)
# needs to be called on the main thread to properly update
# the menubar actions. alive=False enables IonOptics>Peak Center
# d = lambda:self.trait_set(alive=False)
# still necessary with qt? and tasks
if on_end:
on_end()
self.trait_set(alive=False)
if timeout:
evt.set()
self.spectrometer.restore_integration()
def _get_position(self, pos, detector, use_dac=False, update_isotopes=True):
"""
pos can be str or float
"Ar40", "39.962", 39.962
to set in DAC space set use_dac=True
"""
if pos == NULL_STR:
return
spec = self.spectrometer
mag = spec.magnet
if isinstance(detector, str):
det = spec.get_detector(detector)
else:
det = detector
self.debug('detector {}'.format(det))
if use_dac:
dac = pos
else:
self.debug('POSITION {} {}'.format(pos, detector))
if isinstance(pos, str):
try:
pos = float(pos)
except ValueError:
# pos is isotope
if update_isotopes:
# if the pos is an isotope then update the detectors
spec.update_isotopes(pos, detector)
pos = self.get_mass(pos)
mag.mass_change(pos)
# pos is mass i.e 39.962
dac = mag.map_mass_to_dac(pos, det.name)
dac = spec.correct_dac(det, dac)
return dac
def _coincidence(self):
self.coincidence.get_peak_center()
self.info('coincidence finished')
self.spectrometer.restore_integration()
# ===============================================================================
# handler
# ===============================================================================
def _coincidence_config_default(self):
config = None
p = os.path.join(paths.hidden_dir, 'coincidence_config.p')
if os.path.isfile(p):
try:
with open(p) as rfile:
config = pickle.load(rfile)
config.detectors = dets = self.spectrometer.detectors
config.detector = next((di for di in dets if di.name == config.detector_name), None)
except Exception, e:
print 'coincidence config', e
if config is None:
config = CoincidenceConfig()
config.detectors = self.spectrometer.detectors
config.detector = config.detectors[0]
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
return config
def _position_changed(self):
if self.position is not None:
t = Thread(target=self._move_to_position, args=(self.position, self.use_autocenter))
t.start()
self._position_thread = t
def _back_button_fired(self):
pos, kw = self.linear_move_history.pop(-1)
t = Thread(target=self.stage_controller.linear_move, args=pos, kwargs=kw)
t.start()
self.move_thread = t
class BaseStageManager(Manager):
keyboard_focus = Event
canvas_editor_klass = LaserComponentEditor
tray_calibration_manager = Instance(TrayCalibrationManager)
stage_map_klass = LaserStageMap
stage_map_name = Str
stage_map_names = List
stage_map = Instance(BaseStageMap)
canvas = Instance(MapCanvas)
# root = Str(paths.map_dir)
calibrated_position_entry = String(enter_set=True, auto_set=False)
move_thread = None
temp_position = None
temp_hole = None
root = Str
# use_modified = Bool(True) # set true to use modified affine calculation
def motor_event_hook(self, name, value, *args, **kw):
pass
def goto_position(self, pos):
raise NotImplementedError
def refresh_stage_map_names(self):
sms = get_stage_map_names(root=self.root)
self.stage_map_names = sms
def load(self):
self.refresh_stage_map_names()
psm = self._load_previous_stage_map()
sms = self.stage_map_names
sm = None
if psm in sms:
sm = psm
elif sms:
sm = sms[0]
if sm:
self.stage_map_name = ''
self.stage_map_name = sm
def kill(self):
r = super(BaseStageManager, self).kill()
self._save_stage_map()
return r
@property
def stage_map_path(self):
return os.path.join(paths.hidden_dir, '{}.stage_map'.format(self.id))
def canvas_editor_factory(self):
return self.canvas_editor_klass(keyboard_focus='keyboard_focus')
def move_to_hole(self, hole, **kw):
self._move(self._move_to_hole, hole, name='move_to_hole', **kw)
def get_calibrated_position(self, pos, key=None):
smap = self.stage_map
# use a affine transform object to map
canvas = self.canvas
ca = canvas.calibration_item
# check if a calibration applies to this hole
hole_calibration = get_hole_calibration(smap.name, key)
if hole_calibration:
self.debug('Using hole calibration')
ca = hole_calibration
if ca:
rot = ca.rotation
cpos = ca.center
scale = ca.scale
self.debug('Calibration parameters: '
'rot={:0.3f}, cpos={} scale={:0.3f}'.format(
rot, cpos, scale))
pos = smap.map_to_calibration(pos, cpos, rot, scale=scale)
return pos
def update_axes(self):
"""
"""
self.info('querying axis positions')
self._update_axes()
# private
def _update_axes(self):
pass
def _move_to_hole(self, key, correct_position=True, **kw):
pass
def _stop(self):
pass
def _move(self, func, pos, name=None, *args, **kw):
if pos is None:
return
if self.move_thread and self.move_thread.isRunning():
self._stop()
if name is None:
name = func.__name__
self.move_thread = Thread(name='stage.{}'.format(name),
target=func,
args=(pos, ) + args,
kwargs=kw)
self.move_thread.start()
def _canvas_factory(self):
raise NotImplementedError
def _stage_map_changed_hook(self):
pass
# handlers
def _calibrated_position_entry_changed(self, new):
self.debug('User entered calibrated position {}'.format(new))
self.goto_position(new)
def _stage_map_name_changed(self, new):
if new:
self.debug('setting stage map to {}'.format(new))
root = self.root
path = os.path.join(root, add_extension(new, '.txt'))
sm = self.stage_map_klass(file_path=path)
self.tray_calibration_manager.load_calibration(stage_map=new)
self.canvas.set_map(sm)
self.canvas.request_redraw()
self.stage_map = sm
self._stage_map_changed_hook()
# defaults
def _root_default(self):
return paths.map_dir
def _tray_calibration_manager_default(self):
t = TrayCalibrationManager(parent=self, canvas=self.canvas)
return t
def _canvas_default(self):
return self._canvas_factory()
def _save_stage_map(self):
p = self.stage_map_path
self.info('saving stage_map {} to {}'.format(self.stage_map_name, p))
with open(p, 'wb') as f:
pickle.dump(self.stage_map_name, f)
def _load_previous_stage_map(self):
p = self.stage_map_path
if os.path.isfile(p):
self.info('loading previous stage map from {}'.format(p))
with open(p, 'rb') as f:
try:
sm = pickle.load(f)
if not sm.endswith('.center'):
return sm
except (pickle.PickleError, ValueError):
pass
def execute(self):
self.canceled = False
t = Thread(target=self._execute)
t.start()
self._t = t
class FusionsLaserManager(LaserManager):
"""
"""
laser_controller = Instance(FusionsLogicBoard)
fiber_light = Instance(FiberLight)
# optics_view = Instance(OpticsView)
# beam = DelegatesTo('laser_controller')
# beammin = DelegatesTo('laser_controller')
# beammax = DelegatesTo('laser_controller')
# update_beam = DelegatesTo('laser_controller')
# beam_enabled = DelegatesTo('laser_controller')
# # beam_enabled = Bool(True)
#
# zoom = DelegatesTo('laser_controller')
# zoommin = DelegatesTo('laser_controller')
# zoommax = DelegatesTo('laser_controller')
# update_zoom = DelegatesTo('laser_controller')
# execute_button = DelegatesTo('laser_script_executor')
# execute_label = DelegatesTo('laser_script_executor')
pointer = Event
pointer_state = Bool(False)
pointer_label = Property(depends_on='pointer_state')
step_heat_manager = None
lens_configuration = Str('gaussian')
lens_configuration_dict = Dict
lens_configuration_names = List
power_timer = None
brightness_timer = None
power_graph = None
_prev_power = 0
record_brightness = Bool
# recording_zoom = Float
# record = Event
# record_label = Property(depends_on='_recording_power_state')
_recording_power_state = Bool(False)
simulation = DelegatesTo('laser_controller')
data_manager = None
_data_manager_lock = None
_current_rid = None
# brightness_meter = Instance(BrightnessPIDManager)
chiller = Any
motor_event = Event
_degas_thread = None
@on_trait_change('laser_controller:refresh_canvas')
def refresh_canvas(self):
if self.stage_manager:
self.stage_manager.canvas.request_redraw()
# ===============================================================================
# IExtractionDevice interface
# ===============================================================================
def extract(self, power, **kw):
self.enable_laser()
self.set_laser_power(power, **kw)
def end_extract(self):
self.disable_laser()
self.stop_pattern()
def open_motor_configure(self):
self.laser_controller.open_motor_configure()
# def _record_fired(self):
# if self._recording_power_state:
# save = self.db_save_dialog()
# self.stop_power_recording(delay=0, save=save)
# else:
# t = Thread(name='fusions.power_record',
# target=self.start_power_recording, args=('Manual',))
# t.start()
# self._recording_power_state = not self._recording_power_state
def bind_preferences(self, pref_id):
self.debug('binding preferences')
super(FusionsLaserManager, self).bind_preferences(pref_id)
bind_preference(self, 'recording_zoom',
'{}.recording_zoom'.format(pref_id))
bind_preference(self, 'record_brightness',
'{}.record_brightness'.format(pref_id))
self.debug('preferences bound')
def set_light(self, value):
self.set_light_state(value > 0)
self.set_light_intensity(value)
def set_light_state(self, state):
if state:
self.fiber_light.power_off()
else:
self.fiber_light.power_on()
def set_light_intensity(self, v):
self.fiber_light.intensity = min(max(0, v), 100)
@on_trait_change('pointer')
def pointer_ononff(self):
"""
"""
self.pointer_state = not self.pointer_state
self.laser_controller.set_pointer_onoff(self.pointer_state)
def get_laser_watts(self):
return self._requested_power
def get_coolant_temperature(self, **kw):
"""
"""
chiller = self.chiller
if chiller is not None:
return chiller.get_coolant_out_temperature(**kw)
def get_coolant_status(self, **kw):
chiller = self.chiller
if chiller is not None:
return chiller.get_faults(**kw)
def do_motor_initialization(self, name):
if self.laser_controller:
motor = self.laser_controller.get_motor(name)
if motor is not None:
n = 4
from pychron.core.ui.progress_dialog import myProgressDialog
pd = myProgressDialog(max=n, size=(550, 15))
pd.open()
motor.initialize(progress=pd)
pd.close()
def set_beam_diameter(self, bd, force=False, **kw):
"""
"""
result = False
motor = self.get_motor('beam')
if motor is not None:
if motor.enabled or force:
self.set_motor('beam', bd, **kw)
result = True
else:
self.info('beam disabled by lens configuration {}'.format(
self.lens_configuration))
return result
def set_zoom(self, z, **kw):
"""
"""
self.set_motor('zoom', z, **kw)
def set_motor_lock(self, name, value):
m = self.get_motor(name)
if m is not None:
m.locked = to_bool(value)
return True
def set_motor(self, *args, **kw):
self.motor_event = (args, kw)
return self.laser_controller.set_motor(*args, **kw)
def get_motor(self, name):
return next(
(mi for mi in self.laser_controller.motors if mi.name == name),
None)
def do_autofocus(self, **kw):
if self.use_video:
am = self.stage_manager.autofocus_manager
am.passive_focus(block=True, **kw)
def take_snapshot(self, *args, **kw):
if self.use_video:
return self.stage_manager.snapshot(auto=True,
inform=False,
*args,
**kw)
def start_video_recording(self, name='video', *args, **kw):
if self.use_video:
self.stage_manager.start_recording(basename=name)
def stop_video_recording(self, *args, **kw):
if self.use_video:
self.stage_manager.stop_recording()
def degasser_factory(self):
from pychron.mv.degas.degasser import Degasser
dm = Degasser(
laser_manager=self,
video=self.stage_manager.video,
)
return dm
def do_machine_vision_degas(self, lumens, duration, new_thread=False):
if self.use_video:
dm = self.degasser_factory()
def func():
dm.degas(lumens, duration)
if new_thread:
self._degas_thread = Thread(target=func)
self._degas_thread.start()
else:
func()
def get_brightness(self):
if self.use_video:
return self.stage_manager.get_brightness()
else:
return super(FusionsLaserManager, self).get_brightness()
def is_degassing(self):
if self._degas_thread:
return self._degas_thread.isRunning()
# ===============================================================================
# pyscript interface
# ===============================================================================
def _move_to_position(self, position, autocenter):
if self.stage_manager is not None:
if isinstance(position, tuple):
if len(position) > 1:
x, y = position[:2]
self.stage_manager.linear_move(x, y)
if len(position) == 3:
self.stage_manager.set_z(position[2])
else:
self.stage_manager.move_to_hole(position)
return True
def set_stage_map(self, mapname):
if self.stage_manager is not None:
self.stage_manager.set_stage_map(mapname)
def _enable_hook(self, **kw):
resp = self.laser_controller._enable_laser(**kw)
if self.laser_controller.simulation:
resp = True
return resp
def _disable_hook(self):
resp = self.laser_controller._disable_laser()
if self.laser_controller.simulation:
resp = True
return resp
def show_motion_controller_manager(self):
"""
"""
stage_controller = self.stage_manager.stage_controller
package = 'pychron.managers.motion_controller_managers'
if 'Aerotech' in stage_controller.__class__.__name__:
klass = 'AerotechMotionControllerManager'
package += '.aerotech_motion_controller_manager'
else:
klass = 'NewportMotionControllerManager'
package += '.newport_motion_controller_manager'
module = __import__(package, globals(), locals(), [klass], -1)
factory = getattr(module, klass)
m = factory(motion_controller=stage_controller)
self.open_view(m)
# ========================= views =========================
def get_control_buttons(self):
"""
"""
return [
('enable', 'enable_label', None),
]
# def get_control_items(self):
# '''
# '''
# # return Item('laser_controller', show_label=False,
# # editor=InstanceEditor(view='control_view'),
# # style='custom',
# # springy=False, height= -100)
#
# # return self.laser_controller.get_control_group()
# s = [('zoom', 'zoom', {}),
# ('beam', 'beam', {'enabled_when':'object.beam_enabled'})
# ]
# return self._update_slider_group_factory(s)
# def get_lens_configuration_group(self):
# return Item('lens_configuration',
# editor=EnumEditor(values=self.lens_configuration_names)
# )
# def get_optics_group(self):
# csliders = self.get_control_items()
# vg = HGroup(csliders,
# show_border=True,
# label='Optics', springy=False
# )
#
# lens_config = self.get_lens_configuration_group()
# if lens_config:
# vg.content.insert(0, lens_config)
#
# return vg
# def get_control_button_group(self):
# grp = HGroup(spring, Item('enabled_led', show_label=False, style='custom', editor=LEDEditor()),
# self._button_group_factory(self.get_control_buttons(), orientation='h'),
# # springy=True
# )
# return grp
def get_power_group(self):
power_grp = VGroup(
self.get_control_button_group(),
HGroup(
Item('requested_power',
style='readonly',
format_str='%0.2f',
width=100), spring,
Item('units', show_label=False, style='readonly'), spring),
# Item('laser_script_executor', show_label=False, style='custom'),
# self._button_factory('execute_button', 'execute_label'),
show_border=True,
# springy=True,
label='Power')
ps = self.get_power_slider()
if ps:
# ps.springy = True
power_grp.content.append(ps)
return power_grp
# def get_additional_group(self):
# og = Group(Item('laser_controller', show_label=False,
# editor=InstanceEditor(view='control_view'),
# style='custom'),
# label='Optics',
# )
# ac = Group(
# og,
# show_border=True,
# label='Additional Controls',
# layout='tabbed')
#
# aclist = self.get_additional_controls()
# if aclist is None:
# og.label = 'Optics'
# og.show_border = True
# ac = og
# else:
# for ai in aclist:
# ac.content.append(ai)
# return ac
# def get_control_group(self):
# '''
# '''
# power_grp = self.get_power_group()
# pulse_grp = Group(Item('pulse', style='custom', show_label=False),
# label='Pulse', show_border=True
# )
# power_grp = HGroup(power_grp, pulse_grp)
# ac = self.get_additional_group()
# g = HGroup(power_grp, ac)
#
# return g
def _get_pointer_label(self):
"""
"""
return 'Pointer ON' if not self.pointer_state else 'Pointer OFF'
def _get_record_label(self):
return 'Record' if not self._recording_power_state else 'Stop'
def _get_record_brightness(self):
return self.record_brightness and self._get_machine_vision(
) is not None
# ========================= defaults =======================
# def get_power_database(self):
# from pychron.database.adapters.power_adapter import PowerAdapter
#
# db = PowerAdapter(name=self.dbname,
# kind='sqlite')
# return db
# def get_power_calibration_database(self):
# from pychron.database.adapters.power_calibration_adapter import PowerCalibrationAdapter
#
# db = PowerCalibrationAdapter(name=self.dbname,
# kind='sqlite')
# return db
# def _subsystem_default(self):
# '''
# '''
# return ArduinoSubsystem(name='arduino_subsystem_2')
# def _brightness_meter_default(self):
# if self.use_video:
# b = BrightnessPIDManager(parent=self)
# # b.brightness_manager.video = self.stage_manager.video
#
# return b
def _fiber_light_default(self):
"""
"""
return FiberLight(name='fiber_light')
class BaseStageManager(Manager):
keyboard_focus = Event
canvas_editor_klass = LaserComponentEditor
tray_calibration_manager = Instance(TrayCalibrationManager)
stage_map_klass = LaserStageMap
stage_map_name = Str
stage_map_names = List
stage_map = Instance(BaseStageMap)
canvas = Instance(MapCanvas)
root = Str(paths.map_dir)
calibrated_position_entry = String(enter_set=True, auto_set=False)
move_thread = None
temp_position = None
temp_hole = None
use_modified = Bool(True) # set true to use modified affine calculation
def goto_position(self, pos):
raise NotImplementedError
def refresh_stage_map_names(self):
sms = list_directory2(self.root, '.txt', remove_extension=True)
us = list_directory2(paths.user_points_dir, '.yaml', remove_extension=True)
if us:
sms.extend(us)
self.stage_map_names = sms
def load(self):
self.refresh_stage_map_names()
psm = self._load_previous_stage_map()
sms = self.stage_map_names
sm = None
if psm in sms:
sm = psm
elif sms:
sm = sms[0]
if sm:
self.stage_map_name = sm
if self.stage_map:
self.canvas.set_map(self.stage_map)
self.canvas.request_redraw()
# self.stage_maps = []
# config = self.get_configuration()
# if config:
# load the stage maps
# mapfiles = self.config_get(config, 'General', 'mapfiles')
# self.stage_map_names = mapfiles.split(',')
# for mapfile in mapfiles.split(','):
# path = os.path.join(paths.map_dir, mapfile.strip())
# sm = StageMap(file_path=path)
# sm.load_correction_file()
# self.stage_maps.append(sm)
# load user points as stage map
# for di in os.listdir(paths.user_points_dir):
# if di.endswith('.yaml'):
# path = os.path.join(paths.user_points_dir, di)
# sm = self.stage_map_klass(file_path=path)
# self.stage_maps.append(sm)
# load the saved stage map
# sp = self._get_stage_map_by_name(self._load_previous_stage_map())
# if sp is not None:
# sm = sp
# self.stage_map_name = sm
# load the points file
# self.canvas.load_points_file(self.points_file)
# load defaults
# self._default_z = self.config_get(config, 'Defaults', 'z', default=13, cast='float')
# self.canvas.set_map(sm)
# self.canvas.request_redraw()
def kill(self):
r = super(BaseStageManager, self).kill()
self._save_stage_map()
return r
@property
def stage_map_path(self):
return os.path.join(paths.hidden_dir, '{}.stage_map'.format(self.id))
def canvas_editor_factory(self):
return self.canvas_editor_klass(keyboard_focus='keyboard_focus')
def move_to_hole(self, hole, **kw):
self._move(self._move_to_hole, hole, name='move_to_hole', **kw)
def get_calibrated_position(self, pos, key=None):
smap = self.stage_map
# use a affine transform object to map
canvas = self.canvas
ca = canvas.calibration_item
# check if a calibration applies to this hole
hole_calibration = get_hole_calibration(smap.name, key)
if hole_calibration:
self.debug('Using hole calibration')
ca = hole_calibration
if ca:
rot = ca.rotation
cpos = ca.center
scale = ca.scale
self.debug('Calibration parameters: rot={:0.3f}, cpos={} scale={:0.3f}'.format(rot, cpos, scale))
pos = smap.map_to_calibration(pos, cpos, rot,
scale=scale,
use_modified=self.use_modified)
return pos
def update_axes(self):
"""
"""
self.info('querying axis positions')
self._update_axes()
# private
def _update_axes(self):
pass
def _move_to_hole(self, key, correct_position=True):
pass
def _stop(self):
pass
def _move(self, func, pos, name=None, *args, **kw):
if pos is None:
return
if self.move_thread and self.move_thread.isRunning():
self._stop()
if name is None:
name = func.func_name
self.move_thread = Thread(name='stage.{}'.format(name),
target=func, args=(pos,) + args, kwargs=kw)
self.move_thread.start()
def _canvas_factory(self):
raise NotImplementedError
# handlers
def _calibrated_position_entry_changed(self, new):
self.debug('User entered calibrated position {}'.format(new))
self.goto_position(new)
def _stage_map_name_changed(self, new):
if new:
self.debug('setting stage map to {}'.format(new))
sm = self.stage_map_klass(file_path=os.path.join(self.root, add_extension(new, '.txt')))
self.stage_map = sm
self.tray_calibration_manager.load_calibration(stage_map=new)
self.canvas.set_map(sm)
self.canvas.request_redraw()
# defaults
def _tray_calibration_manager_default(self):
t = TrayCalibrationManager(parent=self,
canvas=self.canvas)
return t
def _canvas_default(self):
return self._canvas_factory()
def _save_stage_map(self):
p = self.stage_map_path
self.info('saving stage_map {} to {}'.format(self.stage_map_name, p))
with open(p, 'wb') as f:
pickle.dump(self.stage_map_name, f)
def _load_previous_stage_map(self):
p = self.stage_map_path
if os.path.isfile(p):
self.info('loading previous stage map from {}'.format(p))
with open(p, 'rb') as f:
try:
return pickle.load(f)
except pickle.PickleError:
pass
class IonOpticsManager(Manager):
reference_detector = Instance(BaseDetector)
reference_isotope = Any
magnet_dac = Range(0.0, 6.0)
graph = Instance(Graph)
peak_center_button = Button('Peak Center')
stop_button = Button('Stop')
alive = Bool(False)
spectrometer = Any
peak_center = Instance(PeakCenter)
coincidence = Instance(Coincidence)
peak_center_config = Instance(PeakCenterConfigurer)
# coincidence_config = Instance(CoincidenceConfig)
canceled = False
peak_center_result = None
_centering_thread = None
def close(self):
self.cancel_peak_center()
def cancel_peak_center(self):
self.alive = False
self.canceled = True
self.peak_center.canceled = True
self.peak_center.stop()
self.info('peak center canceled')
def get_mass(self, isotope_key):
spec = self.spectrometer
molweights = spec.molecular_weights
return molweights[isotope_key]
def set_mftable(self, name=None):
"""
if mt is None set to the default mftable located at setupfiles/spectrometer/mftable.csv
:param mt:
:return:
"""
if name and name != os.path.splitext(os.path.basename(
paths.mftable))[0]:
self.spectrometer.use_deflection_correction = False
else:
self.spectrometer.use_deflection_correction = True
self.spectrometer.magnet.set_mftable(name)
def get_position(self, *args, **kw):
kw['update_isotopes'] = False
return self._get_position(*args, **kw)
def position(self, pos, detector, *args, **kw):
dac = self._get_position(pos, detector, *args, **kw)
mag = self.spectrometer.magnet
self.info('positioning {} ({}) on {}'.format(pos, dac, detector))
return mag.set_dac(dac)
def do_coincidence_scan(self, new_thread=True):
if new_thread:
t = Thread(name='ion_optics.coincidence', target=self._coincidence)
t.start()
self._centering_thread = t
def setup_coincidence(self):
pcc = self.coincidence_config
pcc.dac = self.spectrometer.magnet.dac
info = pcc.edit_traits()
if not info.result:
return
detector = pcc.detector
isotope = pcc.isotope
detectors = [d for d in pcc.additional_detectors]
# integration_time = pcc.integration_time
if pcc.use_nominal_dac:
center_dac = self.get_position(isotope, detector)
elif pcc.use_current_dac:
center_dac = self.spectrometer.magnet.dac
else:
center_dac = pcc.dac
# self.spectrometer.save_integration()
# self.spectrometer.set_integration(integration_time)
cs = Coincidence(spectrometer=self.spectrometer,
center_dac=center_dac,
reference_detector=detector,
reference_isotope=isotope,
additional_detectors=detectors)
self.coincidence = cs
return cs
def get_center_dac(self, det, iso):
spec = self.spectrometer
det = spec.get_detector(det)
molweights = spec.molecular_weights
mass = molweights[iso]
dac = spec.magnet.map_mass_to_dac(mass, det.name)
# correct for deflection
return spec.correct_dac(det, dac)
def do_peak_center(self,
save=True,
confirm_save=False,
warn=False,
new_thread=True,
message='',
on_end=None,
timeout=None):
self.debug('doing pc')
self.canceled = False
self.alive = True
self.peak_center_result = None
args = (save, confirm_save, warn, message, on_end, timeout)
if new_thread:
t = Thread(name='ion_optics.peak_center',
target=self._peak_center,
args=args)
t.start()
self._centering_thread = t
return t
else:
self._peak_center(*args)
def setup_peak_center(self,
detector=None,
isotope=None,
integration_time=1.04,
directions='Increase',
center_dac=None,
plot_panel=None,
new=False,
standalone_graph=True,
name='',
show_label=False,
window=0.015,
step_width=0.0005,
min_peak_height=1.0,
percent=80,
deconvolve=None,
use_interpolation=False,
interpolation_kind='linear',
dac_offset=None,
calculate_all_peaks=False,
config_name=None,
use_configuration_dac=True):
if deconvolve is None:
n_peaks, select_peak = 1, 1
if dac_offset is not None:
use_dac_offset = True
spec = self.spectrometer
spec.save_integration()
self.debug('setup peak center. detector={}, isotope={}'.format(
detector, isotope))
self._setup_config()
pcc = None
if detector is None or isotope is None:
self.debug('ask user for peak center configuration')
self.peak_center_config.load(dac=spec.magnet.dac)
if config_name:
self.peak_center_config.active_name = config_name
info = self.peak_center_config.edit_traits()
if not info.result:
return
else:
pcc = self.peak_center_config.active_item
elif config_name:
self.peak_center_config.load(dac=spec.magnet.dac)
self.peak_center_config.active_name = config_name
pcc = self.peak_center_config.active_item
if pcc:
if not detector:
detector = pcc.active_detectors
if not isotope:
isotope = pcc.isotope
directions = pcc.directions
integration_time = pcc.integration_time
window = pcc.window
min_peak_height = pcc.min_peak_height
step_width = pcc.step_width
percent = pcc.percent
use_interpolation = pcc.use_interpolation
interpolation_kind = pcc.interpolation_kind
n_peaks = pcc.n_peaks
select_peak = pcc.select_n_peak
use_dac_offset = pcc.use_dac_offset
dac_offset = pcc.dac_offset
calculate_all_peaks = pcc.calculate_all_peaks
if center_dac is None and use_configuration_dac:
center_dac = pcc.dac
spec.set_integration_time(integration_time)
period = int(integration_time * 1000 * 0.9)
if not isinstance(detector, (tuple, list)):
detector = (detector, )
ref = detector[0]
ref = self.spectrometer.get_detector(ref)
self.reference_detector = ref
self.reference_isotope = isotope
if center_dac is None:
center_dac = self.get_center_dac(ref, isotope)
if len(detector) > 1:
ad = detector[1:]
else:
ad = []
pc = self.peak_center
if not pc or new:
pc = PeakCenter()
pc.trait_set(center_dac=center_dac,
period=period,
window=window,
percent=percent,
min_peak_height=min_peak_height,
step_width=step_width,
directions=directions,
reference_detector=ref,
additional_detectors=ad,
reference_isotope=isotope,
spectrometer=spec,
show_label=show_label,
use_interpolation=use_interpolation,
interpolation_kind=interpolation_kind,
n_peaks=n_peaks,
select_peak=select_peak,
use_dac_offset=use_dac_offset,
dac_offset=dac_offset,
calculate_all_peaks=calculate_all_peaks)
self.peak_center = pc
graph = pc.graph
graph.name = name
if plot_panel:
plot_panel.set_peak_center_graph(graph)
else:
graph.close_func = self.close
if standalone_graph:
# set graph window attributes
graph.window_title = 'Peak Center {}({}) @ {:0.3f}'.format(
ref, isotope, center_dac)
graph.window_width = 300
graph.window_height = 250
open_view(graph)
return self.peak_center
# private
def _setup_config(self):
config = self.peak_center_config
config.detectors = self.spectrometer.detector_names
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
def _get_peak_center_config(self, config_name):
if config_name is None:
config_name = 'default'
config = self.peak_center_config.get(config_name)
config.detectors = self.spectrometer.detectors_names
if config.detector_name:
config.detector = next(
(di for di in config.detectors if di == config.detector_name),
None)
if not config.detector:
config.detector = config.detectors[0]
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
return config
def _timeout_func(self, timeout, evt):
st = time.time()
while not evt.is_set():
if not self.alive:
break
if time.time() - st > timeout:
self.warning(
'Peak Centering timed out after {}s'.format(timeout))
self.cancel_peak_center()
break
time.sleep(0.01)
def _peak_center(self, save, confirm_save, warn, message, on_end, timeout):
pc = self.peak_center
spec = self.spectrometer
ref = self.reference_detector
isotope = self.reference_isotope
if timeout:
evt = Event()
self.timeout_thread = Thread(target=self._timeout_func,
args=(timeout, evt))
self.timeout_thread.start()
dac_d = pc.get_peak_center()
self.peak_center_result = dac_d
if dac_d:
args = ref, isotope, dac_d
self.info('new center pos {} ({}) @ {}'.format(*args))
det = spec.get_detector(ref)
dac_a = spec.uncorrect_dac(det, dac_d)
self.info('dac uncorrected for HV and deflection {}'.format(dac_a))
if save:
if confirm_save:
msg = 'Update Magnet Field Table with new peak center- {} ({}) @ RefDetUnits= {}'.format(
*args)
save = self.confirmation_dialog(msg)
if save:
spec.magnet.update_field_table(det, isotope, dac_a,
message)
spec.magnet.set_dac(dac_d)
elif not self.canceled:
msg = 'centering failed'
if warn:
self.warning_dialog(msg)
self.warning(msg)
# needs to be called on the main thread to properly update
# the menubar actions. alive=False enables IonOptics>Peak Center
# d = lambda:self.trait_set(alive=False)
# still necessary with qt? and tasks
if on_end:
on_end()
self.trait_set(alive=False)
if timeout:
evt.set()
self.spectrometer.restore_integration()
def _get_position(self,
pos,
detector,
use_dac=False,
update_isotopes=True):
"""
pos can be str or float
"Ar40", "39.962", 39.962
to set in DAC space set use_dac=True
"""
if pos == NULL_STR:
return
spec = self.spectrometer
mag = spec.magnet
if isinstance(detector, str):
det = spec.get_detector(detector)
else:
det = detector
self.debug('detector {}'.format(det))
if use_dac:
dac = pos
else:
self.debug('POSITION {} {}'.format(pos, detector))
if isinstance(pos, str):
try:
pos = float(pos)
except ValueError:
# pos is isotope
if update_isotopes:
# if the pos is an isotope then update the detectors
spec.update_isotopes(pos, detector)
pos = self.get_mass(pos)
mag.mass_change(pos)
# pos is mass i.e 39.962
dac = mag.map_mass_to_dac(pos, det.name)
dac = spec.correct_dac(det, dac)
return dac
def _coincidence(self):
self.coincidence.get_peak_center()
self.info('coincidence finished')
self.spectrometer.restore_integration()
# ===============================================================================
# handler
# ===============================================================================
def _coincidence_config_default(self):
config = None
p = os.path.join(paths.hidden_dir, 'coincidence_config.p')
if os.path.isfile(p):
try:
with open(p) as rfile:
config = pickle.load(rfile)
config.detectors = dets = self.spectrometer.detectors
config.detector = next(
(di for di in dets if di.name == config.detector_name),
None)
except Exception, e:
print 'coincidence config', e
if config is None:
config = CoincidenceConfig()
config.detectors = self.spectrometer.detectors
config.detector = config.detectors[0]
keys = self.spectrometer.molecular_weights.keys()
config.isotopes = sort_isotopes(keys)
return config