"""
automated sample finder for the Y axis (TESTING)

the script first runs a coarse scan to find the lower and upper edges of the sample.
after that it runs a fine scan on either edge.

set the scienta to a clear peak in fixed mode.
"""

import math

# estimated center of the sample
START_POS = 0.0
# coarse scan range = estimated size of the sample + margins
COARSE_RANGE = 10.0
# scienta dwell time (fixed mode)
DWELL_TIME = 0.1


# --- do not edit below ---

RELATIVE = False
LATENCY = 0.0
ZIGZAG = False
ENDSCAN = False

SENSORS = (Counts, SampleCurrent, RefCurrent, MachineCurrent)
MOTORS = (ManipulatorY)
RANGE = (START_POS + COARSE_RANGE / 2., START_POS - COARSE_RANGE / 2.)

Scienta.setExposure(DWELL_TIME)
#scienta_time = DWELL_TIME + 0.1

# time per scienta acquisition in seconds
trig_scienta()
time1 = time.time()
trig_scienta()
time.sleep(0.01)
time2 = time.time()
scienta_time = (time2 - time1) + 1.
print "step time: ", scienta_time        
        
STEP = 0.25
SPEED = MOTORS[0].getSpeed()
fly_time = abs(RANGE[1] - RANGE[0]) / SPEED
STEPS = int(fly_time / scienta_time) + 1

print "coarse scan"
print "speed: ", SPEED
print "scan time: ", fly_time

set_exec_pars(keep=True)
adjust_sensors()
set_adc_averaging()

result = cscan(MOTORS, SENSORS, RANGE[0], RANGE[1], STEPS, time=fly_time, before_read=before_readout, after_read = after_readout, check_positions = False)

readable = result.getReadable(0)
positions = result.getPositions(0)
min_counts = min(readable)
max_counts = max(readable)
thresh = (max_counts - min_counts) / 2. + min_counts
print "threshhold: ", thresh

sample_positions = [pos for idx, pos in enumerate(positions) if readable[idx] >= thresh]
lo_edge = min(sample_positions)
hi_edge = max(sample_positions)
print "lower edge, upper edge: ", lo_edge, ", ", hi_edge


RANGE = (lo_edge - 0.4, lo_edge + 0.4)
STEP = 0.025
SPEED = STEP / scienta_time
fly_time = abs(RANGE[1] - RANGE[0]) / SPEED
STEPS = int(fly_time / scienta_time) + 1

print "lower edge scan"
print "speed: ", SPEED
print "scan time: ", fly_time

cscan(MOTORS, SENSORS, RANGE[0], RANGE[1], STEPS, time=fly_time, before_read=before_readout, after_read = after_readout, check_positions = False)


RANGE = (hi_edge - 0.4, hi_edge + 0.4)
STEP = 0.025
SPEED = STEP / scienta_time
fly_time = abs(RANGE[1] - RANGE[0]) / SPEED
STEPS = int(fly_time / scienta_time) + 1

print "upper edge scan"
print "speed: ", SPEED
print "scan time: ", fly_time

cscan(MOTORS, SENSORS, RANGE[0], RANGE[1], STEPS, time=fly_time, before_read=before_readout, after_read = after_readout, check_positions = False)

MOTORS.move((lo_edge + hi_edge) / 2)