#Number of cycles must be small otherwise generates a following error
def before_read(position, scan):  
    global total_time, steps,d_output  
    import time
    if d_output ==1:
        print('enter before_read')
    start = time.time()
    caput("X07MB-OP2:SMPL",1)
    time.sleep(0.75)
    if d_output ==1:
        print "Waiting..."
    cawait ("X07MB-OP2:SMPL-DONE",1, 10000)
    print "Done"
    t = time.time()-start
    if d_output ==1:
        print t
    if t > (total_time/steps):
        print "Before took too long, step = ", (total_time/steps)
    if d_output ==1:
        print('leave before_read')
    # end before_read
    print(t)

    
def after(record, scan):
    pass

from mathutils import *
from plotutils import *

#setup_plotting(line_plots = [mca_1])

print('running')
#  scan definition

x0=-0.84

x1=-0.875
cycles = 4
total_time=20.
# General definitions 
Motor     = ScanY
RBV       = ScanY_RBV

d_output=0    # 1+ debugging output
# general preactions
caput("X07MB-OP2:START-CSMPL",0)   # cont sampling off 
time.sleep(0.1)
caput("X07MB-OP2:TOTAL-CYCLES",1)
time.sleep(0.1)
caput("X07MB-OP2:SMPL",1)              # start one cycle to get system in defined state
time.sleep(0.1)

#cscan(ScanX, [keith_1] , 18, 18.3, 100, latency = 0.0, time = 2.0,  before_read = before_read, after_read = None)
n_cycles=cycles+1
dwell=(n_cycles)*0.2  # time per step

steps=int(total_time/dwell)
speed=(x1-x0)/total_time
#caput(Motor.getChannelName()+".VBAS",speed*.5)

caput("X07MB-OP2:TOTAL-CYCLES",cycles)
print(' parameters for scan ')
print('range',x0,x1)
print('total time',total_time)
print('steps ',steps, '   cycles ' ,cycles)
print('speed',speed)

print(x0,x1,dwell,total_time,steps,speed,speed*0.5)

#ScanX.config.minSpeed = speed*.5
#ScanX.config.save()

# OTF
#ret = cscan(Motor, [keith_1,keith_2,keith_3,RBV] , x0, x1, steps=steps, latency =0.0, time = total_time,  before_read = before_read, after_read = None, domain_axis="Time")
#ret = cscan(Motor, [keith_1,keith_2,keith_3,RBV] , x0, x1, steps=steps, latency =0.0, time = total_time,  before_read = before_read, after_read = None)

# step by step
ret = lscan(Motor, [keith_1,keith_2, RBV] , x0, x1, steps, latency = 0.0, relative = False, passes = 1, zigzag = False, before_read = before_read, after_read = None, title = None)

#General postactions

caput(Motor.getChannelName()+'.VBAS',0.125)

caput("X07MB-OP2:TOTAL-CYCLES",5)
time.sleep(0.1)
caput("X07MB-OP2:START-CSMPL",1)
time.sleep(0.1)
caput("X07MB-OP2:SMPL",1)



# now plot the data 


# read data from data set 

y = ret.getReadable(1)
x = ret.getPositions(0)

# create processed tab 
p = plot(y, xdata=x, title="Processed")[0]

#function = interpolate(y,x,"cubic")

d = deriv(y,x)                # calc derivative 

plot_function(p, interpolate(d,x,"cubic"), "Deriv", x)

p.setLegendVisible(True)
(normalization, mean_val, sigma) = fit_gaussian(y, x)
print (' ===================================== ')
print ('RESULT GAUISSIAN FIT')
print ('sigma',sigma)
print ('position',mean_val)


fitted_gaussian_function = Gaussian(normalization, mean_val, sigma)
plot_function(p, fitted_gaussian_function, "Fit", x)

p.addText(min(x), max(y), get_exec_pars().path, Color.RED)

#plots = get_plot_snapshots("Processed")
#p2 = plot(y, xdata=x, title="Processed_2")[0]
#plot_function(p2, interpolate(d,x,"cubic"), "Deriv", x)

plots = get_plot_snapshots("Processed")

print plots