"""
Multi-peak search and gaussian fitting
""" 

from mathutils import estimate_peak_indexes, fit_gaussians, create_fit_point_list

start = 1
end = 30
step_size = 0.2

result= lscan(sout,sinp,start,end,[step_size,],0.05)

path = get_current_data_group()
set_attribute(path, "ApertureX", apertureX.read())

readable = result.getReadable(0)
positions = result.getPositions(0)

threshold = (min(readable) + max(readable))/2
min_peak_distance = 5.0

peaks = estimate_peak_indexes(readable, positions, threshold, min_peak_distance)
print "Peak indexes: " + str(peaks)
print "Peak x: " + str(map(lambda x:positions[x], peaks))
print "Peak y: " + str(map(lambda x:readable[x], peaks))

log("Highest peak index = " +str(peaks[0]))

#Manually adding a dataset
data = [ [1,2,3,4,5],  [2,3,4,5,6],  [3,4,5,6,7]]
path="group/data2"
save_dataset(path, data)

gaussians = fit_gaussians(readable, positions, peaks)


plots = plot([readable],["Multi-peak search"],[positions])
for i in range(len(peaks)):
    peak = peaks[i]
    (norm, mean, sigma) = gaussians[i]
    if abs(mean - positions[peak]) < min_peak_distance:
        print "Peak -> " +  str(mean)
        plots[0].addMarker(mean, None, "N="+str(round(norm,2)), None)
    else:
        print "Invalid gaussian fit: " +  str(mean)