###############################################################################
#Scan the PSSS photon energy
#Purpose: To find and centre the PSSS photon energy so the measured spectrum is centred on the camera chip

#PARAMETERS
#User inputs - define energy range to scan below by running the appropiate cell
#Below is for a large scan range assuming offset from machine upto $\pm$ 300 eV

#If running from editor
if get_exec_pars().source == CommandSource.ui:   
    RANGE_OFF = None
    RANGE_FROM = 11100
    RANGE_TO = 11300
    STEPS = 5 #60
    NUM_SHOTS= 10 #100
    PLOT=None
p = plot(None, title="Data")[0] if (PLOT is None) else PLOT
p.clear()
p.removeMarker(None)
p.setLegendVisible(True)
p.addSeries(LinePlotSeries("PSSS Spectrum Average")) 

if RANGE_OFF is not None:    
    RANGE_FROM = energy_machine.read()-RANGE_OFF
    RANGE_TO = energy_machine.read()+RANGE_OFF

run("cpython/wrapper")




#Scan and take data
class PSSS_energy(Writable):
    def write(self, value):
        if not is_dry_run():
            psss_energy.write(value)
            exec_cpython("/ioc/modules/qt/PSSS_motion.py", args = ["-m1", "SARFE10-PSSS059"])
            # python / ioc / modules / qt / PSSS_motion.py - m1 SARFE10 - PSSS059
        time.sleep(1)
        print(value)

en = PSSS_energy()
en.alias = "energy"

av = create_averager(psss_spectrum_y, NUM_SHOTS, interval=-1, name="spectrum_average")
av_samples = av.samples
av_samples.alias = "spectrum_samples"


def after_read(record, scan):
    p.getSeries(0).setData(psss_spectrum_x.take(), record[av])
    p.setTitle("Energy = %1.3f" %(record[en]))
      
r = lscan(en, (av, av_samples), RANGE_FROM, RANGE_TO, STEPS, latency=0.0, after_read = after_read, save=False )
average, samples, energy_range =  r.getReadable(0), r.getReadable(1), r.getPositions(0)    

[amp, mean_val, sigma, offset],centre_line_out  = fit_energy(RANGE_FROM, RANGE_TO, STEPS+1, NUM_SHOTS, samples)

if not (RANGE_FROM < mean_val < RANGE_TO or RANGE_TO < mean_val < RANGE_FROM):
    raise Exception ("Invalid fit mean: " + str(mean_val))  

    
measured_offset = energy_machine.read() - mean_val
#Set fitted energy
print "measured offset", measured_offset

en.write(mean_val)


#Plot
"""
plt.figure(figsize=[10,5])
plt.subplot(121)
plt.title('PSSS scan of set photon energy')
plt.pcolormesh(np.arange(0,Scan_spec.shape[2]), Energy_range, Scan_spec.mean(axis=1),cmap='CMRmap')
plt.vlines(int(Scan_spec.shape[2]/2), Energy_range[0], Energy_range[-1],linestyles='--', colors='orange')
plt.xlim([0,Scan_spec.shape[2]])
plt.xlabel('Camera pixel')
plt.ylabel('Set PSSS energy [eV] \n SARFE10-PSSS059:ENERGY')

plt.subplot(122)
plt.title('At camera centre pixel %1i \nCalibrated energy = %.1f [eV]\n Offset from machine = %.1f [eV]'%(int(Scan_spec.shape[2]/2),popt[1],measured_offset))
plt.plot(centre_line_out,Energy_range,linewidth = 2, color = 'orange',label ='measured')
plt.plot(gaus(Energy_range_fit,*popt),Energy_range_fit,'r:',label='fit')
plt.xticks([])
plt.legend()
plt.grid(True)
"""

p.clear()
p.setTitle("")
plot_gauss_fit(energy_range, centre_line_out, gauss_pars=(offset, amp, mean_val, sigma), p=PLOT, title = "Data")


set_return(mean_val)