Changes by Chris and project fixes
This commit is contained in:
Gobbo Alexandre
45
script/cpython/psss.py
Executable file
45
script/cpython/psss.py
Executable file
@@ -0,0 +1,45 @@
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import numpy as np
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from scipy.optimize import curve_fit
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import sys
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def gaus(x, a, x0, sigma, offset):
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return offset + a * np.exp(-(x - x0) ** 2 / (2 * sigma ** 2))
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#Return [amp, mean_val, sigma, offset]
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def fit_energy(e_from, e_to, steps, num_shots, data):
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energy_range = np.linspace(e_from, e_to, steps)
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energy_range_fit = np.linspace(energy_range[0], energy_range[-1], len(energy_range)*10)
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centre_line_out = data[:,:,int(data.shape[2]/2)].mean(axis=1)
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try:
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popt,pcov = curve_fit(gaus,energy_range,centre_line_out,p0=[1,energy_range[np.argmax(centre_line_out)],energy_range.mean()*1e-3,1e3*num_shots])
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except:
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raise Exception('Fit failed: spectrum might not be near scan range center \n' + str(sys.exc_info()[1]))
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#print('Fit failed: spectrum might not be near scan range center')
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#return None
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max_ind = np.argmax(centre_line_out)
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max_photon_energy=energy_range[max_ind]
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print(max_photon_energy)
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return popt, centre_line_out
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#Return [amp, mean_val, sigma, offset]
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def fit_crystal_height(xstal_from, xstal_to, steps, data):
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xstal_range = np.linspace(xstal_from, xstal_to, steps)
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projection = data.mean(axis=1).mean(axis=1)
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offset = np.mean(projection[0:100])
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signal_centre = xstal_range[np.argmax(projection)]
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xstal_range_fit = np.linspace(xstal_range[0], xstal_range[-1], len(xstal_range)*10)
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try:
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popt,pcov = curve_fit(gaus,xstal_range,projection,p0=[100,signal_centre,-0.2,offset])
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except:
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raise Exception('Fit failed: spectrum might not be near scan range center \n' + str(sys.exc_info()[1]))
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#print('Fit failed: spectrum might not be near scan range center')
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#return None
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return popt, projection
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def get_signal_centre(data, data_range):
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projection = data.mean(axis=1).mean(axis=1)
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signal_centre = data_range[np.argmax(projection)]
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return signal_centre, projection
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32
script/cpython/psss_plot.py
Executable file
32
script/cpython/psss_plot.py
Executable file
@@ -0,0 +1,32 @@
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import numpy as np
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import matplotlib.pyplot as plt
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def gaus(x, a, x0, sigma, offset):
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return offset + a * np.exp(-(x - x0) ** 2 / (2 * sigma ** 2))
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def plot_energy(E_from, E_to, steps, Scan_spec, popt, measured_offset):
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Energy_range = np.linspace(E_from, E_to, steps)
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centre_line_out = Scan_spec[:,:,int(Scan_spec.shape[2]/2)].mean(axis=1)
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Energy_range_fit = np.linspace(Energy_range[0], Energy_range[-1], len(Energy_range)*10)
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plt.figure(figsize=[10,5])
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plt.subplot(121)
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plt.title('PSSS scan of set photon energy')
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plt.pcolormesh(np.arange(0,Scan_spec.shape[2]), Energy_range, Scan_spec.mean(axis=1),cmap='CMRmap')
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plt.vlines(int(Scan_spec.shape[2]/2), Energy_range[0], Energy_range[-1],linestyles='--', colors='orange')
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plt.xlim([0,Scan_spec.shape[2]])
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plt.xlabel('Camera pixel')
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plt.ylabel('Set PSSS energy [eV] \n SARFE10-PSSS059:ENERGY')
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plt.subplot(122)
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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))
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plt.plot(centre_line_out,Energy_range,linewidth = 2, color = 'orange',label ='measured')
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try:
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plt.plot(gaus(Energy_range_fit,*popt),Energy_range_fit,'r:',label='fit')
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except:
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pass
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plt.xticks([])
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plt.legend()
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plt.grid(True)
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36
script/cpython/wrapper.py
Executable file
36
script/cpython/wrapper.py
Executable file
@@ -0,0 +1,36 @@
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from jeputils import *
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RELOAD_CPYTHON = not App.isDetached()
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def fit_energy(e_from, e_to, steps, num_shots, data):
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data = to_array(data, 'd')
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dims = [len(data), len(data[0]), len(data[0][0])]
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data = Convert.flatten(data)
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arr = to_npa(data, dims)
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popt, centre_line_out = call_jep("cpython/psss", "fit_energy", [e_from, e_to, steps, num_shots, arr], reload=RELOAD_CPYTHON)
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return popt.getData(), centre_line_out.getData()
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def fit_crystal_height(xstal_from, xstal_to, steps, data):
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data = to_array(data, 'd')
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dims = [len(data), len(data[0]), len(data[0][0])]
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data = Convert.flatten(data)
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arr = to_npa(data, dims)
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popt, projection = call_jep("cpython/psss", "fit_crystal_height", [xstal_from, xstal_to, steps, arr], reload=RELOAD_CPYTHON)
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return popt.getData(), projection.getData()
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def get_signal_centre(data, data_range):
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data = to_array(data, 'd')
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dims = [len(data), len(data[0]), len(data[0][0])]
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data = Convert.flatten(data)
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arr = to_npa(data, dims)
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data_range = to_npa(to_array(data_range, 'd'))
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signal_centre, projection = call_jep("cpython/psss", "get_signal_centre", [arr, data_range], reload=RELOAD_CPYTHON)
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return signal_centre, projection.getData()
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def plot_energy(e_from, e_to, steps, data, popt, measured_offset):
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data = to_array(data, 'd')
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dims = [len(data), len(data[0]), len(data[0][0])]
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data = Convert.flatten(data)
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arr = to_npa(data, dims)
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ret = call_jep("cpython/psss_plot", "plot_energy", [e_from, e_to, steps, arr, popt, measured_offset], reload=RELOAD_CPYTHON)
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return ret
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177
script/local.py
177
script/local.py
@@ -2,6 +2,183 @@
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# Deployment specific global definitions - executed after startup.py
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###################################################################################################
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from mathutils import estimate_peak_indexes, fit_gaussians, create_fit_point_list
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from mathutils import fit_polynomial,fit_gaussian, fit_harmonic, calculate_peaks, fit_gaussian_offset
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from mathutils import PolynomialFunction, Gaussian, HarmonicOscillator, GaussianOffset
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from plotutils import plot_function, plot_data
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import java.awt.Color as Color
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run("psss/psss")
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###################################################################################################
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# DRY RUN
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###################################################################################################
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def set_dry_run(value):
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global dry_run
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dry_run = value
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def is_dry_run():
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if "dry_run" in globals():
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return True if dry_run else False
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return False
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###################################################################################################
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# Machine utilities
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###################################################################################################
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def is_laser_on():
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return (caget ("SIN-TIMAST-TMA:Beam-Las-Delay-Sel",'d') == 0 )
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def is_timing_ok():
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return caget("SIN-TIMAST-TMA:SOS-COUNT-CHECK") == 0
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def get_repetition_rate():
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return caget("SIN-TIMAST-TMA:Evt-15-Freq-I")
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###################################################################################################
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# Shortcut to maths utilities
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###################################################################################################
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def gfit(ydata, xdata = None):
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"""
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Gaussian fit
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"""
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if xdata is None:
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xdata = frange(0, len(ydata), 1)
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#ydata = to_list(ydata)
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#xdata = to_list(xdata)
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max_y= max(ydata)
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index_max = ydata.index(max_y)
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max_x= xdata[index_max]
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print "Max index:" + str(index_max),
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print " x:" + str(max_x),
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print " y:" + str(max_y)
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gaussians = fit_gaussians(ydata, xdata, [index_max,])
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(norm, mean, sigma) = gaussians[0]
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p = plot([ydata],["data"],[xdata], title="Fit" )[0]
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fitted_gaussian_function = Gaussian(norm, mean, sigma)
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scale_x = [float(min(xdata)), float(max(xdata)) ]
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points = max((len(xdata)+1), 100)
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resolution = (scale_x[1]-scale_x[0]) / points
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fit_y = []
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fit_x = frange(scale_x[0],scale_x[1],resolution, True)
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for x in fit_x:
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fit_y.append(fitted_gaussian_function.value(x))
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p.addSeries(LinePlotSeries("fit"))
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p.getSeries(1).setData(fit_x, fit_y)
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if abs(mean - xdata[index_max]) < ((scale_x[0] + scale_x[1])/2):
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print "Mean -> " + str(mean)
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p.addMarker(mean, None, "Mean="+str(round(norm,2)), Color.MAGENTA.darker())
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return (norm, mean, sigma)
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else:
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p.addMarker(max_x, None, "Max="+str(round(max_x,2)), Color.GRAY)
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print "Invalid gaussian fit: " + str(mean)
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return (None, None, None)
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def hfit(ydata, xdata = None):
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"""
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Harmonic fit
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"""
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if xdata is None:
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xdata = frange(0, len(ydata), 1)
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max_y= max(ydata)
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index_max = ydata.index(max_y)
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max_x= xdata[index_max]
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start,end = min(xdata), max(xdata)
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(amplitude, angular_frequency, phase) = fit_harmonic(ydata, xdata)
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fitted_harmonic_function = HarmonicOscillator(amplitude, angular_frequency, phase)
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print "amplitude = ", amplitude
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print "angular frequency = ", angular_frequency
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print "phase = ", phase
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f = angular_frequency/ (2* math.pi)
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print "frequency = ", f
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resolution = 4.00 # 1.00
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fit_y = []
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for x in frange(start,end,resolution, True):
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fit_y.append(fitted_harmonic_function.value(x))
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fit_x = frange(start, end+resolution, resolution)
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p = plot(ydata,"data", xdata, title="HFit")[0]
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p.addSeries(LinePlotSeries("fit"))
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p.getSeries(1).setData(fit_x, fit_y)
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#m = (phase + math.pi)/ angular_frequency
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m = -phase / angular_frequency
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if (m<start):
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m+=(1.0/f)
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if start <=m <=end:
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print "fit = ", m
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p.addMarker(m, None, "Fit="+str(round(m ,2)), Color.MAGENTA.darker())
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return (amplitude, angular_frequency, phase, True, m, fit_x, fit_y)
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else:
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print "max = ",max_x
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p.addMarker(max_x, None, "Max="+str(round(max_x ,2)), Color.MAGENTA.darker())
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return (amplitude, angular_frequency, phase, False, max_x, fit_x, fit_y)
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def plot_gauss_fit(xdata, ydata, gauss_pars=None, p=None, title = "Data"):
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if gauss_pars is None:
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gauss_pars= fit_gaussian_offset(ydata, xdata, None)
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(offset, amp, mean_value, sigma) = gauss_pars
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print "Gauss plot: ", (offset, amp, mean_value, sigma)
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fitted_gaussian_function = GaussianOffset(offset, amp, mean_value, abs(sigma))
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if p is None:
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p = plot(None, title=title)[0]
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p.clear()
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plot_data(p, ydata, title, xdata=xdata, show_points = True, color=Color.BLUE)
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fit_range = frange(xdata[0],xdata[-1],float(xdata[1]-xdata[0])/100, True)
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plot_function(p, fitted_gaussian_function, "Gauss", fit_range, show_points=False, color=Color.RED)
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p.setLegendVisible(True)
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p.addMarker(mean_value, None, "Mean=" + str(round(mean_value,2)), Color.LIGHT_GRAY)
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return p,(amp, mean_value, sigma)
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###################################################################################################
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# Tools
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###################################################################################################
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def elog(title, message, attachments = [], author = None, category = "Info", domain = "", logbook = "Bernina", encoding=1):
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"""
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Add entry to ELOG.
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"""
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if author is None:
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author = "pshell" #get_context().user.name
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typ = "pshell"
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entry = ""
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cmd = 'G_CS_ELOG_add -l "' + logbook + '" '
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cmd = cmd + '-a "Author=' + author + '" '
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cmd = cmd + '-a "Type=' + typ + '" '
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cmd = cmd + '-a "Entry=' + entry + '" '
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cmd = cmd + '-a "Title=' + title + '" '
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cmd = cmd + '-a "Category=' + category + '" '
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cmd = cmd + '-a "Domain=' + domain + '" '
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for attachment in attachments:
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cmd = cmd + '-f "' + attachment + '" '
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cmd = cmd + '-n ' + str(encoding)
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cmd = cmd + ' "' + message + '"'
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#print cmd
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#os.system (cmd)
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#print os.popen(cmd).read()
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import subprocess
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proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
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(out, err) = proc.communicate()
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if (err is not None) and err!="":
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raise Exception(err)
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print out
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try:
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return int(out[out.find("ID=") +3 : ])
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except:
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print out
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@@ -10,6 +10,11 @@ if get_exec_pars().source == CommandSource.ui:
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STEPS = 10 #20
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NUM_SHOTS= 10 # 100
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PLOT=None
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# get current camera ROIs and then set to max for scan
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roi_min = psss_roi_min.read()
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roi_max = psss_roi_max.read()
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psss_roi_min.write(1)
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psss_roi_max.write(2000)
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p = plot(None, title="Data")[0] if (PLOT is None) else PLOT
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p.clear()
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@@ -21,10 +26,10 @@ run("cpython/wrapper")
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#Setup and functions setup¶
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if not is_dry_run():
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xstal_height=Channel("SARFE10-PSSS059:MOTOR_Y3.VAL", name="xstal_height")
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else:
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xstal_height=DummyRegister("xstal_height")
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#if not is_dry_run(): # C.arrell commented out 20.01.21
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xstal_height=Channel("SARFE10-PSSS059:MOTOR_Y3.VAL", name="xstal_height")
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#else:
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# xstal_height=DummyRegister("xstal_height")
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av = create_averager(psss_spectrum_y, NUM_SHOTS, interval=-1, name="spectrum_average")
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av_samples = av.samples
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@@ -54,25 +59,12 @@ if not (RANGE_FROM < mean_val < RANGE_TO or RANGE_TO < mean_val < RANGE_FROM):
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xstal_height.write(mean_val)
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xstal_height.close()
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# return ROI to inital value
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psss_roi_min.write(roi_min)
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psss_roi_max.write(roi_max)
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#Plots
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"""
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plt.figure(figsize=[10,5])
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plt.subplot(121)
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plt.title('PSSS scan of crystal height')
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plt.pcolormesh(energy_axis, xstal_range, Scan_spec.mean(axis=1),cmap='CMRmap')
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plt.xlim([energy_axis[0],energy_axis[-1]])
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plt.ylim([xstal_range[0], xstal_range[-1]])
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plt.xlabel('PSSS energy axis')
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plt.ylabel('Set crystal position [mm] \n'+PSSS_xstal_height_name[0:-4])
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plt.subplot(122)
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plt.plot(projection,xstal_range,linewidth = 2, color = 'orange',label ='projected signal')
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plt.plot(gaus(xstal_range_fit,*popt),xstal_range_fit,'r:',label='fit')
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plt.ylim([xstal_range[0], xstal_range[-1]])
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plt.title('Signal max at %.3f [mm] (from fit)'%popt[1])
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plt.xticks([])
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plt.legend()
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plt.grid(True)
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"""
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p.clear()
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p.setTitle("")
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plot_gauss_fit(xstal_range, projection, gauss_pars=(offset, amp, mean_val, sigma), p=p, title = "Data")
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@@ -26,15 +26,19 @@ if RANGE_OFF is not None:
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run("cpython/wrapper")
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# get current camera ROIs and then set to max for scan
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roi_min = psss_roi_min.read()
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roi_max = psss_roi_max.read()
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psss_roi_min.write(1)
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psss_roi_max.write(2000)
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#Scan and take data
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class PSSS_energy(Writable):
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def write(self, value):
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if not is_dry_run():
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psss_energy.write(value)
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exec_cpython("/ioc/modules/qt/PSSS_motion.py", args = ["-m1", "SARFE10-PSSS059"])
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#if not is_dry_run():
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psss_energy.write(value)
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exec_cpython("/ioc/modules/qt/PSSS_motion.py", args = ["-m1", "SARFE10-PSSS059"])
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# python / ioc / modules / qt / PSSS_motion.py - m1 SARFE10 - PSSS059
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time.sleep(1)
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print(value)
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@@ -53,10 +57,14 @@ def after_read(record, scan):
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r = lscan(en, (av, av_samples), RANGE_FROM, RANGE_TO, STEPS, latency=0.0, after_read = after_read, save=False )
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average, samples, energy_range = r.getReadable(0), r.getReadable(1), r.getPositions(0)
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||||
# return ROI to inital value
|
||||
psss_roi_min.write(roi_min)
|
||||
psss_roi_max.write(roi_max)
|
||||
|
||||
[amp, mean_val, sigma, offset],centre_line_out = fit_energy(RANGE_FROM, RANGE_TO, STEPS+1, NUM_SHOTS, samples)
|
||||
[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))
|
||||
|
||||
|
||||
@@ -67,26 +75,6 @@ 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")
|
||||
|
||||
Reference in New Issue
Block a user