Changes by Chris and project fixes

script/cpython/psss.py

@@ -0,0 +1,45 @@
+import numpy as np
+from scipy.optimize import curve_fit
+import sys
+
+
+def gaus(x, a, x0, sigma, offset):
+    return offset + a * np.exp(-(x - x0) ** 2 / (2 * sigma ** 2))
+
+#Return [amp, mean_val, sigma, offset]
+def fit_energy(e_from, e_to, steps, num_shots, data):
+    energy_range = np.linspace(e_from, e_to, steps)
+    energy_range_fit = np.linspace(energy_range[0], energy_range[-1], len(energy_range)*10)
+    centre_line_out = data[:,:,int(data.shape[2]/2)].mean(axis=1)
+    try:
+        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])
+    except:
+        raise Exception('Fit failed: spectrum might not be near scan range center \n' + str(sys.exc_info()[1]))
+        #print('Fit failed: spectrum might not be near scan range center')
+        #return None
+    max_ind = np.argmax(centre_line_out)
+    max_photon_energy=energy_range[max_ind]
+    print(max_photon_energy)
+    return popt, centre_line_out
+
+
+#Return [amp, mean_val, sigma, offset]
+def fit_crystal_height(xstal_from, xstal_to, steps, data):
+    xstal_range = np.linspace(xstal_from, xstal_to, steps)
+    projection = data.mean(axis=1).mean(axis=1)
+    offset = np.mean(projection[0:100])
+    signal_centre = xstal_range[np.argmax(projection)]
+    xstal_range_fit = np.linspace(xstal_range[0], xstal_range[-1], len(xstal_range)*10)
+    try:
+        popt,pcov = curve_fit(gaus,xstal_range,projection,p0=[100,signal_centre,-0.2,offset])
+    except:
+        raise Exception('Fit failed: spectrum might not be near scan range center \n' + str(sys.exc_info()[1]))
+        #print('Fit failed: spectrum might not be near scan range center')
+        #return None
+    return popt, projection
+
+
+def get_signal_centre(data, data_range):
+    projection = data.mean(axis=1).mean(axis=1)
+    signal_centre = data_range[np.argmax(projection)]
+    return signal_centre, projection

script/cpython/psss_plot.py

@@ -0,0 +1,32 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+def gaus(x, a, x0, sigma, offset):
+    return offset + a * np.exp(-(x - x0) ** 2 / (2 * sigma ** 2))
+    
+def plot_energy(E_from, E_to, steps, Scan_spec, popt, measured_offset):
+    Energy_range = np.linspace(E_from, E_to, steps)
+    centre_line_out = Scan_spec[:,:,int(Scan_spec.shape[2]/2)].mean(axis=1)
+    Energy_range_fit = np.linspace(Energy_range[0], Energy_range[-1], len(Energy_range)*10)
+
+    
+    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')
+    try:
+        plt.plot(gaus(Energy_range_fit,*popt),Energy_range_fit,'r:',label='fit')
+    except:
+        pass
+    plt.xticks([])
+    plt.legend()
+    plt.grid(True)  

script/cpython/wrapper.py

@@ -0,0 +1,36 @@
+from jeputils import *
+
+RELOAD_CPYTHON = not App.isDetached()
+
+def fit_energy(e_from, e_to, steps, num_shots, data):
+    data = to_array(data, 'd')    
+    dims = [len(data), len(data[0]), len(data[0][0])]
+    data = Convert.flatten(data)
+    arr = to_npa(data, dims)
+    popt, centre_line_out =  call_jep("cpython/psss", "fit_energy", [e_from, e_to, steps, num_shots, arr], reload=RELOAD_CPYTHON)
+    return popt.getData(), centre_line_out.getData()
+
+def fit_crystal_height(xstal_from, xstal_to, steps, data):
+    data = to_array(data, 'd')    
+    dims = [len(data), len(data[0]), len(data[0][0])]
+    data = Convert.flatten(data)
+    arr = to_npa(data, dims)
+    popt, projection =  call_jep("cpython/psss", "fit_crystal_height", [xstal_from, xstal_to, steps, arr], reload=RELOAD_CPYTHON)
+    return popt.getData(), projection.getData()
+
+def get_signal_centre(data, data_range):
+    data = to_array(data, 'd')    
+    dims = [len(data), len(data[0]), len(data[0][0])]
+    data = Convert.flatten(data)   
+    arr = to_npa(data, dims)
+    data_range = to_npa(to_array(data_range, 'd'))
+    signal_centre, projection =  call_jep("cpython/psss", "get_signal_centre", [arr, data_range], reload=RELOAD_CPYTHON)
+    return signal_centre, projection.getData()
+
+def plot_energy(e_from, e_to, steps, data, popt, measured_offset):
+    data = to_array(data, 'd')    
+    dims = [len(data), len(data[0]), len(data[0][0])]
+    data = Convert.flatten(data)
+    arr = to_npa(data, dims)
+    ret =  call_jep("cpython/psss_plot", "plot_energy", [e_from, e_to, steps, arr, popt, measured_offset], reload=RELOAD_CPYTHON)
+    return ret