201 lines
6.6 KiB
Python
Executable File
201 lines
6.6 KiB
Python
Executable File
###################################################################################################
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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, Gaussian
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from mathutils import fit_polynomial,fit_gaussian, fit_harmonic, calculate_peaks
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from mathutils import PolynomialFunction, Gaussian, HarmonicOscillator
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import math
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import random
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import java.awt.Color as Color
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def fit(ydata, xdata = None):
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"""
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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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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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p = plot([ydata],["data"],[xdata], title="Fit" )[0]
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if gaussians[0] is None:
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p.addMarker(max_x, None, "Max="+str(round(max_x,2)), Color.GRAY)
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print "Fitting error"
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return (None, None, None)
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(norm, mean, sigma) = gaussians[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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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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resolution = 0.01
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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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fit_max = -phase / angular_frequency
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if (fit_max<start):
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fit_max+=(1.0/f)
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print "fit max= ", fit_max
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p.addMarker(fit_max, None, "Fit max="+str(round(fit_max ,2)), Color.MAGENTA.darker())
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return (amplitude, angular_frequency, phase, fit_max)
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def elogllrf(subject, message, system, subsystem, section, attachments = []):
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"""
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Add entry to ELOG of LLRF: https://elog-gfa.psi.ch/LLRF/
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Example: elogllrf("Hallo Test", "Das ist meine Nachricht...","LLRF", "General", "SINEG01")
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"""
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import getpass
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author = "pshell/" + getpass.getuser()
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cmd = 'G_CS_ELOG_add -l "LLRF" '
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cmd = cmd + '-a "Author=' + author + '" '
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cmd = cmd + '-a "Subject=' + subject + '" '
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cmd = cmd + '-a "Section=' + section + '" '
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cmd = cmd + '-a "System=' + system + '" '
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cmd = cmd + '-a "Subsystem=' + subsystem + '" '
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cmd = cmd + '-a "Machine=SwissFEL" '
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cmd = cmd + '-a "Domain=All"'
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for attachment in attachments:
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cmd = cmd + ' -f "' + attachment + '" '
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#print attachment
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cmd = cmd + ' -x -n 1'
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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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def get_plot_snapshots(title = None, file_type = "jpg", temp_path = controller.setup.getContextPath()):
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"""
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Returns list with file names of plots snapshots from a plotting context.
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"""
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sleep(0.02) #Give some time to plot to be finished - it is not sync with acquisition
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ret = []
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for p in get_plots(title):
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file_name = os.path.abspath(temp_path + "/" + p.getTitle() + "." + file_type)
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p.saveSnapshot(file_name , file_type)
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ret.append(file_name)
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return ret
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class Sinusoid(ReadonlyRegisterBase):
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def doRead(self):
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if not hasattr(self, 'step') : self.step = 10
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self.x = self.x + self.step if hasattr(self, 'x') else 0.0
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noise = (random.random() - 0.5) * 0.2
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return math.sin(self.x * math.pi / 180.0) + noise
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add_device(Sinusoid("sim"), True)
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#------------- CAS --------------------
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import ch.psi.pshell.epics.CAS as CAS
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#CAS.setServerPort(5070)
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class ArrayDevice(ReadonlyRegisterBase, ReadonlyRegisterArray):
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def doRead(self):
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return self.take()
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def getSize(self):
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global scan_result
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return len(self.take())
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def append(self, value):
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c = self.take()
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c.append(value)
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self.set(c)
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def set(self, value):
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self.onReadout(to_array(value, 'd'))
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class ScalarDevice(RegisterBase):
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def doRead(self):
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return self.val if hasattr(self, 'val') else 0.0
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def doWrite(self, val):
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self.val = val
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add_device(ArrayDevice("scan_pos"), True)
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add_device(ArrayDevice("scan_val"), True)
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add_device(ScalarDevice("scan_start"), True)
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add_device(ScalarDevice("scan_stop"), True)
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add_device(ScalarDevice("scan_step"), True)
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scan_start.write(-10.0)
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scan_stop.write(10.0)
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scan_step.write(1.0)
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if not controller.localMode:
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CAS.setServerPort(12345)
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cas1=CAS("PSHELL:scanpos",scan_pos, "double")
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cas2=CAS("PSHELL:scanval",scan_val, "double")
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cas3=CAS("PSHELL:scanstart",scan_start, "double")
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cas4=CAS("PSHELL:scanstop",scan_stop, "double")
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cas5=CAS("PSHELL:scanstep",scan_step, "double")
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#scan_pos.set([] )
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#scan_val.set([])
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#TODO: this is workaround to CAS not supporting dynamic arrays
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MAX_ARRAY_DEV_SIZE = 5000
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scan_pos.set([0.0,] * MAX_ARRAY_DEV_SIZE )
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scan_val.set([0.0,] * MAX_ARRAY_DEV_SIZE )
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