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fluorescence_spectrum.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import time
import gevent
import numpy as np
import os
import pickle
from xray_experiment import xray_experiment
from fluorescence_detector import fluorescence_detector
from goniometer import goniometer
from fast_shutter import fast_shutter
from safety_shutter import safety_shutter
from transmission import transmission as transmission_motor
class fluorescence_spectrum(xray_experiment):
specific_parameter_fields = [{'name': 'position', 'type': '', 'description': ''},
{'name': 'integration_time', 'type': '', 'description': ''},
{'name': 'nchannels', 'type': '', 'description': ''},
{'name': 'calibration', 'type': '', 'description': ''},
{'name': 'energies', 'type': '', 'description': ''},
{'name': 'spectrum', 'type': '', 'description': ''},
{'name': 'dead_time', 'type': '', 'description': ''},
{'name': 'real_count_time', 'type': '', 'description': ''},
{'name': 'input_count_rate', 'type': '', 'description': ''},
{'name': 'output_count_rate', 'type': '', 'description': ''},
{'name': 'calculated_dead_time', 'type': '', 'description': ''},
{'name': 'events_in_run', 'type': '', 'description': ''}]
def __init__(self,
name_pattern,
directory,
integration_time=5,
transmission=1.,
insertion_timeout=2,
position=None,
photon_energy=None,
flux=None,
snapshot=False,
zoom=None,
diagnostic=None,
analysis=None,
simulation=None,
display=False,
parent=None):
if hasattr(self, 'parameter_fields'):
self.parameter_fields += fluorescence_spectrum.specific_parameter_fields
else:
self.parameter_fields = fluorescence_spectrum.specific_parameter_fields[:]
xray_experiment.__init__(self,
name_pattern,
directory,
position=position,
photon_energy=photon_energy,
transmission=transmission,
flux=flux,
snapshot=snapshot,
zoom=zoom,
diagnostic=diagnostic,
analysis=analysis,
simulation=simulation)
self.description = 'XRF spectrum, Proxima 2A, SOLEIL, %s' % time.ctime(self.timestamp)
self.detector = fluorescence_detector()
self.integration_time = integration_time
self.transmission = transmission
self.insertion_timeout = insertion_timeout
self.display = display
self.parent = parent
self.total_expected_exposure_time = self.integration_time
self.total_expected_wedges = 1
self.spectrum = None
self.energies = None
def get_calibration(self):
return self.detector.get_calibration()
def get_nchannels(self):
return len(self.get_channels())
def get_dead_time(self):
return self.detector.get_dead_time()
def get_real_count_time(self):
return self.detector.get_real_time()
def get_input_count_rate(self):
return self.detector.get_input_count_rate()
def get_output_count_rate(self):
return self.detector.get_output_count_rate()
def get_calculated_dead_time(self):
return self.detector.get_calculated_dead_time()
def get_events_in_run(self):
return self.detector.get_events_in_run()
def prepare(self):
_start = time.time()
print('prepare')
self.protective_cover.insert()
self.check_directory(self.directory)
if self.snapshot == True:
print('taking image')
self.camera.set_exposure(0.05)
self.camera.set_zoom(self.zoom)
self.goniometer.insert_backlight()
self.goniometer.extract_frontlight()
self.goniometer.set_position(self.reference_position)
self.goniometer.wait()
self.image = self.get_image()
self.rgbimage = self.get_rgbimage()
self.goniometer.set_data_collection_phase(wait=True)
self.detector.insert()
self.set_photon_energy(self.photon_energy, wait=True)
self.set_transmission(self.transmission)
self.detector.set_integration_time(self.integration_time)
if self.safety_shutter.closed():
self.safety_shutter.open()
if self.position != None:
self.goniometer.set_position(self.position)
else:
self.position = self.goniometer.get_position()
self.write_destination_namepattern(self.directory, self.name_pattern)
self.energy_motor.turn_off()
self.goniometer.wait()
while time.time() - _start < self.insertion_timeout:
time.sleep(self.detector.sleeptime)
def run(self):
#gevent.sleep(0.1)
self.fast_shutter.open()
self.spectrum = self.detector.get_point()
self.fast_shutter.close()
def clean(self):
print('clean')
_start = time.time()
self.detector.extract()
self.end_time = time.time()
self.save_spectrum()
self.collect_parameters()
self.save_parameters()
self.save_log()
self.save_plot()
if self.diagnostic == True:
self.save_diagnostics()
print('clean finished in %.4f seconds' % (time.time() - _start))
def stop(self):
self.fast_shutter.close()
self.detector.stop()
def abort(self):
self.fast_shutter.md2.abort()
self.stop()
def analyze(self):
self.save_plot()
def get_channels(self):
channels = np.arange(0, 2048)
return channels
def get_energies(self):
'''return energies in eV'''
a, b, c = self.detector.get_calibration()
channels = self.get_channels()
energies = a + b*channels + c*channels**2
return energies
def save_spectrum(self):
filename = os.path.join(self.directory, '%s.dat' % self.name_pattern)
self.energies = self.get_energies()
self.channels = self.get_channels()
X = np.array(list(zip(self.channels, self.spectrum, self.energies)))
self.header ='#F %s\n#D %s\n#N %d\n#L channel counts energy\n' % (filename, time.ctime(self.timestamp), X.shape[1])
try:
np.savetxt(filename, X, header=self.header)
except:
f = open(filename, 'a')
f.write(self.header)
np.savetxt(f, X)
f.close()
def save_plot(self):
return
import pylab
pylab.figure(figsize=(16, 9))
pylab.title(self.description, fontsize=22)
pylab.xlabel('energy [eV]', fontsize=18)
pylab.ylabel('intensity [a.u.]', fontsize=18)
pylab.plot(self.get_energies(), self.spectrum)
pylab.xlim([0, 20480])
pylab.savefig(r'%s' % os.path.join(self.directory, '%s_full.png' % self.name_pattern))
if self.display:
pylab.show()
def main():
import optparse
parser = optparse.OptionParser()
parser.add_option('-d', '--directory', default='/tmp', type=str, help='directory (default=%default)')
parser.add_option('-n', '--name_pattern', default='xrf', type=str, help='name_pattern (default=%default)')
parser.add_option('-i', '--integration_time', default=5, type=float, help='integration_time (default=%default s)')
parser.add_option('-t', '--transmission', default=1., type=float, help='transmission (default=%default %)')
parser.add_option('-p', '--photon_energy', default=15000, type=float, help='transmission (default=%default eV)')
parser.add_option('-D', '--display', action='store_true', help='Display the plot')
options, args = parser.parse_args()
fs = fluorescence_spectrum(options.name_pattern,
options.directory,
integration_time=options.integration_time,
photon_energy=options.photon_energy,
transmission=options.transmission,
display=options.display)
filename = '%s_parameters.pickle' % fs.get_template()
if not os.path.isfile(filename):
fs.execute()
elif options.analysis == True:
fs.save_spectrum()
fs.save_plot()
if __name__ == '__main__':
main()