forked from MartinSavko/experimental_methods
/
beamcenter_calibration.py
executable file
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/
beamcenter_calibration.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
single position oscillation scan
'''
import gevent
from gevent.monkey import patch_all
patch_all()
import traceback
import logging
import time
import itertools
import os
import pickle
from experiment import experiment
from diffraction_experiment import diffraction_experiment
from detector import detector
from goniometer import goniometer
from energy import energy as energy_motor
from transmission import transmission as transmission_motor
from omega_scan import omega_scan
class beamcenter_calibration(diffraction_experiment):
specific_parameter_fields = set(['photon_energies',
'tss',
'txs',
'tzs',
'nscans',
'handle_detector_beamstop',
'direct_beam'])
def __init__(self,
directory,
name_pattern = 'pe_%.3feV_ts_%.3fmm_tx_%.3fmm_tz_%.3fmm_$id',
photon_energies=None,
tss=None,
txs=None,
tzs=None,
scan_range=0.1,
scan_exposure_time=0.025,
angle_per_frame=0.1,
direct_beam=True,
analysis=None,
handle_detector_beamstop=False):
experiment.__init__(self,
name_pattern=name_pattern,
directory=directory,
analysis=analysis)
self.directory = directory
self.name_pattern = name_pattern
self.photon_energies = photon_energies
self.tss = tss
self.txs = txs
self.tzs = tzs
self.scan_range = scan_range
self.scan_exposure_time = scan_exposure_time
self.angle_per_frame = angle_per_frame
self.direct_beam = direct_beam
self.nimages = int(self.scan_range/self.angle_per_frame)
#actuators
self.detector = detector()
self.goniometer = goniometer()
self.energy_motor = energy_motor()
self.transmission_motor = transmission_motor()
self.capillary_park_position = 80
self.aperture_park_position = 80
self.detector_beamstop_park_position = 18.5
self.handle_detector_beamstop = handle_detector_beamstop
self.parameter_fields = self.parameter_fields.union(beamcenter_calibration.specific_parameter_fields)
print 'self.parameter_fields', self.parameter_fields
def get_scan_range(self):
return self.scan_range
def get_scan_exposure_time(self):
return self.scan_exposure_time
def get_angle_per_frame(self):
return self.angle_per_frame
def get_nimages(self):
return self.nimages
def get_direct_beam(self):
return self.direct_beam
def get_handle_detector_beamstop(self):
return self.handle_detector_beamstop
def get_photon_energies(self):
return self.photon_energies
def get_tss(self):
return self.tss
def get_txs(self):
return self.txs
def get_tzs(self):
return self.tzs
def get_nscans(self):
return self.nscans
def prepare(self):
self.detector.check_dir(self.directory)
self.goniometer.set_data_collection_phase(wait=True)
if self.handle_detector_beamstop:
self.detector_beamstop_initial_position = self.detector.beamstop.get_z()
self.detector_initial_ts = self.detector.position.ts.get_position()
self.detector_initial_tz = self.detector.position.tz.get_position()
self.detector_initial_tx = self.detector.position.tx.get_position()
self.capillary_initial_position = self.goniometer.md2.capillaryverticalposition
self.aperture_initial_position = self.goniometer.md2.apertureverticalposition
self.initial_position = self.goniometer.get_position()
if self.handle_detector_beamstop:
print 'detector_beamstop_initial_position', self.detector_beamstop_initial_position
print 'self.detector_initial_ts', self.detector_initial_ts
print 'self.detector_initial_tx', self.detector_initial_tx
print 'self.detector_initial_tz', self.detector_initial_tz
print 'self.capillary_initial_position', self.capillary_initial_position
print 'self.aperture_initial_position', self.aperture_initial_position
print 'self.initial_position', self.initial_position
if self.direct_beam == True:
self.goniometer.md2.capillaryverticalposition = self.capillary_park_position
self.goniometer.wait()
self.goniometer.md2.apertureverticalposition = self.aperture_park_position
self.goniometer.wait()
if self.handle_detector_beamstop:
self.detector.beamstop.set_z(self.detector_beamstop_park_position)
self.goniometer.md2.saveaperturebeamposition()
self.goniometer.md2.savecapillarybeamposition()
if self.photon_energies == None:
self.photon_energies = [self.energy_motor.get_energy()]
if self.tss == None:
self.tss = [self.detector.position.ts.get_position()]
if self.txs == None:
self.txs = [self.detector.position.tx.get_position()]
if self.tzs == None:
self.tzs = [self.detector.position.tz.get_position()]
print 'photon_energies', self.photon_energies
print 'tss', self.tss
print 'txs', self.txs
print 'tzs', self.tzs
def get_transmission(self, photon_energy, default_transmision=0.002):
if photon_energy > 1e3:
photon_energy *= 1e-3
if photon_energy > 7 and photon_energy <= 10:
transmission = 0.003
elif photon_energy > 14 and photon_energy<=16.5:
transmission = 0.008
elif photon_energy > 16.5:
transmission = 0.015
else:
transmission = default_transmision
return transmission * 0.06
def clean(self):
try:
self.collect_parameters()
except:
print traceback.print_exc()
self.save_parameters()
self.save_log()
self.detector.disarm()
if self.direct_beam == True:
self.goniometer.wait()
self.goniometer.md2.capillaryverticalposition = self.capillary_initial_position
time.sleep(0.2)
self.goniometer.wait()
self.goniometer.md2.apertureverticalposition = self.aperture_initial_position
time.sleep(0.2)
self.goniometer.wait()
self.goniometer.md2.saveaperturebeamposition()
self.goniometer.md2.savecapillarybeamposition()
if self.handle_detector_beamstop:
self.detector.beamstop.set_z(self.detector_beamstop_initial_position)
self.transmission_motor.set_transmission(10)
self.energy_motor.set_energy(12.65)
self.detector.position.ts.set_position(350)
self.detector.position.tx.set_position(self.detector_initial_tx)
self.detector.position.tz.set_position(self.detector_initial_tz)
def efficient_order(self, sequence, current_value):
if abs(current_value - sequence[0]) > abs(current_value - sequence[-1]):
return sequence[::-1]
else:
return sequence[:]
def run(self):
self._start = time.time()
self.nscans = 0
#for pe, ts, tx ,tz in itertools.product(self.photon_energies, self.tss, self.txs, self.tzs):
for pe in self.efficient_order(self.photon_energies, self.energy_motor.get_energy()):
for ts in self.efficient_order(self.tss, self.detector.position.ts.get_position()):
for tx in self.efficient_order(self.txs, self.detector.position.tx.get_position()):
for tz in self.efficient_order(self.tzs, self.detector.position.tz.get_position()):
if pe<30:
pe *= 1e3
name_pattern = self.name_pattern % (pe, ts, tx, tz)
print 'name_pattern', name_pattern
print 'photon_energy', pe
if self.direct_beam == True:
transmission = self.get_transmission(pe)
else:
transmission = None
if self.nscans % 10 == 0 and self.nscans != 0 and self.direct_beam != True:
self.initial_position['AlignmentY'] += 0.015
s = omega_scan(name_pattern,
self.directory,
scan_range=self.scan_range,
scan_exposure_time=self.scan_exposure_time,
angle_per_frame=self.angle_per_frame,
position = self.initial_position,
photon_energy=pe,
detector_distance=ts,
detector_vertical=tz,
detector_horizontal=tx,
transmission=transmission,
nimages_per_file=1)
print 's.parameter_fields', s.parameter_fields
s.execute()
self.nscans += 1
def analyze(self):
pass
#def save_parameters(self):
#self.parameters = {}
#self.parameters['timestamp'] = self.timestamp
#self.parameters['name_pattern'] = self.name_pattern
#self.parameters['directory'] = self.directory
#self.parameters['photon_energies'] = self.photon_energies
#self.parameters['tss'] = self.tss
#self.parameters['txs'] = self.txs
#self.parameters['tzs'] = self.tzs
#self.parameters['scan_range'] = self.scan_range
#self.parameters['scan_exposure_time'] = self.scan_exposure_time
#self.parameters['angle_per_frame'] = self.angle_per_frame
#self.parameters['nimages'] = self.nimages
#self.parameters['nscans'] = self.nscans
#self.parameters['duration'] = self.end_time - self.start_time
#self.parameters['start_time'] = self.start_time
#self.parameters['end_time'] = self.end_time
#f = open(os.path.join(self.directory, '%s_parameters.pickle' % 'beamcenter_calibration'), 'w')
#pickle.dump(self.parameters, f)
#f.close()
#def save_log(self):
#'''method to save the experiment details in the log file'''
#f = open(os.path.join(self.directory, '%s.log' % self.name_pattern), 'w')
#keyvalues = self.parameters.items()
#keyvalues.sort()
#for key, value in keyvalues:
#f.write('%s: %s\n' % (key, value))
#f.close()
def main():
import optparse
parser = optparse.OptionParser()
parser.add_option('-n', '--name_pattern', default='pe_%.3feV_ts_%.3fmm_tx_%.3fmm_tz_%.3fmm_$id', type=str, help='Prefix default=%default')
parser.add_option('-d', '--directory', default='/nfs/ruche/proxima2a-spool/2017_Run5/%s/Commissioning/beamcenter_calibration/direct_beam_b' % time.strftime('%Y-%m-%d'), type=str, help='Destination directory default=%default')
parser.add_option('-r', '--scan_range', default=0.1, type=float, help='Scan range [deg]')
parser.add_option('-e', '--scan_exposure_time', default=0.1, type=float, help='Scan exposure time [s]')
#parser.add_option('-s', '--scan_start_angle', default=0, type=float, help='Scan start angle [deg]')
parser.add_option('-a', '--angle_per_frame', default=0.1, type=float, help='Angle per frame [deg]')
#parser.add_option('-f', '--image_nr_start', default=1, type=int, help='Start image number [int]')
#parser.add_option('-i', '--position', default=None, type=str, help='Gonio alignment position [dict]')
#parser.add_option('-p', '--photon_energy', default=None, type=float, help='Photon energy ')
#parser.add_option('-t', '--detector_distance', default=None, type=float, help='Detector distance')
#parser.add_option('-o', '--resolution', default=None, type=float, help='Resolution [Angstroem]')
#parser.add_option('-x', '--flux', default=None, type=float, help='Flux [ph/s]')
parser.add_option('-D', '--direct_beam', action='store_true', help='Do apply transmission correction -- for direct beam measurements.')
options, args = parser.parse_args()
print 'options', options
#s = scan(**vars(options))
#s.execute()
import numpy as np
distances = list(np.arange(105, 1052., 50))
#distances = [125, 150, 200]
#distances = [98, 500, 1000]
#energies = [12.65] #[7., 8, 9, 10, 10836., 11, 12, 14, 16] #list(np.arange(6500, 18501, 1000))
#energies = np.linspace(6700, 17600, 7.)
energies = [12650]
txs = [20.50]
tzs = [44.50]
#distances = [175, 450, 875]i
#energies = [12650.]
#txs = [19., 20., 21.30, 22., 23., 24.]
#tzs = [10., 15., 19.13, 25., 30., 35., 40., 50.]
bcc = beamcenter_calibration(options.directory,
photon_energies=energies,
tss=distances,
txs=txs,
tzs=tzs,
scan_range=options.scan_range,
scan_exposure_time=options.scan_exposure_time,
angle_per_frame=options.angle_per_frame,
#scan_start_angle=options.scan_start_angle,
direct_beam=options.direct_beam)
bcc.execute()
if __name__ == '__main__':
main()