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helical_scan.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
helical scan
'''
import os
import time
import pickle
import traceback
from omega_scan import omega_scan
class helical_scan(omega_scan):
actuator_names = ['Omega', 'AlignmentX', 'AlignmentY', 'AlignmentZ', 'CentringX', 'CentringY']
specific_parameter_fields = [{'name': 'position_start', 'type': 'dict', 'description': 'dictionary with motor names as keys and their positions in mm as values'},
{'name': 'position_end', 'type': 'dict', 'description': 'dictionary with motor names as keys and their positions in mm as values'}]
def __init__(self,
name_pattern='test_$id',
directory='/tmp',
scan_range=180,
scan_exposure_time=18,
scan_start_angle=0,
angle_per_frame=0.1,
image_nr_start=1,
position_start=None,
position_end=None,
kappa=None,
phi=None,
photon_energy=None,
resolution=None,
detector_distance=None,
detector_vertical=None,
detector_horizontal=None,
transmission=None,
flux=None,
snapshot=False,
ntrigger=1,
nimages_per_file=400,
zoom=None,
diagnostic=None,
analysis=None,
simulation=None,
parent=None,
beware_of_top_up=True,
beware_of_download=False,
generate_cbf=True,
generate_h5=True):
if hasattr(self, 'parameter_fields'):
self.parameter_fields += helical_scan.specific_parameter_fields
else:
self.parameter_fields = helical_scan.specific_parameter_fields[:]
omega_scan.__init__(self,
name_pattern=name_pattern,
directory=directory,
scan_range=scan_range,
scan_exposure_time=scan_exposure_time,
scan_start_angle=scan_start_angle,
angle_per_frame=angle_per_frame,
image_nr_start=image_nr_start,
kappa=kappa,
phi=phi,
photon_energy=photon_energy,
resolution=resolution,
detector_distance=detector_distance,
detector_vertical=detector_vertical,
detector_horizontal=detector_horizontal,
transmission=transmission,
flux=flux,
snapshot=snapshot,
ntrigger=ntrigger,
nimages_per_file=nimages_per_file,
zoom=zoom,
diagnostic=diagnostic,
analysis=analysis,
simulation=simulation,
parent=parent,
beware_of_top_up=beware_of_top_up,
beware_of_download=beware_of_download,
generate_cbf=generate_cbf,
generate_h5=generate_h5)
self.description = 'Helical scan, Proxima 2A, SOLEIL, %s' % time.ctime(self.timestamp)
self.position_start = self.goniometer.check_position(position_start)
self.position_end = self.goniometer.check_position(position_end)
self.total_expected_exposure_time = self.scan_exposure_time
self.total_expected_wedges = 1
def run(self, wait=True):
self._start = time.time()
if self.beware_of_top_up and self.scan_exposure_time <= self.machine_status.get_top_up_period():
self.check_top_up()
task_id = self.goniometer.helical_scan(self.position_start, self.position_end, self.scan_start_angle, self.scan_range, self.scan_exposure_time, wait=wait)
self.md2_task_info = self.goniometer.get_task_info(task_id)
def main():
import optparse
position_start = "{'AlignmentX': -0.10198379516601541, 'AlignmentY': -1.5075817417454083, 'AlignmentZ': -0.14728600084459487, 'CentringX': -0.73496162280701749, 'CentringY': 0.37533442982456139}"
position_end = "{'AlignmentX': -0.10198379516601541, 'AlignmentY': -1.0274660058923679, 'AlignmentZ': -0.14604777073215836, 'CentringX': -0.41848684210526316, 'CentringY': -0.083777412280701749}"
parser = optparse.OptionParser()
parser.add_option('-n', '--name_pattern', default='helical_test_$id', type=str, help='Prefix default=%default')
parser.add_option('-d', '--directory', default='/nfs/data/default', type=str, help='Destination directory default=%default')
parser.add_option('-r', '--scan_range', default=180, type=float, help='Scan range [deg]')
parser.add_option('-e', '--scan_exposure_time', default=18, 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('-B', '--position_start', default=position_start, type=str, help='Gonio alignment start position [dict]')
parser.add_option('-E', '--position_end', default=position_end, type=str, help='Gonio alignment end 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('-m', '--transmission', default=None, type=float, help='Transmission. Number in range between 0 and 1.')
parser.add_option('-A', '--analysis', action='store_true', help='If set will perform automatic analysis.')
parser.add_option('-D', '--diagnostic', action='store_true', help='If set will record diagnostic information.')
parser.add_option('-S', '--simulation', action='store_true', help='If set will record diagnostic information.')
options, args = parser.parse_args()
print('options', options)
print('args', args)
hs = helical_scan(**vars(options))
filename = os.path.join(options.directory, options.name_pattern) + '_parameters.pickle'
if not os.path.isfile(filename):
hs.execute()
elif options.analysis == True:
hs.analyze()
def test():
position_start = "{'AlignmentX': -0.10198379516601541, 'AlignmentY': -1.5075817417454083, 'AlignmentZ': -0.14728600084459487, 'CentringX': -0.73496162280701749, 'CentringY': 0.37533442982456139}"
position_end = "{'AlignmentX': -0.10198379516601541, 'AlignmentY': -1.0274660058923679, 'AlignmentZ': -0.14604777073215836, 'CentringX': -0.41848684210526316, 'CentringY': -0.083777412280701749}"
hs = helical_scan(position_start=eval(position_start), position_end=eval(position_end))
if __name__ == '__main__':
main()