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diffraction_experiment.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import time
import pickle
import logging
import traceback
import h5py
import gevent
import datetime
import re
import glob
import json
import numpy as np
import subprocess
from xray_experiment import xray_experiment
class diffraction_experiment(xray_experiment):
specific_parameter_fields = [{'name': 'kappa', 'type': 'float', 'description': 'kappa position in degrees'},
{'name': 'phi', 'type': 'float', 'description': 'phi position in degrees'},
{'name': 'resolution', 'type': 'float', 'description': ''},
{'name': 'detector_distance', 'type': 'float', 'description': ''},
{'name': 'detector_vertical_position', 'type': 'float', 'description': ''},
{'name': 'detector_horizontal_position', 'type': 'float', 'description': ''},
{'name': 'detector_ts_intention', 'type': 'float', 'description': ''},
{'name': 'detector_tz_intention', 'type': 'float', 'description': ''},
{'name': 'detector_tx_intention', 'type': 'float', 'description': ''},
{'name': 'nimages_per_file', 'type': 'int', 'description': ''},
{'name': 'image_nr_start', 'type': 'int', 'description': ''},
{'name': 'total_expected_wedges', 'type': 'float', 'description': ''},
{'name': 'total_expected_exposure_time', 'type': 'float', 'description': ''},
{'name': 'beam_center_x', 'type': 'float', 'description': ''},
{'name': 'beam_center_y', 'type': 'float', 'description': ''},
{'name': 'sequence_id', 'type': 'int', 'description': ''},
{'name': 'frames_per_second', 'type': 'float', 'description': 'number of frames per second'},
{'name': 'overlap', 'type': 'float', 'description': 'overlap'},
{'name': 'beware_of_download', 'type': 'bool', 'description': 'wait for expected files'},
{'name': 'generate_cbf', 'type': 'bool', 'description': 'generate CBFs'},
{'name': 'generate_h5', 'type': 'bool', 'description': 'generate h5'},
{'name': 'nimages', 'type': 'int', 'description': 'number of images per trigger'},]
def __init__(self,
name_pattern,
directory,
frames_per_second=None,
nimages_per_file=400,
nimages=10,
position=None,
kappa=None,
phi=None,
chi=None,
photon_energy=None,
resolution=None,
detector_distance=None,
detector_vertical=None,
detector_horizontal=None,
transmission=None,
flux=None,
ntrigger=1,
snapshot=True,
zoom=None,
diagnostic=None,
analysis=None,
conclusion=None,
simulation=None,
parent=None,
mxcube_parent_id=None,
mxcube_gparent_id=None,
beware_of_top_up=False,
beware_of_download=False,
generate_cbf=True,
generate_h5=True):
logging.debug('diffraction_experiment __init__ len(diffraction_experiment.specific_parameter_fields) %d' % len(diffraction_experiment.specific_parameter_fields))
if hasattr(self, 'parameter_fields'):
self.parameter_fields += diffraction_experiment.specific_parameter_fields
else:
self.parameter_fields = diffraction_experiment.specific_parameter_fields[:]
logging.debug('xray_experiment __init__ len(self.parameters_fields) %d' % len(self.parameter_fields))
self.resolution = resolution
self.detector_distance = detector_distance
self.detector_vertical = detector_vertical
self.detector_horizontal = detector_horizontal
xray_experiment.__init__(self,
name_pattern,
directory,
position=position,
photon_energy=photon_energy,
transmission=transmission,
flux=flux,
ntrigger=ntrigger,
snapshot=snapshot,
zoom=zoom,
diagnostic=diagnostic,
analysis=analysis,
conclusion=conclusion,
simulation=simulation,
parent=parent,
mxcube_parent_id=mxcube_parent_id,
mxcube_gparent_id=mxcube_gparent_id,
beware_of_top_up=beware_of_top_up)
self.format_dictionary = {'directory': self.directory, 'name_pattern': self.name_pattern}
self.description = 'Diffraction experiment, Proxima 2A, SOLEIL, %s' % time.ctime(self.timestamp)
self.actuator = self.goniometer
self.frames_per_second = frames_per_second
self.nimages_per_file = nimages_per_file
self.nimages = nimages
self.ntrigger = ntrigger
self.beware_of_download = beware_of_download
self.generate_cbf = generate_cbf
self.generate_h5 = generate_h5
if kappa == None:
try:
self.kappa = self.goniometer.md2.kappaposition
except:
self.kappa = None
else:
self.kappa = kappa
if phi == None:
try:
self.phi = self.goniometer.md2.phiposition
except:
self.phi = None
else:
self.phi = phi
if chi == None:
try:
self.chi = self.goniometer.md2.chiposition
except:
self.chi = None
else:
self.chi = chi
# Set resolution: detector_distance takes precedence
# if neither specified, takes currect detector_distance
print('diffraction_experiment current, specified detector_distance and specified, resolution start', self.get_detector_distance(), self.detector_distance, self.resolution)
if self.detector_distance == None and self.resolution == None:
self.detector_distance = self.detector.position.ts.get_position()
if self.detector_distance != None:
self.resolution = self.resolution_motor.get_resolution_from_distance(self.detector_distance, wavelength=self.wavelength)
elif self.resolution != None:
self.detector_distance = self.resolution_motor.get_distance_from_resolution(self.resolution, wavelength=self.wavelength)
else:
print('There seem to be a problem with logic for detector distance determination. Please check')
print('diffraction_experiment detector_distance and resolution end', self.detector_distance, self.resolution)
self.observations = []
self.observation_fields = ['chronos', 'progress']
self.dozor_launched = 0
def get_master(self):
master = h5py.File(self.get_master_filename(), 'r')
return master
def get_master_filename(self):
return '%s_master.h5' % self.get_template()
def get_parameters(self):
if os.path.isfile(self.get_parameters_filename()):
self.parameters = self.load_parameters_from_file()
return self.parameters
if os.path.isfile(self.get_master_filename()) and self.parameters == {}:
parameters = {}
master = self.get_master()
for key in ['detector_distance', 'beam_center_x', 'beam_center_y']:
parameters[key] = master['/entry/instrument/detector/%s' % key][()]
for key in ['nimages', 'ntrigger']:
parameters[key] = int(master['/entry/instrument/detector/detectorSpecific/%s' % key][()])
parameters['wavelength'] = master['/entry/sample/beam/incident_wavelength'][()]
parameters['detector_distance'] *= 1e3
parameters['resolution'] = self.resolution_motor.get_resolution_from_distance(parameters['detector_distance'], parameters['wavelength'])
parameters['timestamp'] = datetime.datetime.timestamp(datetime.datetime.fromisoformat(master['/entry/instrument/detector/detectorSpecific/data_collection_date'][()].decode()))
self.parameters = parameters
return self.parameters
def get_expected_files(self):
expected_files = ['%s_master.h5' % self.name_pattern]
nimages_per_file = self.get_nimages_per_file()
nimages = self.get_nimages()
ntrigger = self.get_ntrigger()
total_number_of_images = nimages * ntrigger
accounted_for = 0
k = 0
while accounted_for < total_number_of_images:
k += 1
data_file = '%s_data_%06d.h5' % (self.name_pattern, k)
expected_files.append(data_file)
accounted_for += nimages_per_file
expected_files.sort()
return expected_files
def get_downloaded_files(self, expected_files=None, directory=None):
if expected_files is None:
expected_files = self.get_expected_files()
if directory is None:
directory = self.directory
listdir = os.listdir(directory)
already = []
for f in expected_files:
if f in listdir:
already.append(f)
return already
def expected_files_present(self, expected_files=None, directory=None):
if expected_files is None:
expected_files = self.get_expected_files()
if directory is None:
directory = self.directory
listdir = os.listdir(directory)
answer = False
for f in expected_files:
if f not in listdir:
return answer
return True
def get_download_progress(self, expected_files=None, directory=None):
if expected_files is None:
expected_files = self.get_expected_files()
if directory is None:
directory = self.directory
already = self.get_downloaded_files(expected_files=expected_files, directory=directory)
download_progress = 100 * len(already)/len(expected_files)
return download_progress
def wait_for_expected_files(self, timeout=60, naptime=0.5, expected_files=None, directory=None, symbols=['-','\\','|','/']):
if expected_files is None:
expected_files = self.get_expected_files()
if directory is None:
direcotry = self.directory
self.logger.info('waiting for expected files %s' % expected_files)
_start = time.time()
k = 0
while not self.expected_files_present(expected_files=expected_files, directory=directory) and time.time()-_start < timeout:
print('{progress:.1f}% {symbol:s}'.format(progress=self.get_download_progress(expected_files, directory), symbol="%s\r" % symbols[ k%len(symbols) ]), end=' ')
sys.stdout.flush()
gevent.sleep(naptime)
k += 1
self.logger.info('wait for expected files took %.4f seconds' % (time.time() - _start))
def get_degrees_per_frame(self):
'''get degrees per frame'''
return self.angle_per_frame
def get_fps(self):
return self.get_frames_per_second()
def get_frames_per_second(self):
'''get frames per second'''
return self.get_nimages()/self.scan_exposure_time
def get_dps(self):
return self.get_degrees_per_second()
def get_degrees_per_second(self):
'''get degrees per second'''
return self.get_scan_speed()
def get_scan_speed(self):
'''get scan speed'''
return self.scan_range/self.scan_exposure_time
def get_frame_time(self):
'''get frame time'''
return self.scan_exposure_time/self.get_nimages()
def get_reference_position(self):
return self.get_position()
def get_position(self):
'''get position '''
if self.position is None:
return self.goniometer.get_position()
else:
return self.position
def set_position(self, position=None):
'''set position'''
if position is None:
self.position = self.goniometer.get_position()
else:
self.position = position
self.goniometer.set_position(self.position)
self.goniometer.wait()
self.goniometer.save_position()
def get_kappa(self):
return self.kappa
def set_kappa(self, kappa):
self.kappa = kappa
def get_phi(self):
return self.phi
def set_phi(self, phi):
self.phi = phi
def get_chi(self):
return self.chi
def set_chi(self):
self.chi = chi
def get_md2_task_info(self):
return self.md2_task_info
def set_nimages(self, nimages):
self.nimages = nimages
def get_nimages(self):
try:
nimages = self.parameters['nimages']
except:
nimages = int(self.nimages)
return nimages
def get_scan_range(self):
return self.scan_range
def set_scan_range(self, scan_range):
self.scan_range = scan_range
def get_scan_exposure_time(self):
return self.scan_exposure_time
def set_scan_exposure_time(self, scan_exposure_time):
self.scan_exposure_time = scan_exposure_time
def get_scan_start_angle(self):
return self.scan_start_angle
def set_scan_start_angle(self, scan_start_angle):
self.scan_start_angle = scan_start_angle
def get_angle_per_frame(self):
return self.angle_per_frame
def set_angle_per_frame(self, angle_per_frame):
self.angle_per_frame = angle_per_frame
def set_ntrigger(self, ntrigger):
self.ntrigger = ntrigger
def get_ntrigger(self):
try:
ntrigger = self.parameters['ntrigger']
except:
ntrigger = int(self.ntrigger)
return int(self.ntrigger)
def set_resolution(self, resolution=None):
if resolution != None:
self.resolution = resolution
self.resolution_motor.set_resolution(resolution)
def get_resolution(self):
return self.resolution_motor.get_resolution()
def get_detector_distance(self):
return self.detector.position.ts.get_position()
def set_detector_distance(self, position, wait=True):
self.detector_ts_moved = self.detector.set_ts_position(position, wait=wait)
def get_detector_vertical_position(self):
return self.detector.position.tz.get_position()
def set_detector_vertical_position(self, position, wait=True):
self.detector_tz_moved = self.detector.position.tz.set_position(position, wait=wait)
def get_detector_horizontal_position(self):
return self.detector.position.tx.get_position()
def set_detector_horizontal_position(self, position, wait=True):
self.detector_tx_moved = self.detector.position.tx.set_position(position, wait=wait)
def get_sequence_id(self):
return self.sequence_id
def get_detector_ts_intention(self):
return self.detector_distance
def get_detector_tz_intention(self):
return self.detector_vertical
def get_detector_tx_intention(self):
return self.detector_horizontal
def get_detector_ts(self):
return self.get_detector_distance()
def get_detector_tz(self):
return self.get_detector_vertical_position()
def get_detector_tx(self):
return self.get_detector_horizontal_position()
def get_detector_vertical(self):
return self.detector_vertical
def set_detector_vertical(self, detector_vertical):
self.detector_vertical = detector_vertical
def get_detector_horizontal(self):
return self.detector_horizontal
def set_detector_horizontal(self, detector_horizontal):
self.detector_horizontal = detector_horizontal
def set_nimages_per_file(self, nimages_per_file):
self.nimages_per_file = nimages_per_file
def get_nimages_per_file(self):
return int(self.nimages_per_file)
def set_image_nr_start(self):
self.image_nr_start = image_nr_start
def get_image_nr_start(self):
return int(self.image_nr_start)
def set_total_expected_wedges(self, total_expected_wedges):
self.total_expected_wedges = total_expected_wedges
def get_total_expected_wedges(self):
return self.total_expected_wedges
def set_total_expected_exposure_time(self, total_expected_exposure_time):
self.total_expected_exposure_time = total_expected_exposure_time
def get_total_expected_exposure_time(self):
return self.total_expected_exposure_time
def set_beam_center_x(self, beam_center_x):
self.beam_center_x = beam_center_x
def get_beam_center_x(self):
return self.beam_center_x
def set_beam_center_y(self, beam_center_y):
self.beam_center_y = beam_center_y
def get_beam_center_y(self):
return self.beam_center_y
def check_downloader(self):
self.check_server(server_name='downloader')
def get_overlap(self, overlap=0., scan_start_angles=[], scan_range=0., min_scan_range=0.025):
parameters = self.get_parameters()
if 'scan_start_angles' in parameters:
scan_start_angles = parameters['scan_start_angles']
scan_range = parameters['scan_range']
elif hasattr(self, 'scan_start_angles'):
scan_start_angles = self.get_scan_start_angles()
scan_range = self.get_scan_range()
if scan_range < min_scan_range:
scan_range = 0.
if len(scan_start_angles) > 1:
delta = scan_start_angles[0] - scan_start_angles[1]
overlap = delta + scan_range
self.logger.info('get_overlap returns %.2f' % overlap)
return overlap
def get_dozor_directory(self):
return os.path.join('{directory}/process/dozor_{name_pattern}'.format(**self.format_dictionary))
def get_dozor_control_card_filename(self):
return '%s.dat' % self.name_pattern
def get_dozor_log_filename(self):
dozor_control_card_filename = self.get_dozor_control_card_filename()
dozor_log_filename = dozor_control_card_filename.replace('.dat', '_dozor.log')
return dozor_log_filename
def create_dozor_control_card(self, dozor_major_version=2):
'''
dozor_major_version == 1
dozor parameters
!-----------------
detector eiger9m
!
exposure 0.025
spot_size 3
detector_distance 200
X-ray_wavelength 0.9801
fraction_polarization 0.99
pixel_min 0
pixel_max 100000
!
ix_min 1
ix_max 1067
iy_min 1029
iy_max 1108
!
orgx 1454.26
orgy 1731.02
oscillation_range 0.001
image_step 1
starting_angle 75
!
first_image_number 1
number_images 1
name_template_image mesh1_?????.cbf
dozor_major_version == 2
dozor parameters
!-----------------
detector eiger9m
nx 3110
ny 3269
pixel 0.075
exposure 0.0043
detector_distance 115
X-ray_wavelength 0.980133704735
fraction_polarization 0.99
orgx 1453
orgy 1731
oscillation_range 0.1
starting_angle 0.0
number_images 3600
first_image_number 1
name_template_image /dev/shm/s1_1_h5/s1_1_??????.h5
library /nfs/data/plugin.so
pixel_min 0
pixel_max 10712
spot_size 3
beamstop_distance 20
beamstop_size 0.5
beamstop_vertical 0
image_step 1
end
'''
try:
os.makedirs(self.get_dozor_directory())
except OSError:
pass
parameters = self.get_parameters()
if 'frame_time' not in parameters:
parameters['frame_time'] = 1./parameters['frames_per_second']
if 'angle_per_frame' not in parameters:
parameters['angle_per_frame'] = 0.001
if parameters['angle_per_frame'] <= 0.001:
parameters['angle_per_frame_dozor'] = 0.
else:
parameters['angle_per_frame_dozor'] = parameters['angle_per_frame']
if 'scan_start_angles' in parameters:
starting_angle = parameters['scan_start_angles'][0]
elif 'scan_start_angle' in parameters:
starting_angle = parameters['scan_start_angle']
else:
starting_angle = 0.
if 'nimages' in parameters:
self.nimages = parameters['nimages']
else:
self.nimages = parameters['total_expected_exposure_time']/parameters['frame_time']
if 'ntrigger' in parameters:
self.ntrigger = parameters['ntrigger']
elif 'scan_start_angles' in parameters:
self.ntrigger = len(parameters['scan_start_angles'])
else:
self.ntrigger = 1
self.format_dictionary['cbf_directory'] = self.get_cbf_directory()
name_template_image = '{cbf_directory}/{name_pattern}_??????.cbf.gz'.format(**self.format_dictionary)
self.logger.info('deciding whether to create ordered cbf links get_overlap: %.4f, angle_per_frame_dozor: %.4f' % (self.get_overlap(), parameters['angle_per_frame_dozor']))
if self.get_overlap() != 0.:
self.create_ordered_cbf_links()
name_template_image = os.path.join(self.get_dozor_directory(), '{name_pattern}_ordered_??????.cbf.gz'.format(**self.format_dictionary))
dozor_parameters = {'detector': 'eiger9m',
'exposure': parameters['frame_time'],
'spot_size': 3,
'nx': 3110,
'ny': 3269,
'pixel': 0.075,
'detector_distance': parameters['detector_distance'],
'X-ray_wavelength': parameters['wavelength'],
'fraction_polarization': 0.99,
'pixel_min': 0,
'pixel_max': self.detector.get_countrate_correction_count_cutoff(),
'ix_min': 1,
'ix_max': int(parameters['beam_center_x']) + 50,
'iy_min': int(parameters['beam_center_y']) - 50,
'iy_max': int(parameters['beam_center_y']) + 50,
'orgx': int(parameters['beam_center_x']),
'orgy': int(parameters['beam_center_y']),
'oscillation_range': parameters['angle_per_frame_dozor'],
'image_step': 1,
'beamstop_distance': 20,
'beamstop_size': 1.,
'beamstop_vertical': 0,
'starting_angle': starting_angle,
'first_image_number': 1,
'library': '/nfs/data/xds-zcbf.so',
'number_images': self.nimages * self.ntrigger,
'name_template_image': name_template_image}
input_file = 'dozor parameters\n'
input_file += '!-----------------\n'
for parameter in ['detector', 'exposure', 'spot_size', 'detector_distance', 'X-ray_wavelength', 'fraction_polarization', 'pixel_min', 'pixel_max', 'orgx', 'orgy', 'oscillation_range', 'image_step', 'starting_angle', 'first_image_number', 'number_images', 'name_template_image']:
input_file += '%s %s\n' % (parameter, dozor_parameters[parameter])
if dozor_major_version < 2:
for parameter in ['ix_min', 'ix_max', 'iy_min', 'iy_max']:
input_file += '%s %s\n' % (parameter, dozor_parameters[parameter])
else:
for parameter in ['nx', 'ny', 'pixel', 'beamstop_distance', 'beamstop_size', 'beamstop_vertical', 'library']:
input_file += '%s %s\n' % (parameter, dozor_parameters[parameter])
input_file += 'end\n'
f = open(os.path.join(self.get_dozor_directory(), self.get_dozor_control_card_filename()), 'w')
f.write(input_file)
f.close()
def get_cbf_directory(self):
#cbf_directory = '{directory}/{name_pattern}_cbf'.format(**self.format_dictionary)
cbf_directory = '{directory}'.format(**self.format_dictionary)
return cbf_directory
def get_cbf_template(self):
return os.path.join(self.get_cbf_directory(), '{name_pattern:s}_%06d.cbf.gz'.format(name_pattern=self.get_name_pattern()))
def get_spot_list_directory(self):
return os.path.join(self.get_cbf_directory(), 'spot_list')
def get_spot_file_template(self):
return os.path.join(self.get_spot_list_directory(), '{name_pattern:s}_%06d.adx.gz'.format(name_pattern=self.get_name_pattern()))
def get_list_of_spot_files(self):
return glob.glob(os.path.join(self.get_spot_list_directory(), '*.adx.gz'))
def get_list_of_cbf_files(self):
return glob.glob(os.path.join(self.get_cbf_directory(), '*.cbf.gz'))
def create_ordered_cbf_links(self):
self.logger.info('create_ordered_cbf_links')
os.chdir(self.get_dozor_directory())
os.system('touch %s' % self.get_cbf_directory())
cbfs = glob.glob('%s/%s_*.cbf.gz' % (self.get_cbf_directory(), self.name_pattern))
if cbfs == []:
self.logger.info('no cbfs generated please check')
return
cbfs.sort()
for k, cbf in enumerate(cbfs):
try:
os.symlink(cbf, '%s_ordered_%06d.cbf.gz' % (self.name_pattern, k+1))
except OSError:
pass
def run_dials(self):
self.logger.info('run_dials')
if os.path.isfile('{directory}/process/dials_{name_pattern}/dials.find_spots.log'.format(**self.format_dictionary)):
return
spot_find_line = 'source /usr/local/dials/dials_env.sh; mkdir -p {directory}/process/dials_{name_pattern}; cd {directory}/process/dials_{name_pattern}; touch {directory}; echo $(pwd); dials.find_spots shoebox=False per_image_statistics=True spotfinder.filter.ice_rings.filter=True nproc=80 ../../{name_pattern}_master.h5 &'.format(**self.format_dictionary)
if os.uname()[1] != 'process1':
spot_find_line = 'ssh process1 "%s"&' % spot_find_line
self.logger.info('spot_find_line %s' % spot_find_line)
os.system(spot_find_line)
def get_dials_results(self):
if not os.path.isdir(self.get_process_dir()):
os.mkdir(self.get_process_dir())
if not os.path.isfile('%s/dials.find_spots.log' % self.get_process_dir()):
while not os.path.exists('%s_master.h5' % self.get_template()):
os.system('touch %s' % self.directory)
gevent.sleep(0.25)
self.run_dials()
dials_process_output = "%s/dials.find_spots.log" % self.get_process_dir()
print('dials process output', dials_process_output)
os.system('touch %s' % os.path.dirname(dials_process_output))
if os.path.isfile(dials_process_output):
a = commands.getoutput("grep '|' %s" % dials_process_output ).split('\n')
#dials_results = self.get_nspots_nimage(a)
dials_results = np.array(list(map(int, commands.getoutput("grep '|' {directory}/process/dials_{name_pattern}/dials.find_spots.log | grep -v image | cut -d '|' -f 3".format(**self.format_dictionary)).split('\n'))))
return dials_results
def get_dials_raw_results(self):
results_file = self.get_dials_raw_results_filename()
if not os.path.isfile(results_file):
self.results = self.get_dials_results()
elif self.results == None:
self.results = pickle.load(open(results_file))
return self.results
def get_nspots_nimage(self, a):
results = {}
for line in a:
try:
nimage, nspots, nspots_no_ice, total_intensity = list(map(int, re.findall('\| (\d*)\s*\| (\d*)\s*\| (\d*)\s*\| (\d*)\s*\|', line)[0]))
results[nimage] = {}
results[nimage]['dials_spots'] = nspots_no_ice
results[nimage]['dials_all_spots'] = nspots
results[nimage]['dials_total_intensity'] = total_intensity
except:
print(traceback.print_exc())
return results
def parse_find_spots(self):
def get_nspots_nimage(a):
results = {}
for line in a:
try:
nimage, nspots, nspots_no_ice, total_intensity = list(map(int, re.findall('\| (\d*)\s*\| (\d*)\s*\| (\d*)\s*\| (\d*)\s*\|', line)[0]))
#nspots, nimage = map(int, re.findall('Found (\d*) strong pixels on image (\d*)', line)[0])
results[nimage] = {}
results[nimage]['dials_spots'] = nspots_no_ice
results[nimage]['dials_all_spots'] = nspots
results[nimage]['dials_total_intensity'] = total_intensity
except:
self.logger.info(traceback.format_exc())
return results
search_line = "grep '|' {directory}/process/dials_{name_pattern}/dials.find_spots.log".format(**{'directory': self.directory, 'name_pattern': self.name_pattern})
a = commands.get_output(search_line).split('\n')
results = get_nspots_nimage(a)
return results
def run_dozor(self, force=False, binning=1, blocking=False):
self.logger.info('run_dozor force=%s blocking=%s' % (force, blocking))
_start = time.time()
process_directory = self.get_dozor_directory()
if not force and os.path.isfile(os.path.join(self.get_dozor_directory(), self.get_dozor_control_card_filename())):
self.logger.info('dozor was already executed, please use force flag if you want to run it again')
return
if not force and os.path.isfile(os.path.join(process_directory, 'dozor_average.dat')):
self.logger.info('dozor was already executed, and completed, please use force flag if you want to run it again')
return
if not os.path.isfile(self.get_dozor_control_card_filename()):
self.create_dozor_control_card()
dozor_line = 'cd {directory}; dozor -bin {binning:d} -b -p -wg -rd -s -pall {control_card} | tee {log_file}'.format(**{'directory': process_directory, 'control_card': self.get_dozor_control_card_filename(), 'log_file': os.path.join(self.get_dozor_directory(), self.get_dozor_log_filename()), 'binning': binning})
if not blocking:
dozor_line += '&'
if os.uname()[1] != 'process1':
dozor_line = 'ssh process1 "%s"' % dozor_line
if not blocking:
dozor_line += '&'
self.logger.info('dozor_line %s' % dozor_line)
os.system(dozor_line)
if blocking:
self.logger.info('dozor analysis took %.4f seconds' % (time.time() - _start))
def get_dozor_raw_results(self):
return open(os.path.join(self.get_dozor_directory(), self.get_dozor_log_filename())).read()
def get_dozor_results(self, blocking=False, timeout=30):
self.run_dozor(blocking=blocking)
_start = time.time()
no_spots_mainscore_resolution = re.compile('\\s+([\\d]+).*\|\\s+([\\d]+).*\|.*\|\\s+([\\d\.]+)\\s+[\\d\.]+\\s+([\\d\.]+).*')
#spots = re.compile('[\\s]+[\\d]+[\\s]+([\\d]+)[\\s]+[\\d\\.]+[\\s]+[\\d\\.]+[\\s]+[\\d\\.]+[\\s]+[\\d\\.]+[\\s]+[\\d\\.]+')
results_filename = os.path.join(self.get_dozor_directory(), 'dozor_average.dat')
while not os.path.isfile(results_filename) and time.time()-_start < timeout:
time.sleep(0.5)
self.logger.info('Waiting for dozor results to appear')
os.system('touch %s' % self.get_dozor_directory())
results_file = self.get_dozor_raw_results()
raw_results = no_spots_mainscore_resolution.findall(results_file)
results = np.array([list(map(float,item)) for item in raw_results])
return results
def write_xds_inp_init(self):
template = ''' JOB= {jobs:s}
DATA_RANGE= {img_start:d} {img_end:d}
SPOT_RANGE= {img_start:d} {img_end:d}
BACKGROUND_RANGE= {background_img_start:d} {background_img_end:d}
SPOT_MAXIMUM-CENTROID= 2.0
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 3
STRONG_PIXEL= 3.0
OSCILLATION_RANGE= {angle_per_frame:.4f}
STARTING_ANGLE= 0.0
STARTING_FRAME= 1
X-RAY_WAVELENGTH= {wavelength:.4f}
NAME_TEMPLATE_OF_DATA_FRAMES= img/{name_pattern:s}_??????.cbf.gz
DETECTOR_DISTANCE= {detector_distance:.2f}
DETECTOR= EIGER MINIMUM_VALID_PIXEL_VALUE= 0 OVERLOAD= 12457
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
NX= 3110 NY= 3269 QX= 0.075 QY= 0.075
ORGX= {beam_center_x:.4f} ORGY= {beam_center_y:.4f}
ROTATION_AXIS= 1.000000 0.000000 0.000000
INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0
FRACTION_OF_POLARIZATION= 0.99
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
SPACE_GROUP_NUMBER= 0
UNIT_CELL_CONSTANTS= 0 0 0 0 0 0
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 5500 30000
INCLUDE_RESOLUTION_RANGE= 50 {resolution:.2f}
RESOLUTION_SHELLS= 15.0 7.0 {resolution:.2f}
TRUSTED_REGION= 0.0 1.42
STRICT_ABSORPTION_CORRECTION= FALSE
TEST_RESOLUTION_RANGE= 20 4.97
GAIN= 1.0
LIB= /nfs/data/xds-zcbf.so
!=== Added Keywords ===!
MAXIMUM_NUMBER_OF_JOBS= {maximum_number_of_jobs:d}
MAXIMUM_NUMBER_OF_PROCESSORS= {maximum_number_of_processors:d}
FRIEDEL'S_LAW= TRUE
EXCLUDE_RESOLUTION_RANGE= 3.930 3.870 !ice-ring at 3.897 Angstrom
EXCLUDE_RESOLUTION_RANGE= 3.700 3.640 !ice-ring at 3.669 Angstrom
EXCLUDE_RESOLUTION_RANGE= 3.470 3.410 !ice-ring at 3.441 Angstrom
EXCLUDE_RESOLUTION_RANGE= 2.700 2.640 !ice-ring at 2.671 Angstrom
EXCLUDE_RESOLUTION_RANGE= 2.280 2.220 !ice-ring at 2.249 Angstrom
EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong
EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak
EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong
EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak
SENSOR_THICKNESS= 0.45
DATA_RANGE_FIXED_SCALE_FACTOR= 1 100 1.0
'''
print('%s' % self.format_dictionary)
xds_inp_text = template.format(**self.format_dictionary)
process_directory = '{directory}/process/xds_{name_pattern}'.format(**self.format_dictionary)
xds_inp_file = open(os.path.join(process_directory, 'XDS.INP'), 'w')
xds_inp_file.write(xds_inp_text)
print('xds_inp_text')
xds_inp_file.close()
def execute_xds(self):
logging.info('execute_xds')
self.write_xds_inp_init()
execute_line = 'cd {process_directory}; touch {directory}; echo $(pwd); ln -s ../../ img; xds_par &'.format(**self.format_dictionary)
if os.uname()[1] != 'process1':
execute_line = 'ssh process1 "%s"' % execute_line
logging.info('spot_find_line %s' % execute_line)
os.system(execute_line)
def run_xds(self, force=False, background_images=18, binning=None, blocking=True):
logging.info('run_xds')
process_directory = '{directory}/process/xds_{name_pattern}'.format(**self.format_dictionary)
if not force and os.path.isfile(os.path.join(process_directory, 'COLSPOT.LP')):
return
if not os.path.isdir(process_directory):
os.makedirs(process_directory)
parameters = self.get_parameters()
for key in ['resolution', 'wavelength', 'detector_distance', 'beam_center_x', 'beam_center_y']:
self.format_dictionary[key] = parameters[key]
self.format_dictionary['process_directory'] = process_directory
self.format_dictionary['img_start'] = 1
self.format_dictionary['img_end'] = int(parameters['ntrigger'] * parameters['nimages'])
self.format_dictionary['nimages'] = int(parameters['nimages'])
self.format_dictionary['angle_per_frame'] = 0.001 # parameters['angle_per_frame']
if not os.path.isfile(os.path.join(process_directory, 'INIT.LP')) or force:
self.format_dictionary['jobs']= 'XYCORR INIT'
self.format_dictionary['maximum_number_of_jobs'] = 1
self.format_dictionary['maximum_number_of_processors'] = min(background_images, 99)
self.format_dictionary['background_img_start'] = max(1, int(parameters['nimages']/2 - background_images/2))
self.format_dictionary['background_img_end'] = min(parameters['nimages']*parameters['ntrigger'], int(parameters['nimages']/2 + background_images/2))
self.execute_xds()
self.format_dictionary['jobs'] = 'COLSPOT'
self.format_dictionary['maximum_number_of_jobs'] = min(self.get_ntrigger(), 99)
self.format_dictionary['maximum_number_of_processors'] = min(self.get_nimages(), 99)
self.execute_xds()
def get_xds_directory(self):
return os.path.join('{directory}/process/xds_{name_pattern}'.format(**self.format_dictionary))
def get_xds_raw_results_filename(self):
return os.path.join(self.get_xds_directory(), 'COLSPOT.LP')
def get_xds_raw_results(self):
return open(self.get_xds_raw_results_filename()).read()
def get_xds_results(self, blocking=False, timeout=30):
_start = time.time()
self.run_xds()
while not os.path.isfile(self.get_xds_raw_results_filename()) and time.time()-_start < timeout:
time.sleep(0.5)
logging.info('Waiting for xds results to appear')
os.system('touch %s' % self.get_xds_directory())
spots = re.compile('[\s]+[\d]+[\s]+[\d]+[\s]+([\d]+)[\s]+[\d]+')
colspot = self.get_xds_raw_results()
results = np.array(list(map(int, spots.findall(colspot))))
return results
def get_stream_header_appendix(self):
beam_center_x, beam_center_y = self.beam_center.get_beam_center(wavelength=self.wavelength, ts=self.detector_distance, tx=self.detector_horizontal, tz=self.detector_vertical)
header_appendix =\
{"htype": "dhappendix",
"path": self.directory, #os.path.join(self.directory, '%s_cbf' % self.name_pattern),
#"path": self.directory.replace('/nfs/data2', '/dev/shm'),
"template": "%s_??????" % self.name_pattern,
"detector_distance": self.detector_distance/1000.,
"wavelength": self.wavelength,
"beam_center_x": beam_center_x,
"beam_center_y": beam_center_y,
"omega_start": self.scan_start_angle,
"omega_increment": self.angle_per_frame,
"two_theta_start": 0,
"kappa_start": self.kappa,
"phi_start": self.phi,
"overlap": self.get_overlap(),
"start_number": self.image_nr_start,
"user": self.get_login(),
"compression": 1,
"processing": 1,
"binning": 1,
"beamstop_distance": 20,
"beamstop_size": 1.,
"beamstop_vertical": 0,
"frames_per_wedge": self.get_nimages(),
"count_cutoff": self.detector.get_countrate_correction_count_cutoff()}
return json.dumps(header_appendix)
def program_detector(self, photon_energy_delta=0.5, angle_delta=0.002, time_delta=0, filewriter=True, stream=True):
_start = time.time()
if stream:
if self.detector.get_stream_disabled():
self.detector.initialize_stream()
self.detector.set_stream_enabled()
else:
if self.detector.get_stream_enabled():
self.detector.set_stream_disabled()
if filewriter:
if self.detector.get_filewriter_disabled():
self.detector.initialize_filewriter()
self.detector.set_filewriter_enabled()
else:
if self.detector.get_filewriter_enabled():
self.detector.set_filewriter_disabled()
self.detector.set_standard_parameters(nimages_per_file=self.get_nimages_per_file())
self.detector.set_name_pattern(self.get_full_name_pattern())
#self.detector.clear_monitor()
if self.detector.get_ntrigger() != self.get_ntrigger():
self.detector.set_ntrigger(self.get_ntrigger())
if self.detector.get_nimages() != self.get_nimages():
self.detector.set_nimages(self.get_nimages())
frame_time = self.get_frame_time()
if abs(self.detector.get_frame_time() - frame_time) >= time_delta:
self.detector.set_frame_time(frame_time)
count_time = frame_time - self.detector.get_detector_readout_time()
if abs(self.detector.get_count_time() - count_time) >= time_delta:
self.detector.set_count_time(count_time)
if abs(self.detector.get_omega() - self.scan_start_angle) >= angle_delta:
self.detector.set_omega(self.scan_start_angle)
if self.angle_per_frame <= 0.001:
self.detector.set_omega_increment(0)
else:
self.detector.set_omega_increment(self.angle_per_frame)
if abs(self.detector.get_kappa() - self.kappa) >= angle_delta:
self.detector.set_kappa(self.kappa)
if abs(self.detector.get_phi() - self.phi) >= angle_delta:
self.detector.set_phi(self.phi)
if abs(self.detector.get_chi() - self.chi) >= angle_delta:
self.detector.set_chi(self.chi)
if abs(self.detector.get_photon_energy() - self.photon_energy) >= photon_energy_delta:
self.detector.set_photon_energy(self.photon_energy)
if self.detector.get_image_nr_start() != self.image_nr_start:
self.detector.set_image_nr_start(self.image_nr_start)
if self.simulation != True:
beam_center_x, beam_center_y = self.beam_center.get_beam_center(wavelength=self.wavelength, ts=self.detector_distance, tx=self.detector_horizontal, tz=self.detector_vertical)
else:
beam_center_x, beam_center_y = 1430, 1550
self.beam_center_x, self.beam_center_y = beam_center_x, beam_center_y
if abs(self.detector.get_beam_center_x() - beam_center_x) >= angle_delta:
self.detector.set_beam_center_x(beam_center_x)