import os
import numpy
import autoprocess.errors
from autoprocess.parsers import xds
from autoprocess.utils import log, misc, programs, xdsio
from autoprocess.utils.choices import Choices
from autoprocess.utils.misc import Table
_logger = log.get_module_logger(__name__)
PROBLEMS = Choices(
(1, 'index_origin', 'Detector origin not optimal.'),
(2, 'multiple_subtrees',
'Indexed reflections belong to multiple subtrees.'),
(3, 'poor_solution', 'Poor solution, indexing refinement problems.'),
(4, 'non_integral', 'Indices deviate significantly from integers.'),
(5, 'unindexed_spots', 'Too many un-indexed spots.'),
(6, 'spot_accuracy',
'Spots deviate significantly from expected positions.'),
(7, 'dimension_2d', 'Clusters are not 3-Dimensional.'),
(8, 'few_spots', 'Insufficient spots available.'),
(9, 'failed', 'Indexing failed for unknown reason.'))
CODES = {
xds.SPOT_LIST_NOT_3D: PROBLEMS.dimension_2d,
xds.INSUFFICIENT_INDEXED_SPOTS: PROBLEMS.unindexed_spots,
xds.INSUFFICIENT_SPOTS: PROBLEMS.few_spots,
xds.POOR_SOLUTION: PROBLEMS.spot_accuracy,
xds.REFINE_ERROR: PROBLEMS.poor_solution,
import os
import sys
from autoprocess.engine.process import Manager
from autoprocess.utils import log
from autoprocess.utils import misc
logger = log.get_module_logger('auto.integrate')
def main(args):
if args.dir:
os.chdir(args.dir)
try:
checkpoint = misc.load_chkpt()
except IOError:
logger.error(
'Must be in, or provide a valid directory from previous session.')
sys.exit(1)
app = Manager(checkpoint=checkpoint)
# update app and overwrite options
overwrite = {'optimize': args.opt, 'backup': args.backup}
if args.anom != app.options['anomalous']:
overwrite['anomalous'] = args.anom
if args.frames:
overwrite['data_range'] = tuple(map(int, args.frames.split('-')))
if args.exclude:
overwrite['skip_frames'] = [
import sys
import os
from autoprocess.engine.process import Manager
from autoprocess.utils import log
from autoprocess.utils import misc
from autoprocess.utils import xtal
logger = log.get_module_logger('auto.symmetry')
def main(args):
if args.dir:
os.chdir(args.dir)
try:
checkpoint = misc.load_chkpt()
except IOError:
logger.error('Must be in, or provide a valid directory from previous session.')
sys.exit(1)
app = Manager(checkpoint=checkpoint)
overwrite = {
'backup': args.backup,
'chiral': (not args.nonchiral)
}
if args.anom != app.options['anomalous']:
overwrite['anomalous'] = args.anom
if args.res:
overwrite['resolution'] = args.res
import sys
import os
from autoprocess.engine.process import Manager
from autoprocess.utils import log
from autoprocess.utils import misc
logger = log.get_module_logger('auto.strategy')
def main(args):
if args.dir:
os.chdir(args.dir)
try:
chkpt = misc.load_chkpt()
except IOError:
logger.error('This command must be run within a data processing directory.')
sys.exit(1)
app = Manager(checkpoint=chkpt)
overwrite = {
'backup': args.backup
}
if args.anom != app.options['anomalous']:
overwrite['anomalous'] = args.anom
if args.res:
overwrite['resolution'] = args.res
app.run(resume_from=(chkpt['run_position'][0], 'strategy'), overwrite=overwrite)
import sys
import os
from autoprocess.engine.process import Manager
from autoprocess.utils import log
from autoprocess.utils import misc
logger = log.get_module_logger('auto.scale')
def main(args):
if args.dir:
os.chdir(args.dir)
try:
checkpoint = misc.load_chkpt()
except IOError:
logger.error(
'Must be in, or provide a valid directory from previous session.')
sys.exit(1)
app = Manager(checkpoint=checkpoint)
overwrite = {'backup': args.backup}
if args.anom != app.options['anomalous']:
overwrite['anomalous'] = args.anom
if args.res:
overwrite['resolution'] = args.res
app.run(resume_from=(checkpoint['run_position'][0], 'scaling'),
overwrite=overwrite)
import os
import sys
from autoprocess.engine.process import Manager
from autoprocess.utils import log
from autoprocess.utils import misc
logger = log.get_module_logger('auto.process')
def main(args):
if len(args.images) >= 1:
options = {
'images': args.images,
'anomalous': bool(args.anom),
'mode': 'simple',
'backup': args.backup,
'chiral': (not args.nonchiral),
'solve-small': args.formula,
'directory': args.dir,
'prefix': [] if not args.prefix else args.prefix.split(',')
}
if args.screen:
options['mode'] = 'screen'
elif args.mad:
options['mode'] = 'mad'
options['anomalous'] = True
elif len(args.images) > 1:
options['mode'] = 'merge'
if len(options['prefix']) != len(args.images):
import os
import sys
from autoprocess.utils import log, misc
from autoprocess.engine import reporting
logger = log.get_module_logger('auto.report')
def main(args):
if args.dir:
os.chdir(args.dir)
try:
data = misc.load_chkpt()
reporting.save_report(data['datasets'], data['options'])
except IOError:
logger.error(
'Must be in, or provide a valid directory from previous session.')
def run(args):
try:
log.log_to_console()
main(args)
except KeyboardInterrupt:
sys.exit(1)
import re
import socket
from autoprocess.utils.log import get_module_logger
from twisted.internet import reactor
from twisted.spread import pb
logger = get_module_logger(__name__)
class ServerClientFactory(pb.PBClientFactory):
def buildProtocol(self, addr):
broker = pb.PBClientFactory.buildProtocol(self, addr)
pb.PBClientFactory.clientConnectionMade(self, broker)
return broker
class PBClient(object):
"""
A Perspective Broker Client
:param address: string representing the <address>:<port> of the server
"""
NAME = 'PB Server'
def __init__(self, address):
super().__init__()
self.address = address
self.name = self.NAME
self.connection = None
self.factory = None
from autoprocess.utils.ellipse import fit_ellipse
SHARE_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'share')
try:
from scipy.signal import savgol_filter
except:
from autoprocess.utils.misc import savgol_filter
warnings.filterwarnings('ignore')
XSTEP = 0.05
BACKSTOP_OFFSET = 200
CENTER_SEARCH_LIMIT = 500
logger = log.get_module_logger('powder')
class Fit2DFile(object):
def __init__(self, filename, format):
self.rawfile = filename
self.format = format
path, ext = os.path.splitext(self.rawfile)
if self.format == 'TIFF':
self.filename = '{}.{}'.format(path, 'tiff')
else:
self.filename = self.rawfile
self.name = os.path.basename(path)
def __enter__(self):
if self.format == 'TIFF':