def __init__(self, inp, output, logger=None):
logger.info('FindBeamCenter.__init__')
self.st = time.time()
self.input,self.cpu,self.verbose,self.clean,self.ram,self.red = inp
self.output = output
self.logger = logger
#Setting up data input
self.setup = self.input[1]
self.header = self.input[2]
self.header2 = False
if self.input[3].has_key('distance'):
self.header2 = self.input[3]
self.preferences = self.input[4]
else:
self.preferences = self.input[3]
self.controller_address = self.input[-1]
#Number of labelit runs to fine tune beam center and spacing from original
#Should be even number for symmetry around original beam center
self.iterations2 = 10
self.iterations2_space = 0.3
#self.iterations2 = 15
#self.iterations2_space = 0.1
#Sets the limit of the std dev (mm) of either x or y beam position in the top 10% of the solutions.
self.std_dev = 0.1
#Sets settings to check output on my machine and does not send results to database.
#******BEAMLINE SPECIFIC*****
self.cluster_use = BLspec.checkCluster()
if self.cluster_use:
self.test = False
else:
self.test = True
#******BEAMLINE SPECIFIC*****
#this is where I have chosen to place my results
self.labelit_results = {}
self.labelit_summary = False
#Labelit settings
self.twotheta = False
self.multiproc = True
self.labelit_jobs = {}
self.results = {}
self.runs = {}
self.pool = {}
#Settings for all programs
self.x_beam = self.header.get('beam_center_x')
self.y_beam = self.header.get('beam_center_y')
self.working_dir = self.setup.get('work')
#self.sg = self.header.get('spacegroup','None')
self.distance = os.path.basename(self.working_dir)
self.vendortype = Utils.getVendortype(self,self.header)
Process.__init__(self,name='FindBeamCenter')
self.start()
def __init__(self,input,logger=None):
logger.info('AutoStats.__init__')
self.st = time.time()
self.input = input
self.logger = logger
self.working_dir = self.input[0].get('dir',os.getcwd())
self.datafile = self.input[0].get('data',False)
self.gui = self.input[0].get('gui',True)
self.clean = self.input[0].get('clean',True)
self.test = self.input[0].get('test',False)
self.controller_address = self.input[0].get('control',False)
self.verbose = self.input[0].get('verbose',False)
self.clean = False
self.verbose = True
#Check if precession photo info included in input
if self.input[0].has_key('run'):
self.pp = True
else:
self.pp = False
self.stats_timer = 180
self.xtriage_log = []
self.jobs_output = {}
self.pids = {}
self.xtriage_results = False
self.xtriage_summary = False
self.pts = False
self.twin = False
self.molrep_log = False
self.molrep_results = False
self.molrep_summary = False
self.NCS_results = False
self.sample_type = False
self.failed = False
self.input_sg = False
self.solvent_content = 0.55
#******BEAMLINE SPECIFIC*****
#self.cluster_use = Utils.checkCluster()
self.cluster_use = BLspec.checkCluster()
#******BEAMLINE SPECIFIC*****
if self.test:
self.clean = False
Process.__init__(self,name='AutoStats')
self.start()
def __init__(self,inp,output,logger=None):
logger.info('LabelitAction.__init__')
self.st = time.time()
self.input,self.clean,self.test,self.verbose,self.vendortype,self.red = inp
self.output2 = output
self.logger = logger
self.labelit_jobs = {}
self.pool = {}
self.working_dir = os.getcwd()
self.multiproc = True
#******BEAMLINE SPECIFIC*****
#self.cluster_use = Utils.checkCluster()
self.cluster_use = BLspec.checkCluster()
#******BEAMLINE SPECIFIC*****
#initialize the thread
Process.__init__(self,name='LabelitAction')
#start the process
self.start()
def main():
"""
This pipeline has to be run on a computer cluster. It launches many Labelit autoindexing runs varying input beamcenter
for each distance, then looks at all the refined beam center outputs and fits to a 6th order polymonial.
"""
#start logging
import logging,logging.handlers
LOG_FILENAME = os.path.join(os.getcwd(),'rapd.log')
#inp = Input.input()
# Set up a specific logger with our desired output level
logger = logging.getLogger('RAPDLogger')
logger.setLevel(logging.DEBUG)
# Add the log message handler to the logger
handler = logging.handlers.RotatingFileHandler(LOG_FILENAME,maxBytes=10000000,backupCount=5)
#add a formatter
formatter = logging.Formatter("%(asctime)s - %(message)s")
handler.setFormatter(formatter)
logger.addHandler(handler)
logger.info('__init__')
import argparse
#Parse the command line for commands.
parser = argparse.ArgumentParser(description='Run job on computer cluster.')
parser.add_argument('inp' ,nargs='*', type=str, help='folder')
args = vars(parser.parse_args())
if len(args['inp']) == 0:
image_dir = raw_input('In what folder do the direct beam shots exist?: ')
else:
image_dir = args['inp'][0]
#if Utils.checkCluster():
if BLspec.checkCluster():
#Creates the input dict and passes it to the Handler.
Handler(createInput(image_dir,logger),logger=logger)
else:
#Connect to the cluster and rerun this script if not launched on computer cluster.
RunCluster(image_dir,logger=logger)
def __init__(self, input, output=None, logger=None):
logger.info('LabelitPP.__init__')
self.st = time.time()
self.input = input
self.output = output
self.logger = logger
self.working_dir = self.input[0].get('dir', os.getcwd())
self.gui = self.input[0].get('gui', True)
self.test = self.input[0].get('test', False)
self.clean = self.input[0].get('clean', True)
self.controller_address = self.input[0].get('control', False)
self.verbose = self.input[0].get('verbose', False)
#Number of Labelit iterations to run. (Default is 4) added 2 more to test new Labelit options
self.iterations = 6
#Set times for processes. 'False' to disable.
self.stats_timer = 180
self.labelit_timer = 120
self.labelitpp_timer = False
self.labelit_input = False
self.labelit_log = {}
self.labelit_log['0'] = []
self.labelit_results = {}
self.labelitpp_results = False
self.labelit_jobs = {}
self.labelit_summary = False
self.labelit_failed = False
self.failed = False
self.pp_jobs = {}
self.pids = {}
#Labelit settings
self.index_number = False
self.spacegroup = 'None'
self.min_spots = False
self.ignore_user_cell = False
self.ignore_user_SG = False
self.blank_image = False
self.pseudotrans = False
self.min_good_spots = False
self.twotheta = False
self.multiproc = True
#For rerunning Labelit when it does not index correctly with a pair.
self.cycle = 0
if self.input[0].has_key('run'):
#Variables I call in more than one place
self.total = self.input[0].get('run').get('total')
#For determining detector type. Should move to rapd_site probably.
if self.input[0].get('run').get('fullname')[-3:] == 'cbf':
if float(self.input[0].get('run').get('x_beam')) > 200.0:
self.vendortype = 'Pilatus-6M'
else:
self.vendortype = 'ADSC-HF4M'
else:
self.vendortype = 'ADSC'
"""
#if self.input[0].get('run').get('fullname')[-3:] == 'cbf':
if float(self.input[0].get('run').get('x_beam')) > 200.0:
self.pilatus = True
else:
self.pilatus = False
"""
else:
self.failed = True
#******BEAMLINE SPECIFIC*****
#self.cluster_use = Utils.checkCluster()
self.cluster_use = BLspec.checkCluster()
#******BEAMLINE SPECIFIC*****
if self.test:
self.clean = False
Process.__init__(self, name='LabelitPP')
self.start()
def __init__(self, input, output=None, logger=None):
logger.info('LabelitPP.__init__')
self.st = time.time()
self.input = input
self.output = output
self.logger = logger
self.working_dir = self.input[0].get('dir',os.getcwd())
self.gui = self.input[0].get('gui',True)
self.test = self.input[0].get('test',False)
self.clean = self.input[0].get('clean',True)
self.controller_address = self.input[0].get('control',False)
self.verbose = self.input[0].get('verbose',False)
#Number of Labelit iterations to run. (Default is 4) added 2 more to test new Labelit options
self.iterations = 6
#Set times for processes. 'False' to disable.
self.stats_timer = 180
self.labelit_timer = 120
self.labelitpp_timer = False
self.labelit_input = False
self.labelit_log = {}
self.labelit_log['0'] = []
self.labelit_results = {}
self.labelitpp_results = False
self.labelit_jobs = {}
self.labelit_summary = False
self.labelit_failed = False
self.failed = False
self.pp_jobs = {}
self.pids = {}
#Labelit settings
self.index_number = False
self.spacegroup = 'None'
self.min_spots = False
self.ignore_user_cell = False
self.ignore_user_SG = False
self.blank_image = False
self.pseudotrans = False
self.min_good_spots = False
self.twotheta = False
self.multiproc = True
#For rerunning Labelit when it does not index correctly with a pair.
self.cycle = 0
if self.input[0].has_key('run'):
#Variables I call in more than one place
self.total = self.input[0].get('run').get('total')
#For determining detector type. Should move to rapd_site probably.
if self.input[0].get('run').get('fullname')[-3:] == 'cbf':
if float(self.input[0].get('run').get('x_beam')) > 200.0:
self.vendortype = 'Pilatus-6M'
else:
self.vendortype = 'ADSC-HF4M'
else:
self.vendortype = 'ADSC'
"""
#if self.input[0].get('run').get('fullname')[-3:] == 'cbf':
if float(self.input[0].get('run').get('x_beam')) > 200.0:
self.pilatus = True
else:
self.pilatus = False
"""
else:
self.failed = True
#******BEAMLINE SPECIFIC*****
#self.cluster_use = Utils.checkCluster()
self.cluster_use = BLspec.checkCluster()
#******BEAMLINE SPECIFIC*****
if self.test:
self.clean = False
Process.__init__(self,name='LabelitPP')
self.start()
def __init__(self, input, logger=None):
logger.info('AutoMolRep.__init__')
self.st = time.time()
self.input = input
self.logger = logger
#Setting up data input
self.setup = self.input[1]
self.data = self.input[2]
self.preferences = self.input[3]
self.controller_address = self.input[-1]
#For testing individual modules
self.test = False
#Removes junk files and directories at end.
self.clean = False
#Calculate ADF for all solutions
self.adf = True
self.verbose = True
#variables to set
#self.phaser_timer = 600 #Timer will be double for full Phaser
self.phaser_timer = False
self.phaser_results = {}
self.phaser_jobs = []
self.output = {}
self.cell_summary = False
self.pdb_summary = False
self.pdb_percent = False
self.percent = False
self.tooltips = False
self.cell2 = False
self.solvent_content = False
self.input_sg = False
self.pdb_code = False
self.run_before = False
self.dres = False
self.large_cell = False
self.sample_type = self.preferences.get('sample_type','Protein')
self.datafile = Utils.convertUnicode(self,self.data.get('original').get('mtz_file',None))
if self.datafile == None:
self.datafile = Utils.convertUnicode(self,self.preferences.get('request').get('input_sca'))
self.nmol = self.preferences.get('request').get('nmol',False)
#Used for printing summary html
self.pdb_name = self.preferences.get('request').get('pdb_name',False)
if self.pdb_name == None:
self.pdb_name = False
self.input_pdb = Utils.convertUnicode(self,self.preferences.get('request').get('pdb',None))
if self.input_pdb == None:
self.input_pdb = Utils.convertUnicode(self,self.preferences.get('request').get('pdb_code',None))
#Used in SummaryCell for label.
if self.input_pdb != None:
self.pdb_code = True
#Check if running from beamline and turn off testing if I forgot to.
if self.preferences.get('request').has_key('request_type'):
self.gui = True
self.test = False
self.verbose = False
else:
self.gui = False
#******BEAMLINE SPECIFIC*****
#self.cluster_use = Utils.checkCluster()
self.cluster_use = BLspec.checkCluster()
#******BEAMLINE SPECIFIC*****
Process.__init__(self,name='AutoMolRep')
#starts the new process
self.start()
