def run(args, verbose=False):
from libtbx.utils import Sorry
import os
from spotfinder.command_line.signal_strength import master_params
from spotfinder.servers import LoggingFramework
# For the Apache server version, do not allow site, user, or dataset preferences
# all parameters are to be passed in through the http: query line
logfile = LoggingFramework()
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(home_scope="distl")
for key in args.keys():
arg = "%s=%s" % (key, args.get(key, ""))
try:
command_line_params = argument_interpreter.process(arg=arg)
except Exception:
return str(Sorry("Unknown file or keyword: %s" % arg))
else:
phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
# working_params.show()
if not os.path.isfile(params.distl.image):
return str(Sorry("%s is not a readable file" % params.distl.image))
print "Image: %s" % params.distl.image
from spotfinder.applications import signal_strength
try:
signal_strength.run_signal_strength(params)
except Exception:
import traceback
logger = StringIO.StringIO()
logger.write("Sorry, can't process %s. Please contact authors.\n" % params.distl.image)
traceback.print_exc(file=logger)
return str(Sorry(logger.getvalue()))
return logfile.getvalue()
def run(args, verbose=False):
from libtbx.utils import Sorry
import os
from spotfinder.command_line.signal_strength import master_params
from spotfinder.servers import LoggingFramework
#For the Apache server version, do not allow site, user, or dataset preferences
#all parameters are to be passed in through the http: query line
logfile = LoggingFramework()
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
for key in args.keys():
arg = "%s=%s" % (key, args.get(key, ""))
try:
command_line_params = argument_interpreter.process(arg=arg)
except Exception:
return str(Sorry("Unknown file or keyword: %s" % arg))
else:
phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
#working_params.show()
if not os.path.isfile(params.distl.image):
return str(Sorry("%s is not a readable file" % params.distl.image))
print "Image: %s" % params.distl.image
from spotfinder.applications import signal_strength
try:
signal_strength.run_signal_strength(params)
except Exception:
import traceback
logger = StringIO()
logger.write("Sorry, can't process %s. Please contact authors.\n" %
params.distl.image)
traceback.print_exc(file=logger)
return str(Sorry(logger.getvalue()))
return logfile.getvalue()
def do_GET_run(self,
qs): #similar to the run() function in apache.py module
from libtbx.utils import Sorry
import os
from spotfinder.servers import LoggingFramework
base_params = copy.deepcopy(common_parameters_singleton)
argument_interpreter = base_params.command_line_argument_interpreter()
phil_objects = []
for key in qs.keys():
arg = "%s=%s" % (key, qs.get(key, "")[0])
try:
command_line_params = argument_interpreter.process(arg=arg)
except Exception:
return str(Sorry("Unknown file or keyword: %s" % arg))
else:
phil_objects.append(command_line_params)
working_params = base_params.fetch(sources=phil_objects)
params = working_params.extract()
#working_params.show()
if not os.path.isfile(params.distl.image):
return str(Sorry("%s is not a readable file" % params.distl.image))
print "Image: %s" % params.distl.image
logfile = LoggingFramework()
from spotfinder.applications import signal_strength
try:
signal_strength.run_signal_strength(params)
except Exception:
import traceback
logger = StringIO()
logger.write(
"Sorry, can't process %s. Please contact authors.\n" %
params.distl.image)
traceback.print_exc(file=logger)
return str(Sorry(logger.getvalue()))
return logfile.getvalue()
def do_GET_run(self,qs): #similar to the run() function in apache.py module
from libtbx.utils import Sorry
import os
from spotfinder.servers import LoggingFramework
base_params = copy.deepcopy(common_parameters_singleton)
argument_interpreter = base_params.command_line_argument_interpreter()
phil_objects = []
for key in qs.keys():
arg = "%s=%s"%(key,qs.get(key,"")[0])
try: command_line_params = argument_interpreter.process(arg=arg)
except Exception: return str(Sorry("Unknown file or keyword: %s" % arg))
else: phil_objects.append(command_line_params)
working_params = base_params.fetch(sources=phil_objects)
params = working_params.extract()
#working_params.show()
if not os.path.isfile(params.distl.image):
return str(Sorry("%s is not a readable file" % params.distl.image))
print "Image: %s"%params.distl.image
logfile = LoggingFramework()
from spotfinder.applications import signal_strength
try:
signal_strength.run_signal_strength(params)
except Exception:
import traceback
logger = StringIO.StringIO()
logger.write(
"Sorry, can't process %s. Please contact authors.\n"% params.distl.image)
traceback.print_exc(file=logger)
return str(Sorry( logger.getvalue() ))
return logfile.getvalue()
def run(args, verbose=False):
from libtbx.utils import Sorry
try:
from dials.array_family import flex
except ImportError:
return str(Sorry("DIALS is not configured"))
from iotbx.phil import parse
import os
from spotfinder.servers import LoggingFramework
from dials.array_family import flex
from dxtbx.model.experiment_list import ExperimentListFactory
phil_scope = parse("""
file_name = None
.type = str
frame_number = None
.type = int
stats = True
.type = bool
include scope dials.algorithms.spot_finding.factory.phil_scope
""",
process_includes=True)
#For the Apache server version, do not allow site, user, or dataset preferences
#all parameters are to be passed in through the http: query line
logfile = LoggingFramework()
phil_objects = []
for key in args.keys():
arg = "%s=%s" % (key, args.get(key, ""))
try:
phil_objects.append(parse(arg))
except Exception:
return str(Sorry("Unknown file or keyword: %s" % arg))
working_params = phil_scope.fetch(sources=phil_objects)
params = working_params.extract()
#working_params.show()
if not os.path.isfile(params.file_name):
return str(Sorry("%s is not a readable file" % params.file_name))
print "Image: %s\n" % params.file_name
try:
experiments = ExperimentListFactory.from_filenames([params.file_name])
assert len(experiments) == 1
if len(experiments[0].imageset
) > 0 and params.frame_number is not None:
print "Frame number", params.frame_number
experiments[0].imageset = experiments[0].imageset[
params.frame_number:params.frame_number + 1]
experiments[0].scan = experiments[0].imageset.get_scan()
reflections = flex.reflection_table.from_observations(
experiments, params)
if params.stats:
from dials.algorithms.spot_finding.per_image_analysis import stats_single_image
print stats_single_image(experiments[0].imageset,
reflections,
i=None,
resolution_analysis=True,
plot=False)
except Exception:
import traceback
logger = StringIO()
logger.write("Sorry, can't process %s. Please contact authors.\n" %
params.file_name)
traceback.print_exc(file=logger)
return str(Sorry(logger.getvalue())) + logfile.getvalue()
print "Found %d strong reflections" % len(reflections)
return logfile.getvalue()