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_distl(self, params):
""" Performs a quick DISTL spotfinding and returns Bragg spots information.
"""
from spotfinder.applications import signal_strength
# run DISTL spotfinder
with misc.Capturing() as distl_output:
Org = signal_strength.run_signal_strength(params)
# Extract relevant spotfinding info
for frame in Org.S.images.keys():
saturation = Org.Files.imageindex(frame).saturation
Bragg_spots = [flex.sum(spot.wts) for spot in Org.S.images[frame]['inlier_spots']]
return Bragg_spots
def run_distl(self, params):
""" Performs a quick DISTL spotfinding and returns Bragg spots information.
"""
from spotfinder.applications import signal_strength
# run DISTL spotfinder
with misc.Capturing() as distl_output:
Org = signal_strength.run_signal_strength(params)
# Extract relevant spotfinding info
for frame in Org.S.images.keys():
saturation = Org.Files.imageindex(frame).saturation
Bragg_spots = [
flex.sum(spot.wts)
for spot in Org.S.images[frame]['inlier_spots']
]
return Bragg_spots
def run_one(path, *command_line, **kwargs):
args = ["distl.image=%s"%path,
"distl.res.outer=2.1",
"distl.detector_format_version=CXI 5.1",
]
horizons_phil = cxi_phil.cxi_versioned_extract(
copy.deepcopy(args),list(command_line))
global parameters
parameters.horizons_phil = horizons_phil
from spotfinder.applications import signal_strength
info = signal_strength.run_signal_strength(horizons_phil)
if kwargs.get("display",False):
work = wrapper_of_callback(info)
work.display_with_callback(path)
def run_one(path, *command_line, **kwargs):
args = ["distl.image=%s"%path,
"distl.res.outer=2.1",
"distl.detector_format_version=CXI 5.1",
]
horizons_phil = cxi_phil.cxi_versioned_extract(
copy.deepcopy(args),list(command_line))
global parameters
parameters.horizons_phil = horizons_phil
from spotfinder.applications import signal_strength
info = signal_strength.run_signal_strength(horizons_phil)
if kwargs.get("display",False):
work = wrapper_of_callback(info)
work.display_with_callback(path)
def run_distl(self, params):
""" Performs a quick DISTL spotfinding and returns Bragg spots information.
"""
from spotfinder.applications import signal_strength
# run DISTL spotfinder
try:
with util.Capturing() as distl_output:
Org = signal_strength.run_signal_strength(params)
except NotImplementedError as e:
print("NOT IMPLEMENTED ERROR FOR {}".format(self.img))
# Extract relevant spotfinding info
for frame in Org.S.images.keys():
saturation = Org.Files.imageindex(frame).saturation
Bragg_spots = [
flex.sum(spot.wts)
for spot in Org.S.images[frame]['inlier_spots']
]
return Bragg_spots
def run(args, verbose=False):
from libtbx.utils import Sorry
import os
from spotfinder.command_line.signal_strength import master_params
#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
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
from spotfinder.servers.apache_utils import LongLineSimpleNode as SimpleNode
from spotfinder.applications import signal_strength
logger = StringIO()
top = SimpleNode("spotfinder")
try:
for key in args.keys():
arg = "%s=%s" % (key, args.get(key, ""))
command_line_params = argument_interpreter.process(arg=arg)
phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
top.child(SimpleNode(tag="file_name", contents=params.distl.image))
if not os.path.isfile(params.distl.image):
raise Sorry("%s not a readable file" % params.distl.image)
Org = signal_strength.run_signal_strength(params)
assert len(list(Org.S.images.keys())) == 1 # there is only one image
key = list(Org.S.images.keys())[0]
# List of spots between specified high- and low-resolution limits
if Org.S.images[key].has_extended_key('lo_pass_resolution_spots'):
spots = Org.S.images[key]['lo_pass_resolution_spots']
elif Org.S.images[key].has_extended_key('inlier_spots'):
spots = Org.S.images[key]['inlier_spots']
else:
spots = []
if Org.S.images[key].has_extended_key('N_spots_total'):
total = "%d" % Org.S.images[key]["N_spots_total"]
else:
total = "0"
if Org.S.images[key].has_extended_key('resolution'):
resolution = Org.S.images[key]['resolution']
elif Org.S.images[key].has_extended_key('distl_resolution'):
resolution = Org.S.images[key]['distl_resolution']
else:
resolution = 0.0
top.child(SimpleNode(tag="total_spots", contents=total))
top.child(SimpleNode(tag="good_spots", contents="%d" % len(spots)))
top.child(SimpleNode(tag="resolution", contents="%.3f" % resolution))
if len(Org.S.reporters[key]) == 0:
top.child(SimpleNode(tag="total_integrated", contents="0"))
top.child(SimpleNode(tag="mean_isigi", contents="0"))
else:
reporter = Org.S.reporters[key][-1]
normalizer = reporter.weights.sum()
summation = 0
for x in range(reporter.S_table_rows):
summation += reporter.weights[x] * reporter.MeanIsigI[x]
top.child(
SimpleNode(tag="mean_isigi",
contents="%.3f" % (summation / normalizer)))
integrated = reporter.Integrated.sum()
top.child(
SimpleNode(tag="integrated", contents="%.3f" % integrated))
except Exception as e:
top.child(SimpleNode(tag="status", contents=repr(e)))
top.emit(logger)
return logger.getvalue()
top.child(SimpleNode(tag="status", contents="OK"))
top.emit(logger)
return logger.getvalue()
def run(args, command_name="distl.signal_strength"):
help_str = """explanation:
Local background and background standard deviation are determined.
Pixels are classified as signal if > minimum_signal_height sigmas above background.
Signals are chosen as spot maxima if > minimum_spot_height sigmas above background.
Spots are grown around the maxima, and retained if they fit minimal area criteria.
Total number of candidates at this stage is reported as "Spot Total"
Ice rings are eliminated by at least two different algorithms (rings of high pixel
values and rings of high spot count).
Resolution filters are applied if given on the command line.
Total number of candidates at this stage is reported as "In-Resolution Total"
Other spot-quality filters are applied to give the number of "Good Bragg Candidates".
Method 1 Resolution is a published legacy algorithm (Zhang et al, 2006) no longer used.
Method 2 Resolution reflects drop off of spot count as a function of resolution shell,
but is overridden by command line input of distl.res.outer
Signal strength of the Good Bragg Candidates is then presented as integrated area of
the spot above local background, expressed in pixel-analog/digital units.
Very verbose output is available by setting distl.verbose=True
Full documentation: http://cci.lbl.gov/publications/download/ccn_jul2010_page18.pdf
"""
if (len(args) == 0
or args[0] in ["H", "h", "-H", "-h", "help", "--help", "-help"]):
print "usage: %s image_filename [parameter=value ...]" % command_name
print "example: %s lysozyme_001.img distl.res.outer=2.0 distl.res.inner=6.0 distl.minimum_spot_area=8" % command_name
master_params.show(attributes_level=1, expert_level=1)
print help_str
return
print "%s: characterization of candidate Bragg spots" % command_name
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
image_file_name = None
moving_pdb_file_name = None
for arg in args:
if (os.path.isfile(arg)):
if (image_file_name is None): image_file_name = arg
else: raise Sorry("Too many file names.")
else:
try:
command_line_params = argument_interpreter.process(arg=arg)
except KeyboardInterrupt:
raise
except Exception:
raise 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()
def raise_missing(what):
raise Sorry("""\
Missing file name for %(what)s structure:
Please add
%(what)s=file_name
to the command line to specify the %(what)s structure.""" % vars())
if (image_file_name is None):
if (params.distl.image is None): raise_missing("file name")
else:
params.distl.image = image_file_name
print "#Parameters used:"
print "#phil __ON__"
print
working_params = master_params.format(python_object=params)
working_params.show(expert_level=1)
print
print "#phil __OFF__"
print
#Now actually run the program logic
from spotfinder.applications import signal_strength
return signal_strength.run_signal_strength(working_params.extract())
def run(args, command_name="distl.signal_strength"):
help_str="""explanation:
Local background and background standard deviation are determined.
Pixels are classified as signal if > minimum_signal_height sigmas above background.
Signals are chosen as spot maxima if > minimum_spot_height sigmas above background.
Spots are grown around the maxima, and retained if they fit minimal area criteria.
Total number of candidates at this stage is reported as "Spot Total"
Ice rings are eliminated by at least two different algorithms (rings of high pixel
values and rings of high spot count).
Resolution filters are applied if given on the command line.
Total number of candidates at this stage is reported as "In-Resolution Total"
Other spot-quality filters are applied to give the number of "Good Bragg Candidates".
Method 1 Resolution is a published legacy algorithm (Zhang et al, 2006) no longer used.
Method 2 Resolution reflects drop off of spot count as a function of resolution shell,
but is overridden by command line input of distl.res.outer
Signal strength of the Good Bragg Candidates is then presented as integrated area of
the spot above local background, expressed in pixel-analog/digital units.
Very verbose output is available by setting distl.verbose=True
Full documentation: http://cci.lbl.gov/publications/download/ccn_jul2010_page18.pdf
"""
if (len(args) == 0 or args[0] in ["H","h","-H","-h","help","--help","-help"]):
print "usage: %s image_filename [parameter=value ...]" % command_name
print "example: %s lysozyme_001.img distl.res.outer=2.0 distl.res.inner=6.0 distl.minimum_spot_area=8"%command_name
master_params.show(attributes_level=1,expert_level=1)
print help_str
return
print "%s: characterization of candidate Bragg spots"%command_name
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
image_file_name = None
moving_pdb_file_name = None
for arg in args:
if (os.path.isfile(arg)):
if (image_file_name is None): image_file_name = arg
else: raise Sorry("Too many file names.")
else:
try: command_line_params = argument_interpreter.process(arg=arg)
except KeyboardInterrupt: raise
except Exception: raise 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()
def raise_missing(what):
raise Sorry("""\
Missing file name for %(what)s structure:
Please add
%(what)s=file_name
to the command line to specify the %(what)s structure.""" % vars())
if (image_file_name is None):
if (params.distl.image is None): raise_missing("file name")
else:
params.distl.image = image_file_name
print "#Parameters used:"
print "#phil __ON__"
print
working_params = master_params.format(python_object=params)
working_params.show(expert_level=1)
print
print "#phil __OFF__"
print
#Now actually run the program logic
from spotfinder.applications import signal_strength
return signal_strength.run_signal_strength(working_params.extract())
def run(args, verbose=False):
from libtbx.utils import Sorry
import os
from spotfinder.command_line.signal_strength import master_params
#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
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
from spotfinder.servers.apache_utils import LongLineSimpleNode as SimpleNode
from spotfinder.applications import signal_strength
logger = StringIO.StringIO()
top = SimpleNode("spotfinder")
try:
for key in args.keys():
arg = "%s=%s"%(key,args.get(key,""))
command_line_params = argument_interpreter.process(arg=arg)
phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
top.child(SimpleNode(tag="file_name",contents=params.distl.image))
if not os.path.isfile(params.distl.image):
raise Sorry("%s not a readable file"%params.distl.image)
Org = signal_strength.run_signal_strength(params)
assert len(Org.S.images.keys())==1 # there is only one image
key = Org.S.images.keys()[0]
# List of spots between specified high- and low-resolution limits
if Org.S.images[key].has_key('lo_pass_resolution_spots'):
spots = Org.S.images[key]['lo_pass_resolution_spots']
elif Org.S.images[key].has_key('inlier_spots'):
spots = Org.S.images[key]['inlier_spots']
else:
spots = []
if Org.S.images[key].has_key('N_spots_total'):
total = "%d"%Org.S.images[key]["N_spots_total"]
else:
total = "0"
if Org.S.images[key].has_key('resolution'):
resolution = Org.S.images[key]['resolution']
elif Org.S.images[key].has_key('distl_resolution'):
resolution = Org.S.images[key]['distl_resolution']
else:
resolution = 0.0
top.child(SimpleNode(tag="total_spots",contents=total))
top.child(SimpleNode(tag="good_spots",contents="%d"%len(spots)))
top.child(SimpleNode(tag="resolution",contents="%.3f"%resolution))
if len(Org.S.reporters[key])==0:
top.child(SimpleNode(tag="total_integrated",contents="0"))
top.child(SimpleNode(tag="mean_isigi",contents="0"))
else:
reporter = Org.S.reporters[key][-1]
normalizer = reporter.weights.sum()
summation = 0;
for x in xrange(reporter.S_table_rows):
summation += reporter.weights[x] * reporter.MeanIsigI[x]
top.child(SimpleNode(tag="mean_isigi",contents="%.3f"%(summation/normalizer)))
integrated = reporter.Integrated.sum()
top.child(SimpleNode(tag="integrated",contents="%.3f"%integrated))
except Exception,e:
top.child(SimpleNode(tag="status",contents=repr(e)))
top.emit(logger)
return logger.getvalue()