def get_spotfinder_data(self, params):
pointdata = []
test_pattern = False
if (
test_pattern is True
and self.raw_image.__class__.__name__.find("CSPadDetector") >= 0
):
key_count = -1
for key, asic in self.raw_image._tiles.items():
key_count += 1
focus = asic.focus()
for slow in range(0, focus[0], 20):
for fast in range(0, focus[1], 20):
slowpic, fastpic = self.flex_image.tile_readout_to_picture(
key_count, slow, fast
)
mr1, mr2 = self.picture_fast_slow_to_map_relative(
fastpic, slowpic
)
pointdata.append((mr1, mr2, {"data": key}))
elif self.raw_image.__class__.__name__.find("CSPadDetector") >= 0:
from cxi_xdr_xes.cftbx.spotfinder.speckfinder import spotfind_readout
key_count = -1
for key, asic in self.raw_image._tiles.items():
key_count += 1
indexing = spotfind_readout(
readout=asic, peripheral_margin=params.spotfinder.peripheral_margin
)
for spot in indexing:
slow = int(round(spot[0]))
fast = int(round(spot[1]))
slowpic, fastpic = self.flex_image.tile_readout_to_picture(
key_count, slow, fast
)
mr1, mr2 = self.picture_fast_slow_to_map_relative(fastpic, slowpic)
pointdata.append((mr1, mr2, {"data": key}))
else:
from spotfinder.command_line.signal_strength import master_params
working_params = master_params.fetch(
sources=[]
) # placeholder for runtime mods
working_params.show(expert_level=1)
distl_params = working_params.extract()
spotfinder, frameno = self.raw_image.get_spotfinder(distl_params)
spots = spotfinder.images[frameno]["spots_total"]
for spot in spots:
mr = self.picture_fast_slow_to_map_relative(
spot.max_pxl_y() + 0.5, spot.max_pxl_x() + 0.5
)
# spot.ctr_mass_y() + 0.5, spot.ctr_mass_x() + 0.5)
pointdata.append(mr)
return pointdata
def get_initial_cxi_scope():
from spotfinder.command_line.signal_strength import master_params
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
object1 = argument_interpreter.process(arg="distl.detector_tiling=%s" %
run3_cxi_limits().as_string())
working_params = master_params.fetch(sources=[object1])
return working_params.extract()
def run(args, command_name="distl.image_viewer"):
help_str = """Same as distl.signal_strength (type that command for help) except that
the image_viewer starts up an interactive GUI to visualize spotfinder spots.
"""
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
working_params = master_params.format(python_object=params)
#working_params.show(expert_level=1)
#Now actually run the program logic
from spotfinder.applications import image_viewer as app_image_viewer
modeler = app_image_viewer.run_signal_strength_class(
params=working_params.extract())
modeler.view()
def get_initial_cxi_scope():
from spotfinder.command_line.signal_strength import master_params
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
object1 = argument_interpreter.process(arg=
"distl.detector_tiling=%s"%run3_cxi_limits().as_string())
working_params = master_params.fetch(sources=[object1])
return working_params.extract()
def run(args, command_name="distl.image_viewer"):
help_str="""Same as distl.signal_strength (type that command for help) except that
the image_viewer starts up an interactive GUI to visualize spotfinder spots.
"""
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
working_params = master_params.format(python_object=params)
#working_params.show(expert_level=1)
#Now actually run the program logic
from spotfinder.applications import image_viewer as app_image_viewer
modeler = app_image_viewer.run_signal_strength_class(params=working_params.extract())
modeler.view()
def get_spotfinder_data(self, params):
pointdata = []
test_pattern = False
if test_pattern is True and self.raw_image.__class__.__name__.find("CSPadDetector") >= 0:
key_count = -1
for key, asic in self.raw_image._tiles.iteritems():
key_count += 1
focus = asic.focus()
for slow in xrange(0,focus[0],20):
for fast in xrange(0,focus[1],20):
slowpic,fastpic = self.flex_image.tile_readout_to_picture(key_count,slow,fast)
mr1,mr2 = self.picture_fast_slow_to_map_relative(fastpic,slowpic)
pointdata.append((mr1,mr2,{"data":key}))
elif (self.raw_image.__class__.__name__.find("CSPadDetector") >= 0):
from cxi_xdr_xes.cftbx.spotfinder.speckfinder import spotfind_readout
key_count = -1
for key, asic in self.raw_image._tiles.iteritems():
key_count += 1
indexing = spotfind_readout(
readout=asic,
peripheral_margin=params.spotfinder.peripheral_margin)
for spot in indexing:
slow = int(round(spot[0]))
fast = int(round(spot[1]))
slowpic,fastpic = self.flex_image.tile_readout_to_picture(key_count,slow,fast)
mr1,mr2 = self.picture_fast_slow_to_map_relative(fastpic,slowpic)
pointdata.append((mr1,mr2,{"data":key}))
else:
from spotfinder.command_line.signal_strength import master_params
working_params = master_params.fetch(sources = []) #placeholder for runtime mods
working_params.show(expert_level=1)
distl_params = working_params.extract()
spotfinder,frameno = self.raw_image.get_spotfinder(distl_params)
spots = spotfinder.images[frameno]["spots_total"]
for spot in spots:
mr = self.picture_fast_slow_to_map_relative(
spot.max_pxl_y() + 0.5, spot.max_pxl_x() + 0.5)
# spot.ctr_mass_y() + 0.5, spot.ctr_mass_x() + 0.5)
pointdata.append(mr)
return pointdata
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 run(args, command_name="distl.mp_spotfinder_server_read_file"):
help_str = """Multiprocessing server to find Bragg spots & quantify signal strength.
Full documentation: http://cci.lbl.gov/publications/download/ccn_jul2010_page18.pdf
Allowed parameters:
"""
if (len(args) >= 1
and args[0] in ["H", "h", "-H", "-h", "help", "--help", "-help"]):
print("usage: %s [parameter=value ...]" % command_name)
print("example: %s distl.port=8125 distl.processors=8" % command_name)
print(help_str)
return
else:
print(help_str)
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
for arg in args:
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()
working_params = master_params.format(python_object=params)
#working_params.show()
screen = 100
for D in working_params.all_definitions():
fp = D.object.full_path()
if fp in ["distl.image", "distl.verbose", "distl.pdf_output"]: continue
name = " %s=%s" % (D.object.full_path(), D.object.extract())
help = D.object.help
if D.object.expert_level > 1: continue
if len(name) + len(help) < screen and len(name) < 36:
print("%-36s" % name, "[%s]" % help)
else:
print("%-36s" % name, end=' ')
tokens = ("[%s]" % help).split()
reserve = min(screen - 36, screen - len(name))
while len(tokens) > 0:
reserve -= len(tokens[0])
if len(tokens[0]) > (screen - 36): break
while reserve < 0:
print()
print(" " * 36, end=' ')
reserve = screen - 36
print(tokens.pop(0), end=' ')
print()
#Now actually run the program logic
from spotfinder.servers import mp_spotfinder_server_read_file as srv
NUMBER_OF_PROCESSES = params.distl.processors
srv.generate_common_parameters(working_params)
server_address = ('', params.distl.port)
srv.image_request_handler.protocol_version = "HTTP/1.0"
print("Serving %d-process HTTP on" % NUMBER_OF_PROCESSES,
server_address[0], "port", server_address[1], "...")
print("To exit press Ctrl-C")
srv.runpool(server_address, NUMBER_OF_PROCESSES, srv.image_request_handler)
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.mp_spotfinder_server_read_file"):
help_str="""Multiprocessing server to find Bragg spots & quantify signal strength.
Full documentation: http://cci.lbl.gov/publications/download/ccn_jul2010_page18.pdf
Allowed parameters:
"""
if (len(args)>=1 and args[0] in ["H","h","-H","-h","help","--help","-help"]):
print "usage: %s [parameter=value ...]" % command_name
print "example: %s distl.port=8125 distl.processors=8"%command_name
print help_str
return
else: print help_str
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="distl")
for arg in args:
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()
working_params = master_params.format(python_object=params)
#working_params.show()
screen = 100
for D in working_params.all_definitions():
fp = D.object.full_path()
if fp in ["distl.image", "distl.verbose", "distl.pdf_output"]: continue
name = " %s=%s"%(D.object.full_path(),D.object.extract())
help = D.object.help
if D.object.expert_level > 1: continue
if len(name) + len(help) < screen and len(name) < 36:
print "%-36s"%name,"[%s]"%help
else:
print "%-36s"%name,
tokens = ("[%s]"%help).split()
reserve = min(screen-36,screen-len(name))
while len(tokens)>0:
reserve -= len(tokens[0])
if len(tokens[0])>(screen-36):break
while reserve<0:
print
print " "*36,
reserve = screen-36
print tokens.pop(0),
print
#Now actually run the program logic
from spotfinder.servers import mp_spotfinder_server_read_file as srv
NUMBER_OF_PROCESSES = params.distl.processors
srv.generate_common_parameters(working_params)
server_address = ('', params.distl.port)
srv.image_request_handler.protocol_version = "HTTP/1.0"
print "Serving %d-process HTTP on"%NUMBER_OF_PROCESSES, server_address[0], "port", server_address[1], "..."
print "To exit press Ctrl-C"
srv.runpool(server_address,NUMBER_OF_PROCESSES,srv.image_request_handler)
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()
