def dxtbx_spotfinder_factory(phil_params): from dxtbx.format.Registry import Registry reader = Registry.find(phil_params.distl.image[0]) from spotfinder.dxtbx_toolbox.practical_heuristics import heuristics_base Spotfinder = heuristics_base(phil_params) return Spotfinder
def dxtbx_spotfinder_factory(phil_params):
import dxtbx.format.Registry
reader = dxtbx.format.Registry.get_format_class_for_file(
phil_params.distl.image[0])
from spotfinder.dxtbx_toolbox.practical_heuristics import heuristics_base
Spotfinder = heuristics_base(phil_params)
return Spotfinder
def spotfinder_factory(absrundir,frames,phil_params):
local_frames=frames.frames()
A = frames.images[0]
#A.readHeader()--deprecate this because it squashes any overrides
# from dataset_preferences processed in imagefiles.py
pd = {'directory':frames.filenames.FN[0].cwd,
'template': frames.filenames.FN[0].template,
'identifier':frames.filenames.FN[0].fileroot,
'vendortype':A.vendortype,
'binning':'%d'%A.bin,
'distance':'%f'%A.distance,
'wavelength':'%f'%A.wavelength,
'deltaphi':'%f'%A.deltaphi,
}
#temp values for getting coordinate convention
pd['pixel_size']='%f'%A.pixel_size
pd['size1']='%f'%A.size1
pd['size2']='%f'%A.size2
pd['ybeam'] = '%f'%A.beamy
pd['xbeam'] = '%f'%A.beamx
try:
pd['twotheta'] = '%f'%A.twotheta
except Exception:
pd['twotheta'] = '0.0'
from spotfinder.applications.practical_heuristics import heuristics_base
Spotfinder = heuristics_base(pd,phil_params)
from libtbx import easy_mp
def run_spotfinder(args):
assert len(args) == 2
framenumber, frames = args
try:
assert Spotfinder.images.has_key(framenumber)
except Exception:
Spotfinder.register_frames(framenumber,frames)
if phil_params.spotfinder_verbose: Spotfinder.show()
return Spotfinder
iterable = [(framenumber, frames) for framenumber in local_frames]
results = easy_mp.parallel_map(
func=run_spotfinder,
iterable=iterable,
processes=phil_params.distl.nproc,
method="multiprocessing",
preserve_order=True
)
for result in results:
Spotfinder.images.update(result.images)
return Spotfinder
def get_spotfinder(self, distl_params
): #following heuristics_base.register_frames() example
#application-specific adjustments to parameters
#XXX this should probably be a deep copy of parameters.
if distl_params.distl.res.inner != None:
distl_params.distl_lowres_limit = distl_params.distl.res.inner
if distl_params.distl.res.outer != None:
distl_params.force_method2_resolution_limit = distl_params.distl.res.outer
distl_params.distl_highres_limit = distl_params.distl.res.outer
distl_params.distl_force_binning = False
distl_params.distl_permit_binning = False
distl_params.wedgelimit = 1
distl_params.spotfinder_header_tests = False
#unusual location for min spot area tests...
from iotbx.detectors.context.config_detector import beam_center_convention_from_image_object
beam_center_convention_from_image_object(self, distl_params)
# end special min spot area treatment
from spotfinder.applications.practical_heuristics import heuristics_base
from spotfinder.diffraction.imagefiles import file_names
class empty:
pass
E = empty()
E.argv = ["Empty", self.filename]
names = file_names(E)
this_frame = names.frames()[0]
process_dictionary = dict(
twotheta="%f" % self.twotheta,
ybeam="%f" % self.beamy,
xbeam="%f" % self.beamx,
distance="%f" % self.distance,
wavelength="%f" % self.wavelength,
template=[
item.template for item in names.FN if item.number == this_frame
][0],
)
Spotfinder = heuristics_base(process_dictionary, distl_params)
Spotfinder.images[this_frame] = Spotfinder.oneImage(
this_frame, Spotfinder.pd, self)
Spotfinder.determine_maxcell(this_frame, Spotfinder.pd)
Spotfinder.images[this_frame]['spotoutput']['relpath'] = self.filename
from spotfinder.applications.stats_distl import pretty_image_stats
pretty_image_stats(Spotfinder, this_frame)
return Spotfinder, this_frame
def get_spotfinder(self,distl_params): #following heuristics_base.register_frames() example
#application-specific adjustments to parameters
#XXX this should probably be a deep copy of parameters.
if distl_params.distl.res.inner!=None:
distl_params.distl_lowres_limit = distl_params.distl.res.inner
if distl_params.distl.res.outer!=None:
distl_params.force_method2_resolution_limit = distl_params.distl.res.outer
distl_params.distl_highres_limit = distl_params.distl.res.outer
distl_params.distl_force_binning = False
distl_params.distl_permit_binning = False
distl_params.wedgelimit = 1
distl_params.spotfinder_header_tests = False
#unusual location for min spot area tests...
from iotbx.detectors.context.config_detector import beam_center_convention_from_image_object
beam_center_convention_from_image_object(self,distl_params)
# end special min spot area treatment
from spotfinder.applications.practical_heuristics import heuristics_base
from spotfinder.diffraction.imagefiles import file_names
class empty:pass
E = empty()
E.argv = ["Empty",self.filename]
names = file_names(E)
this_frame = names.frames()[0]
process_dictionary = dict(twotheta = "%f"%self.twotheta,
ybeam = "%f"%self.beamy,
xbeam = "%f"%self.beamx,
distance = "%f"%self.distance,
wavelength = "%f"%self.wavelength,
template = [item.template for item in names.FN if item.number==this_frame][0],
)
Spotfinder = heuristics_base(process_dictionary,distl_params)
Spotfinder.images[this_frame] = Spotfinder.oneImage(this_frame,
Spotfinder.pd, self)
Spotfinder.determine_maxcell(this_frame,Spotfinder.pd)
Spotfinder.images[this_frame]['spotoutput']['relpath']=self.filename
from spotfinder.applications.stats_distl import pretty_image_stats
pretty_image_stats(Spotfinder,this_frame)
return Spotfinder,this_frame
def spotfinder_factory(absrundir, frames, phil_params):
local_frames = frames.frames()
A = frames.images[0]
#A.readHeader()--deprecate this because it squashes any overrides
# from dataset_preferences processed in imagefiles.py
pd = {
'directory': frames.filenames.FN[0].cwd,
'template': frames.filenames.FN[0].template,
'identifier': frames.filenames.FN[0].fileroot,
'vendortype': A.vendortype,
'binning': '%d' % A.bin,
'distance': '%f' % A.distance,
'wavelength': '%f' % A.wavelength,
'deltaphi': '%f' % A.deltaphi,
}
#temp values for getting coordinate convention
pd['pixel_size'] = '%f' % A.pixel_size
pd['size1'] = '%f' % A.size1
pd['size2'] = '%f' % A.size2
pd['ybeam'] = '%f' % A.beamy
pd['xbeam'] = '%f' % A.beamx
try:
pd['twotheta'] = '%f' % A.twotheta
except Exception:
pd['twotheta'] = '0.0'
from spotfinder.applications.practical_heuristics import heuristics_base
Spotfinder = heuristics_base(pd, phil_params)
for framenumber in local_frames:
try:
assert framenumber in Spotfinder.images
except Exception:
Spotfinder.register_frames(framenumber, frames)
if phil_params.spotfinder_verbose: Spotfinder.show()
return Spotfinder
def spotfinder_factory(absrundir,frames,phil_params):
local_frames=frames.frames()
A = frames.images[0]
#A.readHeader()--deprecate this because it squashes any overrides
# from dataset_preferences processed in imagefiles.py
pd = {'directory':frames.filenames.FN[0].cwd,
'template': frames.filenames.FN[0].template,
'identifier':frames.filenames.FN[0].fileroot,
'vendortype':A.vendortype,
'binning':'%d'%A.bin,
'distance':'%f'%A.distance,
'wavelength':'%f'%A.wavelength,
'deltaphi':'%f'%A.deltaphi,
}
#temp values for getting coordinate convention
pd['pixel_size']='%f'%A.pixel_size
pd['size1']='%f'%A.size1
pd['size2']='%f'%A.size2
pd['ybeam'] = '%f'%A.beamy
pd['xbeam'] = '%f'%A.beamx
try:
pd['twotheta'] = '%f'%A.twotheta
except Exception:
pd['twotheta'] = '0.0'
from spotfinder.applications.practical_heuristics import heuristics_base
Spotfinder = heuristics_base(pd,phil_params)
for framenumber in local_frames:
try:
assert Spotfinder.images.has_key(framenumber)
except Exception:
Spotfinder.register_frames(framenumber,frames)
if phil_params.spotfinder_verbose: Spotfinder.show()
return Spotfinder
