def get_spot_convention(imagefile):
# Maybe 2 if RAXIS else 0..
return 2
from spotfinder.command_line.signal_strength import master_params
phil_params = master_params.extract()
imageobject = iotbx.detectors.ImageFactory(G["file"][start_frame])
beam_center_convention_from_image_object(imageobject, phil_params)
print "SPOT CONVENTION=", phil_params.spot_convention
return phil_params.spot_convention
def get_spot_convention(imagefile):
# Maybe 2 if RAXIS else 0..
return 2
from spotfinder.command_line.signal_strength import master_params
phil_params = master_params.extract()
imageobject = iotbx.detectors.ImageFactory(G["file"][start_frame])
beam_center_convention_from_image_object(imageobject, phil_params)
print "SPOT CONVENTION=", phil_params.spot_convention
return phil_params.spot_convention
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 initialize_viewer_properties(self, phil_parameters, verbose=True):
self._invert_beam_center = False
from iotbx.detectors.context.config_detector import \
beam_center_convention_from_image_object
bc = beam_center_convention_from_image_object(self, phil_parameters)
if verbose:
print "beam center convention: %d" % bc
# FIXME what about 2-4 & 6-7?
if (bc == 0):
self._invert_beam_center = True
self._invert_y = True
elif (bc == 1):
self._invert_y = False
elif (bc == 5):
self._invert_y = True
self.image_size_fast = self.size2 # width
self.image_size_slow = self.size1 # height
self.pixel_resolution = self.pixel_size
def initialize_viewer_properties(self,phil_parameters,verbose=True):
self._invert_beam_center = False
from iotbx.detectors.context.config_detector import \
beam_center_convention_from_image_object
bc = beam_center_convention_from_image_object(self,phil_parameters)
if verbose:
print "beam center convention: %d" % bc
# FIXME what about 2-4 & 6-7?
if (bc == 0) :
self._invert_beam_center = True
self._invert_y = True
elif (bc == 1) :
self._invert_y = False
elif (bc == 5) :
self._invert_y = True
self.image_size_fast = self.size2 # width
self.image_size_slow = self.size1 # height
self.pixel_resolution = self.pixel_size
def site_modifications(self,imageobject,filenameobject):
from iotbx.detectors.context.config_detector\
import beam_center_convention_from_image_object
beam_center_convention = beam_center_convention_from_image_object(imageobject,self.phil_params)
#we may elect to override the beam position globally for LABELIT.
#Case I. The user has provided a tuple of floats, superceding all else
if self.phil_params.autoindex_override_beam != None:
imageobject.parameters['BEAM_CENTER_X'],\
imageobject.parameters['BEAM_CENTER_Y']=\
self.phil_params.autoindex_override_beam
imageobject.beam_center_reference_frame = "imageblock"
#Case II. An XY convention has been defined.
elif beam_center_convention != 0:
convert_beam_instrument_to_imageblock(imageobject,beam_center_convention)
if self.phil_params.autoindex_override_distance != None:
imageobject.parameters['DISTANCE']=self.phil_params.autoindex_override_distance
if self.phil_params.autoindex_override_wavelength != None:
imageobject.parameters['WAVELENGTH']=self.phil_params.autoindex_override_wavelength
if self.phil_params.autoindex_override_deltaphi != None:
if self.verbose:
print "Overriding deltaphi not fully supported: contact authors"
print "Altering deltaphi",(filenameobject.number-1)*self.phil_params.autoindex_override_deltaphi
imageobject.parameters['OSC_RANGE']=self.phil_params.autoindex_override_deltaphi
imageobject.parameters['OSC_START']=(filenameobject.number-1)*self.phil_params.autoindex_override_deltaphi
# override twotheta angle
if self.phil_params.autoindex_override_twotheta != None:
imageobject.parameters['TWOTHETA']=\
self.phil_params.autoindex_override_twotheta
if self.phil_params.image_specific_osc_start != None:
imageobject.parameters['OSC_START']= \
eval("(%s)(%d)"%(
self.phil_params.image_specific_osc_start,filenameobject.number))
#take care of unbinned Quantum 315
if (self.phil_params.distl_permit_binning and \
imageobject.size1 > 4000 and imageobject.vendortype=="ADSC") or \
self.phil_params.distl_force_binning:
imageobject.setBin(2)
self.phil_params.distl.minimum_spot_area = min(
self.phil_params.distl.minimum_spot_area,
self.phil_params.distl_binned_image_spot_size)
if imageobject.vendortype=="MARCCD":
#This section corrects for the fact that ESRF writes the mar ccd header
# with beam center in mm instead of pixels.
detector_center_in_mm = 0.5*imageobject.size1*imageobject.pixel_size
one_tenth_error = 0.1*detector_center_in_mm
#offset between given beam and detector center
import math
def distance(a,b):
return math.sqrt((a[0]-b[0])*(a[0]-b[0])+(a[1]-b[1])*(a[1]-b[1]))
offset1=distance( (detector_center_in_mm,detector_center_in_mm),
(imageobject.beamx,imageobject.beamy) )
if offset1>one_tenth_error:
newx = imageobject.beamx/imageobject.pixel_size
newy = imageobject.beamy/imageobject.pixel_size
#offset between corrected beam and detector center
offset2=distance( (detector_center_in_mm,detector_center_in_mm),
(newx,newy) )
if offset2<one_tenth_error:
imageobject.parameters['BEAM_CENTER_X'] = newx
imageobject.parameters['BEAM_CENTER_Y'] = newy
#Furthermore the x and y are transposed in the one example we've been given
convert_beam_instrument_to_imageblock(imageobject,
beam_center_convention,force=True)
if self.verbose:
print "Mar CCD image appears to have beam center %.2f %.2f in mm instead of pixels"%(
imageobject.beamx,imageobject.beamy)
def site_modifications(self,imageobject,filenameobject):
from iotbx.detectors.context.config_detector\
import beam_center_convention_from_image_object
beam_center_convention = beam_center_convention_from_image_object(imageobject,self.phil_params)
#we may elect to override the beam position globally for LABELIT.
#Case I. The user has provided a tuple of floats, superceding all else
if self.phil_params.autoindex_override_beam != None:
imageobject.parameters['BEAM_CENTER_X'],\
imageobject.parameters['BEAM_CENTER_Y']=\
self.phil_params.autoindex_override_beam
imageobject.beam_center_reference_frame = "imageblock"
#Case II. An XY convention has been defined.
elif beam_center_convention != 0:
convert_beam_instrument_to_imageblock(imageobject,beam_center_convention)
if self.phil_params.autoindex_override_distance != None:
imageobject.parameters['DISTANCE']=self.phil_params.autoindex_override_distance
if self.phil_params.autoindex_override_wavelength != None:
imageobject.parameters['WAVELENGTH']=self.phil_params.autoindex_override_wavelength
if self.phil_params.autoindex_override_deltaphi != None:
if self.verbose:
print "Overriding deltaphi not fully supported: contact authors"
print "Altering deltaphi",(filenameobject.number-1)*self.phil_params.autoindex_override_deltaphi
imageobject.parameters['OSC_RANGE']=self.phil_params.autoindex_override_deltaphi
imageobject.parameters['OSC_START']=(filenameobject.number-1)*self.phil_params.autoindex_override_deltaphi
# override twotheta angle
if self.phil_params.autoindex_override_twotheta != None:
imageobject.parameters['TWOTHETA']=\
self.phil_params.autoindex_override_twotheta
if self.phil_params.image_specific_osc_start != None:
imageobject.parameters['OSC_START']= \
eval("(%s)(%d)"%(
self.phil_params.image_specific_osc_start,filenameobject.number))
#take care of unbinned Quantum 315
if (self.phil_params.distl_permit_binning and \
imageobject.size1 > 4000) or \
self.phil_params.distl_force_binning:
imageobject.setBin(2)
self.phil_params.distl.minimum_spot_area = min(
self.phil_params.distl.minimum_spot_area,
self.phil_params.distl_binned_image_spot_size)
if imageobject.vendortype=="MARCCD":
#This section corrects for the fact that ESRF writes the mar ccd header
# with beam center in mm instead of pixels.
detector_center_in_mm = 0.5*imageobject.size1*imageobject.pixel_size
one_tenth_error = 0.1*detector_center_in_mm
#offset between given beam and detector center
import math
def distance(a,b):
return math.sqrt((a[0]-b[0])*(a[0]-b[0])+(a[1]-b[1])*(a[1]-b[1]))
offset1=distance( (detector_center_in_mm,detector_center_in_mm),
(imageobject.beamx,imageobject.beamy) )
if offset1>one_tenth_error:
newx = imageobject.beamx/imageobject.pixel_size
newy = imageobject.beamy/imageobject.pixel_size
#offset between corrected beam and detector center
offset2=distance( (detector_center_in_mm,detector_center_in_mm),
(newx,newy) )
if offset2<one_tenth_error:
imageobject.parameters['BEAM_CENTER_X'] = newx
imageobject.parameters['BEAM_CENTER_Y'] = newy
#Furthermore the x and y are transposed in the one example we've been given
convert_beam_instrument_to_imageblock(imageobject,
beam_center_convention,force=True)
if self.verbose:
print "Mar CCD image appears to have beam center %.2f %.2f in mm instead of pixels"%(
imageobject.beamx,imageobject.beamy)
