def module_or_slice_from_http_request(request):
# edit out data from list
tags = {}
for item in request.keys():
assert len(request[item]) == 1 #list with one element
tags[item] = request[item][0]
if len(tags[item]) < 1000: #short items could be converted to numbers
try:
tags[item] = float(tags[item])
if tags[item] == round(tags[item], 0):
tags[item] = int(tags[item])
except Exception:
pass
#print "posted data types",item, type(tags[item]), tags[item]
# tags dictionary is now conditioned as to type
tags_class = attributes_from_dict(tags)
#Vendor selector.
if tags["vendortype"].lower().find("adsc") >= 0:
P = ADSCModule()
elif tags["vendortype"].lower().find("pilatus") >= 0:
P = PilatusSlice()
P.moduleindex = tags["moduleindex"]
P.object = StringIO(tags["adsc_data"])
P.copy_common_attributes_from_parent_instance(tags_class)
P.parameters = {}
for item in [
'DISTANCE', 'PHI', 'WAVELENGTH', 'TWOTHETA', 'OSC_RANGE',
'CCD_IMAGE_SATURATION', 'OSC_START', 'DETECTOR_SN', 'PIXEL_SIZE',
'SIZE1', 'SIZE2', 'BEAM_CENTER_X', 'BEAM_CENTER_Y'
]:
P.parameters[item] = tags[item]
from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_imageblock
convert_beam_instrument_to_imageblock(P, P.beam_center_convention)
P.slice_callback = P.slice_callback_with_high_performance_http_data
return P
def module_or_slice_from_http_request(request):
# edit out data from list
tags = {}
for item in request.keys():
assert len(request[item])==1 #list with one element
tags[item]=request[item][0]
if len(tags[item]) < 1000: #short items could be converted to numbers
try:
tags[item] = float(tags[item])
if tags[item]==round(tags[item],0):
tags[item]= int(tags[item])
except Exception: pass
#print "posted data types",item, type(tags[item]), tags[item]
# tags dictionary is now conditioned as to type
tags_class = attributes_from_dict(tags)
#Vendor selector.
if tags["vendortype"].lower().find("adsc")>=0:
P = ADSCModule()
elif tags["vendortype"].lower().find("pilatus")>=0:
P = PilatusSlice()
P.moduleindex = tags["moduleindex"]
P.object = StringIO.StringIO(tags["adsc_data"])
P.copy_common_attributes_from_parent_instance(tags_class)
P.parameters = {}
for item in ['DISTANCE', 'PHI', 'WAVELENGTH',
'TWOTHETA', 'OSC_RANGE',
'CCD_IMAGE_SATURATION', 'OSC_START', 'DETECTOR_SN', 'PIXEL_SIZE',
'SIZE1','SIZE2','BEAM_CENTER_X','BEAM_CENTER_Y'
]:
P.parameters[item] = tags[item]
from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_imageblock
convert_beam_instrument_to_imageblock(P,P.beam_center_convention)
P.slice_callback = P.slice_callback_with_high_performance_http_data
return P
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 set_beam_center_convention(self, beam_center_convention):
from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_imageblock
convert_beam_instrument_to_imageblock(self, beam_center_convention)
def set_beam_center_convention(self,beam_center_convention): from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_imageblock convert_beam_instrument_to_imageblock(self,beam_center_convention)
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)
