def module_parameters(self,object):
param = object.parameters
#unchanged parameters first:
result = {}
for item in ['DISTANCE', 'PHI', 'WAVELENGTH',
'TWOTHETA', 'OSC_RANGE',
'CCD_IMAGE_SATURATION', 'OSC_START', 'DETECTOR_SN', 'PIXEL_SIZE',
]:
result[item]=copy.copy(param[item])
#other parameters keep a record of parent settings; but child
# settings are deduced on-the-fly once the data are read.
for item in ['SIZE1','SIZE2','BEAM_CENTER_X','BEAM_CENTER_Y',
]:
result["PARENT_"+item]=copy.copy(param[item])
#the final parameters require a knowledge of the module boundaries.
# In this implementation, these boundaries are determined on the fly
# from the raw data, implying an up-front file read.
# The only way to avoid this (not implemented here) is to encode
# the vendor- & model-specific module boundaries.
object.read()
nullvalue = vendor_specific_null_value(object)
ID = image_divider(data = object.linearintdata, nullvalue=nullvalue)
print "module slow interval",ID.tile_slow_interval(self.moduleindex).first, ID.tile_slow_interval(self.moduleindex).last
print "module fast interval",ID.tile_fast_interval(self.moduleindex).first, ID.tile_fast_interval(self.moduleindex).last
result["SIZE1"] = ID.tile_slow_interval(self.moduleindex).size()
result["SIZE2"] = ID.tile_fast_interval(self.moduleindex).size()
print "size1",result["SIZE1"],"size2",result["SIZE2"]
return result
def slice_callback_with_object_data(self):
self.object.read()
nullvalue = self.object.vendor_specific_null_value
ID = image_divider(data=self.object.linearintdata, nullvalue=nullvalue)
assert 0 <= self.moduleindex < ID.module_count()
new_data_array = ID.tile_data(self.moduleindex)
if self.object.linearintdata.__dict__.get("bin2by2") == True:
new_data_array.bin2by2 = True
del self.object #once the data are copied, no need to keep the original
return new_data_array
def slice_callback_with_object_data(self):
self.object.read()
nullvalue = self.object.vendor_specific_null_value
ID = image_divider(data = self.object.linearintdata, nullvalue=nullvalue)
assert 0 <= self.moduleindex < ID.module_count()
new_data_array = ID.tile_data(self.moduleindex)
if self.object.linearintdata.__dict__.get("bin2by2")==True:
new_data_array.bin2by2=True
del self.object #once the data are copied, no need to keep the original
return new_data_array
def set_beam_center_convention(self,beam_center_convention):
#previously part of the module_parameters function
#from iotbx.detectors.context.config_detector import beam_center_convention_from_image_object
#beam_center_convention = beam_center_convention_from_image_object(object)
print "CC",beam_center_convention
assert self.object.beam_center_reference_frame == "instrument"
nullvalue = self.object.vendor_specific_null_value
ID = image_divider(data = self.object.linearintdata, nullvalue=nullvalue)
from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_module
self.parameters['BEAM_CENTER_X'],self.parameters['BEAM_CENTER_Y'] = convert_beam_instrument_to_module(
self.object, ID, self.moduleindex, beam_center_convention)
self.beam_center_reference_frame = "imageblock"
self.beam_center_convention = beam_center_convention
print "old beam center",self.object.parameters['BEAM_CENTER_X'],self.object.parameters['BEAM_CENTER_Y']
print "for module", self.moduleindex,"beam x,y is", self.parameters['BEAM_CENTER_X'],self.parameters['BEAM_CENTER_Y']
def module_parameters(self, object):
param = object.parameters
#unchanged parameters first:
result = {}
for item in [
'DISTANCE',
'PHI',
'WAVELENGTH',
'TWOTHETA',
'OSC_RANGE',
'CCD_IMAGE_SATURATION',
'OSC_START',
'DETECTOR_SN',
'PIXEL_SIZE',
]:
result[item] = copy.copy(param[item])
#other parameters keep a record of parent settings; but child
# settings are deduced on-the-fly once the data are read.
for item in [
'SIZE1',
'SIZE2',
'BEAM_CENTER_X',
'BEAM_CENTER_Y',
]:
result["PARENT_" + item] = copy.copy(param[item])
#the final parameters require a knowledge of the module boundaries.
# In this implementation, these boundaries are determined on the fly
# from the raw data, implying an up-front file read.
# The only way to avoid this (not implemented here) is to encode
# the vendor- & model-specific module boundaries.
object.read()
nullvalue = vendor_specific_null_value(object)
ID = image_divider(data=object.linearintdata, nullvalue=nullvalue)
print("module slow interval",
ID.tile_slow_interval(self.moduleindex).first,
ID.tile_slow_interval(self.moduleindex).last)
print("module fast interval",
ID.tile_fast_interval(self.moduleindex).first,
ID.tile_fast_interval(self.moduleindex).last)
result["SIZE1"] = ID.tile_slow_interval(self.moduleindex).size()
result["SIZE2"] = ID.tile_fast_interval(self.moduleindex).size()
print("size1", result["SIZE1"], "size2", result["SIZE2"])
return result
def set_beam_center_convention(self, beam_center_convention):
#previously part of the module_parameters function
#from iotbx.detectors.context.config_detector import beam_center_convention_from_image_object
#beam_center_convention = beam_center_convention_from_image_object(object)
print "CC", beam_center_convention
assert self.object.beam_center_reference_frame == "instrument"
nullvalue = self.object.vendor_specific_null_value
ID = image_divider(data=self.object.linearintdata, nullvalue=nullvalue)
from iotbx.detectors.beam_center_convention import convert_beam_instrument_to_module
self.parameters['BEAM_CENTER_X'], self.parameters[
'BEAM_CENTER_Y'] = convert_beam_instrument_to_module(
self.object, ID, self.moduleindex, beam_center_convention)
self.beam_center_reference_frame = "imageblock"
self.beam_center_convention = beam_center_convention
print "old beam center", self.object.parameters[
'BEAM_CENTER_X'], self.object.parameters['BEAM_CENTER_Y']
print "for module", self.moduleindex, "beam x,y is", self.parameters[
'BEAM_CENTER_X'], self.parameters['BEAM_CENTER_Y']
def do_main(filepath, force_binning, convention, host, port):
absfile = os.path.abspath(filepath)
Q = get_labelit_image_object(absfile, convention)
if force_binning:
Q.setBin(2)
Q.show_header()
get_spotfinder_url(Q, host, port)
from iotbx.detectors import image_divider
number_of_modules = image_divider(
Q.linearintdata, Q.vendor_specific_null_value).module_count()
for x in range(number_of_modules):
file = "file://%s?slice=%d" % (absfile, x)
Q = get_labelit_image_object(file, convention)
if force_binning:
Q.setBin(2)
Q.show_header()
get_spotfinder_url(Q, host, port)
def effective_tiling_as_flex_int_impl(self, **kwargs):
assert self.reference_image is not None
IT = flex.int()
from iotbx.detectors import image_divider
if self.reference_image.linearintdata is None:
self.reference_image.readHeader()
self.reference_image.read()
null_value = self.reference_image.vendor_specific_null_value
divider = image_divider(self.reference_image.linearintdata, null_value)
for i in range(divider.module_count()):
slow = divider.tile_slow_interval(i)
fast = divider.tile_fast_interval(i)
IT.append(slow.first)
IT.append(fast.first)
IT.append(slow.last + 1)
IT.append(fast.last + 1)
return IT
def do_main(filepath, force_binning, convention, host, port):
absfile = os.path.abspath(filepath)
Q = get_labelit_image_object(absfile, convention)
if force_binning:
Q.setBin(2)
Q.show_header()
get_spotfinder_url(Q,host,port)
from iotbx.detectors import image_divider
number_of_modules = image_divider(
Q.linearintdata,
Q.vendor_specific_null_value
).module_count()
for x in xrange(number_of_modules):
file = "file://%s?slice=%d"%(absfile,x)
Q = get_labelit_image_object(file, convention)
if force_binning:
Q.setBin(2)
Q.show_header()
get_spotfinder_url(Q,host,port)
def effective_tiling_as_flex_int_impl(self, **kwargs):
assert self.reference_image is not None
IT = flex.int()
from iotbx.detectors import image_divider
if self.reference_image.linearintdata is None:
self.reference_image.readHeader()
self.reference_image.read()
null_value = self.reference_image.vendor_specific_null_value
divider = image_divider(
self.reference_image.linearintdata,
null_value
)
for i in range(divider.module_count()):
slow = divider.tile_slow_interval(i)
fast = divider.tile_fast_interval(i)
IT.append(slow.first)
IT.append(fast.first)
IT.append(slow.last+1)
IT.append(fast.last+1)
return IT
