def overwrite_from_phil(params, detector, beam=None):
'''
Overwrite from phil parameters
'''
from cctbx.eltbx import attenuation_coefficient
# Override any panel parameters
for panel_params in params.detector.panel:
panel = detector[panel_params.id]
if panel_params.name is not None:
panel.set_name(panel_params.name)
if panel_params.type is not None:
panel.set_type(panel_params.type)
if panel_params.gain is not None:
panel.set_gain(panel_params.gain)
if panel_params.pixel_size is not None:
panel.set_pixel_size(panel_params.pixel_size)
if panel_params.image_size is not None:
panel.set_image_size(panel_params.image_size)
if panel_params.trusted_range is not None:
panel.set_trusted_range(panel_params.trusted_range)
if panel_params.thickness is not None:
panel.set_thickness(panel_params.thickness)
if panel_params.material is not None:
panel.set_material(panel_params.material)
if panel_params.parallax_correction is None:
if isinstance(panel.get_px_mm_strategy(),
ParallaxCorrectedPxMmStrategy):
panel_params.parallax_correction = True
else:
panel_params.parallax_correction = False
if panel_params.parallax_correction is True:
if beam is None:
raise RuntimeError("No beam for parallax correction")
table = attenuation_coefficient.get_table(panel.get_material())
mu = table.mu_at_angstrom(beam.get_wavelength()) / 10.0
t0 = panel.get_thickness()
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
else:
panel.set_px_mm_strategy(SimplePxMmStrategy())
axes = [
panel_params.fast_axis, panel_params.slow_axis,
panel_params.origin
]
if axes.count(None) != 3:
if panel_params.fast_axis is None:
panel_params.fast_axis = panel.get_local_fast_axis()
if panel_params.slow_axis is None:
panel_params.slow_axis = panel.get_local_slow_axis()
if panel_params.origin is None:
panel_params.origin = panel.get_local_origin()
panel.set_local_frame(panel_params.fast_axis,
panel_params.slow_axis,
panel_params.origin)
# Create the hierarchy
if params.detector.hierarchy is not None:
root = detector.hierarchy()
if params.detector.hierarchy.name is not None:
root.set_name(params.detector.hierarchy.name)
if (params.detector.hierarchy.fast_axis is not None
or params.detector.hierarchy.slow_axis is not None
or params.detector.hierarchy.origin is not None):
if params.detector.hierarchy.fast_axis is None:
params.detector.hierarchy.fast_axis = root.get_fast_axis()
if params.detector.hierarchy.slow_axis is None:
params.detector.hierarchy.slow_axis = root.get_slow_axis()
if params.detector.hierarchy.origin is None:
params.detector.hierarchy.origin = root.get_origin()
root.set_frame(params.detector.hierarchy.fast_axis,
params.detector.hierarchy.slow_axis,
params.detector.hierarchy.origin)
def get_group(node, index):
if len(index) == 0:
return node
return get_group(node[index[0]], index[1:])
for group_params in params.detector.hierarchy.group:
group = get_group(root, group_params.id)
if group_params.name is not None:
group.set_name(group_params.name)
if (group_params.fast_axis is not None
or group_params.slow_axis is not None
or group_params.origin is not None):
if group_params.fast_axis is None:
group_params.fast_axis = group.get_local_fast_axis()
if group_params.slow_axis is None:
group_params.slow_axis = group.get_local_slow_axis()
if group_params.origin is None:
group_params.origin = group.get_local_origin()
group.set_local_frame(group_params.fast_axis,
group_params.slow_axis,
group_params.origin)
if len(group_params.panel) != 0:
raise RuntimeError("Can't reassign panels in groups")
# Return the detector
return detector
def generate_from_phil(params, beam=None):
'''
Create a new detector model from phil parameters
'''
from cctbx.eltbx import attenuation_coefficient
detector = Detector()
# Create a list of panels
panel_list = {}
for panel_params in params.detector.panel:
panel = Panel()
if panel_params.name is not None:
panel.set_name(panel_params.name)
if panel_params.type is not None:
panel.set_type(panel_params.type)
if panel_params.gain is not None:
panel.set_gain(panel_params.gain)
if panel_params.pixel_size is not None:
panel.set_pixel_size(panel_params.pixel_size)
else:
raise RuntimeError('No pixel size set')
if panel_params.image_size is not None:
panel.set_image_size(panel_params.image_size)
else:
raise RuntimeError('No image size set')
if panel_params.trusted_range is not None:
panel.set_trusted_range(panel_params.trusted_range)
else:
raise RuntimeError('No trusted range set')
if panel_params.thickness is not None:
panel.set_thickness(panel_params.thickness)
if panel_params.material is not None:
panel.set_material(panel_params.material)
if panel_params.parallax_correction is True:
if panel_params.material is None:
raise RuntimeError("No material for parallax correction")
if panel_params.thickness is None:
raise RuntimeError("No thickness for parallax correction")
if beam is None:
raise RuntimeError("No beam for parallax correction")
table = attenuation_coefficient.get_table(
panel_params.material)
mu = table.mu_at_angstrom(beam.get_wavelength()) / 10.0
t0 = panel_params.thickness
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
if panel_params.fast_axis is None:
panel_params.fast_axis = (1, 0, 0)
if panel_params.slow_axis is None:
panel_params.slow_axis = (0, 1, 0)
if panel_params.origin is None:
panel_params.origin = (0, 0, 0)
panel.set_local_frame(panel_params.fast_axis,
panel_params.slow_axis, panel_params.origin)
if panel_params.id in panel_list:
raise RuntimeError('Multiple panels with id=%d' %
panel_params.id)
panel_list[panel_params.id] = panel
# Create the hierarchy
panel_counter = 0
root = detector.hierarchy()
if params.detector.hierarchy.name is not None:
root.set_name(params.detector.hierarchy.name)
if params.detector.hierarchy.fast_axis is None:
params.detector.hierarchy.fast_axis = (1, 0, 0)
if params.detector.hierarchy.slow_axis is None:
params.detector.hierarchy.slow_axis = (0, 1, 0)
if params.detector.hierarchy.origin is None:
params.detector.hierarchy.origin = (0, 0, 0)
root.set_frame(params.detector.hierarchy.fast_axis,
params.detector.hierarchy.slow_axis,
params.detector.hierarchy.origin)
def get_parent(node, index):
if len(index) == 0:
return node
return get_parent(node[index[0]], index[1:])
for group_params in params.detector.hierarchy.group:
parent = get_parent(root, group_params.id[:-1])
assert len(parent) == group_params.id[-1]
group = parent.add_group()
if group_params.name is not None:
group.set_name(group_params.name)
if group_params.fast_axis is None:
group_params.fast_axis = (1, 0, 0)
if group_params.slow_axis is None:
group_params.slow_axis = (0, 1, 0)
if group_params.origin is None:
group_params.origin = (0, 0, 0)
group.set_local_frame(group_params.fast_axis,
group_params.slow_axis, group_params.origin)
for panel_id in group_params.panel:
assert panel_id == panel_counter
group.add_panel(panel_list[panel_id])
panel_counter += 1
if panel_counter == 0:
for panel_id in range(max(panel_list.keys()) + 1):
detector.add_panel(panel_list[panel_id])
elif panel_counter != len(panel_list):
raise RuntimeError("Inconsistent number of panels in hierarchy")
# Return detector
return detector
