def write_instrument_to_hexrd_config(self, instr):
iconfig = HexrdConfig().instrument_config_none_euler_convention
# Add this so the calibration crystal gets written
cal_crystal = iconfig.get('calibration_crystal')
output_dict = instr.write_config(calibration_dict=cal_crystal)
# Convert back to whatever convention we were using before
eac = HexrdConfig().euler_angle_convention
if eac is not None:
convert_tilt_convention(output_dict, None, eac)
# Add the saturation levels, as they seem to be missing
sl = 'saturation_level'
for det in output_dict['detectors'].keys():
output_dict['detectors'][det][sl] = iconfig['detectors'][det][sl]
# Save the previous iconfig to restore the statuses
prev_iconfig = HexrdConfig().config['instrument']
# Update the config
HexrdConfig().config['instrument'] = output_dict
# This adds in any missing keys. In particular, it is going to
# add in any "None" detector distortions
HexrdConfig().set_detector_defaults_if_missing()
# Add status values
HexrdConfig().add_status(output_dict)
# Set the previous statuses to be the current statuses
HexrdConfig().set_statuses_from_prev_iconfig(prev_iconfig)
def set_euler_angle_convention(self, new_conv, convert_config=True):
allowed_conventions = [{
'axes_order': 'xyz',
'extrinsic': True
}, {
'axes_order': 'zxz',
'extrinsic': False
}, None]
if new_conv not in allowed_conventions:
default_conv = constants.DEFAULT_EULER_ANGLE_CONVENTION
print('Warning: Euler angle convention not allowed:', new_conv)
print('Setting the default instead:', default_conv)
new_conv = default_conv
if convert_config:
# First, convert all the tilt angles
old_conv = self._euler_angle_convention
utils.convert_tilt_convention(self.config['instrument'], old_conv,
new_conv)
# Set the variable
self._euler_angle_convention = copy.deepcopy(new_conv)
self.euler_angle_convention_changed.emit()
def save_instrument_config(self, output_file):
default = self.filter_instrument_config(self.config['instrument'])
eac = self.euler_angle_convention
if eac is not None:
# Convert it to None convention before saving
utils.convert_tilt_convention(default, eac, None)
with open(output_file, 'w') as f:
yaml.dump(default, f, Dumper=NumPyIncludeDumper)
def save_instrument_config(self, output_file):
default = self.filter_instrument_config(self.config['instrument'])
eac = self.euler_angle_convention
if eac != (None, None):
# Convert it to None convention before saving
new_conv = (None, None)
utils.convert_tilt_convention(default, eac, new_conv)
with open(output_file, 'w') as f:
yaml.dump(default, f)
def restore_instrument_config_backup(self):
self.config['instrument'] = copy.deepcopy(
self.instrument_config_backup)
old_eac = self.instrument_config_backup_eac
new_eac = self.euler_angle_convention
if old_eac != new_eac:
# Convert it to whatever convention we are using
utils.convert_tilt_convention(self.config['instrument'], old_eac,
new_eac)
self.rerender_needed.emit()
self.update_active_material_energy()
def set_detector_defaults(self, det):
if det not in self.detector_defaults.keys():
return
for key, value in self.detector_defaults[det].items():
HexrdConfig().set_instrument_config_val(
['detectors', det, 'transform', key, 'value'], value)
self.detector_defaults[det]
eac = {'axes_order': 'zxz', 'extrinsic': False}
convert_tilt_convention(HexrdConfig().config['instrument'], None, eac)
self.detector_defaults[det]['tilt'] = (
HexrdConfig().get_instrument_config_val(
['detectors', det, 'transform', 'tilt', 'value']))
self.new_config_loaded.emit()
def load_instrument_config(self, yml_file):
with open(yml_file, 'r') as f:
self.config['instrument'] = yaml.load(f, Loader=yaml.FullLoader)
eac = self.euler_angle_convention
if eac != (None, None):
# Convert it to whatever convention we are using
old_conv = (None, None)
utils.convert_tilt_convention(self.config['instrument'], old_conv,
eac)
# Set any required keys that might be missing to prevent key errors
self.set_defaults_if_missing()
self.create_internal_config(self.config['instrument'])
# Create a backup
self.backup_instrument_config()
self.update_active_material_energy()
return self.config['instrument']
def load_instrument_config(self, yml_file):
old_detectors = self.detector_names
with open(yml_file, 'r') as f:
self.config['instrument'] = yaml.load(f, Loader=NumPyIncludeLoader)
eac = self.euler_angle_convention
if eac is not None:
# Convert it to whatever convention we are using
utils.convert_tilt_convention(self.config['instrument'], None, eac)
# Set any required keys that might be missing to prevent key errors
self.set_defaults_if_missing()
# Remove any 'None' distortion dicts from the detectors
utils.remove_none_distortions(self.config['instrument'])
self.create_internal_config(self.config['instrument'])
# Create a backup
self.backup_instrument_config()
# Temporarily turn off overlays. They will be updated later.
self.clear_overlay_data()
prev = self.show_overlays
self.config['materials']['show_overlays'] = False
self.update_visible_material_energies()
self.update_active_material_energy()
self.config['materials']['show_overlays'] = prev
self.instrument_config_loaded.emit()
new_detectors = self.detector_names
if old_detectors != new_detectors:
self.detectors_changed.emit()
else:
# Still need a deep rerender
self.deep_rerender_needed.emit()
return self.config['instrument']
def set_euler_angle_convention(self,
axes_order='xyz',
extrinsic=True,
convert_config=True):
new_conv = (axes_order, extrinsic)
allowed_combinations = [('xyz', True), ('zxz', False), (None, None)]
if new_conv not in allowed_combinations:
print('Warning: Euler angle convention not allowed:', new_conv)
print('Setting the default instead:', allowed_combinations[0])
new_conv = allowed_combinations[0]
if convert_config:
# First, convert all the tilt angles
old_conv = self._euler_angle_convention
utils.convert_tilt_convention(self.config['instrument'], old_conv,
new_conv)
# Set the variable
self._euler_angle_convention = new_conv
def run_powder_calibration():
# Set up the tilt calibration mapping
rme = HexrdConfig().rotation_matrix_euler()
# Set up the instrument
iconfig = HexrdConfig().instrument_config_none_euler_convention
instr = instrument.HEDMInstrument(instrument_config=iconfig,
tilt_calibration_mapping=rme)
flags = HexrdConfig().get_statuses_instrument_format()
if len(flags) != len(instr.calibration_flags):
msg = 'Length of internal flags does not match instr.calibration_flags'
raise Exception(msg)
instr.calibration_flags = flags
# Plane data and images
plane_data = HexrdConfig().active_material.planeData
img_dict = HexrdConfig().current_images_dict()
# tolerances for patches
tth_tol = HexrdConfig().config['calibration']['powder']['tth_tol']
eta_tol = HexrdConfig().config['calibration']['powder']['eta_tol']
pktype = HexrdConfig().config['calibration']['powder']['pk_type']
# powder calibrator
pc = PowderCalibrator(instr, plane_data, img_dict,
tth_tol=tth_tol, eta_tol=eta_tol,
pktype=pktype)
# make instrument calibrator
ic = InstrumentCalibrator(pc)
use_robust_optimization = False
ic.run_calibration(use_robust_optimization)
# We might need to use this at some point
# data_dict = pc._extract_powder_lines()
# Add this so the calibration crystal gets written
cal_crystal = iconfig.get('calibration_crystal')
output_dict = instr.write_config(calibration_dict=cal_crystal)
# Convert back to whatever convention we were using before
eac = HexrdConfig().euler_angle_convention
if eac is not None:
convert_tilt_convention(output_dict, None, eac)
# Add the saturation levels, as they seem to be missing
sl = 'saturation_level'
for det in output_dict['detectors'].keys():
output_dict['detectors'][det][sl] = iconfig['detectors'][det][sl]
# Save the previous iconfig to restore the statuses
prev_iconfig = HexrdConfig().config['instrument']
# Update the config
HexrdConfig().config['instrument'] = output_dict
# This adds in any missing keys. In particular, it is going to
# add in any "None" detector distortions
HexrdConfig().set_detector_defaults_if_missing()
# Add status values
HexrdConfig().add_status(output_dict)
# Set the previous statuses to be the current statuses
HexrdConfig().set_statuses_from_prev_iconfig(prev_iconfig)
def instrument_config_none_euler_convention(self):
iconfig = self.instrument_config
eac = self.euler_angle_convention
utils.convert_tilt_convention(iconfig, eac, None)
return iconfig
def run_line_picked_calibration(line_data):
# Set up the tilt calibration mapping
rme = HexrdConfig().rotation_matrix_euler()
print('Setting up the instrument...')
# Set up the instrument
iconfig = HexrdConfig().instrument_config_none_euler_convention
instr = instrument.HEDMInstrument(instrument_config=iconfig,
tilt_calibration_mapping=rme)
flags = HexrdConfig().get_statuses_instrument_format()
if np.count_nonzero(flags) == 0:
msg = 'There are no refinable parameters'
raise Exception(msg)
if len(flags) != len(instr.calibration_flags):
msg = 'Length of internal flags does not match instr.calibration_flags'
raise Exception(msg)
print('Running optimization...')
# Run calibration
opt_result = calibrate_instrument_from_picks(instr,
line_data,
param_flags=flags,
xtol=1e-4,
ftol=1e-4)
if not opt_result.success:
print('Optimization failed!')
return False
print('Optimization succeeded!')
# Add this so the calibration crystal gets written
cal_crystal = iconfig.get('calibration_crystal')
output_dict = instr.write_config(calibration_dict=cal_crystal)
# Convert back to whatever convention we were using before
eac = HexrdConfig().euler_angle_convention
if eac is not None:
convert_tilt_convention(output_dict, None, eac)
# Add the saturation levels, as they seem to be missing
sl = 'saturation_level'
for det in output_dict['detectors'].keys():
output_dict['detectors'][det][sl] = iconfig['detectors'][det][sl]
print('Updating the config')
# Save the previous iconfig to restore the statuses
prev_iconfig = HexrdConfig().config['instrument']
# Update the config
HexrdConfig().config['instrument'] = output_dict
# This adds in any missing keys. In particular, it is going to
# add in any "None" detector distortions
HexrdConfig().set_detector_defaults_if_missing()
# Add status values
HexrdConfig().add_status(output_dict)
# Set the previous statuses to be the current statuses
HexrdConfig().set_statuses_from_prev_iconfig(prev_iconfig)
return True
