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pyTransfocator_general.py 21.08 KiB
import numpy as np
import tomllib
import xraylib
from transfocator_calcs import lookup_diameter, materials_to_deltas, materials_to_linear_attenuation
from transfocator_calcs import find_levels, calc_lookup_table, get_densities
MAT_MACRO = 'MAT'
NLENS_MACRO = 'NUMLENS'
RADIUS_MACRO = 'RADIUS'
LOC_MACRO = 'LOC'
THICKERR_MACRO = 'THICKERR'
'''
Config variables
Beam Properties
energy : energy in keV
L_und : undulator length in m
sigmaH_e : Sigma electron source size in H direction in m
sigmaV_e : Sigma electron source size in V direction in m
sigmaHp : Sigma electron divergence in H direction in rad
sigmaVp_e : Sigma electron divergence in V direction in rad
Beamline properties
d_StoL1 : Source-to-CRL1 distance, in m
d_StoL2 : Source-to-CRL2 distance, in m
d_Stof : Source-to-focus distance, in m
CRL properties
d_min : Minimum thickness at the apex in m
stack_d : Stack thickness in m
'''
DEFAULT_CONFIG = {'beam':{'energy': 15, 'L_und': 4.7, 'sigmaH_e': 14.8e-6,
'sigmaV_e': 3.7e-6, 'sigmaHp_e': 2.8e-6, 'sigmaVp_e': 1.5e-6},
'beamline': {'d_StoL1': 51.9, 'd_StoL2': 62.1, 'd_Stof': 66.2},
'crl':{'stack_d': 50.0e-3, 'd_min': 3.0e-5}}
class transfocator():
def __init__(self, crl_setup = None, beam_config = DEFAULT_CONFIG['beam'],
beamline_config = DEFAULT_CONFIG['beamline'],
crl_config = DEFAULT_CONFIG['crl']):
self.verbose = True
if crl_setup is None:
beam = beam_config
beamline = beamline_config
crl = crl_config
# slits = slits_config
else:
with open(crl_setup, "rb") as f:
config = tomllib.load(f)
beam = config['beam']
beamline = config['beamline']
crl = config['crl']
# slits = config['slits']
self.beam = {}
self.setupSource(beam)
self.bl = {}
self.setupBeamline(beamline)
self.crl = {}
self.setupCRL(crl)
self.slits = [{'H':0,'V':0}]
# self.slit1_H = 0
# self.slit1_V = 0
# Initialize lens variables -- TODO -- this is done via a subs file -- are any of these needed prior to that loading?
self.numlens = np.array([1, 1, 1, 1, 1, 1, 2, 4, 8, 16]) # CRL1 number of lenses in each stack (was L1_n)
self.radius = np.array([2.0e-3, 1.0e-3, 5.0e-4, 3.0e-4, 2.0e-4, 1.0e-4, 1.0e-4, 1.0e-4, 1.0e-4, 1.0e-4]) # CRL1 lens radius in each stack (was L1_R)
self.materials = np.array(["Be", "Be", "Be", "Be", "Be", "Be", "Be", "Be", "Be", "Be"]) # CRL1 lens material in each stack (was L1_mater)
self.lens_loc = np.array([4.5, 3.5, 2.5, 1.5, 0.5, -0.5, -1.5, -2.5, -3.5, -4.5])*self.crl['stack_d'] # CRL1 lens stack location relative to center stack, positive means upstream (was L1_Loc)
self.lens_thickerr = np.array([1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6, 1.4e-6, 2.0e-6, 2.8e-6, 4.0e-6]) # CRL1 lens RMS thickness error (was L1_HE)
self.Lens_diameter_table = [
(50, 450.0),
(100, 632.0),
(200, 894.0),
(300, 1095.0),
(500, 1414.0),
(1000, 2000.0),
(1500, 2450.0),
]
# Convert the lookup table to a dictionary for faster lookup
self.Lens_diameter_dict = {int(col1): col2 for col1, col2 in self.Lens_diameter_table}
self.energy = 0 # gets value from an ao (incoming beam energy)
self.focalSize = 0 # get value from an ao (desired focal length)
self.lenses = 0 # sets integer (2^10) whose binary representation indicates which lenses are in or out
self.num_stacks = 10 # Number of lenses in system
self.lookupTable = []
self.thickerr_flag = True
def setupSource(self, beam_properties):
'''
Beam properties can have entries for the following
energy : energy in keV
L_und : undulator length in m
sigmaH_e : Sigma electron source size in H direction in m
sigmaV_e : Sigma electron source size in V direction in m
sigmaHp_e : Sigma electron divergence in H direction in rad
sigmaVp_e : Sigma electron divergence in V direction in rad
'''
self.setEnergy(beam_properties['energy'])
self.L_und = beam_properties['L_und']
self.sigmaH_e = beam_properties['sigmaH_e']
self.sigmaV_e = beam_properties['sigmaV_e']
self.sigmaHp_e = beam_properties['sigmaHp_e']
self.sigmaVp_e = beam_properties['sigmaVp_e']
self.setupSourceEnergyDependent()
def setupSourceEnergyDependent(self):
'''
Fill in later
'''
self.beam['sigmaH'] = (self.sigmaH_e**2 + self.wl*self.L_und/2/np.pi/np.pi)**0.5
self.beam['sigmaV'] = (self.sigmaV_e**2 + self.wl*self.L_und/2/np.pi/np.pi)**0.5
self.beam['sigmaHp'] = (self.sigmaHp_e**2 + self.wl/self.L_und/2)**0.5
self.beam['sigmaVp'] = (self.sigmaVp_e**2 + self.wl/self.L_und/2)**0.5
def setupBeamline(self, beamline_properties, num=1):
'''
Beamline properties can contain entries for the following
d_StoL1 : Source-to-CRL1 distance, in m
d_Stof : Source-to-sample distance, in m
'''
self.bl['d_StoL1'] = beamline_properties['d_StoL1']
self.bl['d_Stof'] = beamline_properties['d_Stof']
def setupCRL(self, crl_properties):
'''
CRL properties can contiain entries for the following
d_min : Minimum thickness at the apex in m
stack_d : Stack thickness in m
'''
self.crl['d_min'] = crl_properties['d_min']
self.crl['stack_d'] = crl_properties['stack_d']
def setupSlits(self, slit_properties):
'''
Slit properties can contain entries for the following
'''
pass
def setupLookupTable(self, subs_file, n_lenses):
'''
lookup table created after IOC startup
energy and slit size are updated before this is called
'''
print(80*'#')
print('Setting up lens control...')
self.num_stacks = n_lenses
self.num_configs = 2**self.num_stacks
self.configs = np.arange(self.num_configs)
# self.energy = energy
#read in substitutions file
try:
subsFile = open(subs_file,"r")
except:
raise RuntimeError(f"Substiution file ({subsFile}) not found.")
subsFileContent = subsFile.readlines()
subsFile.close()
macros = subsFileContent[2].replace('{','').replace('}','').replace(',','').split()
lens_properties = {key: [] for key in macros} # dictionary of lists
for i in range(self.num_stacks):
try:
xx = subsFileContent[3+i].replace('{','').replace('}','').replace(',','').replace('"','').split()
lens_properties[macros[0]].append(xx[0])
lens_properties[macros[1]].append(xx[1])
lens_properties[macros[2]].append(xx[2])
lens_properties[macros[3]].append(xx[3])
lens_properties[macros[4]].append(xx[4])
lens_properties[macros[5]].append(xx[5])
lens_properties[macros[6]].append(xx[6])
except:
raise RuntimeError(f"Number of lenses ({self.num_stacks}) doesn't match substitution file")
self.numlens = []
self.radius = []
self.materials = []
self.lens_loc = []
self.lens_thickerr = []
# get number of lens for each lens stack from lens properties dictionary-list
print('Getting lens materials...')
if NLENS_MACRO in macros:
self.numlens = np.array([int(i) for i in lens_properties[NLENS_MACRO]])
print('Number of lens read in.\n')
else:
raise RuntimeError(f"Number of lenses macro ({NLENS_MACRO}) not found in substituion file")
# get radii for each lens from lens properties dictionary-list
print('Getting lens\' radii...')
if RADIUS_MACRO in macros:
self.radius = np.array([float(i) for i in lens_properties[RADIUS_MACRO]])
print('Radius of lenses read in.\n')
else:
raise RuntimeError(f"Radius macro ({RADIUS_MACRO}) not found in substituion file")
# get materials from lens properties dictionary-list
print('Getting lens materials...')
if MAT_MACRO in macros:
self.materials = lens_properties[MAT_MACRO]
print('Lens material read in.\n')
else:
raise RuntimeError(f"Material macro ({MAT_MACRO}) not found in substituion file")
# get densities from local definition (for compounds) or from xraylib (for elements)
densities = get_densities(self.materials)
self.densities = np.array([densities[material] for material in self.materials])
# get location of each lens from lens properties dictionary-list
print('Getting lens\' locations...')
if LOC_MACRO in macros:
self.lens_loc = np.array([float(i)*self.crl['stack_d'] for i in lens_properties[LOC_MACRO]])
print('Location of lenses read in.\n')
else:
raise RuntimeError(f"Location macro ({LOC_MACRO}) not found in substituion file")
# get thicknesses errprfrom lens properties dictionary-list
print('Getting lens thickness error...')
if THICKERR_MACRO in macros:
self.lens_thickerr = np.array([float(i) for i in lens_properties[THICKERR_MACRO]])
print('Lens thickness errors read in.\n')
else:
raise RuntimeError(f"Thickness errors macro ({THICKERR_MACRO}) not found in substituion file")
print('Constructing lookup table...')
self.construct_lookup_table()
print('Lookup table calculation complete.\n')
print('Transfocator control setup complete.')
print(80*'#')
def construct_lookup_table(self):
arr_a, arr_b, arr_c = calc_lookup_table(self.num_configs, self.radius,
self.materials, self.energy, self.wl,
self.numlens,
self.lens_loc, self.beam, self.bl,
self.crl, self.slits[0]['H'], self.slits[0]['V'],
self.lens_thickerr, flag_HE = self.thickerr_flag,
verbose = self.verbose)
self.lookupTable = arr_a
self.sorted_invF_index = arr_b
self.sorted_invF = arr_c
# self.sort_lookup_table()
self.updateEnergyRBV()
self.updateSlitSizeRBV('hor')
self.updateSlitSizeRBV('vert')
self.updateLookupWaveform()
self.updateInvFWaveform()
self.updateLookupConfigs()
def setFocalSizeActual(self):
'''
'''
# self.focalSize_actual = self.culledTable[self.culledIndex]
self.focalSize_actual = self.lookupTable[self.indexSorted]
def find_config(self):
'''
User selected focal size, this function finds nearest acheivable focal
size from the lookup table
'''
# Code to search lookup table for nearest focal size to desired; note the
# lookup table is already sorted by 1/f
if self.verbose: print(f'Searching for config closest to {self.focalSize}')
# simple approach
# self.indexSorted = np.argmin(np.abs(self.lookupTable - self.focalSize))
# XS approach -- can handle nan but in pydev application don't have a good
# way to "transmit" errors (i.e. no solution found) to user.
indices, _ = find_levels(self.lookupTable, self.focalSize, direction='forward')[0]
self.indexSorted = indices[0]
if self.verbose: print(f'1/f-sorted config index found at {self.indexSorted}')
self.index = self.sorted_invF_index[self.indexSorted]
if self.verbose: print(f'Config index found at {self.index}')
# Update PVs
self.setFocalSizeActual()
self.updateLensConfigPV()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def getPreviewFocalSize(self, sortedIndex):
'''
'''
fSize_preview = self.lookupTable[sortedIndex]
if self.verbose: print(f'Preview focal sizes for {sortedIndex} is {fSize_preview}')
pydev.iointr('new_preview', fSize_preview)
def setSlitSize(self, size, slit):
'''
Update proper slit size
'''
if slit == 'hor':
# self.slit1_H = float(size) # H slit size before CRL 1
self.slits[0]['H'] = float(size) # H slit size before CRL 1
elif slit == 'vert':
# self.slit1_V = float(size) # V slit size before CRL 1
self.slits[0]['V'] = float(size) # V slit size before CRL 1
else:
raise RuntimeError(f"Slit identifier ({slit}) not recognized. Should be 'hor' or 'vert'")
def updateSlitSize(self, size, slit):
'''
Slit size updates are propagated to CRL object from EPICS. The beam
size lookup table is then recalculated.
'''
self.setSlitSize(size, slit)
if self.verbose:
if slit == 'hor':
# print(f'Horizontal slit size updated to {self.slit1_H} m')
print(f"Horizontal slit size updated to {self.slits[0]['H']} m")
elif slit == 'vert':
# print(f'Vertical slit size updated to {self.slit1_V} m')
print(f"Vertical slit size updated to {self.slits[0]['V']} m")
def setEnergy(self, energy):
'''
Sets various forms of energy
'''
if energy > 0.0001:
self.energy = float(energy)
self.energy_eV = self.energy*1000.0 # Energy in keV
self.wl = 1239.84 / (self.energy_eV * 10**9) #Wavelength in nm(?)
if self.verbose: print(f'Setting energy to {self.energy} keV')
def updateE(self, energy):
'''
Beam energy updates are propagated to CRL object from EPICS. The beam
size lookup table is then recalculated.
'''
if energy > 0.0001:
# Energy variable sent from IOC as a string
self.setEnergy(energy)
# Update beam properties that are dependent on energy
self.setupSourceEnergyDependent()
else:
if verbose: print(f'Invalid energy setting: {energy} kev; staying at {self.energy} keV')
def updateFsize(self, focalSize):
'''
User updates desired focal size. Lookup table is traversed to find nearest
to desired.
'''
# focalPoint variable sent from IOC as a string
self.focalSize = float(focalSize)
self.find_config()
def updateIndex(self, sortedIndex):
'''
User has updated desired sorted index
'''
self.indexSorted = int(sortedIndex)
self.index = self.sorted_invF_index[self.indexSorted]
# Update PVs
self.setFocalSizeActual()
self.updateLensConfigPV()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def setThickerrFlag(self, flag):
'''
User has updated thickness error flag so that ...
'''
self.thickerr_flag = int(flag)
if self.verbose: print(f'Thickness Error Flag set to {flag}')
self.updateThickerrFlagRBV()
def updateThickerrFlagRBV(self):
'''
Thickness error flag has been updated
'''
if self.verbose: print(f'Thickness Error Flag RBV set to {self.thickerr_flag}')
pydev.iointr('updated_thickerr_Flag', self.thickerr_flag)
def updateLensConfigPV(self):
'''
'''
self.config = self.configs[self.index]
pydev.iointr('new_lenses', int(self.config))
def updateLensRBV(self):
'''
'''
pydev.iointr('new_index', int(self.indexSorted))
def updateEnergyRBV(self):
'''
'''
pydev.iointr('updated_E', float(self.energy))
def updateSlitSizeRBV(self, slit):
'''
Update proper slit size
'''
if slit == 'hor':
# pydev.iointr('updated_slitSize_H', float(self.slit1_H))
# if self.verbose: print(f'Horizontal slit size RBV updated to {self.slit1_H} m')
pydev.iointr('updated_slitSize_H', float(self.slits[0]['H']))
if self.verbose: print(f"Horizontal slit size RBV updated to {self.slits[0]['H']} m")
elif slit == 'vert':
# pydev.iointr('updated_slitSize_V', float(self.slit1_V))
# if self.verbose: print(f'Vertical slit size RBV updated to {self.slit1_V} m')
pydev.iointr('updated_slitSize_V', float(self.slits[0]['V']))
if self.verbose: print(f"Vertical slit size RBV updated to {self.slits[0]['V']} m")
def updateFocalSizeRBVs(self):
'''
'''
pydev.iointr('new_fSize', self.focalSize_actual)
def updateVerbosity(self, verbosity):
'''
Turn on minor printing
'''
print(f'Verbosity set to {verbosity}')
self.verbose = int(verbosity)
def updateLookupWaveform(self):
'''
Puts lookup table focal sizes into waveform PV
'''
pydev.iointr('new_lookupTable', self.lookupTable.tolist())
def updateInvFWaveform(self):
'''
Puts invF list into waveform PV
'''
pydev.iointr('new_invFind_list', self.sorted_invF_index.tolist())
pydev.iointr('new_invF_list', self.sorted_invF.tolist())
def updateLookupConfigs(self):
'''
Puts lookup table config integers into waveform PV
'''
pydev.iointr('new_configs', self.configs.tolist())
class singleTF(transfocator):
def __init__(self, crl_setup = None, beam_config = DEFAULT_CONFIG['beam'],
beamline_config = DEFAULT_CONFIG['beamline'],
crl_config = DEFAULT_CONFIG['crl']):
super().__init__(crl_setup = crl_setup, beam_config = beam_config,
beamline_config = beamline_config, crl_config = crl_config)
def updateConfig(self, config_BW):
'''
When user manually changes lenses, this gets focal size and displays it
along with updated RBVs but it doesn't set the config PV
'''
self.index = int(config_BW)
# Find the configuration in the 1/f sorted list
self.indexSorted = self.sorted_invF_index.tolist().index(self.index)
self.setFocalSizeActual()
self.updateLensRBV()
self.updateFocalSizeRBVs()
class doubleTF(transfocator):
def __init__(self, crl_setup = None, beam_config = DEFAULT_CONFIG['beam'],
beamline_config = DEFAULT_CONFIG['beamline'],
crl_config = DEFAULT_CONFIG['crl']):
super().__init__(crl_setup = crl_setup, beam_config = beam_config,
beamline_config = beamline_config, crl_config = crl_config)
def updateConfig1(self, config_BW):
'''
When user manually changes lenses, this gets focal size and displays it
along with updated RBVs but it doesn't set the config PV
'''
self.index = int(config_BW)
# Find the configuration in the 1/f sorted list
#TODO how to find in double-list? ?????
self.indexSorted = self.sorted_invF_index.tolist().index(self.index)
self.setFocalSizeActual()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def updateConfig2(self, config_BW):
'''
When user manually changes lenses, this gets focal size and displays it
along with updated RBVs but it doesn't set the config PV
'''
self.index = int(config_BW)
# Find the configuration in the 1/f sorted list
#TODO how to find in double-list? ?????
self.indexSorted = self.sorted_invF_index.tolist().index(self.index)
self.setFocalSizeActual()
self.updateLensRBV()
self.updateFocalSizeRBVs()
class singeTFandKB(transfocator):
pass