import numpy as np
import tomllib
from scipy.optimize import root_scalar
import xraylib
from transfocator_calcs import lookup_diameter, materials_to_deltas, materials_to_linear_attenuatio, calc_lookup_table
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_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},
'beam_line': {'d_StoL': 51.9, 'd_Stof': 66.2},
'crl':{'stack_d': 50.0e-3, 'd_min': 3.0e-5}}
"""
pyDevice TO DO:
WHAT inputs change the focal size arrays? Energy, what else?
WHAT inputs change the search through the arrays? desired focal size, what else?
IOC init functions
-get lens stack parameters (# of lenses in each stack, radius, location, thickness, thickness error) -- from substitution file but put into PVs? Update with autosave?
-get source info
-energy from from ID IOC
-hor/vert sizes and divergence (also energy dependent)
-lens diameter table? What is it doing?
-desired focal size is changed --> what needs updating? --> nothing, just need to search focal size array again
-multiple flags: is focal size achievable? is it achievable at sample?
recalc function -- should probably be same as init function
-energy is updated --> what needs updating?
-what else could user/staff change? sample position?
"""
'''
Update the following to accommodate XS code
'''
class singleTF():
def __init__(self, crl_setup = None, beam_config = DEFAULT_CONFIG['beam'],
beamline_config = DEFAULT_CONFIG['beamline'],
crl_config = DEFAULT_CONFIG['crl'],
slits_config = DEFAULT_CONFIG['slits']):
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.setupSource(beam)
self.setupBeamline(beamline)
self.setupCRL(crl)
# TODO is setupSlits necessary?
self.setupSlits(slits)
# 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])*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)
#<----- lens diameter stuff done in transfocator calcs, should this be removed from here?
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 Lens_diameter_table}
# end lens diameter stuff ------->
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 (2^12) whose binary representation indicates which lenses are in or out
self.num_lense = 12 # Number of lenses in system
self.verbosity = True
self.lookupTable = []
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 : Sigma electron divergence in H direction in rad
sigmaVp_e : Sigma electron divergence in V direction in rad
'''
self.setEnergy(beam_properites['energy'])
self.beam['L_und'] = beam_properties['L_und']
self.beam['sigmaH_e'] = beam_properties['sigmaH_e']
self.beam['sigmaV_e'] = beam_properties['sigmaV_e']
self.beam['sigmaHp_e'] = beam_properties['sigmaHp_e']
self.beam['sigmaVp_e'] = beam_properties['sigmaVp_e']
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):
'''
Beamline properties can contain entries for the following
d_StoL1 : Source-to-CRL1 distance, in m
d_Stof : Source-to-focus distance, in m
'''
self.bl['d_StoL'] = beam_properties['d_StoL']
self.bl['d_Stof'] = beam_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 contiain entries for the following
'''
pass
def setLensCount(self, lensCount):
self.numLens =
def setupLookupTable(self, subs_file, n_lenses, energy = 8.0):
'''
lookup table created after IOC startup (after transfocator materials and
thicknesses are set
'''
print(80*'#')
print('Setting up lens control...')
self.num_lenses = n_lenses
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_lenses):
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_lenses}) doesn't match substitution file")
self.numlens = []
self.radius = []
self.materials = []
self.lens_loc = []
self.lens_thickerr = []
# get number of lens for each lens from lens properties dictionary-list
print('Getting lens materials...')
if NLENS_MACRO in macros:
self.numlens = 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 RAD_MACRO in macros:
self.radius = lens_properties[RAD_MACRO]
print('Radius of lenses read in.\n')
else:
raise RuntimeError(f"Radius macro ({RAD_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 = [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 = lens_properties[LOC_MACRO]*self.stack_d
print('Location of lenses read in.\n')
else:
raise RuntimeError(f"Location macro ({RAD_MACRO}) not found in substituion file")
# get thicknesses errprfrom lens properties dictionary-list
print('Getting lens thickness error...')
if TERR_MACRO in macros:
self.lens_thickerr = [float(i) for i in lens_properties[TERR_MACRO]]
print('Lens thickness errors read in.\n')
else:
raise RuntimeError(f"Thickness errors macro ({TERR_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):
self.lookupTable = calc_lookup_table(self.num_configs, self.radius,
self.material, self.energy, self.numlens,
self.lens_loc, self.beam, self.bl,
self.crl, self.slit1_H, self.slit1_V,
self.lens_thickerr, flag_HE = self.thickerr_flag)
self.cull_lookup_table()
def cull_lookup_table(self):
'''
Culls the lookup table based on lenses that are locked and or disabled
'''
self.culledSize = 2**(self.num_lenses - (self.outMask | self.inMask).bit_count())
if self.verbose: print(f'Operating spaced now at {self.culledSize} configurations')
if self.verbose: print(f'Culling table with in mask {self.inMask} and out mask {self.outMask}')
self.culledConfigs = np.empty(self.culledSize, dtype=int)
self.culledTable = np.empty(self.culledSize)
j = 0
for i in range(2**self.num_lenses):
if ((i & self.outMask == 0) and (i & self.inMask == self.inMask)):
self.culledConfigs[j]=i
self.culledTable[j] = self.lookupTable[i]
j += 1
self.sort_lookup_table()
def sort_lookup_table(self):
'''
'''
if self.verbose: print(f'Sorting culled lookup table of length {len(self.culledTable)}')
self.sorted_index = np.argsort(self.culledTable)
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.configIndex = int(config_BW)
self.configIndexSorted = self.sorted_index.tolist().index(self.configIndex)
self.setFocalSizeActual()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def setInMask(self, inMask):
'''
update mask for lenses that are locked in
'''
self.inMask = int(inMask)
self.cull_lookup_table()
if self.verbose: print(f'Converting culled index via in Mask')
self.convertCulledIndex()
if self.verbose: print(f'Updating transfocator RBV via in Mask')
self.updateLensRBV()
if self.verbose: print(f'Setting in mask RBV to {self.inMask}')
pydev.iointr('new_inMask', int(self.inMask))
def setOutMask(self, outMask):
'''
update mask for lenses that must remain out (either disabled or locked)
'''
self.outMask = int(outMask)
self.cull_lookup_table()
if self.verbose: print(f'Converting culled index via out Mask')
self.convertCulledIndex()
if self.verbose: print(f'Updating transfocator RBV via out Mask')
self.updateLensRBV()
if self.verbose: print(f'Setting out mask RBV to {self.outMask}')
pydev.iointr('new_outMask', int(self.outMask))
def convertCulledIndex(self):
'''
When available configs change, need to update index so that tweaks
continue to work
'''
if self.verbose: print('Converting ...')
self.culledIndex = (np.where(self.culledConfigs == self.config))[0][0]
if self.verbose: print(f'Culled index is {self.culledIndex}')
self.culledIndexSorted = self.sorted_index.tolist().index(self.culledIndex)
if self.verbose: print(f'Sorted culled index is {self.culledIndexSorted}')
def setFocalSizeActual(self):
'''
'''
self.focalSize_actual = self.culledTable[self.culledIndex]
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
if self.verbose: print(f'Searching for config closest to {self.focalSize}')
self.culledIndex = np.argmin(np.abs(self.culledTable - self.focalSize))
if self.verbose: print(f'Config index found at {self.culledIndex}')
self.culledIndexSorted = self.sorted_index.tolist().index(self.culledIndex)
if self.verbose: print(f'Sorted config index found at {self.culledIndexSorted}')
# Update PVs
self.setFocalSizeActual()
self.updateLensConfigPV()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def setSlitSize(self, size, slit):
'''
Update proper slit size
'''
if slit = 'hor':
self.slit1_H = float(size) # H slit size before CRL 1
elif slit == 'vert':
self.slit1_V = float(size) # V slit size before CRL 1
else
# Need error handling
break
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(self, size, slit)
# Testing calling the lookup table reconstruction in EPICS instead of python
# self.construct_lookup_table()
def setEnergy(self, energy):
'''
Sets various forms of energy
'''
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(?)
def updateE(self, energy):
'''
Beam energy updates are propagated to CRL object from EPICS. The beam
size lookup table is then recalculated.
'''
# Energy variable sent from IOC as a string
self.setEnergy(energy)
self.construct_lookup_table()
# Do I need to find what the current config would produce as far as focal size and location?
# self.focalSizeRBV =
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.culledIndexSorted = int(sortedIndex)
self.culledIndex = self.sorted_index[self.culledIndexSorted]
# Update PVs
self.setFocalSizeActual()
self.updateLensConfigPV()
self.updateLensRBV()
self.updateFocalSizeRBVs()
def updateThickerrFlag(self, flag):
'''
User has updated thickness error flag so that ...
'''
self.thickerr_flag = flag
def updateLensConfigPV(self):
'''
'''
self.config = self.culledConfigs[self.culledIndex]
pydev.iointr('new_lenses', int(self.config))
def updateLensRBV(self):
'''
'''
pydev.iointr('new_index', int(self.culledIndexSorted))
def updateEnergyRBV(self):
'''
'''
pydev.iointr('updated_E', int(self.energy))
def updateSlitSizeRBV(self, size, slit):
'''
Update proper slit size
'''
if slit = 'hor':
pydev.iointr('updated_slitSize_H', int(self.slit1_H))
elif slit == 'vert':
pydev.iointr('updated_slitSize_V', int(self.slit1_V))
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)