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Commit 2ed9d490 authored by 29iduser's avatar 29iduser
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fixed table scans

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iexcode/instruments/scanRecord.py
+ 2
− 5
View file @ 2ed9d490
......@@ -928,11 +928,8 @@ class ScanRecord:
if kwargs['debug']:
print('fillin: ',val_pv,rbv_pv,myarray[0],myarray[-1])
if posNum == 1:
#clear positioners
self.positioners_clear(**kwargs)
#set to table mode
caput(scan_pv+".P"+str(posNum)+"SM","TABLE")
#set to table mode
caput(scan_pv+".P"+str(posNum)+"SM","TABLE")
#write new positioners
caput(scan_pv+".P"+str(posNum)+"PV",val_pv) #Drive
caput(scan_pv+".R"+str(posNum)+"PV",rbv_pv) #Read
......
iexcode/macros/hkl_iex.py
+ 116
− 119
View file @ 2ed9d490
......@@ -17,6 +17,7 @@ from ophyd import PseudoSingle
from ophyd import SoftPositioner
from epics import caget,caput
import iexcode.instruments.cfg as iex
from iexcode.instruments.conversions_constants import Lambda2eV, eV2Lambda
from iexcode.instruments.kappa_angle_calcs import EtoK
from iexcode.instruments.Motors import *
......@@ -51,24 +52,14 @@ select_diffractometer(fourc)
print(f"\n{fourc.name} modes: {fourc.engine.modes}")
# Define motors RBVs:
""" kappa_motor_dict = _kappa_motor_dictionary()
kappa_motor_dict = _kappa_motor_dictionary()
tth_rbv = EpicsSignalRO(kappa_motor_dict['tth'][0], name="tth_rbv")
omega_rbv = EpicsSignalRO(kappa_motor_dict['th'][0], name="omega_rbv")
chi_rbv = EpicsSignalRO(kappa_motor_dict['chi'][0], name="chi_rbv")
phi_rbv = EpicsSignalRO(kappa_motor_dict['phi'][0], name="phi_rbv")
kth_rbv = EpicsSignalRO(kappa_motor_dict['kth'][0], name="kth_rbv")
kap_rbv = EpicsSignalRO(kappa_motor_dict['kap'][0], name="kap_rbv")
kphi_rbv =EpicsSignalRO(kappa_motor_dict['kphi'][0], name="phi_rbv") """
print('We are here')
tth_rbv = EpicsSignalRO('29idKappa:m9.RBV', name="tth_rbv")
omega_rbv = EpicsSignalRO('29idKappa:Euler_ThetaRBV', name="omega_rbv")
chi_rbv = EpicsSignalRO('29idKappa:Euler_ChiRBV', name="chi_rbv")
phi_rbv = EpicsSignalRO('29idKappa:Euler_PhiRBV', name="phi_rbv")
kth_rbv = EpicsSignalRO('29idKappa:m8.RBV', name="kth_rbv")
kap_rbv = EpicsSignalRO('29idKappa:m7.RBV', name="kap_rbv")
kphi_rbv =EpicsSignalRO('29idKappa:m1.RBV', name="tth_rbv")
kphi_rbv =EpicsSignalRO(kappa_motor_dict['kphi'][0], name="phi_rbv")
# SPEC equivalent of setmode.
......@@ -164,9 +155,7 @@ UB_update_wavelength()
####### Tools and functions:
## Where motor: wh(fourc)
def wh(E=None,sync=True,diffractometer=fourc):
"""
1117.KAPPA29ID_sim> wh
......@@ -501,26 +490,29 @@ def UBcalc(r1,r2,sync=True):
caput('29idKappa:UBor2',np.array([h,k,l,omega,chi,phi,tth]))
return fourc.calc.sample.UB
def UBrbv():
def UB_get():
"""
returns the UB matrix
"""
UB=caget('29idKappa:UBmatrix') # flattened to a 9x1 matrix
return(UB.reshape(3,3)) # reshape to a 3x3 matrix
def UBenergy(eV=getE()):
"""Update diffractometer energy.
To sync to beamline energy, use UBenergy(getE())"""
"""
Updates diffractometer energy.
"""
fourc.calc.wavelength = eV2Lambda(eV)
print("\nCurrent energy: "+str(round(Lambda2eV(fourc.calc.wavelength),2)))
UB_update_wavelength
def UBenergy_rbv():
"""Return diffractometer energy. """
print("\nUB_energy: "+str(round(Lambda2eV(fourc.calc.wavelength),2)))
UB_update_wavelength()
def UBenergy_get():
"""
Returns the diffractometer energy.
"""
eV=Lambda2eV(fourc.calc.wavelength)
print("\nCurrent energy: "+str(round(eV,2)))
############## start editing here
def _hkl_scan_detectors(scanning=True,hkl_arrays=[],**kwargs):
def _hkl_scan_detectors_set(scanning=True,hkl_arrays=[],**kwargs):
"""
adds/remove hkl detectors from the scanRecord
scanning = True (adds)
......@@ -554,38 +546,60 @@ def _hkl_scan_detectors(scanning=True,hkl_arrays=[],**kwargs):
print(caget(ArrayCalc+".DESC")+" = [D"+str(Det_h+i)+"]")
def _scan_hkl_array(mytable,**kwargs):
def _scan_hkl_fillin(hkl_tables,**kwargs):
"""
Uses bluesky pyhkl to calculate the motor positions for an hkl scan:
Uses bluesky pyhkl to calculate the motor positions for an hkl scan
and fills in the scanRecord; does not press go
mytable = _hkl_array(hkl1,hkl2,npts,eV)
hkl_tables = _hkl_array(hkl1,hkl2,npts,eV)
= (table_omega, table_chi, table_phi, table_tth)
where hkl_tables = hkl_calc_scan_arrays(hkl1,hkl2,npts,hv)
Save the corresponding table into a txt file (CSV) as scan_####.txt
Logging is automatic
**kwargs are the optional logging arguments see scanlog() for details
scan_dim = 1
"""
iex.BL.motors.scan_table('phi',table_phi,**kwargs)
def scanhkl(hkl1,hkl2,npts,**kwargs):
"""
With hkl1=[h1,k1,l1] and hkl2=[h2,k2,l2]
npts = number of point
cts = count time
**kwargs:
energy: changes the photon energy (if execute=False only changes energy in UB)
execute True/False to scan/print trajectory
comment:
scaler_cnts: to change the acquire time
"""
kwargs.setdefault('execute',True)
kwargs.setdefault('hv',getE())
if 'comment' in kwargs:
log_print(kwargs['comment'])
hkl_tables=hkl_calc_scan_arrays(hkl1,hkl2,npts,kwargs['hv'])
print("Number of accessible reflections: ",str(len(hkl_tables[4])))
kwargs.setdefault('scan_dim',1)
kwargs.setdefault('positioner_settling_time',0.2)
kwargs.setdefault('execute',True)
# Extract individual arrays:
table_omega = mytable[0]
table_chi = mytable[1]
table_phi = mytable[2]
table_tth = mytable[3]
table_hkl = mytable[4]
array_h = mytable[4][:,0]
array_k = mytable[4][:,1]
array_l = mytable[4][:,2]
_hkl_scan_detectors(scanning=True,hkl_arrays=[array_h,array_k,array_l],**kwargs)
table_omega = hkl_tables[0]
table_chi = hkl_tables[1]
table_phi = hkl_tables[2]
table_tth = hkl_tables[3]
table_hkl = hkl_tables[4]
array_h = hkl_tables[4][:,0]
array_k = hkl_tables[4][:,1]
array_l = hkl_tables[4][:,2]
_hkl_scan_detectors_set(scanning=True,hkl_arrays=[array_h,array_k,array_l],**kwargs)
for motor in ['tth','th','chi','phi']:
print('motor = [D'+str(kappa_motors_detNum(motor))+']')
# Fill-in sscan record:
# Fill-in scanRecord:
execute = kwargs['execute']
kwargs.update({'execute':False})
iex.BL.motors.scan_table('tth',table_tth,**kwargs)
......@@ -594,63 +608,59 @@ def _scan_hkl_array(mytable,**kwargs):
kwargs.update({'positioner_num':3})
iex.BL.motors.scan_table('chi',table_chi,**kwargs)
kwargs.update({'positioner_num':4})
iex.BL.motors.scan_table('phi',table_phi,**kwargs)
# Scanning
if execute:
scan_go(**kwargs)
# Setting everything back
scan_after_table_reset(**kwargs)
scan_positioners_clear(**kwargs)
_hkl_scan_detectors(scanning=False,hkl_arrays=[],**kwargs)
# Setting everything back
scan_after_table_reset(**kwargs)
scan_positioners_clear(**kwargs)
_hkl_scan_detectors_set(scanning=False,hkl_arrays=[],**kwargs)
else:
return hkl_tables
def scanhkl(hkl1,hkl2,npts,cts,**kwargs):
def scanhkl_test(hkl1,hkl2,npts,**kwargs):
"""
With hkl1=[h1,k1,l1] and hkl2=[h2,k2,l2]
npts = number of point
cts = count time
Print the hkl trajectory for hkl1=[h1,k1,l1] and hkl2=[h2,k2,l2]
**kwargs:
energy: changes the photon energy (if execute=False only changes energy in UB)
execute True/False to scan/print trajectory
comment:
"""
kwargs.setdefault('execute',True)
kwargs['scaler_cts'] = cts
kwargs.setdefault('hv',energy)
hkl_tables=hkl_calc_scan_arrays(hkl1,hkl2,npts,kwargs['hv'])
return hkl_tables
if 'comment' in kwargs:
log_print(kwargs['comment'])
if 'energy' in kwargs:
E = kwargs['energy']
else:
E=getE()
def hkl_write_array(hkl1,hkl2,npts,**kwargs):
"""
writes the hkl trajectories to a text file
UBenergy(E)
myarray=_hkl_array(hkl1,hkl2,npts,E)
print("Number of accessible reflections: ",str(len(myarray[4])))
if kwargs['execute']:
_scan_hkl_array(myarray,**kwargs)
else:
cahkl_table(myarray[4])
**kwargs:
energy: changes the photon energy (if execute=False only changes energy in UB)
filepath: default = userpath\hkl
separator: defautl = ','
"""
kwargs.setdefault('hv',getE())
kwargs.setdefault('filepath',"/home/beams/29IDUSER/Documents/User_Folders/"+mda_user_name()+'/hkl/')
kwargs.setdefault(separator,',')
#Need to make this smarter to not record unobtainable hkl reflections - data size missmatch
def scanhkl_test(hkl1,hkl2,npts,ct,E=None):
'''Print the hkl trajectory for hkl1=[h1,k1,l1] and hkl2=[h2,k2,l2]
If E = None (default), uses the current beamline energy.
'''
if E is None:
E=getE()
cahkl_table(_hkl_array(hkl1,hkl2,npts,E)[4])
fileName='scan_'+str.zfill(str(mda_fileNum()),0)+'.txt'
separator = kwargs['separator']
hkl_table = hkl_calc_scan_arrays(hkl1,hkl2,npts,**kwargs)
with open(join(kwargs['filepath'], fileName), "a+") as f:
f.write('h'+separator+'k'+separator+'l'+separator+'tth'+separator+'th'+separator+'chi'+separator+'phi'+'\n')
for (i) in range(len(hkl_table[1])):
f.write(str(hkl_table[1][i])+separator+str(hkl_table[2][i])+separator+str(hkl_table[3][i])+separator+str(hkl_table[4][i])+separator+str(hkl_table[5][i])+separator+str(hkl_table[6][i])+separator+str(hkl_table[7][i])+'\n')
print('\nWriting hkl table to:',join(kwargs['filepath'], fileName))
def _hkl_array(hkl_start,hkl_stop,npts,eV):
def hkl_calc_scan_arrays(hkl_start,hkl_stop,npts,hv=getE()):
"""
Uses bluesky pyhkl to calculate a numpy array with the motors' trajectory for a given hkl scan.
and returns the hkl_tables=(omega,chi,phi,tth,hkl)
"""
# Set diffractometer energy:
fourc.calc.wavelength = eV2Lambda(eV)
UB_update_wavelength()
UBenergy(hv)
# Generate a list of hkl position
list_hkl_in = fourc.calc.calc_linear_path(hkl_start,hkl_stop,npts, num_params=3)
......@@ -679,57 +689,44 @@ def _hkl_array(hkl_start,hkl_stop,npts,eV):
def table2csv(hkl_table,filePath=None,separator=','):
#Need to make this smarter to not record unobtainable hkl reflections - data size missmatch
if filePath is None:
user=iex.BL.mda.user_name()
filePath="/home/beams/29IDUSER/Documents/User_Folders/"+user+'/hkl/'
scanNum=hkl_table[0]
scanNumstr=str.zfill(str(scanNum),0)
fileName='scan_'+scanNumstr+'.txt'
with open(join(filePath, fileName), "a+") as f:
f.write('h'+separator+'k'+separator+'l'+separator+'tth'+separator+'th'+separator+'chi'+separator+'phi'+'\n')
for (i) in range(len(hkl_table[1])):
f.write(str(hkl_table[1][i])+separator+str(hkl_table[2][i])+separator+str(hkl_table[3][i])+separator+str(hkl_table[4][i])+separator+str(hkl_table[5][i])+separator+str(hkl_table[6][i])+separator+str(hkl_table[7][i])+'\n')
print('\nWriting hkl table to:',join(filePath, fileName))
def scanhkl_E(StartStopStepLists,hkl,cts,ID_tracking,mono_offset=0,return_table=False,**kwargs):
def scanhkl_E(hv_list, hkl=get_hkl(), **kwargs):
"""
Uses bluesky pyhkl to calculate the motor positions for an energy scan at constant Q:
hkl=(h,k,l); if hkl=None, uses the current hkl position
cts = acquisition time
ID_tracking: if True, scans the ID; if False, scan mono only
mono_offset => if you want to artificially shift the energy for the reciprocal space calulation (eg to match known hkl indexes)
hv_list = [[start1,stop1,step1], [start1,stop1,step1],...]; list of lists for the different scan ranges
Note duplicates are removed and the resulting array is sorted in ascending order
StartStopStepLists is a list of lists for the different scan ranges
StartStopStepList[[start1,stop1,step1],[start2,stop2,step2],...]
Note duplicates are removed and the resulting array is sorted in ascending order
hkl=(h,k,l); if hkl=None, uses the current hkl position
Logging is automatic
**kwargs are the optional logging arguments see scanlog() for details
**kwargs
scaler_cts: to change the acquisition time
ID_tracking: True/False (default=False)
mono_offset: if you want to artificially shift the energy for the reciprocal space calulation (eg to match known hkl indexes)
write_file: True/False to write csv file (default=True)
execute: True/False
"""
kwargs.setdefault('execute',True)
kwargs.setdefault('positioner_settling_time',0.2)
kwargs.setdefault('positioner_after_scan',"STAY")
kwargs['scaler_cts']=cts
kwargs.setdefault('ID_tracking',False)
kwargs.setdefault('mono_offset',0)
kwargs.setdefault('write_file',True)
# caget beamline parameters:
scanIOC = iex.BL.mda.ioc
scanIOC = mda_ioc()
ID_Mode, ID_QP, ID_SP, ID_RBV, hv, grt = energy_get_all()
if hkl == None:
hkl=get_hkl()
print('hkl = '+str(hkl))
print('hkl = '+str(hkl))
# Target hkl:
h,k,l = hkl
# Create energy trajectory (can have variable step size):
mytable_hv=make_table(StartStopStepLists)
mytable_hv=make_table(hv_list)
UB_update_wavelength()
......@@ -743,7 +740,7 @@ def scanhkl_E(StartStopStepLists,hkl,cts,ID_tracking,mono_offset=0,return_table=
# Compute motor positions for each energy point & append to the motor tables:
for eV in mytable_hv:
fourc.calc.wavelength = eV2Lambda(eV+mono_offset)
fourc.calc.wavelength = eV2Lambda(eV+kwargs['mono_offset'])
e_omega=round(fourc.calc.forward((h,k,l))[0][0],5)
e_chi = round(fourc.calc.forward((h,k,l))[0][1],5)
e_phi = round(fourc.calc.forward((h,k,l))[0][2],5)
......@@ -764,7 +761,7 @@ def scanhkl_E(StartStopStepLists,hkl,cts,ID_tracking,mono_offset=0,return_table=
kwargs.update({'positioner_num':3})
iex.BL.motors.scan_table('th',mytable_omega,**kwargs)
if ID_tracking:# moving ID - at the moment this replaces chi:
if kwargs['ID_tracking']:# moving ID - at the moment this replaces chi:
kwargs.update({'positioner_num':4})
ID_array=np.array([])
ID_mode,ID_QP_ratio,ID_sp,ID_rbv,hv,grt = energy_get_all(verbose=False)
......@@ -787,10 +784,10 @@ def scanhkl_E(StartStopStepLists,hkl,cts,ID_tracking,mono_offset=0,return_table=
# Setting everything back
scan_after_table_reset(**kwargs)
scan_positioners_clear(**kwargs)
_hkl_scan_detectors(scanning=False,hkl_arrays=[],**kwargs)
_hkl_scan_detectors_set(scanning=False,hkl_arrays=[],**kwargs)
# to be saved in text file like scanhkl:
if return_table:
if not ID_tracking: mytable_ID=None
if kwargs['write_file']:
if not kwargs['ID_tracking']: mytable_ID=None
return FileNum,mytable_hv.tolist(),mytable_ID.tolist(),mytable_omega.tolist(),mytable_chi.tolist() ,mytable_phi.tolist() ,mytable_tth.tolist()
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