diff --git a/iexcode/instruments/VLS_PGM.py b/iexcode/instruments/VLS_PGM.py
index 4aae5e76c4331f820c8eb345b0383ab1e1b73db1..cb1f34624b4e2548b09f2bebe3a4fdba0fb4abdc 100644
--- a/iexcode/instruments/VLS_PGM.py
+++ b/iexcode/instruments/VLS_PGM.py
@@ -13,6 +13,8 @@ from iexcode.instruments.IEX_BL_config import *
from iexcode.instruments.utilities import print_warning_message,read_dict
from iexcode.instruments.scanRecord import *
+
+
##############################################################################################################
################################ mono ##############################
##############################################################################################################
@@ -84,21 +86,29 @@ def _mono_mirror_num():
"""returns the current mirror num"""
return caget('29idmonoMIR_TYPE_MON')
-def _mono_pvs(grt_num=None,mir_num=None):
+def mono_pvs():
+ """
+ returns a dictionary with the pvs for energy, energy_sp and grt_density
+ """
+ d={'energy':"29idmono:ENERGY_MON",
+ 'energy_sp':"29idmono:ENERGY_SP",
+ 'grt_density':"29idmono:GRT_DENSITY",
+ }
+ return d
+
+def _mono_pvs_extended(grt_num=None,mir_num=None):
"""
returns a dictionary with all the mono pvs
"""
+
if grt_num is None:
grt_num = _mono_grating_num()
if mir_num is None:
mir_num = _mono_mirror_num()
ext=_mono_extensions()
-
- d={
- 'energy':"29idmono:ENERGY_MON",
- 'energy_sp':"29idmono:ENERGY_SP",
- 'grt_density':"29idmono:GRT_DENSITY",
+ d = mono_pvs()
+ d.update({
'grt_offset':'29idmonoGRT:P_OFFSETS.'+ext[grt_num],
'grt_b2':'29idmonoGRT:B2_CALC.'+ext[grt_num],
'grt_pos':'29idmonoGRT:X_DEF_POS.'+ext[grt_num],
@@ -136,10 +146,8 @@ def _mono_pvs(grt_num=None,mir_num=None):
'mir_pos':'29idmonoMIR:X_DEF_POS.'+ext[mir_num],
'mono_stop':"29idmono:STOP_CMD.PROC",
'cff':'29idmono:CC_MON',
- 'arm':'29idmono:PARAMETER.G'
-
-
- }
+ 'arm':'29idmono:PARAMETER.G',
+ })
return d
def mono_get_all_extended(verbose=False):
@@ -156,7 +164,7 @@ def mono_get_all_extended(verbose=False):
ext=_mono_extensions()
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
vals={
'grt_num':grt_num,
'mir_num':mir_num,
@@ -220,7 +228,7 @@ def mono_energy_set(hv_eV,verbose=True):
Previously: SetMono
"""
hv_min, hv_max = mono_energy_range()
- pv = _mono_pvs()['energy_sp']
+ pv = _mono_pvs_extended()['energy_sp']
if hv_min <= hv_eV <= hv_max:
caput(pv,hv_eV,wait=True,timeout=60)
time.sleep(2.5)
@@ -241,8 +249,8 @@ def mono_scan_pvs():
"""
returns the pvs to be used in scanning
"""
- val_pv = _mono_pvs()['energy_sp']
- rbv_pv = _mono_pvs()['energy']
+ val_pv = _mono_pvs_extended()['energy_sp']
+ rbv_pv = _mono_pvs_extended()['energy']
return val_pv, rbv_pv
def mono_status_get():
@@ -255,7 +263,7 @@ def mono_status_get():
Previously Mono_Status
"""
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
mir_P_status = int(caget(pvs['mir_P_status']))
grt_P_status = int(caget(pvs['grt_P_status']))
mir_X_status = int(caget(pvs['mir_X_status']))
@@ -301,7 +309,7 @@ def _mono_optic_change(optic,name, verbose=True):
print_warning_message(name+' not a valid '+optic)
return
- pvs = _mono_pvs ()
+ pvs = _mono_pvs_extended ()
if optic == 'grating':
type_get = mono_grating_get()
type_sp = pvs['grt_type_sp']
@@ -339,7 +347,7 @@ def mono_resest_pitch():
resets the MIR and GRT pitch interlocks after a following error or limit
Previoulsy part of SetMono
"""
- pv=_mono_pvs()
+ pv=_mono_pvs_extended()
caput(pv['grt_P_stop'],1)
time.sleep(1)
caput(pv['mir_P_stop'],1)
@@ -352,7 +360,7 @@ def mono_kill():
Previously: Kill_Mono
"""
- pv=_mono_pvs()
+ pv=_mono_pvs_extended()
caput(pv['grt_P_kill'],1)
caput(pv['mir_P_kill'],1)
caput(pv['grt_X_kill'],1)
@@ -368,7 +376,7 @@ def mono_stop():
Previously: Stop_Mono
"""
- pv=_mono_pvs()
+ pv=_mono_pvs_extended()
caput(pv['mono_stop'],1)
time.sleep(5)
@@ -378,7 +386,7 @@ def mono_enable():
Previously: Enable_Mono
"""
- pv=_mono_pvs()
+ pv=_mono_pvs_extended()
caput(pv['grt_P_enable'],1)
caput(pv['mir_P_enable'],1)
caput(pv['grt_X_enable'],1)
@@ -392,7 +400,7 @@ def mono_limits_reset():
Previously: Reset_Mono_Limits
"""
- pv=_mono_pvs()['energy_sp']
+ pv=_mono_pvs_extended()['energy_sp']
caput(pv+".DRVL",200)
caput(pv+".LOW",200)
caput(pv+".LOLO",200)
@@ -404,7 +412,7 @@ def mono_parameters_pv(grt_num=None,mir_num=None):
"""
returns dictionary with mono_parameter for current grating/mirror
"""
- pvs=_mono_pvs(grt_num,mir_num)
+ pvs=_mono_pvs_extended(grt_num,mir_num)
d={
@@ -617,7 +625,7 @@ def mono_angles_set(alpha,beta): #JM modified to monitor the ready, moving seque
"""
alpha=alpha*1.0
beta=beta*1.0
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
#don't wait during move so they move in parallel (less likely to crash)
caput(pvs['mir_P_sp'],alpha)
@@ -636,7 +644,7 @@ def mono_pink_beam():
Previously: Mono_pinkbeam
"""
mono_angles_set(0,0)
- pvs=_mono_pvs()
+ pvs=_mono_pvs_extended()
mono_motor_move('MIR:X',-52,wait=False)
mono_motor_move('GRT:X',210,wait=True)
@@ -654,7 +662,7 @@ def mono_CC():
caput("29idmono:ENERGY_SP", 440)
def mono_grating_offset_get(grt_num=None):
- pvs=_mono_pvs(grt_num,None)
+ pvs=_mono_pvs_extended(grt_num,None)
return caget(pvs['grt_offset'])
def mono_grating_offset_set(val,grt_num=None):
@@ -663,12 +671,12 @@ def mono_grating_offset_set(val,grt_num=None):
Previously: Mono_Set_GRT0
"""
- pvs=_mono_pvs(grt_num,None)
+ pvs=_mono_pvs_extended(grt_num,None)
caput(pvs['grt_offset'],val)
mono_get_all_extended(verbose=True)
def mono_mirror_offset_get(mir_num=None):
- pvs=_mono_pvs(None,mir_num)
+ pvs=_mono_pvs_extended(None,mir_num)
return caget(pvs['mir_offset'])
def mono_mirror_offset_set(val,mir_num=None):
@@ -677,7 +685,7 @@ def mono_mirror_offset_set(val,mir_num=None):
Previously: Mono_Set_MIR0
"""
- pvs=_mono_pvs(None,mir_num)
+ pvs=_mono_pvs_extended(None,mir_num)
caput(pvs['mir_offset'],val)
mono_get_all_extended(verbose=True)
@@ -713,7 +721,7 @@ def mono_grating_mirror_offsets_set(mirror_offset):
mono_get_all_extended(verbose=True)
def mono_grating_b2_get(grt_num=None):
- pvs = _mono_pvs(grt_num,None)
+ pvs = _mono_pvs_extended(grt_num,None)
return caget(pvs['grt_b2'])
def mono_grating_b2_set(val,grt_num=None):
@@ -722,7 +730,7 @@ def mono_grating_b2_set(val,grt_num=None):
Previously: Mono_Set_b2
"""
hv = mono_energy_get()
- pvs = _mono_pvs(grt_num,None)
+ pvs = _mono_pvs_extended(grt_num,None)
caput(pvs['grt_b2t'],val)
time.sleep(1)
@@ -755,7 +763,7 @@ def mono_cff_set(val,tune_num):
Previously: Mono_Set_cff
"""
hv = mono_energy_get()
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
#get current info
current_vals = mono_get_all_extended(verbose=False)
@@ -780,7 +788,7 @@ def mono_cff_set(val,tune_num):
print('Differences : ',grt_dif,mir_dif)
def mono_arm_get():
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
return caget(pvs(['arm']))
def mono_arm_set(distance_mm):
@@ -790,7 +798,7 @@ def mono_arm_set(distance_mm):
Previously: Mono_Set_ExitArm
"""
hv = mono_energy_get()
- pvs = _mono_pvs()
+ pvs = _mono_pvs_extended()
#get current info
current_vals = mono_get_all_extended(verbose=False)
diff --git a/iexcode/instruments/cfg.py b/iexcode/instruments/cfg.py
index e5767b1f89575b95bc1f02a1289cbd67d843febe..c44dc83474f83e1d93f3b602f0521ff1b134a056 100644
--- a/iexcode/instruments/cfg.py
+++ b/iexcode/instruments/cfg.py
@@ -5,4 +5,5 @@ BL=None
mpa=None
kappa_detectors_dictionary={}
-EA=None
\ No newline at end of file
+EA=None
+vortex = None
\ No newline at end of file
diff --git a/iexcode/macros/A_hutch/A_hutch.py b/iexcode/macros/A_hutch/A_hutch.py
index f9b41d07d2ad1823f608fc249ba1f4e56b129406..90d49ec60bb150580e63509b51d21b6cd1485e30 100644
--- a/iexcode/macros/A_hutch/A_hutch.py
+++ b/iexcode/macros/A_hutch/A_hutch.py
@@ -199,7 +199,8 @@ def _Ahutch_detector_dictionary():
12:"29idb:ca12:read",
13:"29idb:ca13:read",
14:"29idb:ca14:read",
- 15:"29idb:ca15:read"
+ 15:"29idb:ca15:read",
+ 68:"29idb:ca14:read",
}
Kappa_scalers={
diff --git a/iexcode/macros/Kappa/__init__.py b/iexcode/macros/Kappa/__init__.py
index 1580436f76c2e3aa81a033e81f5377d9677f1977..f3db549d2cd0c4cc3e7661080c0742401009a1ca 100644
--- a/iexcode/macros/Kappa/__init__.py
+++ b/iexcode/macros/Kappa/__init__.py
@@ -7,7 +7,7 @@ from iexcode.instruments.kappa_angle_calcs import *
from iexcode.instruments.m3r_align import *
from iexcode.instruments.m3r import *
from iexcode.instruments.MPA import *
-from iexcode.instruments.vortex import *
+from iexcode.instruments.Vortex import *
from iexcode.instruments.SRS_current_amplifiers import *
from iexcode.macros.Kappa.Kappa_mca import *
diff --git a/iexcode/macros/Kappa/hkl_iex.py b/iexcode/macros/Kappa/hkl_iex.py
index 9e9038b2bcabaf8ba4bc86a7241b37fa674905e2..852befa63809b8b0859ebedf5731715e74ed0011 100644
--- a/iexcode/macros/Kappa/hkl_iex.py
+++ b/iexcode/macros/Kappa/hkl_iex.py
@@ -55,6 +55,7 @@ class FourCircleDiffractometer(SimulatedE4CV):
# create the 4-circle diffractometer object
fourc = FourCircleDiffractometer('', name="fourc")
select_diffractometer(fourc)
+az_ref = [0, 0, 1]
# What the available modes with this diffractometer?
print(f"\n{fourc.name} modes: {fourc.engine.modes}")
@@ -381,7 +382,12 @@ def sample_new(name,A,B,C,Alpha,Beta,Gamma):
lattice=Lattice(
a=A, b=B, c=C,
alpha=Alpha, beta=Beta, gamma=Gamma))
- print(mysample)
+ # print(mysample)
+ print(f'Sample = {mysample.name}')
+ print(f'Lattice = {mysample.lattice}')
+ print(f'U = {mysample.U}')
+ print(f'UB = {mysample.UB}')
+ print(f'Reflections: {mysample.reflections}')
_UB_put('UBsample',fourc.calc.sample.name)
_UB_put('UBlattice',fourc.calc.sample.lattice)
except ValueError:
@@ -846,7 +852,7 @@ def pa(diffractometer=fourc):
print(f'\treal space = {a:.3f} {b:.3f} {c:.3f} / {alpha:.3f} {beta:.3f} {gamma:.3f}')
print(f'\treciprocal space = {r_a:.3f} {r_b:.3f} {r_c:.3f} / {r_alpha:.3f} {r_beta:.3f} {r_gamma:.3f}\n')
print(f'Azimuthal Reference:')
- # print(f'\tH K L = {fourc.az_ref[0]} {fourc.az_ref[1]} {fourc.az_ref[2]}')
+ print(f'\tH K L = {az_ref[0]} {az_ref[1]} {az_ref[2]}')
print(f'[U]: \n{np.round(sample.U, 3)}\n')
print(f'[UB]: \n{np.round(sample.UB, 3)}')
@@ -917,12 +923,60 @@ def set_az(g_haz, g_kaz, g_laz):
'''
set azimutal orientation
'''
- pass
+ az_ref = [g_haz, g_kaz, g_laz]
+
+
+def angle_between(v1, v2):
+ angle = np.arccos(np.dot(v1, v2)/(np.linalg.norm(v1)*np.linalg.norm(v2)))
+ return np.rad2deg(angle)
+
+
+def rot(v, axis, deg):
+ rad = np.deg2rad(deg)
+ if axis.lower()=='x':
+ r = np.array([[1, 0, 0],[0, np.cos(rad), -np.sin(rad)],[0, np.sin(rad), np.cos(rad)]])
+ elif axis.lower()=='y':
+ r = np.array([[np.cos(rad), 0, np.sin(rad)],[0, 1, 0],[-np.sin(rad), 0, np.cos(rad)]])
+ elif axis.lower()=='z':
+ r = np.array([[np.cos(rad), -np.sin(rad), 0],[np.sin(rad), np.cos(rad), 0],[0, 0, 1]])
+ else:
+ print('axis should be either x, y, or z')
+ return np.dot(r, v)
+
+
+def calc_psi_alpha_beta(az_ref=az_ref):
+ h = getattr(fourc, 'h').position
+ k = getattr(fourc, 'k').position
+ l = getattr(fourc, 'l').position
+ omega_now = omega_rbv.get()
+ phi_now = phi_rbv.get()
+ chi_now = chi_rbv.get()
+ tth_now = tth_rbv.get()
+
+ incident = np.array((1, 0, 0))
+ diffracted = np.array((np.cos(np.deg2rad(tth_now)), np.sin(np.deg2rad(tth_now)), 0))
+ q_hkl = diffracted - incident
+ q_hkl /= np.linalg.norm(q_hkl)
+ scattering_plane = np.array((0, 0, 1))
+ az_now = np.dot(fourc.calc.sample.UB, az_ref)
+ az_now = rot(az_now, 'y', phi_now)
+ az_now = rot(az_now, 'x', 90-chi_now)
+ az_now = rot(az_now, 'z', omega_now)
+ az_now /= np.linalg.norm(az_now)
+ az_projected = az_now - np.dot(az_now, q_hkl)*q_hkl
+ incident_projected = incident - np.dot(incident, q_hkl)*q_hkl
+ incident_projected /= np.linalg.norm(incident_projected)
+ az_projected_x = np.dot(az_projected, incident_projected)
+ az_projected_y = np.dot(az_projected, (0, 0, -1))
+ psi = np.rad2deg(np.arctan2(az_projected_y, az_projected_x))
+ alpha = angle_between(incident, az_now) - 90
+ beta = 90-angle_between(az_now, diffracted)
+ return psi, alpha, beta
def fixed_alpha(alpha):
'''
- fix alpha mode, which is not avaiable in hklpy as of 202408. Need to use external variables
+ fix alpha mode, which is not avaiable in hklpy as of 202408. Need to use external variables az_ref
SPEC modes:
g_mode =
diff --git a/iexcode/macros/Octupole/__init__.py b/iexcode/macros/Octupole/__init__.py
index fa65535336ff20838febdbfc8eb13ba8d6a12417..3027ecbd4e41485b37991be793429771835eae3e 100644
--- a/iexcode/macros/Octupole/__init__.py
+++ b/iexcode/macros/Octupole/__init__.py
@@ -5,6 +5,6 @@ from iexcode.macros.Octupole_macros.Octupole_mca import *
from iexcode.instruments.m3r_align import *
from iexcode.instruments.m3r import *
-from iexcode.instruments.vortex import *
+from iexcode.instruments.Vortex import *
from iexcode.instruments.SRS_current_amplifiers import *
\ No newline at end of file
diff --git a/iexcode/macros/resolution.py b/iexcode/macros/resolution.py
index b1aaa8f9c2b88a22618cf33e01d7aa4942b5af94..851f93640cf317cf465bb9971aa4f4ea6de555e9 100644
--- a/iexcode/macros/resolution.py
+++ b/iexcode/macros/resolution.py
@@ -3,14 +3,19 @@ import numpy as np
from epics import caget
-#import iexcode.instruments.cfg as iex
+import iexcode.instruments.cfg as iex
from iexcode.instruments.IEX_BL_config import BLconfig_endstation_name
from iexcode.instruments.utilities import take_closest_value
from iexcode.macros.xrays.xrays import getE, slit_get
from iexcode.instruments.VLS_PGM import mono_grating_get
-from iexcode.instruments.electron_analyzer import EA, resolution_EA, SES_slit_get
+
+from iexcode.instruments.electron_analyzer import resolution_EA, SES_slit_get
+
+
from iexcode.instruments.ARPES import ARPES_extra_pvs
from iexcode.instruments.scanRecord import *
+
+
#############################################################################################################
############################## Resolution ##############################
#############################################################################################################
@@ -26,7 +31,7 @@ def resolution():
if BLconfig_endstation_name() == "ARPES":
slit_SES = SES_slit_get()
- PE = int(EA.PassEnergy)
+ PE = int(iex.EA.PassEnergy)
Tsample = caget(ARPES_extra_pvs()['TA'])
resolution_ARPES(grt,hv_eV,slit_size,PE,slit_SES,Tsample,verbose=True)
print("Calculate: resolution_ARPES(grt,hv_eV,slit_size,PE,slit_SES,Tsample)")
@@ -97,6 +102,8 @@ def resolution_ARPES(grt,hv_eV,slit_size,PE,slit_SES,T,verbose=True):
"""
resolution of the ARPES
"""
+
+
bl = resolution_beamline(grt,hv_eV,slit_size,verbose=False)
KbT = T*25/300
SES = resolution_EA(PE,slit_SES)
diff --git a/iexcode/macros/staff/ID_energy_calibration.py b/iexcode/macros/staff/ID_energy_calibration.py
index d2aaa738f1c893440a575a3a47b4ffd7298dca6e..57d5a24d3313e70a96ab17370d5ce109e75497bf 100644
--- a/iexcode/macros/staff/ID_energy_calibration.py
+++ b/iexcode/macros/staff/ID_energy_calibration.py
@@ -16,9 +16,9 @@ import iexcode.instruments.cfg as iex
#from iexcode.macros.xrays.xrays import *
from iexcode.macros.xrays.xrays import _energy_range_min_max, polarization, apertures_set
from iexcode.instruments.AUX100_diode import current2flux
-from iexcode.instruments.IEX_VPU import ID_QP_ratio_get, ID_set_eV
+from iexcode.instruments.IEX_VPU import ID_QP_ratio_get, ID_set_eV, ID_pvs
from iexcode.instruments.VLS_PGM import mono_grating_density_get, mono_grating_get, mono_energy_set, mono_scan
-
+from iexcode.instruments.VLS_PGM import mono_pvs
from iexcode.instruments.diagnostics import diagnostics_all_out
from iexcode.instruments.m3r import m3r_branch
from iexcode.instruments.m3r_align import m3r_align
@@ -26,8 +26,17 @@ from iexcode.instruments.m3r_align import m3r_align
from iexcode.instruments.utilities import range_up, read_dict, today
from iexcode.instruments.Logfile import log_name_set,log_print
-from iexplot.mda_quick_plot import *
+from iexplot.mda_quick_plot import *
+from iexplot.utilities import make_num_list
+from iexplot.pynData.nmda import nmda
+from iexplot.IEX_funcs import IEX_scanNum_fpath
+
+#mono max and min energies
+global plotMin,plotMax,ID_dict_path
+plotMin = 100
+plotMax = 3000
+ID_dict_path = '/home/beams22/29IDUSER/Documents/User_Macros/Macros_29id/IEX_Dictionaries/Dict_IDCal.txt'
##############################################################################################################
################################ ID calibration scripts ##############################
##############################################################################################################
@@ -128,276 +137,201 @@ def ID_calibration_scan(ID_start,ID_stop,ID_step,bandwidth=10,QP=None,Harm=1,sca
######################################### IDCalibration fitting ###################################
###############################################################################################
+#======================= fitting and plotting ==================================
+def calibration_metadata_pvs():
+ d = {
+ 'id_sp':ID_pvs()['energy_sp'],
+ 'id_rbv':ID_pvs()['energy_rbv'],
+ 'id_mode':ID_pvs()['mode_rbv'],
+ 'mono_grt_den':mono_pvs()['grt_density'],
+ }
+ return d
-def id_calibration_fit(first_scan,last_scan,det,PolyRank,**kwargs):
-
+
+
+def calibration_read_mda(*scans,detNum,**kwargs):
+ """
+ *scans
+ **kwargs:
- #id_calibration_fit(FirstLast[0],FirstLast[1],det,poly_order,mytitle=mytitle,countby=countby,plotMin=plt_min,plotMax=plt_max,plotType=plotType,filepath=filepath,prefix=prefix)
"""
- Fits calibration curves fpr each GRTs and modes included in the data set. Creates 3 dictionnaries:
+ kwargs.setdefault('ext','mda')
+
+ modeDict={'CW, RCP':'RCP','CCW, LCP':'LCP','H':'H','V':'V'}
+ grtDict={1200:'MEG',2400:'HEG'}
+
+ scanNum_list = make_num_list(*scans)
- coefs={[GRT][mode][[breakpoint1,[coefs]],[breakpoint2,[coefs]...}
- xdata= {[GRT][mode][[breakpoint1,[flux curve x axis]],[breakpoint2,[flux curve x axis]...}
- fdata= {[GRT][mode][[breakpoint1,[flux curve y axis]],[breakpoint2,[flux curve y axis]...}
+ data_detNum = []
+ data_mono_rbv = []
+ id_sp_eV = []
+ id_mode =[]
+ grt_name = []
+ mono_max = []
+ current_max = []
+ flux_max =[]
+ mono_res = []
+ current_res=[]
+ flux_res = []
+
+ for scanNum in scanNum_list:
+ #read the data
+ fpath = IEX_scanNum_fpath(scanNum,fullpath=True,**kwargs)
+ mda = nmda(fpath)
+
+ x = mda.posx[0].data
+ data_mono_rbv.append(x)
+ y = mda.det[detNum].data
+ data_detNum.append(y)
- kwargs:
- countby = 1 by default
- mytitle = '' by default
- plotMin = min x range for plotting (default 250)
- plotMax = max x range for plotting (default 3000)
- plotType = ['dif,'fit,'flux'], full set by default
- filepath = None, uses current mda filepath unless specified
- e.g. user : filepath='/net/s29data/export/data_29idc/2018_2/UserName/mda/'
- e.g. staff: filepath='/net/s29data/export/data_29idb/2018_2/mda/'
- prefix = None, uses current mda prefix unless specified
- scanIOC = None, uses BL_ioc() unless specified
+ #extra pvs
+ id_sp_eV.append(mda.header.all[meta_data_pvs()['id_sp']][2][0]*1000)
+ key = mda.header.all[meta_data_pvs()['id_mode']][2]
+ id_mode.append(modeDict[key])
+ key = mda.header.all[meta_data_pvs()['mono_grt_den']][2][0]
+ grt_name.append(grtDict[key])
+ #find max current
+ hv,current,flux = calibration_find_max(x,y)
+ mono_max.append(hv)
+ current_max.append(current)
+ flux_max.append(flux)
+
+ return data_mono_rbv,data_detNum, id_sp_eV, id_mode,grt_name,mono_max, current_max, flux_max
+
+
+def calibration_find_max(mono_rbv,intensity):
"""
+ Finds the max intensity from a series of mono scans and
+ returns mono_energy_maxI,id_sp,current,flux
- kwargs.setdefault('countby',1)
- kwargs.setdefault('mytitle','')
- kwargs.setdefault('plotMin',225)
- kwargs.setdefault('plotMax',3000)
- kwargs.setdefault('plotType',['fit','dif','flux'])
- kwargs.setdefault('filepath',iex.BL.mda.filepath())
- kwargs.setdefault('prefix',iex.BL.mda.prefix())
-
- countby=kwargs['countby']
- mytitle=kwargs['mytitle']
- plotMin=kwargs['plotMin']
- plotMax=kwargs['plotMax']
- filepath=kwargs['filepath']
- prefix=kwargs['prefix']
-
+ intensity = data_detNum
+ mono_rbv = data_mono_rbv
- def calibration_curve(first,last,det,countby,filepath,prefix):
- mono_list=[]
- ID_list=[]
- max_list=[]
- flux_list=[]
- print("filepath = ",filepath)
- print("prefix = ",prefix)
- print("First scan = ",first)
- print("Last scan = ",last)
- for i in range(first,last,countby):
- x,y,x_name,y_name=mda_1D(i,det,1,0,filepath,prefix) #mda_1D(ScanNum,DetectorNum,coeff=1,bckg=0,filepath=None,prefix=None,scanIOC=None):
- v,w,v_name,w_name=mda_1D(i, 4 ,1,0,filepath,prefix)
- if y != []:
- n=y.index(max(y)) # finds the peak max intensity index
- e=round(x[n],2) # finds the corresponding mono energy
- sp=round(w[2]*1000,0) # reads the ID set point
- mono_list.append(e)
- max_list.append(max(y))
- ID_list.append(sp)
- flux_list.append(current2flux(max(y)),e,p=None)
- return mono_list,ID_list,max_list,flux_list
-
- Mono_max,ID_SP,int_max,flux=calibration_curve(first_scan,last_scan+1,det,countby,filepath,prefix)
- nPt_gaus=200
- x_HR = np.linspace(Mono_max[0], Mono_max[-1], nPt_gaus)
+ """
- # Data
- xdata = np.array(Mono_max)
- ydata = np.array(ID_SP)
- zdata = np.array(int_max)
- fdata = np.array(flux)
- # Fitting
- coefs = poly.polyfit(xdata, ydata, PolyRank)
- ffit_HR = poly.polyval(x_HR, coefs)
- ffit_Coarse = poly.polyval(xdata, coefs)
- # Residual
- Dif=np.array(ID_SP)-np.array(ffit_Coarse)
- ratio=(np.array(ID_SP)-np.array(ffit_Coarse))/(np.array(ID_SP)/100)
- # Plot differences
- #print('plotMin = ',str(plotMin))
- if 'dif' in kwargs['plotType']:
- fig = plt.figure(figsize=(12,6))
- plt.plot(Mono_max,ID_SP,marker='x',markersize=5,color='g',linewidth=0,label='data')
- plt.plot(x_HR,ffit_HR,color='b',label='SP-fit')
- plt.plot(xdata,Dif*100,marker='x',color='r',label='Dif x100')
- plt.plot(xdata,ratio*1000,marker='x',color='g',label='Difx1000/ID')
- plt.ylabel('ID SP')
- plt.xlabel('Mono')
- plt.xlim(plotMin,plotMax)
- plt.legend(ncol=2, shadow=True, title=mytitle, fancybox=True)
- plt.grid(linestyle='-', linewidth='0.5', color='grey')
- plt.show()
- # Plot raw data + fit
- if 'fit' in kwargs['plotType']:
- fig = plt.figure(figsize=(12,6))
- a1 = fig.add_axes([0,0,1,1])
- a1.plot(xdata+Dif,zdata,marker='*',markersize=10,color='r',linewidth=0,label='Interpolated ID SP')
- for i in range(first_scan,last_scan+1):
- x,y,x_name,y_name=mda_1D(i,det,1,0,filepath,prefix)
- a1.plot(x,y,color='b')
- a1.set_xlim(plotMin,plotMax)
- a1.set(xlabel='Mono')
- a1.set(ylabel='ID SP')
- a1.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
- a1.grid(linestyle='-', linewidth='0.5', color='grey')
- plt.legend(ncol=2, shadow=True, title=mytitle, fancybox=True)
- plt.show()
- # Plot flux curves:
- fdata_x=xdata+Dif
- if 'flux' in kwargs['plotType']:
- fig = plt.figure(figsize=(12,6))
- a1 = fig.add_axes([0,0,1,1])
- a1.plot(fdata_x,fdata,color='r',linewidth=1,label='Flux curves')
- a1.set_xlim(plotMin,plotMax)
- a1.set(xlabel='Mono')
- a1.set(ylabel='ID SP')
- a1.set_yscale('log')
- #a1.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
- a1.grid(linestyle='-', linewidth='0.5', color='grey')
- plt.legend(ncol=2, shadow=True, title=mytitle, fancybox=True)
- plt.show()
- return coefs, fdata_x,fdata
-
-
-def read_id_files(first,last,filepath=None,prefix=None,q=True):
+ # finds the peak max intensity index
+ intensity_max = np.max(intensity)
+ index_max = list(intensity).index(intensity_max)
+ mono_max = round(mono_rbv[index_max],2)
+ flux_max = current2flux(intensity_max,mono_max,verbose=False)
+ return mono_max,intensity_max,flux_max
+
+def Au_bkpt(id_sp_eV,Au=2100):
"""
- Reads extra PVs
- Return a list of [[ScanNum,ID_SP,grt,mode],...] for mda files between first and last.
+ returns the index for the id setpoint closest to Au
"""
- if filepath == None:
- filepath=iex.BL.mda.filepath()
- if prefix == None:
- prefix=iex.BL.mda.prefix()[:-1]
- elif prefix[-1] == "_":
- prefix=prefix[:-1]
- mydata=mdaFile(first,last,filepath=filepath,prefix=prefix,q=q)
- value=[]
- modeDict={'CW, RCP':'RCP','CCW, LCP':'LCP','H':'H','V':'V'}
- grtDict={1200:'MEG',2400:'HEG'}
- for mdaNum in mydata.scanList:
- if first<=mdaNum<=last:
- extraPVs=mydata.header[mdaNum].all
- try:
- ID=round(extraPVs['ID29:EnergySet.VAL'][2][0]*1000,2)
- mode=modeDict[extraPVs['ID29:ActualMode'][2]] # extraPVs return 'CW, RCP'
- grt=grtDict[extraPVs['29idmono:GRT_DENSITY'][2][0]] # extraPVs return 1200
- except KeyError:
- ID=round(extraPVs[b'ID29:EnergySet.VAL'][2][0]*1000,2)
- mode=modeDict[str(extraPVs[b'ID29:ActualMode'][2])[2:-1]]
- grt=grtDict[extraPVs[b'29idmono:GRT_DENSITY'][2][0]] # extraPVs return 1200
- if len(value)>0 and value[-1][1:] == [ID,grt,mode]:
- pass
- else:
- value.append([mdaNum,ID,grt,mode])
- return value
-
-
-
-def id2num(ID,grt,mode,first=0,last=inf,ignore=[],filepath=None,prefix=None,q=True): # Not efficient - requires to read all 600 files everytime
+ Au=2100
+ sp_Au = take_closest_value(id_sp_eV,Au)
+ n = id_sp_eV.index(sp_Au)
+ if sp_Au <= Au:
+ return n
+ else:
+ return n-1
+
+def calibration_bkpts(id_sp_eV,**kwargs):
"""
- Return ScanNum corresponding to a given ID_SP from ExtraPVs (using mdaFile)
"""
- if filepath == None:
- filepath=iex.BL.mda.filepath()
- if prefix == None:
- prefix=iex.BL.mda.prefix()[:-1]
- elif prefix[-1] == "_":
- prefix=prefix[:-1]
- ScanNum = 0
- data_list = read_id_files(first,last,filepath,prefix,q)
- data_short=[x for x in data_list if x[2:]==[grt,mode] and x[0] not in ignore]
- step=data_short[1][1]-data_short[0][1]
- precision=int(step/2)
- ID1=ID-precision
- ID2=ID+precision
- ScanNum=[x[0] for x in data_short if ID1<= x[1]<= ID2]
- if len(ScanNum)==0: result=None
- else: result=ScanNum[0]
- return result
-
-
-
-def num2id(ScanNum,grt,mode,first=0,last=inf,ignore=[],filepath=None,prefix=None,q=True): # Not efficient - requires to read all 600 files everytime
+ kwargs.setdefault('bkpts',[0,Au_bkpt(id_sp_eV)])
+ n1,n2 = kwargs['bkpts']
+ return n1,n2
+
+
+def calibration_do_fitting(mono_vals,id_sp_eV,**kwargs):
"""
- Return ID SP corresponding to a given ScanNum from ExtraPVs (using mdaFile)
+ fits the ID set point vs the mono values to a polynomial of rank PolyRand
+ returns id_sp_eV_fit,coefs
+ **kwargs
+ poly_rank (default: 1)
"""
- if filepath == None:
- filepath=iex.BL.mda.filepath()
- if prefix == None:
- prefix=iex.BL.mda.prefix()[:-1]
- elif prefix[-1] == "_":
- prefix=prefix[:-1]
- ID = 0
- data_short=[]
- data_list = read_id_files(first,last,filepath,prefix,q)
- data_short=[x for x in data_list if x[2:]==[grt,mode] and x[0] not in ignore]
- ID=[x[1] for x in data_short if x[0] == ScanNum]
- return ID[0]
-
-
-
-def extract_id(first,last,ignore=[],breakpts={'RCP':[600],'H':[400,600],'V':[600],'LCP':[600],'HEG':[],'MEG':[2200,2475]},filepath=None,prefix=None,q=True):
+ kwargs.setdefault('poly_rank',1)
+
+ xdata = np.array(mono_vals)
+ ydata = np.array(id_sp_eV)
+
+ # Fitting
+ n1,n2 = calibration_bkpts(id_sp_eV,**kwargs)
+ coefs = poly.polyfit(xdata[n1:n2], ydata[n1:n2], 4)
+ ft = poly.polyval(np.array(mono_vals), coefs)
+
+ return ft,coefs
+
+def calibration_interp_fit(mono_vals,coefs,**kwargs):
+ """
+ interpolates the mono_values with kwarg[npts] (default: 200)
+ and calculates id_setpoint based on the fit
+ returns mono_new, id_new
+ """
+ kwargs.setdefault('npts',200)
+ mono_new = np.linspace(mono_vals[0], mono_vals[-1], kwargs['npts'])
+ id_new = poly.polyval(mono_new, coefs)
+ return mono_new, id_new
+
+def calibration_calc_delta(id_sp_eV, id_sp_eV_fit):
+ """
+ returns the difference between the ID setpint and the interpolated value
+ """
+ id_delta = np.array(id_sp_eV) - id_sp_eV_fit
+ return id_delta
+
+def calibration_plot_fit(hv_max,id_sp_eV,id_sp_eV_fit,**kwargs):
"""
- Breaksdown the info from a calibration files into grt & mode with the corresponding breakpoints (hardcoded):
- [[first, last, 'HEG', 'RCP', [600]],
- [first, last, 'HEG', 'H', [400, 600]]...]
+ plots the fit to t
"""
- if filepath == None:
- filepath=iex.BL.mda.filepath()
- if prefix == None:
- prefix=iex.BL.mda.prefix()[:-1]
- elif prefix[-1] == "_":
- prefix=prefix[:-1]
- IDlog=read_id_files(first,last,filepath,prefix,q)
- #breakpts={'RCP':[600],'H':[400,600],'V':[600],'LCP':[600],'HEG':[],'MEG':[2200]}
- #breakpts={'RCP':[600],'H':[400,600],'V':[600],'LCP':[600],'HEG':[],'MEG':[2200]}
- #breakpts={'RCP':[600],'H':[600],'V':[600],'LCP':[600],'HEG':[],'MEG':[2200,2475]} # FR changed H breakpoints, missing low energy scans 06/14/2021
- data=[]
- for grt in ['HEG','MEG']:
- for mode in ['RCP','H','V','LCP']:
- tmp=[x for x in IDlog if x[2:]==[grt,mode] and x[0] not in ignore]
- #print(tmp)
- if len(tmp)>0:
- tmp=[tmp[0][0],tmp[-1][0],grt,mode,breakpts[mode]+breakpts[grt]]
- data.append(tmp)
- return data
-
-
-
-def update_id_dict(first,last,det,update_file,ignore,**kwargs):
+ fig = plt.figure(figsize=(12,6))
+ #plotting data and difference between fit and data
+ plt.subplot(2,1,1)
+ plt.plot(hv_max, id_sp_eV,color='r',marker='o',label='data')
+ plt.plot(hv_max, id_sp_eV_fit,color='k',label='fit')
+ n1,n2 = calibration_bkpts(id_sp_eV,**kwargs)
+ plt.vlines(id_sp_eV[n2],plotMin,plotMax,color='g',label='breakpoint')
+ plt.legend()
+ plt.grid(linestyle='-', linewidth='0.5', color='grey')
+
+ #difference plot
+ plt.subplot(2,1,2)
+ plt.plot(hv_max,id_delta,marker='.',label='difference')
+ plt.legend()
+ n1,n2 = calibration_bkpts(id_sp_eV)
+ ylims=np.min(id_delta[n1:n2]),np.max(id_delta[n1:n2])
+ plt.ylim(ylims)
+ plt.grid(linestyle='-', linewidth='0.5', color='grey')
+
+def calibration_plot_data(data_mono_rbv,data_detNum,hv_max,current_max):
+ fig = plt.figure(figsize=(12,6))
+ a1 = fig.add_axes([0,0,1,1])
+ #plotting interpolated ID setpoint
+ a1.plot(np.array(hv_max)+id_delta,np.array(current_max),marker='*',markersize=10,color='r',linewidth=0,label='Interpolated ID SP')
+ #plotting data curves
+ for i,intensity in enumerate(data_detNum):
+ a1.plot(data_mono_rbv[i],data_detNum[i],color='b')
+ #plt.xlim(kwargs['plotMin'],['plotMax'])
+ a1.set(xlabel='Mono')
+ a1.set(ylabel='Intensity')
+ a1.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
+ a1.grid(linestyle='-', linewidth='0.5', color='grey')
+ plt.legend(ncol=2, shadow=True, title='', fancybox=True)
+
+def ID_calibration_analysis(*scans,detNum=15,**kwargs):
"""
Calculate new calibration curve for a full set of data.'
But what if the set is not complete? To be addressed by Future Me
If update_file == True (ONLY):
- \tupdate the ID dictionary '/home/beams22/29IDUSER/Documents/User_Macros/Macros_29id/IEX_Dictionaries/Dict_IDCal.txt'
+ \tupdate the ID dictionary ''
"""
-
- if update_file == True:
- foo=input('\nAre you sure you want to update the ID calibration dictionary?\n>')
- if foo == 'Y' or foo == 'y' or foo == 'yes'or foo == 'YES' or foo == 'Yes':
- foo = 'yes'
- print('\nWill save new dictionary to: \'/home/beams22/29IDUSER/Documents/User_Macros/Macros_29id/IEX_Dictionaries/Dict_IDCal.txt\'\n')
- else:
- print('\nCalibration curves will not be saved.\n')
- else:
- print('\nCalibration curves will not be saved.\n')
-
- kwargs.setdefault('countby',1)
kwargs.setdefault('mytitle','')
- kwargs.setdefault('plotMin',225)
- kwargs.setdefault('plotMax',3000)
+ kwargs.setdefault('plotMin',plotMin)
+ kwargs.setdefault('plotMax',plotMax)
kwargs.setdefault('plotType',['fit','dif','flux'])
- kwargs.setdefault('filepath',iex.BL.mda.filepath())
- kwargs.setdefault('prefix',iex.BL.mda.prefix())
- kwargs.setdefault('q',True)
- kwargs.setdefault('breakpts',{'RCP':[600],'H':[400,600],'V':[600],'LCP':[600],'HEG':[],'MEG':[2200,2475]})
+ kwargs.setdefault('filepath',mda_filepath())
+ kwargs.setdefault('prefix',mda_prefix())
+ kwargs.setdefault('verbose',False)
+ kwargs.setdefault('breakpts',calibration_breakpts())
-
- breakpts=kwargs['breakpts']
- plotType=kwargs['plotType']
- filepath=kwargs['filepath']
- prefix=kwargs['prefix']
- q=kwargs['q']
-
- ID_data=extract_id(first,last,ignore,breakpts,filepath,prefix,q)
+ #extract_id returns data
+ id_sp, id_mode,grt_name,hv_max, current_max, flux_max = calibration_read_mda(*scans,detNum,**kwargs)
##### Extract parameters:
-
mode_dict ={'RCP':0,'LCP':1,'V':2,'H':3}
id_coef={}
new_id_function={}
@@ -454,16 +388,15 @@ def update_id_dict(first,last,det,update_file,ignore,**kwargs):
if grt=='MEG' and ID[1]>2900:
poly_order=5
plt_min=ID[0]-200
- print('det =',det)
+ print('det =',detNum)
print('poly_order =',poly_order)
subkwargs=kwargs # kwargs contains plotType, filepath, prefix and q
newkwargs={'mytitle':mytitle,'countby':countby,"plotMin":plt_min,'plotMax':plt_max}
subkwargs.update(newkwargs)
- #print(newkwargs)
- #print(FirstLast[0],FirstLast[1])
- #result,energy_data,flux_data=id_calibration_fit(FirstLast[0],FirstLast[1],det,poly_order,subkwargs)
- result,energy_data,flux_data=id_calibration_fit(FirstLast[0],FirstLast[1],det,poly_order,mytitle=mytitle,countby=countby,plotMin=plt_min,plotMax=plt_max,plotType=['fit','dif'],filepath=filepath,prefix=prefix)
+
+ result,energy_data,flux_data=id_calibration_fit(FirstLast[0],FirstLast[1],detNum,poly_order,mytitle=mytitle,countby=countby,plotMin=plt_min,plotMax=plt_max,plotType=['fit','dif'],filepath=filepath,prefix=prefix)
+
tmp0.append([cutoff[1],result.tolist()])
tmp1.append([cutoff[1],energy_data])
tmp2.append([cutoff[1],flux_data])
@@ -477,37 +410,3 @@ def update_id_dict(first,last,det,update_file,ignore,**kwargs):
flux_dict[grt]=id_flux
##### Read & update old dictionary:
-
- try:
- id_function=read_dict('Dict_IDCal.txt')
- print(id_function)
- id_function.update(new_id_function)
-
- except KeyError:
- print("Unable to read previous dictionary")
-
-
- if update_file == True and foo == 'yes':
- filepath = "/home/beams22/29IDUSER/Documents/User_Macros/Macros_29id/IEX_Dictionaries/"
- filename = 'Dict_IDCal.txt'
-
- with open(join(filepath, filename), "a+") as f:
- f.write('\n======= '+today()+': \n')
- f.write(str(id_function))
- f.write('\n')
- print('\nWriting dictionary to:',join(filepath, filename))
-
- if update_file == True and foo == 'yes':
- filepath = "/home/beams22/29IDUSER/Documents/User_Macros/Macros_29id/IEX_Dictionaries/"
- filename = 'Flux_Curves.txt'
-
- with open(join(filepath, filename), "a+") as f:
- f.write('\n======= '+today()+': \n')
- f.write('\n----- flux_x:\n')
- f.write(str(energy_dict))
- f.write('\n----- flux_y:\n')
- f.write(str(flux_dict))
- f.write('\n')
- print('\nWriting flux curves to:',join(filepath, filename))
-
- return id_function,energy_dict,flux_dict