From 880368870c7b556fa2814434dbcca8163e256a75 Mon Sep 17 00:00:00 2001
From: jmcchesn <jmcchesn@aps.anl.gov>
Date: Thu, 8 Sep 2022 11:09:12 -0500
Subject: [PATCH] debugging
---
iexcode/cheatsheet.txt | 2 +
iexcode/instruments/Kappa.py | 10 +++--
iexcode/instruments/Motors.py | 1 -
iexcode/instruments/cfg.py | 2 +-
iexcode/instruments/staff.py | 1 +
iexcode/instruments/vortex.py | 8 ++--
iexcode/macros/Kappa_optimization.py | 63 +++++++++++++++-------------
iexcode/macros/quick_plot.py | 46 +++++++-------------
8 files changed, 63 insertions(+), 70 deletions(-)
diff --git a/iexcode/cheatsheet.txt b/iexcode/cheatsheet.txt
index 1a5bfd1..2cc6961 100644
--- a/iexcode/cheatsheet.txt
+++ b/iexcode/cheatsheet.txt
@@ -29,6 +29,8 @@ ca_detector_list => list of detectors which are used in a given branch ('b for b
ca_average => turns on averaging for all Keithleys in ca_list
ca_reset_all => resets all Keithleys in all branches
SRS => class for SRS current amplifiers
+.get
+.setgain
current2flux => calculates the flux based on the current reading in an AUX100 photodiode
flux2current => calculates the current reading for a given flux for and AUX100 photodiode
diff --git a/iexcode/instruments/Kappa.py b/iexcode/instruments/Kappa.py
index d5b1668..86a4a84 100644
--- a/iexcode/instruments/Kappa.py
+++ b/iexcode/instruments/Kappa.py
@@ -1,3 +1,4 @@
+from json import detect_encoding
import numpy as np
from time import sleep
from math import floor
@@ -25,12 +26,15 @@ from iexcode.instruments.shutters import branch_shutter_close
#branch specific
from iexcode.instruments.slits import slit3D_get
#endstation specific
-from iexcode.instruments.kappa_det import kappa_Detector
+from iexcode.instruments.kappa_det import Kappa_Detector
from iexcode.instruments.scalers import scaler_cts
from iexcode.instruments.MPA import MPA, mpa_ROI_reset
from iexcode.instruments.spec_stuff import folders_spec
default_ioc = '29idKappa:'
+
+global tey,d3,d4,mesh,kappa_scaler_pv,tth_pv,tthdet
+
#############################################################################
def kappa_init(*userName,**kwargs):
"""
@@ -76,7 +80,7 @@ def kappa_init(*userName,**kwargs):
iex.BL.mda.log('kappa',user_name,_kappa_log_header(),_kappa_log_entries)
#global detectors
- global tey,d3,d4,mesh,kappa_scaler_pv,tth_pv,tthdet
+
tey = SRS("29idMZ0:scaler1.S2", '29idd:A1')
d3 = SRS("29idMZ0:scaler1.S3", '29idd:A2')
d4 = SRS("29idMZ0:scaler1.S4", '29idd:A3')
@@ -84,7 +88,7 @@ def kappa_init(*userName,**kwargs):
kappa_scaler_pv = '29idMZ0:scaler1.CNT'
tth_pv = _kappa_motor_dictionary('tth')[3]
iex.mpa = MPA()
- tthdet = kappa_Detector(kappa_Motors)
+ tthdet = Kappa_Detector(kappa_Motors)
#resetting everything
if kwargs['reset']:
diff --git a/iexcode/instruments/Motors.py b/iexcode/instruments/Motors.py
index e4e9a2c..5e7756b 100644
--- a/iexcode/instruments/Motors.py
+++ b/iexcode/instruments/Motors.py
@@ -1,5 +1,4 @@
import time
-from math import floor
from epics import caget, caput
diff --git a/iexcode/instruments/cfg.py b/iexcode/instruments/cfg.py
index 9de5488..8e9c946 100644
--- a/iexcode/instruments/cfg.py
+++ b/iexcode/instruments/cfg.py
@@ -1,3 +1,3 @@
BL=None
-mpa=None
\ No newline at end of file
+mpa=None
diff --git a/iexcode/instruments/staff.py b/iexcode/instruments/staff.py
index 2624d35..4206824 100644
--- a/iexcode/instruments/staff.py
+++ b/iexcode/instruments/staff.py
@@ -1,6 +1,7 @@
from os import listdir,mkdir,chmod
from os.path import join, isfile, exists
+import iexcode.instruments.cfg as iex
from iexcode.instruments.ARPES import folders_ARPES, ARPES_init
from iexcode.instruments.kappa import folders_kappa, kappa_init
diff --git a/iexcode/instruments/vortex.py b/iexcode/instruments/vortex.py
index b57d15d..aa71435 100644
--- a/iexcode/instruments/vortex.py
+++ b/iexcode/instruments/vortex.py
@@ -1,4 +1,4 @@
-from this import d
+from time import sleep
from epics import caput, caget
import iexcode.instruments.cfg as iex
@@ -39,7 +39,7 @@ def mca_scaler(time_sec):
def mca_run(time_sec):
caput(vortex_pv+'mca1.PRTM',time_sec)
sleep(0.1)
- caput(vortex_pv'mca1EraseStart',1,wait=True,timeout = 100000)
+ caput(vortex_pv+'mca1EraseStart',1,wait=True,timeout = 100000)
def mca_off():
@@ -54,7 +54,7 @@ def mca_on():
def _mca_file_setup():
mda_saveData=saveData_get_all(iex.BL.mda.ioc)
- caput(vortex_pv+'saveData_fileSystem',mda_saveData[fileSystem])
+ caput(vortex_pv+'saveData_fileSystem',mda_saveData['fileSystem'])
caput(vortex_pv+'saveData_subDir', '/'+ mda_saveData['subDir']+'/S'+str(mda_saveData['scanNumber']))
caput(vortex_pv+'saveData_scanNumber',1)
@@ -97,7 +97,7 @@ def scanmca(add_mca=True,save_image=False,**kwargs):
sleep(1)
if save_image:
_mca_file_setup()
- chkmcasave()
+ mca_check_save()
else:
#remove vortex trigger and detectors
iex.BL.mda.triggers_clear()
diff --git a/iexcode/macros/Kappa_optimization.py b/iexcode/macros/Kappa_optimization.py
index 54a89ae..fac1150 100644
--- a/iexcode/macros/Kappa_optimization.py
+++ b/iexcode/macros/Kappa_optimization.py
@@ -1,4 +1,11 @@
+from time import sleep
+from iexcode.instruments.utilities import *
+from iexcode.instruments.kappa import uan
+from iexcode.instruments.kappa import tey,d3,d4,mesh,kappa_scaler_pv,tth_pv,tthdet
+from iexcode.instruments.Motors import *
+from iexcode.instruments.scanRecord import last_mda
+from iexcode.macros.quick_plot import *
##### Kappa Optimization scans - 2022 versions #####
@@ -17,16 +24,16 @@ def Find_kth_zero(th_0,th_180):
def align_d4(z0,th):
''' th = 0 or 180
'''
- setdet('d4')
+ tthdet.set('d4')
sleep(1)
uan(0,th)
mvz(z0-1500)
- setgain('d4',10,'uA')
+ d4.setgain(10,'uA')
dscantth(-0.25,0.25,0.01)
sleep(1)
- setgain('d4',1,'nA')
+ d4.setgain(1,'nA')
mvz(z0)
- n=LastMDA()
+ n=last_mda()
fit_mda(n,25,0,'poly',graph=False)
tth0=fit_d4(n)
print('tth0 = '+str(round(tth0,3)))
@@ -38,12 +45,12 @@ def align_z0_chi0(question=True):
if question:
foo=input_d('Are you at th=90/270, chi=0, phi=90 (Y or N)? >')
if foo == 'Y'.lower() or foo == 'yes'.lower():
- setdet('d3')
+ tthdet.set('d3')
sleep(1)
mvtth(0)
dscanz(-750,750,50)
sleep(1)
- n=LastMDA()
+ n=last_mda()
fit_mda(n,25,0,'poly',graph=False)
z0=fit_z(n)
print('z0 = '+str(round(z0,0)))
@@ -53,27 +60,25 @@ def align_z0_chi0(question=True):
print('Canceling')
return
else:
- setdet('d3')
+ tthdet.set('d3')
sleep(1)
mvtth(0)
dscanz(-750,750,50)
sleep(1)
- n=LastMDA()
+ n=last_mda()
fit_mda(n,25,0,'poly',graph=False)
z0=fit_z(n)
print('z0 = '+str(round(z0,0)))
playsound()
return z0
-
-
def align_z0(omega):
- setdet('d3')
+ tthdet.set('d3')
sleep(1)
uan(0,omega)
dscanz(-750,750,50)
sleep(1)
- n=LastMDA()
+ n=last_mda()
#fit_mda(n,25,0,'poly',graph=False)
#z0=fit_z(n)
#print('z0 = '+str(round(z0,0)))
@@ -82,12 +87,12 @@ def align_z0(omega):
def align_z180(omega):
- setdet('d3')
+ tthdet.set('d3')
sleep(1)
uan(0,180+omega)
dscanz(-750,750,50)
sleep(1)
- n=LastMDA()
+ n=last_mda()
#fit_mda(n,25,0,'poly',graph=False)
#z180=fit_z(n)
#print('z180 = '+str(round(z180,0)))
@@ -95,15 +100,15 @@ def align_z180(omega):
#return z180
def align_th0(omega,z):
- setdet('d4')
+ tthdet.set('d4')
sleep(1)
#uan(20,10+omega)
uan(30,15+omega)
mvz(z)
sleep(30)
- setgain('d4',1,'nA')
+ d4.setgain(1,'nA')
dscanth(-0.25,0.25,0.01)
- n=LastMDA()
+ n=last_mda()
fit_mda(n,25,0,'poly',graph=False)
th_spec=fit_d4(n)
print('th specular = '+str(round(th_spec,3)))
@@ -115,14 +120,14 @@ def align_th0(omega,z):
def align_th180(omega,z):
- setdet('d4')
+ tthdet.set('d4')
sleep(1)
uan(-30,180+omega-15)
#uan(-20,180+omega-10)
mvz(z)
- setgain('d4',1,'nA')
+ d4.setgain(1,'nA')
dscanth(-0.25,0.25,0.01)
- n=LastMDA()
+ n=last_mda()
fit_mda(n,25,0,'poly',graph=False)
th_spec=fit_d4(n)
print('th specular = '+str(round(th_spec,3)))
@@ -147,13 +152,13 @@ def Opt_d4(iteration,moveZ,graph='y',srs=None,start=-0.5,stop=0.5,step=0.04):
current_det=caget('29idKappa:userStringSeq6.STR1',as_string=True)
if current_det != 'd4':
print('Switching detector to d4')
- setdet('d4')
+ tthdet.set('d4')
mvtth(0)
if moveZ is not None:
mvz(z-1000)
for i in range(iteration):
scantth(start,stop,step,'relative')
- scannum=LastMDA()
+ scannum=last_mda()
tth0=fit_mda(scannum,det,tth_w,'gauss',graph=graph)
mvtth(tth0)
mvz(z)
@@ -164,7 +169,7 @@ def Opt_z0(iteration,movetth,movekth,det='d4',srs=None,graph='y'):
current_det=caget('29idKappa:userStringSeq6.STR1',as_string=True)
if current_det != det:
print('Switching detector to '+det)
- setdet(det)
+ tthdet.set(det)
if det=='d3' and srs==None: det=20
if det=='d3' and srs!=None: det=33
if det=='d4' and srs==None: det=21
@@ -175,11 +180,11 @@ def Opt_z0(iteration,movetth,movekth,det='d4',srs=None,graph='y'):
mvkth(movekth)
if iteration>1:
scanz(-2000,2000,250,'relative')
- scannum=LastMDA()
+ scannum=last_mda()
z0=fit_mda(scannum,det,z_w,'erf',graph=graph)
mvz(z0)
scanz(-700,700,50,'relative')
- scannum=LastMDA()
+ scannum=last_mda()
z0=fit_mda(scannum,det,z_w,'erf',graph=graph)
mvz(z0)
return z0,scannum
@@ -188,7 +193,7 @@ def Opt_kth(kth_0,theta,det='d4',srs=None,graph='y'):
current_det=caget('29idKappa:userStringSeq6.STR1',as_string=True)
if current_det != det:
print('Switching detector to '+det)
- setdet(det)
+ tthdet.set(det)
if det == 'd4':
if srs==None: det=21
else: det=34
@@ -200,12 +205,12 @@ def Opt_kth(kth_0,theta,det='d4',srs=None,graph='y'):
mvtth(theta*2)
mvkth(kth_0+theta)
scankth(-0.5*i,0.5*i,0.05*i,'relative')
- new_kth=fit_mda(LastMDA(),det,0.1,'gauss',graph=graph)
+ new_kth=fit_mda(last_mda(),det,0.1,'gauss',graph=graph)
mvkth(new_kth)
scankth(-0.2*i,0.2*i,0.02*i,'relative')
- new_kth=fit_mda(LastMDA(),det,0.1,'gauss',graph=graph)
+ new_kth=fit_mda(last_mda(),det,0.1,'gauss',graph=graph)
mvkth(new_kth)
- scannum=LastMDA()
+ scannum=last_mda()
kth0=round(new_kth-theta,3)
print('\nkth0 = ',kth0)
print('To plot use:')
diff --git a/iexcode/macros/quick_plot.py b/iexcode/macros/quick_plot.py
index c49d213..f8210df 100755
--- a/iexcode/macros/quick_plot.py
+++ b/iexcode/macros/quick_plot.py
@@ -1,24 +1,11 @@
-"""
-#ScanFunctions_plot.py
-how to copy tabs in stabs and not spaces jupyter
-
-For Fanny: Converting spaces to tabs from the terminal
-cp ScanFunctions_IEX.py ScanFunctions_IEXbackup.py
-sed -e 's/ /\t/g' ScanFunctions_IEXbackup.py > ScanFunctions_IEX.py
-"""
-#### Other utilities:
-import csv
from os import listdir
from os.path import join, isfile, dirname
+
+### Data analysis:
from scipy.optimize import curve_fit
from scipy.special import erf
import numpy.polynomial.polynomial as poly
-import ast
-
-### Data analysis:
-from inspect import CO_ASYNC_GENERATOR
-from sre_constants import CATEGORY_DIGIT
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
@@ -28,15 +15,10 @@ from netCDF4 import Dataset
##### APS / 29ID-IEX:
-from IEX_plotting_and_analysis.mda import readMDA,scanDim
-from IEX_plotting_and_analysis.IEX_nData import *
-
-try:
- from epics import caget
- from ..instruments.IEX_BL_config import BL
- from ..instruments.utilities import read_dict,today
- from ..instruments.slits import apertures_set
- from IEXcode.iexcode.current_amplifiers import current2flux
+from epics import caget
+from iexplot.mda import readMDA,scanDim
+import iexcode.instruments.cfg as iex
+from iexcode.instruments.current_amplifiers import current2flux
except:
print("EPICS package and dependent functions are not installed")
@@ -146,9 +128,9 @@ def mda_unpack(ScanNum,filepath=None,prefix=None):
"""
try:
if filepath is None:
- filepath = BL.mda.filepath
+ filepath = iex.BL.mda.filepath()
if prefix is None:
- prefix = BL.mda.prefix
+ prefix = iex.BL.mda.prefix()
except:
print('Please specify filepath and prefix, BL is not defined')
@@ -1243,7 +1225,7 @@ def fit_mda(scannum,det,FWHM_or_PolyOrder,fct,hkl_positionner=False,xrange=None,
- if BL.endstation == 'Kappa' and fct != 'poly':
+ if iex.BL.endstation_name == 'kappa' and fct != 'poly':
try:
title=title + ' centroid = '+str(centroid_avg(scannum))
except:
@@ -1525,21 +1507,21 @@ def fit_hkl(mydata,n,pos,det,FWHM,fct='gauss',xrange=None,title='',marker='x',gr
return center
-def fit_d4(n=BL.mda.lastFileNum()):
+def fit_d4(n=iex.BL.mda.lastFileNum()):
d4=fit_mda(n,34,0.1,'gauss',title='mda_'+str(n).zfill(4))
return round(d4,3)
-def fit_d3(n=BL.mda.lastFileNum()):
+def fit_d3(n=iex.BL.mda.lastFileNum()):
d3=fit_mda(n,33,3,'gauss',title='mda_'+str(n).zfill(4))
return round(d3,3)
-def fit_z(n=BL.mda.lastFileNum(),d=33):
+def fit_z(n=iex.BL.mda.lastFileNum(),d=33):
z=fit_mda(n,d,500,'erf',title='mda_'+str(n).zfill(4))
return round(z,0)
def plotd():
dets=[34,33,35]
- n=BL.mda.lastFileNum()
+ n=iex.BL.mda.lastFileNum()
d=dets[caget('29idKappa:det:set')]
plot_mda(n,d,title='mda_'+str(n).zfill(4))
@@ -1805,7 +1787,7 @@ class mdaFile:
def __init__(self,first=1,last=None,name='mydata',filepath=None,prefix=None,q=False):
if filepath == None:
- filepath = BL.mda.filepath()
+ filepath = iex.BL.mda.filepath()
self.path = filepath
self._name = name
self._first = first
--
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