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srx-coord-energy-sdd.py
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srx-coord-energy-sdd.py
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#! /usr/bin/env /usr/bin/python2.7
#backwards compatible (i.e., reverts to X raster move Y, hfm, vhm scan if no Z
#values given) three dimensional fast mirror scan. Scan is likely to be very
#fast with respect to motor heating issues. use --wait command line option
#if two transverse stages are scanned with sub-millimeter steps
#add file logging
#ycchen 03/12/15, modified one line to include current readout from bpm02: if detstr=='xf05bpm03' or detstr=='xf05bpm04':
#drop electron BPM readbacks and add preliminary support for xspress3
#refine support for xspress3. push configuration from script, write a single hdf5
import signal
import sys
import os
import time
from epics import PV
import math
from optparse import OptionParser
import string
import decimal
import matplotlib.pyplot as plt
import numpy as np
import srxslit
import SRXenergy
#can we signal handle in python??
def sigint_handler(signal,frame):
global simulate
global fp
if simulate != True:
fp.close()
x3h5capture.put(0)
print "!!!!!!!!! stopped"
else:
print "Ctrl-C detected...exiting"
sys.exit()
signal.signal(signal.SIGINT,sigint_handler)
def sigtstp_handler(signal,frame):
print "Ctrl-z detected. Scan paused."
raw_input('Press enter to resume.')
signal.signal(signal.SIGTSTP,sigtstp_handler)
#target array: (xpos, at_position)(ypos, at_position)
tar = []
tar.append([])
tar[0].append(0.)
tar[0].append(1)
tar.append([])
tar[1].append(0.)
tar[1].append(1)
tar.append([])
tar[2].append(0.)
tar[2].append(1)
#deadband in motor units
dbd = .001
#simulate motor moves
simulate=False
global shut_open
shut_open = False
global current
current = False
global T_stop
T_stop = False
global x3h5capture
x3h5capture=PV('XSPRESS3-EXAMPLE:HDF5:Capture')
def cbf_shut(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
global shut_open
if value==1:
shut_open=True
else:
shut_open=False
def cbf_curr(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
global current
if value<50.:
current=False
else:
current=True
#callback to check on motor position
def cbfx(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
if indeadband(float(tar[0][0]),float(value),dbd)==1:
tar[0][1] = 0
else:
tar[0][1] = 1
def cbfy(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
if indeadband(float(tar[1][0]),float(value),dbd)==1:
tar[1][1] = 0
else:
tar[1][1] = 1
def cbfz(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
if indeadband(float(tar[2][0]),float(value),dbd)==1:
tar[2][1] = 0
else:
tar[2][1] = 1
def cbf_temp(pvname=None,value=None,char_value=None,type=None,enum_strs=None,**kw):
#thresh_temp=80.
thresh_temp = 120.
global T_stop
if (value > thresh_temp):
T_stop=True
else:
T_stop=False
#manual deadband
def indeadband(com,act,dbd):
if math.fabs(math.fabs(com)-math.fabs(act))<float(dbd):
return 1
else:
return 0
def main(argv=None):
global dbd
global simulate
global fp
global shut_open
global current
global T_stop
dSi111=SRXenergy.d111
dbragg=SRXenergy.dBragg
#parse command line options
usage = "usage: %prog [options]\nData files are written to /data/<year>/<month>/<day>/"
parser = OptionParser(usage)
parser.add_option("--wait", action="store", type="float", dest="stall", help="wait at each step [seconds]")
parser.add_option("--config",action="store", type="string", dest="fname", help="name of config file")
parser.add_option("--simulate", action="store_true", dest="sim", default=False, help="simulate motor moves and bursting")
parser.add_option("--checkbeam", action="store_true", dest="checkbeam", default=False, help="only acquire when beam is on")
parser.add_option("--acqtime", action="store", type="float", dest="acqt", help="image integration time [sec]")
parser.add_option("--acqnum", action="store", type="int", dest="acqn", help="images to collect")
(options,args) = parser.parse_args()
#open log file
D0=time.localtime()[0]
D1=time.localtime()[1]
D2=time.localtime()[2]
D3=time.localtime()[3]
D4=time.localtime()[4]
cd=os.getcwd()
fstr='/nfs/xf05id1/data/'
if sys.argv[0][0]=='.':
out_filename=fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/'+'log_'+repr(D0)+'_'+repr(D1)+'_'+repr(D2)+'_'+repr(D3)+'_'+repr(D4)+'_'+\
string.split(string.strip(sys.argv[0],'./'),'/')[0]+'.txt'
else:
out_filename=fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/'+'log_'+repr(D0)+'_'+repr(D1)+'_'+repr(D2)+'_'+repr(D3)+'_'+repr(D4)+'_'+\
string.split(string.strip(sys.argv[0],'./'),'/')[5]+'.txt'
try:
os.chdir(fstr+repr(D0))
except OSError:
try:
os.mkdir(fstr+repr(D0))
except Exception:
print 'cannot create directory: '+fstr+repr(D0)
sys.exit()
try:
os.chdir(fstr+repr(D0)+'/'+repr(D1))
except OSError:
try:
os.mkdir(fstr+repr(D0)+'/'+repr(D1))
except Exception:
print 'cannot create directory: '+fstr+repr(D0)+'/'+repr(D1)
sys.exit()
try:
os.chdir(fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2))
except OSError:
try:
os.mkdir(fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2))
except Exception:
print 'cannot create directory: '+fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)
sys.exit()
try:
fp=open(out_filename,'a')
except Exception:
print 'cannot open file: '+out_filename
sys.exit()
try:
os.chdir(fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/'+'HDF5')
except OSError:
try:
os.mkdir(fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/'+'HDF5')
except Exception:
print 'cannot create directory: '+fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/'+'HDF5'
sys.exit()
# H5path=fstr+repr(D0)+'/'+repr(D1)+'/'+repr(D2)+'/HDF5'
#H5path='/epics/data/2015-3/300198'
H5path='/epics/data/2015-3/in-house'
os.chdir(cd)
fp.write('#')
fp.write(', '.join(sys.argv))
fp.write('\n')
#open list of scan points
try:
fconfig=open(options.fname)
except Exception:
print "cannot open file containing scan points. Error opening: "+options.fname
sys.exit()
fstr='#a default string'
pN=0
angle=list()
ivu=list()
t2gap=list()
while fstr.rsplit().__len__() > 0:
if (fstr[0] is not '#'):
pN=pN+1
angle.append(fstr.rsplit()[0])
ivu.append(fstr.rsplit()[1])
t2gap.append(fstr.rsplit()[2])
fstr=fconfig.readline()
fconfig.close()
#initialize PVs and callbacks
detstr='XF:05IDA{IM:1}'
bmot = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:P}Mtr.VAL')
bmot_cur = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:P}Mtr.RBV')
bmot_stop = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:P}Mtr.STOP')
umot = PV('SR:C5-ID:G1{IVU21:1-Mtr:2}Inp:Pos')
umot_cur = PV('SR:C5-ID:G1{IVU21:1-LEnc}Gap')
umot_go = PV('SR:C5-ID:G1{IVU21:1-Mtr:2}Sw:Go')
gmot = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:X2}Mtr.VAL')
gmot_cur = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:X2}Mtr.RBV')
gmot_stop = PV('XF:05IDA-OP:1{Mono:HDCM-Ax:X2}Mtr.STOP')
shut_status=PV('SR:C05-EPS{PLC:1}Shutter:Sum-Sts')
beam_current=PV('SR:C03-BI{DCCT:1}I:Total-I')
bragg_temp=PV('XF:05IDA-OP:1{Mono:HDCM-Ax:P}T-I')
norm0=PV('XF:05IDD-BI:1{BPM:01}.S20')
norm1=PV('XF:05IDD-BI:1{BPM:01}.S21')
norm2=PV('XF:05IDD-BI:1{BPM:01}.S22')
norm3=PV('XF:05IDD-BI:1{BPM:01}.S23')
wb=srxslit.nsls2slit(tb='XF:05IDA-OP:1{Slt:1-Ax:T}',bb='XF:05IDA-OP:1{Slt:1-Ax:B}',ib='XF:05IDA-OP:1{Slt:1-Ax:I}',ob='XF:05IDA-OP:1{Slt:1-Ax:O}')
pb=srxslit.nsls2slit(ib='XF:05IDA-OP:1{Slt:2-Ax:I}',ob='XF:05IDA-OP:1{Slt:2-Ax:O}')
ssa=srxslit.nsls2slit(tb='XF:05IDB-OP:1{Slt:SSA-Ax:T}', bb='XF:05IDB-OP:1{Slt:SSA-Ax:B}', ob='XF:05IDB-OP:1{Slt:SSA-Ax:O}',ib='XF:05IDB-OP:1{Slt:SSA-Ax:I}')
x3acq=PV('XSPRESS3-EXAMPLE:Acquire')
x3erase=PV('XSPRESS3-EXAMPLE:ERASE')
x3acqtime=PV('XSPRESS3-EXAMPLE:AcquireTime')
x3acqnum=PV('XSPRESS3-EXAMPLE:NumImages')
x3tmode=PV('XSPRESS3-EXAMPLE:TriggerMode')
x3h5path=PV('XSPRESS3-EXAMPLE:HDF5:FilePath')
x3h5fname=PV('XSPRESS3-EXAMPLE:HDF5:FileName')
x3h5fnum=PV('XSPRESS3-EXAMPLE:HDF5:FileNumber')
x3h5vdim=PV('XSPRESS3-EXAMPLE:HDF5:NumExtraDims')
x3h5size=PV('XSPRESS3-EXAMPLE:HDF5:ExtraDimSizeN')
x3h5d1=PV('XSPRESS3-EXAMPLE:HDF5:ExtraDimSizeX')
x3h5d2=PV('XSPRESS3-EXAMPLE:HDF5:ExtraDimSizeY')
#report ROIs for channels and counts at each point
x3ch1roi0min=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI1_LLM')
x3ch1roi0max=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI1_HLM')
x3ch1roi0ct=PV('XSPRESS3-EXAMPLE:C1_ROI1:Value_RBV')
x3ch1roi1min=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI2_LLM')
x3ch1roi1max=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI2_HLM')
x3ch1roi1ct=PV('XSPRESS3-EXAMPLE:C1_ROI2:Value_RBV')
x3ch1roi2min=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI3_LLM')
x3ch1roi2max=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI3_HLM')
x3ch1roi2ct=PV('XSPRESS3-EXAMPLE:C1_ROI3:Value_RBV')
x3ch2roi0min=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI1_LLM')
x3ch2roi0max=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI1_HLM')
x3ch2roi0ct=PV('XSPRESS3-EXAMPLE:C2_ROI1:Value_RBV')
x3ch2roi1min=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI2_LLM')
x3ch2roi1max=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI2_HLM')
x3ch2roi1ct=PV('XSPRESS3-EXAMPLE:C2_ROI2:Value_RBV')
x3ch2roi2min=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI3_LLM')
x3ch2roi2max=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI3_HLM')
x3ch2roi2ct=PV('XSPRESS3-EXAMPLE:C2_ROI3:Value_RBV')
x3ch3roi0min=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI1_LLM')
x3ch3roi0max=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI1_HLM')
x3ch3roi0ct=PV('XSPRESS3-EXAMPLE:C3_ROI1:Value_RBV')
x3ch3roi1min=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI2_LLM')
x3ch3roi1max=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI2_HLM')
x3ch3roi1ct=PV('XSPRESS3-EXAMPLE:C3_ROI2:Value_RBV')
x3ch3roi2min=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI3_LLM')
x3ch3roi2max=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI3_HLM')
x3ch3roi2ct=PV('XSPRESS3-EXAMPLE:C3_ROI3:Value_RBV')
#claim ROI 4 for our own use. we will integrate over all 4096 channels.
x3ch1roi3min=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI4_LLM')
x3ch1roi3max=PV('XSPRESS3-EXAMPLE:C1_MCA_ROI4_HLM')
x3ch1roi3ct=PV('XSPRESS3-EXAMPLE:C1_ROI4:Value_RBV')
x3ch2roi3min=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI4_LLM')
x3ch2roi3max=PV('XSPRESS3-EXAMPLE:C2_MCA_ROI4_HLM')
x3ch2roi3ct=PV('XSPRESS3-EXAMPLE:C2_ROI4:Value_RBV')
x3ch3roi3min=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI4_LLM')
x3ch3roi3max=PV('XSPRESS3-EXAMPLE:C3_MCA_ROI4_HLM')
x3ch3roi3ct=PV('XSPRESS3-EXAMPLE:C3_ROI4:Value_RBV')
dett=PV('XF:05IDD-ES:1{EVR:1-Out:FP3}Src:Scale-SP')
deti=PV('XF:05IDA{IM:1}Per-SP')
detinit=PV('XF:05IDA{IM:1}Cmd:Init')
det0 = PV(detstr+'Cur:I0-I')
det1 = PV(detstr+'Cur:I1-I')
det2 = PV(detstr+'Cur:I2-I')
det3 = PV(detstr+'Cur:I3-I')
bmot.info
bmot_cur.info
bmot_stop.info
umot.info
umot_cur.info
umot_go.info
gmot.info
gmot_cur.info
gmot_stop.info
det0.info
det1.info
det2.info
det3.info
bragg_temp.info
bmot_cur.add_callback(cbfx)
bmot_cur.run_callbacks()
umot_cur.add_callback(cbfy)
umot_cur.run_callbacks()
gmot_cur.add_callback(cbfz)
gmot_cur.run_callbacks()
shut_status.add_callback(cbf_shut)
beam_current.add_callback(cbf_curr)
shut_status.run_callbacks()
beam_current.run_callbacks()
bragg_temp.add_callback(cbf_temp)
bragg_temp.run_callbacks()
x3h5path.put(H5path)
x3h5fname.put(repr(D0)+'_'+repr(D1)+'_'+repr(D2)+'_'+repr(D3)+'_'+repr(D4)+'_')
x3h5fnum.put(0)
x3acqtime.put(options.acqt)
x3acqnum.put(options.acqn)
x3tmode.put(1)
x3ch1roi3min.put(0)
x3ch2roi3min.put(0)
x3ch3roi3min.put(0)
x3ch1roi3max.put(4096)
x3ch2roi3max.put(4096)
x3ch3roi3max.put(4096)
#h5 set up
x3h5vdim.put(1)
x3h5size.put(options.acqn)
x3h5d1.put(pN)
x3h5d2.put(0)
roits=x3ch3roi3ct.timestamp
dett.put(3)
#overhead on triggering F460
deti.put(float(options.acqn)*options.acqt*.9)
detinit.put(1)
#check command line options
if options.stall == None:
twait = 0.
else:
twait = options.stall
str='#NSLS-II SRX'+time.asctime()
fp.write(str)
fp.write('\n')
str='# Start time is '+time.asctime()
print str
fp.write(str)
fp.write('\n')
if options.sim is True:
str=" -----simulating motor moves and bursts-----"
print str
fp.write(str)
fp.write('\n')
else:
x3h5capture.put(1)
dett.put(4)
time.sleep(2)
while x3h5capture.get() == 0:
time.sleep(0.5)
dett.put(3)
str='# bragg: %(br)6.4f ; undulator: %(un)6.4f ; gap: %(cg)f ; ROI1 %(roi1i)d:%(roi1a)d ; ROI2 %(roi2i)d:%(roi2a)d ; ROI3 %(roi3i)d:%(roi3a)d'%\
{"br":bmot_cur.get(),"un":umot_cur.get(), "cg":gmot_cur.get(),'roi1i':x3ch1roi0min.get(), 'roi1a':x3ch1roi0max.get(), 'roi2i':x3ch1roi1min.get(), 'roi2a':x3ch1roi1max.get(), 'roi3i':x3ch1roi2min.get(), 'roi3a':x3ch1roi2max.get()}
print str
fp.write(str)
fp.write('\n')
str="# --------------------"
print str
fp.write(str)
fp.write('\n')
str="# bragg u-gap c-gap energy I0-1 I0-2 I0-3 I0-4 time ROI-1 ROI-2 ROI-3 ROI-4 intensity"
print str
fp.write(str)
fp.write('\n')
LN=0
oldsig=det0.get()
t0=time.time()
sig0=0.
sig1=0.
sig2=0.
sig3=0.
nsig0=0.
nsig1=0.
nsig2=0.
nsig3=0.
for x in range(0,pN):
tar[0][1] = 1
tar[0][0] = float(angle[x])
tar[1][1] = 1
tar[1][0] = float(ivu[x])
tar[2][1] = 1
tar[2][0] = float(t2gap[x])
#if tar[0][0] is the original position, raise "in position" flag
if indeadband(float(tar[0][0]),float(bmot_cur.get()),dbd)==1:
tar[0][1] = 0
if indeadband(float(tar[1][0]),float(umot_cur.get()),dbd)==1:
tar[1][1] = 0
if indeadband(float(tar[2][0]),float(gmot_cur.get()),dbd)==1:
tar[2][1] = 0
if options.sim is False:
bmot.put(tar[0][0])
umot.put(tar[1][0])
gmot.put(tar[2][0])
time.sleep(1)
umot_go.put(0)
else:
tar[0][1]=0
tar[1][1]=0
tar[2][1]=0
while (tar[0][1] == 1) or (tar[1][1] == 1) or(tar[2][1] == 1):
time.sleep(0.05)
if LN > 400:
umot_go.put(0)
LN=0
else:
LN=LN+1
if options.sim is False:
time.sleep(twait)
while ( options.checkbeam and (shut_open == False or beam_current == False)) or T_stop==True:
print "Stopped. Waiting for scan conditions to return to normal."
if shut_open == False:
print "\t->shutter is closed"
elif beam_current == False:
print "\t->Ring current is below threshold"
elif T_stop==True:
print "\t->HDCM pitch motor is too hot"
else:
print "\t->why not have a nice cup of tea or hit ctrl-C?"
time.sleep(60.)
x3erase.put(1)
dett.put(4)
nsig0=norm0.get()
nsig1=norm1.get()
nsig2=norm2.get()
nsig3=norm3.get()
#??
# sig0=sig1=sig2=sig3=3
sig0=sig1=sig2=sig3=0
for i in range(0,options.acqn):
x3acq.put(1)
while ( x3ch3roi3ct.get()==0.0 or x3ch3roi3ct.timestamp==roits):
time.sleep(0.02)
sig0=sig0+x3ch1roi0ct.get()+x3ch2roi0ct.get()+x3ch3roi0ct.get()
sig1=sig1+x3ch1roi1ct.get()+x3ch2roi1ct.get()+x3ch3roi1ct.get()
sig2=sig2+x3ch1roi2ct.get()+x3ch2roi2ct.get()+x3ch3roi2ct.get()
sig3=sig3+x3ch1roi3ct.get()+x3ch2roi3ct.get()+x3ch3roi3ct.get()
# sig0=sig0+x3ch2roi0ct.get()+x3ch3roi0ct.get()
# sig1=sig1+x3ch2roi1ct.get()+x3ch3roi1ct.get()
# sig2=sig2+x3ch2roi2ct.get()+x3ch3roi2ct.get()
# sig3=sig3+x3ch2roi3ct.get()+x3ch3roi3ct.get()
roits=x3ch3roi3ct.timestamp
signal0=float(det1.get())
while (signal0==0.0):
signal0=float(det1.get())
# while(signal0 == oldsig):
# signal0=det0.get()
# oldsig=signal0
dett.put(3)
else:
while ( options.checkbeam and (shut_open == False or beam_current == False)):
print "Stopped. Waiting for beam to return."
time.sleep(60.)
signal0=0.
nsig1=0
nsig2=0
nsig3=0
tn=time.time()-t0
if options.sim is False:
# str=' %(B)8.4f %(U)8.4f %(G)8.3f %(E)8.2f %(C0)10.7e %(C1)10.7e %(C2)10.7e %(C3)10.7e %(T)d %(ROI1)d %(ROI2)d %(ROI3)d %(ROI4)d %(T1)10.7e'%{"B":float(bmot_cur.get()), "U":float(umot_cur.get()), "G":float(gmot_cur.get()), "C0":nsig0, "C1":nsig1, "C2":nsig2, "C3":nsig3, "ROI1":sig0,'T':tn,"ROI2":sig1,"ROI3":sig2,"ROI4":sig3,"T1":signal0,"E":12398.4 / (2 * 3.13029665951 * math.sin((bmot_cur.get()+0.323658778534)/180.*np.pi))}
str=' %(B)8.4f %(U)8.4f %(G)8.3f %(E)8.2f %(C0)10.7e %(C1)10.7e %(C2)10.7e %(C3)10.7e %(T)d %(ROI1)d %(ROI2)d %(ROI3)d %(ROI4)d %(T1)10.7e'%{"B":float(bmot_cur.get()), "U":float(umot_cur.get()), "G":float(gmot_cur.get()), "C0":nsig0, "C1":nsig1, "C2":nsig2, "C3":nsig3, "ROI1":sig0,'T':tn,"ROI2":sig1,"ROI3":sig2,"ROI4":sig3,"T1":signal0,"E":12398.4 / (2 * dSi111 * math.sin((bmot_cur.get()+dbragg)/180.*np.pi))}
print str
fp.write(str)
fp.write('\n')
else:
str=' B= %(B)8.4f U= %(U)8.4f G= %(G)8.3f : %(C0)10.7e %(C1)10.7e %(C2)10.7e %(C3)10.7e %(ROI)d %(T)d'%{"B":tar[0][0], "U":tar[1][0], "G":tar[2][0], "C0":signal0, "C1":nsig1, "C2":nsig2, "C3":nsig3, "ROI":x3ch1roi0ct.get(),'T':time.time()}
print str
fp.write(str)
fp.write('\n')
str='#End time is '+time.asctime()
print str
fp.write(str)
fp.write('\n')
fp.close()
return 0
if __name__ == "__main__":
sys.exit(main())