add preliminary PBMotionAnalyzer.py

This commit is contained in:
2016-12-22 10:13:32 +01:00
parent b98456b6ad
commit 6e31c7e705
6 changed files with 235 additions and 181 deletions

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#!/usr/bin/env python
# *-----------------------------------------------------------------------*
# | |
# | Copyright (c) 2015 by Paul Scherrer Institute (http://www.psi.ch) |
# | |
# | Author Thierry Zamofing (thierry.zamofing@psi.ch) |
# *-----------------------------------------------------------------------*
'''
gathers data on powerpmac and plot
#mode bits:
0 1 configure acquisition -> needs -c
1 2 start acquisition ->Gather.Enable=2
2 4 stop acquisition ->Gather.Enable=0
3 8 wait acquisition stopped ->while(1){if(Gather.Enable==0) break}
4 16 upload acquisition
5 32 plot acquisition -> needs -a (or -c)
mode 1+2+8+16+32 | user sets a stop
mode 1+2 | motion, wait some time| #mode 4+16+32
mode 1+8+16+32 | start acqu, do motion stop acqu.
verbose bits:
1 basic info
2 wait progress
4 upload progress
#config file example:
{
"channels": [
"Motor[1].ActPos",
"Motor[9].ActPos",
"Motor[10].ActPos",
"Motor[11].ActPos",
"PowerBrick[0].GpioData[0]"
],
"axes": [
[0, "b", "ActPos 1"],
[1, "g", "ActPos_9"],
[2, "r", "ActPos_10"],
[3, "m", "ActPos_11"],
[4, ["bits", 15, 3], "GPIO"]],
"gather": {
"MaxSamples":1000,
"Period":10
}
}
Acquired time is:MaxSamples*Period*.2
'''
#gatherPlot
#channels -c '[Sys.ServoCount,Motor[1].ActPos,Motor[9].ActPos,Motor[10].ActPos,Motor[11].ActPos,PowerBrick[0].GpioData[0]]'
#axis -a '(((0,1),'b','ActPos 1'), ((0,2),'g','ActPos 9'), ((0,3),'r','ActPos 10'), ((0,4),'m','ActPos 11'), ((0,5),('bits',14,18),'GPIO'))
#('bits',14,18) means decode bits 14-18
#
#check: Gather.Enable Gather.Index
#on PPMAC do something like:
#Gather.Items=6
#Gather.MaxSamples=10000
#Gather.Period=10
#Gather.Addr[0]=Sys.ServoCount.a
#Gather.Addr[1]=Motor[1].ActPos.a
#Gather.Addr[2]=Motor[9].ActPos.a
#Gather.Addr[3]=Motor[10].ActPos.a
#Gather.Addr[4]=Motor[11].ActPos.a
#Gather.Addr[5]=PowerBrick[0].GpioData[0].a
#
#Gather.Enable=2
## move the motor[1]
#Gather.Enable=0
#
#1;&1;#1->1000X
#k;j=0;P1=1000
#b3r
# to run that script without password, make first an ssh connection e.g. ssh root@PPMACZT84
#
import os, sys, json
import numpy as np
import matplotlib as mpl
import subprocess as sprc
class GatherPlot:
def __init__(self):
pass
def plot1(self):
import matplotlib.pyplot as plt
fnLoc='/tmp/gather.txt'
data = np.genfromtxt(fnLoc, delimiter=' ')
x=np.arange(data.shape[0])*2. #-> msec
pass #-> needs -a (or -c)
fig=plt.figure()
ax0 = fig.add_subplot(1,1,1)
ax0.set_xlabel('msec')
ax=[ax0,]
axArgs=[(0,'r','A'),(1,'g','B'),(2,'b','C')]
for i in range(len(axArgs)-1):
ax.append(ax0.twinx())
fig.subplots_adjust(right=0.75)
n=(len(ax)-2);dx=.2/n
for i in range(n):
ax[2+i].spines['right'].set_position(('axes', 1+dx*(1+i)))
ax[2+i].set_frame_on(True)
ax[2+i].patch.set_visible(False)
for i in range(len(axArgs)):
idx,param,lbl=axArgs[i]
col=param
ax[i].set_ylabel(lbl, color=col)
ax[i].plot(x, data[:,idx], color=col)
ax[i].tick_params(axis='y', colors=col)
plt.show()
def plot(self):
import matplotlib.pyplot as plt
fnLoc='/tmp/gather.txt'
data = np.genfromtxt(fnLoc, delimiter=' ')
fig=plt.figure()
ax0 = fig.add_subplot(1,1,1)
ax0.set_xlabel('msec')
ax=[ax0,]
#fig.subplots_adjust(right=0.75)
col='b'
#idx=1
#ax[0].set_ylabel(ch[idx], color=col)
x=data[:,1]
y=data[:,2]
hl=ax[0].plot(x, y, color=col)
ax[0].tick_params(axis='y', colors=col)
cid = fig.canvas.mpl_connect('scroll_event', self.onclick)
fig.obj=self
self.data=data
#self.ch=ch
self.idx=1
self.ax=ax
self.col=col
self.hl=hl
plt.show()
@staticmethod
def onclick(event):
#print 'button=%s, x=%d, y=%d, xdata=%f, ydata=%f'%(
# event.button, event.x, event.y, event.xdata, event.ydata)
obj=event.canvas.figure.obj
if event.button=='up':
if obj.idx<len(obj.ch)-1:
obj.idx+=1
else:
if obj.idx>0:
obj.idx-=1
obj.ax[0].set_ylabel(obj.ch[obj.idx], color=obj.col)
d=obj.data[:,obj.idx]
if obj.args.diff:
d=np.diff(d)
obj.hl[0].set_ydata(d)
#obj.ax[0].plot(x, obj.data[:,obj.idx]obj.data[:,obj.idx]obj.data[:,obj.idx], color=obj.col)
min=bottom=d.min()
max=d.max()
delta=(max-min)/10.
obj.ax[0].set_ylim(bottom=min-delta,top=max+delta,emit=True,auto=True)
event.canvas.figure.show()
if __name__=='__main__':
gp=GatherPlot()
gp.plot()

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#!/usr/bin/env python
# *-----------------------------------------------------------------------*
# | |
# | Copyright (c) 2016 by Paul Scherrer Institute (http://www.psi.ch) |
# | |
# | Author Thierry Zamofing (thierry.zamofing@psi.ch) |
# *-----------------------------------------------------------------------*
'''
shape an optimal path with given points
verbose bits:
1 basic info
2 plot sorting steps
4 list program
4 upload progress
8 plot gather path
#config file example:
{
"points": [
[100,523],[635,632],[756,213],
"sequencer":[
'gen_grid_points(w=10,h=10,pitch=100,rnd=.2)',
'sort_points()',
'gen_prog(file="/tmp/shapepath.prg")',
'plot_gather()']
}
Sequencer functions are:
- generate points (if not in the 'points' configuration)
gen_rand_points(self,n=107,scale=1000)
gen_grid_points(w=10,h=10,pitch=100,rnd=.2)
- sorting points:
sort_points(self)
- generate/download/execute motion progran, upload trace of motors (gather data)
gen_prog(self,prgId=2,file=None,host=None)
if host=None nothing will be downloaded/executed and trace of motors will not be uploaded
if file=None the program will not be saved and nothing will be executed
- plot gathered data
plot_gather()
this makes only sence, if motion has been executed and data can be gathered from the powerbrick
Acquired time is:MaxSamples*Period*.2
'''
import os, sys, json
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import subprocess as sprc
import telnetlib
from utilities import *
class ShapePath:
def __init__(self,args):
if args.cfg:
fh=open(args.cfg,'r')
s=fh.read()
cfg=json.loads(s, object_hook=ConvUtf8)
s=json.dumps(cfg, indent=2, separators=(',', ': '));print s
else:
#cfg={"points": [[100,523],[635,632],[756,213]],"sequencer":['sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
#cfg={"sequencer":['gen_rand_points(n=107, scale=1000)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
#cfg={"sequencer":['gen_grid_points(w=10,h=10,pitch=100,rnd=.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
#cfg={"sequencer":['gen_grid_points(w=10,h=10,pitch=100,rnd=0.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg")','plot_gather()']}
#cfg = {"sequencer": ['gen_rand_points(n=107, scale=1000)', 'sort_points()','plot_gather()']}
cfg={"sequencer":['gen_grid_points(w=20,h=20,pitch=50,rnd=.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
cfg={"sequencer":['gen_grid_points(w=20,h=20,pitch=50,rnd=.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg")','plot_gather()']}
#cfg={"sequencer":['gen_rand_points(n=400, scale=1000)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
self.cfg=dotdict(cfg)
self.args=args
def run(self):
print('args='+str(self.args))
print('cfg='+str(self.cfg))
try:
self.points=np.array(self.cfg.points)
except AttributeError:
pass
try:
sequencer= self.cfg.pop('sequencer')
except KeyError:
print('no command sequence to execute')
else:
dryrun=self.args.dryrun
for cmd in sequencer:
print '>'*5+' '+cmd+' '+'<'*5
if not dryrun:
eval('self.' + cmd)
def gen_rand_points(self,n=107,scale=1000):
np.random.seed(0)
#data=np.random.randint(0,1000,(30,2))
pts=np.random.rand(n,2)*scale
self.points=pts
def gen_grid_points(self,w=10,h=10,pitch=100,rnd=.2):
np.random.seed(0)
xx,yy=np.meshgrid(range(w), range(h))
pts=np.array([xx.reshape(-1),yy.reshape(-1)],dtype=np.float).transpose()*pitch
if rnd != 0:
pts+=(np.random.rand(pts.shape[0],2)*(rnd*pitch))
self.points=pts
def gen_prog(self,prgId=2,file=None,host=None,mode=0):
prg=[]
gather={"MaxSamples":100000, "Period":10 }
#channels=["Motor[1].ActPos","Motor[2].ActPos","Motor[3].ActPos"]
channels=["Motor[1].ActPos","Motor[2].ActPos","Motor[3].ActPos","Motor[1].DesPos","Motor[2].DesPos","Motor[3].DesPos"]
prg.append('Gather.Enable=0')
prg.append('Gather.Items=%d'%len(channels))
for k,v in gather.iteritems():
prg.append('Gather.%s=%d'%(k,v))
for i,c in enumerate(channels):
prg.append('Gather.Addr[%d]=%s.a'%(i,c))
prg.append('open prog %d'%(prgId))
# this uses Coord[1].Tm and limits with MaxSpeed
prg.append('Gather.Enable=2')
if mode==0:
prg.append(' linear abs')
data=self.points
for idx in range(data.shape[0]):
prg.append('X(%f) Y(%f)'%tuple(data[idx,:]))
prg.append('dwell 100')
if mode==1:
pass
prg.append('Gather.Enable=0')
prg.append('close')
prg.append('&1\nb%dr\n'%prgId)
if self.args.verbose & 4:
for ln in prg:
print(ln)
if file is not None:
fh=open(file,'w')
fh.write('\n'.join(prg))
fh.close()
if host is not None:
cmd ='gpasciiCommander --host '+host+' '+ file
print cmd
p = sprc.Popen(cmd, shell=True)#, stdout=sprc.PIPE, stderr=sprc.STDOUT)
#res=p.stdout.readlines(); print res
retval = p.wait()
#gather -u /var/ftp/gather/out.txt
cmd ='PBGatherPlot -m24 -v7 --host '+host
print cmd
p = sprc.Popen(cmd, shell=True)#, stdout=sprc.PIPE, stderr=sprc.STDOUT)
retval = p.wait()
self.prg=prg
def sort_points(self):
pts=self.points
verb=self.args.verbose
#if verb&2:
# self.plot_points(pts)
#sort points along y
pts=pts[pts[:, 1].argsort()]
#if verb&2:
# self.plot_points(pts)
#group sorting
cnt=pts.shape[0]
idx=np.ndarray(cnt,dtype=np.int32)
grp_cnt=int(np.sqrt(cnt))
grp_sz=int(np.ceil(float(cnt)/grp_cnt))
for i in range(grp_cnt):
a=i*grp_sz
#print a,a+grp_sz
if i%2:
idx[a:a+grp_sz]=a+pts[a:a+grp_sz,0].argsort()[::-1]
else:
idx[a:a+grp_sz]=a+pts[a:a+grp_sz,0].argsort()
#print(idx)
pts=pts[idx]
if verb&2:
self.plot_points(pts)
plt.show()
self.points=pts
@staticmethod
def onclick(event):
print 'button=%s, x=%d, y=%d, xdata=%f, ydata=%f'%(
event.button, event.x, event.y, event.xdata, event.ydata)
obj=event.canvas.figure.obj
def plot_points(self,pts):
fig=plt.figure()
ax = fig.add_subplot(1,1,1)
#hl=ax[0].plot(x, y, color=col)
hl=ax.plot(pts[:,0],pts[:,1],'r.')
hl=ax.plot(pts[:,0],pts[:,1],'y--')
cid = fig.canvas.mpl_connect('button_press_event', self.onclick)
fig.obj=self
self.ax=ax
self.hl=hl
def plot_gather(self,fnLoc='/tmp/gather.txt'):
pts=self.points
rec = np.genfromtxt(fnLoc, delimiter=' ')
fig=plt.figure()
ax = fig.add_subplot(1,1,1)
#hl=ax[0].plot(x, y, color=col)
hl=ax.plot(pts[:,0],pts[:,1],'r.')
hl=ax.plot(pts[:,0],pts[:,1],'y--')
hl = ax.plot(rec[:, 4], rec[:, 5], 'b-')
hl=ax.plot(rec[:,1],rec[:,2],'g-')
ax.xaxis.set_label_text('x-pos um')
ax.yaxis.set_label_text('y-pos um')
cid = fig.canvas.mpl_connect('button_press_event', self.onclick)
fig.obj=self
self.ax=ax
self.hl=hl
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
err=np.sqrt((rec[:,1]-rec[:,4])**2+(rec[:,1]-rec[:,4])**2)
hl = ax.plot(err, 'r-')
ax.xaxis.set_label_text('time (10x servo cycle)')
ax.yaxis.set_label_text('pos-error um')
plt.show()
if __name__=='__main__':
from optparse import OptionParser, IndentedHelpFormatter
class MyFormatter(IndentedHelpFormatter):
'helper class for formating the OptionParser'
def __init__(self):
IndentedHelpFormatter.__init__(self)
def format_epilog(self, epilog):
if epilog:
return epilog
else:
return ""
def parse_args():
'main command line interpreter function'
#usage: gpasciiCommunicator.py --host=PPMACZT84 myPowerBRICK.cfg
(h, t)=os.path.split(sys.argv[0]);cmd='\n '+(t if len(h)>3 else sys.argv[0])+' '
exampleCmd=('--host=PPMAC1391 -m 63 --cfg gather.cfg',
'samplePowerBrick.cfg',
'-n stackCheck1.cfg',
'--host=PPMACZT84 stackCheck1.cfg',
'--host=PPMACZT84 stackCheck1.cfg -v15',
)
epilog=__doc__+'''
Examples:'''+''.join(map(lambda s:cmd+s, exampleCmd))+'\n '
fmt=MyFormatter()
parser=OptionParser(epilog=epilog, formatter=fmt)
parser.add_option('-v', '--verbose', type="int", dest='verbose', help='verbosity bits (see below)', default=0)
parser.add_option('-n', '--dryrun', action='store_true', help='dryrun to stdout')
parser.add_option('--cfg', help='config file containing json configuration structure')
(args, other)=parser.parse_args()
args.other=other
sp=ShapePath(args)
sp.run()
#------------------ Main Code ----------------------------------
#ssh_test()
ret=parse_args()
exit(ret)

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#!/usr/bin/env python
#*-----------------------------------------------------------------------*
#| |
#| Copyright (c) 2016 by Paul Scherrer Institute (http://www.psi.ch) |
#| |
#| Author Thierry Zamofing (thierry.zamofing@psi.ch) |
#*-----------------------------------------------------------------------*
'''
utilities classes
'''
import logging, h5py, re, zlib, zmq, json
import numpy as np
from libDetXR import *
import time
class dotdict(dict):
"""dot.notation access to dictionary attributes"""
def __init__(self,arg=None,**kwargs):
if arg!=None:
self.__fill__(arg)
self.__fill__(kwargs)
def __fill__(self,kw):
for k,v in kw.iteritems():
if type(v)==dict:
self[k]=dotdict(v)
else:
self[k]=v
if type(v)==list:
for i,w in enumerate(v):
if type(w)==dict:
v[i]=dotdict(w)
pass
def __dir__(self):
l=dir(object)
#l.extend(self.keys())
l.extend(map(str,self.keys()))
return l
def __getattr__(self, attr):
#return self.get(attr)
try:
return self[attr]
except KeyError as e:
raise AttributeError("%r instance has no attribute %r" % (self.__class__, attr))
def __repr__(self):
return '<' + dict.__repr__(self)[1:-1] + '>'
def PrettyPrint(self,indent=0):
for k,v in self.iteritems():
if type(v)==dotdict:
print ' '*indent,str(k)+':'
v.PrettyPrint(indent+2)
else:
print ' '*indent+str(k)+'\t'+str(v)
__setattr__= dict.__setitem__
__delattr__= dict.__delitem__
#__getattr__= dict.__getattr__
def ConvUtf8(s):
'convert unicoded json object to ASCII encoded'
#http://stackoverflow.com/questions/956867/how-to-get-string-objects-instead-of-unicode-ones-from-json-in-python
if isinstance(s, dict):
return {ConvUtf8(key): ConvUtf8(value) for key, value in s.iteritems()}
elif isinstance(s, list):
return [ConvUtf8(element) for element in s]
elif isinstance(s, unicode):
return s.encode('utf-8')
else:
return s
class GpasciiCommunicator():
'''Communicates with the Delta Tau gpascii programm
'''
gpascii_ack="\x06\r\n"
gpascii_inp='Input\r\n'
def connect(self, host, username='root', password='deltatau',prompt='ppmac# '):
p=telnetlib.Telnet(host)
print p.read_until('login: ')
p.write(username+'\n')
print p.read_until('Password: ')
p.write(password+'\n')
print p.read_until(prompt) # command prompt
p.write('gpascii -2\n') # execute gpascii command
print p.read_until(self.gpascii_inp)
return p