add preliminary PBMotionAnalyzer.py
This commit is contained in:
@@ -1,180 +0,0 @@
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#!/usr/bin/env python
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# *-----------------------------------------------------------------------*
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# | |
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# | Copyright (c) 2015 by Paul Scherrer Institute (http://www.psi.ch) |
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# | |
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# | Author Thierry Zamofing (thierry.zamofing@psi.ch) |
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# *-----------------------------------------------------------------------*
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'''
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gathers data on powerpmac and plot
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#mode bits:
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0 1 configure acquisition -> needs -c
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1 2 start acquisition ->Gather.Enable=2
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2 4 stop acquisition ->Gather.Enable=0
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3 8 wait acquisition stopped ->while(1){if(Gather.Enable==0) break}
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4 16 upload acquisition
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5 32 plot acquisition -> needs -a (or -c)
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mode 1+2+8+16+32 | user sets a stop
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mode 1+2 | motion, wait some time| #mode 4+16+32
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mode 1+8+16+32 | start acqu, do motion stop acqu.
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verbose bits:
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1 basic info
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2 wait progress
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4 upload progress
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#config file example:
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{
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"channels": [
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"Motor[1].ActPos",
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"Motor[9].ActPos",
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"Motor[10].ActPos",
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"Motor[11].ActPos",
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"PowerBrick[0].GpioData[0]"
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],
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"axes": [
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[0, "b", "ActPos 1"],
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[1, "g", "ActPos_9"],
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[2, "r", "ActPos_10"],
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[3, "m", "ActPos_11"],
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[4, ["bits", 15, 3], "GPIO"]],
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"gather": {
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"MaxSamples":1000,
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"Period":10
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}
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}
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Acquired time is:MaxSamples*Period*.2
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'''
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#gatherPlot
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#channels -c '[Sys.ServoCount,Motor[1].ActPos,Motor[9].ActPos,Motor[10].ActPos,Motor[11].ActPos,PowerBrick[0].GpioData[0]]'
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#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'))
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#('bits',14,18) means decode bits 14-18
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#
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#check: Gather.Enable Gather.Index
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#on PPMAC do something like:
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#Gather.Items=6
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#Gather.MaxSamples=10000
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#Gather.Period=10
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#Gather.Addr[0]=Sys.ServoCount.a
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#Gather.Addr[1]=Motor[1].ActPos.a
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#Gather.Addr[2]=Motor[9].ActPos.a
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#Gather.Addr[3]=Motor[10].ActPos.a
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#Gather.Addr[4]=Motor[11].ActPos.a
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#Gather.Addr[5]=PowerBrick[0].GpioData[0].a
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#
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#Gather.Enable=2
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## move the motor[1]
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#Gather.Enable=0
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#
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#1;&1;#1->1000X
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#k;j=0;P1=1000
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#b3r
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# to run that script without password, make first an ssh connection e.g. ssh root@PPMACZT84
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#
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import os, sys, json
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import numpy as np
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import matplotlib as mpl
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import subprocess as sprc
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class GatherPlot:
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def __init__(self):
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pass
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def plot1(self):
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import matplotlib.pyplot as plt
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fnLoc='/tmp/gather.txt'
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data = np.genfromtxt(fnLoc, delimiter=' ')
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x=np.arange(data.shape[0])*2. #-> msec
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pass #-> needs -a (or -c)
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fig=plt.figure()
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ax0 = fig.add_subplot(1,1,1)
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ax0.set_xlabel('msec')
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ax=[ax0,]
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axArgs=[(0,'r','A'),(1,'g','B'),(2,'b','C')]
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for i in range(len(axArgs)-1):
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ax.append(ax0.twinx())
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fig.subplots_adjust(right=0.75)
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n=(len(ax)-2);dx=.2/n
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for i in range(n):
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ax[2+i].spines['right'].set_position(('axes', 1+dx*(1+i)))
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ax[2+i].set_frame_on(True)
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ax[2+i].patch.set_visible(False)
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for i in range(len(axArgs)):
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idx,param,lbl=axArgs[i]
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col=param
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ax[i].set_ylabel(lbl, color=col)
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ax[i].plot(x, data[:,idx], color=col)
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ax[i].tick_params(axis='y', colors=col)
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plt.show()
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def plot(self):
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import matplotlib.pyplot as plt
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fnLoc='/tmp/gather.txt'
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data = np.genfromtxt(fnLoc, delimiter=' ')
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fig=plt.figure()
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ax0 = fig.add_subplot(1,1,1)
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ax0.set_xlabel('msec')
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ax=[ax0,]
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#fig.subplots_adjust(right=0.75)
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col='b'
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#idx=1
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#ax[0].set_ylabel(ch[idx], color=col)
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x=data[:,1]
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y=data[:,2]
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hl=ax[0].plot(x, y, color=col)
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ax[0].tick_params(axis='y', colors=col)
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cid = fig.canvas.mpl_connect('scroll_event', self.onclick)
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fig.obj=self
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self.data=data
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#self.ch=ch
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self.idx=1
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self.ax=ax
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self.col=col
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self.hl=hl
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plt.show()
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@staticmethod
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def onclick(event):
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#print 'button=%s, x=%d, y=%d, xdata=%f, ydata=%f'%(
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# event.button, event.x, event.y, event.xdata, event.ydata)
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obj=event.canvas.figure.obj
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if event.button=='up':
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if obj.idx<len(obj.ch)-1:
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obj.idx+=1
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else:
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if obj.idx>0:
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obj.idx-=1
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obj.ax[0].set_ylabel(obj.ch[obj.idx], color=obj.col)
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d=obj.data[:,obj.idx]
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if obj.args.diff:
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d=np.diff(d)
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obj.hl[0].set_ydata(d)
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#obj.ax[0].plot(x, obj.data[:,obj.idx]obj.data[:,obj.idx]obj.data[:,obj.idx], color=obj.col)
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min=bottom=d.min()
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max=d.max()
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delta=(max-min)/10.
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obj.ax[0].set_ylim(bottom=min-delta,top=max+delta,emit=True,auto=True)
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event.canvas.figure.show()
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if __name__=='__main__':
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gp=GatherPlot()
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gp.plot()
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270
cfg/shapepath.py
270
cfg/shapepath.py
@@ -1,270 +0,0 @@
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#!/usr/bin/env python
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# *-----------------------------------------------------------------------*
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# | |
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# | Copyright (c) 2016 by Paul Scherrer Institute (http://www.psi.ch) |
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# | |
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# | Author Thierry Zamofing (thierry.zamofing@psi.ch) |
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# *-----------------------------------------------------------------------*
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'''
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shape an optimal path with given points
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verbose bits:
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1 basic info
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2 plot sorting steps
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4 list program
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4 upload progress
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8 plot gather path
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#config file example:
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{
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"points": [
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[100,523],[635,632],[756,213],
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"sequencer":[
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'gen_grid_points(w=10,h=10,pitch=100,rnd=.2)',
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'sort_points()',
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'gen_prog(file="/tmp/shapepath.prg")',
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'plot_gather()']
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}
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Sequencer functions are:
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- generate points (if not in the 'points' configuration)
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gen_rand_points(self,n=107,scale=1000)
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gen_grid_points(w=10,h=10,pitch=100,rnd=.2)
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- sorting points:
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sort_points(self)
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- generate/download/execute motion progran, upload trace of motors (gather data)
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gen_prog(self,prgId=2,file=None,host=None)
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if host=None nothing will be downloaded/executed and trace of motors will not be uploaded
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if file=None the program will not be saved and nothing will be executed
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- plot gathered data
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plot_gather()
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this makes only sence, if motion has been executed and data can be gathered from the powerbrick
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Acquired time is:MaxSamples*Period*.2
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'''
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import os, sys, json
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import numpy as np
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import matplotlib as mpl
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import matplotlib.pyplot as plt
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import subprocess as sprc
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import telnetlib
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from utilities import *
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class ShapePath:
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def __init__(self,args):
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if args.cfg:
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fh=open(args.cfg,'r')
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s=fh.read()
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cfg=json.loads(s, object_hook=ConvUtf8)
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s=json.dumps(cfg, indent=2, separators=(',', ': '));print s
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else:
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#cfg={"points": [[100,523],[635,632],[756,213]],"sequencer":['sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
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#cfg={"sequencer":['gen_rand_points(n=107, scale=1000)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
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#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()']}
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#cfg={"sequencer":['gen_grid_points(w=10,h=10,pitch=100,rnd=0.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg")','plot_gather()']}
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#cfg = {"sequencer": ['gen_rand_points(n=107, scale=1000)', 'sort_points()','plot_gather()']}
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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()']}
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cfg={"sequencer":['gen_grid_points(w=20,h=20,pitch=50,rnd=.2)','sort_points()','gen_prog(file="/tmp/shapepath.prg")','plot_gather()']}
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#cfg={"sequencer":['gen_rand_points(n=400, scale=1000)','sort_points()','gen_prog(file="/tmp/shapepath.prg",host="SAROP11-CPPM-MOT6871")','plot_gather()']}
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self.cfg=dotdict(cfg)
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self.args=args
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def run(self):
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print('args='+str(self.args))
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print('cfg='+str(self.cfg))
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try:
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self.points=np.array(self.cfg.points)
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except AttributeError:
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pass
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try:
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sequencer= self.cfg.pop('sequencer')
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except KeyError:
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print('no command sequence to execute')
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else:
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dryrun=self.args.dryrun
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for cmd in sequencer:
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print '>'*5+' '+cmd+' '+'<'*5
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if not dryrun:
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eval('self.' + cmd)
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def gen_rand_points(self,n=107,scale=1000):
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np.random.seed(0)
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#data=np.random.randint(0,1000,(30,2))
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pts=np.random.rand(n,2)*scale
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self.points=pts
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def gen_grid_points(self,w=10,h=10,pitch=100,rnd=.2):
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np.random.seed(0)
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xx,yy=np.meshgrid(range(w), range(h))
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pts=np.array([xx.reshape(-1),yy.reshape(-1)],dtype=np.float).transpose()*pitch
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if rnd != 0:
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pts+=(np.random.rand(pts.shape[0],2)*(rnd*pitch))
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self.points=pts
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def gen_prog(self,prgId=2,file=None,host=None,mode=0):
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prg=[]
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gather={"MaxSamples":100000, "Period":10 }
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#channels=["Motor[1].ActPos","Motor[2].ActPos","Motor[3].ActPos"]
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channels=["Motor[1].ActPos","Motor[2].ActPos","Motor[3].ActPos","Motor[1].DesPos","Motor[2].DesPos","Motor[3].DesPos"]
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prg.append('Gather.Enable=0')
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prg.append('Gather.Items=%d'%len(channels))
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for k,v in gather.iteritems():
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prg.append('Gather.%s=%d'%(k,v))
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for i,c in enumerate(channels):
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prg.append('Gather.Addr[%d]=%s.a'%(i,c))
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prg.append('open prog %d'%(prgId))
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# this uses Coord[1].Tm and limits with MaxSpeed
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prg.append('Gather.Enable=2')
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if mode==0:
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prg.append(' linear abs')
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data=self.points
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for idx in range(data.shape[0]):
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prg.append('X(%f) Y(%f)'%tuple(data[idx,:]))
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prg.append('dwell 100')
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if mode==1:
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pass
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prg.append('Gather.Enable=0')
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prg.append('close')
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prg.append('&1\nb%dr\n'%prgId)
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if self.args.verbose & 4:
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for ln in prg:
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print(ln)
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if file is not None:
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fh=open(file,'w')
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fh.write('\n'.join(prg))
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fh.close()
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if host is not None:
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cmd ='gpasciiCommander --host '+host+' '+ file
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print cmd
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p = sprc.Popen(cmd, shell=True)#, stdout=sprc.PIPE, stderr=sprc.STDOUT)
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#res=p.stdout.readlines(); print res
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retval = p.wait()
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#gather -u /var/ftp/gather/out.txt
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cmd ='PBGatherPlot -m24 -v7 --host '+host
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print cmd
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p = sprc.Popen(cmd, shell=True)#, stdout=sprc.PIPE, stderr=sprc.STDOUT)
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retval = p.wait()
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self.prg=prg
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def sort_points(self):
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pts=self.points
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verb=self.args.verbose
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#if verb&2:
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# self.plot_points(pts)
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#sort points along y
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pts=pts[pts[:, 1].argsort()]
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#if verb&2:
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# self.plot_points(pts)
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#group sorting
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cnt=pts.shape[0]
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idx=np.ndarray(cnt,dtype=np.int32)
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grp_cnt=int(np.sqrt(cnt))
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grp_sz=int(np.ceil(float(cnt)/grp_cnt))
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for i in range(grp_cnt):
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a=i*grp_sz
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#print a,a+grp_sz
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if i%2:
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idx[a:a+grp_sz]=a+pts[a:a+grp_sz,0].argsort()[::-1]
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else:
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idx[a:a+grp_sz]=a+pts[a:a+grp_sz,0].argsort()
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#print(idx)
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pts=pts[idx]
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if verb&2:
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self.plot_points(pts)
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plt.show()
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self.points=pts
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@staticmethod
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def onclick(event):
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print 'button=%s, x=%d, y=%d, xdata=%f, ydata=%f'%(
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event.button, event.x, event.y, event.xdata, event.ydata)
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obj=event.canvas.figure.obj
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def plot_points(self,pts):
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fig=plt.figure()
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ax = fig.add_subplot(1,1,1)
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#hl=ax[0].plot(x, y, color=col)
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hl=ax.plot(pts[:,0],pts[:,1],'r.')
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hl=ax.plot(pts[:,0],pts[:,1],'y--')
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cid = fig.canvas.mpl_connect('button_press_event', self.onclick)
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fig.obj=self
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self.ax=ax
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self.hl=hl
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def plot_gather(self,fnLoc='/tmp/gather.txt'):
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pts=self.points
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rec = np.genfromtxt(fnLoc, delimiter=' ')
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fig=plt.figure()
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ax = fig.add_subplot(1,1,1)
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#hl=ax[0].plot(x, y, color=col)
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hl=ax.plot(pts[:,0],pts[:,1],'r.')
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hl=ax.plot(pts[:,0],pts[:,1],'y--')
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hl = ax.plot(rec[:, 4], rec[:, 5], 'b-')
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hl=ax.plot(rec[:,1],rec[:,2],'g-')
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ax.xaxis.set_label_text('x-pos um')
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ax.yaxis.set_label_text('y-pos um')
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cid = fig.canvas.mpl_connect('button_press_event', self.onclick)
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fig.obj=self
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self.ax=ax
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self.hl=hl
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fig = plt.figure()
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ax = fig.add_subplot(1, 1, 1)
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err=np.sqrt((rec[:,1]-rec[:,4])**2+(rec[:,1]-rec[:,4])**2)
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hl = ax.plot(err, 'r-')
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ax.xaxis.set_label_text('time (10x servo cycle)')
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ax.yaxis.set_label_text('pos-error um')
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plt.show()
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if __name__=='__main__':
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from optparse import OptionParser, IndentedHelpFormatter
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class MyFormatter(IndentedHelpFormatter):
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'helper class for formating the OptionParser'
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def __init__(self):
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IndentedHelpFormatter.__init__(self)
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def format_epilog(self, epilog):
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if epilog:
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return epilog
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else:
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return ""
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def parse_args():
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'main command line interpreter function'
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#usage: gpasciiCommunicator.py --host=PPMACZT84 myPowerBRICK.cfg
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(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)
|
||||
@@ -1,93 +0,0 @@
|
||||
#!/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
|
||||
|
||||
Reference in New Issue
Block a user