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helicalscan wip

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This commit is contained in:
zamofing_t
2017-12-07 16:59:58 +01:00
parent f91ce6ad93
commit 9a663ac251
6 changed files with 491 additions and 134 deletions
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385
python/helicalscan.py
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@@ -7,7 +7,27 @@
# *-----------------------------------------------------------------------*
'''
tools to setup and execute a helical scan of a cristal
#THIS IS JUST TESTING CODE TO SOLVE FINDING THE ROTATION CENTER
motors CX CZ RY FY
7 8 1 2
Mot 1: Rotation stage LS Mecapion MDM-DC06DNC0H 32 poles = 1 rev = 16*2048=32768 phase_step
Mot 2: Stage Y Parker MX80L D11 25mm one pole cycle = 13mm = 2048 phase_step
Mot 3: Stage X Parker MX80L D11 25mm one pole cycle = 13mm = 2048 phase_step
Mot/Enc 4: camera base plate X
Mot/Enc 5: camera base plate Y
Mot 6: Backlight 2.3A
Mot 7: Stada Stepper: 670mA 200 poles 1 rev = 100*2048 phase_step (2 stepper motor)
Mot 8: Stada Stepper: 670mA 200 poles 1 rev = 100*2048 phase_step (2 stepper motor)
verbose bits:
#1 basic info
#2 plot sorting steps
4 list program
#4 upload progress
#8 plot gather path
'''
import os, sys, json
@@ -17,7 +37,7 @@ import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d as plt3d
import matplotlib.animation as anim
from matplotlib.widgets import Slider
import subprocess as sprc
from utilities import *
d2r=2*np.pi/360
@@ -129,12 +149,12 @@ class HelicalScan:
def test_coord_trf(self):
self.calcParam()
param = self.param
y, w, dx, dz = (4.3, .1, 0.2, 0.3)
print 'input : fy:%.3g dx:%.3g dz:%.3g w:%.3g' % (y, dx, dz, w / d2r)
(fy, w, cx, cz) = self.inv_transform(y, w, dx, dz)
print 'inv_trf: fy:%.3g cx:%.3g cz:%.3g w:%.3g' % (fy, cx, cz, w / d2r)
(y, w, dx, dz) = self.fwd_transform(fy, w, cx, cz)
print 'fwd_trf: fy:%.3g dx:%.3g dz:%.3g w:%.3g' % (y, dx, dz, w / d2r)
dx, dz, w, y, = (0.2,0.3,0.1,4.3)
print 'input : dx:%.3g dz:%.3g w:%.3g fy:%.3g' % (dx,dz,w/d2r,y)
(cx,cz,w,fy) = self.inv_transform(dx,dz,w,y)
print 'inv_trf: cx:%.3g cz:%.3g w:%.3g fy:%.3g' % (cx,cz,w/d2r,fy)
(dx, dz,w,y) = self.fwd_transform(cx,cz,w,fy)
print 'fwd_trf: dx:%.3g dz:%.3g w:%.3g fy:%.3g' % (dx,dz,w/d2r,y)
# plt.ion()
# fig = plt.figure()
@@ -145,8 +165,7 @@ class HelicalScan:
# def my_anim_func3(self,idx):
# self.hCrist,pt=self.pltCrist(cx=0,ty=0,cz=0,w=10*idx*d2r,h=self.hCrist)
def interactive_fy_cx_cz_w(self):
def interactive_cx_cz_w_fy(self):
fig = plt.figure()
self.manip=False#True#False
self.ax=ax=plt3d.Axes3D(fig,[0.02, 0.15, 0.96, 0.83])
@@ -158,24 +177,24 @@ class HelicalScan:
ctr=param[:,0:3].mean(0)[::-1]
self.axSetCenter(ctr,10)
axFy = plt.axes([0.1, 0.01, 0.8, 0.02])
axCx = plt.axes([0.1, 0.04, 0.8, 0.02])
axCz = plt.axes([0.1, 0.07, 0.8, 0.02])
axW = plt.axes([0.1, 0.10, 0.8, 0.02])
axCx=plt.axes([0.1, 0.01, 0.8, 0.02])
axCz=plt.axes([0.1, 0.04, 0.8, 0.02])
axW =plt.axes([0.1, 0.07, 0.8, 0.02])
axFy=plt.axes([0.1, 0.10, 0.8, 0.02])
if self.manip:
lz=ax.get_xlim()
lx=ax.get_ylim()
ly=ax.get_zlim()
else:
lx = ly=lz=[-5,5]
self.sldFy = sFy = Slider(axFy, 'fy', ly[0], ly[1], valinit=(ly[0]+ly[1])/2.)
self.sldCx = sCx = Slider(axCx, 'cx', lx[0], lx[1], valinit=(lx[0]+lx[1])/2.)
self.sldCz = sCz = Slider(axCz, 'cz', lz[0], lz[1], valinit=(lz[0]+lz[1])/2.)
self.sldW =sW = Slider(axW, 'ang', -180., 180.0, valinit=0)
sFy.on_changed(self.update_fy_cx_cz_w)
sCx.on_changed(self.update_fy_cx_cz_w)
sCz.on_changed(self.update_fy_cx_cz_w)
sW.on_changed(self.update_fy_cx_cz_w)
self.sldCx=sCx=Slider(axCx, 'cx', lx[0], lx[1], valinit=(lx[0]+lx[1])/2.)
self.sldCz=sCz=Slider(axCz, 'cz', lz[0], lz[1], valinit=(lz[0]+lz[1])/2.)
self.sldW =sW =Slider(axW, 'ang', -180., 180.0, valinit=0)
self.sldFy=sFy=Slider(axFy, 'fy', ly[0], ly[1], valinit=(ly[0]+ly[1])/2.)
sCx.on_changed(self.update_cx_cz_w_fy)
sCz.on_changed(self.update_cx_cz_w_fy)
sW.on_changed(self.update_cx_cz_w_fy)
sFy.on_changed(self.update_cx_cz_w_fy)
hCrist,pt=self.pltCrist()
@@ -186,18 +205,19 @@ class HelicalScan:
(z_i, y_i, x_i, r_i, phi_i)=param[i]
p[i,0]=x_i+r_i*np.sin(phi_i) # x= x_i+r_i*cos(phi_i+w)+cx
p[i,1]=y_i # y= y_i
p[i,2] =z_i+r_i*np.cos(phi_i) # z= z_i+r_i*sin(phi_i*w)
p[i,2]=z_i+r_i*np.cos(phi_i) # z= z_i+r_i*sin(phi_i*w)
print p
ofs=(p[1]+p[0])/2. # = center of the cristal
m=Trf.trans(*ofs); self.hOrig=self.pltOrig(m)
plt.show()
def update_fy_cx_cz_w(self,val):
fy = self.sldFy.val
def update_cx_cz_w_fy(self,val):
cx = self.sldCx.val
cz = self.sldCz.val
w = self.sldW.val
w = self.sldW.val
fy = self.sldFy.val
if self.manip:
param = self.param
# param[i]=(z_i, y_i, x_i, r_i,phi_i)
@@ -218,7 +238,8 @@ class HelicalScan:
#l.set_ydata(amp * np.sin(2 * np.pi * freq * t))
self.fig.canvas.draw_idle()
def interactive_y_dx_dz_w(self):
def interactive_dx_dz_w_y(self):
fig = plt.figure()
self.ax=ax=plt3d.Axes3D(fig,[0.02, 0.15, 0.96, 0.83])
ax.set_xlabel('Z');ax.set_ylabel('X');ax.set_zlabel('Y')
@@ -230,21 +251,21 @@ class HelicalScan:
ctr=(0,0,0)
self.axSetCenter(ctr,10)
axY = plt.axes([0.1, 0.01, 0.8, 0.02])
axDx = plt.axes([0.1, 0.04, 0.8, 0.02])
axDz = plt.axes([0.1, 0.07, 0.8, 0.02])
axW = plt.axes([0.1, 0.10, 0.8, 0.02])
axDx=plt.axes([0.1, 0.01, 0.8, 0.02])
axDz=plt.axes([0.1, 0.04, 0.8, 0.02])
axW =plt.axes([0.1, 0.07, 0.8, 0.02])
axY =plt.axes([0.1, 0.10, 0.8, 0.02])
lx=[-1,1];ly=[0,1];lz=[-1,1]
ly = param[:,1]
self.sldY = sY = Slider(axY, 'y', ly[0], ly[1], valinit=(ly[0]+ly[1])/2.)
self.sldDx = sDx = Slider(axDx, 'dx', lx[0], lx[1], valinit=(lx[0]+lx[1])/2.)
self.sldDz = sDz = Slider(axDz, 'dz', lz[0], lz[1], valinit=(lz[0]+lz[1])/2.)
self.sldW =sW = Slider(axW, 'ang', -180., 180.0, valinit=0)
sY.on_changed(self.update_y_dx_dz_w)
sDx.on_changed(self.update_y_dx_dz_w)
sDz.on_changed(self.update_y_dx_dz_w)
sW.on_changed(self.update_y_dx_dz_w)
self.sldDx=sDx=Slider(axDx, 'dx', lx[0], lx[1], valinit=(lx[0]+lx[1])/2.)
self.sldDz=sDz=Slider(axDz, 'dz', lz[0], lz[1], valinit=(lz[0]+lz[1])/2.)
self.sldW =sW =Slider(axW, 'ang', -180., 180.0, valinit=0)
self.sldY =sY =Slider(axY, 'y', ly[0], ly[1], valinit=(ly[0]+ly[1])/2.)
sDx.on_changed(self.update_dx_dz_w_y)
sDz.on_changed(self.update_dx_dz_w_y)
sW.on_changed(self.update_dx_dz_w_y)
sY.on_changed(self.update_dx_dz_w_y)
# param[i]=(z_i, y_i, x_i, r_i,phi_i)
@@ -263,21 +284,23 @@ class HelicalScan:
self.hCrist=hCrist;self.fig=fig
plt.show()
def update_y_dx_dz_w(self,val):
y = self.sldY.val
def update_dx_dz_w_y(self,val):
dx = self.sldDx.val
dz = self.sldDz.val
w = self.sldW.val
y = self.sldY.val
w=w*d2r
(fy, w, cx, cz)=self.inv_transform(y,w,dx,dz)
(cx,cz,w,fy)=self.inv_transform(dx,dz,w,y)
#print (cx,cz,w,fy)
self.hCrist,pt=self.pltCrist(-fy,-cx,-cz,w,self.hCrist)
self.fig.canvas.draw_idle()
def fwd_transform(self,fy,w,cx,cz):
def fwd_transform(self,cx,cz,w,fy):
#cx,cy: coarse stage
#input: fy,w,cx,cz
#output: y,w,dx,dz
#input: cx,cz,w,fy
#output: dx,dz,w,y
# param[i]=(z_i, y_i, x_i, r_i,phi_i)
param=self.param
@@ -297,12 +320,13 @@ class HelicalScan:
dx=cx-v[0]
dz=cz-v[2]
y=v[1]
res=(y,w,dx,dz)
res=(dx,dz,w,y)
return res
def inv_transform(self,y,w,dx=0,dz=0):
#input: y,w,dx,dz
#output: y,w,cx,cz
def inv_transform(self,dx,dz,w,y):
#input: dx,dz,w,y
#output: cx,cz,w,fy
#dx,dy: deviation from cristal center line
param=self.param
p=np.ndarray((param.shape[0], 3))
@@ -321,7 +345,7 @@ class HelicalScan:
cx=dx+v[0]
cz=dz+v[2]
fy=v[1]
res=(fy,w,cx,cz)
res=(cx,cz,w,fy)
return res
@@ -366,6 +390,7 @@ class HelicalScan:
hb.set_3d_properties((o[1], o[1] + b[1]))
return h
def pltCrist(self,fy=0,cx=0,cz=0,w=0,h=None):
#h are the handles
if h is None:
@@ -414,6 +439,7 @@ class HelicalScan:
#h+=(hs,hp[0])
return (h,pt)
@staticmethod
def meas_rot_ctr(y,per=1):
# find the amplitude bias and phase of an equidistant sampled sinus
@@ -436,11 +462,252 @@ class HelicalScan:
ax.set_ylim(v[0]-l2, v[0]+l2);
ax.set_zlim(v[1]-l2, v[1]+l2)
def my_anim_func(idx,hs,horig):
print('anim')
a=idx*.01*2*np.pi
m=Trf.rotY(a)
hs.pltOrig(m,horig)
def gen_coord_trf_code(self,file=None,host=None):
param=self.param
prg = []
prg.append('''
// Set the motors as inverse kinematic axes in CS 1
//motors CX CZ RY FY
// 7 8 1 2
&1
#7->I
#8->I
#1->I
#2->I
open forward
define(qCX='L7', qCZ='L8', qW='L1', qFY='L2')
define(DX='C6', DZ='C8', W='C1', Y='C7')
//coord X Z B Y
define(p0_x='L10', p0_y='L11', p0_z='L12')
define(p1_x='L13', p1_y='L14', p1_z='L15')
define(f='L16')
send 1"forward kinematic\\n"''')
for i in range(2):
#https://stackoverflow.com/questions/3471999/how-do-i-merge-two-lists-into-a-single-list
l=[j for i in zip((i,) * param.shape[1], list(param[i])) for j in i]
prg.append(" define(z_%i=%g, y_%i=%g, x_%i=%g, r_%i=%g, phi_%i=%g)"%tuple(l))
prg.append('''
p0_x=x_0+r_0*sin(phi_0+W)
p1_x=x_1+r_1*sin(phi_1+W)
p0_y=y_0
p1_y=y_1
p0_z=z_0+r_0*cos(phi_0+W)
p1_z=z_1+r_1*cos(phi_0+W)
f=(qFY-y_0)/(y_1-y_0)
p0_x=p0_x+f*(p1_x-p0_x)
p0_y=p0_y+f*(p1_y-p0_y)
p0_z=p0_z+f*(p1_z-p0_z)
DX=qCX-p0_x
DZ=qCZ-p0_z
Y=qFY
W=qW
D0=$000001c2; //B=$2 X=$40 Y=$80 Z=$100 hex(2+int('40',16)+int('80',16)+int('100',16)) -> 0x1c2
close
''')
prg.append('''
open inverse
define(DX='C6', DZ='C8', W='C1', Y='C7')
//coord X Z B Y
//D0 is set to $000001c2
define(qCX='L7', qCZ='L8', qW='L1', qFY='L2')
define(p0_x='L10', p0_y='L11', p0_z='L12')
define(p1_x='L13', p1_y='L14', p1_z='L15')
define(f='L16')
send 1"inverse kinematic\\n"''')
for i in range(2):
# https://stackoverflow.com/questions/3471999/how-do-i-merge-two-lists-into-a-single-list
l = [j for i in zip((i,) * param.shape[1], list(param[i])) for j in i]
prg.append(" define(z_%i=%g, y_%i=%g, x_%i=%g, r_%i=%g, phi_%i=%g)" % tuple(l))
prg.append('''
p0_x=x_0+r_0*sin(phi_0+W)
p1_x=x_1+r_1*sin(phi_1+W)
p0_y=y_0
p1_y=y_1
p0_z=z_0+r_0*cos(phi_0+W)
p1_z=z_1+r_1*cos(phi_0+W)
f=(qFY-y_0)/(y_1-y_0)
p0_x=p0_x+f*(p1_x-p0_x)
p0_y=p0_y+f*(p1_y-p0_y)
p0_z=p0_z+f*(p1_z-p0_z)
qCX=DX+p0_x
qCZ=DZ+p0_z
qFY=Y
qW=W
close
''')
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 = '/home/zamofing_t/scripts/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
def gen_prog(self,prgId=2,file=None,host=None,mode=0,**kwargs):
'''
kwargs:
acq_per : acquire period: acquire data all acq_per servo loops (default=1)
pt2pt_time : time to move from one point to the next point
'''
prg=[]
acq_per=kwargs.get('acq_per',1)
gather={"MaxSamples":1000000, "Period":acq_per}
#Sys.ServoPeriod is dependent of !common() macro
ServoPeriod= .2 #0.2ms
#ServoPeriod = .05
self.meta = {'timebase': ServoPeriod*gather['Period']}
#channels=["Motor[1].ActPos","Motor[2].ActPos","Motor[3].ActPos"]
channels=["Motor[7].ActPos","Motor[8].ActPos","Motor[1].ActPos","Motor[2].ActPos"]
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
if mode==-1: #### jog a 10mm square
pos=self.points
prg.append(' linear abs')
prg.append('X(%g) Y(%g)' % tuple(pos[0, :]))
prg.append('dwell 10')
prg.append('Gather.Enable=2')
prg.append('jog2:10000')
prg.append('dwell 100')
prg.append('jog3:10000')
prg.append('dwell 100')
prg.append('jog2:-10000')
prg.append('dwell 100')
prg.append('jog3:-10000')
prg.append('dwell 100')
prg.append('Gather.Enable=0')
elif mode==0: #### linear motion
pos=self.points
prg.append(' linear abs')
prg.append('X(%g) Y(%g)' % tuple(pos[0, :]))
prg.append('dwell 10')
prg.append('Gather.Enable=2')
prg.append(' linear abs')
for idx in range(pos.shape[0]):
prg.append('X%g Y%g'%tuple(pos[idx,:]))
prg.append('dwell 100')
prg.append('Gather.Enable=0')
elif mode==1: #### pvt motion
try:
pt2pt_time=kwargs['pt2pt_time'] #how many ms to move to next point (pt2pt_time)
except KeyError:
print('missing pt2pt_time, use default=100ms')
pt2pt_time=100.
try:
cnt=kwargs['cnt'] #move path multiple times
except KeyError:
cnt=1
try:
pt=self.ptsCorr
except AttributeError:
pt=self.points
vel=pt[2:,:]-pt[:-2,:]
#pv is an array of posx posy velx vely
pv=np.ndarray(shape=(pt.shape[0]+2,4),dtype=pt.dtype)
pv[:]=np.NaN
#pv[ 0,(0,1)]=2*pt[0,:]-pt[1,:]
pv[ 0,(0,1)]=pt[0,:]
pv[ 1:-1,(0,1)]=pt
#pv[ -1,(0,1)]=2*pt[-1,:]-pt[-2,:]
pv[ -1,(0,1)]=pt[-1,:]
pv[(0,0,-1,-1),(2,3,2,3)]=0
dist=pv[2:,(0,1)] - pv[:-2,(0,1)]
pv[ 1:-1,(2,3)] = 1000.*dist/(2.*pt2pt_time)
prg.append(' linear abs')
prg.append('X%g Y%g' % tuple(pv[0, (0,1)]))
prg.append('dwell 10')
prg.append('Gather.Enable=2')
if cnt>1:
prg.append('P100=%d'%cnt)
prg.append('N100:')
prg.append(' pvt%g abs'%pt2pt_time) #100ms to next position
for idx in range(1,pv.shape[0]):
prg.append('X%g:%g Y%g:%g'%tuple(pv[idx,(0,2,1,3)]))
prg.append('X%g Y%g' % tuple(pv[-1, (0,1)]))
if cnt>1:
prg.append('dwell 10')
prg.append('P100=P100-1')
prg.append('if(P100>0)')
prg.append('{')
prg.append(' linear abs')
prg.append('X%g Y%g' % tuple(pv[0, (0,1)]))
prg.append('dwell 100')
prg.append('goto 100')
prg.append('}')
else:
prg.append('dwell 1000')
prg.append('Gather.Enable=0')
elif mode==2: #### spline motion
try:
pt2pt_time=kwargs['pt2pt_time'] #how many ms to move to next point (pt2pt_time)
except KeyError:
print('missing pt2pt_time, use default=100ms')
pt2pt_time=100.
pos=self.points
pcor=np.ndarray(pos.shape,dtype=pos.dtype);pcor[:]=np.NaN
pcor[(0,-1),:]=pos[(0,-1),:]
pcor[1:-1,:]=(-pos[0:-2,:]+8*pos[1:-1,:]-pos[2:,:])/6.
#pcor=pos
prg.append(' linear abs')
prg.append('X(%g) Y(%g)' % tuple(pcor[0, :]))
prg.append('dwell 10')
prg.append('Gather.Enable=2')
prg.append(' spline%g abs'%pt2pt_time) #100ms to next position
for idx in range(pcor.shape[0]):
prg.append('X%g Y%g'%tuple(pcor[idx,:]))
prg.append('dwell 100')
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
if __name__=='__main__':
from optparse import OptionParser, IndentedHelpFormatter
@@ -479,11 +746,13 @@ Examples:'''+''.join(map(lambda s:cmd+s, exampleCmd))+'\n '
hs=HelicalScan(args)
#hs.sequencer()
hs.args.verbose=255;hs.calcParam();hs.gen_coord_trf_code('/tmp/helicalscan.cfg','MOTTEST-CPPM-CRM0485')
#return
hs.test_find_rot_ctr()
hs.test_find_rot_ctr(n=5. ,per=1.,bias=2.31,ampl=4.12,phi=24.6)
hs.test_coord_trf()
hs.interactive_fy_cx_cz_w()
hs.interactive_y_dx_dz_w()
hs.interactive_cx_cz_w_fy()
hs.interactive_dx_dz_w_y()
#------------------ Main Code ----------------------------------