enhance syncronization -> parameters in setup_sync

-> sp.setup_sync(verbose=args.verbose&0x40,timeOfs=0.03,timeCor=0.0005) - cleanup code - add motion markers - add debug data - rework triggerSync - BUT nothing should change in Sync
2022-10-04 16:39:13 +02:00
parent 7a968aac96
commit 20c6d690e8
6 changed files with 438 additions and 202 deletions
--- a/Readme.md
+++ b/Readme.md
@@ -1274,4 +1274,194 @@ Make z to move over the grid.


 ?? what are the PV for the camera, zoom etc ???
+```
+
+
+30.9.22 Debug Synchronization
+=============================
+
+https://docs.google.com/document/d/1soSuCZYyfGf_ntcgG_Y1_WeGuo_687OuFn0s4sMj1uY/edit
+
+
+remote ssh tunnel + start gather_server
+---------------------------------------
+```
+PPMAC=SAR-CPPM-EXPMX1
+rsync -va ~/Documents/prj/SwissFEL/PBTools/pbtools/gather/gather_server root@$PPMAC:/tmp/
+lsof -i -n | grep '127.0.0.1:1000'
+ssh -L 10001:localhost:22 root@$PPMAC 'uname -a'
+ssh -L 10002:localhost:2332 root@$PPMAC 'uname -a'
+ssh root@$PPMAC
+LD_LIBRARY_PATH=/opt/ppmac/libppmac/ /tmp/gather_server
+```
+
+cleanup /tmp/
+-------------
+```
+PPMAC=SAR-CPPM-EXPMX1
+ssh root@$PPMAC rm /tmp/gather_server /tmp/triggerSync
+ssh root@$PPMAC ls -l /tmp
+```
+
+start debug tools
+-----------------
+```
+PPMAC=SAR-CPPM-EXPMX1
+PBInspect --host=$PPMAC&
+gpasciiCommander --host $PPMAC -i
+ssh root@$PPMAC
+ssh root@$PPMAC rm /tmp/gather_server /tmp/triggerSync
+ssh root@$PPMAC ls -l /tmp
+```
+
+restart IOC
+-----------
+```
+ssh saresc-cons-03
+PPMAC=SAR-CPPM-EXPMX1
+telnet $PPMAC 50001
+Ctrl-X
+dbgf SAR-CPPM-EXPMX1:MOD_VER
+
+caget SAR-CPPM-EXPMX1:MOD_VER
+
+```
+
+checking versions
+-----------------
+```
+git: 7a968aac967
+asyn             427.0.2
+motorBase        alpha_220518
+asynMotor        alpha_220518
+powerPmac        alpha_220518
+PB_COMMON        2.0.1
+gpasciiCommander 0.9.0
+ESB_MX           0.0.2
+```
+
+zamofing_t@ganymede:~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX$
+git loggraph -10
+* 7a968aa 2022-09-20 (HEAD -> master, tag: latest, tag: 0.0.2, psigithub/master) change speeds and directions [Thierry Zamofing] 
+* 00588f8 2022-09-16 minor changes [Thierry Zamofing] 
+* d52a6ce 2022-08-30 minor changes [Thierry Zamofing] 
+* f47e111 2022-05-20 (tag: 0.0.1) add DET_Z motor [Thierry Zamofing] 
+* 8e5b15e 2022-05-20 wip [Thierry Zamofing] 
+* 399282c 2019-03-20 enhance triggering [Thierry Zamofing] 
+* eda8caf 2019-03-19 wip [Thierry Zamofing] 
+* 0c45705 2019-03-08 optimize [Thierry Zamofing] 
+* c962ebd 2019-03-06 documentation [Thierry Zamofing] 
+
+git reset --hard 7a968aa
+rmake -e LIBVERSION=42.42.42 uninstall install
+-> restart IOC
+
+ssh root@$PPMAC rm /tmp/triggerSync
+cd python
+git dt latest -- shapepath.py
+./shapepath.py --host=localhost:10001:10002
+
+removing test verion
+ssh sf-lc7 ls -l /ioc/modules/ESB_MX/
+ssh sf-lc7 rm -rf /ioc/modules/ESB_MX/42.42.42
+
+
+IOC locations
+-------------
+```
+~/Documents/prj/SwissFEL/epics_ioc_boot_sf/ESC_all/ESB_MX_PowerBrick
+They are just using the new alphy driver. That should have no impact on the motion config.
+```
+
+
+Current (old) Synchronization
+-----------------------------
+```
+default:
+/ESB_MX/src/triggerSync/triggerSync.c -> read usage 
+simulate start trigger -> pshm->Coord[1].Q[10]=1 to simulate a Jungfrau aquire start\n\
+simulate frame trigger -> pshm->Coord[1].Q[11]
+Coord[1].Q[0] is incremented at each trigger
+
+Coord[1].DesTimeBase is adjusted at each frame trigger
+
+Coord[1].pDesTimeBase=Coord[1].DesTimeBase.a
+
+
+gpascii: set  Gather.Enable=1
+PMAC:    LD_LIBRARY_PATH=/opt/ppmac/libppmac/ /tmp/triggerSync 10 0 11 -> wait for start trigger
+gpascii: set Start trigger:  pshm->Coord[1].Q[10]=1 or set EVR that generates the trigger
+PMAC: start Gather (Gather.Enable=2)
+      count and sync frames: 
+      Coord[1].Q[0] = frame counter
+gpascii: stop Gather -> Gather.Enable=0
+PMAC: triggerSync stops when Gather.Enable=0
+
+
+```
+
+Enhanced Synchronization
+------------------------
+```
+(to be tested)
+Coord[1].pDesTimeBase=Coord[1].DesTimeBase.a
+For “external time base”, in which the coordinate system’s time base value is proportional to the
+frequency of an incoming encoder signal or pulse train, Coord[x].pDesTimeBase should be set
+to EncTable[i].DeltaPos.a
+
+Setup EncTable:
+EncTable[n].type = (3)Software 1/T encoder extension (5)Four-byte read 32 bit int (11) Float 32f or 64f
+
+The ERV are mapped to
+//Power PMAC Software Reference Manual.pdf Gate3[i].Chan[j].Status -> page 919 UserFlag
+(gate3_1->Chan[0].Status&0x800) = Gate3[1].Chan[0].UserFlag Trigger start
+(gate3_1->Chan[1].Status&0x800) = Gate3[1].Chan[1].UserFlag Trigger frame
+
+
+Use EncTable 20 as Frame counter
+Gate3[1].Chan[1].EncCtrl = $encctrl
+EncTable[20].type = 3
+EncTable[20].pEnc = Gate3[1].Chan[1].UserFlag.a (is same as Gate3[1].Chan[1].Status) thus it will not work
+EncTable[20].pEnc1 = Gate3[1].Chan[0].TimerA.a
+EncTable[20].index1 = 0
+EncTable[20].index2 = 0
+EncTable[20].index3 = 0
+EncTable[20].index4 = 0
+EncTable[20].index5 = 0
+EncTable[20].ScaleFactor = 1/256
+-> THIS DOES NOT WORK WITH CURRENT CONNECTIONS !
+-> ONE PHYSICAL ENCODER WOULD NEED PULSE AND DIRECTION INPUT AND SET Gate3[1].Chan[1].EncCtrl TO 'pulse and direction' mode
+
+
+> Sys.Ddata[0]=Sys.Ddata[0]+10
+
+Use EncTable 20 as Frame counter
+Gate3[1].Chan[1].EncCtrl = $encctrl
+EncTable[20].type = 11 //loating point read
+EncTable[20].pEnc = Sys.Ddata[0].a
+EncTable[20].pEnc1 = Gate3[1].Chan[0].TimerA.a
+EncTable[20].index1 = 0
+EncTable[20].index2 = 0
+EncTable[20].index3 = 0
+EncTable[20].index4 = 0
+EncTable[20].index5 = 99 //multiply with 100
+EncTable[20].index5 = 1 //float64
+EncTable[20].ScaleFactor = 1/256
+EncTable[20].ScaleFactor=1E-3
+
+
+Use EncTable 20 as Frame counter
+EncTable[20].type = 1 //32 Bit uint
+EncTable[20].pEnc = Sys.Udata[0].a
+EncTable[20].index1 = 0
+EncTable[20].index2 = 0
+EncTable[20].index3 = 0
+EncTable[20].index4 = 0
+EncTable[20].index5 = 0
+EncTable[20].index5 = 0
+EncTable[20].ScaleFactor=1E-3
+
+
+2.1 trigger zu spät
+1.9 trigger zu früh

--- a/python/MXMotion.py
+++ b/python/MXMotion.py
@@ -7,6 +7,8 @@
 # *-----------------------------------------------------------------------*
 '''
 Coord[1].Q[0] : sync points when using setup_sync(mode=2)
+                -3: when armed (at start position)
+                -2: triggerSync waiting for start trigger
                0: after setup_sync(mode=2) call
                idx: index of position during run
                -1:  pvt motion is finished
@@ -44,7 +46,7 @@ class MotionBase:
    self.meta={'srv_per':ServoPeriod,'pt2pt_time':40,'sync_flag':0,'sync_mode':2}
    self.meta.update(kwargs)

-  def setup_sync(self, crdId=1, prgId=2,verbose=False, timeOfs=0.):
+  def setup_sync(self, crdId=1, prgId=2,verbose=False, timeOfs=0.,timeCor=0.):
    '''setup the timing synchronization for the motion program
       kwargs:
        sync_mode : default=2
@@ -88,41 +90,43 @@ class MotionBase:
      flag0='Coord[{crdId}].Q[10]'.format(crdId=crdId) if sync_flag&1 else 'Gate3[1].Chan[0].UserFlag'
      flag1='Coord[{crdId}].Q[11]'.format(crdId=crdId) if sync_flag&2 else 'Gate3[1].Chan[1].UserFlag'
      if sync_mode==1:
-        prg = '''
-  Coord[{crdId}].Q[0]=-2
-  Coord[{crdId}].TimeBaseSlew=1 //1E-4 is default
-  Coord[{crdId}].DesTimeBase=0
-  while({flag0}==0){{}}
-  Coord[{crdId}].Q[0]=-1
-  Gather.Enable=2
-  while({flag1}==0){{}}
-  Coord[1].DesTimeBase=Sys.ServoPeriod
-  '''.format(crdId=crdId, flag0=flag0, flag1=flag1)
+        prg = f'\n{flag0}=0\n' if sync_flag&1 else ''
+        prg += f'''
+Coord[{crdId}].Q[0]=-2 motion program started and armed
+Coord[{crdId}].TimeBaseSlew=1 //1E-4 is default
+Coord[{crdId}].DesTimeBase=0
+while({flag0}==0){{}}
+Coord[{crdId}].Q[0]=-1
+Gather.Enable=2
+while({flag1}==0){{}}
+Coord[1].DesTimeBase=Sys.ServoPeriod
+'''
      else:
-        prg = '''
-  //Gather.Enable=2 is done in the sync program
-  Coord[1].TimeBaseSlew=1 //1E-4 is default 
-  Coord[1].DesTimeBase=0
-  //Coord[1].Q[0]=-1 is done in the sync program
-        '''.format(crdId=crdId, flag0=flag0, flag1=flag1)
+        prg = f'''
+//Gather.Enable=2 is done in the triggerSync program
+Coord[1].TimeBaseSlew=1 //1E-4 is default
+Coord[1].DesTimeBase=0
+Coord[1].Q[0]=-3 //motion program started and waits. Arm(-2) is done in triggerSync program
+'''

      self.sync_prg = prg
      #download and start triggerSync code
      comm=self.comm
      if comm is None: return

-      arg=0 #argument to pass to triggerSync program
-      if sync_mode==2:arg+=1  #synchronize
-      arg+=sync_flag*2        #simulated or real triggers
-      if verbose: arg+=8
-      if sync_mode==2 or arg&4:
+      mode=0 #mode to pass to triggerSync program
+      if sync_mode==2:mode+=1  #synchronize
+      mode+=sync_flag*2        #simulated or real triggers
+      if verbose: mode+=8
+      if sync_mode==2 or mode&4:
        sftp = comm.sftp
        dst = '/tmp/triggerSync'
        src = os.path.abspath(os.path.join(os.path.dirname(__file__), 'triggerSync'))
        sftp.put(src, dst)
        sftp.chmod(dst, 0o755)
        cmd = 'LD_LIBRARY_PATH=/opt/ppmac/libppmac/ ' + dst
-        cmd+=' %g %g %d'%(pt2pt_time,timeOfs,arg)
+        #cmd+=' %d %g %g %g'%(mode,pt2pt_time,timeOfs,timeCor)
+        cmd+=' %d %g %g'%(mode,pt2pt_time+timeCor,timeOfs)
        self.cmdSync = cmd
        print ('starting '+cmd)
        self.syncShell=comm.shell_channel(cmd)
--- a/python/shapepath.py
+++ b/python/shapepath.py
@@ -17,63 +17,36 @@ verbose bits:
 0x20 plot pvt trajectory (before motion)
 0x40 print sync details

-Gather motor order

-idx    0                 1                 2                 3                 4                 5                 6
-OLD    Motor[3].ActPos   Motor[2].ActPos   Motor[1].ActPos   Motor[3].DesPos   Motor[2].DesPos   Motor[1].DesPos   Gate3[1].Chan[1].UserFlag
+    if mode&1:
+      self.plot_trajectory()
+
+    if mode&2:
+      self.plot_pos_error()
+
+    if mode&4:
+      self.plot_bode(xy=(3,1),mode=31,db=True) # FX
+      self.plot_bode(xy=(2,0),mode=31,db=True) # FY
+
+    if mode&8:
+      self.plot_trigger_jitter()
+
+
+Gather motor order
+idx    0                 1                 2                 3                 4
 NEW    Motor[1].ActPos   Motor[2].ActPos   Motor[1].DesPos   Motor[2].DesPos   Gate3[1].Chan[1].UserFlag
 NEW           y.ActPos          x.ActPos          y.DesPos          x.DesPos   Gate3[1].Chan[1].UserFlag
-OLD->NEW
-0->none
-1->1
-2->0
-3->none
-4->3
-5->2

 Mot 1: Stage Y Parker MX80L D11 25mm               one pole cycle = 13mm = 2048 phase_step
 Mot 2: Stage X Parker MX80L D11 25mm               one pole cycle = 13mm = 2048 phase_step
 Mot 3: Rotation stage LS Mecapion MDM-DC06DNC0H    32 poles = 1 rev = 16*2048=32768 phase_step
 Mot 4: Stage X Stada Stepper                       670mA 200 poles 1 rev = 100*2048 phase_step (2 stepper motor)
 Mot 5: Stage Z Stada Stepper                       670mA 200 poles 1 rev = 100*2048 phase_step (2 stepper motor)
-Enc 6: Interferometer Y
-Enc 7: Interferometer X
-
-
-tunnel PowerBrick port locally
------------------------------
-Port 22 on PowerBrick is the ssh server port
-Port 2332 on PowerBrick is the gather port of gather_server
-
-PPMAC=SAR-CPPM-EXPMX1
-
-rsync -vai ~/Documents/prj/SwissFEL/PBTools/pbtools/gather/gather_server root@$PPMAC:/tmp/
-ssh root@$PPMAC
-LD_LIBRARY_PATH=/opt/ppmac/libppmac/ /tmp/gather_server
-
-
-
-rsync -vai ~/Documents/prj/SwissFEL/PBTools/pbtools/gather/gather_server root@$PPMAC:/tmp
-
-ssh -L 10001:localhost:22 root@$PPMAC 'uname -a'
-ssh -L 10002:localhost:2332 root@$PPMAC 'uname -a'
-> this tunnels port 22 and 2332 of $PPMAC to 10001 and 10002 of localhost
-('uname -a' is just to execute a command and return, because the port remains open)
-
-Tests:
-nc localhost 10001
-nc localhost 10002
-
-list close ssh tunnel
---------------------
-lsof -i -n | egrep 'ssh'
-lsof -i -n | grep '127.0.0.1:1000'
-
-

+s.a. https://docs.google.com/document/d/1soSuCZYyfGf_ntcgG_Y1_WeGuo_687OuFn0s4sMj1uY/
 '''
+
 from __future__ import print_function
-#from __future__ import absolute_import,division,generators,nested_scopes,print_function,unicode_literals,with_statement
 try: raw_input;input=raw_input
 except NameError: pass

@@ -305,7 +278,7 @@ class DebugPlot:
    hl = ax.plot(pts[:, 0], pts[:, 1], 'r.', label='points')
    hl += ax.plot(pts[:, 0], pts[:, 1], 'y--', label='direct')
    hl += ax.plot(rec[:, 3], rec[:, 2], 'b-', label='DesPos')  # desired path
-    hl += ax.plot(rec[:, 1], rec[:, 0], 'g-', label='ActPos')  # actual path
+    hl += ax.plot(rec[:, 1], rec[:, 0], 'g.', label='ActPos')  # actual path
    try:
      pvt = self.pvt
    except AttributeError:
@@ -333,6 +306,23 @@ class DebugPlot:
    ax2.legend(loc='best')
    plt.show(block=False)

+  def plot_dbg(self):
+    rec = self.rec  # yA,xA,yD,xD,trig
+    ts=self.meta['srv_per']*self.meta['acq_per']
+    fig = plt.figure('debug plot')
+    ax = fig.add_subplot(1, 1, 1)
+    t=np.arange(rec.shape[0],dtype=np.uint32)
+    #address=("Motor[1].ActPos", "Motor[2].ActPos", "Motor[1].DesPos", "Motor[2].DesPos", "Gate3[1].Chan[1].UserFlag","EncTable[20].DeltaPos")
+
+    hl = []
+    rec[0, 5]=rec[0, 6]=0
+    hl += ax.plot(t, rec[:, 6], 'rx', label='EncTable[20].DeltaPos')
+    hl += ax.plot(t, rec[:, 5], 'b-', label='Coord[1].TimeBase')
+    hl += ax.plot(t, rec[:, 4], 'g.', label='Gate3[1].Chan[1].UserFlag')
+    ax.xaxis.set_label_text('ms (timebase: %g ms per data point)' % ts)
+    ax.legend(loc='best')
+    plt.show(block=False)
+
  def plot_gather(self,mode=255):
    try:
      meta=self.meta
@@ -355,6 +345,10 @@ class DebugPlot:
    if mode&8:
      self.plot_trigger_jitter()

+    #self.plot_dbg()
+
+
+
    plt.show(block=False)

  def plot_bode(self,xy=(0,1),mode=25,db=True):
@@ -445,8 +439,8 @@ class DebugPlot:
    plt.show(block=False)

  def load_npz(self,fn='/tmp/shapepath.npz'):
-    fh=np.load(fn)
-    for k,v in fh.iteritems():
+    fh=np.load(fn,allow_pickle=True)
+    for k,v in fh.items():
      setattr(self,k,v)
    self.meta=self.meta.item()

@@ -571,15 +565,6 @@ class ShapePath(MotionBase):
      for x in np.arange(mult)*shift:
        stack.append(pts+(x,y))
    pts=np.vstack(stack)
-
-
-    #xx,yy=np.meshgrid(range(w), range(h))
-    #pts=np.array([xx.reshape(-1),yy.reshape(-1)],dtype=np.float).transpose()*pitch
-    #if xy:
-    #else:
-
-    #  smlpitch
-    #pts+=ofs
    self.points=pts


@@ -654,36 +639,26 @@ class ShapePath(MotionBase):
    comm=self.comm
    gt=self.gather
    gt.set_phasemode(False)
-    if self.meta['sync_flag']&2:
+    meta=self.meta
+    if meta['sync_flag']&2:
      address=("Motor[1].ActPos","Motor[2].ActPos","Motor[1].DesPos","Motor[2].DesPos","Coord[1].Q[11]")
    else:
      address=("Motor[1].ActPos","Motor[2].ActPos","Motor[1].DesPos","Motor[2].DesPos","Gate3[1].Chan[1].UserFlag")
-
+      #address=("Motor[1].ActPos","Motor[2].ActPos","Motor[1].DesPos","Motor[2].DesPos","Gate3[1].Chan[1].UserFlag","EncTable[20].PrevEnc")
+      #address=("Motor[1].ActPos", "Motor[2].ActPos", "Motor[1].DesPos", "Motor[2].DesPos", "Gate3[1].Chan[1].UserFlag","Coord[1].TimeBase","EncTable[20].DeltaPos")
    gtMaxLn=gt.set_address(*address)
    if acq_per is None:
      ovhdTime=100
-      acq_per=int(np.ceil((self.meta['pt2pt_time']*self.points.shape[0]+ovhdTime)/(gtMaxLn*self.meta['srv_per'])))
+      acq_per=int(np.ceil((meta['pt2pt_time']*self.points.shape[0]+ovhdTime)/(gtMaxLn*meta['srv_per'])))
    gt.set_property(MaxSamples=1000000, Period=acq_per)
    #gt.set_property(Period=acq_per)
-    self.meta.update({'acq_per':acq_per,'address':address})
+    meta.update({'acq_per':acq_per,'address':address})

  def setup_coord_trf(self,fx='X',fy='Y',cz='0'):
    # FY:1,  FX:2,  ROT_Y:3,  CX:4,  CZ:5,
    if self.comm is None: return
    comm = self.comm
    gpascii = comm.gpascii
-    prg = '''&1a
-#1->   Y
-#2->   X
-#3->   A
-&0#4->0
-&0#5->0
-&0#6->0
-&0#7->0
-#1..3j/
-//#8->0
-//#1..8j/
-'''
    prg=f'''&1a
 &1#3->0
 &1#4->0
@@ -699,7 +674,6 @@ class ShapePath(MotionBase):
 #5->{cz}
 #1,2,5j/
 '''
-
    gpascii.send_block(prg)

  def setup_motion(self,prgId=2,fnPrg=None,mode=0,**kwargs):
@@ -719,6 +693,22 @@ class ShapePath(MotionBase):
                numPad : number of padding points to reduce aliasing (default=16)
      '''
      prg=['close all buffers','open prog %d'%(prgId)]
+
+      #Use EncTable 20 as Frame counter
+      #dont use Coord[1].DesTimeBase as the time base but use the virtual encoder:
+      # Coord[1].pDesTimeBase=Coord[1].DesTimeBase.a #(default)
+      prg.append('''\
+EncTable[20].type = 1 //32 Bit uint
+EncTable[20].pEnc = Sys.Udata[0].a
+EncTable[20].index1 = 0
+EncTable[20].index2 = 0
+EncTable[20].index3 = 0
+EncTable[20].index4 = 0
+EncTable[20].index5 = 0
+EncTable[20].index5 = 0
+EncTable[20].ScaleFactor=1E-3
+//Coord[1].pDesTimeBase=EncTable[20].DeltaPos.a
+''')
      verb=self.verbose
      comm=self.comm
      if comm is not None:
@@ -768,7 +758,8 @@ class ShapePath(MotionBase):
          plt.show(block=False)

        pv[1:-1, (2, 3)]*=CoordFeedTime #scaling for Deltatau
-        prg.append('  linear abs')
+        prg.append('linear abs')
+        #prg.append('X%g Y%g' % tuple(pv[0, (0,1)]-(120,120)))
        prg.append('X%g Y%g' % tuple(pv[0, (0,1)]))
        prg.append('dwell 10')
        try: prg.extend(self.sync_prg.split('\n'))
@@ -781,6 +772,10 @@ class ShapePath(MotionBase):
        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)]))
+          #if idx%78==10: #sync data all 256 points
+          #  prg.append('Coord[1].Q[12]=Sys.ServoCount')
+          #  #prg.append(f'Coord[1].Q[13]={idx}')
+          #  prg.append(f'Coord[1].Q[13]=Motor[1].DesPos')
        prg.append('X%g Y%g' % tuple(pv[-1, (0,1)]))
        if cnt>1:
          prg.append('dwell 10')
@@ -813,6 +808,7 @@ class ShapePath(MotionBase):

  def gather_upload(self,fnRec=None):
    gt=self.gather
+    comm=self.comm
    gt.wait_stopped(verbose=True)
    self.rec=rec=gt.upload()

@@ -824,23 +820,24 @@ class ShapePath(MotionBase):
      del self.syncShell

    pts=self.points
-    ofsy=-rec[0,2]+pts[0,1]
-    ofsx=-rec[0,3]+pts[0,0]
-    rec[:,(1,3)]+=ofsx
-    rec[:,(0,2)]+=ofsy
+
+    ofsy=comm.gpascii.get_variable("Motor[1].HomePos", type_=float)
+    ofsx=comm.gpascii.get_variable("Motor[2].HomePos", type_=float)
+    rec[:,(0,2)]-=ofsy
+    rec[:,(1,3)]-=ofsx
    if fnRec:
      np.savez_compressed(fnRec, rec=rec, pts=pts, meta=self.meta)


 if __name__=='__main__':
-  #import logging
-  #logger = logging.getLogger(__name__)
-  #logger = logging.getLogger('pbtools.misc.pp_comm')
-  #logger.setLevel(logging.DEBUG)
-  #logging.basicConfig(format=('%(asctime)s %(name)-12s '
-  #                            '%(levelname)-8s %(message)s'),
-  #                    datefmt='%m-%d %H:%M',
-  #                    )
+  import logging
+  _log=logging.getLogger(__name__)
+  logging.getLogger('pbtools.misc.pp_comm').setLevel(logging.INFO)
+  logging.getLogger('paramiko').setLevel(logging.WARNING)
+  logging.getLogger('matplotlib').setLevel(logging.INFO)
+  #https://docs.python.org/3/library/logging.html#logging.Formatter add %(name)s to identify the logger
+  logging.basicConfig(level=logging.DEBUG, format='%(levelname)s:%(module)s:%(lineno)d:%(funcName)s:%(message)s ')
+  import argparse

  def unique_filename(fnBase):
    i = 0;
@@ -854,20 +851,6 @@ if __name__=='__main__':


  def run_test(args):
-    #dp=DebugPlot();dp.plot_gather();return
-    #import socket
-    #s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)  # create an INET, STREAMing socket
-    #s.settimeout(.1)
-    #try:
-    #  port=22 #ssh port
-    #  s.connect((args.host, port))  # try to connect to port
-    #  s.close()
-    #except (socket.error, socket.gaierror) as e:
-    #  comm=gather=None
-    #else:
-    #  comm = PPComm(host=args.host)
-    #  gather = Gather(comm)
-
    hpp=args.host.split(':')
    param={'host':hpp[0]}
    if len(hpp)>1:
@@ -885,7 +868,7 @@ if __name__=='__main__':
    #sp = ShapePath(comm, gather, args.verbose,sync_mode=0,pt2pt_time=10)

    #simulated start and frame trigger no sync
-    sp = ShapePath(comm, gather, args.verbose,sync_mode=1,sync_flag=3)
+    #sp = ShapePath(comm, gather, args.verbose,sync_mode=1,sync_flag=3)

    #simulated start and frame trigger with sync
    #sp = ShapePath(comm, gather, args.verbose,sync_mode=2,sync_flag=3)
@@ -894,7 +877,7 @@ if __name__=='__main__':
    #sp = ShapePath(comm, gather, args.verbose,sync_mode=1,sync_flag=1)

    #simulated start real frame trigger with sync
-    #sp = ShapePath(comm, gather, args.verbose,sync_mode=2,sync_flag=1)
+    sp = ShapePath(comm, gather, args.verbose,sync_mode=2,sync_flag=1)

    fn='/tmp/shapepath'
    #fn =unique_filename('ShapePathAnalyser/records/19_01_24/spiral')
@@ -927,18 +910,36 @@ if __name__=='__main__':
    #sp.gen_spiral_points(rStart=100,rInc=130,numSeg=4,numCir=2, ofs=(0, 0))
    #sp.gen_grid_points(w=20,h=20,pitch=100,rnd=0,ofs=(0,+2000));sp.sort_points(False);
    #sp.gen_grid_points(w=5,h=10,pitch=100,rnd=0,ofs=(0,+2000));sp.sort_points(False,10);
-    sp.gen_grid_points(w=125,h=125,pitch=3,rnd=0,ofs=(0,+2000));sp.sort_points(False,125);   sp.meta['pt2pt_time']=5
- 
+
+    #sp.gen_grid_points(w=50,h=50,pitch=120,rnd=0,ofs=(0,+2000));sp.sort_points(False,50);   sp.meta['pt2pt_time']=10
+    #sp.gen_grid_points(w=16,h=16,pitch=120,rnd=0,ofs=(0,+2000));sp.sort_points(False,16);   sp.meta['pt2pt_time']=10
+    #12.5x12.5
+    sp.gen_grid_points(w=78,h=78,pitch=120,rnd=0,ofs=(-10000,-12000));sp.sort_points(False,78);   sp.meta['pt2pt_time']=10
+    #23.0x23.0 -> only 3 data points from shot to shot: 6,9,12,14,17,20...
+    #sp.gen_grid_points(w=162,h=162,pitch=120,rnd=0,ofs=(-10000,-12000));sp.sort_points(False,162);   sp.meta['pt2pt_time']=10
+
    #sp.gen_grid_points(w=1,h=10,pitch=100,rnd=0,ofs=(0,0))
    #sp.gen_spiral_points(rStart=100,rInc=20,numSeg=8,numCir=32, ofs=(0, 0))
    #sp.gen_spiral_points(rStart=100,rInc=10,numSeg=2,numCir=32, phase=45, ofs=(0, 0))
    #sp.gen_spiral_points(rStart=100,rInc=10,numSeg=4,numCir=32, ofs=(0, 0))
    #sp.gen_closed_shifted()

-    gtMaxLn=116508;ovhdTime=100
+    gtMaxLn=int(sp.comm.gpascii.get_variable('Gather.MaxLines')) # 116508
+    if gtMaxLn==0:
+      sp.setup_gather(acq_per=1)
+      gtMaxLn=int(sp.comm.gpascii.get_variable('Gather.MaxLines')) # 116508
+
+    ovhdTime=100
    acq_per=int(np.ceil((sp.meta['pt2pt_time']*sp.points.shape[0]+ovhdTime)/(gtMaxLn*sp.meta['srv_per'])))
+    if args.verbose&0x01:
+      print(f'''\
+Gather.MaxLines:{gtMaxLn}
+Gather.Period:  {acq_per}
+meta: {sp.meta}
+Filename: {fn}.[prg|npz]
+''')
    sp.setup_gather(acq_per=acq_per)
-    sp.setup_sync(verbose=args.verbose&32,timeOfs=0.05)
+    sp.setup_sync(verbose=args.verbose&0x40,timeOfs=0.03,timeCor=0.0005)
    sp.setup_coord_trf() # reset to shape path system
    #sp.meta['pt2pt_time']=10 #put between setup_sync and setup_motion to have more motion points than FEL syncs
    sp.setup_motion(fnPrg=fn+'.prg', mode=3, scale=1.,dwell=10)
@@ -946,8 +947,11 @@ if __name__=='__main__':
    #sp.setup_motion(fnPrg=fn + '.prg', mode=1, scale=0,dwell=10)
    sp.homing()      #homing if needed
    sp.run()         #start motion program
+    print('wait_armed')
    sp.wait_armed()  # wait until motors are at first position
+    print('trigger')
    sp.trigger(0.5) #send a start trigger (if needed) ater given time
+    print('progress..')
    if not comm is None:
      while True:
        p=sp.progress()
@@ -955,55 +959,31 @@ if __name__=='__main__':
        print('progress %d/%d'%(p,sp.points.shape[0]));time.sleep(.1)
      sp.gather_upload(fnRec=fn+'.npz')
      dp=DebugPlot(sp);dp.plot_gather(mode=11)
-
    print('done')
    plt.show(block=False)
    input('press return')

-
-    #sp.plot_points(sp.points);plt.show()
-
-
-
-    #>>>run gather and plot trajectory<<<
-    #return
-
-
-  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=('-v15',
-                '--host=localhost:10001:10002'
-               )
-    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('--host', help='hostname', default='SAR-CPPM-EXPMX1')
+                '--host=localhost:10001:10002 -v 0x5d',
+                '--host=localhost:10001:10002 -v 0x59'
+                )
+    epilog=__doc__+'\nExamples:'+''.join(map(lambda s:cmd+s, exampleCmd))+'\n '
+    parser=argparse.ArgumentParser(epilog=epilog, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument("-m", "--mode", type=lambda x:int(x, 0), help="mode (see bitmasks) default=0x%(default)x", default=0xff)
+    parser.add_argument('-v', '--verbose', type=lambda x:int(x, 0), dest='verbose', help='verbosity bits (see below) default=0x%(default)x', default=0x00)
+    parser.add_argument('--host', help='hostname', default='SAR-CPPM-EXPMX1')
    #parser.add_option('--host', help='hostname', default='localhost:10001:10002')
-    #parser.add_option('--host', help='hostname')

-    (args, other)=parser.parse_args()
-    args.other=other
+    args=parser.parse_args()
+    _log.info('Arguments:{}'.format(args.__dict__))
    run_test(args)
 #------------------ Main Code ----------------------------------
+
+  #dp=DebugPlot('/tmp/shapepath.npz');dp.plot_gather(mode=11);plt.show()
+  #exit(0)
  #ssh_test()
  ret=parse_args()
  exit(ret)
--- a/src/triggerSync/Makefile
+++ b/src/triggerSync/Makefile
@@ -1,12 +1,13 @@
 #HOST=MOTTEST-CPPM-CRM0573
 HOST=SAR-CPPM-EXPMX1

-XENOMAI_INC_DIR=/opt/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/include
-XENOMAI_LIB_DIR=/opt/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/lib
+#XENOMAI_INC_DIR=/opt/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/include
+#XENOMAI_LIB_DIR=/opt/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/lib
+
+XENOMAI_INC_DIR=/tmp/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/include
+XENOMAI_LIB_DIR=/tmp/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/lib

 INC=-I/opt/eldk-4.2/PPMAC_rootfs-7-wheezy/opt/ppmac/libppmac -I/opt/eldk-4.2/PPMAC_rootfs-7-wheezy/opt/ppmac/rtpmac -I$(XENOMAI_INC_DIR)
-
-
 LIB=-L/opt/eldk-4.2/PPMAC_rootfs-7-wheezy/opt/ppmac/libppmac -lppmac -L/opt/eldk-4.2/PPMAC_rootfs-7-wheezy/usr/local/xenomai-2.6.2.1/lib -lnative -lxenomai -lpthread_rt -lpthread -lrt -ldl

 CC=/opt/eldk-4.2/usr/bin/ppc_4xxFP-g++
@@ -14,8 +15,15 @@ LD=$(CC)

 all: triggerSync

+triggerSync.o: $(XENOMAI_INC_DIR)
+
+$(XENOMAI_INC_DIR):
+	mkdir -p /tmp/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/
+	rsync -vai root@$(HOST):/usr/local/xenomai-2.6.2.1/ /tmp/powerpc-465-rootfs/usr/local/xenomai-2.6.2.1/
+
+
 %.o: %.c
-	$(CC) -g $(INC) -c $^ -o $@
+	$(CC) -g $(INC) -c $< -o $@

 triggerSync: triggerSync.o
 	$(LD) -g $(LIB) $^ -o $@
--- a/src/triggerSync/triggerSync
+++ b/src/triggerSync/triggerSync
--- a/src/triggerSync/triggerSync.c
+++ b/src/triggerSync/triggerSync.c
@@ -33,11 +33,23 @@
 extern struct SHM *pshm;
 static char mode=0;
 static float mtPt2Pt=40.f; //motion point to point time
-static float timeOfs=0.f; //time ofset
+static float timeOfs=0.f; //time ofset  (start time adjustment)
+static float timeCor=0.f; //time correction (frame to frame time adjustment)
+
 #define CLOCK_RES 1e-9 //Clock resolution is 1 ns by default

 #define  SIMFLAG0 (pshm->Coord[1].Q[10])
 #define  SIMFLAG1 (pshm->Coord[1].Q[11])
+
+//EncTable[20].pEnc= Coord[1].Q[12].a does not work
+//EncTable[20].pEnc= Sys.Udata[0].a works uint32
+//EncTable[20].pEnc= Sys.Idata[0].a works int32
+//EncTable[20].pEnc= Sys.Fdata[0].a works float32
+//EncTable[20].pEnc= Sys.Ddata[0].a works float64
+//#define  ENCVAL (*((double *)pushm+0))
+#define  ENCVAL (*((unsigned int *)pushm+0))
+
+
 //#define  SIMFLAG0 (pshm->P[10])
 //#define  SIMFLAG1 (pshm->P[11])
 //Power PMAC Software Reference Manual.pdf Gate3[i].Chan[j].Status -> page 919 UserFlag
@@ -76,6 +88,14 @@ void trigsync_func(void *arg)
    printf("ending trigsync_func because Gather.Enable==0\n");
    return;
  }
+
+  //unsigned int lastQ12=0; //Q12 value for further sync
+  double mxActPos,mxDesPos,mxHomePos=pshm->Motor[2].HomePos;
+  double myActPos,myDesPos,myHomePos=pshm->Motor[1].HomePos;
+
+  printf("Wait motion program arrived at start position...\n");
+  while(pshm->Coord[1].Q[0]!=-3)
+    rt_task_wait_period(NULL);
  pshm->Coord[1].Q[0]=-2;
  srvPer=pshm->ServoPeriod;

@@ -93,29 +113,30 @@ void trigsync_func(void *arg)
  }
  printf("Flag 0: %.5f ms\n", (rt_timer_read() - rtStart)/1E6);

-  pshm->Gather.Enable=2; //start gathering data
-  pshm->Coord[1].Q[0]=-1;
  if(mode&4)
  {
+    while(SIMFLAG1)
+      rt_task_wait_period(NULL);
    while(!SIMFLAG1)
      rt_task_wait_period(NULL);
  }
  else
  {
+    while(FLAG1)
+      rt_task_wait_period(NULL);
    while(!FLAG1)
      rt_task_wait_period(NULL);
  }
-//puts("waitFlag1");
-//gate3_1->Chan[1].Status f057f77f
-//gate3_1->Chan[1].Status f057ff7f
-//printf("gate3_1->Chan[1].Status %x\n",gate3_1->Chan[1].Status);
+  //FEL shot arrived FLAG1 0->1: first frame trigger before first cristall
+  pshm->Gather.Enable=2; //start gathering data
+  pshm->Coord[1].Q[0]=-1;
+  ENCVAL=0;

  printf("Flag 1: %.5f ms\n", (rt_timer_read() - rtStart)/1E6);
  rtStart=rtLast=rt_timer_read();
  scStart=scLast=pshm->ServoCount;
  mtAct=0.f;
  pshm->Coord[1].Q[0]=0;
-  srvPer=0.2f;
  //pshm->Coord[1].DesTimeBase=srvPer;  //start motion at default speed
  pshm->Coord[1].DesTimeBase=srvPer*(mtPt2Pt+timeOfs)/mtPt2Pt;  //start motion at default speed
  if(mode&8)
@@ -134,24 +155,53 @@ void trigsync_func(void *arg)
    else
    {
      while(FLAG1)
+      {
        rt_task_wait_period(NULL);
+        ENCVAL=( (i-1)*mtPt2Pt + (pshm->ServoCount-scLast)*srvPer )*1000;
+      }

      while(!FLAG1)
+      {
        rt_task_wait_period(NULL);
+        ENCVAL=( (i-1)*mtPt2Pt + (pshm->ServoCount-scLast)*srvPer )*1000;
+      }
    }
-    //FEL shot arrived
+    //FEL shot arrived FLAG1 0->1
+    //ENCVAL+=mtPt2Pt*1000; //ENCVAL in us
+    ENCVAL=i*mtPt2Pt*1000; //ENCVAL in us
    rtCur = rt_timer_read();
    scCur=pshm->ServoCount;
+    //if (lastQ12!=(unsigned int)pshm->Coord[1].Q[12])
+    //{
+    //  //'Coord[1].Q[12]=Sys.ServoCount'
+    //  //'Coord[1].Q[13]={idxOfPoint}'
+    //  //type of pshm->Coord[1].Q[12] is double
+    //  lastQ12=(unsigned int)pshm->Coord[1].Q[12]; //saved ServoCount in program code
+
+    //  //mxActPos=pshm->Motor[2].ActPos;mxDesPos=pshm->Motor[2].DesPos;
+    //  //myActPos=pshm->Motor[1].ActPos;myDesPos=pshm->Motor[1].DesPos;
+
+    //  //printf("*** SYNC *** Trigger count:%d,  ProgIdx:%d, ServoCount diff:%d-%d=%d", i, (unsigned int)pshm->Coord[1].Q[13], lastQ12,scCur, lastQ12-scCur);
+    //  printf("*** SYNC *** Trigger count:%d,  myDesPos:%.2f, ServoCount diff:%d-%d=%d\n", i, pshm->Coord[1].Q[13]-myHomePos, lastQ12,scCur, lastQ12-scCur);
+    //  //printf(" X,Y ActPos:(%.5g %.5g) DesPos:(%.5g %.5g)\n", mxActPos-mxHomePos, myActPos-myHomePos, mxDesPos-mxHomePos, myDesPos-myHomePos);
+    //}
+
    rtDiff=rtCur-rtLast;
    scDiff=scCur-scLast;

-    mtAct+=scDiff*srvPer;
+    mtAct+=scDiff*srvPer+timeCor;
    mtDes=i*mtPt2Pt+timeOfs;
    srvPer=(mtPt2Pt+mtDes-mtAct)/scDiff;
+    //srvPer=pshm->ServoPeriod; //default speed
    pshm->Coord[1].DesTimeBase=srvPer;
    pshm->Coord[1].Q[0]++;
    if(mode&8)
-      printf("Trigger count:%d, rtDiff:%.3fms scDiff:%d mtAct:%.3f mtDes:%.3f srvPer:%.6f\n", i, rtDiff/1E6,scDiff, mtAct,mtDes,srvPer);
+    {
+      mxActPos=pshm->Motor[2].ActPos;mxDesPos=pshm->Motor[2].DesPos;
+      myActPos=pshm->Motor[1].ActPos;myDesPos=pshm->Motor[1].DesPos;
+      printf(" X,Y ActPos:(%.5g %.5g) DesPos:(%.5g %.5g) ", mxActPos-mxHomePos, myActPos-myHomePos, mxDesPos-mxHomePos, myDesPos-myHomePos);
+      printf("Trigger count:%d, rtDiff:%.3fms scDiff:%d mtAct:%.3f mtDes:%.3f srvPer:%.6f ENCVAL:%u \n", i, rtDiff/1E6,scDiff, mtAct,mtDes,srvPer,ENCVAL);
+    }
    rtLast=rtCur;
    scLast=scCur;
  }
@@ -163,12 +213,13 @@ void trigsim_func(void *arg)
  RT_TASK *curtask;
  RT_TASK_INFO curtaskinfo;
  int iret = 0;
+  int loopPeriod=1e7;//Expressed in ticks (this is the default task period)
  curtask = rt_task_self();
  rt_task_inquire(curtask, &curtaskinfo);
  //Print the info
-  //printf("Starting task %s with period of %f ms ....\n", curtaskinfo.name,10*1E6/1E6);
+  printf("Starting task %s with period of %f ms ....\n", curtaskinfo.name,loopPeriod/1E6);
  //Make the task periodic with a specified loop period
-  //rt_task_set_periodic(NULL, TM_NOW, 10*1E6);
+  //rt_task_set_periodic(NULL, TM_NOW, loopPeriod); //not critical here because not polling but rt_task_sleep_until ...
  printf("Starting task %s \n", curtaskinfo.name);

  int i,j=0;
@@ -180,9 +231,8 @@ void trigsim_func(void *arg)

  for(i=0,rtSlice=rtStart;;i++)
  {
-    rtSlice=rtStart+i*40*1E6; // a slice is 40 ms
-    //rtSlice=rtStart+i*40.2*1E6; // a slice is 40 ms
-    //rtSlice+=(rand()%(int)(1*1E6)); //0.1ms jitter
+    rtSlice=rtStart+i*mtPt2Pt*1E6; // a slice is mtPt2Pt ms
+    //rtSlice+=(rand()%(int)(1*1E6)); //0.1ms jitter to test sync
    rt_task_sleep_until(rtSlice); //in ns
    if(mode&4)
    {
@@ -275,6 +325,11 @@ mode:\n\
 bit2:4: simulate frame trigger\n\
 bit3:8: verbose\n\
 \n\
+pt2ptTime:  point to point time in ms (default=10, float value)\n\
+timeOfs:    once added time offset in ms (default=0, float value)\n\
+scl:        scale factor (so far unused, default=1, float value)\n\
+\n\
+\n\
 simulate start trigger:\n\
 set pshm->Coord[1].Q[10]=1 to simulate a Jungfrau aquire start\n\
 \n\
@@ -297,7 +352,7 @@ Coord[1].Q[0]= 0 : got frame trigger 0\n\
 Coord[1].Q[0] is incremented at each trigger\n\
 sync task ends when Gather.Enable==0\n\
 ";
-  printf("usage:\n%s pt2ptTime timeOfs mode\n",cmd);
+  printf("usage:\n%s mode pt2ptTime timeOfs(default=0) scl(default=1)\n",cmd);
  puts(s);
  return -1;
 }
@@ -308,22 +363,21 @@ int main(int argc, char *argv[])
    int initialized=0;
    int i;
    char *s;
-    if(argc!=4)
-      return usage(argv[0]);
-    mtPt2Pt=strtof(argv[1], &s);
-    if (argv[1]==s)
-      return usage(argv[0]);
-    timeOfs=strtof(argv[2], &s);
-    if (argv[2]==s)
-      return usage(argv[0]);
-    mode=(int)strtol(argv[3], &s, 10);
-    if (argv[3]==s)
+    if(argc<2)
      return usage(argv[0]);
+    mode=(int)strtol(argv[1], &s, 10);
+    if (argc>2)
+      mtPt2Pt=strtof(argv[2], &s);
+    if (argc>3)
+      timeOfs=strtof(argv[3], &s);
+    if (argc>4)
+      timeCor=strtof(argv[4], &s);
    puts(argv[0]);
    puts(argv[1]);
-    puts(argv[2]);
-    puts(argv[3]);
-    printf("mtPt2Pt:%g timeOfs:%g mode:%d\n",mtPt2Pt,timeOfs,mode);
+    //puts(argv[2]);
+    //puts(argv[3]);
+    //puts(argv[4]);
+    printf("mode:%d mtPt2Pt:%3.8gms timeOfs:%3.8gms timeCor:%3.8gms\n",mode,mtPt2Pt,timeOfs,timeCor);
    if ((err = InitLibrary()) != 0) {
        abort();
    }