first steps in helicalscan

python/helicalscan.py

@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+# *-----------------------------------------------------------------------*
+# |                                                                       |
+# |  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+# |                                                                       |
+# |              Author Thierry Zamofing (thierry.zamofing@psi.ch)        |
+# *-----------------------------------------------------------------------*
+'''
+tools to setup and execute a helical scan of a cristal
+#THIS IS JUST TESTING CODE TO SOLVE FINDING THE ROTATION CENTER
+'''
+
+import os, sys, json
+import numpy as np
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+from utilities import *
+
+class HelicalScan:
+    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:
+        fn='/tmp/shapepath4'
+        #fn='/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/data/'+time.strftime('%y-%m-%d-%H_%M_%S')
+        #cfg = {"sequencer": ['gen_grid_points(w=5,h=5,pitch=100,rnd=0.4)', 'sort_points()','gen_prog(file="'+fn+'.prg",host="SAR-CPPM-EXPMX1",mode=1,pt2pt_time=10,cnt=1)', 'plot_gather("'+fn+'.npz")']}
+        #cfg = {"sequencer": ['test_find_rot_ctr()']}
+        cfg = {"sequencer": ['test_find_rot_ctr(n=5. ,per=1. ,phi=24.6  ,bias=2.31,ampl=4.12)']}
+
+      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 meas_rot_ctr(self,y,per=1):
+      # find the amplitude bias and phase of an equidistant sampled sinus
+      # it needs at least 3 measurements e.g. at 0,120 240 deg or 0 90 180 270 deg
+      # per is the number of persiods, default is 1 period =360 deg
+      n=len(y)
+      f = np.fft.fft(y)
+      idx=int(per)
+      bias=np.absolute(f[0]/n)
+      phase=np.angle(f[idx])
+      ampl=np.absolute(f[idx])*2/n
+      return (bias,phase,ampl)
+
+    def test_find_rot_ctr(self,n=3. ,per=1. ,phi=37  ,bias=4.1,ampl=2.4):
+      # find the rotation center, amplitude out of n (niminum 3) measurements
+      # n    number of equidistant measurements
+      # per  number of periods (full rotation of all measurements nut be a interger value for precise measurements)
+      # phi  phase
+      # bias bias value
+      # ampl amplitude
+
+      t = np.arange(n)
+      y=ampl*np.cos(2*np.pi*(per/n*t+phi/360.))+bias
+      sp = np.fft.fft(y)
+      freq = np.fft.fftfreq(t.shape[-1])
+      plt.figure(1)
+      plt.subplot(311)
+      plt.plot(t,y,'b.-')
+      plt.subplot(312)
+      #plt.plot(t, sp.real,'b.-', t, sp.imag,'r.-')
+      plt.step(t, sp.real,'b.-', t, sp.imag,'r.-', where='mid')
+      #plt.stem(t, sp.real,'b-')
+      #plt.plot(freq, sp.real,'b.-', freq, sp.imag,'r.-')
+
+      idx=int(per)
+      bias=np.absolute(sp[0]/n)
+      phase=np.angle(sp[idx])
+      ampl=np.absolute(sp[idx]) * 2 / n
+      print('bias: '+str(bias))
+      print('phase: '+str(phase*360./2/np.pi))
+      print('amplitude: '+str(ampl))
+
+      plt.subplot(313)
+      t2 = np.linspace(0,2*np.pi,64)
+      y2=ampl*np.cos(t2+phase)+bias
+      plt.plot(t2,y2,'g-')
+      plt.stem(t/n*2*np.pi*per,y,'b-')
+
+
+      plt.show()
+      pass
+
+
+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=('-n',
+                '-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('--xy', action='store_true', help='sort x,y instead y,x')
+    parser.add_option('--cfg', help='config file containing json configuration structure')
+
+    (args, other)=parser.parse_args()
+    args.other=other
+
+    sp=HelicalScan(args)
+    sp.run()
+#------------------ Main Code ----------------------------------
+  #ssh_test()
+  ret=parse_args()
+  exit(ret)