hooke/plugin/multidistance.py

   1 # -*- coding: utf-8 -*-
   2 from libhooke import WX_GOOD, ClickedPoint
   3 import wxversion
   4 wxversion.select(WX_GOOD)
   5 from wx import PostEvent
   6 import numpy as np
   7 import scipy as sp
   8 import copy
   9 import os.path
  10 import time
  11
  12 import warnings
  13 warnings.simplefilter('ignore',np.RankWarning)
  14
  15
  16 class multidistanceCommands(object):
  17
  18     def do_multidistance(self,args):
  19      '''
  20      MULTIDISTANCE
  21      multidistance.py
  22      Based on the convolution recognition automatically give the distances between the peaks found.
  23      The command allow also to remove the unwanted peaks that can be due to interference.
  24      When you first issue the command, it will ask for the filename. If you are giving the filename
  25      of an existing file, autopeak will resume it and append measurements to it. If you are giving
  26      a new filename, it will create the file and append to it until you close Hooke.
  27      You can also define a minimun deviation of the peaks.
  28
  29      Syntax:
  30      multidistance [deviation]
  31      deviation = number of times the convolution signal is above the noise absolute deviation.
  32      '''
  33
  34      def find_current_peaks(noflatten, a):
  35             #Find peaks.
  36             if len(a)==0:
  37                  a=self.convfilt_config['mindeviation']
  38             try:
  39                  abs_devs=float(a)
  40             except:
  41                  print "Bad input, using default."
  42                  abs_devs=self.convfilt_config['mindeviation']
  43
  44             defplot=self.current.curve.default_plots()[0]
  45             if not noflatten:
  46                 flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
  47                 defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
  48             pk_loc,peak_size=self.has_peaks(defplot, abs_devs)
  49             return pk_loc, peak_size
  50
  51
  52      noflatten=False
  53      peaks_location, peak_size=find_current_peaks(noflatten, args)
  54
  55      #if no peaks, we have nothing to plot. exit.
  56      if len(peaks_location)==0:
  57             return
  58
  59      #otherwise, we plot the peak locations.
  60      xplotted_ret=self.plots[0].vectors[1][0]
  61      yplotted_ret=self.plots[0].vectors[1][1]
  62      xgood=[xplotted_ret[index] for index in peaks_location]
  63      ygood=[yplotted_ret[index] for index in peaks_location]
  64
  65      recplot=self._get_displayed_plot()
  66      recplot.vectors.append([xgood,ygood])
  67      if recplot.styles==[]:
  68          recplot.styles=[None,None,'scatter']
  69          recplot.colors=[None,None,None]
  70      else:
  71          recplot.styles+=['scatter']
  72          recplot.colors+=[None]
  73
  74      self._send_plot([recplot])
  75
  76      print 'Peaks to ignore (0,1...n from contact point,return to take all)'
  77      print 'N to discard measurement'
  78      exclude_raw=raw_input('Input:')
  79      if exclude_raw=='N':
  80         print 'Discarded.'
  81         return
  82
  83      if not exclude_raw=='':
  84         exclude=exclude_raw.split(',')
  85         #we convert in numbers the input
  86         try:
  87             exclude=[int(item) for item in exclude]
  88         except:
  89             print 'Bad input, taking nothing.'
  90             return
  91
  92 #    we remove the peaks that we don't want from the list, we need a counter beacause if we remove
  93 #    a peaks the other peaks in the list are shifted by one at each step
  94         count=0
  95         for a in exclude:
  96           if (a==0):
  97              peaks_location=peaks_location[1:]
  98           else:
  99              new_a=a-count
 100              peaks_location=  peaks_location[0:new_a]+peaks_location[new_a+1:]
 101              peak_size=            peak_size[0:new_a]+peak_size[new_a+1:]
 102           count+=1
 103
 104      #we calculate the distance vector
 105      dist=[]
 106      for i in range(len(peaks_location)-1):
 107          dist.append(xplotted_ret[peaks_location[i]]-xplotted_ret[peaks_location[i+1]])
 108
 109
 110
 111
 112
 113         #Save file info
 114      if self.autofile=='':
 115             self.autofile=raw_input('Multidistance filename? (return to ignore) ')
 116             if self.autofile=='':
 117                 print 'Not saved.'
 118                 return
 119
 120      if not os.path.exists(self.autofile):
 121             f=open(self.autofile,'w+')
 122             f.write('Analysis started '+time.asctime()+'\n')
 123             f.write('----------------------------------------\n')
 124             f.write('; Delta Distance length (m)\n')
 125             f.write(self.current.path+'\n')
 126             for o in dist:
 127                f.write(";")
 128                f.write(str(o))
 129             f.write("\n")
 130             f.close()
 131
 132      print 'Saving...'
 133      f=open(self.autofile,'a+')
 134
 135      f.write(self.current.path+'\n')
 136      for i in dist:
 137           f.write(";")
 138           f.write(str(i))
 139
 140      f.write("\n")
 141      f.close()