hooke/plugin/multidistance.py

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