curvetools.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
  13 class curvetoolsCommands:
  14
  15       def print_prec(self, arr, prec):
  16          try:
  17            nparr=np.array(arr)
  18            np.set_printoptions(precision=prec)
  19            #we remove the parentesis if the array is longer that 1
  20            if len(nparr)>1:
  21              strvals=str(nparr)[1:-1]
  22            return strvals
  23          except:
  24            return "Error in the array."
  25
  26       def fit_interval_nm(self,start_index,plot,nm,backwards):
  27           '''
  28           Calculates the number of points to fit, given a fit interval in nm
  29           start_index: index of point
  30           plot: plot to use
  31           backwards: if true, finds a point backwards.
  32           '''
  33           whatset=1 #FIXME: should be decidable
  34           x_vect=plot.vectors[1][0]
  35
  36           c=0
  37           i=start_index
  38           start=x_vect[start_index]
  39           maxlen=len(x_vect)
  40           while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
  41               if i==0 or i==maxlen-1: #we reached boundaries of vector!
  42                   return c
  43
  44               if backwards:
  45                   i-=1
  46               else:
  47                   i+=1
  48               c+=1
  49           return c
  50
  51
  52
  53       def find_current_peaks(self,noflatten, a=True, maxpeak=True):
  54             #Find peaks.
  55             if a==True:
  56                   a=self.convfilt_config['mindeviation']
  57             try:
  58                   abs_devs=float(a)
  59             except:
  60                   print "Bad input, using default."
  61                   abs_devs=self.convfilt_config['mindeviation']
  62
  63             defplot=self.current.curve.default_plots()[0]
  64             if not noflatten:
  65                 flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
  66                 defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
  67             pk_location,peak_size=self.has_peaks(defplot, abs_devs, maxpeak)
  68             return pk_location, peak_size
  69
  70
  71       def pickup_contact_point(self,N=1,whatset=1):
  72             '''macro to pick up the contact point by clicking'''
  73             contact_point=self._measure_N_points(N=1, whatset=1)[0]
  74             contact_point_index=contact_point.index
  75             self.wlccontact_point=contact_point
  76             self.wlccontact_index=contact_point.index
  77             self.wlccurrent=self.current.path
  78             return contact_point, contact_point_index
  79
  80
  81
  82       def baseline_points(self,peak_location, displayed_plot):
  83             clicks=self.config['baseline_clicks']
  84             if clicks==0:
  85                 self.basepoints=[]
  86                 base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
  87                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
  88                 base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
  89                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
  90             elif clicks>0:
  91                 print 'Select baseline'
  92                 if clicks==1:
  93                     self.basepoints=self._measure_N_points(N=1, whatset=1)
  94                     base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
  95                     self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
  96                 else:
  97                     self.basepoints=self._measure_N_points(N=2, whatset=1)
  98
  99             self.basecurrent=self.current.path
 100             return self.basepoints
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