hooke/plugin/curvetools.py

   1 # Copyright
   2
   3 from ..libhooke import WX_GOOD, ClickedPoint
   4
   5 import wxversion
   6 wxversion.select(WX_GOOD)
   7 from wx import PostEvent
   8 import numpy as np
   9 import scipy as sp
  10 import copy
  11 import os.path
  12 import time
  13
  14
  15 class curvetoolsCommands:
  16
  17       def fit_interval_nm(self,start_index,plot,nm,backwards):
  18           '''
  19           Calculates the number of points to fit, given a fit interval in nm
  20           start_index: index of point
  21           plot: plot to use
  22           backwards: if true, finds a point backwards.
  23           '''
  24           whatset=1 #FIXME: should be decidable
  25           x_vect=plot.vectors[1][0]
  26
  27           c=0
  28           i=start_index
  29           start=x_vect[start_index]
  30           maxlen=len(x_vect)
  31           while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
  32               if i==0 or i==maxlen-1: #we reached boundaries of vector!
  33                   return c
  34
  35               if backwards:
  36                   i-=1
  37               else:
  38                   i+=1
  39               c+=1
  40           return c
  41
  42
  43
  44       def find_current_peaks(self,noflatten, a=True, maxpeak=True):
  45             #Find peaks.
  46             if a==True:
  47                   a=self.convfilt_config['mindeviation']
  48             try:
  49                   abs_devs=float(a)
  50             except:
  51                   print "Bad input, using default."
  52                   abs_devs=self.convfilt_config['mindeviation']
  53
  54             defplot=self.current.curve.default_plots()[0]
  55             if not noflatten:
  56                 flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
  57                 defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
  58             pk_location,peak_size=self.has_peaks(defplot, abs_devs, maxpeak)
  59             return pk_location, peak_size
  60
  61
  62       def pickup_contact_point(self,N=1,whatset=1):
  63             '''macro to pick up the contact point by clicking'''
  64             contact_point=self._measure_N_points(N=1, whatset=1)[0]
  65             contact_point_index=contact_point.index
  66             self.wlccontact_point=contact_point
  67             self.wlccontact_index=contact_point.index
  68             self.wlccurrent=self.current.path
  69             return contact_point, contact_point_index
  70
  71
  72
  73       def baseline_points(self,peak_location, displayed_plot):
  74             clicks=self.config['baseline_clicks']
  75             if clicks==0:
  76                 self.basepoints=[]
  77                 base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
  78                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
  79                 base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
  80                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
  81             elif clicks>0:
  82                 print 'Select baseline'
  83                 if clicks==1:
  84                     self.basepoints=self._measure_N_points(N=1, whatset=1)
  85                     base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
  86                     self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
  87                 else:
  88                     self.basepoints=self._measure_N_points(N=2, whatset=1)
  89
  90             self.basecurrent=self.current.path
  91             return self.basepoints
  92
  93
  94
  95 class InfoCommand (Command):
  96     """Execute a system command and report the output.
  97     """
  98     def __init__(self):
  99         super(SystemCommand, self).__init__(
 100             name='system',
 101             arguments=[
 102                 Argument(
 103     name='command', type='string', optional=False, count=-1,
 104     help="""
 105 Command line to execute.
 106 """.strip())
 107 ],
 108             help=self.__doc__)
 109
 110     def _run(self, hooke, inqueue, outqueue, params):
 111         os.system(params['command'])
 112
 113     def do_info(self,args):
 114         '''
 115         INFO
 116         ----
 117         Returns informations about the current curve.
 118         '''
 119         print 'Path: ',self.current.path
 120         print 'Experiment: ',self.current.curve.experiment
 121         print 'Filetype: ',self.current.curve.filetype
 122         for plot in self.current.curve.default_plots():
 123             for set in plot.vectors:
 124                 lengths=[len(item) for item in set]
 125                 print 'Data set size: ',lengths
 126
 127
 128     def help_current(self):
 129         print '''
 130 CURRENT
 131 Prints the current curve path.
 132 ------
 133 Syntax: current
 134         '''
 135     def do_current(self,args):
 136         print self.current.path
 137
 138
 139     def help_txt(self):
 140         print '''
 141 TXT
 142 Saves the current curve as a text file
 143 Columns are, in order:
 144 X1 , Y1 , X2 , Y2 , X3 , Y3 ...
 145
 146 -------------
 147 Syntax: txt [filename] {plot to export}
 148         '''
 149     def do_txt(self,args):
 150
 151         def transposed2(lists, defval=0):
 152             '''
 153             transposes a list of lists, i.e. from [[a,b,c],[x,y,z]] to [[a,x],[b,y],[c,z]] without losing
 154             elements
 155             (by Zoran Isailovski on the Python Cookbook online)
 156             '''
 157             if not lists: return []
 158             return map(lambda *row: [elem or defval for elem in row], *lists)
 159
 160         whichplot=0
 161         args=args.split()
 162         if len(args)==0:
 163             filename=linp.safeinput('Filename?',[self.current.path+'.txt'])
 164         else:
 165             filename=linp.checkalphainput(args[0],self.current.path+'.txt',[])
 166             try:
 167                 whichplot=int(args[1])
 168             except:
 169                 pass
 170
 171         try:
 172             outofplot=self.plots[whichplot].vectors
 173         except:
 174             print "Plot index out of range."
 175             return 0
 176
 177         columns=[]
 178         for dataset in self.plots[whichplot].vectors:
 179             for i in range(0,len(dataset)):
 180                 columns.append([])
 181                 for value in dataset[i]:
 182                     columns[-1].append(str(value))
 183
 184         rows=transposed2(columns, 'nan')
 185         rows=[' , '.join(item) for item in rows]
 186         text='\n'.join(rows)
 187
 188         txtfile=open(filename,'w+')
 189         #Save units of measure in header
 190         txtfile.write('X:'+self.plots[whichplot].units[0]+'\n')
 191         txtfile.write('Y:'+self.plots[whichplot].units[1]+'\n')
 192         txtfile.write(text)
 193         txtfile.close()