hooke/plugin/curvetools.py

   1 # Copyright (C) 2010 Fabrizio Benedetti
   2 #                    W. Trevor King <wking@drexel.edu>
   3 #
   4 # This file is part of Hooke.
   5 #
   6 # Hooke is free software: you can redistribute it and/or
   7 # modify it under the terms of the GNU Lesser General Public
   8 # License as published by the Free Software Foundation, either
   9 # version 3 of the License, or (at your option) any later version.
  10 #
  11 # Hooke is distributed in the hope that it will be useful,
  12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 # GNU Lesser General Public License for more details.
  15 #
  16 # You should have received a copy of the GNU Lesser General Public
  17 # License along with Hooke.  If not, see
  18 # <http://www.gnu.org/licenses/>.
  19
  20 from ..libhooke import WX_GOOD, ClickedPoint
  21
  22 import wxversion
  23 wxversion.select(WX_GOOD)
  24 from wx import PostEvent
  25 import numpy as np
  26 import scipy as sp
  27 import copy
  28 import os.path
  29 import time
  30
  31
  32 class curvetoolsCommands:
  33
  34       def fit_interval_nm(self,start_index,plot,nm,backwards):
  35           '''
  36           Calculates the number of points to fit, given a fit interval in nm
  37           start_index: index of point
  38           plot: plot to use
  39           backwards: if true, finds a point backwards.
  40           '''
  41           whatset=1 #FIXME: should be decidable
  42           x_vect=plot.vectors[1][0]
  43
  44           c=0
  45           i=start_index
  46           start=x_vect[start_index]
  47           maxlen=len(x_vect)
  48           while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
  49               if i==0 or i==maxlen-1: #we reached boundaries of vector!
  50                   return c
  51
  52               if backwards:
  53                   i-=1
  54               else:
  55                   i+=1
  56               c+=1
  57           return c
  58
  59
  60
  61       def find_current_peaks(self,noflatten, a=True, maxpeak=True):
  62             #Find peaks.
  63             if a==True:
  64                   a=self.convfilt_config['mindeviation']
  65             try:
  66                   abs_devs=float(a)
  67             except:
  68                   print "Bad input, using default."
  69                   abs_devs=self.convfilt_config['mindeviation']
  70
  71             defplot=self.current.curve.default_plots()[0]
  72             if not noflatten:
  73                 flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
  74                 defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
  75             pk_location,peak_size=self.has_peaks(defplot, abs_devs, maxpeak)
  76             return pk_location, peak_size
  77
  78
  79       def pickup_contact_point(self,N=1,whatset=1):
  80             '''macro to pick up the contact point by clicking'''
  81             contact_point=self._measure_N_points(N=1, whatset=1)[0]
  82             contact_point_index=contact_point.index
  83             self.wlccontact_point=contact_point
  84             self.wlccontact_index=contact_point.index
  85             self.wlccurrent=self.current.path
  86             return contact_point, contact_point_index
  87
  88
  89
  90       def baseline_points(self,peak_location, displayed_plot):
  91             clicks=self.config['baseline_clicks']
  92             if clicks==0:
  93                 self.basepoints=[]
  94                 base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
  95                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
  96                 base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
  97                 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
  98             elif clicks>0:
  99                 print 'Select baseline'
 100                 if clicks==1:
 101                     self.basepoints=self._measure_N_points(N=1, whatset=1)
 102                     base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
 103                     self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
 104                 else:
 105                     self.basepoints=self._measure_N_points(N=2, whatset=1)
 106
 107             self.basecurrent=self.current.path
 108             return self.basepoints
 109
 110
 111
 112 class InfoCommand (Command):
 113     """Execute a system command and report the output.
 114     """
 115     def __init__(self):
 116         super(SystemCommand, self).__init__(
 117             name='system',
 118             arguments=[
 119                 Argument(
 120     name='command', type='string', optional=False, count=-1,
 121     help="""
 122 Command line to execute.
 123 """.strip())
 124 ],
 125             help=self.__doc__)
 126
 127     def _run(self, hooke, inqueue, outqueue, params):
 128         os.system(params['command'])
 129
 130     def do_info(self,args):
 131         '''
 132         INFO
 133         ----
 134         Returns informations about the current curve.
 135         '''
 136         print 'Path: ',self.current.path
 137         print 'Experiment: ',self.current.curve.experiment
 138         print 'Filetype: ',self.current.curve.filetype
 139         for plot in self.current.curve.default_plots():
 140             for set in plot.vectors:
 141                 lengths=[len(item) for item in set]
 142                 print 'Data set size: ',lengths
 143
 144
 145     def help_current(self):
 146         print '''
 147 CURRENT
 148 Prints the current curve path.
 149 ------
 150 Syntax: current
 151         '''
 152     def do_current(self,args):
 153         print self.current.path
 154
 155
 156     def help_txt(self):
 157         print '''
 158 TXT
 159 Saves the current curve as a text file
 160 Columns are, in order:
 161 X1 , Y1 , X2 , Y2 , X3 , Y3 ...
 162
 163 -------------
 164 Syntax: txt [filename] {plot to export}
 165         '''
 166     def do_txt(self,args):
 167
 168         def transposed2(lists, defval=0):
 169             '''
 170             transposes a list of lists, i.e. from [[a,b,c],[x,y,z]] to [[a,x],[b,y],[c,z]] without losing
 171             elements
 172             (by Zoran Isailovski on the Python Cookbook online)
 173             '''
 174             if not lists: return []
 175             return map(lambda *row: [elem or defval for elem in row], *lists)
 176
 177         whichplot=0
 178         args=args.split()
 179         if len(args)==0:
 180             filename=linp.safeinput('Filename?',[self.current.path+'.txt'])
 181         else:
 182             filename=linp.checkalphainput(args[0],self.current.path+'.txt',[])
 183             try:
 184                 whichplot=int(args[1])
 185             except:
 186                 pass
 187
 188         try:
 189             outofplot=self.plots[whichplot].vectors
 190         except:
 191             print "Plot index out of range."
 192             return 0
 193
 194         columns=[]
 195         for dataset in self.plots[whichplot].vectors:
 196             for i in range(0,len(dataset)):
 197                 columns.append([])
 198                 for value in dataset[i]:
 199                     columns[-1].append(str(value))
 200
 201         rows=transposed2(columns, 'nan')
 202         rows=[' , '.join(item) for item in rows]
 203         text='\n'.join(rows)
 204
 205         txtfile=open(filename,'w+')
 206         #Save units of measure in header
 207         txtfile.write('X:'+self.plots[whichplot].units[0]+'\n')
 208         txtfile.write('Y:'+self.plots[whichplot].units[1]+'\n')
 209         txtfile.write(text)
 210         txtfile.close()