hooke/plugin/massanalysis.py

   1 # Copyright (C) 2008-2012 Massimo Sandal <devicerandom@gmail.com>
   2 #                         W. Trevor King <wking@tremily.us>
   3 #
   4 # This file is part of Hooke.
   5 #
   6 # Hooke is free software: you can redistribute it and/or modify it under the
   7 # terms of the GNU Lesser General Public License as published by the Free
   8 # Software Foundation, either version 3 of the License, or (at your option) any
   9 # later version.
  10 #
  11 # Hooke is distributed in the hope that it will be useful, but WITHOUT ANY
  12 # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
  13 # A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
  14 # details.
  15 #
  16 # You should have received a copy of the GNU Lesser General Public License
  17 # along with Hooke.  If not, see <http://www.gnu.org/licenses/>.
  18
  19 """Global analysis of force curves with various parameters
  20
  21 Requires:
  22 libpeakspot.py
  23 flatfilts.py
  24 """
  25
  26 import numpy as np
  27 import csv
  28
  29 from .. import libpeakspot as lps
  30 from .. import curve as lhc
  31 from .. import libhooke as lh
  32
  33 class massanalysisCommands(object):
  34
  35     def _plug_init(self):
  36         self.mass_variables={}
  37         self.interesting_variables=['curve','firstpeak_distance','lastpeak_distance','Npeaks','median_distance','mean_distance']
  38         self._clean_data()
  39
  40     def _clean_data(self):
  41         for variable in self.interesting_variables:
  42             self.mass_variables[variable]=[]
  43
  44     def peak_position_from_contact(self, item, locations):
  45         '''
  46         calculates X distance of a peak from the contact point
  47         '''
  48         item.identify(self.drivers)
  49
  50         real_positions=[]
  51         cut_index=self.find_contact_point()
  52
  53         #we assume the first is the plot with the force curve
  54         plot=item.curve.default_plots()[0]
  55         xret=plot.vectors[1][0]
  56
  57         start_x=xret[cut_index]
  58
  59         real_positions=[abs((xret[index])-(start_x)) for index in locations]
  60         #close all open files
  61         item.curve.close_all()
  62         #needed to avoid *big* memory leaks!
  63         del item.curve
  64         del item
  65         return real_positions
  66
  67     def do_maplist(self,args):
  68         '''
  69         MAPLIST
  70         (flatfilts.py)
  71         ----
  72         pass
  73         '''
  74         self._clean_data() #if we recall it, clean previous data!
  75         min_deviation=self.convfilt_config['mindeviation']
  76
  77
  78         c=0
  79         for item in self.current_list:
  80             try:
  81                 peak_location,peak_size=self.exec_has_peaks(item, min_deviation)
  82                 real_positions=self.peak_position_from_contact(item, peak_location)
  83
  84                 self.mass_variables['Npeaks'].append(len(peak_location))
  85
  86                 if len(peak_location) > 1:
  87                     self.mass_variables['firstpeak_distance'].append(min(real_positions))
  88                     self.mass_variables['lastpeak_distance'].append(max(real_positions))
  89
  90                     distancepeaks=[]
  91                     for index in range(len(real_positions)-1):
  92                         distancepeaks.append(real_positions[index+1]-real_positions[index])
  93                 else:
  94                     self.mass_variables['firstpeak_distance'].append(0)
  95                     self.mass_variables['lastpeak_distance'].append(0)
  96
  97                 if len(peak_location) > 2:
  98                     self.mass_variables['median_distance'].append(np.median(distancepeaks))
  99                     self.mass_variables['mean_distance'].append(np.mean(distancepeaks))
 100                 else:
 101                     self.mass_variables['median_distance'].append(0)
 102                     self.mass_variables['mean_distance'].append(0)
 103
 104                 print 'curve',c
 105             except SyntaxError:
 106                 print 'curve',c,'not mapped'
 107                 pass
 108
 109             c+=1
 110
 111     def do_plotmap(self,args):
 112         '''
 113         '''
 114         args=args.split()
 115         if len(args)>1:
 116             x=self.mass_variables[args[0]]
 117             y=self.mass_variables[args[1]]
 118         else:
 119             print 'Give me two arguments between those:'
 120             print self.interesting_variables
 121             return
 122
 123         scattermap=lhc.PlotObject()
 124         scattermap.vectors=[[]]
 125         scattermap.vectors[0].append(x)
 126         scattermap.vectors[0].append(y)
 127
 128         scattermap.units=[args[0],args[1]]
 129         scattermap.styles=['scatter']
 130         scattermap.destination=1
 131
 132         self._send_plot([scattermap])
 133
 134     def do_savemaps(self,args):
 135         '''
 136         args=filename
 137         '''
 138
 139         '''
 140         def csv_write_cols(data, f):
 141
 142             #from Bruno Desthuillers on comp.lang.python
 143
 144             writer = csv.writer(f)
 145             keys = data.keys()
 146             writer.writerow(dict(zip(keys,keys)))
 147             for row in zip(*data.values()):
 148                 writer.writerow(dict(zip(keys, row)))
 149         '''
 150
 151         f=open(args,'wb')
 152         lh.csv_write_dictionary(f,self.mass_variables)
 153         f.close()