hooke/plugin/massanalysis.py

   1 '''
   2 massanalysis.py
   3
   4 Global analysis of force curves with various parameters
   5
   6 Requires:
   7 libpeakspot.py
   8 flatfilts.py
   9 '''
  10
  11
  12 import libpeakspot as lps
  13 import libhookecurve as lhc
  14 import libhooke as lh
  15 import numpy as np
  16
  17 import csv
  18
  19 class massanalysisCommands:
  20
  21     def _plug_init(self):
  22         self.mass_variables={}
  23         self.interesting_variables=['curve','firstpeak_distance','lastpeak_distance','Npeaks','median_distance','mean_distance']
  24         self._clean_data()
  25
  26     def _clean_data(self):
  27         for variable in self.interesting_variables:
  28             self.mass_variables[variable]=[]
  29
  30     def peak_position_from_contact(self, item, locations):
  31         '''
  32         calculates X distance of a peak from the contact point
  33         '''
  34         item.identify(self.drivers)
  35
  36         real_positions=[]
  37         cut_index=self.find_contact_point()
  38
  39         #we assume the first is the plot with the force curve
  40         plot=item.curve.default_plots()[0]
  41         xret=plot.vectors[1][0]
  42
  43         start_x=xret[cut_index]
  44
  45         real_positions=[abs((xret[index])-(start_x)) for index in locations]
  46         #close all open files
  47         item.curve.close_all()
  48         #needed to avoid *big* memory leaks!
  49         del item.curve
  50         del item
  51         return real_positions
  52
  53     def do_maplist(self,args):
  54         '''
  55         MAPLIST
  56         (flatfilts.py)
  57         ----
  58         pass
  59         '''
  60         self._clean_data() #if we recall it, clean previous data!
  61         min_deviation=self.convfilt_config['mindeviation']
  62
  63
  64         c=0
  65         for item in self.current_list:
  66             try:
  67                 peak_location,peak_size=self.exec_has_peaks(item, min_deviation)
  68                 real_positions=self.peak_position_from_contact(item, peak_location)
  69
  70                 self.mass_variables['Npeaks'].append(len(peak_location))
  71
  72                 if len(peak_location) > 1:
  73                     self.mass_variables['firstpeak_distance'].append(min(real_positions))
  74                     self.mass_variables['lastpeak_distance'].append(max(real_positions))
  75
  76                     distancepeaks=[]
  77                     for index in range(len(real_positions)-1):
  78                         distancepeaks.append(real_positions[index+1]-real_positions[index])
  79                 else:
  80                     self.mass_variables['firstpeak_distance'].append(0)
  81                     self.mass_variables['lastpeak_distance'].append(0)
  82
  83                 if len(peak_location) > 2:
  84                     self.mass_variables['median_distance'].append(np.median(distancepeaks))
  85                     self.mass_variables['mean_distance'].append(np.mean(distancepeaks))
  86                 else:
  87                     self.mass_variables['median_distance'].append(0)
  88                     self.mass_variables['mean_distance'].append(0)
  89
  90                 print 'curve',c
  91             except SyntaxError:
  92                 print 'curve',c,'not mapped'
  93                 pass
  94
  95             c+=1
  96
  97     def do_plotmap(self,args):
  98         '''
  99         '''
 100         args=args.split()
 101         if len(args)>1:
 102             x=self.mass_variables[args[0]]
 103             y=self.mass_variables[args[1]]
 104         else:
 105             print 'Give me two arguments between those:'
 106             print self.interesting_variables
 107             return
 108
 109         scattermap=lhc.PlotObject()
 110         scattermap.vectors=[[]]
 111         scattermap.vectors[0].append(x)
 112         scattermap.vectors[0].append(y)
 113
 114         scattermap.units=[args[0],args[1]]
 115         scattermap.styles=['scatter']
 116         scattermap.destination=1
 117
 118         self._send_plot([scattermap])
 119
 120     def do_savemaps(self,args):
 121         '''
 122         args=filename
 123         '''
 124
 125         '''
 126         def csv_write_cols(data, f):
 127
 128             #from Bruno Desthuillers on comp.lang.python
 129
 130             writer = csv.writer(f)
 131             keys = data.keys()
 132             writer.writerow(dict(zip(keys,keys)))
 133             for row in zip(*data.values()):
 134                 writer.writerow(dict(zip(keys, row)))
 135         '''
 136
 137         f=open(args,'wb')
 138         lh.csv_write_dictionary(f,self.mass_variables)
 139         f.close()