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