hooke/plugin/massanalysis.py

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