Replace .config rather than reconstructing plugins, drivers, and UIs.

[hooke.git] / hooke / plugin / massanalysis.py

diff --git a/hooke/plugin/massanalysis.py b/hooke/plugin/massanalysis.py
index e3d3830063ea67cd5204719eeaf9780df3de83f8..c657af9ddb302db0771a2f4ce39a142840bb60f2 100644 (file)
--- a/hooke/plugin/massanalysis.py
+++ b/hooke/plugin/massanalysis.py
@@ -1,30 +1,43 @@
-#!/usr/bin/env python
+# Copyright (C) 2008-2010 Massimo Sandal <devicerandom@gmail.com>
+#                         W. Trevor King <wking@drexel.edu>
+#
+# This file is part of Hooke.
+#
+# Hooke is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# Hooke is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General
+# Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with Hooke.  If not, see
+# <http://www.gnu.org/licenses/>.
 
-'''
-massanalysis.py
-
-Global analysis of force curves with various parameters
+"""Global analysis of force curves with various parameters
 
 Requires:
 libpeakspot.py
 flatfilts.py
-'''
-
+"""
 
-import libpeakspot as lps
-import libhookecurve as lhc
-import libhooke as lh
 import numpy as np
-
 import csv
 
-class massanalysisCommands:
+from .. import libpeakspot as lps
+from .. import curve as lhc
+from .. import libhooke as lh
+
+class massanalysisCommands(object):
 
     def _plug_init(self):
-        self.mass_variables={}        
+        self.mass_variables={}
         self.interesting_variables=['curve','firstpeak_distance','lastpeak_distance','Npeaks','median_distance','mean_distance']
         self._clean_data()
-        
+
     def _clean_data(self):
         for variable in self.interesting_variables:
             self.mass_variables[variable]=[]
@@ -33,18 +46,18 @@ class massanalysisCommands:
         '''
         calculates X distance of a peak from the contact point
         '''
-        item.identify(self.drivers)        
-        
+        item.identify(self.drivers)
+
         real_positions=[]
         cut_index=self.find_contact_point()
-        
+
         #we assume the first is the plot with the force curve
         plot=item.curve.default_plots()[0]
         xret=plot.vectors[1][0]
-        
+
         start_x=xret[cut_index]
-        
-        real_positions=[abs((xret[index])-(start_x)) for index in locations] 
+
+        real_positions=[abs((xret[index])-(start_x)) for index in locations]
         #close all open files
         item.curve.close_all()
         #needed to avoid *big* memory leaks!
@@ -61,39 +74,39 @@ class massanalysisCommands:
         '''
         self._clean_data() #if we recall it, clean previous data!
         min_deviation=self.convfilt_config['mindeviation']
-          
-        
+
+
         c=0
         for item in self.current_list:
             try:
                 peak_location,peak_size=self.exec_has_peaks(item, min_deviation)
                 real_positions=self.peak_position_from_contact(item, peak_location)
-                
+
                 self.mass_variables['Npeaks'].append(len(peak_location))
-                
+
                 if len(peak_location) > 1:
                     self.mass_variables['firstpeak_distance'].append(min(real_positions))
                     self.mass_variables['lastpeak_distance'].append(max(real_positions))
-                    
+
                     distancepeaks=[]
                     for index in range(len(real_positions)-1):
                         distancepeaks.append(real_positions[index+1]-real_positions[index])
                 else:
                     self.mass_variables['firstpeak_distance'].append(0)
-                    self.mass_variables['lastpeak_distance'].append(0)    
-                    
+                    self.mass_variables['lastpeak_distance'].append(0)
+
                 if len(peak_location) > 2:
                     self.mass_variables['median_distance'].append(np.median(distancepeaks))
-                    self.mass_variables['mean_distance'].append(np.mean(distancepeaks))    
+                    self.mass_variables['mean_distance'].append(np.mean(distancepeaks))
                 else:
                     self.mass_variables['median_distance'].append(0)
-                    self.mass_variables['mean_distance'].append(0)   
-                
+                    self.mass_variables['mean_distance'].append(0)
+
                 print 'curve',c
             except SyntaxError:
                 print 'curve',c,'not mapped'
                 pass
-            
+
             c+=1
 
     def do_plotmap(self,args):
@@ -107,37 +120,35 @@ class massanalysisCommands:
             print 'Give me two arguments between those:'
             print self.interesting_variables
             return
-            
+
         scattermap=lhc.PlotObject()
         scattermap.vectors=[[]]
         scattermap.vectors[0].append(x)
         scattermap.vectors[0].append(y)
-        
+
         scattermap.units=[args[0],args[1]]
         scattermap.styles=['scatter']
         scattermap.destination=1
-        
+
         self._send_plot([scattermap])
-        
+
     def do_savemaps(self,args):
         '''
         args=filename
         '''
-        
+
         '''
         def csv_write_cols(data, f):
-            
+
             #from Bruno Desthuillers on comp.lang.python
-            
+
             writer = csv.writer(f)
             keys = data.keys()
             writer.writerow(dict(zip(keys,keys)))
             for row in zip(*data.values()):
-                writer.writerow(dict(zip(keys, row))) 
+                writer.writerow(dict(zip(keys, row)))
         '''
-        
+
         f=open(args,'wb')
         lh.csv_write_dictionary(f,self.mass_variables)
         f.close()
-        
-        
\ No newline at end of file