X-Git-Url: http://git.tremily.us/?p=hooke.git;a=blobdiff_plain;f=hooke%2Fplugin%2Fprocplots.py;fp=procplots.py;h=b7826aed227cc2499adf0778c9365ddb6db1c24f;hp=8c58f70d764ee7f002c9e30f08a6c290639bffdc;hb=41ef0130e16c0cf8d2c0f1acc9e06986d62f7607;hpb=7fc996abaf986c43c0354ac3b4127ed7876ad41a;ds=sidebyside

diff --git a/procplots.py b/hooke/plugin/procplots.py
old mode 100755
new mode 100644
similarity index 88%
rename from procplots.py
rename to hooke/plugin/procplots.py
index 8c58f70..b7826ae
--- a/procplots.py
+++ b/hooke/plugin/procplots.py
@@ -1,27 +1,27 @@
-#!/usr/bin/env python
-
 '''
 PROCPLOTS
 Processed plots plugin for force curves.
 
 Licensed under the GNU GPL version 2
 '''
-from libhooke import WX_GOOD
+from ..libhooke import WX_GOOD
 import wxversion
 wxversion.select(WX_GOOD)
 
 import wx
-import libhookecurve as lhc
 import numpy as np
 import scipy as sp
 import scipy.signal
 import copy
 
-class procplotsCommands:
-    
+from .. import libhookecurve as lhc
+
+
+class procplotsCommands(object):
+
     def _plug_init(self):
         pass
-               
+
     def do_derivplot(self,args):
         '''
         DERIVPLOT
@@ -29,30 +29,30 @@ class procplotsCommands:
         Plots the derivate (actually, the discrete differentiation) of the current force curve
         ---------
         Syntax: derivplot
-        '''                
-        dplot=self.derivplot_curves()               
-        plot_graph=self.list_of_events['plot_graph']       
+        '''
+        dplot=self.derivplot_curves()
+        plot_graph=self.list_of_events['plot_graph']
         wx.PostEvent(self.frame,plot_graph(plots=[dplot]))
-        
+
     def derivplot_curves(self):
         '''
         do_derivplot helper function
-        
+
         create derivate plot curves for force curves.
-        '''    
+        '''
         dplot=lhc.PlotObject()
-        dplot.vectors=[]       
-        
+        dplot.vectors=[]
+
         for vector in self.plots[0].vectors:
             dplot.vectors.append([])
             dplot.vectors[-1].append(vector[0][:-1])
             dplot.vectors[-1].append(np.diff(vector[1]))
-        
+
         dplot.destination=1
         dplot.units=self.plots[0].units
-        
-        return dplot        
-            
+
+        return dplot
+
     def do_subtplot(self,args):
         '''
         SUBTPLOT
@@ -62,42 +62,42 @@ class procplotsCommands:
         Syntax: subtplot
         '''
         #FIXME: sub_filter and sub_order must be args
-        
+
         if len(self.plots[0].vectors) != 2:
             print 'This command only works on a curve with two different plots.'
             pass
-        
+
         outplot=self.subtract_curves(sub_order=1)
-        
-        plot_graph=self.list_of_events['plot_graph']       
+
+        plot_graph=self.list_of_events['plot_graph']
         wx.PostEvent(self.frame,plot_graph(plots=[outplot]))
-        
+
     def subtract_curves(self, sub_order):
         '''
         subtracts the extension from the retraction
-        ''' 
+        '''
         xext=self.plots[0].vectors[0][0]
         yext=self.plots[0].vectors[0][1]
         xret=self.plots[0].vectors[1][0]
         yret=self.plots[0].vectors[1][1]
-        
+
         #we want the same number of points
         maxpoints_tot=min(len(xext),len(xret))
         xext=xext[0:maxpoints_tot]
         yext=yext[0:maxpoints_tot]
         xret=xret[0:maxpoints_tot]
         yret=yret[0:maxpoints_tot]
-    
+
         if sub_order:
             ydiff=[yretval-yextval for yretval,yextval in zip(yret,yext)]
         else: #reverse subtraction (not sure it's useful, but...)
-            ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]    
-        
+            ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]
+
         outplot=copy.deepcopy(self.plots[0])
         outplot.vectors[0][0], outplot.vectors[1][0] = xext,xret #FIXME: if I use xret, it is not correct!
         outplot.vectors[1][1]=ydiff
         outplot.vectors[0][1]=[0 for item in outplot.vectors[1][0]]
-        
+
         return outplot
 
 
@@ -110,21 +110,21 @@ class procplotsCommands:
             median_filter=customvalue
         else:
             median_filter=self.config['medfilt']
-         
+
         if median_filter==0:
             return plot
-         
+
         if float(median_filter)/2 == int(median_filter)/2:
             median_filter+=1
-            
+
         nplots=len(plot.vectors)
         c=0
         while c<nplots:
             plot.vectors[c][1]=scipy.signal.medfilt(plot.vectors[c][1],median_filter)
             c+=1
-        
+
         return plot
-    
+
 
     def plotmanip_correct(self, plot, current, customvalue=None):
         '''
@@ -134,24 +134,24 @@ class procplotsCommands:
         - the deflection() vector is as long as the X of extension + the X of retraction
         - plot.vectors[0][0] is the X of extension curve
         - plot.vectors[1][0] is the X of retraction curve
-        
+
         FIXME: both this method and the picoforce driver have to be updated, deflection() must return
         a more senseful data structure!
         '''
         #use only for force spectroscopy experiments!
         if current.curve.experiment != 'smfs':
             return plot
-    
+
         if customvalue != None:
             execute_me=customvalue
         else:
             execute_me=self.config['correct']
         if not execute_me:
             return plot
-     
+
         defl_ext,defl_ret=current.curve.deflection()
         #halflen=len(deflall)/2
-    
+
         plot.vectors[0][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[0][0],defl_ext)]
         plot.vectors[1][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[1][0],defl_ret)]
 
@@ -197,11 +197,11 @@ class procplotsCommands:
         #DEPRECATED
         if self.config['detrigger']==0:
             return plot
-        
+
         cutindex=2
         startvalue=plot.vectors[0][0][0]
-        
-        for index in range(len(plot.vectors[0][0])-1,2,-2):  
+
+        for index in range(len(plot.vectors[0][0])-1,2,-2):
            if plot.vectors[0][0][index]>startvalue:
                 cutindex=index
            else:
@@ -209,12 +209,12 @@ class procplotsCommands:
 
         plot.vectors[0][0]=plot.vectors[0][0][:cutindex]
         plot.vectors[0][1]=plot.vectors[0][1][:cutindex]
-        
+
         return plot
-    '''       
-           
-           
-    
+    '''
+
+
+
 #FFT---------------------------
     def fft_plot(self, vector):
         '''
@@ -222,22 +222,22 @@ class procplotsCommands:
         '''
         fftplot=lhc.PlotObject()
         fftplot.vectors=[[]]
-               
+
         fftlen=len(vector)/2 #need just 1/2 of length
-        fftplot.vectors[-1].append(np.arange(1,fftlen).tolist()) 
-        
+        fftplot.vectors[-1].append(np.arange(1,fftlen).tolist())
+
         try:
             fftplot.vectors[-1].append(abs(np.fft(vector)[1:fftlen]).tolist())
         except TypeError: #we take care of newer NumPy (1.0.x)
             fftplot.vectors[-1].append(abs(np.fft.fft(vector)[1:fftlen]).tolist())
-        
-        
+
+
         fftplot.destination=1
-        
-        
+
+
         return fftplot
-        
-    
+
+
     def do_fft(self,args):
         '''
         FFT
@@ -245,15 +245,15 @@ class procplotsCommands:
         Plots the fast Fourier transform of the selected plot
         ---
         Syntax: fft [top,bottom] [select] [0,1...]
-        
+
         By default, fft performs the Fourier transform on all the 0-th data set on the
         top plot.
-        
+
         [top,bottom]: which plot is the data set to fft (default: top)
         [select]: you pick up two points on the plot and fft only the segment between
         [0,1,...]: which data set on the selected plot you want to fft (default: 0)
         '''
-        
+
         #args parsing
         #whatplot = plot to fft
         #whatset = set to fft in the plot
@@ -270,7 +270,7 @@ class procplotsCommands:
                 whatset=int(arg)
             except ValueError:
                 pass
-        
+
         if select:
             points=self._measure_N_points(N=2, whatset=whatset)
             boundaries=[points[0].index, points[1].index]
@@ -278,9 +278,8 @@ class procplotsCommands:
             y_to_fft=self.plots[whatplot].vectors[whatset][1][boundaries[0]:boundaries[1]] #y
         else:
             y_to_fft=self.plots[whatplot].vectors[whatset][1] #y
-        
-        fftplot=self.fft_plot(y_to_fft)               
+
+        fftplot=self.fft_plot(y_to_fft)
         fftplot.units=['frequency', 'power']
-        plot_graph=self.list_of_events['plot_graph']       
+        plot_graph=self.list_of_events['plot_graph']
         wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))
-