Update SurfacePositionModel to match new diag/scale interpretation.

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

diff --git a/hooke/plugin/multidistance.py b/hooke/plugin/multidistance.py
index c93900fb85675e17d5a07a663406442acbc8b790..7c8291ac4135680619a098ac28d779a77c4033bc 100644 (file)
--- a/hooke/plugin/multidistance.py
+++ b/hooke/plugin/multidistance.py
@@ -1,5 +1,24 @@
-# -*- coding: utf-8 -*-
-from libhooke import WX_GOOD, ClickedPoint
+# Copyright (C) 2009-2010 Fabrizio Benedetti
+#                         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/>.
+
+from hooke.libhooke import WX_GOOD, ClickedPoint
+
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
@@ -13,8 +32,8 @@ import warnings
 warnings.simplefilter('ignore',np.RankWarning)
 
 
-class multidistanceCommands:
-    
+class multidistanceCommands(object):
+
     def do_multidistance(self,args):
      '''
      MULTIDISTANCE
@@ -25,43 +44,26 @@ class multidistanceCommands:
      of an existing file, autopeak will resume it and append measurements to it. If you are giving
      a new filename, it will create the file and append to it until you close Hooke.
      You can also define a minimun deviation of the peaks.
-     
+
      Syntax:
      multidistance [deviation]
      deviation = number of times the convolution signal is above the noise absolute deviation.
      '''
 
-     def find_current_peaks(noflatten, a):
-            #Find peaks.
-           if len(a)==0:
-                 a=self.convfilt_config['mindeviation']
-            try:
-                 abs_devs=float(a)
-            except:
-                print "Bad input, using default."
-                 abs_devs=self.convfilt_config['mindeviation']
-
-            defplot=self.current.curve.default_plots()[0]
-            if not noflatten:
-                flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
-                defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
-            pk_loc,peak_size=self.has_peaks(defplot, abs_devs)
-            return pk_loc, peak_size
-
       
      noflatten=False
-     peaks_location, peak_size=find_current_peaks(noflatten, args)
+     peaks_location, peak_size=self.find_current_peaks(noflatten)
      
      #if no peaks, we have nothing to plot. exit.
      if len(peaks_location)==0:
             return
-        
+
      #otherwise, we plot the peak locations.
      xplotted_ret=self.plots[0].vectors[1][0]
      yplotted_ret=self.plots[0].vectors[1][1]
      xgood=[xplotted_ret[index] for index in peaks_location]
      ygood=[yplotted_ret[index] for index in peaks_location]
-        
+
      recplot=self._get_displayed_plot()
      recplot.vectors.append([xgood,ygood])
      if recplot.styles==[]:
@@ -79,7 +81,7 @@ class multidistanceCommands:
      if exclude_raw=='N':
         print 'Discarded.'
         return
-     
+
      if not exclude_raw=='':
         exclude=exclude_raw.split(',')
        #we convert in numbers the input
@@ -100,13 +102,13 @@ class multidistanceCommands:
              peaks_location=  peaks_location[0:new_a]+peaks_location[new_a+1:]
              peak_size=            peak_size[0:new_a]+peak_size[new_a+1:]
           count+=1
-     
+
      #we calculate the distance vector
      dist=[]
      for i in range(len(peaks_location)-1):
          dist.append(xplotted_ret[peaks_location[i]]-xplotted_ret[peaks_location[i+1]])
-     
-     
+
+
 
 
 
@@ -116,7 +118,7 @@ class multidistanceCommands:
             if self.autofile=='':
                 print 'Not saved.'
                 return
-        
+
      if not os.path.exists(self.autofile):
             f=open(self.autofile,'w+')
             f.write('Analysis started '+time.asctime()+'\n')
@@ -128,14 +130,14 @@ class multidistanceCommands:
               f.write(str(o))
             f.write("\n")
             f.close()
-            
+
      print 'Saving...'
      f=open(self.autofile,'a+')
-        
+
      f.write(self.current.path+'\n')
      for i in dist:
           f.write(";")
           f.write(str(i))
 
-     f.write("\n")            
+     f.write("\n")
      f.close()