Merged with trunk

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

diff --git a/hooke/plugin/flatfilts.py b/hooke/plugin/flatfilts.py
index 47eab591e46db9b4ef819637a26b85ac108c4386..e19964c71a2dfd01c8f710916402a16e35a024a2 100644 (file)
--- a/hooke/plugin/flatfilts.py
+++ b/hooke/plugin/flatfilts.py
@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 '''
 FLATFILTS
 
@@ -136,8 +139,8 @@ class flatfiltsCommands(object):
     #-----CONVFILT-------------------------------------------------
     #-----Convolution-based peak recognition and filtering.
     #Requires the libpeakspot.py library
-
-    def has_peaks(self, plot, abs_devs=None):
+    
+    def has_peaks(self, plot, abs_devs=None, maxpeak=True, window=10):
         '''
         Finds peak position in a force curve.
         FIXME: should be moved in libpeakspot.py
@@ -165,14 +168,26 @@ class flatfiltsCommands(object):
         noise_level=lps.noise_absdev(convoluted[cut_index:], self.convfilt_config['positive'], self.convfilt_config['maxcut'], self.convfilt_config['stable'])
         above=lps.abovenoise(convoluted,noise_level,cut_index,abs_devs)
         peak_location,peak_size=lps.find_peaks(above,seedouble=self.convfilt_config['seedouble'])
-
-        #take the maximum
+                
+        #take the minimum or the maximum of a peak
         for i in range(len(peak_location)):
             peak=peak_location[i]
-            maxpk=min(yret[peak-10:peak+10])
-            index_maxpk=yret[peak-10:peak+10].index(maxpk)+(peak-10)
-            peak_location[i]=index_maxpk
-
+            valpk=min(yret[peak-window:peak+window])  #maximum in force (near the unfolding point)
+            index_pk=yret[peak-window:peak+window].index(valpk)+(peak-window)            
+
+            if maxpeak==False:
+               valpk=max(yret[peak:peak+window]) #minimum in force, near the baseline
+               index_pk=yret[peak:peak+window].index(valpk)+(peak)
+
+#  Let's explain that for the minimum.  Immaging that we know that there is a peak at position/region 100 and you have found its y-value,
+#  Now you look in the array, from 100-10 to 100+10  (if the window is 10).
+#  This "100-10 to 100+10" is substancially a new array with its index. In this array you have 20
+#  elements, so the index of your y-value will be 10.
+#  Now to find the index in the TOTAL array you have to add the "position" of the "region" (that in this case
+#  correspond to 100) and also substract the window size ---> (+100-10)
+
+            peak_location[i]=index_pk
+            
         return peak_location,peak_size
 
 
@@ -310,6 +325,9 @@ class flatfiltsCommands(object):
                 item.curve=None #empty the item object, to further avoid memory leak
                 notflat_list.append(item)
 
+            for i in range(1000):
+                k=0
+
         #Warn that no flattening had been done.
         if not ('flatten' in self.config['plotmanips']):
             print 'Flatten manipulator was not found. Processing was done without flattening.'