Run update-copyright.py.

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

diff --git a/hooke/plugin/pcluster.py b/hooke/plugin/pcluster.py
index 2e166201dbf13f051e40e21fa846f09bafde2388..45bb9c7e5b8b3db63207b426266fd43b57989075 100644 (file)
--- a/hooke/plugin/pcluster.py
+++ b/hooke/plugin/pcluster.py
@@ -1,5 +1,25 @@
+# Copyright (C) 2009-2012 Massimo Sandal <devicerandom@gmail.com>
+#                         Pancaldi Paolo <pancaldi.paolo@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/>.
+
+from ..libhooke import WX_GOOD, ClickedPoint, config_file_path
+
 from mdp import pca
-from libhooke import WX_GOOD, ClickedPoint
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
@@ -8,9 +28,11 @@ import scipy as sp
 import copy
 import os.path
 import time
-import libhookecurve as lhc
 import pylab as pyl
 
+from .. import curve as lhc
+
+
 import warnings
 warnings.simplefilter('ignore',np.RankWarning)
 
@@ -28,13 +50,9 @@ class pclusterCommands(object):
         Automatically measures peaks and extracts informations for further clustering
         (c)Paolo Pancaldi, Massimo Sandal 2009
         '''
-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\'
         blindw = str(self.convfilt_config['blindwindow'])
         pclus_dir = "pCluster_blind"+blindw+"_"+time.strftime("%Y%m%d_%H%M")
-        self.my_work_dir = os.getcwd()+slash+pclus_dir+slash
+        self.my_work_dir = os.path.join(os.getcwd(), pclus_dir)
         self.my_curr_dir = os.path.basename(os.getcwd())
         os.mkdir(self.my_work_dir)
 
@@ -73,31 +91,7 @@ class pclusterCommands(object):
         f.write('----------------------------------------\n')
         f.write('; Peak number  ;  1 peak Length (nm) ; 1 peak Force (pN) ;  2 peak Length (nm) ; 2 peak Force (pN) ;  3 peak Length (nm) ; 3 peak Force (pN) ;  4 peak Length (nm) ; 4 peak Force (pN) ;  5 peak Length (nm) ; 5 peak Force (pN) ;  6 peak Length (nm) ; 6 peak Force (pN) ;  7 peak Length (nm) ; 7 peak Force (pN) ;  8 peak Length (nm) ; 8 peak Force (pN)\n')
         f.close()
-
-        # ------ FUNCTION ------
-        def fit_interval_nm(start_index,plot,nm,backwards):
-            '''
-            Calculates the number of points to fit, given a fit interval in nm
-            start_index: index of point
-            plot: plot to use
-            backwards: if true, finds a point backwards.
-            '''
-            whatset=1 #FIXME: should be decidable
-            x_vect=plot.vectors[1][0]
-
-            c=0
-            i=start_index
-            start=x_vect[start_index]
-            maxlen=len(x_vect)
-            while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
-                if i==0 or i==maxlen-1: #we reached boundaries of vector!
-                    return c
-                if backwards:
-                    i-=1
-                else:
-                    i+=1
-                c+=1
-            return c
+        
 
         def plot_informations(itplot,pl_value):
             '''
@@ -116,9 +110,9 @@ class pclusterCommands(object):
             cindex=self.find_contact_point(itplot[0]) #Automatically find contact point <158, libhooke.ClickedPoint>
             contact_point=self._clickize(itplot[0].vectors[1][0], itplot[0].vectors[1][1], cindex)
             self.basepoints=[]
-            base_index_0=peak_location[-1]+fit_interval_nm(peak_location[-1], itplot[0], self.config['auto_right_baseline'],False)
+            base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], itplot[0], self.config['auto_right_baseline'],False)
             self.basepoints.append(self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],base_index_0))
-            base_index_1=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, itplot[0], self.config['auto_left_baseline'],False)
+            base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, itplot[0], self.config['auto_left_baseline'],False)
             self.basepoints.append(self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],base_index_1))
             self.basecurrent=self.current.path
             boundaries=[self.basepoints[0].index, self.basepoints[1].index]
@@ -343,14 +337,7 @@ class pclusterCommands(object):
         '''
 
         # reads the columns of pca
-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\'
-        self.my_hooke_dir = self.config['hookedir']+slash
-        #self.my_work_dir = os.getcwd()+slash+"pCluster_"+time.strftime("%Y%m%d_%H%M")+slash
-        #self.my_curr_dir = os.path.basename(os.getcwd())
-        conf=open(self.my_hooke_dir+"pca_config.txt")
+        conf=open(config_file_path("pca_config.txt"), 'r')
         config = conf.readlines()
         conf.close()