hooke/plugin/showconvoluted.py

   1 # Copyright (C) 2009-2012 Rolf Schmidt <rschmidt@alcor.concordia.ca>
   2 #                         W. Trevor King <wking@drexel.edu>
   3 #
   4 # This file is part of Hooke.
   5 #
   6 # Hooke is free software: you can redistribute it and/or modify it
   7 # under the terms of the GNU Lesser General Public License as
   8 # published by the Free Software Foundation, either version 3 of the
   9 # License, or (at your option) any later version.
  10 #
  11 # Hooke is distributed in the hope that it will be useful, but WITHOUT
  12 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
  13 # or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General
  14 # Public License for more details.
  15 #
  16 # You should have received a copy of the GNU Lesser General Public
  17 # License along with Hooke.  If not, see
  18 # <http://www.gnu.org/licenses/>.
  19
  20 """This plugin contains a plotmanipulator to show the convoluted curve.
  21 """
  22
  23 import libpeakspot
  24
  25 class showconvolutedCommands:
  26
  27     #def _plug_init(self):
  28         #pass
  29
  30     def plotmanip_showconvoluted(self, plot, curve):
  31         '''
  32         BEGIN: taken from procplots.py
  33         might need some tweaking
  34         '''
  35         #use only for force spectroscopy experiments!
  36         if curve.driver.experiment != 'smfs':
  37             return plot
  38
  39         '''
  40         END: taken from procplots.py
  41         '''
  42
  43         #need to convert the string that contains the list into a list
  44         #convolution = eval(self.config['convfilt']['convolution']['value'])
  45         convolution = eval(self.GetStringFromConfig('flatfilts', 'convfilt', 'convolution'))
  46
  47         xRet = plot.vectors[1][0]
  48         yRet = plot.vectors[1][1]
  49         convoluted = libpeakspot.conv_dx(yRet, convolution)
  50         #convoluted=libpeakspot.conv_dx(yRet, [-20, -10, -6, 0, 12, 12, 12])
  51         plot.add_set(xRet, convoluted)
  52         #plot.vectors[1][1]=[i for i in convoluted]
  53         #set contact point plot style to 'plot'
  54         #and the color to red
  55         plot.styles.append('plot')
  56         plot.colors.append('black')
  57         #peak_location, peak_size = self.has_peaks(plot, blindwindow, convolution, minpeaks)
  58         peak_locations, peak_sizes = self.has_peaks(plot, curve)
  59
  60         if peak_locations:
  61             peak_locations_x = []
  62             peak_locations_y = []
  63             for location in peak_locations:
  64                 peak_locations_x.append(xRet[location])
  65                 peak_locations_y.append(yRet[location])
  66             plot.add_set(peak_locations_x, peak_locations_y)
  67             plot.styles.append('scatter')
  68             plot.colors.append('green')
  69             plot.add_set(peak_locations_x, peak_sizes)
  70             plot.styles.append('scatter')
  71             plot.colors.append('magenta')
  72
  73         #Return the plot object.
  74         return plot