1 # Copyright (C) 2009-2010 Fabrizio Benedetti
2 # Massimo Sandal <devicerandom@gmail.com>
3 # W. Trevor King <wking@drexel.edu>
5 # This file is part of Hooke.
7 # Hooke is free software: you can redistribute it and/or modify it
8 # under the terms of the GNU Lesser General Public License as
9 # published by the Free Software Foundation, either version 3 of the
10 # License, or (at your option) any later version.
12 # Hooke is distributed in the hope that it will be useful, but WITHOUT
13 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
14 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
15 # Public License for more details.
17 # You should have received a copy of the GNU Lesser General Public
18 # License along with Hooke. If not, see
19 # <http://www.gnu.org/licenses/>.
21 """The `cut` module provides :class:`CutPlugin` and
27 from ..command import Command, Argument, Failure
28 from ..plugin import Plugin
31 class CutPlugin (Plugin):
33 super(CutPlugin, self).__init__(name='cut')
34 self._commands = [CutCommand(self)]
37 # Define common or complicated arguments
39 def current_curve_callback(hooke, command, argument, value):
40 playlist = hooke.playlists.current()
42 raise Failure('No playlists loaded')
43 curve = playlist.current()
45 raise Failure('No curves in playlist %s' % playlist.name)
48 CurveArgument = Argument(
49 name='curve', type='curve', callback=current_curve_callback,
51 :class:`hooke.curve.Curve` to cut from. Defaults to the current curve.
57 class CutCommand (Command):
58 """Cut the selected signal between two points and write it to a file.
60 The data is saved in TAB-delimited ASCII text. A "#" prefixed
61 header will optionally appear at the beginning of the file naming
64 def __init__(self, plugin):
65 super(CutCommand, self).__init__(
69 Argument(name='block', aliases=['set'], type='int', default=0,
71 Data block to save. For an approach/retract force curve, `0` selects
72 the approaching curve and `1` selects the retracting curve.
74 Argument(name='bounds', type='point', optional=False, count=2,
76 Indicies of points bounding the selected data.
78 Argument(name='output', type='file', default='cut.dat',
80 File name for the output data.
82 Argument(name='header', type='bool', default=True,
84 True if you want the column-naming header line.
87 help=self.__doc__, plugin=plugin)
89 def _run(self, hooke, inqueue, outqueue, params):
90 if params['curve'] == None:
91 params['curve'] = hooke.playlists.current().current()
93 i_min = min([p.index for p in params['points']])
94 i_max = max([p.index for p in params['points']])
96 data = params['curve'][params['bound']]
97 cut_data = data[i_min:i_max+1,:] # slice rows from row-major data
98 # +1 to include data[i_max] row
100 f = open(params['output'], 'w')
101 if params['header'] == True:
102 f.write('# %s \n' % ('\t'.join(cut_data.info['columns'])))
103 numpy.savetxt(f, cut_data, delimiter='\t')