1 # Copyright (C) 2008-2010 Alberto Gomez-Casado
3 # Massimo Sandal <devicerandom@gmail.com>
4 # W. Trevor King <wking@drexel.edu>
6 # This file is part of Hooke.
8 # Hooke is free software: you can redistribute it and/or
9 # modify it under the terms of the GNU Lesser General Public
10 # License as published by the Free Software Foundation, either
11 # version 3 of the License, or (at your option) any later version.
13 # Hooke is distributed in the hope that it will be useful,
14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 # GNU Lesser General Public License for more details.
18 # You should have received a copy of the GNU Lesser General Public
19 # License along with Hooke. If not, see
20 # <http://www.gnu.org/licenses/>.
22 """The ``curve`` module provides :class:`CurvePlugin` and several
23 associated :class:`hooke.command.Command`\s for handling
24 :mod:`hooke.curve` classes.
29 from ..command import Command, Argument, Failure
30 from ..curve import Data
31 from ..plugin import Builtin
32 from ..plugin.playlist import current_playlist_callback
33 from ..util.calculus import derivative
34 from ..util.fft import unitary_avg_power_spectrum
37 class CurvePlugin (Builtin):
39 super(CurvePlugin, self).__init__(name='curve')
41 InfoCommand(self), ExportCommand(self),
42 DifferenceCommand(self), DerivativeCommand(self),
43 PowerSpectrumCommand(self)]
46 # Define common or complicated arguments
48 def current_curve_callback(hooke, command, argument, value):
51 playlist = current_playlist_callback(hooke, command, argument, value)
52 curve = playlist.current()
54 raise Failure('No curves in %s' % playlist)
57 CurveArgument = Argument(
58 name='curve', type='curve', callback=current_curve_callback,
60 :class:`hooke.curve.Curve` to act on. Defaults to the current curve
61 of the current playlist.
67 class InfoCommand (Command):
68 """Get selected information about a :class:`hooke.curve.Curve`.
70 def __init__(self, plugin):
73 Argument(name='all', type='bool', default=False, count=1,
74 help='Get all curve information.'),
76 self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
77 'blocks', 'block sizes']
78 for field in self.fields:
80 name=field, type='bool', default=False, count=1,
81 help='Get curve %s' % field))
82 super(InfoCommand, self).__init__(
83 name='curve info', arguments=args,
84 help=self.__doc__, plugin=plugin)
86 def _run(self, hooke, inqueue, outqueue, params):
88 for key in self.fields:
89 fields[key] = params[key]
90 if reduce(lambda x,y: x and y, fields.values()) == False:
91 params['all'] = True # No specific fields set, default to 'all'
92 if params['all'] == True:
93 for key in self.fields:
96 for key in self.fields:
97 if fields[key] == True:
98 get = getattr(self, '_get_%s' % key.replace(' ', '_'))
99 lines.append('%s: %s' % (key, get(params['curve'])))
100 outqueue.put('\n'.join(lines))
102 def _get_name(self, curve):
105 def _get_path(self, curve):
108 def _get_experiment(self, curve):
109 return curve.info.get('experiment', None)
111 def _get_driver(self, curve):
114 def _get_filetype(self, curve):
115 return curve.info.get('filetype', None)
117 def _get_note(self, curve):
118 return curve.info.get('note', None)
120 def _get_blocks(self, curve):
121 return len(curve.data)
123 def _get_block_sizes(self, curve):
124 return [block.shape for block in curve.data]
126 class ExportCommand (Command):
127 """Export a :class:`hooke.curve.Curve` data block as TAB-delimeted
130 def __init__(self, plugin):
131 super(ExportCommand, self).__init__(
135 Argument(name='block', aliases=['set'], type='int', default=0,
137 Data block to save. For an approach/retract force curve, `0` selects
138 the approaching curve and `1` selects the retracting curve.
140 Argument(name='output', type='file', default='curve.dat',
142 File name for the output data. Defaults to 'curve.dat'
145 help=self.__doc__, plugin=plugin)
147 def _run(self, hooke, inqueue, outqueue, params):
148 data = params['curve'].data[int(params['block'])] # HACK, int() should be handled by ui
149 numpy.savetxt(params['output'], data, delimiter='\t')
151 class DifferenceCommand (Command):
152 """Calculate the derivative (actually, the discrete differentiation)
153 of a curve data block.
155 See :func:`hooke.util.calculus.derivative` for implementation
158 def __init__(self, plugin):
159 super(DifferenceCommand, self).__init__(
160 name='block difference',
163 Argument(name='block one', aliases=['set one'], type='int',
166 Block A in A-B. For an approach/retract force curve, `0` selects the
167 approaching curve and `1` selects the retracting curve.
169 Argument(name='block two', aliases=['set two'], type='int',
171 help='Block B in A-B.'),
172 Argument(name='x column', type='int', default=0,
174 Column of data block to differentiate with respect to.
176 Argument(name='f column', type='int', default=1,
178 Column of data block to differentiate.
181 help=self.__doc__, plugin=plugin)
183 def _run(self, hooke, inqueue, outqueue, params):
184 a = params['curve'].data[params['block one']]
185 b = params['curve'].data[params['block two']]
186 assert a[:,params['x column']] == b[:,params['x column']]
187 out = Data((a.shape[0],2), dtype=a.dtype)
188 out[:,0] = a[:,params['x column']]
189 out[:,1] = a[:,params['f column']] - b[:,params['f column']]
192 class DerivativeCommand (Command):
193 """Calculate the difference between two blocks of data.
195 def __init__(self, plugin):
196 super(DerivativeCommand, self).__init__(
197 name='block derivative',
200 Argument(name='block', aliases=['set'], type='int', default=0,
202 Data block to differentiate. For an approach/retract force curve, `0`
203 selects the approaching curve and `1` selects the retracting curve.
205 Argument(name='x column', type='int', default=0,
207 Column of data block to differentiate with respect to.
209 Argument(name='f column', type='int', default=1,
211 Column of data block to differentiate.
213 Argument(name='weights', type='dict', default={-1:-0.5, 1:0.5},
215 Weighting scheme dictionary for finite differencing. Defaults to
216 central differencing.
219 help=self.__doc__, plugin=plugin)
221 def _run(self, hooke, inqueue, outqueue, params):
222 data = params['curve'].data[params['block']]
223 outqueue.put(derivative(
224 block, x_col=params['x column'], f_col=params['f column'],
225 weights=params['weights']))
227 class PowerSpectrumCommand (Command):
228 """Calculate the power spectrum of a data block.
230 def __init__(self, plugin):
231 super(PowerSpectrumCommand, self).__init__(
232 name='block power spectrum',
235 Argument(name='block', aliases=['set'], type='int', default=0,
237 Data block to act on. For an approach/retract force curve, `0`
238 selects the approaching curve and `1` selects the retracting curve.
240 Argument(name='f column', type='int', default=1,
242 Column of data block to differentiate with respect to.
244 Argument(name='freq', type='float', default=1.0,
248 Argument(name='chunk size', type='int', default=2048,
250 Number of samples per chunk. Use a power of two.
252 Argument(name='overlap', type='bool', default=False,
254 If `True`, each chunk overlaps the previous chunk by half its length.
255 Otherwise, the chunks are end-to-end, and not overlapping.
258 help=self.__doc__, plugin=plugin)
260 def _run(self, hooke, inqueue, outqueue, params):
261 data = params['curve'].data[params['block']]
262 outqueue.put(unitary_avg_power_spectrum(
263 data[:,params['f column']], freq=params['freq'],
264 chunk_size=params['chunk size'],
265 overlap=params['overlap']))