hooke/plugin/curve.py

   1 # Copyright (C) 2008-2010 Alberto Gomez-Casado
   2 #                         Fabrizio Benedetti
   3 #                         Massimo Sandal <devicerandom@gmail.com>
   4 #                         W. Trevor King <wking@drexel.edu>
   5 #
   6 # This file is part of Hooke.
   7 #
   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.
  12 #
  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.
  17 #
  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/>.
  21
  22 """The ``curve`` module provides :class:`CurvePlugin` and several
  23 associated :class:`hooke.command.Command`\s for handling
  24 :mod:`hooke.curve` classes.
  25 """
  26
  27 import numpy
  28
  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
  35
  36
  37 class CurvePlugin (Builtin):
  38     def __init__(self):
  39         super(CurvePlugin, self).__init__(name='curve')
  40         self._commands = [
  41             InfoCommand(self), ExportCommand(self),
  42             DifferenceCommand(self), DerivativeCommand(self),
  43             PowerSpectrumCommand(self)]
  44
  45
  46 # Define common or complicated arguments
  47
  48 def current_curve_callback(hooke, command, argument, value):
  49     if value != None:
  50         return value
  51     playlist = current_playlist_callback(hooke, command, argument, value)
  52     curve = playlist.current()
  53     if curve == None:
  54         raise Failure('No curves in %s' % playlist)
  55     return curve
  56
  57 CurveArgument = Argument(
  58     name='curve', type='curve', callback=current_curve_callback,
  59     help="""
  60 :class:`hooke.curve.Curve` to act on.  Defaults to the current curve
  61 of the current playlist.
  62 """.strip())
  63
  64
  65 # Define commands
  66
  67 class InfoCommand (Command):
  68     """Get selected information about a :class:`hooke.curve.Curve`.
  69     """
  70     def __init__(self, plugin):
  71         args = [
  72             CurveArgument,
  73             Argument(name='all', type='bool', default=False, count=1,
  74                      help='Get all curve information.'),
  75             ]
  76         self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
  77                        'blocks', 'block sizes']
  78         for field in self.fields:
  79             args.append(Argument(
  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)
  85
  86     def _run(self, hooke, inqueue, outqueue, params):
  87         fields = {}
  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:
  94                 fields[key] = True
  95         lines = []
  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))
 101
 102     def _get_name(self, curve):
 103         return curve.name
 104
 105     def _get_path(self, curve):
 106         return curve.path
 107
 108     def _get_experiment(self, curve):
 109         return curve.info.get('experiment', None)
 110
 111     def _get_driver(self, curve):
 112         return curve.driver
 113
 114     def _get_filetype(self, curve):
 115         return curve.info.get('filetype', None)
 116
 117     def _get_note(self, curve):
 118         return curve.info.get('note', None)
 119
 120     def _get_blocks(self, curve):
 121         return len(curve.data)
 122
 123     def _get_block_sizes(self, curve):
 124         return [block.shape for block in curve.data]
 125
 126 class ExportCommand (Command):
 127     """Export a :class:`hooke.curve.Curve` data block as TAB-delimeted
 128     ASCII text.
 129
 130     A "#" prefixed header will optionally appear at the beginning of
 131     the file naming the columns.
 132     """
 133     def __init__(self, plugin):
 134         super(ExportCommand, self).__init__(
 135             name='export block',
 136             arguments=[
 137                 CurveArgument,
 138                 Argument(name='block', aliases=['set'], type='int', default=0,
 139                          help="""
 140 Data block to save.  For an approach/retract force curve, `0` selects
 141 the approaching curve and `1` selects the retracting curve.
 142 """.strip()),
 143                 Argument(name='output', type='file', default='curve.dat',
 144                          help="""
 145 File name for the output data.  Defaults to 'curve.dat'
 146 """.strip()),
 147                 Argument(name='header', type='bool', default=True,
 148                          help="""
 149 True if you want the column-naming header line.
 150 """.strip()),
 151                 ],
 152             help=self.__doc__, plugin=plugin)
 153
 154     def _run(self, hooke, inqueue, outqueue, params):
 155         data = params['curve'].data[int(params['block'])] # HACK, int() should be handled by ui
 156
 157         f = open(params['output'], 'w')
 158         if params['header'] == True:
 159             f.write('# %s \n' % ('\t'.join(data.info['columns'])))
 160         numpy.savetxt(f, data, delimiter='\t')
 161         f.close()
 162
 163 class DifferenceCommand (Command):
 164     """Calculate the derivative (actually, the discrete differentiation)
 165     of a curve data block.
 166
 167     See :func:`hooke.util.calculus.derivative` for implementation
 168     details.
 169     """
 170     def __init__(self, plugin):
 171         super(DifferenceCommand, self).__init__(
 172             name='block difference',
 173             arguments=[
 174                 CurveArgument,
 175                 Argument(name='block one', aliases=['set one'], type='int',
 176                          default=1,
 177                          help="""
 178 Block A in A-B.  For an approach/retract force curve, `0` selects the
 179 approaching curve and `1` selects the retracting curve.
 180 """.strip()),
 181                 Argument(name='block two', aliases=['set two'], type='int',
 182                          default=0,
 183                          help='Block B in A-B.'),
 184                 Argument(name='x column', type='int', default=0,
 185                          help="""
 186 Column of data block to differentiate with respect to.
 187 """.strip()),
 188                 Argument(name='f column', type='int', default=1,
 189                          help="""
 190 Column of data block to differentiate.
 191 """.strip()),
 192                 ],
 193             help=self.__doc__, plugin=plugin)
 194
 195     def _run(self, hooke, inqueue, outqueue, params):
 196         a = params['curve'].data[params['block one']]
 197         b = params['curve'].data[params['block two']]
 198         assert a[:,params['x column']] == b[:,params['x column']]
 199         out = Data((a.shape[0],2), dtype=a.dtype)
 200         out[:,0] = a[:,params['x column']]
 201         out[:,1] = a[:,params['f column']] - b[:,params['f column']]
 202         outqueue.put(out)
 203
 204 class DerivativeCommand (Command):
 205     """Calculate the difference between two blocks of data.
 206     """
 207     def __init__(self, plugin):
 208         super(DerivativeCommand, self).__init__(
 209             name='block derivative',
 210             arguments=[
 211                 CurveArgument,
 212                 Argument(name='block', aliases=['set'], type='int', default=0,
 213                          help="""
 214 Data block to differentiate.  For an approach/retract force curve, `0`
 215 selects the approaching curve and `1` selects the retracting curve.
 216 """.strip()),
 217                 Argument(name='x column', type='int', default=0,
 218                          help="""
 219 Column of data block to differentiate with respect to.
 220 """.strip()),
 221                 Argument(name='f column', type='int', default=1,
 222                          help="""
 223 Column of data block to differentiate.
 224 """.strip()),
 225                 Argument(name='weights', type='dict', default={-1:-0.5, 1:0.5},
 226                          help="""
 227 Weighting scheme dictionary for finite differencing.  Defaults to
 228 central differencing.
 229 """.strip()),
 230                 ],
 231             help=self.__doc__, plugin=plugin)
 232
 233     def _run(self, hooke, inqueue, outqueue, params):
 234         data = params['curve'].data[params['block']]
 235         outqueue.put(derivative(
 236                 block, x_col=params['x column'], f_col=params['f column'],
 237                 weights=params['weights']))
 238
 239 class PowerSpectrumCommand (Command):
 240     """Calculate the power spectrum of a data block.
 241     """
 242     def __init__(self, plugin):
 243         super(PowerSpectrumCommand, self).__init__(
 244             name='block power spectrum',
 245             arguments=[
 246                 CurveArgument,
 247                 Argument(name='block', aliases=['set'], type='int', default=0,
 248                          help="""
 249 Data block to act on.  For an approach/retract force curve, `0`
 250 selects the approaching curve and `1` selects the retracting curve.
 251 """.strip()),
 252                 Argument(name='f column', type='int', default=1,
 253                          help="""
 254 Column of data block to differentiate with respect to.
 255 """.strip()),
 256                 Argument(name='freq', type='float', default=1.0,
 257                          help="""
 258 Sampling frequency.
 259 """.strip()),
 260                 Argument(name='chunk size', type='int', default=2048,
 261                          help="""
 262 Number of samples per chunk.  Use a power of two.
 263 """.strip()),
 264                 Argument(name='overlap', type='bool', default=False,
 265                          help="""
 266 If `True`, each chunk overlaps the previous chunk by half its length.
 267 Otherwise, the chunks are end-to-end, and not overlapping.
 268 """.strip()),
 269                 ],
 270             help=self.__doc__, plugin=plugin)
 271
 272     def _run(self, hooke, inqueue, outqueue, params):
 273         data = params['curve'].data[params['block']]
 274         outqueue.put(unitary_avg_power_spectrum(
 275                 data[:,params['f column']], freq=params['freq'],
 276                 chunk_size=params['chunk size'],
 277                 overlap=params['overlap']))