#
# 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 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.
+# 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
:mod:`hooke.curve` classes.
"""
+import numpy
+
from ..command import Command, Argument, Failure
from ..curve import Data
from ..plugin import Builtin
from ..plugin.playlist import current_playlist_callback
from ..util.calculus import derivative
from ..util.fft import unitary_avg_power_spectrum
+from ..util.si import ppSI, split_data_label
class CurvePlugin (Builtin):
def __init__(self):
super(CurvePlugin, self).__init__(name='curve')
self._commands = [
- InfoCommand(self), ExportCommand(self),
- DifferenceCommand(self), DerivativeCommand(self),
- PowerSpectrumCommand(self)]
+ GetCommand(self), InfoCommand(self), DeltaCommand(self),
+ ExportCommand(self), DifferenceCommand(self),
+ DerivativeCommand(self), PowerSpectrumCommand(self)]
# Define common or complicated arguments
# Define commands
+class GetCommand (Command):
+ """Return a :class:`hooke.curve.Curve`.
+ """
+ def __init__(self, plugin):
+ super(GetCommand, self).__init__(
+ name='get curve', arguments=[CurveArgument],
+ help=self.__doc__, plugin=plugin)
+
+ def _run(self, hooke, inqueue, outqueue, params):
+ outqueue.put(params['curve'])
+
class InfoCommand (Command):
"""Get selected information about a :class:`hooke.curve.Curve`.
"""
def _get_block_sizes(self, curve):
return [block.shape for block in curve.data]
+
+class DeltaCommand (Command):
+ """Get distance information between two points.
+
+ With two points A and B, the returned distances are A-B.
+ """
+ def __init__(self, plugin):
+ super(DeltaCommand, self).__init__(
+ name='delta',
+ arguments=[
+ CurveArgument,
+ Argument(name='block', type='int', default=0,
+ help="""
+Data block that points are selected from. For an approach/retract
+force curve, `0` selects the approaching curve and `1` selects the
+retracting curve.
+""".strip()),
+ Argument(name='point', type='point', optional=False, count=2,
+ help="""
+Indicies of points bounding the selected data.
+""".strip()),
+ Argument(name='SI', type='bool', default=False,
+ help="""
+Return distances in SI notation.
+""".strip())
+ ],
+ help=self.__doc__, plugin=plugin)
+
+ def _run(self, hooke, inqueue, outqueue, params):
+ data = params['curve'].data[params['block']]
+ As = data[params['point'][0],:]
+ Bs = data[params['point'][1],:]
+ ds = [A-B for A,B in zip(As, Bs)]
+ if params['SI'] == False:
+ out = [(name, d) for name,d in zip(data.info['columns'], ds)]
+ else:
+ out = []
+ for name,d in zip(data.info['columns'], ds):
+ n,units = split_data_label(name)
+ out.append(
+ (n, ppSI(value=d, unit=units, decimals=2)))
+ outqueue.put(out)
+
+
class ExportCommand (Command):
"""Export a :class:`hooke.curve.Curve` data block as TAB-delimeted
ASCII text.
+
+ A "#" prefixed header will optionally appear at the beginning of
+ the file naming the columns.
"""
def __init__(self, plugin):
super(ExportCommand, self).__init__(
Argument(name='block', aliases=['set'], type='int', default=0,
help="""
Data block to save. For an approach/retract force curve, `0` selects
-the approacing curve and `1` selects the retracting curve.
+the approaching curve and `1` selects the retracting curve.
""".strip()),
Argument(name='output', type='file', default='curve.dat',
help="""
File name for the output data. Defaults to 'curve.dat'
+""".strip()),
+ Argument(name='header', type='bool', default=True,
+ help="""
+True if you want the column-naming header line.
""".strip()),
],
help=self.__doc__, plugin=plugin)
def _run(self, hooke, inqueue, outqueue, params):
data = params['curve'].data[params['block']]
+
f = open(params['output'], 'w')
- data.tofile(f, sep='\t')
+ if params['header'] == True:
+ f.write('# %s \n' % ('\t'.join(data.info['columns'])))
+ numpy.savetxt(f, data, delimiter='\t')
f.close()
class DifferenceCommand (Command):
- """Calculate the derivative (actually, the discrete differentiation)
- of a curve data block.
-
- See :func:`hooke.util.calculus.derivative` for implementation
- details.
+ """Calculate the difference between two blocks of data.
"""
def __init__(self, plugin):
super(DifferenceCommand, self).__init__(
default=1,
help="""
Block A in A-B. For an approach/retract force curve, `0` selects the
-approacing curve and `1` selects the retracting curve.
+approaching curve and `1` selects the retracting curve.
""".strip()),
Argument(name='block two', aliases=['set two'], type='int',
default=0,
help='Block B in A-B.'),
Argument(name='x column', type='int', default=0,
help="""
-Column of data block to differentiate with respect to.
+Column of data to return as x values.
""".strip()),
- Argument(name='f column', type='int', default=1,
+ Argument(name='y column', type='int', default=1,
help="""
-Column of data block to differentiate.
+Column of data block to difference.
""".strip()),
],
help=self.__doc__, plugin=plugin)
assert a[:,params['x column']] == b[:,params['x column']]
out = Data((a.shape[0],2), dtype=a.dtype)
out[:,0] = a[:,params['x column']]
- out[:,1] = a[:,params['f column']] - b[:,params['f column']]
+ out[:,1] = a[:,params['y column']] - b[:,params['y column']]
outqueue.put(out)
class DerivativeCommand (Command):
- """Calculate the difference between two blocks of data.
+ """Calculate the derivative (actually, the discrete differentiation)
+ of a curve data block.
+
+ See :func:`hooke.util.calculus.derivative` for implementation
+ details.
"""
def __init__(self, plugin):
super(DerivativeCommand, self).__init__(
Argument(name='block', aliases=['set'], type='int', default=0,
help="""
Data block to differentiate. For an approach/retract force curve, `0`
-selects the approacing curve and `1` selects the retracting curve.
+selects the approaching curve and `1` selects the retracting curve.
""".strip()),
Argument(name='x column', type='int', default=0,
help="""
Argument(name='block', aliases=['set'], type='int', default=0,
help="""
Data block to act on. For an approach/retract force curve, `0`
-selects the approacing curve and `1` selects the retracting curve.
+selects the approaching curve and `1` selects the retracting curve.
""".strip()),
- Argument(name='f column', type='int', default=1,
+ Argument(name='column', type='int', default=1,
help="""
-Column of data block to differentiate with respect to.
+Column of data block containing time-series data.
""".strip()),
Argument(name='freq', type='float', default=1.0,
help="""
def _run(self, hooke, inqueue, outqueue, params):
data = params['curve'].data[params['block']]
outqueue.put(unitary_avg_power_spectrum(
- data[:,params['f column']], freq=params['freq'],
+ data[:,params['column']], freq=params['freq'],
chunk_size=params['chunk size'],
overlap=params['overlap']))
projects / hooke.git / blobdiff