# -*- coding: utf-8 -*-
#
-# Copyright (C) 2008-2010 Alberto Gomez-Casado
-# Fabrizio Benedetti
-# Massimo Sandal <devicerandom@gmail.com>
-# W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2010-2012 W. Trevor King <wking@tremily.us>
#
# 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
-# <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Lesser General Public License
+# along with Hooke. If not, see <http://www.gnu.org/licenses/>.
"""The ``flatfilt`` module provides :class:`FlatFiltPlugin` and
several associated :class:`~hooke.command.Command`\s for removing flat
See Also
--------
-:mod:`~hooke.plugin.convfilt` for a convolution-based filter for
-:class:`~hooke.experiment.VelocityClamp` experiments.
+:mod:`~hooke.plugin.convfilt` for a convolution-based filter.
"""
import copy
from ..command import Argument, Success, Failure, UncaughtException
from ..config import Setting
from ..curve import Data
-from ..experiment import VelocityClamp
-from ..plugin import Plugin, argument_to_setting
-from ..plugin.curve import ColumnAddingCommand
-from ..plugin.playlist import FilterCommand
from ..util.fit import PoorFit
from ..util.peak import (find_peaks, peaks_to_mask,
find_peaks_arguments, Peak, _kwargs)
from ..util.si import join_data_label, split_data_label
+from . import Plugin, argument_to_setting
+from .curve import ColumnAddingCommand
+from .playlist import FilterCommand
class FlatFiltPlugin (Plugin):
new_columns=[
('output peak column', 'flat filter peaks', """
Name of the column (without units) to use as the peak output.
-""".split()),
+""".strip()),
],
arguments=[
Argument(name='peak info name', type='string',
default='flat filter peaks',
help="""
-Name (without units) for storing the list of peaks in the `.info`
-dictionary.
+Name for storing the list of peaks in the `.info` dictionary.
""".strip()),
] + plugin_arguments,
help=self.__doc__, plugin=plugin)
def _run(self, hooke, inqueue, outqueue, params):
- params = self.__setup_params(hooke=hooke, params=params)
+ self._add_to_command_stack(params)
+ params = self._setup_params(hooke=hooke, params=params)
block = self._block(hooke=hooke, params=params)
dist_data = self._get_column(hooke=hooke, params=params,
column_name='distance column')
values=peaks_to_mask(def_data, peaks) * def_data)
outqueue.put(peaks)
- def __setup_params(self, hooke, params):
+ def _setup_params(self, hooke, params):
"""Setup `params` from config and return the z piezo and
deflection arrays.
"""
curve = self._curve(hooke=hooke, params=params)
- if curve.info['experiment'] != VelocityClamp:
- raise Failure('%s operates on VelocityClamp experiments, not %s'
- % (self.name, curve.info['experiment']))
for key,value in params.items():
if value == None and key in self.plugin.config:
# Use configured default value.
name,def_unit = split_data_label(params['deflection column'])
params['output peak column'] = join_data_label(
params['output peak column'], def_unit)
- params['peak info name'] = join_data_label(
- params['peak info name'], def_unit)
return params
def _peak_name(self, params, index):
def __init__(self, plugin):
flat_peaks = [c for c in plugin._commands
if c.name == 'flat filter peaks'][0]
- flat_peaks_arg_names = [a.name for a in flat_peaks.arguments]
+ flat_peaks_arguments = [a for a in flat_peaks.arguments
+ if a.name not in ['help', 'stack']]
+ flat_peaks_arg_names = [a.name for a in flat_peaks_arguments]
plugin_arguments = [a for a in plugin._arguments
if a.name not in flat_peaks_arg_names]
- arguments = flat_peaks.arguments + plugin_arguments
+ arguments = flat_peaks_arguments + plugin_arguments
super(FlatFilterCommand, self).__init__(
plugin, name='flat filter playlist')
self.arguments.extend(arguments)
params['curve'] = curve
inq = Queue()
outq = Queue()
- filt_command = [c for c in hooke.commands
- if c.name=='flat filter peaks'][0]
+ filt_command = hooke.command_by_name['flat filter peaks']
filt_command.run(hooke, inq, outq, **params)
peaks = outq.get()
if isinstance(peaks, UncaughtException) \
projects / hooke.git / blobdiff