-# Copyright
+# Copyright (C) 2009-2010 Fabrizio Benedetti
+# Massimo Sandal <devicerandom@gmail.com>
+# W. Trevor King <wking@drexel.edu>
+#
+# 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 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/>.
"""The `cut` module provides :class:`CutPlugin` and
:class:`CutCommand`.
"""
+import numpy
+
from ..command import Command, Argument, Failure
from ..plugin import Plugin
class CutPlugin (Plugin):
def __init__(self):
super(CutPlugin, self).__init__(name='cut')
-
- def commands(self):
- return [CutCommand()]
+ self._commands = [CutCommand(self)]
# Define common or complicated arguments
class CutCommand (Command):
"""Cut the selected signal between two points and write it to a file.
- The data is saved in TAB-delimited ASCII text, where the first column
- is "x" and the second is "y". There is no header row.
+ The data is saved in TAB-delimited ASCII text. A "#" prefixed
+ header will optionally appear at the beginning of the file naming
+ the columns.
"""
- def __init__(self):
+ def __init__(self, plugin):
super(CutCommand, self).__init__(
name='cut',
arguments=[
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='bounds', type='point', optional=False, count=2,
help="""
Argument(name='output', type='file', default='cut.dat',
help="""
File name for the output data.
+""".strip()),
+ Argument(name='header', type='bool', default=True,
+ help="""
+True if you want the column-naming header line.
""".strip()),
],
- help=self.__doc__)
+ help=self.__doc__, plugin=plugin)
def _run(self, hooke, inqueue, outqueue, params):
if params['curve'] == None:
cut_data = data[i_min:i_max+1,:] # slice rows from row-major data
# +1 to include data[i_max] row
- f = open(params['output'], 'w')
- cut_data.tofile(f, sep='\t')
+ f = open(params['output'], 'w')
+ if params['header'] == True:
+ f.write('# %s \n' % ('\t'.join(cut_data.info['columns'])))
+ numpy.savetxt(f, cut_data, delimiter='\t')
f.close()