Add os.path.expanduser() wrappers to user-supplied paths.

[hooke.git] / hooke / plugin / cut.py

diff --git a/hooke/plugin/cut.py b/hooke/plugin/cut.py
index 369cfcc3b7fa86d49df9ac776a7953e8bd5f8e41..6aef07695bd38ea16ee8444c95d387a29c2f5e1c 100644 (file)
--- a/hooke/plugin/cut.py
+++ b/hooke/plugin/cut.py
@@ -1,17 +1,39 @@
+# 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 os.path
+
+import numpy
+
 from ..command import Command, Argument, Failure
-from ..plugin import Plugin
+from . 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
@@ -37,10 +59,11 @@ CurveArgument = Argument(
 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=[
@@ -48,7 +71,7 @@ class CutCommand (Command):
                 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="""
@@ -57,9 +80,13 @@ Indicies of points bounding the selected data.
                 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:
@@ -72,6 +99,8 @@ File name for the output data.
         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(os.path.expanduser(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()