hooke> remove_cantilever_from_extension --block retract
hooke> flat_peaks_to_polymer_peaks --block retract
hooke> polymer_fit_peaks --block retract
+ hooke> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
This stores the fit parameters in the block's
-:attr:`~hooke.curve.Data.info` dictionary (see each command's `Help`_
-for details). To access the parameters, save the playlist,::
-
- hooke> save_playlist --output mylist.hkp
-
-load it with PyYAML_::
+:attr:`~hooke.curve.Data.info` dictionary and also appends them to
+:file:`data.yaml` (see each command's `Help`_ for details). To access
+the parameters, load :file:`data.yaml` with PyYAML_::
$ python
>>> import yaml
>>> import hooke.util.yaml
- >>> mylist = yaml.load(open('mylist.hkp', 'r'))
-
-navigate to your curve,::
-
- >>> mylist.jump(1234)
+ >>> data = yaml.load(open('data.yaml', 'r'))
-and extract your parameter.::
+and extract your parameter::
- >>> mylist.current().data[1].info['polymer peak 0']['contour length (m)']
+ >>> data['20071120a_i27_t33.100']['retract']['polymer peak 0']['contour length (m)']
2.124...e-08
-You can also get a list of all available parameters::
-
- >>> mylist.current().data[1].info['polymer peak 0'].keys()
- ['model', 'contour length (m)', 'temperature (K)', 'fit',
- 'persistence length (m)']
-
-or just pprint_ the whole thing::
-
- >>> from pprint import pprint
- >>> pprint(mylist.current().data[1].info['polymer peak 0'])
- {'contour length (m)': 2.1248220207858103e-08,
- 'fit': {'active fitted parameters': 3.7024307200788127,
- 'active parameters': 3.7024307200788127,
- 'convergence flag': 1,
- 'covariance matrix': None,
- 'data scale factor': 5.2716380732198972e-10,
- 'fitted parameters': -2.5663294148411571,
- 'info': {'fjac': None,
- 'fvec': None,
- 'ipvt': None,
- 'nfev': 16,
- 'qtf': None},
- 'initial parameters': [-0.69314718055994529],
- 'message': 'Both actual and predicted relative reductions in the sum of squares\n are at most 0.000000',
- 'rescaled': True,
- 'scale': None},
- 'model': u'WLC',
- 'persistence length (m)': 4.0000000000000001e-10,
- 'temperature (K)': 301.0}
-
.. _PyYAML: http://pyyaml.org/
-.. _pprint: http://docs.python.org/library/pprint.html
-
-.. todo:: UI access to block (and curve?) info dicts. Someone should
- make a tree-based object browser ;).
-
-.. todo:: Playlists currently drop all :class:`~hooke.curve.Data`
- instances when they are unloaded, so you can't extract the fitted
- parameters from unloaded curves. We'll need a way to export chosen
- curve attributes to file.
Command stacks
~~~~~~~~~~~~~~
hooke> remove_cantilever_from_extension --block retract
hooke> flat_peaks_to_polymer_peaks --block retract
hooke> polymer_fit_peaks --block retract
- hooke> export_block --block retract --output myblock.dat
+ hooke> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
hooke> stop_command_capture
hooke> apply_command_stack_to_playlist
"""
import copy
+import re
import numpy
+import yaml
from ..command import Command, Argument, Failure
from ..command_stack import CommandStack
def __init__(self):
super(CurvePlugin, self).__init__(name='curve')
self._commands = [
- GetCommand(self), InfoCommand(self), DeltaCommand(self),
- ExportCommand(self), DifferenceCommand(self),
+ GetCommand(self), InfoCommand(self), BlockInfoCommand(self),
+ DeltaCommand(self), ExportCommand(self), DifferenceCommand(self),
DerivativeCommand(self), PowerSpectrumCommand(self),
ClearStackCommand(self)]
return [block.shape for block in curve.data]
+class BlockInfoCommand (BlockCommand):
+ """Get selected information about a :class:`hooke.curve.Curve` data block.
+ """
+ def __init__(self, plugin):
+ super(BlockInfoCommand, self).__init__(
+ name='block info', arguments=[
+ Argument(
+ name='key', count=-1, optional=False,
+ help='Dot-separted (.) key selection regexp.'),
+ Argument(
+ name='output',
+ help="""
+File name for the output (appended).
+""".strip()),
+ ],
+ help=self.__doc__, plugin=plugin)
+
+ def _run(self, hooke, inqueue, outqueue, params):
+ block = self._block(hooke, params)
+ values = {'index': self._block_index(hooke, params)}
+ for key in params['key']:
+ keys = [(0, key.split('.'), block.info)]
+ while len(keys) > 0:
+ index,key_stack,info = keys.pop(0)
+ regexp = re.compile(key_stack[index])
+ matched = False
+ for k,v in info.items():
+ if regexp.match(k):
+ matched = True
+ new_stack = copy.copy(key_stack)
+ new_stack[index] = k
+ if index+1 == len(key_stack):
+ vals = values
+ for k in new_stack[:-1]:
+ if k not in vals:
+ vals[k] = {}
+ vals = vals[k]
+ vals[new_stack[-1]] = v
+ else:
+ keys.append((index+1, new_stack, v))
+ if matched == False:
+ raise ValueError('no match found for %s in %s'
+ % (key_stack[index], key))
+ if params['output'] != None:
+ curve = self._curve(hooke, params)
+ with open(params['output'], 'a') as f:
+ yaml.dump({curve.name:{
+ 'path': curve.path,
+ block.info['name']: values
+ }}, f)
+ outqueue.put(values)
+
+
class DeltaCommand (BlockCommand):
"""Get distance information between two points.
--- /dev/null
+# Copyright (C) 2010 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/>.
+
+"""
+>>> import os
+>>> from uuid import uuid4
+>>> from hooke.hooke import Hooke, HookeRunner
+>>> h = Hooke()
+>>> r = HookeRunner()
+>>> h = r.run_lines(h, ['load_playlist test/data/test']) # doctest: +ELLIPSIS
+<FilePlaylist test.hkp>
+Success
+<BLANKLINE>
+
+>>> file_name = '%s.block' % uuid4()
+>>> block_info_already_exists = os.path.exists(file_name)
+>>> block_info_already_exists
+False
+>>> h = r.run_lines(h, ['block_info --output %s name columns "raw info.file*"'
+... % file_name]) # doctest: +ELLIPSIS, +REPORT_UDIFF
+{'index': 0, 'name': 'approach', 'columns': ['z piezo (m)', 'deflection (m)'], 'raw info': {'filetype': 'picoforce'}}
+Success
+<BLANKLINE>
+>>> with open(file_name, 'r') as f:
+... text = f.read()
+>>> if block_info_already_exists == False:
+... os.remove(file_name)
+>>> print text
+picoforce.000:
+ approach:
+ columns: [z piezo (m), deflection (m)]
+ index: 0
+ name: approach
+ raw info: {filetype: picoforce}
+ path: /tmp/hooke/test/data/picoforce.000
+<BLANKLINE>
+"""
projects / hooke.git / commitdiff