-# Copyright (C) 2010 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 `curve` module provides :class:`Curve` and :class:`Data` for
storing force curves.
"""
+from copy_reg import dispatch_table
+from copy import _reconstruct, _copy_dispatch
+import logging
import os.path
+
import numpy
+from .command_stack import CommandStack
+
class NotRecognized (ValueError):
def __init__(self, curve):
super(NotRecognized, self).__init__(msg)
self.curve = data
+
class Data (numpy.ndarray):
"""Stores a single, continuous data set.
[ 20., 21.]])
>>> d.info
{'columns': ['distance (m)', 'force (N)']}
+
+ The information gets passed on to slices.
+
>>> row_a = d[:,0]
>>> row_a
Data([ 0., 10., 20.])
>>> row_a.info
{'columns': ['distance (m)', 'force (N)']}
+
+ The data-type is also pickleable, to ensure we can move it between
+ processes with :class:`multiprocessing.Queue`\s.
+
+ >>> import pickle
+ >>> s = pickle.dumps(d)
+ >>> z = pickle.loads(s)
+ >>> z
+ Data([[ 0., 1.],
+ [ 10., 11.],
+ [ 20., 21.]])
+ >>> z.info
+ {'columns': ['distance (m)', 'force (N)']}
+
+ The data-type is also YAMLable (see :mod:`hooke.util.yaml`).
+
+ >>> import yaml
+ >>> s = yaml.dump(d)
+ >>> print s
+ !hooke.curve.DataInfo
+ columns: [distance (m), force (N)]
+ <BLANKLINE>
+ >>> z = yaml.load(s)
+ >>> z
+ Data([], shape=(0, 0), dtype=float32)
"""
def __new__(subtype, shape, dtype=numpy.float, buffer=None, offset=0,
strides=None, order=None, info=None):
self.info = getattr(obj, 'info', {})
# We do not need to return anything
+ def __reduce__(self):
+ """Collapse an instance for pickling.
+
+ Returns
+ -------
+ reconstruct : callable
+ Called to create the initial version of the object.
+ args : tuple
+ A tuple of arguments for `reconstruct`
+ state : (optional)
+ The state to be passed to __setstate__, if present.
+ iter : iterator (optional)
+ Yielded items will be appended to the reconstructed
+ object.
+ dict : iterator (optional)
+ Yielded (key,value) tuples pushed back onto the
+ reconstructed object.
+ """
+ base_reduce = list(numpy.ndarray.__reduce__(self))
+ # tack our stuff onto ndarray's setstate portion.
+ base_reduce[2] = (base_reduce[2], (self.info,))
+ return tuple(base_reduce)
+
+ def __setstate__(self, state):
+ base_class_state,own_state = state
+ numpy.ndarray.__setstate__(self, base_class_state)
+ self.info, = own_state
+
class Curve (object):
"""A grouped set of :class:`Data` runs from the same file with metadata.
would consist of the approach data and the retract data. Metadata
would be the temperature, cantilever spring constant, etc.
- Two important :attr:`info` settings are `filetype` and
- `experiment`. These are two strings that can be used by Hooke
- commands/plugins to understand what they are looking at.
-
- * `.info['filetype']` should contain the name of the exact
- filetype defined by the driver (so that filetype-speciofic
- commands can know if they're dealing with the correct filetype).
- * `.info['experiment']` should contain an instance of a
- :class:`hooke.experiment.Experiment` subclass to identify the
- experiment type. For example, various
- :class:`hooke.driver.Driver`\s can read in force-clamp data, but
- Hooke commands could like to know if they're looking at force
- clamp data, regardless of their origin.
+ Each :class:`Data` block in :attr:`data` must contain an
+ :attr:`info['name']` setting with a unique (for the parent
+ curve) name identifying the data block. This allows plugins
+ and commands to access individual blocks.
+
+ Each curve maintiains a :class:`~hooke.command_stack.CommandStack`
+ (:attr:`command_stack`) listing the commands that have been
+ applied to the `Curve` since loading.
+
+ The data-type is pickleable, to ensure we can move it between
+ processes with :class:`multiprocessing.Queue`\s.
+
+ >>> import pickle
+ >>> import yaml
+ >>> from .engine import CommandMessage
+ >>> c = Curve(path='some/path')
+
+ We add a recursive reference to `c` as you would get from
+ :meth:`hooke.plugin.curve.CurveCommand._add_to_command_stack`.
+
+ >>> c.command_stack.append(CommandMessage('curve info', {'curve':c}))
+
+ >>> s = pickle.dumps(c)
+ >>> z = pickle.loads(s)
+ >>> z
+ <Curve path>
+ >>> z.command_stack
+ [<CommandMessage curve info {curve: <Curve path>}>]
+ >>> z.command_stack[-1].arguments['curve'] == z
+ True
+ >>> print yaml.dump(c) # doctest: +REPORT_UDIFF
+ &id001 !!python/object:hooke.curve.Curve
+ command_stack: !!python/object/new:hooke.command_stack.CommandStack
+ listitems:
+ - !!python/object:hooke.engine.CommandMessage
+ arguments:
+ curve: *id001
+ command: curve info
+ explicit_user_call: true
+ name: path
+ path: some/path
+ <BLANKLINE>
+
+ However, if we try and serialize the command stack first, we run
+ into `Python issue 1062277`_.
+
+ .. _Python issue 1062277: http://bugs.python.org/issue1062277
+
+ >>> pickle.dumps(c.command_stack)
+ Traceback (most recent call last):
+ ...
+ assert id(obj) not in self.memo
+ AssertionError
+
+ YAML still works, though.
+
+ >>> print yaml.dump(c.command_stack) # doctest: +REPORT_UDIFF
+ &id001 !!python/object/new:hooke.command_stack.CommandStack
+ listitems:
+ - !!python/object:hooke.engine.CommandMessage
+ arguments:
+ curve: !!python/object:hooke.curve.Curve
+ command_stack: *id001
+ name: path
+ path: some/path
+ command: curve info
+ explicit_user_call: true
+ <BLANKLINE>
"""
def __init__(self, path, info=None):
- #the data dictionary contains: {name of data: list of data sets [{[x], [y]}]
+ self.__setstate__({'path':path, 'info':info})
+
+ def __str__(self):
+ return str(self.__unicode__())
+
+ def __unicode__(self):
+ return u'<%s %s>' % (self.__class__.__name__, self.name)
+
+ def __repr__(self):
+ return self.__str__()
+
+ def set_path(self, path):
+ if path != None:
+ path = os.path.expanduser(path)
self.path = path
- self.driver = None
- self.data = None
- if info == None:
- info = {}
- self.info = info
- self.name = os.path.basename(path)
+ if self.name == None and path != None:
+ self.name = os.path.basename(path)
+
+ def _setup_default_attrs(self):
+ # .data contains: {name of data: list of data sets [{[x], [y]}]
+ # ._hooke contains a Hooke instance for Curve.load()
+ self._default_attrs = {
+ '_hooke': None,
+ 'command_stack': [],
+ 'data': None,
+ 'driver': None,
+ 'info': {},
+ 'name': None,
+ 'path': None,
+ }
+
+ def __getstate__(self):
+ state = dict(self.__dict__) # make a copy of the attribute dict.
+ del(state['_hooke'])
+ return state
+
+ def __setstate__(self, state):
+ self._setup_default_attrs()
+ self.__dict__.update(self._default_attrs)
+ if state == True:
+ return
+ self.__dict__.update(state)
+ self.set_path(getattr(self, 'path', None))
+ if self.info in [None, {}]:
+ self.info = {}
+ if type(self.command_stack) == list:
+ self.command_stack = CommandStack()
+
+ def __copy__(self):
+ """Set copy to preserve :attr:`_hooke`.
+
+ :meth:`getstate` drops :attr:`_hooke` for :mod:`pickle` and
+ :mod:`yaml` output, but it should be preserved (but not
+ duplicated) during copies.
+
+ >>> import copy
+ >>> class Hooke (object):
+ ... pass
+ >>> h = Hooke()
+ >>> d = Data(shape=(3,2), info={'columns':['distance (m)', 'force (N)']})
+ >>> for i in range(3): # initialize d
+ ... for j in range(2):
+ ... d[i,j] = i*10 + j
+ >>> c = Curve(None)
+ >>> c.data = [d]
+ >>> c.set_hooke(h)
+ >>> c._hooke # doctest: +ELLIPSIS
+ <hooke.curve.Hooke object at 0x...>
+ >>> c._hooke == h
+ True
+ >>> c2 = copy.copy(c)
+ >>> c2._hooke # doctest: +ELLIPSIS
+ <hooke.curve.Hooke object at 0x...>
+ >>> c2._hooke == h
+ True
+ >>> c2.data
+ [Data([[ 0., 1.],
+ [ 10., 11.],
+ [ 20., 21.]])]
+ >>> d.info
+ {'columns': ['distance (m)', 'force (N)']}
+ >>> id(c2.data[0]) == id(d)
+ True
+ """
+ copier = _copy_dispatch.get(type(self))
+ if copier:
+ return copier(self)
+ reductor = dispatch_table.get(type(self))
+ if reductor:
+ rv = reductor(self)
+ else:
+ # :class:`object` implements __reduce_ex__, see :pep:`307`.
+ rv = self.__reduce_ex__(2)
+ y = _reconstruct(self, rv, 0)
+ y.set_hooke(self._hooke)
+ return y
+
+ def __deepcopy__(self, memo):
+ """Set deepcopy to preserve :attr:`_hooke`.
+
+ :meth:`getstate` drops :attr:`_hooke` for :mod:`pickle` and
+ :mod:`yaml` output, but it should be preserved (but not
+ duplicated) during copies.
+
+ >>> import copy
+ >>> class Hooke (object):
+ ... pass
+ >>> h = Hooke()
+ >>> d = Data(shape=(3,2), info={'columns':['distance (m)', 'force (N)']})
+ >>> for i in range(3): # initialize d
+ ... for j in range(2):
+ ... d[i,j] = i*10 + j
+ >>> c = Curve(None)
+ >>> c.data = [d]
+ >>> c.set_hooke(h)
+ >>> c._hooke # doctest: +ELLIPSIS
+ <hooke.curve.Hooke object at 0x...>
+ >>> c._hooke == h
+ True
+ >>> c2 = copy.deepcopy(c)
+ >>> c2._hooke # doctest: +ELLIPSIS
+ <hooke.curve.Hooke object at 0x...>
+ >>> c2._hooke == h
+ True
+ >>> c2.data
+ [Data([[ 0., 1.],
+ [ 10., 11.],
+ [ 20., 21.]])]
+ >>> d.info
+ {'columns': ['distance (m)', 'force (N)']}
+ >>> id(c2.data[0]) == id(d)
+ False
+ """
+ reductor = dispatch_table.get(type(self))
+ if reductor:
+ rv = reductor(self)
+ else:
+ # :class:`object` implements __reduce_ex__, see :pep:`307`.
+ rv = self.__reduce_ex__(2)
+ y = _reconstruct(self, rv, 1, memo)
+ y.set_hooke(self._hooke)
+ return y
+
+ def set_hooke(self, hooke=None):
+ if hooke != None:
+ self._hooke = hooke
def identify(self, drivers):
"""Identify the appropriate :class:`hooke.driver.Driver` for
the curve file (`.path`).
"""
+ if 'filetype' in self.info:
+ driver = [d for d in drivers if d.name == self.info['filetype']]
+ if len(driver) == 1:
+ driver = driver[0]
+ if driver.is_me(self.path):
+ self.driver = driver
+ return
for driver in drivers:
if driver.is_me(self.path):
self.driver = driver # remember the working driver
return
raise NotRecognized(self)
- def load(self):
+ def load(self, hooke=None):
"""Use the driver to read the curve into memory.
+
+ Also runs any commands in :attr:`command_stack`. All
+ arguments are passed through to
+ :meth:`hooke.command_stack.CommandStack.execute`.
"""
- data,info = self.driver.read(self.path)
+ self.set_hooke(hooke)
+ log = logging.getLogger('hooke')
+ log.debug('loading curve %s with driver %s' % (self.name, self.driver))
+ data,info = self.driver.read(self.path, self.info)
self.data = data
for key,value in info.items():
self.info[key] = value
+ if self._hooke != None:
+ self.command_stack.execute(self._hooke)
+ elif len(self.command_stack) > 0:
+ log.warn(
+ 'could not execute command stack for %s without Hooke instance'
+ % self.name)
def unload(self):
"""Release memory intensive :attr:`.data`.
"""
+ log = logging.getLogger('hooke')
+ log.debug('unloading curve %s' % self.name)
self.data = None
projects / hooke.git / blobdiff