Add multi-y TODO comment to gui.panel.plot

[hooke.git] / hooke / curve.py

diff --git a/hooke/curve.py b/hooke/curve.py
index 5aeaeaac887f3bc3cc26f0b8ead8a73098deb7ee..7e3d084c213e909ae2d36ba74a35b608232ab514 100644 (file)
--- a/hooke/curve.py
+++ b/hooke/curve.py
@@ -1,12 +1,41 @@
-"""The curve module provides :class:`Curve` and :class:`Data` for storing
-force curves.
+# 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/>.
+
+"""The `curve` module provides :class:`Curve` and :class:`Data` for
+storing force curves.

 """
 
 import os.path
 import numpy
 
 """
 
 import os.path
 import numpy
 

-from .driver import NotRecognized

 
 

+class NotRecognized (ValueError):
+    def __init__(self, curve):
+        self.__setstate__(curve)
+
+    def __getstate__(self):
+        return self.curve
+
+    def __setstate__(self, data):
+        if isinstance(data, Curve):
+            msg = 'Not a recognizable curve format: %s' % data.path
+            super(NotRecognized, self).__init__(msg)
+            self.curve = data

 
 class Data (numpy.ndarray):
     """Stores a single, continuous data set.
 
 class Data (numpy.ndarray):
     """Stores a single, continuous data set.


@@ -15,16 +44,52 @@ class Data (numpy.ndarray):
 
     See :mod:`numpy.doc.subclassing` for the peculiarities of
     subclassing :class:`numpy.ndarray`.
 
     See :mod:`numpy.doc.subclassing` for the peculiarities of
     subclassing :class:`numpy.ndarray`.

+
+    Examples
+    --------
+
+    >>> d = Data(shape=(3,2), info={'columns':['distance (m)', 'force (N)']})
+    >>> type(d)
+    <class 'hooke.curve.Data'>
+    >>> for i in range(3): # initialize d
+    ...    for j in range(2):
+    ...        d[i,j] = i*10 + j
+    >>> d
+    Data([[  0.,   1.],
+           [ 10.,  11.],
+           [ 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)']}

     """
     """

-    def __new__(self, subtype, shape, dtype=numpy.float, buffer=None, offset=0,
+    def __new__(subtype, shape, dtype=numpy.float, buffer=None, offset=0,

                 strides=None, order=None, info=None):
         """Create the ndarray instance of our type, given the usual
         input arguments.  This will call the standard ndarray
         constructor, but return an object of our type.
         """
                 strides=None, order=None, info=None):
         """Create the ndarray instance of our type, given the usual
         input arguments.  This will call the standard ndarray
         constructor, but return an object of our type.
         """

-        obj = np.ndarray.__new__(subtype=subtype, shape=shape, dtype=dtype,
-                                 buffer=buffer, offset=offset, strides=strides,
-                                 order=order)
+        obj = numpy.ndarray.__new__(
+            subtype, shape, dtype, buffer, offset, strides, order)

         # add the new attribute to the created instance
         if info == None:
             info = {}
         # add the new attribute to the created instance
         if info == None:
             info = {}


@@ -39,6 +104,34 @@ class Data (numpy.ndarray):
         self.info = getattr(obj, 'info', {})
         # We do not need to return anything
 
         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.
 
 class Curve (object):
     """A grouped set of :class:`Data` runs from the same file with metadata.


@@ -61,26 +154,42 @@ class Curve (object):
       Hooke commands could like to know if they're looking at force
       clamp data, regardless of their origin.
     """
       Hooke commands could like to know if they're looking at force
       clamp data, regardless of their origin.
     """

-    def __init__(self, path):
+    def __init__(self, path, info=None):

         #the data dictionary contains: {name of data: list of data sets [{[x], [y]}]
         self.path = path
         self.driver = None
         #the data dictionary contains: {name of data: list of data sets [{[x], [y]}]
         self.path = path
         self.driver = None

-        self.data = []
-        self.info = None
+        self.data = None
+        if info == None:
+            info = {}
+        self.info = info

         self.name = os.path.basename(path)
         self.name = os.path.basename(path)

-        self.notes = ''

 
     def identify(self, drivers):
         """Identify the appropriate :class:`hooke.driver.Driver` for
         the curve file (`.path`).
         """
 
     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
         for driver in drivers:
             if driver.is_me(self.path):
                 self.driver = driver # remember the working driver
                 return

-        raise NotRecognized(self.path)
+        raise NotRecognized(self)

 
     def load(self):
         """Use the driver to read the curve into memory.
         """
 
     def load(self):
         """Use the driver to read the curve into memory.
         """

-        pass
+        data,info = self.driver.read(self.path, self.info)
+        self.data = data
+        for key,value in info.items():
+            self.info[key] = value
+
+    def unload(self):
+        """Release memory intensive :attr:`.data`.
+        """
+        self.data = None