Merge pull request #111 from toddrjen/cleanups

Various Cleanups

Author: toddrjen

doc/source/developers_guide.rst

@@ -38,10 +38,10 @@ a GitHub account and then set to watch the repository at `GitHub Repository`_
 Requirements
 ------------
 
-    * Python_ 2.6, 2.7, 3.1 or 3.2
+    * Python_ 2.6, 2.7, or 3.3
     * numpy_ >= 1.3.0
     * quantities_ >= 0.9.0
-    * if using Python 2.6 or 3.1, unittest2_ >= 0.5.1
+    * if using Python 2.6, unittest2_ >= 0.5.1
     * Setuptools >= 0.7
     * nose_ >= 0.11.1 (for running tests)
     * Sphinx_ >= 0.6.4 (for building documentation)
@@ -96,7 +96,7 @@ on your system::
 
     $ cd neo/test
 
-With Python 2.7 or 3.2::
+With Python 2.7 or 3.3::
 
     $ python -m unittest discover
     $ python3 -m unittest discover
@@ -195,9 +195,10 @@ open a pull request on GitHub
 Python 3
 --------
 
-Neo core should work with both recent versions of Python 2 (versions 2.6 and 2.7)
-and Python 3. Neo IO modules should ideally work with both Python 2 and 3, but
-certain modules may only work with one or the other (see :doc:`install`).
+Neo core should work with both recent versions of Python 2 (versions 2.6 and
+2.7) and Python 3 (version 3.3). Neo IO modules should ideally work with both
+Python 2 and 3, but certain modules may only work with one or the other
+(see :doc:`install`).
 
 So far, we have managed to write code that works with both Python 2 and 3.
 Mainly this involves avoiding the ``print`` statement (use ``logging.info``
@@ -218,7 +219,7 @@ Coding standards and style
 --------------------------
 
 All code should conform as much as possible to `PEP 8`_, and should run with
-Python 2.6, 2.7, 3.1, 3.2, and 3.3.
+Python 2.6, 2.7, and 3.3.
 
 You can use the `pep8`_ program to check the code for PEP 8 conformity.
 You can also use `flake8`_, which combines pep8 and pyflakes.

examples/read_files.py

@@ -15,16 +15,17 @@
 
 #create a reader
 reader = neo.io.PlexonIO(filename='File_plexon_3.plx')
-# read the block
-bl = reader.read(cascade=True, lazy=False)
-print bl
+# read the blocks
+blks = reader.read(cascade=True, lazy=False)
+print blks
 # acces to segments
-for seg in bl.segments:
-    print seg
-    for asig in seg.analogsignals:
-        print asig
-    for st in seg.spiketrains:
-        print st
+for blk in blks:
+    for seg in blk.segments:
+        print seg
+        for asig in seg.analogsignals:
+            print asig
+        for st in seg.spiketrains:
+            print st
 
 
 # CED Spike2 files

examples/simple_plot_with_matplotlib.py

@@ -6,6 +6,7 @@
 import urllib
 
 import numpy as np
+import quantities as pq
 from matplotlib import pyplot
 
 import neo
@@ -21,12 +22,17 @@
 for seg in bl.segments:
     fig = pyplot.figure()
     ax1 = fig.add_subplot(2, 1, 1)
-    ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
+    ax2 = fig.add_subplot(2, 1, 2)
     ax1.set_title(seg.file_origin)
-    for asig in seg.analogsignals:
-        ax1.plot(asig.times, asig)
-    for s, st in enumerate(seg.spiketrains):
-        print st.units
-        ax2.plot(st, s*np.ones(st.size), linestyle='None',
-                 marker='|', color='k')
+    mint = 0 * pq.s
+    maxt = np.inf * pq.s
+    for i, asig in enumerate(seg.analogsignals):
+        times = asig.times.rescale('s').magnitude
+        asig = asig.rescale('mV').magnitude
+        ax1.plot(times, asig)
+
+    trains = [st.rescale('s').magnitude for st in seg.spiketrains]
+    colors = pyplot.cm.jet(np.linspace(0, 1, len(seg.spiketrains)))
+    ax2.eventplot(trains, colors=colors)
+
 pyplot.show()

neo/core/analogsignal.py

@@ -365,55 +365,55 @@ def _copy_data_complement(self, other):
                      "description", "channel_index", "annotations"):
             setattr(self, attr, getattr(other, attr, None))
 
-    def _apply_operator(self, other, op):
+    def _apply_operator(self, other, op, *args):
         '''
         Handle copying metadata to the new :class:`BaseAnalogSignal`
         after a mathematical operation.
         '''
         self._check_consistency(other)
         f = getattr(super(BaseAnalogSignal, self), op)
-        new_signal = f(other)
+        new_signal = f(other, *args)
         new_signal._copy_data_complement(self)
         return new_signal
 
-    def __add__(self, other):
+    def __add__(self, other, *args):
         '''
         Addition (+)
         '''
-        return self._apply_operator(other, "__add__")
+        return self._apply_operator(other, "__add__", *args)
 
-    def __sub__(self, other):
+    def __sub__(self, other, *args):
         '''
         Subtraction (-)
         '''
-        return self._apply_operator(other, "__sub__")
+        return self._apply_operator(other, "__sub__", *args)
 
-    def __mul__(self, other):
+    def __mul__(self, other, *args):
         '''
         Multiplication (*)
         '''
-        return self._apply_operator(other, "__mul__")
+        return self._apply_operator(other, "__mul__", *args)
 
-    def __truediv__(self, other):
+    def __truediv__(self, other, *args):
         '''
         Float division (/)
         '''
-        return self._apply_operator(other, "__truediv__")
+        return self._apply_operator(other, "__truediv__", *args)
 
-    def __div__(self, other):
+    def __div__(self, other, *args):
         '''
         Integer division (//)
         '''
-        return self._apply_operator(other, "__div__")
+        return self._apply_operator(other, "__div__", *args)
 
     __radd__ = __add__
     __rmul__ = __sub__
 
-    def __rsub__(self, other):
+    def __rsub__(self, other, *args):
         '''
         Backwards subtraction (other-self)
         '''
-        return self.__mul__(-1) + other
+        return self.__mul__(-1, *args) + other
 
     def _repr_pretty_(self, pp, cycle):
         '''
@@ -437,8 +437,6 @@ def _pp(line):
                 pp.text(line)
         if hasattr(self, "channel_index"):
             _pp("channel index: {0}".format(self.channel_index))
-        elif hasattr(self, "channel_indexes"):
-            _pp("channel indices: %s" % self.channel_indexes)
         for line in ["sampling rate: {0}".format(self.sampling_rate),
                      "time: {0} to {1}".format(self.t_start, self.t_stop)
                      ]:

neo/core/irregularlysampledsignal.py

@@ -229,14 +229,14 @@ def __ne__(self, other):
         '''
         return not self.__eq__(other)
 
-    def _apply_operator(self, other, op):
+    def _apply_operator(self, other, op, *args):
         '''
         Handle copying metadata to the new :class:`IrregularlySampledSignal`
         after a mathematical operation.
         '''
         self._check_consistency(other)
         f = getattr(super(IrregularlySampledSignal, self), op)
-        new_signal = f(other)
+        new_signal = f(other, *args)
         new_signal._copy_data_complement(self)
         return new_signal
 
@@ -273,40 +273,40 @@ def _copy_data_complement(self, other):
                      "description", "channel_index", "annotations"):
             setattr(self, attr, getattr(other, attr, None))
 
-    def __add__(self, other):
+    def __add__(self, other, *args):
         '''
         Addition (+)
         '''
-        return self._apply_operator(other, "__add__")
+        return self._apply_operator(other, "__add__", *args)
 
-    def __sub__(self, other):
+    def __sub__(self, other, *args):
         '''
         Subtraction (-)
         '''
-        return self._apply_operator(other, "__sub__")
+        return self._apply_operator(other, "__sub__", *args)
 
-    def __mul__(self, other):
+    def __mul__(self, other, *args):
         '''
         Multiplication (*)
         '''
-        return self._apply_operator(other, "__mul__")
+        return self._apply_operator(other, "__mul__", *args)
 
-    def __truediv__(self, other):
+    def __truediv__(self, other, *args):
         '''
         Float division (/)
         '''
-        return self._apply_operator(other, "__truediv__")
+        return self._apply_operator(other, "__truediv__", *args)
 
-    def __div__(self, other):
+    def __div__(self, other, *args):
         '''
         Integer division (//)
         '''
-        return self._apply_operator(other, "__div__")
+        return self._apply_operator(other, "__div__", *args)
 
     __radd__ = __add__
     __rmul__ = __sub__
 
-    def __rsub__(self, other):
+    def __rsub__(self, other, *args):
         '''
         Backwards subtraction (other-self)
         '''