neo.units module (Issue278)

doc/source/api_reference.rst

@@ -6,4 +6,4 @@ API Reference
 .. testsetup:: *
 
     from neo import SpikeTrain
-    import quantities as pq
+    from neo import units as un

doc/source/core.rst

@@ -66,7 +66,7 @@ cut across the simple container hierarchy.
 NumPy compatibility
 ===================
 
-Neo data objects inherit from :py:class:`Quantity`, which in turn inherits from NumPy
+Neo data objects inherit from :py:class:`Quantity` (by using units module), which in turn inherits from NumPy
 :py:class:`ndarray`. This means that a Neo :py:class:`AnalogSignal` is also a :py:class:`Quantity`
 and an array, giving you access to all of the methods available for those objects.
 

doc/source/images/generate_diagram.py

@@ -10,7 +10,8 @@
 from datetime import datetime
 
 import numpy as np
-import quantities as pq
+from neo import units as un
+
 from matplotlib import pyplot
 from matplotlib.patches import Rectangle, ArrowStyle, FancyArrowPatch
 from matplotlib.font_manager import FontProperties
@@ -173,7 +174,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
             else:
                 t1 = attrname
 
-            if attrtype == pq.Quantity:
+            if attrtype == un.Quantity:
                 if attr[2] == 0:
                     t2 = 'Quantity scalar'
                 else:

examples/generated_data.py

@@ -6,10 +6,11 @@
 from __future__ import division  # Use same division in Python 2 and 3
 
 import numpy as np
-import quantities as pq
+
 from matplotlib import pyplot as plt
 
 import neo
+from neo import units as un
 
 
 def generate_block(n_segments=3, n_channels=8, n_units=3,
@@ -48,7 +49,7 @@ def generate_block(n_segments=3, n_channels=8, n_units=3,
             sig = np.random.randn(data_samples)
             sig[feature_pos:feature_pos + feature_samples] += wave
 
-            signal = neo.AnalogSignal(sig * pq.mV, sampling_rate=1 * pq.kHz)
+            signal = neo.AnalogSignal(sig * un.mV, sampling_rate=1 * un.kHz)
             seg.analogsignals.append(signal)
             rc.analogsignals.append(signal)
 
@@ -59,7 +60,7 @@ def generate_block(n_segments=3, n_channels=8, n_units=3,
             feature_spikes = np.random.rand(5) * feature_len + feature_time
             spikes = np.hstack([random_spikes, feature_spikes])
 
-            train = neo.SpikeTrain(spikes * pq.s, 1 * pq.s)
+            train = neo.SpikeTrain(spikes * un.s, 1 * un.s)
             seg.spiketrains.append(train)
             u.spiketrains.append(train)
 

examples/simple_plot_with_matplotlib.py

@@ -6,10 +6,12 @@
 import urllib
 
 import numpy as np
-import quantities as pq
+
 from matplotlib import pyplot
 
 import neo
+from neo import units as un
+
 
 url = 'https://portal.g-node.org/neo/'
 # distantfile = url + 'neuroexplorer/File_neuroexplorer_2.nex'
@@ -33,8 +35,8 @@
     ax1 = fig.add_subplot(2, 1, 1)
     ax2 = fig.add_subplot(2, 1, 2)
     ax1.set_title(seg.file_origin)
-    mint = 0 * pq.s
-    maxt = np.inf * pq.s
+    mint = 0 * un.s
+    maxt = np.inf * un.s
     for i, asig in enumerate(seg.analogsignals):
         times = asig.times.rescale('s').magnitude        
         asig = asig.rescale('mV').magnitude

neo/core/analogsignal.py

@@ -22,11 +22,12 @@
 import logging
 
 import numpy as np
-import quantities as pq
 
 from neo.core.baseneo import BaseNeo, MergeError, merge_annotations
 from neo.core.channelindex import ChannelIndex
 
+from neo import units as un
+
 logger = logging.getLogger("Neo")
 
 
@@ -49,7 +50,7 @@ def _get_sampling_rate(sampling_rate, sampling_period):
 
 
 def _new_AnalogSignalArray(cls, signal, units=None, dtype=None, copy=True,
-                          t_start=0*pq.s, sampling_rate=None,
+                          t_start=0*un.s, sampling_rate=None,
                           sampling_period=None, name=None, file_origin=None,
                           description=None,
                           annotations=None):
@@ -64,7 +65,7 @@ def _new_AnalogSignalArray(cls, signal, units=None, dtype=None, copy=True,
                **annotations)
 
 
-class AnalogSignal(BaseNeo, pq.Quantity):
+class AnalogSignal(BaseNeo, un.Quantity):
     '''
     Array of one or more continuous analog signals.
 
@@ -79,10 +80,10 @@ class AnalogSignal(BaseNeo, pq.Quantity):
     *Usage*::
 
         >>> from neo.core import AnalogSignal
-        >>> import quantities as pq
+
         >>>
         >>> sigarr = AnalogSignal([[1, 2, 3], [4, 5, 6]], units='V',
-        ...                            sampling_rate=1*pq.Hz)
+        ...                            sampling_rate=1*un.Hz)
         >>>
         >>> sigarr
         <AnalogSignal(array([[1, 2, 3],
@@ -148,13 +149,13 @@ class AnalogSignal(BaseNeo, pq.Quantity):
 
     _single_parent_objects = ('Segment', 'ChannelIndex')
     _quantity_attr = 'signal'
-    _necessary_attrs = (('signal', pq.Quantity, 2),
-                        ('sampling_rate', pq.Quantity, 0),
-                        ('t_start', pq.Quantity, 0))
+    _necessary_attrs = (('signal', un.Quantity, 2),
+                        ('sampling_rate', un.Quantity, 0),
+                        ('t_start', un.Quantity, 0))
     _recommended_attrs = BaseNeo._recommended_attrs
 
     def __new__(cls, signal, units=None, dtype=None, copy=True,
-                t_start=0 * pq.s, sampling_rate=None, sampling_period=None,
+                t_start=0 * un.s, sampling_rate=None, sampling_period=None,
                 name=None, file_origin=None, description=None,
                 **annotations):
         '''
@@ -168,12 +169,12 @@ def __new__(cls, signal, units=None, dtype=None, copy=True,
         if units is None:
             if not hasattr(signal, "units"):
                 raise ValueError("Units must be specified")
-        elif isinstance(signal, pq.Quantity):
+        elif isinstance(signal, un.Quantity):
             # could improve this test, what if units is a string?
             if units != signal.units:
                 signal = signal.rescale(units)
 
-        obj = pq.Quantity(signal, units=units, dtype=dtype, copy=copy).view(cls)
+        obj = un.Quantity(signal, units=units, dtype=dtype, copy=copy).view(cls)
 
         if obj.ndim == 1:
             obj.shape = (-1, 1)
@@ -189,7 +190,7 @@ def __new__(cls, signal, units=None, dtype=None, copy=True,
         return obj
 
     def __init__(self, signal, units=None, dtype=None, copy=True,
-                 t_start=0 * pq.s, sampling_rate=None, sampling_period=None,
+                 t_start=0 * un.s, sampling_rate=None, sampling_period=None,
                  name=None, file_origin=None, description=None,
                  **annotations):
         '''
@@ -235,7 +236,7 @@ def __array_finalize__(self, obj):
         copied over here.
         '''
         super(AnalogSignal, self).__array_finalize__(obj)
-        self._t_start = getattr(obj, '_t_start', 0 * pq.s)
+        self._t_start = getattr(obj, '_t_start', 0 * un.s)
         self._sampling_rate = getattr(obj, '_sampling_rate', None)
 
         # The additional arguments
@@ -281,11 +282,11 @@ def __getitem__(self, i):
         '''
         obj = super(AnalogSignal, self).__getitem__(i)
         if isinstance(i, int):  # a single point in time across all channels
-            obj = pq.Quantity(obj.magnitude, units=obj.units)
+            obj = un.Quantity(obj.magnitude, units=obj.units)
         elif isinstance(i, tuple):
             j, k = i
             if isinstance(j, int):  # extract a quantity array
-                obj = pq.Quantity(obj.magnitude, units=obj.units)
+                obj = un.Quantity(obj.magnitude, units=obj.units)
             else:
                 if isinstance(j, slice):
                     if j.start:
@@ -413,15 +414,15 @@ def rescale(self, units):
         Return a copy of the AnalogSignal converted to the specified
         units
         '''
-        to_dims = pq.quantity.validate_dimensionality(units)
+        to_dims = un.quantity.validate_dimensionality(units)
         if self.dimensionality == to_dims:
             to_u = self.units
             signal = np.array(self)
         else:
-            to_u = pq.Quantity(1.0, to_dims)
-            from_u = pq.Quantity(1.0, self.dimensionality)
+            to_u = un.Quantity(1.0, to_dims)
+            from_u = un.Quantity(1.0, self.dimensionality)
             try:
-                cf = pq.quantity.get_conversion_factor(from_u, to_u)
+                cf = un.quantity.get_conversion_factor(from_u, to_u)
             except AssertionError:
                 raise ValueError('Unable to convert between units of "%s" \
                                  and "%s"' % (from_u._dimensionality,

neo/core/block.py

@@ -27,7 +27,7 @@ class Block(Container):
 
         >>> from neo.core import (Block, Segment, ChannelIndex,
         ...                       AnalogSignal)
-        >>> from quantities import nA, kHz
+        >>> from neo.units import nA, kHz
         >>> import numpy as np
         >>>
         >>> # create a Block with 3 Segment and 2 ChannelIndex objects

neo/core/channelindex.py

@@ -11,7 +11,7 @@
 from __future__ import absolute_import, division, print_function
 
 import numpy as np
-import quantities as pq
+from neo import units as un
 
 from neo.core.container import Container
 
@@ -32,7 +32,7 @@ class ChannelIndex(Container):
 
         >>> from neo.core import (Block, Segment, ChannelIndex,
         ...                       AnalogSignal)
-        >>> from quantities import nA, kHz
+        >>> from neo.units import nA, kHz
         >>> import numpy as np
         >>>
         >>> # create a Block with 3 Segment and 2 ChannelIndex objects
@@ -120,7 +120,7 @@ class ChannelIndex(Container):
     _necessary_attrs = (('index', np.ndarray, 1, np.dtype('i')),)
     _recommended_attrs = ((('channel_names', np.ndarray, 1, np.dtype('S')),
                            ('channel_ids', np.ndarray, 1, np.dtype('i')),
-                           ('coordinates', pq.Quantity, 2)) +
+                           ('coordinates', un.Quantity, 2)) +
                           Container._recommended_attrs)
 
     def __init__(self, index, channel_names=None, channel_ids=None,

neo/core/epoch.py

@@ -12,10 +12,12 @@
 import sys
 
 import numpy as np
-import quantities as pq
+
 
 from neo.core.baseneo import BaseNeo, merge_annotations
 
+from neo import units as un
+
 PY_VER = sys.version_info[0]
 
 def _new_epoch(cls, times=None, durations=None, labels=None, units=None,
@@ -27,14 +29,14 @@ def _new_epoch(cls, times=None, durations=None, labels=None, units=None,
     return Epoch( times=times, durations=durations, labels=labels, units=units, name=name, file_origin=file_origin,
                  description=description, **annotations)
 
-class Epoch(BaseNeo, pq.Quantity):
+class Epoch(BaseNeo, un.Quantity):
     '''
     Array of epochs.
 
     *Usage*::
 
         >>> from neo.core import Epoch
-        >>> from quantities import s, ms
+        >>> from neo.units import s, ms
         >>> import numpy as np
         >>>
         >>> epc = Epoch(times=np.arange(0, 30, 10)*s,
@@ -67,16 +69,16 @@ class Epoch(BaseNeo, pq.Quantity):
 
     _single_parent_objects = ('Segment',)
     _quantity_attr = 'times'
-    _necessary_attrs = (('times', pq.Quantity, 1),
-                        ('durations', pq.Quantity, 1),
+    _necessary_attrs = (('times', un.Quantity, 1),
+                        ('durations', un.Quantity, 1),
                         ('labels', np.ndarray, 1, np.dtype('S')))
 
     def __new__(cls, times=None, durations=None, labels=None, units=None,
                 name=None, description=None, file_origin=None, **annotations):
         if times is None:
-            times = np.array([]) * pq.s
+            times = np.array([]) * un.s
         if durations is None:
-            durations = np.array([]) * pq.s
+            durations = np.array([]) * un.s
         if labels is None:
             labels = np.array([], dtype='S')
         if units is None:
@@ -90,16 +92,16 @@ def __new__(cls, times=None, durations=None, labels=None, units=None,
             if hasattr(units, 'dimensionality'):
                 dim = units.dimensionality
             else:
-                dim = pq.quantity.validate_dimensionality(units)
+                dim = un.quantity.validate_dimensionality(units)
         # check to make sure the units are time
         # this approach is much faster than comparing the
         # reference dimensionality
         if (len(dim) != 1 or list(dim.values())[0] != 1 or
-                not isinstance(list(dim.keys())[0], pq.UnitTime)):
+                not isinstance(list(dim.keys())[0], un.UnitTime)):
             ValueError("Unit %s has dimensions %s, not [time]" %
                        (units, dim.simplified))
 
-        obj = pq.Quantity.__new__(cls, times, units=dim)
+        obj = un.Quantity.__new__(cls, times, units=dim)
         obj.durations = durations
         obj.labels = labels
         obj.segment = None
@@ -147,7 +149,7 @@ def __repr__(self):
 
     @property
     def times(self):
-        return pq.Quantity(self)
+        return un.Quantity(self)
 
     def merge(self, other):
         '''