Merge branch 'master' into fix/neuralynxrawio_import

Author: JuliaSprenger

.circleci/config.yml

@@ -55,9 +55,12 @@ jobs:
       # run tests!
       - run:
           name: run tests
+          no_output_timeout: 20m
           command: |
             . venv/bin/activate
-            nosetests -v --with-coverage --cover-package=neo
+            nosetests -v --with-coverage --cover-package=neo --debug=neo.test
+      # note that we use --debug to get output while downloading files
+      # without this, CircleCI tends to time out because there's no output for a long time
 
       - run:
           name: coveralls

doc/source/grouping.rst

@@ -111,7 +111,7 @@ Each :class:`ChannelIndex` also contains the list of channels on which that neur
     block.channel_indexes.extend((chx0, chx1))
 
 
-Using :class:`ChannelView` and :class`Group`::
+Using :class:`ChannelView` and :class:`Group`::
 
     import numpy as np
     from quantities import ms, mV, kHz
@@ -136,7 +136,7 @@ Using :class:`ChannelView` and :class`Group`::
     # assign each spiketrain to a neuron (now using Group)
     units = []
     for i, spiketrain in enumerate(spiketrains):
-        unit = Group(spiketrain, name=f"Neuron #{i + 1}")
+        unit = Group([spiketrain], name=f"Neuron #{i + 1}")
         units.append(unit)
 
     # create a ChannelView of the signal for each unit, to show which channels the spikes come from
@@ -150,4 +150,4 @@ Using :class:`ChannelView` and :class`Group`::
 
 
 Now each putative neuron is represented by a :class:`Group` containing the spiktrains of that neuron
-and a view of the signal selecting only those channels from which the spikes were obtained.
+and a view of the signal selecting only those channels from which the spikes were obtained.

doc/source/rawio.rst

@@ -114,8 +114,17 @@ Read signal chunks of data and scale them::
 
 
 There are 3 ways to select a subset of channels: by index (0 based), by id or by name.
-By index is not ambiguous 0 to n-1 (included), for some IOs channel_names (and sometimes channel_ids) have no guarantees to
-be unique, in such cases it would raise an error.
+By index is unambiguous 0 to n-1 (included), whereas for some IOs channel_names
+(and sometimes channel_ids) have no guarantees to
+be unique. In such cases, using names or ids may raise an error.
+
+A selected subset of channels which is passed to get_analog_signal_chunk, get_analog_signal_size,
+or get_analog_signal_t_start has the additional restriction that all such channels must have
+the same t_start and signal_size.
+
+Such subsets of channels may be available in specific RawIOs by using the
+get_group_signal_channel_indexes method, if the RawIO has defined separate
+group_ids for each group with those common characteristics.
 
 Example with BlackrockRawIO for the file FileSpec2.3001::
 

neo/io/__init__.py

@@ -48,6 +48,7 @@
 * :attr:`RawBinarySignalIO`
 * :attr:`RawMCSIO`
 * :attr:`Spike2IO`
+* :attr:`SpikeGLXIO`
 * :attr:`StimfitIO`
 * :attr:`TdtIO`
 * :attr:`TiffIO`
@@ -195,6 +196,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: SpikeGLXIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.StimfitIO
 
     .. autoattribute:: extensions
@@ -273,6 +278,7 @@
 from neo.io.rawbinarysignalio import RawBinarySignalIO
 from neo.io.rawmcsio import RawMCSIO
 from neo.io.spike2io import Spike2IO
+from neo.io.spikeglxio import SpikeGLXIO
 from neo.io.stimfitio import StimfitIO
 from neo.io.tdtio import TdtIO
 from neo.io.tiffio import TiffIO
@@ -316,6 +322,7 @@
     RawBinarySignalIO,
     RawMCSIO,
     Spike2IO,
+    SpikeGLXIO,
     StimfitIO,
     TdtIO,
     TiffIO,

neo/io/spikeglxio.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.spikeglxrawio import SpikeGLXRawIO
+
+
+class SpikeGLXIO(SpikeGLXRawIO, BaseFromRaw):
+    __doc__ = SpikeGLXRawIO.__doc__
+    mode = 'dir'
+
+    def __init__(self, dirname):
+        SpikeGLXRawIO.__init__(self, dirname=dirname)
+        BaseFromRaw.__init__(self, dirname)

neo/rawio/__init__.py

@@ -28,6 +28,7 @@
 * :attr:`RawBinarySignalRawIO`
 * :attr:`RawMCSRawIO`
 * :attr:`Spike2RawIO`
+* :attr:`SpikeGLXRawIO`
 * :attr:`TdtRawIO`
 * :attr:`WinEdrRawIO`
 * :attr:`WinWcpRawIO`
@@ -97,6 +98,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.SpikeGLXRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.TdtRawIO
 
     .. autoattribute:: extensions
@@ -129,6 +134,7 @@
 from neo.rawio.rawbinarysignalrawio import RawBinarySignalRawIO
 from neo.rawio.rawmcsrawio import RawMCSRawIO
 from neo.rawio.spike2rawio import Spike2RawIO
+from neo.rawio.spikeglxrawio import SpikeGLXRawIO
 from neo.rawio.tdtrawio import TdtRawIO
 from neo.rawio.winedrrawio import WinEdrRawIO
 from neo.rawio.winwcprawio import WinWcpRawIO
@@ -150,6 +156,7 @@
     RawBinarySignalRawIO,
     RawMCSRawIO,
     Spike2RawIO,
+    SpikeGLXRawIO,
     TdtRawIO,
     WinEdrRawIO,
     WinWcpRawIO,

neo/rawio/baserawio.py

@@ -654,12 +654,32 @@ def _segment_t_stop(self, block_index, seg_index):
     ###
     # signal and channel zone
     def _get_signal_size(self, block_index, seg_index, channel_indexes):
+        """
+        Return the size of a set of AnalogSignals indexed by channel_indexes.
+
+        All channels indexed must have the same size and t_start.
+        """
         raise (NotImplementedError)
 
     def _get_signal_t_start(self, block_index, seg_index, channel_indexes):
+        """
+        Return the t_start of a set of AnalogSignals indexed by channel_indexes.
+
+        All channels indexed must have the same size and t_start.
+        """
         raise (NotImplementedError)
 
     def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, channel_indexes):
+        """
+        Return the samples from a set of AnalogSignals indexed by channel_indexes.
+
+        All channels indexed must have the same size and t_start.
+
+        RETURNS
+        -------
+            array of samples, with each requested channel in a column
+        """
+
         raise (NotImplementedError)
 
     ###

neo/rawio/examplerawio.py

@@ -25,8 +25,8 @@
     * copy paste neo/rawio/tests/test_examplerawio.py and do the same
 
   3. Step 3 : Create the neo.io class with the wrapper
-    * Create a file in neo/io/ that endith with "io.py"
-    * Create a that inherits both your RawIO class and BaseFromRaw class
+    * Create a file in neo/io/ that ends with "io.py"
+    * Create a class that inherits both your RawIO class and BaseFromRaw class
     * copy/paste from neo/io/exampleio.py
 
   4.Step 4 : IO test
@@ -47,7 +47,7 @@ class ExampleRawIO(BaseRawIO):
     """
     Class for "reading" fake data from an imaginary file.
 
-    For the user, it give acces to raw data (signals, event, spikes) as they
+    For the user, it gives access to raw data (signals, event, spikes) as they
     are in the (fake) file int16 and int64.
 
     For a developer, it is just an example showing guidelines for someone who wants
@@ -58,11 +58,11 @@ class ExampleRawIO(BaseRawIO):
       * Follow the :ref:`io_guiline`
 
     This fake IO:
-        * have 2 blocks
+        * has 2 blocks
         * blocks have 2 and 3 segments
-        * have 16 signal_channel sample_rate = 10000
-        * have 3 unit_channel
-        * have 2 event channel: one have *type=event*, the other have
+        * has 16 signal_channels sample_rate = 10000
+        * has 3 unit_channels
+        * has 2 event channels: one has *type=event*, the other has
           *type=epoch*
 
 
@@ -98,7 +98,7 @@ def _source_name(self):
     def _parse_header(self):
         # This is the central of a RawIO
         # we need to collect in the original format all
-        # informations needed for further fast acces
+        # informations needed for further fast access
         # at any place in the file
         # In short _parse_header can be slow but
         # _get_analogsignal_chunk need to be as fast as possible
@@ -107,12 +107,12 @@ def _parse_header(self):
         # This is mandatory!!!!
         # gain/offset/units are really important because
         # the scaling to real value will be done with that
-        # at the end real_signal = (raw_signal* gain + offset) * pq.Quantity(units)
+        # at the end real_signal = (raw_signal * gain + offset) * pq.Quantity(units)
         sig_channels = []
         for c in range(16):
             ch_name = 'ch{}'.format(c)
             # our channel id is c+1 just for fun
-            # Note that chan_id should be realated to
+            # Note that chan_id should be related to
             # original channel id in the file format
             # so that the end user should not be lost when reading datasets
             chan_id = c + 1
@@ -121,9 +121,9 @@ def _parse_header(self):
             units = 'uV'
             gain = 1000. / 2 ** 16
             offset = 0.
-            # group_id isonly for special cases when channel have diferents
+            # group_id is only for special cases when channels have different
             # sampling rate for instance. See TdtIO for that.
-            # Here this is the general case :all channel have the same characteritics
+            # Here this is the general case: all channel have the same characteritics
             group_id = 0
             sig_channels.append((ch_name, chan_id, sr, dtype, units, gain, offset, group_id))
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)