Get examples working

doc/source/index.rst

@@ -21,4 +21,5 @@ Table of Contents
    rawiolist
    releases
    authors
-   governance
+   governance
+   auto_examples/index

doc/source/rawio.rst

@@ -49,8 +49,8 @@ The :mod:`neo.rawio` API is less flexible than :mod:`neo.io` and has some limita
 
 For an intuitive comparison of :mod:`neo.io` and :mod:`neo.rawio` see:
 
-- :file:`example/read_file_neo_io.py`
-- :file:`example/read_file_neo_rawio.py`
+- :doc:`auto_examples/read_files_neo_io`
+- :doc:`auto_examples/read_files_neo_rawio`
 
 
 One benefit of the :mod:`neo.rawio` API is that a developer
@@ -61,6 +61,22 @@ objects or of the :mod:`quantities` package.
 Basic usage
 ===========
 
+.. Download example files
+
+.. ipython:: python
+   :suppress:
+
+   import os.path
+   from urllib.request import urlretrieve
+
+   url_repo = 'https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/'
+
+   for distantfile in ('plexon/File_plexon_2.plx', 'plexon/File_plexon_3.plx', 'blackrock/FileSpec2.3001.nev', 'blackrock/FileSpec2.3001.ns5'):
+       localfile = f'../examples/{distantfile.split("/")[1]}'
+       if not os.path.exists(localfile):
+          urlretrieve(url_repo + distantfile, localfile)
+
+
 First create a reader from a class:
 
 .. ipython::

examples/convert_to_nwb.py

@@ -0,0 +1,59 @@
+"""
+Converting to NWB using Neo
+===========================
+
+"""
+
+from urllib.request import urlretrieve
+from urllib.parse import quote
+from neo.io import get_io
+
+
+dataset_url = "https://object.cscs.ch/v1/AUTH_63ea6845b1d34ad7a43c8158d9572867/hbp-d000017_PatchClamp-GranuleCells_pub"
+
+folder = "GrC_Subject15_180116"
+
+#filenames = ["180116_0004 IV -70.abf", "180116_0005 CC step.abf", "180116_0006 EPSP.abf"]
+filenames = ["180116_0005 CC step.abf"]
+
+for filename in filenames:
+    datafile_url = f"{dataset_url}/{folder}/{quote(filename)}"
+    local_file = urlretrieve(datafile_url, filename)
+
+
+reader = get_io("180116_0005 CC step.abf")
+data = reader.read()
+
+global_metadata = {
+    "session_start_time": data[0].rec_datetime,
+    "identifier": data[0].file_origin,
+    "session_id": "180116_0005",
+    "institution": "University of Pavia",
+    "lab": "D'Angelo Lab",
+    "related_publications": "https://doi.org/10.1038/s42003-020-0953-x"
+}
+
+#data[0].annotate(**global_metadata)
+
+signal_metadata = {
+    "nwb_group": "acquisition",
+    "nwb_neurodata_type": ("pynwb.icephys", "PatchClampSeries"),
+    "nwb_electrode": {
+        "name": "patch clamp electrode",
+        "description": "The patch-clamp pipettes were pulled from borosilicate glass capillaries "
+                        "(Hilgenberg, Malsfeld, Germany) and filled with intracellular solution "
+                        "(K-gluconate based solution)",
+        "device": {
+           "name": "patch clamp electrode"
+        }
+    },
+    "nwb:gain": 1.0
+}
+
+for segment in data[0].segments:
+    signal = segment.analogsignals[0]
+    signal.annotate(**signal_metadata)
+
+from neo.io import NWBIO
+writer = NWBIO("GrC_Subject15_180116.nwb", mode="w", **global_metadata)
+writer.write(data)

examples/generated_data.py

@@ -1,5 +1,7 @@
 """
-This is an example for creating simple plots from various Neo structures.
+Creating simple plots from various Neo structures
+=================================================
+
 It includes a function that generates toy data.
 """
 

examples/imageseq.py

@@ -1,5 +1,7 @@
 """
-docstring needed here
+ImageSequences
+==============
+
 """
 
 from neo.core import ImageSequence

examples/plot_with_matplotlib.py

@@ -1,5 +1,7 @@
 """
-This is an example for plotting a Neo object with matplotlib.
+Plotting a Neo object with matplotlib
+=====================================
+
 """
 
 import urllib

examples/read_files_neo_io.py

@@ -1,5 +1,7 @@
 """
-This is an example for reading files with neo.io
+Reading files with neo.io
+=========================
+
 """
 
 import urllib

examples/read_files_neo_rawio.py

@@ -1,5 +1,7 @@
 """
-This is an example for reading files with neo.rawio
+Reading files with neo.rawio
+============================
+
 compare with read_files_neo_io.py
 """
 
@@ -52,12 +54,12 @@
 float_waveforms = reader.rescale_waveforms_to_float(raw_waveforms, dtype='float32', spike_channel_index=0)
 print(float_waveforms.shape, float_waveforms.dtype, float_waveforms[0, 0, :4])
 
-# Read event timestamps and times (take anotehr file)
+# Read event timestamps and times (take another file)
 distantfile = url_repo + 'plexon/File_plexon_2.plx'
 localfile = './File_plexon_2.plx'
 urllib.request.urlretrieve(distantfile, localfile)
 
-# Count event per channel
+# Count events per channel
 reader = PlexonRawIO(filename='File_plexon_2.plx')
 reader.parse_header()
 nb_event_channel = reader.event_channels_count()

examples/read_proxy_with_lazy_load.py

@@ -1,5 +1,6 @@
 """
-This is an example demonstrate the lazy load and proxy objects.
+Demonstration of lazy load and proxy objects
+============================================
 
 """
 

examples/roi_demo.py

@@ -1,5 +1,7 @@
 """
-Example of working with RegionOfInterest objects
+Working with RegionOfInterest objects
+=====================================
+
 """
 
 import matplotlib.pyplot as plt

neo/io/asciisignalio.py

@@ -268,8 +268,8 @@ def read_segment(self, lazy=False):
             else:
                 ana_sig = AnalogSignal(signal * self.units, sampling_rate=sampling_rate,
                                        t_start=t_start,
-                                       channel_index=self.usecols or np.arange(signal.shape[1]),
                                        name='multichannel')
+                ana_sig.array_annotate(channel_index=self.usecols or np.arange(signal.shape[1]))
                 seg.analogsignals.append(ana_sig)
         else:
             if self.timecolumn is not None and self.timecolumn < 0: