Merge branch 'dev' into fix/one_photon_series

docs/gallery/advanced_io/linking_data.py

@@ -58,6 +58,8 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_linking_data.png'
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil.tz import tzlocal
 from pynwb import NWBFile
 from pynwb import TimeSeries
@@ -66,7 +68,6 @@
 
 # Create the base data
 start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
-create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
 data = np.arange(1000).reshape((100, 10))
 timestamps = np.arange(100)
 filename1 = 'external1_example.nwb'
@@ -75,36 +76,45 @@
 filename4 = 'external_linkdataset_example.nwb'
 
 # Create the first file
-nwbfile1 = NWBFile(session_description='demonstrate external files',
-                   identifier='NWBE1',
-                   session_start_time=start_time,
-                   file_create_date=create_date)
+nwbfile1 = NWBFile(
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
+)
 # Create the second file
 test_ts1 = TimeSeries(name='test_timeseries1',
                       data=data,
                       unit='SIunit',
                       timestamps=timestamps)
 nwbfile1.add_acquisition(test_ts1)
+
 # Write the first file
-io = NWBHDF5IO(filename1, 'w')
-io.write(nwbfile1)
-io.close()
+with NWBHDF5IO(filename1, 'w') as io:
+    io.write(nwbfile1)
 
 # Create the second file
-nwbfile2 = NWBFile(session_description='demonstrate external files',
-                   identifier='NWBE2',
-                   session_start_time=start_time,
-                   file_create_date=create_date)
+nwbfile2 = NWBFile(
+    session_description='demonstrate external files',
+    identifier=str(uuid4()),
+    session_start_time=start_time,
+)
 # Create the second file
-test_ts2 = TimeSeries(name='test_timeseries2',
-                      data=data,
-                      unit='SIunit',
-                      timestamps=timestamps)
+test_ts2 = TimeSeries(
+    name='test_timeseries2',
+    data=data,
+    unit='SIunit',
+    timestamps=timestamps,
+)
 nwbfile2.add_acquisition(test_ts2)
+
 # Write the second file
-io = NWBHDF5IO(filename2, 'w')
-io.write(nwbfile2)
-io.close()
+with NWBHDF5IO(filename2, 'w') as io:
+    io.write(nwbfile2)
 
 
 #####################
@@ -117,10 +127,11 @@
 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 # Create the first file
-nwbfile4 = NWBFile(session_description='demonstrate external files',
-                   identifier='NWBE4',
-                   session_start_time=start_time,
-                   file_create_date=create_date)
+nwbfile4 = NWBFile(
+    session_description='demonstrate external files',
+    identifier=str(uuid4()),
+    session_start_time=start_time,
+)
 
 
 ####################
@@ -142,10 +153,12 @@
 # To link to the dataset we can simply assign the data object (here `` timeseries_1.data``) to a new ``TimeSeries``
 
 # Create a new timeseries that links to our data
-test_ts4 = TimeSeries(name='test_timeseries4',
-                      data=timeseries_1_data,   # <-------
-                      unit='SIunit',
-                      timestamps=timestamps)
+test_ts4 = TimeSeries(
+    name='test_timeseries4',
+    data=timeseries_1_data,   # <-------
+    unit='SIunit',
+    timestamps=timestamps,
+)
 nwbfile4.add_acquisition(test_ts4)
 
 ####################
@@ -158,23 +171,22 @@
 from hdmf.backends.hdf5.h5_utils import H5DataIO
 
 # Create another timeseries that links to the same data
-test_ts5 = TimeSeries(name='test_timeseries5',
-                      data=H5DataIO(data=timeseries_1_data,     # <-------
-                                    link_data=True),            # <-------
-                      unit='SIunit',
-                      timestamps=timestamps)
+test_ts5 = TimeSeries(
+    name='test_timeseries5',
+    data=H5DataIO(data=timeseries_1_data,     # <-------
+                  link_data=True),            # <-------
+    unit='SIunit',
+    timestamps=timestamps,
+)
 nwbfile4.add_acquisition(test_ts5)
 
 ####################
 # Step 4: Write the data
 # ^^^^^^^^^^^^^^^^^^^^^^^
 #
-from pynwb import NWBHDF5IO
-
-io4 = NWBHDF5IO(filename4, 'w')
-io4.write(nwbfile4,
-          link_data=True)     # <-------- Specify default behavior to link rather than copy data
-io4.close()
+with NWBHDF5IO(filename4, 'w') as io4:
+    io4.write(nwbfile4,
+              link_data=True)     # <-------- Specify default behavior to link rather than copy data
 io1.close()
 
 #####################
@@ -230,17 +242,17 @@
 #
 
 # Create a new NWBFile that links to the external timeseries
-nwbfile3 = NWBFile(session_description='demonstrate external files',
-                   identifier='NWBE3',
-                   session_start_time=start_time,
-                   file_create_date=create_date)
+nwbfile3 = NWBFile(
+    session_description='demonstrate external files',
+    identifier=str(uuid4()),
+    session_start_time=start_time,
+)
 nwbfile3.add_acquisition(timeseries_1)             # <--------
 nwbfile3.add_acquisition(timeseries_2)             # <--------
 
 # Write our third file that includes our two timeseries as external links
-io3 = NWBHDF5IO(filename3, 'w', manager=manager)
-io3.write(nwbfile3)
-io3.close()
+with NWBHDF5IO(filename3, 'w', manager=manager) as io3:
+    io3.write(nwbfile3)
 io1.close()
 io2.close()
 

docs/gallery/domain/brain_observatory.py

@@ -17,8 +17,6 @@
 #     :url: https://gist.githubusercontent.com/nicain/82e6b3d8f9ff5b85ef01a582e41e2389/raw/
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_allenbrainobservatory.png'
-from datetime import datetime
-from dateutil.tz import tzlocal
 
 from allensdk.core.brain_observatory_cache import BrainObservatoryCache
 import allensdk.brain_observatory.stimulus_info as si
@@ -61,7 +59,6 @@
     session_description='Allen Brain Observatory dataset',
     identifier=str(metadata['ophys_experiment_id']),
     session_start_time=metadata['session_start_time'],
-    file_create_date=datetime.now(tzlocal())
 )
 
 

docs/gallery/domain/ecephys.py

@@ -23,6 +23,8 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_ecephys.png'
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil.tz import tzlocal
 
 import numpy as np
@@ -38,14 +40,13 @@
 
 nwbfile = NWBFile(
     session_description="my first synthetic recording",
-    identifier="EXAMPLE_ID",
+    identifier=str(uuid4()),
     session_start_time=datetime.now(tzlocal()),
-    experimenter="Dr. Bilbo Baggins",
+    experimenter=["Baggins, Bilbo", ],
     lab="Bag End Laboratory",
     institution="University of Middle Earth at the Shire",
-    experiment_description="I went on an adventure with thirteen dwarves "
-    "to reclaim vast treasures.",
-    session_id="LONELYMTN",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
 )
 
 #######################

docs/gallery/domain/icephys.py

@@ -24,16 +24,22 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_icephys_sweeptable.png'
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil.tz import tzlocal
 from pynwb import NWBFile
 import numpy as np
 
-nwbfile = NWBFile('my first synthetic recording', 'EXAMPLE_ID', datetime.now(tzlocal()),
-                  experimenter='Dr. Bilbo Baggins',
-                  lab='Bag End Laboratory',
-                  institution='University of Middle Earth at the Shire',
-                  experiment_description='I went on an adventure with thirteen dwarves to reclaim vast treasures.',
-                  session_id='LONELYMTN')
+nwbfile = NWBFile(
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
+)
 
 #######################
 # Device metadata

docs/gallery/domain/images.py

@@ -20,10 +20,13 @@
 """
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_image_data.png'
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil import tz
 
 import numpy as np
 from PIL import Image
+from dateutil.tz import tzlocal
 
 from pynwb import NWBFile, NWBHDF5IO
 from pynwb.base import Images
@@ -48,14 +51,14 @@
 session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
 
 nwbfile = NWBFile(
-    session_description="Mouse exploring an open field",  # required
-    identifier="Mouse5_Day3",  # required
-    session_start_time=session_start_time,  # required
-    session_id="session_1234",  # optional
-    experimenter="My Name",  # optional
-    lab="My Lab Name",  # optional
-    institution="University of My Institution",  # optional
-    related_publications="DOI:10.1016/j.neuron.2016.12.011",  # optional
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
 )
 
 nwbfile

docs/gallery/domain/ophys.py

@@ -21,6 +21,8 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_ophys.png'
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil.tz import tzlocal
 
 import numpy as np
@@ -39,15 +41,14 @@
 
 
 nwbfile = NWBFile(
-    'my first synthetic recording',
-    'EXAMPLE_ID',
-    datetime.now(tzlocal()),
-    experimenter='Dr. Bilbo Baggins',
-    lab='Bag End Laboratory',
-    institution='University of Middle Earth at the Shire',
-    experiment_description='I went on an adventure with thirteen dwarves '
-                           'to reclaim vast treasures.',
-    session_id='LONELYMTN'
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
 )
 
 ####################

docs/gallery/domain/plot_behavior.py

@@ -38,9 +38,11 @@
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_behavior.png'
 
 from datetime import datetime
+from uuid import uuid4
 
 import numpy as np
 from dateutil import tz
+from dateutil.tz import tzlocal
 from pynwb.misc import IntervalSeries
 
 from pynwb.epoch import TimeIntervals
@@ -67,14 +69,14 @@
 session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
 
 nwbfile = NWBFile(
-    session_description="Mouse exploring an open field",  # required
-    identifier="Mouse5_Day3",  # required
-    session_start_time=session_start_time,  # required
-    session_id="session_1234",  # optional
-    experimenter="My Name",  # optional
-    lab="My Lab Name",  # optional
-    institution="University of My Institution",  # optional
-    related_publications="DOI:10.1016/j.neuron.2016.12.011",  # optional
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
 )
 
 nwbfile

docs/gallery/domain/plot_icephys.py

@@ -81,6 +81,8 @@
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_icephys.png'
 # Standard Python imports
 from datetime import datetime
+from uuid import uuid4
+
 from dateutil.tz import tzlocal
 import numpy as np
 import pandas
@@ -211,14 +213,14 @@
 
 # Create the file
 nwbfile = NWBFile(
-    session_description='my first synthetic recording',
-    identifier='EXAMPLE_ID',
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
     session_start_time=datetime.now(tzlocal()),
-    experimenter='Dr. Bilbo Baggins',
-    lab='Bag End Laboratory',
-    institution='University of Middle Earth at the Shire',
-    experiment_description='I went on an adventure with thirteen dwarves to reclaim vast treasures.',
-    session_id='LONELYMTN'
+    experimenter=["Baggins, Bilbo", ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
 )
 
 #####################################################################