def create_general_top(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general top test")
settings["overwrite"] = True
settings["description"] = "test top-level elements in /general"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(DATA_COLLECTION, "DATA_COLLECTION")
neurodata.set_metadata(EXPERIMENT_DESCRIPTION, "EXPERIMENT_DESCRIPTION")
neurodata.set_metadata(EXPERIMENTER, "EXPERIMENTER")
neurodata.set_metadata(INSTITUTION, "INSTITUTION")
neurodata.set_metadata(LAB, "LAB")
neurodata.set_metadata(NOTES, "NOTES")
neurodata.set_metadata(PROTOCOL, "PROTOCOL")
neurodata.set_metadata(PHARMACOLOGY, "PHARMACOLOGY")
neurodata.set_metadata(RELATED_PUBLICATIONS, "RELATED_PUBLICATIONS")
neurodata.set_metadata(SESSION_ID, "SESSION_ID")
neurodata.set_metadata(SLICES, "SLICES")
neurodata.set_metadata(STIMULUS, "STIMULUS")
neurodata.set_metadata(SURGERY, "SURGERY")
neurodata.set_metadata(VIRUS, "VIRUS")
#
neurodata.set_metadata_from_file("source_script", __file__)
#
neurodata.close()
def create_general_extra(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general extracellular test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/extracellular_ephys"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(EXTRA_ELECTRODE_MAP, [[1,1,1], [1,2,3]])
neurodata.set_metadata(EXTRA_ELECTRODE_GROUP, ["p1", "p2"])
neurodata.set_metadata(EXTRA_IMPEDANCE, [1.0e6, 2.0e6])
neurodata.set_metadata(EXTRA_FILTERING, "EXTRA_FILTERING")
neurodata.set_metadata(EXTRA_CUSTOM("EXTRA_CUSTOM"), "EXTRA_CUSTOM")
neurodata.set_metadata(EXTRA_SHANK_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(EXTRA_SHANK_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(EXTRA_SHANK_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(EXTRA_SHANK_CUSTOM("p1", "extra_shank_custom"), "EXTRA_SHANK_CUSTOM")
#
neurodata.set_metadata(EXTRA_SHANK_DESCRIPTION("p2"), "DESCRIPTION")
neurodata.set_metadata(EXTRA_SHANK_LOCATION("p2"), "LOCATION")
neurodata.set_metadata(EXTRA_SHANK_DEVICE("p2"), "DEVICE")
neurodata.set_metadata(EXTRA_SHANK_CUSTOM("p2", "extra_shank_custom"), "EXTRA_SHANK_CUSTOM")
#
neurodata.close()
def create_general_intra(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general intracellular test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/intracellular_ephys"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(INTRA_CUSTOM("intra_custom"), "INTRA_CUSTOM")
#
neurodata.set_metadata(INTRA_ELECTRODE_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(INTRA_ELECTRODE_FILTERING("p1"), "FILTERING")
neurodata.set_metadata(INTRA_ELECTRODE_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(INTRA_ELECTRODE_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(INTRA_ELECTRODE_RESISTANCE("p1"), "RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_SEAL("p1"), "SEAL")
neurodata.set_metadata(INTRA_ELECTRODE_SLICE("p1"), "SLICE")
neurodata.set_metadata(INTRA_ELECTRODE_INIT_ACCESS_RESISTANCE("p1"), "INITIAL_ACCESS_RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_CUSTOM("p1", "intra_electrode_custom"), "INTRA_ELECTRODE_CUSTOM")
#
neurodata.set_metadata(INTRA_ELECTRODE_DESCRIPTION("e2"), "DESCRIPTION")
neurodata.set_metadata(INTRA_ELECTRODE_FILTERING("e2"), "FILTERING")
neurodata.set_metadata(INTRA_ELECTRODE_DEVICE("e2"), "DEVICE")
neurodata.set_metadata(INTRA_ELECTRODE_LOCATION("e2"), "LOCATION")
neurodata.set_metadata(INTRA_ELECTRODE_RESISTANCE("e2"), "RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_SEAL("e2"), "SEAL")
neurodata.set_metadata(INTRA_ELECTRODE_SLICE("e2"), "SLICE")
neurodata.set_metadata(INTRA_ELECTRODE_INIT_ACCESS_RESISTANCE("e2"), "INITIAL_ACCESS_RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_CUSTOM("e2", "intra_electrode_custom"), "INTRA_ELECTRODE_CUSTOM")
#
neurodata.close()
def create_annotation_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("annotation example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test file with AnnotationSeries"
neurodata = nwb.NWB(**settings)
#
annot = neurodata.create_timeseries("AnnotationSeries", name, target)
annot.set_description("This is an AnnotationSeries with sample data")
annot.set_comment("The comment and description fields can store arbitrary human-readable data")
annot.set_source("Observation of Dr. J Doe")
#
annot.add_annotation("Rat in bed, beginning sleep 1", 15.0)
annot.add_annotation("Rat placed in enclosure, start run 1", 933.0)
annot.add_annotation("Rat taken out of enclosure, end run 1", 1456.0)
annot.add_annotation("Rat in bed, start sleep 2", 1461.0)
annot.add_annotation("Rat placed in enclosure, start run 2", 2401.0)
annot.add_annotation("Rat taken out of enclosure, end run 2", 3210.0)
annot.add_annotation("Rat in bed, start sleep 3", 3218.0)
annot.add_annotation("End sleep 3", 4193.0)
#
annot.finalize()
neurodata.close()
def create_general_extra(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier(
"general extracellular test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/extracellular_ephys"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(EXTRA_ELECTRODE_MAP, [[1, 1, 1], [1, 2, 3]])
neurodata.set_metadata(EXTRA_ELECTRODE_GROUP, ["p1", "p2"])
neurodata.set_metadata(EXTRA_IMPEDANCE, [1.0e6, 2.0e6])
neurodata.set_metadata(EXTRA_FILTERING, "EXTRA_FILTERING")
neurodata.set_metadata(EXTRA_CUSTOM("EXTRA_CUSTOM"), "EXTRA_CUSTOM")
neurodata.set_metadata(EXTRA_SHANK_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(EXTRA_SHANK_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(EXTRA_SHANK_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(EXTRA_SHANK_CUSTOM("p1", "extra_shank_custom"),
"EXTRA_SHANK_CUSTOM")
#
neurodata.set_metadata(EXTRA_SHANK_DESCRIPTION("p2"), "DESCRIPTION")
neurodata.set_metadata(EXTRA_SHANK_LOCATION("p2"), "LOCATION")
neurodata.set_metadata(EXTRA_SHANK_DEVICE("p2"), "DEVICE")
neurodata.set_metadata(EXTRA_SHANK_CUSTOM("p2", "extra_shank_custom"),
"EXTRA_SHANK_CUSTOM")
#
neurodata.close()
def create_iface_series(fname, newfile):
settings = {}
settings["filename"] = fname
if newfile:
settings["identifier"] = nwb.create_identifier(
"interface timeseries example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test interface timeseries file"
else:
settings["modify"] = True
neurodata = nwb.NWB(**settings)
#
mod = neurodata.create_module("test module")
iface = mod.create_interface("BehavioralEvents")
ts = neurodata.create_timeseries("TimeSeries", "Ones")
ts.set_data(np.ones(10),
unit="Event",
conversion=1.0,
resolution=float('nan'))
ts.set_value("num_samples", 10)
ts.set_time(np.arange(10))
iface.add_timeseries(ts)
iface.finalize()
mod.finalize()
#
neurodata.close()
def create_new_file(fname, identifier):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier(identifier)
settings["overwrite"] = True
settings["description"] = "softlink test"
return nwb.NWB(**settings)
def create_isi_iface(fname, name):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("reference image test")
settings["overwrite"] = True
settings["description"] = "reference image test"
neurodata = nwb.NWB(**settings)
module = neurodata.create_module(name)
iface = module.create_interface("ImagingRetinotopy")
iface.add_axis_1_phase_map([[1.0, 1.1, 1.2], [2.0, 2.1, 2.2]], "altitude",
.1, .1)
iface.add_axis_2_phase_map([[3.0, 3.1, 3.2], [4.0, 4.1, 4.2]],
"azimuth",
.1,
.1,
unit="degrees")
iface.add_axis_1_power_map([[0.1, 0.2, 0.3], [0.4, 0.5, 0.6]], .1, .1)
iface.add_sign_map([[-.1, .2, -.3], [.4, -.5, .6]])
iface.add_vasculature_image([[1, 0, 129], [2, 144, 0]],
height=.22,
width=.35)
iface.add_focal_depth_image([[1, 0, 129], [2, 144, 0]], bpp=8)
iface.finalize()
module.finalize()
neurodata.close()
def create_annotation_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("annotation example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test file with AnnotationSeries"
neurodata = nwb.NWB(**settings)
#
annot = neurodata.create_timeseries("AnnotationSeries", name, target)
annot.set_description("This is an AnnotationSeries with sample data")
annot.set_comment(
"The comment and description fields can store arbitrary human-readable data"
)
annot.set_source("Observation of Dr. J Doe")
#
annot.add_annotation("Rat in bed, beginning sleep 1", 15.0)
annot.add_annotation("Rat placed in enclosure, start run 1", 933.0)
annot.add_annotation("Rat taken out of enclosure, end run 1", 1456.0)
annot.add_annotation("Rat in bed, start sleep 2", 1461.0)
annot.add_annotation("Rat placed in enclosure, start run 2", 2401.0)
annot.add_annotation("Rat taken out of enclosure, end run 2", 3210.0)
annot.add_annotation("Rat in bed, start sleep 3", 3218.0)
annot.add_annotation("End sleep 3", 4193.0)
#
annot.finalize()
neurodata.close()
def create_linked_series(fname, root):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("link test")
settings["overwrite"] = True
settings["description"] = "time series link test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
#
first = neurodata.create_timeseries("TimeSeries", root+"1", "template")
first.ignore_time()
first.set_value("num_samples", 1)
first.set_data([1], unit="parsec", conversion=1, resolution=1e-12)
first.finalize()
#
second = neurodata.create_timeseries("TimeSeries", root+"2", "stimulus")
second.set_time([2])
second.set_value("num_samples", 1)
second.set_data_as_link(first)
second.finalize()
#
third = neurodata.create_timeseries("TimeSeries", root+"3", "acquisition")
third.set_time_as_link(second)
third.set_value("num_samples", 1)
third.set_data([3], unit="parsec", conversion=1, resolution=1e-9)
third.finalize()
#
neurodata.close()
def create_general_top(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general top test")
settings["overwrite"] = True
settings["description"] = "test top-level elements in /general"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(DATA_COLLECTION, "DATA_COLLECTION")
neurodata.set_metadata(EXPERIMENT_DESCRIPTION, "EXPERIMENT_DESCRIPTION")
neurodata.set_metadata(EXPERIMENTER, "EXPERIMENTER")
neurodata.set_metadata(INSTITUTION, "INSTITUTION")
neurodata.set_metadata(LAB, "LAB")
neurodata.set_metadata(NOTES, "NOTES")
neurodata.set_metadata(PROTOCOL, "PROTOCOL")
neurodata.set_metadata(PHARMACOLOGY, "PHARMACOLOGY")
neurodata.set_metadata(RELATED_PUBLICATIONS, "RELATED_PUBLICATIONS")
neurodata.set_metadata(SESSION_ID, "SESSION_ID")
neurodata.set_metadata(SLICES, "SLICES")
neurodata.set_metadata(STIMULUS, "STIMULUS")
neurodata.set_metadata(SURGERY, "SURGERY")
neurodata.set_metadata(VIRUS, "VIRUS")
#
neurodata.set_metadata_from_file("source_script", __file__)
#
neurodata.close()
def create_general_intra(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general optophysiology test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/optophysiology"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(IMAGE_CUSTOM("image_custom"), "IMAGE_CUSTOM")
#
neurodata.set_metadata(IMAGE_SITE_DESCRIPTION("p1"), "DESCRIPTION")
# MANUAL CHECK
# try storing string - -type system should balk
#neurodata.set_metadata(IMAGE_SITE_MANIFOLD("p1"), "MANIFOLD")
neurodata.set_metadata(IMAGE_SITE_MANIFOLD("p1"), [[[1,2,3],[2,3,4]],[[3,4,5],[4,5,6]]])
neurodata.set_metadata(IMAGE_SITE_INDICATOR("p1"), "INDICATOR")
neurodata.set_metadata(IMAGE_SITE_EXCITATION_LAMBDA("p1"), "EXCITATION_LAMBDA")
neurodata.set_metadata(IMAGE_SITE_CHANNEL_LAMBDA("p1", "red"), "CHANNEL_LAMBDA")
neurodata.set_metadata(IMAGE_SITE_CHANNEL_DESCRIPTION("p1", "red"), "DESCRIPTION")
neurodata.set_metadata(IMAGE_SITE_CHANNEL_LAMBDA("p1", "green"), "CHANNEL_LAMBDA")
neurodata.set_metadata(IMAGE_SITE_CHANNEL_DESCRIPTION("p1", "green"), "DESCRIPTION")
neurodata.set_metadata(IMAGE_SITE_IMAGING_RATE("p1"), "IMAGING_RATE")
neurodata.set_metadata(IMAGE_SITE_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(IMAGE_SITE_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(IMAGE_SITE_CUSTOM("p1", "image_site_custom"), "IMAGE_SITE_CUSTOM")
#
neurodata.close()
def create_empty_file(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("UnitTimes example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test file with spike times in processing module"
neurodata = nwb.NWB(**settings)
return neurodata
def create_empty_file(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("UnitTimes example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test file with spike times in processing module"
neurodata = nwb.NWB(**settings)
return neurodata
def create_refimage(fname, name):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("reference image test")
settings["overwrite"] = True
settings["description"] = "reference image test"
neurodata = nwb.NWB(**settings)
neurodata.create_reference_image([1, 2, 3, 4, 5], name, "raw", "test")
neurodata.close()
def create_refimage(fname, name):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("reference image test")
settings["overwrite"] = True
settings["description"] = "reference image test"
neurodata = nwb.NWB(**settings)
neurodata.create_reference_image([1,2,3,4,5], name, "raw", "test")
neurodata.close()
def create_softlink_reader(fname, name, src_fname, src_name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("softlink reader")
settings["overwrite"] = True
settings["description"] = "softlink test"
neurodata = nwb.NWB(**settings)
source = neurodata.create_timeseries("TimeSeries", name, target)
source.set_data_as_remote_link(src_fname, "acquisition/timeseries/"+src_name+"/data")
source.set_time([345])
source.finalize()
neurodata.close()
def create_softlink_reader(fname, name, src_fname, src_name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("softlink reader")
settings["overwrite"] = True
settings["description"] = "softlink test"
neurodata = nwb.NWB(**settings)
source = neurodata.create_timeseries("TimeSeries", name, target)
source.set_data_as_remote_link(
src_fname, "acquisition/timeseries/" + src_name + "/data")
source.set_time([345])
source.finalize()
neurodata.close()
def create_softlink_source(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("softlink source")
settings["overwrite"] = True
settings["description"] = "time series no data test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
source = neurodata.create_timeseries("TimeSeries", name, target)
source.set_data([234], unit="parsec", conversion=1, resolution=1e-3)
source.set_time([123])
source.finalize()
neurodata.close()
def create_softlink_source(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("softlink source")
settings["overwrite"] = True
settings["description"] = "time series no data test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
source = neurodata.create_timeseries("TimeSeries", name, target)
source.set_data([234], unit="parsec", conversion=1, resolution=1e-3)
source.set_time([123])
source.finalize()
neurodata.close()
def create_notime_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("notime example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test no time"
neurodata = nwb.NWB(**settings)
#
notime = neurodata.create_timeseries("TimeSeries", name, target)
notime.ignore_time()
notime.set_data([0], unit="n/a", conversion=1, resolution=1)
#
notime.finalize()
neurodata.close()
def create_notime_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("notime example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test no time"
neurodata = nwb.NWB(**settings)
#
notime = neurodata.create_timeseries("TimeSeries", name, target)
notime.ignore_time()
notime.set_data([0], unit="n/a", conversion=1, resolution=1)
#
notime.finalize()
neurodata.close()
def create_nodata_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("nodata example")
settings["overwrite"] = True
settings["description"] = "time series no data test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
#
nodata = neurodata.create_timeseries("TimeSeries", name, target)
nodata.ignore_data()
nodata.set_time([0])
#
nodata.finalize()
neurodata.close()
def create_startingtime_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("starting time test")
settings["overwrite"] = True
settings["description"] = "time series starting time test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
#
stime = neurodata.create_timeseries("TimeSeries", name, target)
stime.set_data([0, 1, 2, 3], unit="n/a", conversion=1, resolution=1)
stime.set_value("num_samples", 4)
stime.set_time_by_rate(0.125, 2)
#
stime.finalize()
neurodata.close()
def create_startingtime_series(fname, name, target):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("starting time test")
settings["overwrite"] = True
settings["description"] = "time series starting time test"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
#
stime = neurodata.create_timeseries("TimeSeries", name, target)
stime.set_data([0, 1, 2, 3], unit="n/a", conversion=1, resolution=1)
stime.set_value("num_samples", 4)
stime.set_time_by_rate(0.125, 2)
#
stime.finalize()
neurodata.close()
def create_general_subject(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general top test")
settings["overwrite"] = True
settings["description"] = "test top-level elements in /general"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(SUBJECT, "SUBJECT")
neurodata.set_metadata(SUBJECT_ID, "SUBJECT_ID")
neurodata.set_metadata(SPECIES, "SPECIES")
neurodata.set_metadata(GENOTYPE, "GENOTYPE")
neurodata.set_metadata(SEX, "SEX")
neurodata.set_metadata(AGE, "AGE")
neurodata.set_metadata(WEIGHT, "WEIGHT")
#
neurodata.close()
def create_general_optogen(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("metadata optogenetic test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/optogentics"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(OPTOGEN_CUSTOM("optogen_custom"), "OPTOGEN_CUSTOM")
#
neurodata.set_metadata(OPTOGEN_SITE_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(OPTOGEN_SITE_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(OPTOGEN_SITE_LAMBDA("p1"), "LAMBDA")
neurodata.set_metadata(OPTOGEN_SITE_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(OPTOGEN_SITE_CUSTOM("p1", "optogen_site_custom"), "OPTOGEN_SITE_CUSTOM")
#
neurodata.close()
def create_general_subject(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("general top test")
settings["overwrite"] = True
settings["description"] = "test top-level elements in /general"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(SUBJECT, "SUBJECT")
neurodata.set_metadata(SUBJECT_ID, "SUBJECT_ID")
neurodata.set_metadata(SPECIES, "SPECIES")
neurodata.set_metadata(GENOTYPE, "GENOTYPE")
neurodata.set_metadata(SEX, "SEX")
neurodata.set_metadata(AGE, "AGE")
neurodata.set_metadata(WEIGHT, "WEIGHT")
#
neurodata.close()
def create_isi_iface(fname, name):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("reference image test")
settings["overwrite"] = True
settings["description"] = "reference image test"
neurodata = nwb.NWB(**settings)
module = neurodata.create_module(name)
iface = module.create_interface("ImagingRetinotopy")
iface.add_axis_1_phase_map([[1.0, 1.1, 1.2],[2.0,2.1,2.2]], "altitude", .1, .1)
iface.add_axis_2_phase_map([[3.0, 3.1, 3.2],[4.0,4.1,4.2]], "azimuth", .1, .1, unit="degrees")
iface.add_axis_1_power_map([[0.1, 0.2, 0.3],[0.4, 0.5, 0.6]], .1, .1)
iface.add_sign_map([[-.1, .2, -.3],[.4,-.5,.6]])
iface.add_vasculature_image([[1,0,129],[2,144,0]], height=.22, width=.35)
iface.add_focal_depth_image([[1,0,129],[2,144,0]], bpp=8)
iface.finalize()
module.finalize()
neurodata.close()
def create_general_optogen(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("metadata optogenetic test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/optogentics"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(OPTOGEN_CUSTOM("optogen_custom"), "OPTOGEN_CUSTOM")
#
neurodata.set_metadata(OPTOGEN_SITE_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(OPTOGEN_SITE_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(OPTOGEN_SITE_LAMBDA("p1"), "LAMBDA")
neurodata.set_metadata(OPTOGEN_SITE_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(OPTOGEN_SITE_CUSTOM("p1", "optogen_site_custom"),
"OPTOGEN_SITE_CUSTOM")
#
neurodata.close()
def create_general_intra(fname):
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier(
"general intracellular test")
settings["overwrite"] = True
settings["description"] = "test elements in /general/intracellular_ephys"
neurodata = nwb.NWB(**settings)
#
neurodata.set_metadata(INTRA_CUSTOM("intra_custom"), "INTRA_CUSTOM")
#
neurodata.set_metadata(INTRA_ELECTRODE_DESCRIPTION("p1"), "DESCRIPTION")
neurodata.set_metadata(INTRA_ELECTRODE_FILTERING("p1"), "FILTERING")
neurodata.set_metadata(INTRA_ELECTRODE_DEVICE("p1"), "DEVICE")
neurodata.set_metadata(INTRA_ELECTRODE_LOCATION("p1"), "LOCATION")
neurodata.set_metadata(INTRA_ELECTRODE_RESISTANCE("p1"), "RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_SEAL("p1"), "SEAL")
neurodata.set_metadata(INTRA_ELECTRODE_SLICE("p1"), "SLICE")
neurodata.set_metadata(INTRA_ELECTRODE_INIT_ACCESS_RESISTANCE("p1"),
"INITIAL_ACCESS_RESISTANCE")
neurodata.set_metadata(
INTRA_ELECTRODE_CUSTOM("p1", "intra_electrode_custom"),
"INTRA_ELECTRODE_CUSTOM")
#
neurodata.set_metadata(INTRA_ELECTRODE_DESCRIPTION("e2"), "DESCRIPTION")
neurodata.set_metadata(INTRA_ELECTRODE_FILTERING("e2"), "FILTERING")
neurodata.set_metadata(INTRA_ELECTRODE_DEVICE("e2"), "DEVICE")
neurodata.set_metadata(INTRA_ELECTRODE_LOCATION("e2"), "LOCATION")
neurodata.set_metadata(INTRA_ELECTRODE_RESISTANCE("e2"), "RESISTANCE")
neurodata.set_metadata(INTRA_ELECTRODE_SEAL("e2"), "SEAL")
neurodata.set_metadata(INTRA_ELECTRODE_SLICE("e2"), "SLICE")
neurodata.set_metadata(INTRA_ELECTRODE_INIT_ACCESS_RESISTANCE("e2"),
"INITIAL_ACCESS_RESISTANCE")
neurodata.set_metadata(
INTRA_ELECTRODE_CUSTOM("e2", "intra_electrode_custom"),
"INTRA_ELECTRODE_CUSTOM")
#
neurodata.close()
def create_iface_series(fname, newfile):
settings = {}
settings["filename"] = fname
if newfile:
settings["identifier"] = nwb.create_identifier("interface timeseries example")
settings["overwrite"] = True
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
settings["description"] = "Test interface timeseries file"
else:
settings["modify"] = True
neurodata = nwb.NWB(**settings)
#
mod = neurodata.create_module("test module")
iface = mod.create_interface("BehavioralEvents")
ts = neurodata.create_timeseries("TimeSeries", "Ones")
ts.set_data(np.ones(10), unit="Event", conversion=1.0, resolution=float('nan'))
ts.set_value("num_samples", 10)
ts.set_time(np.arange(10))
iface.add_timeseries(ts)
iface.finalize()
mod.finalize()
#
neurodata.close()
for analysis using drifting gratings, not necessarily the stack of all
frames displayed by the graphics card.
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_abstract_features.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("abstract-feature example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings["description"] = "Test file demonstrating use of the AbstractFeatureSeries"
# create the NWB object. this manages the file
print("Creating " + settings["filename"])
experiment, for example "rat placed in enclosure" or "observed
start of seizure activity".
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_annotations.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("annotation example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings[
"description"] = "Test file demonstrating use of the AbstractFeatureSeries"
Store extracellular ephys data
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_extracellular_ephys.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("extracellular ephys example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings["description"] = "Test file demonstrating a simple extracellular ephys recording"
# create the NWB object. this manages the file
print("Creating " + settings["filename"])
experiment, for example "rat placed in enclosure" or "observed
start of seizure activity".
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_annotations.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("annotation example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings["description"] = "Test file demonstrating use of the AbstractFeatureSeries"
# create the NWB object. this manages the file
this behavior is only determinable by post-processing of acquired
data.
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_behavior.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("behavioral interval example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings["description"] = "Test file demonstrating use of the BehavioralEpochs module interface"
# create the NWB object. this manages the file
print("Creating " + settings["filename"])
the XY delta for each imaging frame necessary to correct for motion.
A third time series is created pointing to the corrected image.
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_motion_correction_2.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("motion correction example 2")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings["description"] = "Test file demonstrating use of the MotionCorrection interface with two cameras"
# create the NWB object. this manages the file
print("Creating " + settings["filename"])
import h5py
import sys
import nwb
import test_utils as ut
import time
# creates file and modifies it multiple times
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("Modification example")
settings["overwrite"] = True
settings["description"] = "Modified empty file"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
neurodata.close()
#time.sleep(1)
settings = {}
settings["filename"] = fname
settings["overwrite"] = False
settings["modify"] = True
neurodata = nwb.NWB(**settings)
neurodata.close()
#time.sleep(1)
the XY delta for each imaging frame necessary to correct for motion.
A third time series is created pointing to the corrected image.
"""
########################################################################
# create a new NWB file
# several settings are specified when doing so. these can be supplied within
# the NWB constructor or defined in a dict, as in in this example
settings = {}
settings["filename"] = "sample_motion_correction.nwb"
# each file should have a descriptive globally unique identifier
# that specifies the lab and this experiment session
# the function nwb.create_identifier() is recommended to use as it takes
# the string and appends the present date and time
settings["identifier"] = nwb.create_identifier("motion correction example")
# indicate that it's OK to overwrite exting file
settings["overwrite"] = True
# specify the start time of the experiment. all times in the NWB file
# are relative to experiment start time
# if the start time is not specified the present time will be used
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
# provide one or two sentences that describe the experiment and what
# data is in the file
settings[
"description"] = "Test file demonstrating use of the MotionCorrection interface"
# create the NWB object. this manages the file
import sys
import nwb
from nwb.nwbco import *
import test_utils as ut
import time
# creates file and modifies it multiple times
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
settings = {}
settings["filename"] = fname
settings["identifier"] = nwb.create_identifier("Modification example")
settings["overwrite"] = True
settings["description"] = "Modified empty file"
settings["start_time"] = "Sat Jul 04 2015 3:14:16"
neurodata = nwb.NWB(**settings)
neurodata.close()
#time.sleep(1)
settings = {}
settings["filename"] = fname
settings["overwrite"] = False
settings["modify"] = True
neurodata = nwb.NWB(**settings)
neurodata.set_metadata(INSTITUTION, "Allen Institute for Brain Science")
neurodata.close()
