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_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_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_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_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_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_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()