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_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_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_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_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_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_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_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"] = "vwx"
settings["overwrite"] = True
settings["description"] = "wxy"
settings["start_time"] = "xyz"
neurodata = nwb.NWB(**settings)
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_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_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_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 openNWB(siteNWB):
""" Open the given NWB file """
outputNWB = deriveOutputNWB(siteNWB)
if not os.path.isfile(outputNWB):
shutil.copyfile(siteNWB, outputNWB)
settings = {}
settings["filename"] = outputNWB
settings["auto_compress"] = True
settings["modify"] = True
try:
return nwb.NWB(**settings)
except:
raise NameError("Could not open the NWB file \"%s\"." % outputNWB)
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()
# 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"])
neurodata = nwb.NWB(**settings)
########################################################################
# create two electrical series, one with a single electrode and one with many
# then create a spike event series
# first create the electrode map
# example simulated recording is made from two 2-electrode probes named
# 'p0' and 'p1'. we need to define the locations of the electrodes
# relative to each probe, and the location of the probes
# electrode coordinates are in meters and their positions
# are relative to each other. the location of the probe itself is
# stored separately. using absolute coordinates here, if they are known,
# is still OK
electrode_map = [[0, 0, 0], [0, 1.5e-6, 0], [0, 0, 0], [0, 3.0e-5, 0]]
electrode_group = [ "p0", "p0", "p1", "p1" ]
def main():
module = PipelineModule()
jin = module.input_data()
infile = jin["input_nwb"]
outfile = jin["output_nwb"]
# a temporary nwb file must be created. this is that file's name
tmpfile = outfile + ".tmp"
# create temp file and make modifications to it using h5py
shutil.copy2(infile, tmpfile)
f = h5py.File(tmpfile, "a")
# change dataset names in acquisition time series to match that
# of existing ephys NWB files
# also rescale the contents of 'data' fields to match the scaling
# in original files
acq = f["acquisition/timeseries"]
sweep_nums = []
for k, v in iteritems(acq):
# parse out sweep number
try:
num = int(k[5:10])
except:
print("Error - unexpected sweep name encountered in IGOR nwb file")
print("Sweep called: '%s'" % k)
print("Expecting 5-digit sweep number between chars 5 and 9")
sys.exit(1)
swp = "Sweep_%d" % num
# rename objects
try:
acq.move(k, swp)
ts = acq[swp]
ts.move("stimulus_description", "aibs_stimulus_description")
except:
print("*** Error renaming HDF5 object in %s" % swp)
type_, value_, traceback_ = sys.exc_info()
print(traceback.print_tb(traceback_))
sys.exit(1)
# rescale contents of data so conversion is 1.0
try:
data = ts["data"]
scale = float(data.attrs["conversion"])
data[...] = data.value * scale
data.attrs["conversion"] = 1.0
except:
print("*** Error rescaling data in %s" % swp)
type_, value_, traceback_ = sys.exc_info()
print(traceback.print_tb(traceback_))
sys.exit(1)
# keep track of sweep numbers
sweep_nums.append("%d" % num)
###################################
#... ditto for stimulus time series
stim = f["stimulus/presentation"]
for k, v in iteritems(stim):
# parse out sweep number
try:
num = int(k[5:10])
except:
print("Error - unexpected sweep name encountered in IGOR nwb file")
print("Sweep called: '%s'" % k)
print("Expecting 5-digit sweep number between chars 5 and 9")
sys.exit(1)
swp = "Sweep_%d" % num
try:
stim.move(k, swp)
except:
print("Error renaming HDF5 group from %s to %s" % (k, swp))
sys.exit(1)
# rescale contents of data so conversion is 1.0
try:
ts = stim[swp]
data = ts["data"]
scale = float(data.attrs["conversion"])
data[...] = data.value * scale
data.attrs["conversion"] = 1.0
except:
print("*** Error rescaling data in %s" % swp)
type_, value_, traceback_ = sys.exc_info()
print(traceback.print_tb(traceback_))
sys.exit(1)
f.close()
####################################################################
# re-open file w/ nwb library and add indexing (epochs)
nd = nwb.NWB(filename=tmpfile, modify=True)
for num in sweep_nums:
ts = nd.file_pointer["acquisition/timeseries/Sweep_" + num]
# sweep epoch
t0 = ts["starting_time"].value
rate = float(ts["starting_time"].attrs["rate"])
n = float(ts["num_samples"].value)
t1 = t0 + (n - 1) * rate
ep = nd.create_epoch("Sweep_" + num, t0, t1)
ep.add_timeseries("stimulus", "stimulus/presentation/Sweep_" + num)
ep.add_timeseries("response", "acquisition/timeseries/Sweep_" + num)
ep.finalize()
if "CurrentClampSeries" in ts.attrs["ancestry"]:
# test pulse epoch
t0 = ts["starting_time"].value
t1 = t0 + PULSE_LEN
ep = nd.create_epoch("TestPulse_" + num, t0, t1)
ep.add_timeseries("stimulus", "stimulus/presentation/Sweep_" + num)
ep.add_timeseries("response",
"acquisition/timeseries/Sweep_" + num)
ep.finalize()
# experiment epoch
t0 = ts["starting_time"].value
t1 = t0 + (n - 1) * rate
t0 += EXPERIMENT_START_TIME
ep = nd.create_epoch("Experiment_" + num, t0, t1)
ep.add_timeseries("stimulus", "stimulus/presentation/Sweep_" + num)
ep.add_timeseries("response",
"acquisition/timeseries/Sweep_" + num)
ep.finalize()
nd.close()
# rescaling the contents of the data arrays causes the file to grow
# execute hdf5-repack to get it back to its original size
try:
print("Repacking hdf5 file with compression")
process = subprocess.Popen(
["h5repack", "-f", "GZIP=4", tmpfile, outfile],
stdout=subprocess.PIPE)
process.wait()
except:
print("Unable to run h5repack on temporary nwb file")
print("--------------------------------------------")
raise
try:
print("Removing temporary file")
os.remove(tmpfile)
except:
print("Unable to delete temporary file ('%s')" % tmpfile)
raise
# done (nothing to return)
module.write_output_data({})
