def test_axis(fname, iname, num):
val = ut.verify_present(fname, iname, "axis_"+num+"_phase_map")
if len(val) != 2 or len(val[0]) != 3:
ut.error("Checking axis-"+num, "wrong dimension")
if num == "1":
if val[0][0] != 1.0:
ut.error("Checking axis-"+num, "wrong contents")
elif num == "2":
if val[0][0] != 3.0:
ut.error("Checking axis-"+num+" contents", "wrong contents")
val = ut.verify_attribute_present(fname, iname+"/axis_"+num+"_phase_map", "unit")
if not ut.strcmp(val, "degrees"):
ut.error("Checking axis-"+num+" unit", "Wrong value")
val = ut.verify_attribute_present(fname, iname+"/axis_"+num+"_phase_map", "dimension")
if val[0] != 2 or val[1] != 3:
ut.error("Double-checking axis-"+num+" dimension", "Wrong value")
val = ut.verify_attribute_present(fname, iname+"/axis_"+num+"_phase_map", "field_of_view")
if val[0] != .1 or val[1] != .1:
ut.error("Checking axis-"+num+" field-of-view", "Wrong value")
# now check power map. it only exists for axis 1
if num == "1":
val = ut.verify_present(fname, iname, "axis_"+num+"_phase_map")
if len(val) != 2 or len(val[0]) != 3:
ut.error("Checking axis-"+num+" power map", "wrong dimension")
val = ut.verify_attribute_present(fname, iname+"/axis_"+num+"_power_map", "dimension")
if val[0] != 2 or val[1] != 3:
ut.error("Double-checking axis-"+num+"-power dimension", "Wrong value")
val = ut.verify_attribute_present(fname, iname+"/axis_"+num+"_power_map", "field_of_view")
if val[0] != .1 or val[1] != .1:
ut.error("Checking axis-"+num+"-power field-of-view", "Wrong value")
def test_append():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
name1 = "annot1"
name2 = "annot2"
create_annotation_series(fname, name1, "acquisition", True)
create_annotation_series(fname, name2, "acquisition", False)
ut.verify_timeseries(fname, name1, "acquisition/timeseries", "TimeSeries")
ut.verify_timeseries(fname, name1, "acquisition/timeseries", "AnnotationSeries")
ut.verify_timeseries(fname, name2, "acquisition/timeseries", "TimeSeries")
ut.verify_timeseries(fname, name2, "acquisition/timeseries", "AnnotationSeries")
ut.verify_attribute_present(fname, "file_create_date", "modification_time")
def test_ts_link():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
root = "root"
create_linked_series(fname, root)
ut.verify_timeseries(fname, root + "1", "stimulus/templates", "TimeSeries")
ut.verify_timeseries(fname, root + "2", "stimulus/presentation",
"TimeSeries")
ut.verify_timeseries(fname, root + "3", "acquisition/timeseries",
"TimeSeries")
##################################################
# make sure data is present in ts using link
val = ut.verify_present(fname, "stimulus/presentation/root2", "data")
if val[0] != 1:
ut.error("Checking link content", "Incorrect value")
# make sure link is documented
val = ut.verify_attribute_present(fname, "stimulus/presentation/root2",
"data_link")
if not ut.search_for_substring(val, "root1"):
ut.error("Checking attribute data_link", "Name missing")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute data_link", "Name missing")
val = ut.verify_attribute_present(fname, "stimulus/templates/root1",
"data_link")
if not ut.search_for_substring(val, "root1"):
ut.error("Checking attribute data_link", "Name missing")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute data_link", "Name missing")
##################################################
# make sure timestamps is present in ts using link
val = ut.verify_present(fname, "acquisition/timeseries/root3",
"timestamps")
if val[0] != 2:
ut.error("Checking link content", "Incorrect value")
# make sure link is documented
val = ut.verify_attribute_present(fname, "stimulus/presentation/root2",
"timestamp_link")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute timestamp_link", "Name missing")
if not ut.search_for_substring(val, "root3"):
ut.error("Checking attribute timestamp_link", "Name missing")
val = ut.verify_attribute_present(fname, "acquisition/timeseries/root3",
"timestamp_link")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute timestamp_link", "Name missing")
if not ut.search_for_substring(val, "root3"):
ut.error("Checking attribute timestamp_link", "Name missing")
def test_image(fname, iname, img):
val = ut.verify_present(fname, iname, img)
if len(val) != 2 or len(val[0]) != 3:
ut.error("Checking image "+img, "wrong dimension")
if val[1][1] != 144:
ut.error("Checking image "+img, "wrong contents")
val = ut.verify_attribute_present(fname, iname+"/"+img, "format")
if not ut.strcmp(val, "raw"):
ut.error("Checking image "+img+" format", "wrong contents")
val = ut.verify_attribute_present(fname, iname+"/"+img, "dimension")
if len(val) != 2 or val[0] != 2 or val[1] != 3:
ut.error("Checking image "+img+" dimension", "wrong contents")
val = ut.verify_attribute_present(fname, iname+"/"+img, "bits_per_pixel")
if val != 8:
ut.error("Checking image "+img+" bpp", "wrong contents")
def test_general_top():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
create_general_top(fname)
test_field(fname, "DATA_COLLECTION")
test_field(fname, "EXPERIMENT_DESCRIPTION")
test_field(fname, "EXPERIMENTER")
test_field(fname, "INSTITUTION")
test_field(fname, "LAB")
test_field(fname, "NOTES")
test_field(fname, "PROTOCOL")
test_field(fname, "PHARMACOLOGY")
test_field(fname, "RELATED_PUBLICATIONS")
test_field(fname, "SESSION_ID")
test_field(fname, "SLICES")
test_field(fname, "STIMULUS")
test_field(fname, "SURGERY")
test_field(fname, "VIRUS")
val = ut.verify_present(fname, "general/", "source_script")
if len(val) < 1000:
ut.error("Checking metadata_from_file", "unexpected field size")
val = ut.verify_attribute_present(fname, "general/source_script",
"neurodata_type")
if val != "Custom" and val != b"Custom":
ut.error("Checking custom tag", "neurodata_type incorrect")
def test_append():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
name1 = "annot1"
name2 = "annot2"
create_annotation_series(fname, name1, "acquisition", True)
create_annotation_series(fname, name2, "acquisition", False)
ut.verify_timeseries(fname, name1, "acquisition/timeseries", "TimeSeries")
ut.verify_timeseries(fname, name1, "acquisition/timeseries",
"AnnotationSeries")
ut.verify_timeseries(fname, name2, "acquisition/timeseries", "TimeSeries")
ut.verify_timeseries(fname, name2, "acquisition/timeseries",
"AnnotationSeries")
ut.verify_attribute_present(fname, "file_create_date", "modification_time")
def test_general_top():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
create_general_top(fname)
test_field(fname, "DATA_COLLECTION")
test_field(fname, "EXPERIMENT_DESCRIPTION")
test_field(fname, "EXPERIMENTER")
test_field(fname, "INSTITUTION")
test_field(fname, "LAB")
test_field(fname, "NOTES")
test_field(fname, "PROTOCOL")
test_field(fname, "PHARMACOLOGY")
test_field(fname, "RELATED_PUBLICATIONS")
test_field(fname, "SESSION_ID")
test_field(fname, "SLICES")
test_field(fname, "STIMULUS")
test_field(fname, "SURGERY")
test_field(fname, "VIRUS")
val = ut.verify_present(fname, "general/", "source_script")
if len(val) < 1000:
ut.error("Checking metadata_from_file", "unexpected field size")
val = ut.verify_attribute_present(fname, "general/source_script", "neurodata_type")
if val != "Custom" and val != b"Custom":
ut.error("Checking custom tag", "neurodata_type incorrect")
def test_refimage_series():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
name = "refimage"
create_refimage(fname, name)
val = ut.verify_present(fname, "acquisition/images/", name)
#if len(val) != 6:
if len(val) != 5:
ut.error("Checking ref image contents", "wrong dimension")
val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "format")
if not ut.strcmp(val, "raw"):
ut.error("Checking ref image format", "Wrong value")
val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "description")
if not ut.strcmp(val, "test"):
ut.error("Checking ref image description", "Wrong value")
def test_refimage_series():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
name = "refimage"
create_refimage(fname, name)
val = ut.verify_present(fname, "acquisition/images/", name)
#if len(val) != 6:
if len(val) != 5:
ut.error("Checking ref image contents", "wrong dimension")
val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "format")
if not ut.strcmp(val, "raw"):
ut.error("Checking ref image format", "Wrong value")
val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "description")
if not ut.strcmp(val, "test"):
ut.error("Checking ref image description", "Wrong value")
def test_sign_map(fname, iname):
val = ut.verify_present(fname, iname, "sign_map")
if len(val) != 2 or len(val[0]) != 3:
ut.error("Checking sign map", "wrong dimension")
if val[1][1] != -.5:
ut.error("Checking sign map", "wrong content")
val = ut.verify_attribute_present(fname, iname+"/sign_map", "dimension")
if len(val) != 2 or val[0] != 2 or val[1] != 3:
ut.error("Checking sign map dimension", "wrong contents")
def test_ts_link():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
root = "root"
create_linked_series(fname, root)
ut.verify_timeseries(fname, root+"1", "stimulus/templates", "TimeSeries")
ut.verify_timeseries(fname, root+"2", "stimulus/presentation", "TimeSeries")
ut.verify_timeseries(fname, root+"3", "acquisition/timeseries", "TimeSeries")
##################################################
# make sure data is present in ts using link
val = ut.verify_present(fname, "stimulus/presentation/root2", "data")
if val[0] != 1:
ut.error("Checking link content", "Incorrect value")
# make sure link is documented
val = ut.verify_attribute_present(fname, "stimulus/presentation/root2", "data_link")
if not ut.search_for_substring(val, "root1"):
ut.error("Checking attribute data_link", "Name missing")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute data_link", "Name missing")
val = ut.verify_attribute_present(fname, "stimulus/templates/root1", "data_link")
if not ut.search_for_substring(val, "root1"):
ut.error("Checking attribute data_link", "Name missing")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute data_link", "Name missing")
##################################################
# make sure timestamps is present in ts using link
val = ut.verify_present(fname, "acquisition/timeseries/root3", "timestamps")
if val[0] != 2:
ut.error("Checking link content", "Incorrect value")
# make sure link is documented
val = ut.verify_attribute_present(fname, "stimulus/presentation/root2", "timestamp_link")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute timestamp_link", "Name missing")
if not ut.search_for_substring(val, "root3"):
ut.error("Checking attribute timestamp_link", "Name missing")
val = ut.verify_attribute_present(fname, "acquisition/timeseries/root3", "timestamp_link")
if not ut.search_for_substring(val, "root2"):
ut.error("Checking attribute timestamp_link", "Name missing")
if not ut.search_for_substring(val, "root3"):
ut.error("Checking attribute timestamp_link", "Name missing")
def test_nodata_series():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
name = "starting_time"
create_startingtime_series(fname, name, "acquisition")
ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries")
ut.verify_absent(fname, "acquisition/timeseries/"+name, "timestamps")
val = ut.verify_present(fname, "acquisition/timeseries/"+name, "starting_time")
if val != 0.125:
ut.error("Checking start time", "Incorrect value")
val = ut.verify_attribute_present(fname, "acquisition/timeseries/starting_time/"+name, "rate")
if val != 2:
ut.error("Checking rate", "Incorrect value")
def test_nodata_series():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
name = "starting_time"
create_startingtime_series(fname, name, "acquisition")
ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries")
ut.verify_absent(fname, "acquisition/timeseries/" + name, "timestamps")
val = ut.verify_present(fname, "acquisition/timeseries/" + name,
"starting_time")
if val != 0.125:
ut.error("Checking start time", "Incorrect value")
val = ut.verify_attribute_present(
fname, "acquisition/timeseries/starting_time/" + name, "rate")
if val != 2:
ut.error("Checking rate", "Incorrect value")
# epoch2 = borg.create_epoch("epoch-2", 1, 4);
epoch2 = f.make_group("<epoch_X>", "epoch-2")
epoch2.set_dataset("start_time", 1)
epoch2.set_dataset("stop_time", 4)
# for i in range(len(tags)-1):
# epoch2.add_tag(tags[i])
epoch2.set_dataset("tags", tags[0:-1])
f.close()
# this test modified because tags are stored as dataset rather than attribute
# tags = ut.verify_attribute_present(fname, "epochs/epoch-1", "tags");
tags = ut.verify_present(fname, "epochs/epoch-1", "tags")
for i in range(len(tags) - 1):
if tags[i + 1] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
# tags = ut.verify_attribute_present(fname, "epochs/epoch-2", "tags");
tags = ut.verify_present(fname, "epochs/epoch-2", "tags")
for i in range(len(tags) - 1):
if tags[i] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
tags = ut.verify_attribute_present(fname, "epochs", "tags")
for i in range(len(tags)):
if tags[i] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
print("%s PASSED" % __file__)
fname = "x" + __file__[1:-3] + ".nwb"
borg = ut.create_new_file(fname, "Epoch tags")
tags = ["tag-a", "tag-b", "tag-c"]
epoch1 = borg.create_epoch("epoch-1", 0, 3);
for i in range(len(tags)-1):
epoch1.add_tag(tags[i+1])
epoch2 = borg.create_epoch("epoch-2", 1, 4);
for i in range(len(tags)-1):
epoch2.add_tag(tags[i])
borg.close()
tags = ut.verify_attribute_present(fname, "epochs/epoch-1", "tags");
for i in range(len(tags)-1):
if tags[i+1] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
tags = ut.verify_attribute_present(fname, "epochs/epoch-2", "tags");
for i in range(len(tags)-1):
if tags[i] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
tags = ut.verify_attribute_present(fname, "epochs", "tags");
for i in range(len(tags)):
if tags[i] not in tags:
ut.error("Verifying epoch tag content", "All tags not present")
