def test_general_intra():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
create_general_intra(fname)
#
val = ut.verify_present(fname, "general/optophysiology/", "image_custom")
if not ut.strcmp(val, "IMAGE_CUSTOM"):
#if val != "IMAGE_CUSTOM" and val != b"IMAGE_CUSTOM":
ut.error("Checking custom", "Field value incorrect")
#
test_field(fname, "DESCRIPTION", "p1")
test_field(fname, "DEVICE", "p1")
test_field(fname, "EXCITATION_LAMBDA", "p1")
test_field(fname, "IMAGE_SITE_CUSTOM", "p1")
test_field(fname, "IMAGING_RATE", "p1")
test_field(fname, "INDICATOR", "p1")
test_field(fname, "LOCATION", "p1")
val = ut.verify_present(fname, "general/optophysiology/p1/", "manifold")
if len(val) != 2 or len(val[0]) != 2 or len(val[0][0]) != 3:
ut.error("Checking manifold", "Incorrect dimensions")
val = ut.verify_present(fname, "general/optophysiology/p1/red/", "description")
if not ut.strcmp(val, "DESCRIPTION"):
ut.error("Checking metadata", "field value incorrect")
val = ut.verify_present(fname, "general/optophysiology/p1/green/", "description")
if not ut.strcmp(val, "DESCRIPTION"):
ut.error("Checking metadata", "field value incorrect")
val = ut.verify_present(fname, "general/optophysiology/p1/red/", "emission_lambda")
if not ut.strcmp(val, "CHANNEL_LAMBDA"):
ut.error("Checking metadata", "field value incorrect")
val = ut.verify_present(fname, "general/optophysiology/p1/green/", "emission_lambda")
if not ut.strcmp(val, "CHANNEL_LAMBDA"):
ut.error("Checking metadata", "field value incorrect")
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_general_intra():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
create_general_intra(fname)
#
val = ut.verify_present(fname, "general/intracellular_ephys/", "intra_custom")
if not ut.strcmp(val, "INTRA_CUSTOM"):
ut.error("Checking custom", "Field value incorrect")
#
test_field(fname, "DESCRIPTION", "p1")
test_field(fname, "FILTERING", "p1")
test_field(fname, "DEVICE", "p1")
test_field(fname, "LOCATION", "p1")
test_field(fname, "RESISTANCE", "p1")
test_field(fname, "SLICE", "p1")
test_field(fname, "SEAL", "p1")
test_field(fname, "INITIAL_ACCESS_RESISTANCE", "p1")
test_field(fname, "INTRA_ELECTRODE_CUSTOM", "p1")
#
test_field(fname, "DESCRIPTION", "e2")
test_field(fname, "FILTERING", "e2")
test_field(fname, "DEVICE", "e2")
test_field(fname, "LOCATION", "e2")
test_field(fname, "RESISTANCE", "e2")
test_field(fname, "SLICE", "e2")
test_field(fname, "SEAL", "e2")
test_field(fname, "INITIAL_ACCESS_RESISTANCE", "e2")
test_field(fname, "INTRA_ELECTRODE_CUSTOM", "e2")
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, "/", "identifier")
if not ut.strcmp(val, "vwx"):
ut.error("Checking file idenfier", "wrong contents")
val = ut.verify_present(fname, "/", "file_create_date")
val = ut.verify_present(fname, "/", "session_start_time")
if not ut.strcmp(val, "xyz"):
ut.error("Checking session start time", "wrong contents")
val = ut.verify_present(fname, "/", "session_description")
if not ut.strcmp(val, "wxy"):
ut.error("Checking session start time", "wrong contents")
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, "/", "identifier")
if not ut.strcmp(val, "vwx"):
ut.error("Checking file idenfier", "wrong contents")
val = ut.verify_present(fname, "/", "file_create_date")
val = ut.verify_present(fname, "/", "session_start_time")
if not ut.strcmp(val, "xyz"):
ut.error("Checking session start time", "wrong contents")
val = ut.verify_present(fname, "/", "session_description")
if not ut.strcmp(val, "wxy"):
ut.error("Checking session start time", "wrong contents")
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_isi_iface():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
name = "test_module"
iname = "processing/" + name + "/ImagingRetinotopy"
create_isi_iface(fname, name)
test_axis(fname, iname, "1")
test_axis(fname, iname, "2")
val = ut.verify_present(fname, iname, "axis_descriptions")
if len(val) != 2:
ut.error("Checking axis_description", "wrong dimension")
if not ut.strcmp(val[0], "altitude") or not ut.strcmp(val[1], "azimuth"):
ut.error("Checking axis_description", "wrong contents")
test_image(fname, iname, "vasculature_image")
test_image(fname, iname, "focal_depth_image")
test_sign_map(fname, iname)
def test_general_optogen():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
create_general_optogen(fname)
#
val = ut.verify_present(fname, "general/optogenetics/", "optogen_custom")
if not ut.strcmp(val, "OPTOGEN_CUSTOM"):
ut.error("Checking custom", "Field value incorrect")
#
test_field(fname, "DESCRIPTION", "p1")
#test_field(fname, "DESCRIPTIONx", "p1")
#test_field(fname, "DESCRIPTION", "p1x")
test_field(fname, "DEVICE", "p1")
test_field(fname, "LAMBDA", "p1")
test_field(fname, "LOCATION", "p1")
val = ut.verify_present(fname, "general/optogenetics/p1/", "optogen_site_custom")
if not ut.strcmp(val, "OPTOGEN_SITE_CUSTOM"):
ut.error("Checking metadata", "field value incorrect")
def test_general_optogen():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
create_general_optogen(fname)
#
val = ut.verify_present(fname, "general/optogenetics/", "optogen_custom")
if not ut.strcmp(val, "OPTOGEN_CUSTOM"):
ut.error("Checking custom", "Field value incorrect")
#
test_field(fname, "DESCRIPTION", "p1")
#test_field(fname, "DESCRIPTIONx", "p1")
#test_field(fname, "DESCRIPTION", "p1x")
test_field(fname, "DEVICE", "p1")
test_field(fname, "LAMBDA", "p1")
test_field(fname, "LOCATION", "p1")
val = ut.verify_present(fname, "general/optogenetics/p1/",
"optogen_site_custom")
if not ut.strcmp(val, "OPTOGEN_SITE_CUSTOM"):
ut.error("Checking metadata", "field value incorrect")
def test_general_subject():
if __file__.startswith("./"):
fname = "x" + __file__[3:-3] + ".nwb"
else:
fname = "x" + __file__[1:-3] + ".nwb"
create_general_subject(fname)
val = ut.verify_present(fname, "general/subject/", "description")
if not ut.strcmp(val, "SUBJECT"):
ut.error("Checking metadata", "field value incorrect")
test_field(fname, "SUBJECT_ID")
test_field(fname, "SPECIES")
test_field(fname, "GENOTYPE")
test_field(fname, "SEX")
test_field(fname, "AGE")
test_field(fname, "WEIGHT")
def test_general_subject():
if __file__.startswith("./"):
fname = "s" + __file__[3:-3] + ".nwb"
else:
fname = "s" + __file__[1:-3] + ".nwb"
create_general_subject(fname)
val = ut.verify_present(fname, "general/subject/", "description")
if not ut.strcmp(val, "SUBJECT"):
ut.error("Checking metadata", "field value incorrect")
test_field(fname, "SUBJECT_ID")
test_field(fname, "SPECIES")
test_field(fname, "GENOTYPE")
test_field(fname, "SEX")
test_field(fname, "AGE")
test_field(fname, "WEIGHT")
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_field(fname, name):
val = ut.verify_present(fname, "general/subject/", name.lower())
if not ut.strcmp(val, name):
ut.error("Checking metadata", "field value incorrect")
def test_field(fname, name):
val = ut.verify_present(fname, "general/subject/", name.lower())
if not ut.strcmp(val, name):
ut.error("Checking metadata", "field value incorrect")
def test_field(fname, name, subdir):
val = ut.verify_present(fname, "general/intracellular_ephys/"+subdir+"/", name.lower())
if not ut.strcmp(val, name):
ut.error("Checking metadata", "field value incorrect")
def test_field(fname, name, subdir):
val = ut.verify_present(fname, "general/optogenetics/"+subdir+"/", name.lower())
if not ut.strcmp(val, name):
ut.error("Checking metadata", "field value incorrect")
