def test_override_email(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--email", "*****@*****.**"])
assert(mod.args["email"] == "*****@*****.**")
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--email", "invalid"])
def test_override_float(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--float", "1.23456789"])
assert(abs(mod.args["float"] - 1.23456789) < 1e-10)
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--float", "invalid"])
def test_override_decimal(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--decimal", "1.23456789"])
assert(mod.args["decimal"] == Decimal("1.23456789"))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--decimal", "invalid"])
def test_override_numpyarray(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--numpyarray", "[[4,3],[2,1]]"])
assert(np.all(mod.args["numpyarray"] == np.array([[4, 3], [2, 1]])))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--numpyarray", "invalid"])
def test_override_boolean(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--boolean", "False"])
assert(not mod.args["boolean"])
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--boolean", "invalid"])
def test_classifier_model_path(self, classifier_model, s3_classifier,
input_data, tmp_path):
ArgSchemaParser(
input_data=input_data, # input_data has local classifier default
schema_type=InferenceInputSchema,
args=[])
s3_input = input_data.copy()
s3_input["classifier_model_path"] = s3_classifier
ArgSchemaParser(input_data=s3_input,
schema_type=InferenceInputSchema,
args=[])
fake_s3 = input_data.copy()
fake_s3["classifier_model_path"] = "s3://my-bucket/fake-hello.txt"
with pytest.raises(ValidationError) as e:
ArgSchemaParser(input_data=fake_s3,
schema_type=InferenceInputSchema,
args=[])
assert "does not exist" in str(e.value)
fake_local = input_data.copy()
fake_local["classifier_model_path"] = str(tmp_path / "hello-again.txt")
with pytest.raises(ValidationError) as e:
ArgSchemaParser(input_data=fake_local,
schema_type=InferenceInputSchema,
args=[])
assert "does not exist" in str(e.value)
def test_override_timedelta(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--timedelta", "0"])
assert(mod.args["timedelta"] == datetime.timedelta(0))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--timedelta", "invalid"])
def test_override_datetime(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--datetime", "1977-05-04T00:00:00"])
assert(mod.args["datetime"] == datetime.datetime(1977, 5, 4, 0, 0, 0))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--datetime", "invalid"])
def test_override_url(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--url", "http://www.alleninstitute.org"])
assert(mod.args["url"] == "http://www.alleninstitute.org")
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--url", "invalid"])
def test_override_number(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--number", "10"])
assert(mod.args["number"] == 10)
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--number", "invalid"])
def test_override_slice(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--slice", "800:3:9000"])
assert(mod.args["slice"] == slice(800, 3, 9000))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--slice", "invalid"])
def test_override_log_level(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--log_level", "CRITICAL"])
assert(mod.args["log_level"] == "CRITICAL")
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--log_level", "invalid"])
def test_override_list(test_data):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--list", "[1000,3000]"])
assert(mod.args["list"] == [1000, 3000])
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--list", "invalid"])
def test_parser_validation(input_dict, raises):
if raises:
with pytest.raises(mm.ValidationError):
ArgSchemaParser(input_data=input_dict,
schema_type=MySchema,
args=[])
else:
ArgSchemaParser(input_data=input_dict, schema_type=MySchema, args=[])
def test_override_uuid(test_data):
val = "1a66e457-4d0f-474a-bb4e-bee91e61e084"
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--uuid", val])
assert(mod.args["uuid"] == uuid.UUID(val))
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--uuid", "invalid"])
def test_override_list_deprecated(deprecated_data):
with pytest.warns(FutureWarning):
mod = ArgSchemaParser(deprecated_data, schema_type=MyDeprecatedSchema,
args=["--list_deprecated", "1000", "3000"])
assert(mod.args["list_deprecated"] == [1000, 3000])
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(deprecated_data,
schema_type=MyDeprecatedSchema,
args=["--list_deprecated", "[1000,3000]"])
def main():
"""Main entry point for running sg-prototype."""
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
output = {}
# YOUR STUFF GOES HERE
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output)
else:
print(mod.get_output_json(output))
def test_bad_output(tmpdir):
file_out = tmpdir.join('test_output_bad.json')
input_parameters = {'output_json': str(file_out)}
mod = ArgSchemaParser(input_data=input_parameters,
output_schema_type=MyOutputSchema,
args=[])
M = [[5, 5], [7, 2]]
Mnp = np.array(M)
output = {"a": "example", "b": "not a number", "M": Mnp}
with pytest.raises(mm.ValidationError):
mod.output(output)
def test_output_unvalidated(tmpdir):
file_out = tmpdir.join('test_output_unvalidated.json')
input_parameters = {'output_json': str(file_out)}
mod = ArgSchemaParser(input_data=input_parameters, args=[])
output = {
"a": "example",
}
mod.output(output)
with open(str(file_out), 'r') as fp:
actual_output = json.load(fp)
assert actual_output == output
def test_override_inputfile(test_data, tmpdir_factory):
input2 = tmpdir_factory.mktemp("input3").join("input2.file")
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--inputfile", str(input2)])
with open(str(input2), "w") as f:
f.write("")
mod = ArgSchemaParser(test_data, schema_type=MySchema,
args=["--inputfile", str(input2)])
assert(mod.args["inputfile"] == str(input2))
assert(os.path.exists(mod.args["inputfile"]) and
os.path.isfile(mod.args["inputfile"]))
def test_invalid_model_registry_env(self, input_data):
# This should run without error
ArgSchemaParser(input_data=input_data,
schema_type=InferenceInputSchema,
args=[])
# Now to test when the model_registry_env field is invalid
invalid_model_registry_env = input_data.copy()
invalid_model_registry_env["model_registry_env"] = "prode"
with pytest.raises(ValidationError) as e:
ArgSchemaParser(input_data=invalid_model_registry_env,
schema_type=InferenceInputSchema,
args=[])
assert "not a valid value for the 'model_registry_env'" in str(e.value)
def main():
"""Main entry point for running AllenSDK Eye Tracking."""
try:
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
istream = CvInputStream(mod.args["input_source"])
ostream = setup_annotation(
istream.frame_shape,
**mod.args.get("annotation", DEFAULT_ANNOTATION))
qc_params = mod.args.get("qc", {})
generate_plots = qc_params.get("generate_plots",
EyeTracker.DEFAULT_GENERATE_QC_OUTPUT)
tracker = EyeTracker(istream, ostream, mod.args.get("starburst", {}),
mod.args.get("ransac",
{}), mod.args["pupil_bounding_box"],
mod.args["cr_bounding_box"], generate_plots,
**mod.args.get("eye_params", {}))
cr_params, pupil_params, cr_err, pupil_err = tracker.process_stream(
start=mod.args.get("start_frame", 0),
stop=mod.args.get("stop_frame", None),
step=mod.args.get("frame_step", 1))
output = write_output(mod.args["output_dir"], cr_params, pupil_params,
tracker.mean_frame)
pupil_intensity = None
if tracker.adaptive_pupil:
pupil_intensity = tracker.pupil_colors
if generate_plots:
write_QC_output(tracker.annotator,
cr_params,
pupil_params,
cr_err,
pupil_err,
tracker.mean_frame,
pupil_intensity=pupil_intensity,
**mod.args)
output["input_parameters"] = mod.args
if "output_json" in mod.args:
mod.output(output, indent=1)
else:
print(json.dumps(mod.get_output_json(output), indent=1))
except marshmallow.ValidationError as e:
print(e)
argparser = schema_argparser(InputParameters())
argparser.print_usage()
def main():
from ._schemas import InputParameters, OutputParameters
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
output = calculate_quality_metrics(mod.args)
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output, indent=2)
else:
print(mod.get_output_json(output))
def main():
from ._schemas import InputParameters, OutputParameters
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
# output = calculate_stimulus_metrics_ondisk(mod.args)
output = calculate_stimulus_metrics_gather(mod.args)
if MPI_rank == 0:
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output, indent=2)
else:
log_info(mod.get_output_json(output))
barrier()
def main():
from ._schemas import InputParameters, OutputParameters
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
output = classify_noise_templates(mod.args)
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output, indent=2)
else:
print(mod.get_output_json(output))
def main():
from ._schemas import InputParameters, OutputParameters
"""Main entry point:"""
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
output = get_psth_events(mod.args)
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output, indent=2)
else:
print(mod.get_output_json(output))
def main():
from ._schemas import InputParameters, OutputParameters
mod = ArgSchemaParser(schema_type=InputParameters,
output_schema_type=OutputParameters)
output = run_automerging(mod.args)
output.update({"input_parameters": mod.args})
if "output_json" in mod.args:
mod.output(output, indent=2)
else:
print(mod.get_output_json(output))
def test_output(tmpdir):
file_out = tmpdir.join('test_output.json')
input_parameters = {'output_json': str(file_out)}
mod = ArgSchemaParser(input_data=input_parameters,
output_schema_type=MyOutputSchema,
args=[])
M = [[5, 5], [7, 2]]
Mnp = np.array(M)
output = {"a": "example", "M": Mnp}
expected_output = {"a": "example", "b": 5, "M": M}
mod.output(output)
with open(str(file_out), 'r') as fp:
actual_output = json.load(fp)
assert actual_output == expected_output
def test_bad_path():
with pytest.raises(mm.ValidationError):
example = {
"input_json": "a bad path",
"output_json": "another example",
"log_level": "DEBUG"}
ArgSchemaParser(input_data=example, args=[])
def test_bad_option():
input_data = {
'a': 4
}
with pytest.raises(mm.ValidationError):
mod = ArgSchemaParser(
input_data=input_data, schema_type=OptionSchema, args=[])