def test_load_xrf_quant_fluor_json_file1(tmp_path):
# 'load_xrf_quant_fluor_json_file' - non-existing file
_, json_path = _get_data_and_json_path(tmp_path)
with pytest.raises(IOError, match=f"File '{json_path}' does not exist"):
load_xrf_quant_fluor_json_file(json_path)
def test_load_xrf_quant_fluor_json_file1(tmp_path):
# 'load_xrf_quant_fluor_json_file' - non-existing file
_, json_path = _get_data_and_json_path(tmp_path)
# 're.escape' is necessary if test is run on Windows
with pytest.raises(IOError,
match=f"File '{re.escape(json_path)}' does not exist"):
load_xrf_quant_fluor_json_file(json_path)
def test_load_xrf_quant_fluor_json_file2(tmp_path):
# 'load_xrf_quant_fluor_json_file' - schema is not matched
data, json_path = _get_data_and_json_path(tmp_path)
# Create file
save_xrf_quant_fluor_json_file(json_path, data)
schema = copy.deepcopy(_xrf_quant_fluor_schema)
# Modify schema, so that it is incorrect
schema["properties"]["scaler_name"] = {"type": "number"} # Supposed to be a string
with pytest.raises(jsonschema.ValidationError):
load_xrf_quant_fluor_json_file(json_path, schema=schema)
def test_save_xrf_quant_fluor_json_file1(tmp_path):
r"""Basic test of function 'save_xrf_standard_yaml_file' and 'load_xrf_standard_yaml_file'"""
data, json_path = _get_data_and_json_path(tmp_path)
# Sample data
save_xrf_quant_fluor_json_file(json_path, data)
data_loaded = load_xrf_quant_fluor_json_file(json_path)
assert data_loaded == data, "Loaded data is not equal to the original data"
def test_save_xrf_quant_fluor_json_file4(tmp_path):
r"""Schema allows some data fields to hold value of ``None``. Test if this works."""
data, json_path = _get_data_and_json_path(tmp_path)
# Modify some elements of the dictionary
data = copy.deepcopy(data)
data["detector_channel"] = None
data["scaler_name"] = None
data["distance_to_sample"] = None
# Sample data
save_xrf_quant_fluor_json_file(json_path, data)
data_loaded = load_xrf_quant_fluor_json_file(json_path)
assert data_loaded == data, "Loaded data is not equal to the original data"
def test_ParamQuantEstimation_3(tmp_path):
standard_data = _standard_data_sample
# 'home_dir' is typically '~', but for testing it is set to 'tmp_dir'
home_dir = tmp_path
config_dir = ".pyxrf"
standards_fln = "quantitative_standards.yaml"
# Create the file with user-defined reference definitions
file_path = os.path.join(home_dir, config_dir, standards_fln)
save_xrf_standard_yaml_file(file_path, standard_data)
# Create the object and load references
pqe = ParamQuantEstimation(home_dir=home_dir)
pqe.load_standards()
# Select first 'user-defined' sample (from '_standard_data_sample' list)
incident_energy = 12.0
img = gen_xrf_map_dict()
# Generate and fill fluorescence data dictionary
pqe.set_selected_standard()
pqe.gen_fluorescence_data_dict(incident_energy=incident_energy)
scaler_name = "sclr"
pqe.fill_fluorescence_data_dict(xrf_map_dict=img, scaler_name=scaler_name)
# Equivalent transformations using functions that are already tested. The sequence
# must give the same result (same functions are called).
qfdd = get_quant_fluor_data_dict(standard_data[0], incident_energy)
fill_quant_fluor_data_dict(qfdd, xrf_map_dict=img, scaler_name=scaler_name)
assert (
pqe.fluorescence_data_dict == qfdd
), "The filled fluorescence data dictionary does not match the expected"
# Test generation of preview (superficial)
pview, msg_warnings = pqe.get_fluorescence_data_dict_text_preview()
# It is expected that the preview will contain 'WARNING:'
assert len(msg_warnings), "Warning is not found in preview"
# Disable warnings
pview, msg_warnings = pqe.get_fluorescence_data_dict_text_preview(
enable_warnings=False)
assert not len(msg_warnings), "Warnings are disabled, but still generated"
# Test function for setting detector channel name
pqe.set_detector_channel_in_data_dict(detector_channel="sum")
assert pqe.fluorescence_data_dict[
"detector_channel"] == "sum", "Detector channel was not set correctly"
# Test function for setting distance to sample
distance_to_sample = 2.5
pqe.set_distance_to_sample_in_data_dict(
distance_to_sample=distance_to_sample)
assert (pqe.fluorescence_data_dict["distance_to_sample"] ==
distance_to_sample), "Distance-to-sample was not set correctly"
# Function for setting Scan ID and Scan UID
scan_id = 65476
scan_uid = "abcdef-12345678" # Some string
qfdd = copy.deepcopy(pqe.fluorescence_data_dict)
pqe.set_optional_parameters(scan_id=scan_id, scan_uid=scan_uid)
set_quant_fluor_data_dict_optional(qfdd,
scan_id=scan_id,
scan_uid=scan_uid)
# We don't check if time is computed correctly (this was checked at different place)
# Time computed at different function calls may be different
qfdd["creation_time_local"] = pqe.fluorescence_data_dict[
"creation_time_local"]
assert pqe.fluorescence_data_dict == qfdd, "Optional parameters are not set correctly"
# Try generating preview again: there should be no warnings
pview, msg_warnings = pqe.get_fluorescence_data_dict_text_preview()
# There should be no warnings in preview (all parameters are set)
assert not len(msg_warnings), "Preview is expected to contain no warnings"
# Test the method 'get_suggested_json_fln'
fln_suggested = pqe.get_suggested_json_fln()
assert (
f"_{pqe.fluorescence_data_dict['serial']}." in fln_suggested
), f"Serial of the reference is not found in the suggested file name {fln_suggested}"
# Test saving calibration data
file_path = os.path.join(tmp_path, fln_suggested)
pqe.save_fluorescence_data_dict(file_path=file_path)
qfdd = load_xrf_quant_fluor_json_file(file_path=file_path)
assert qfdd == prune_quant_fluor_data_dict(
pqe.fluorescence_data_dict
), "Error occurred while saving and loading calibration data dictionary. Dictionaries don't match"
