def test_reading_empty_or_half_file(self):
"""If the ini file is empty or keys are missing, GlobalSettings
reverts to default values."""
with tempfile.TemporaryDirectory() as tmp_dir:
ini_file = Path(tmp_dir, "potku2.ini")
open(ini_file, "a").close()
gs = GlobalSettings(tmp_dir, save_on_creation=False)
# Update directories
self.gs.set_config_dir(tmp_dir)
self.gs.set_request_directory(Path(tmp_dir, "requests"))
self.gs.set_request_directory_last_open(Path(tmp_dir, "requests"))
self.assert_settings_equal(self.gs, gs)
# Save the file
self.gs.save_config()
# Remove every second line from the ini file
with open(ini_file, "r") as f:
lines = f.readlines()
self.assertTrue(1 < len(lines))
with open(ini_file, "w") as f:
for line in lines[::2]:
f.write(line)
gs = GlobalSettings(tmp_dir, save_on_creation=False)
self.assert_settings_equal(self.gs, gs, only_check_same_size=True)
def __init__(self,
parent: BaseTab,
measurement: Measurement,
global_settings: GlobalSettings,
statusbar: Optional[QtWidgets.QStatusBar] = None):
"""Inits depth profile dialog.
Args:
parent: a MeasurementTabWidget.
measurement: a Measurement object
global_settings: a GlobalSettings object
statusbar: a QStatusBar object
"""
super().__init__()
uic.loadUi(gutils.get_ui_dir() / "ui_depth_profile_params.ui", self)
self.parent = parent
self.measurement = measurement
self.statusbar = statusbar
# Connect buttons
self.OKButton.clicked.connect(self._accept_params)
self.cancelButton.clicked.connect(self.close)
locale = QLocale.c()
self.spin_systerr.setLocale(locale)
self.sbox_reference_density.setLocale(locale)
m_name = self.measurement.name
if m_name not in DepthProfileDialog.checked_cuts:
DepthProfileDialog.checked_cuts[m_name] = set()
gutils.fill_cuts_treewidget(self.measurement,
self.treeWidget.invisibleRootItem(),
use_elemloss=True)
self.used_cuts = DepthProfileDialog.checked_cuts[m_name]
gutils.set_btn_group_data(self.group_x_axis_units, DepthProfileUnit)
self.x_axis_units = DepthProfileDialog.x_unit
if self.x_axis_units == DepthProfileUnit.NM:
self._show_reference_density()
else:
self._hide_reference_density()
self.radioButtonNm.clicked.connect(self._show_reference_density)
self.radioButtonAtPerCm2.clicked.connect(self._hide_reference_density)
self.systematic_error = DepthProfileDialog.systerr
self.show_scale_line = DepthProfileDialog.line_scale
self.show_zero_line = DepthProfileDialog.line_zero
self.cross_sections = global_settings.get_cross_sections()
self._show_measurement_settings()
self._show_efficiency_files()
self.exec_()
def test_reading_bad_values(self):
with tempfile.TemporaryDirectory() as tmp_dir:
self.gs.set_config_dir(tmp_dir)
self.gs.set_request_directory(Path(tmp_dir, "requests"))
self.gs.set_request_directory_last_open(Path(tmp_dir, "requests"))
self.gs.save_config()
ini_file = self.gs.get_config_file()
with ini_file.open("r") as f:
lines = f.readlines()
self.assertTrue(1 < len(lines))
with ini_file.open("w") as f:
for line in lines:
if line.strip().startswith("compression_y"):
line = "compression_y = True\n"
elif line.strip().startswith("transpose"):
line = "transpose =\n"
f.write(line)
f.write("foo = bar\n")
f.write("bar\n")
gs = GlobalSettings(config_dir=tmp_dir, save_on_creation=False)
self.assert_settings_equal(self.gs, gs)
def test_initialization(self):
"""Upon initialization, global settings creates a directory containing
an ini file and request directory if save on creation is True.
"""
with tempfile.TemporaryDirectory() as tmp_dir:
path = Path(tmp_dir, "settings")
file = path / "potku2.ini"
global_settings = GlobalSettings(config_dir=path,
save_on_creation=False)
self.assertFalse(path.exists())
self.assertFalse(file.exists())
self.assertFalse(global_settings.get_request_directory().exists())
global_settings = GlobalSettings(config_dir=path,
save_on_creation=True)
self.assertTrue(path.exists())
self.assertTrue(file.exists())
# Request directory is not created
self.assertFalse(global_settings.get_request_directory().exists())
def test_element_simulation_settings(self):
"""This tests that ElementSimulation is run with the correct settings
depending on how 'use_default_settings' and 'use_request_settings'
have been set.
"""
with tempfile.TemporaryDirectory() as tmp_dir:
# File paths
tmp_dir = Path(tmp_dir).resolve()
req_dir = tmp_dir / "req"
sim_dir = req_dir / "Sample_01-foo" / \
f"{Simulation.DIRECTORY_PREFIX}01-bar"
simu_file = sim_dir / "bar.simulation"
# Request
request = Request(
req_dir, "test_req", GlobalSettings(config_dir=tmp_dir), {},
enable_logging=False)
self.assertEqual(req_dir, request.directory)
self.assertEqual("test_req", request.request_name)
# Sample
sample = request.samples.add_sample(name="foo")
self.assertIs(sample, request.samples.samples[0])
self.assertIsInstance(sample, Sample)
self.assertEqual("foo", sample.name)
self.assertEqual(request, sample.request)
self.assertEqual("Sample_01-foo", sample.directory)
# Simulation
sim = sample.simulations.add_simulation_file(
sample, simu_file, 0)
# Disable logging so the logging file handlers do not cause
# an exception when the tmp dir is removed
sim.close_log_files()
self.assertIs(sim, sample.simulations.get_key_value(0))
self.assertIsInstance(sim.detector, Detector)
self.assertIsInstance(sim.run, Run)
self.assertEqual("bar", sim.name)
self.assertEqual(request, sim.request)
self.assertEqual(sample, sim.sample)
# ElementSimulation
rec_elem = RecoilElement(
Element.from_string("Fe"), [Point((1, 1))], name="recoil_name")
elem_sim = sim.add_element_simulation(rec_elem)
self.assertIs(elem_sim, sim.element_simulations[0])
elem_sim.number_of_preions = 2
elem_sim.number_of_ions = 3
self.assertEqual(request, elem_sim.request)
self.assertEqual("Fe-Default", elem_sim.get_full_name())
# Some pre-simulation checks
self.assertIsNot(sim.target, request.default_target)
self.assertIsNot(elem_sim, request.default_element_simulation)
self.assertIsNot(sim.detector, request.default_detector)
self.assertIsNot(sim.run, request.default_run)
self.assertIsNot(sim.run.beam, request.default_run.beam)
self.assertNotEqual(
elem_sim.number_of_ions,
request.default_element_simulation.number_of_ions)
self.assert_expected_settings(elem_sim, request, sim)
def setUp(self) -> None:
self.gs = GlobalSettings(tempfile.gettempdir(), save_on_creation=False)
class TestGlobalSettings(unittest.TestCase):
def setUp(self) -> None:
self.gs = GlobalSettings(tempfile.gettempdir(), save_on_creation=False)
def test_initialization(self):
"""Upon initialization, global settings creates a directory containing
an ini file and request directory if save on creation is True.
"""
with tempfile.TemporaryDirectory() as tmp_dir:
path = Path(tmp_dir, "settings")
file = path / "potku2.ini"
global_settings = GlobalSettings(config_dir=path,
save_on_creation=False)
self.assertFalse(path.exists())
self.assertFalse(file.exists())
self.assertFalse(global_settings.get_request_directory().exists())
global_settings = GlobalSettings(config_dir=path,
save_on_creation=True)
self.assertTrue(path.exists())
self.assertTrue(file.exists())
# Request directory is not created
self.assertFalse(global_settings.get_request_directory().exists())
def test_boolean_getters(self):
self.gs.set_tofe_transposed(False)
self.assertFalse(self.gs.get_tofe_transposed())
self.gs.set_tofe_transposed(True)
self.assertTrue(self.gs.get_tofe_transposed())
self.gs.set_tofe_invert_y(False)
self.assertFalse(self.gs.get_tofe_invert_y())
self.gs.set_tofe_invert_y(True)
self.assertTrue(self.gs.get_tofe_invert_y())
def test_int_getters(self):
self.gs.set_import_coinc_count(555)
self.assertEqual(555, self.gs.get_import_coinc_count())
# Some keys have default values in case conversion fails
self.gs.set_import_coinc_count("seven")
self.assertEqual(10000, self.gs.get_import_coinc_count())
def test_cross_section(self):
self.assertEqual(CrossSection.ANDERSEN, self.gs.get_cross_sections())
self.gs.set_cross_sections(CrossSection.LECUYER)
self.assertEqual(CrossSection.LECUYER, self.gs.get_cross_sections())
self.gs.set_cross_sections(CrossSection.RUTHERFORD)
self.assertEqual(CrossSection.RUTHERFORD, self.gs.get_cross_sections())
def test_ion_division(self):
self.gs.set_ion_division(IonDivision.BOTH)
self.assertEqual(IonDivision.BOTH, self.gs.get_ion_division())
self.gs.set_ion_division(IonDivision.SIM)
self.assertEqual(IonDivision.SIM, self.gs.get_ion_division())
self.gs.set_ion_division(IonDivision.NONE)
self.assertEqual(IonDivision.NONE, self.gs.get_ion_division())
def test_color_scheme(self):
self.gs.set_tofe_color(ToFEColorScheme.DEFAULT)
self.assertEqual(ToFEColorScheme.DEFAULT, self.gs.get_tofe_color())
self.gs.set_tofe_color(ToFEColorScheme.INV_GREYSCALE)
self.assertEqual(ToFEColorScheme.INV_GREYSCALE,
self.gs.get_tofe_color())
self.gs.set_tofe_color(ToFEColorScheme.GREYSCALE)
self.assertEqual(ToFEColorScheme.GREYSCALE, self.gs.get_tofe_color())
def test_element_colors(self):
self.gs.set_element_color("B", "black")
# This is case insensitive
self.assertEqual("black", self.gs.get_element_color("B"))
self.assertEqual("black", self.gs.get_element_color("b"))
# Unknown color returns a default value
self.assertEqual("red", self.gs.get_element_color("foo"))
# New elements can be added
self.gs.set_element_color("foo", "green")
self.assertEqual("green", self.gs.get_element_color("foo"))
def test_minimum_concentration(self):
self.assertEqual(0.0001, self.gs.get_minimum_concentration())
self.gs.set_minimum_concentration(1)
self.assertEqual(1, self.gs.get_minimum_concentration())
self.gs.set_minimum_concentration(0)
# The absolute minimum
self.assertEqual(0.000001, self.gs.get_minimum_concentration())
def test_serialiazation(self):
"""Deserialized GlobalSettings object should have the same
values as the serialized object.
"""
with tempfile.TemporaryDirectory() as tmp_dir:
path = Path(tmp_dir, "settings")
gs1 = GlobalSettings(config_dir=path, save_on_creation=False)
gs1.set_cross_sections(CrossSection.LECUYER)
gs1.set_element_color("He", "blue")
gs1.set_tofe_transposed(False)
gs1.set_request_directory(Path(tmp_dir, "requests2"))
gs1.set_tofe_bin_range_x(444, 555)
gs1.set_num_iterations(13)
gs1.save_config()
gs2 = GlobalSettings(config_dir=path, save_on_creation=False)
self.assert_settings_equal(gs1, gs2)
def test_reading_empty_or_half_file(self):
"""If the ini file is empty or keys are missing, GlobalSettings
reverts to default values."""
with tempfile.TemporaryDirectory() as tmp_dir:
ini_file = Path(tmp_dir, "potku2.ini")
open(ini_file, "a").close()
gs = GlobalSettings(tmp_dir, save_on_creation=False)
# Update directories
self.gs.set_config_dir(tmp_dir)
self.gs.set_request_directory(Path(tmp_dir, "requests"))
self.gs.set_request_directory_last_open(Path(tmp_dir, "requests"))
self.assert_settings_equal(self.gs, gs)
# Save the file
self.gs.save_config()
# Remove every second line from the ini file
with open(ini_file, "r") as f:
lines = f.readlines()
self.assertTrue(1 < len(lines))
with open(ini_file, "w") as f:
for line in lines[::2]:
f.write(line)
gs = GlobalSettings(tmp_dir, save_on_creation=False)
self.assert_settings_equal(self.gs, gs, only_check_same_size=True)
def test_reading_bad_values(self):
with tempfile.TemporaryDirectory() as tmp_dir:
self.gs.set_config_dir(tmp_dir)
self.gs.set_request_directory(Path(tmp_dir, "requests"))
self.gs.set_request_directory_last_open(Path(tmp_dir, "requests"))
self.gs.save_config()
ini_file = self.gs.get_config_file()
with ini_file.open("r") as f:
lines = f.readlines()
self.assertTrue(1 < len(lines))
with ini_file.open("w") as f:
for line in lines:
if line.strip().startswith("compression_y"):
line = "compression_y = True\n"
elif line.strip().startswith("transpose"):
line = "transpose =\n"
f.write(line)
f.write("foo = bar\n")
f.write("bar\n")
gs = GlobalSettings(config_dir=tmp_dir, save_on_creation=False)
self.assert_settings_equal(self.gs, gs)
def assert_settings_equal(self,
gs1: GlobalSettings,
gs2: GlobalSettings,
only_check_same_size=False):
"""Asserts that the two GlobalSettings objects return same values.
If only_check_same_size is True, the return values of
get_element_colors are only checked if they are the same size.
"""
getters = [
method for method in dir(gs1)
if method.startswith("get") or method.startswith("is")
]
for getter in getters:
if getter == "get_element_color":
args = mo.get_element(randomize=True).symbol,
elif getter == "get_import_timing":
args = random.randint(0, 2),
else:
args = ()
val1 = getattr(gs1, getter)(*args)
val2 = getattr(gs2, getter)(*args)
if only_check_same_size:
if getter == "get_element_colors":
if len(val1) != len(val2):
continue
self.assertEqual(val1, val2)
def test_serialiazation(self):
"""Deserialized GlobalSettings object should have the same
values as the serialized object.
"""
with tempfile.TemporaryDirectory() as tmp_dir:
path = Path(tmp_dir, "settings")
gs1 = GlobalSettings(config_dir=path, save_on_creation=False)
gs1.set_cross_sections(CrossSection.LECUYER)
gs1.set_element_color("He", "blue")
gs1.set_tofe_transposed(False)
gs1.set_request_directory(Path(tmp_dir, "requests2"))
gs1.set_tofe_bin_range_x(444, 555)
gs1.set_num_iterations(13)
gs1.save_config()
gs2 = GlobalSettings(config_dir=path, save_on_creation=False)
self.assert_settings_equal(gs1, gs2)
def get_global_settings() -> GlobalSettings:
"""Returns a GlobalSettings object.
"""
return GlobalSettings(config_dir=_TEMP_DIR, save_on_creation=False)