def test_initialization(self):
"""Tests the initialization of a DepthProfile object"""
dp = DepthProfile([1], [2])
self.assertEqual((1, ), dp.depths)
self.assertEqual((2, ), dp.concentrations)
self.assertIsNone(dp.events)
self.assertEqual("total", dp.get_profile_name())
# Currently the order of depth counts, or validity of
# numerical values is not checked so following is ok.
dp = DepthProfile([2, 1], [True, "Foo"])
self.assertEqual((2, 1), dp.depths)
self.assertEqual((True, "Foo"), dp.concentrations)
dp = DepthProfile([1], [2], [3], element=Element.from_string("Si"))
self.assertEqual((1, ), dp.depths)
self.assertEqual((2, ), dp.concentrations)
self.assertEqual((3, ), dp.events)
self.assertEqual("Si", dp.get_profile_name())
self.assertRaises(ValueError, lambda: DepthProfile([], [], []))
self.assertRaises(ValueError, lambda: DepthProfile([], [1]))
self.assertRaises(
ValueError,
lambda: DepthProfile([1], [], [1],
element=Element.from_string("Si")))
self.assertRaises(
ValueError,
lambda: DepthProfile([1], [1], [],
element=Element.from_string("Si")))
def setUpClass(cls):
cls.directory = Path(tempfile.gettempdir())
target = Target(layers=[
Layer("layer1", [
Element.from_string("Li 1.0")
], 0.01, 0.01, start_depth=0.0),
Layer("layer2", [
Element.from_string("Li 0.048"),
Element.from_string("O 0.649"),
Element.from_string("Mn 0.303")
], 90.0, 4.0, start_depth=0.01),
Layer("subtrate", [
Element.from_string("Si 1.0")
], 1000.0, 2.32, start_depth=90.01)
])
cls.mcerd = MCERD(101, {
"recoil_element": mo.get_recoil_element(),
"sim_dir": tempfile.gettempdir(),
"simulation_type": SimulationType.ERD,
"target": target,
"detector": mo.get_detector(),
"beam": mo.get_beam(),
# Following simulation parameters have been determined by the
# rigorous application of the Stetson-Harrison method.
"minimum_scattering_angle": 5.5,
"minimum_main_scattering_angle": 6.5,
"minimum_energy_of_ions": 8.15,
"number_of_recoils": 15,
"simulation_mode": SimulationMode.NARROW,
"number_of_scaling_ions": 14,
"number_of_ions_in_presimu": 100,
"number_of_ions": 1000
}, mo.get_element_simulation().get_full_name())
def test_get_full_name(self):
self.assertEqual("He-bar", self.rec_elem.get_full_name())
rec_elem = RecoilElement(Element.from_string("16O"), [], name=None)
self.assertEqual("16O-Default", rec_elem.get_full_name())
rec_elem = RecoilElement(Element.from_string("16O"), [], name="")
self.assertEqual("16O-Default", rec_elem.get_full_name())
def test_subtraction(self):
dp1 = DepthProfile([0, 1], [2, 3], [1, 2], Element.from_string("Si"))
dp2 = DepthProfile([0, 1], [3, 4], [1, 2], Element.from_string("Si"))
dp3 = dp2 - dp1
self.assertEqual((1, 1), dp3.concentrations)
self.assertEqual((0, 1), dp3.depths)
self.assertIsNone(dp3.events)
self.assertIsNone(dp3.element)
dp3 -= dp3
self.assertEqual((0, 0), dp3.concentrations)
def set_element(self, element: Element):
"""Sets currently selected element.
"""
if not isinstance(element, Element):
try:
element = Element.from_string(element)
except (ValueError, AttributeError):
self._isotope_input.clear()
self.validate()
self.selection_changed.emit()
return
show_st_mass_in_combobox = self._st_mass_input is None
self._symbol_input.setText(element.symbol)
gutils.load_isotopes(element.symbol,
self._isotope_input,
show_std_mass=show_st_mass_in_combobox,
current_isotope=element.isotope)
if self._amount_input is not None and element.amount:
self._amount_input.setValue(element.amount)
self.validate()
self.selection_changed.emit()
def __sortt(self, key):
cut_file = key.split('.')
# TODO use RBS selection to sort (for example m1.35Cl.RBS_Mn.0.cut
# should be sorted by Mn, not Cl)
# TODO provide elements as parameter instead of reinitializing them
# over and over again
return Element.from_string(cut_file[0].strip())
def __sortt(key):
cut_file = key.split('.')
# TODO sort by RBS selection
# TODO provide elements as parameters, do not initialize them here.
# Better yet, use CutFile objects here.
# TODO is measurement removed from the cut file at this point? If
# not, this sorts by measurement instead of element
return Element.from_string(cut_file[0].strip())
def test_equals_prop_based(self):
n = 1000
for _ in range(n):
elem1 = mo.get_element(randomize=True)
elem1_str = str(elem1)
elem2 = Element.from_string(elem1_str)
self.assertIsNot(elem1, elem2)
self.assertEqual(elem1, elem2)
self.assertEqual(hash(elem1), hash(elem2))
def test_hash(self):
e = Element.from_string("H")
hashed_elems = {
e, e,
Element.from_string("H"),
Element.from_string("1H"),
Element.from_string("1H 4.0"),
Element.from_string("1H 4.0"),
Element.from_string("1H 5.0")
}
self.assertEqual(
{
Element.from_string("H"),
Element.from_string("1H"),
Element.from_string("1H 4.0"),
Element.from_string("1H 5.0")
}, hashed_elems)
def test_merging(self):
dp1 = DepthProfile([0, 1, 2, 3, 4], [1, 1, 1, 1, 1], [1, 1, 1, 1, 1],
element=Element.from_string("Si"))
dp2 = DepthProfile([0, 1, 2, 3, 4], [2, 2, 2, 2, 2], [2, 2, 2, 2, 2],
element=Element.from_string("Si"))
dp3 = dp1.merge(dp2, 1, 3)
self.assertEqual(dp1.depths, dp3.depths)
self.assertEqual((1, 2, 2, 2, 1), dp3.concentrations)
self.assertEqual((1, 1, 1, 1, 1), dp3.events)
self.assertEqual("Si", dp3.get_profile_name())
# Original depth profiles remain unchanged
self.assertEqual(dp1.depths, (0, 1, 2, 3, 4))
self.assertEqual(dp2.depths, (0, 1, 2, 3, 4))
self.assertEqual(dp1.concentrations, (1, 1, 1, 1, 1))
self.assertEqual(dp2.concentrations, (2, 2, 2, 2, 2))
self.assertEqual(dp1.events, (1, 1, 1, 1, 1))
self.assertEqual(dp2.events, (2, 2, 2, 2, 2))
self.assertEqual(dp1.element, Element.from_string("Si"))
self.assertEqual(dp2.element, Element.from_string("Si"))
# Testing merging at different depths
dp3 = dp1.merge(dp2, 1, 3.5)
self.assertEqual((1, 2, 2, 2, 1), dp3.concentrations)
dp3 = dp1.merge(dp2, 0.5, 4)
self.assertEqual((1, 2, 2, 2, 2), dp3.concentrations)
dp3 = dp1.merge(dp2, -1, 6)
self.assertEqual((2, 2, 2, 2, 2), dp3.concentrations)
dp3 = dp2.merge(dp1, 4, 6)
self.assertEqual((2, 2, 2, 2, 1), dp3.concentrations)
dp3 = dp2.merge(dp1, 3, 2)
self.assertEqual((2, 2, 2, 2, 2), dp3.concentrations)
def test_adding(self):
dp1 = DepthProfile([0, 1, 2], [10, 11, 12], [21, 22, 23],
element=Element.from_string("Si"))
dp2 = DepthProfile([0, 1, 2], [15, 16, 17], [31, 32, 33],
element=Element.from_string("C"))
dp3 = dp1 + dp2
self.assertIsInstance(dp3, DepthProfile)
self.assertEqual(dp3.depths, (0, 1, 2))
self.assertEqual(dp3.concentrations, (25, 27, 29))
self.assertIsNone(dp3.events)
self.assertEqual(dp3.get_profile_name(), "total")
# DepthProfile can be incremented by another DepthProfile
dp3 += dp3
self.assertEqual(dp3.depths, (0, 1, 2))
self.assertEqual(dp3.concentrations, (50, 54, 58))
self.assertIsNone(dp3.events)
self.assertEqual(dp3.get_profile_name(), "total")
# Arbitrary collection of tuples cannot be added
self.assertRaises(
TypeError, lambda: dp3 + ((0, 1, 2), (10, 11, 12), (21, 22, 23)))
def test_match_elements_to_strs(self):
strs = ["Si", "10C", "C", "12"]
elements = [
Element.from_string("Si"),
Element.from_string("10C"),
Element.from_string("12C"),
Element.from_string("Br")
]
matches = comp.match_elements_to_strs(elements, strs)
self.assertEqual(next(matches), (Element.from_string("Si"), "Si"))
self.assertEqual(next(matches), (Element.from_string("10C"), "10C"))
self.assertEqual(next(matches), (Element.from_string("12C"), "C"))
self.assertEqual(next(matches), (Element.from_string("Br"), None))
# Matches has been exhausted and this will produce an
# exception
self.assertRaises(StopIteration, lambda: next(matches))
def setUpClass(cls):
# default recoil element
cls.elem_4he = RecoilElement(Element.from_string("4He"), [], "red")
# Valid file names for the recoil element
cls.valid_erd_files = ["4He-Default.101.erd", "4He-Default.102.erd"]
# Invalid file names for the recoil element
cls.invalid_erd_files = [
"4He-Default.101", ".4He-Default.102.erd", ".4He-Default..erd",
"4He-Default.101.erf", "4He-Default./.103.erd",
"4He-Default.\\.104.erd", "3He-Default.102.erd"
]
cls.expected_values = [(Path(f), s + 101)
for s, f in enumerate(cls.valid_erd_files)]
def load_properties_from_file(self, file_path: Path):
# TODO create a base class for settings widgets to get rid of this
# copy-paste code
def err_func(err: Exception):
if self.preset_widget is not None:
self.preset_widget.set_status_msg(
f"Failed to load preset: {err}")
values = self._load_json_file(file_path, error_func=err_func)
if not values:
return
try:
values["beam_ion"] = Element.from_string(values["beam_ion"])
self.set_properties(**values)
except KeyError as e:
err_func(f"file contained no {e} key.")
except ValueError as e:
err_func(e)
def test_match_strs_to_elements(self):
strs = ["Si", "10C", "C", "12"]
elements = [
Element.from_string("Si"),
Element.from_string("10C"),
Element.from_string("12C")
]
matches = comp.match_strs_to_elements(strs, elements)
self.assertEqual(("Si", Element.from_string("Si")), next(matches))
self.assertEqual(("10C", Element.from_string("10C")), next(matches))
self.assertEqual(("C", Element.from_string("12C")), next(matches))
self.assertEqual(("12", None), next(matches))
def test_serialization(self):
with tempfile.TemporaryDirectory() as tmp_dir:
file_path = fp.get_recoil_file_path(self.rec_elem, tmp_dir)
self.rec_elem.to_file(tmp_dir)
rec_elem2 = RecoilElement.from_file(file_path,
channel_width=self.ch_width,
rec_type=self.rec_type)
self.compare_rec_elems(self.rec_elem, rec_elem2)
# Test with an empty list of points and no rec_type or ch_width
rec_elem3 = RecoilElement(Element.from_string("O"), [])
file_path = fp.get_recoil_file_path(rec_elem3, tmp_dir)
rec_elem3.to_file(tmp_dir)
rec_elem4 = RecoilElement.from_file(file_path)
self.compare_rec_elems(rec_elem3, rec_elem4)
self.assertFalse(os.path.exists(tmp_dir))
def test_get_erd_file_path(self):
rec_elem = RecoilElement(Element.from_string("He"), [], "red")
self.assertEqual("He-Default.101.erd",
fp.get_erd_file_name(rec_elem, 101))
self.assertEqual("He-Default.102.erd",
fp.get_erd_file_name(rec_elem, 102))
self.assertEqual(
"He-opt.101.erd",
fp.get_erd_file_name(
rec_elem, 101, optim_mode=OptimizationType.RECOIL))
self.assertEqual(
"He-optfl.101.erd",
fp.get_erd_file_name(
rec_elem, 101, optim_mode=OptimizationType.FLUENCE))
self.assertRaises(ValueError,
lambda: fp.get_erd_file_name(rec_elem, 101,
optim_mode="foo"))
def test_iteration(self):
"""Tests that a DepthProfile object can be iterated over."""
# Testing element profile
dp = DepthProfile([i for i in range(10)], [i for i in range(10, 20)],
[i for i in range(20, 30)],
element=Element.from_string("Si"))
x1 = (i for i in range(10))
x2 = (i for i in range(10, 20))
x3 = (i for i in range(20, 30))
for val in dp:
self.assertEqual((next(x1), next(x2), next(x3)), val)
self.assertEqual(10, len(list(dp)))
# Testing total profile
dp = DepthProfile([i for i in range(10)], [i for i in range(10, 20)])
x1 = (i for i in range(10))
x2 = (i for i in range(10, 20))
for val in dp:
self.assertEqual((next(x1), next(x2), 0), val)
self.assertEqual(10, len(list(dp)))
# profile can be iterated over multiple times
for i in range(3):
x1 = (i for i in range(10))
x2 = (i for i in range(10, 20))
for val in dp:
self.assertEqual((next(x1), next(x2), 0), val)
# iteration restarts after break
for val in dp:
self.assertEqual((0, 10, 0), val)
break
for val in dp:
self.assertEqual((0, 10, 0), val)
break
def test_ion_binding(self):
# This is the default beam ion
elem = Element("Cl", 35)
self.assertEqual(elem, self.mesu_widget.beam_ion)
self.assertFalse(self.mesu_widget.are_values_changed())
# Change the ion and assert that values are changed and correct
# values are shown in inputs
elem = Element.from_string("13C")
self.mesu_widget.beam_ion = elem
self.assertTrue(self.mesu_widget.are_values_changed())
self.assertIsNot(elem, self.mesu_widget.beam_ion)
self.assertEqual(elem, self.mesu_widget.beam_ion)
self.assertEqual("C", self.mesu_widget.beamIonButton.text())
self.assertEqual(
13,
self.mesu_widget.isotopeComboBox.currentData()["element"].isotope)
# Set ion to None
self.mesu_widget.beam_ion = None
self.assertIsNone(self.mesu_widget.beam_ion)
self.assertEqual("Select", self.mesu_widget.beamIonButton.text())
self.assertFalse(self.mesu_widget.isotopeComboBox.isEnabled())
def test_from_string(self):
self.assertRaises(ValueError, lambda: Element.from_string(""))
self.assertRaises(ValueError, lambda: Element.from_string("4"))
self.assertRaises(ValueError, lambda: Element.from_string("2 2"))
e = Element.from_string("He")
self.assertEqual("He", e.symbol)
self.assertIsNone(e.isotope)
self.assertEqual(0, e.amount)
e = Element.from_string("4He")
self.assertEqual("He", e.symbol)
self.assertEqual(4, e.isotope)
e = Element.from_string("3H 2")
self.assertEqual("H", e.symbol)
self.assertEqual(3, e.isotope)
self.assertEqual(2, e.amount)
def _accept_params(self, *_):
"""Accept given parameters.
Args:
*_: unused event args
"""
self.status_msg = ""
sbh = StatusBarHandler(self.statusbar)
sbh.reporter.report(10)
try:
output_dir = self.measurement.get_depth_profile_dir()
# Get the filepaths of the selected items
used_cuts = self.used_cuts
DepthProfileDialog.checked_cuts[self.measurement.name] = set(
used_cuts)
# TODO could take care of RBS selection here
elements = [
Element.from_string(fp.name.split(".")[1]) for fp in used_cuts
]
x_unit = self.x_axis_units
DepthProfileDialog.x_unit = x_unit
DepthProfileDialog.line_zero = self.show_zero_line
DepthProfileDialog.line_scale = self.show_scale_line
DepthProfileDialog.systerr = self.systematic_error
DepthProfileDialog.used_eff = self.show_used_eff
DepthProfileDialog.eff_files_str = self.eff_files_str
sbh.reporter.report(20)
# If items are selected, proceed to generating the depth profile
if used_cuts:
self.status_msg = "Please wait. Creating depth profile."
if self.parent.depth_profile_widget:
self.parent.del_widget(self.parent.depth_profile_widget)
# If reference density changed, update value to measurement
if x_unit == DepthProfileUnit.NM:
_, _, _, profile, measurement = \
self.measurement.get_used_settings()
if profile.reference_density != self.reference_density:
profile.reference_density = self.reference_density
measurement.to_file()
self.parent.depth_profile_widget = DepthProfileWidget(
self.parent,
output_dir,
used_cuts,
elements,
x_unit,
DepthProfileDialog.line_zero,
DepthProfileDialog.used_eff,
DepthProfileDialog.line_scale,
DepthProfileDialog.systerr,
DepthProfileDialog.eff_files_str,
progress=sbh.reporter.get_sub_reporter(
lambda x: 30 + 0.6 * x))
sbh.reporter.report(90)
icon = self.parent.icon_manager.get_icon(
"depth_profile_icon_2_16.png")
self.parent.add_widget(self.parent.depth_profile_widget,
icon=icon)
self.close()
else:
self.status_msg = "Please select .cut file[s] to create " \
"depth profiles."
except Exception as e:
error_log = f"Exception occurred when trying to create depth " \
f"profiles: {e}"
self.measurement.log_error(error_log)
finally:
sbh.reporter.report(100)
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 test_eq(self):
self.assertEqual(Element.from_string("He"), Element.from_string("He"))
self.assertEqual(Element.from_string("4He"),
Element.from_string("4He"))
self.assertEqual(Element.from_string("4He 2"),
Element.from_string("4He 2.00"))
self.assertEqual(Element("He", 4, 2), Element("He", 4, 2.00))
self.assertEqual(Element("He", 4, 0), Element("He", 4))
self.assertEqual(Element("He"), Element("He", None))
self.assertNotEqual(Element.from_string("4He 2"),
Element.from_string("4He 1"))
self.assertNotEqual(Element.from_string("3He"),
Element.from_string("4He"))
self.assertNotEqual(Element.from_string("He"),
Element.from_string("4He"))
self.assertNotEqual(Element.from_string("He"),
Element.from_string("H"))
self.assertNotEqual(Element.from_string("H"), "H")
def test_lt(self):
elems = [
Element.from_string("H"),
Element.from_string("He"),
Element.from_string("C"),
Element.from_string("C 2"),
Element.from_string("4C"),
Element.from_string("5C"),
Element.from_string("15Si"),
Element.from_string("Mn"),
Element.from_string("Mn 2"),
Element.from_string("16Mn"),
Element.from_string("243Bk"),
Element.from_string("250Cf")
]
orig_elems = list(elems)
random.shuffle(elems)
self.assertEqual(orig_elems, sorted(elems))
def test_get_mcerd_params(self):
beam = Beam(ion=Element.from_string("4He"), energy=14)
self.assertEqual(["Beam ion: 4He", "Beam energy: 14 MeV"],
beam.get_mcerd_params())
def _make_legend_box(self) -> None:
"""Make legend box for the graph.
"""
box = self.axes.get_position()
if not self._position_set:
self.axes.set_position(
[box.x0, box.y0, box.width * 0.8, box.height])
self._position_set = True
handles, labels = self.axes.get_legend_handles_labels()
# Calculate values to be displayed in the legend box
# TODO make profile_handler use Element objects as keys so
# there is no need to do this conversion
ignored_str = set(str(elem) for elem in self._ignore_from_ratio)
lim_a, lim_b = self._limit_lines.get_range()
if self._absolute_values:
concentrations = self._profile_handler.integrate_concentrations(
lim_a, lim_b)
percentages, moes = {}, {}
else:
percentages, moes = self._profile_handler.calculate_ratios(
ignored_str, lim_a, lim_b, self._systematic_error)
concentrations = {}
# Fixes labels to proper format, with MoE
labels_w_percentages = []
rbs_values = {elem.symbol for elem in self._rbs_list.values()}
for element_str in labels:
element = Element.from_string(element_str)
if element.isotope is None:
element_isotope = ""
else:
element_isotope = str(element.isotope)
rbs_asterisk = "*" if element_str in rbs_values else ""
element_name = f"{element.symbol}{rbs_asterisk}"
elem_lbl = f"$^{{{element_isotope}}}${element_name}"
if not self._absolute_values and percentages[element_str] is not \
None:
percentage = percentages[element_str]
moe = moes[element_str]
rounding = mf.get_rounding_decimals(moe)
if rounding:
str_ratio = f"{round(percentage, rounding)}%"
str_err = f"± {round(moe, rounding)}%"
else:
str_ratio = f"{int(percentage)}%"
str_err = f"± {int(moe)}%"
lbl_str = f"{elem_lbl} {str_ratio:<6} {str_err}"
else:
lbl_str = f"{element_isotope:>3}{element_name:<3}"
# Uses absolute values for the elements instead of percentages.
if self._absolute_values:
conc = concentrations[element_str]
lbl_str = f"{elem_lbl} {round(conc, 3):<7} at./1e15 at./cm²"
labels_w_percentages.append(lbl_str)
leg = self.axes.legend(handles,
labels_w_percentages,
loc=3,
bbox_to_anchor=(1, 0),
borderaxespad=0,
prop={
"size": 11,
"family": "monospace"
})
# If "Show used efficiency files" is checked and text-object is not
# yet created.
if self._show_eff_files and self.eff_text is None:
eff_str = self.used_eff_str.replace("\t", "")
# Set position of text according to amount of lines in the string
line_count = eff_str.count("\n") + 1
y_position_txt = 1 - 0.08 * line_count
x_position_txt = 1.01
self.eff_text = self.axes.text(x_position_txt,
y_position_txt,
eff_str,
transform=self.axes.transAxes,
fontsize=11,
fontfamily="monospace")
for handle in leg.legendHandles:
handle.set_linewidth(3.0)
def on_draw(self):
"""Draw method for matplotlib.
"""
# Values for zoom
x_min, x_max = self.axes.get_xlim()
y_min, y_max = self.axes.get_ylim()
x_min_changed = False
self.axes.clear() # Clear old stuff
self.axes.set_ylabel("Yield (counts)")
self.axes.set_xlabel("Energy (MeV)")
# TODO refactor the draw function so that measurement and simulation
# do not use so many lines of different code
if isinstance(self.parent.parent.obj, Measurement):
element_counts = {}
keys = [item[0] for item in sorted(self.histed_files.items(),
key=lambda x: self.__sortt(
x[0]))]
for key in keys:
cut_file = key.split('.')
cut = self.histed_files[key]
element_object = Element.from_string(cut_file[0])
element = element_object.symbol
isotope = element_object.isotope
if key in self.__ignore_elements:
continue
# Check RBS selection
rbs_string = ""
if len(cut_file) == 3:
if key + ".cut" in self.__rbs_list:
element_object = self.__rbs_list[key + ".cut"]
element = element_object.symbol
isotope = element_object.isotope
rbs_string = "*"
else:
if key in self.__rbs_list:
element_object = self.__rbs_list[key]
element = element_object.symbol
isotope = element_object.isotope
rbs_string = "*"
x, y = get_axis_values(cut)
x_min, x_min_changed = fix_minimum(x, x_min)
if isotope is None:
isotope = ""
# Get color for selection
dirtyinteger = 0
if rbs_string == "*":
color_string = "{0}{1}{2}{3}".format("RBS_", isotope,
element, dirtyinteger)
else:
color_string = "{0}{1}{2}".format(isotope, element,
dirtyinteger)
while color_string in element_counts:
dirtyinteger += 1
if rbs_string == "*":
color_string = "{0}{1}{2}{3}".format("RBS_", isotope,
element,
dirtyinteger)
else:
color_string = "{0}{1}{2}".format(isotope, element,
dirtyinteger)
element_counts[color_string] = 1
if color_string not in self.__selection_colors:
color = "red"
else:
color = self.__selection_colors[color_string]
if len(cut_file) == 3:
label = r"$^{" + str(isotope) + "}$" + element + rbs_string
else:
label = r"$^{" + str(isotope) + "}$" + element \
+ rbs_string + "$_{split: " + cut_file[2] + "}$"
line, = self.axes.plot(x, y, color=color, label=label,
linestyle=self.default_linestyle)
self.plots[key] = line
else: # Simulation energy spectrum
if self.__ignore_elements:
self.files_to_draw = self.remove_ignored_elements()
else:
self.files_to_draw = copy.deepcopy(self.histed_files)
for key, data in self.files_to_draw.items():
# Parse the element symbol and isotope.
file_name = key.name
isotope = ""
symbol = ""
color = None
suffix = ""
if file_name.endswith(".hist"):
measurement_name, isotope_and_symbol, erd_or_rbs, rest = \
file_name.split('.', 3)
if "ERD" in erd_or_rbs:
element = Element.from_string(isotope_and_symbol)
else:
if "RBS_" in erd_or_rbs:
i = erd_or_rbs.index("RBS_")
scatter_element_str = erd_or_rbs[i + len("RBS_"):]
element = Element.from_string(scatter_element_str)
else:
element = Element("")
suffix = "*"
isotope = element.isotope
if isotope is None:
isotope = ""
symbol = element.symbol
rest_split = rest.split(".")
if "no_foil" in rest_split:
# TODO make a function that splits all the necessary
# parts from a file name at once so there is no
# need to do these kinds of checks
rest_split.remove("no_foil")
if len(rest_split) == 2: # regular hist file
label = r"$^{" + str(isotope) + "}$" + symbol + suffix \
+ " (exp)"
else: # split
label = r"$^{" + str(isotope) + "}$" + symbol + suffix \
+ "$_{split: " + rest_split[1] + "}$"" (exp)"
elif file_name.endswith(".simu"):
for s in file_name:
if s != "-":
if s.isdigit():
isotope += s
else:
symbol += s
else:
break
recoil_name_with_end = file_name.split('-', 1)[1]
recoil_name = recoil_name_with_end.split('.')[0]
label = r"$^{" + isotope + "}$" + symbol + " " + recoil_name
for used_recoil in self.__used_recoils:
used_recoil_file_name = \
f"{used_recoil.get_full_name()}.simu"
if used_recoil_file_name == file_name:
color = used_recoil.color
break
else:
label = file_name
x, y = get_axis_values(data)
x_min, x_min_changed = fix_minimum(x, x_min)
if not color:
line, = self.axes.plot(x, y, label=label,
linestyle=self.default_linestyle)
else:
line, = self.axes.plot(x, y, label=label, color=color,
linestyle=self.default_linestyle)
self.plots[key] = line
if self.draw_legend:
if not self.__initiated_box:
self.fig.tight_layout(pad=0.5)
box = self.axes.get_position()
self.axes.set_position([box.x0, box.y0,
box.width * 0.9, box.height])
self.__initiated_box = True
handles, labels = self.axes.get_legend_handles_labels()
self.leg = self.axes.legend(handles,
labels,
loc=3,
bbox_to_anchor=(1, 0),
borderaxespad=0,
prop={'size': 12})
for handle in self.leg.legendHandles:
handle.set_linewidth(3.0)
if 0.09 < x_max < 1.01: # This works...
x_max = self.axes.get_xlim()[1]
if 0.09 < y_max < 1.01:
y_max = self.axes.get_ylim()[1]
# Set limits accordingly
self.axes.set_ylim([y_min, y_max])
if x_min_changed:
self.axes.set_xlim([x_min - self.parent.bin_width, x_max])
else:
self.axes.set_xlim([x_min, x_max])
if self.__log_scale:
self.axes.set_yscale("symlog")
# Remove axis ticks
self.remove_axes_ticks()
# Draw magic
self.canvas.draw()
def __init__(self,
parent: BaseTab,
output_dir: Path,
cut_files: List[Path],
elements: List[Element],
x_units: DepthProfileUnit,
line_zero: bool,
used_eff: bool,
line_scale: bool,
systematic_error: float,
eff_files_str: str,
progress: Optional[ProgressReporter] = None):
"""Inits widget.
Args:
parent: a MeasurementTabWidget.
output_dir: full path to depth file location
cut_files: A list of Cut files.
elements: A list of Element objects that are used in depth profile.
x_units: Units to be used for x-axis of depth profile.
line_zero: A boolean representing if vertical line is drawn at zero.
used_eff: A boolean representing if used eff files are shown.
line_scale: A boolean representing if horizontal line is drawn at
the defined depth scale.
systematic_error: A double representing systematic error.
"""
try:
super().__init__()
uic.loadUi(gutils.get_ui_dir() / "ui_depth_profile.ui", self)
self.parent = parent
self.measurement: Measurement = parent.obj
self.output_dir = output_dir
self.elements = elements
self.x_units = x_units
self.use_cuts = cut_files
self._line_zero_shown = line_zero
self._eff_files_shown = used_eff
self._eff_files_str = eff_files_str
self._line_scale_shown = line_scale
self._systematic_error = systematic_error
if progress is not None:
sub_progress = progress.get_sub_reporter(lambda x: 0.5 * x)
else:
sub_progress = None
depth_files.generate_depth_files(self.use_cuts,
self.output_dir,
self.measurement,
progress=sub_progress)
if progress is not None:
progress.report(50)
# Check for RBS selections.
rbs_list = cut_file.get_rbs_selections(self.use_cuts)
for rbs in rbs_list:
# Search and replace instances of Beam element with scatter
# elements.
# When loading request, the scatter element is already
# replaced. This is essentially done only when creating
# a new Depth Profile graph.
# TODO seems overly complicated. This stuff should be sorted
# before initializing the widget
element = Element.from_string(rbs.split(".")[0])
for i, elem in enumerate(elements):
if elem == element:
elements[i] = rbs_list[rbs]
if self._line_scale_shown:
_, _, _, profile, _ = self.measurement.get_used_settings()
depth_scale = (profile.depth_for_concentration_from,
profile.depth_for_concentration_to)
else:
depth_scale = None
if progress is not None:
sub_progress = progress.get_sub_reporter(
lambda x: 50 + 0.5 * x)
else:
sub_progress = None
self.matplotlib = MatplotlibDepthProfileWidget(
self,
self.output_dir,
self.elements,
rbs_list,
icon_manager=self.parent.icon_manager,
selection_colors=self.measurement.selector.get_colors(),
depth_scale=depth_scale,
x_units=self.x_units,
add_line_zero=self._line_zero_shown,
show_eff_files=self._eff_files_shown,
used_eff_str=self._eff_files_str,
systematic_error=self._systematic_error,
progress=sub_progress)
except Exception as e:
msg = f"Could not create Depth Profile graph: {e}"
self.measurement.log_error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
finally:
if progress is not None:
progress.report(100)
def make_depth_profile(self,
directory: Path,
name: str,
serial_number_m: int,
sample_folder_name: str,
progress=None):
"""Make depth profile from loaded lines from saved file.
Args:
directory: A path to depth files directory.
name: A string representing measurement's name.
serial_number_m: Measurement's serial number.
sample_folder_name: Sample's serial number.
progress: a ProgressReporter object
"""
file = Path(directory, DepthProfileWidget.save_file)
lines = MeasurementTabWidget._load_file(file)
if not lines:
return
m_name = self.obj.name
try:
base = Measurement.DIRECTORY_PREFIX
# TODO add sample prefix
old_folder_prefix = base + "%02d" % serial_number_m
new_folder_prefix = base + "%02d" % self.obj.serial_number
new_sample_name = "Sample_" + "%02d" % \
self.obj.sample.serial_number + "-" + \
self.obj.sample.name
output_dir = self.__confirm_filepath(lines[0].strip(), name,
m_name, old_folder_prefix,
new_folder_prefix,
sample_folder_name,
new_sample_name)
use_cuts = self.__confirm_filepath(lines[2].strip().split("\t"),
name, m_name, old_folder_prefix,
new_folder_prefix,
sample_folder_name,
new_sample_name)
elements_string = lines[1].strip().split("\t")
elements = [
Element.from_string(element) for element in elements_string
]
try:
x_unit = DepthProfileUnit(lines[3].strip())
except ValueError:
x_unit = DepthProfileUnit.ATOMS_PER_SQUARE_CM
line_zero = False
line_scale = False
systerr = 0.0
if len(lines) == 7: # "Backwards compatibility"
line_zero = lines[4].strip() == "True"
line_scale = lines[5].strip() == "True"
systerr = float(lines[6].strip())
DepthProfileDialog.x_unit = x_unit
DepthProfileDialog.checked_cuts[m_name] = set(use_cuts)
DepthProfileDialog.line_zero = line_zero
DepthProfileDialog.line_scale = line_scale
DepthProfileDialog.systerr = systerr
self.depth_profile_widget = DepthProfileWidget(self,
output_dir,
use_cuts,
elements,
x_unit,
line_zero,
line_scale,
systerr,
progress=progress)
icon = self.icon_manager.get_icon("depth_profile_icon_2_16.png")
self.add_widget(self.depth_profile_widget, icon=icon)
except Exception as e:
# We do not need duplicate error logs, log in widget instead
print(e)
def on_draw(self):
"""Draw method for matplotlib.
"""
self.axes.clear() # Clear old stuff
# keys = sorted(self.split.keys())
keys = [
item[0] for item in sorted(self.split.items(),
key=lambda x: self.__sortt(x[0]))
]
for key in keys:
cut_file = key.split('.')
# TODO provide elements as parameter rather than initializing
# them here
element_object = Element.from_string(cut_file[0].strip())
element = element_object.symbol
isotope = element_object.isotope
if key in self.__ignore_elements:
continue
if self.reference_cut_key and key == self.reference_cut_key:
continue
# Check RBS selection
rbs_string = ""
if len(cut_file) == 3:
if key + ".cut" in self.__rbs_list:
element_object = self.__rbs_list[key + ".cut"]
element = element_object.symbol
isotope = element_object.isotope
rbs_string = "*"
else:
if key in self.__rbs_list:
element_object = self.__rbs_list[key]
element = element_object.symbol
isotope = element_object.isotope
rbs_string = "*"
# Get color for selection
if isotope is None:
isotope = ""
if rbs_string == "*":
color_string = "{0}{1}{2}".format("RBS_" + isotope, element,
cut_file[2])
else:
color_string = "{0}{1}{2}".format(isotope, element,
cut_file[2])
color = self.selection_colors.get(color_string, "red")
# Set label text
if len(cut_file) == 3:
label = r"$^{" + str(isotope) + "}$" + element + rbs_string
else:
label = r"$^{" + str(isotope) + "}$" + element + rbs_string \
+ "$_{split: " + cut_file[3] + "}$"
# Modify data if scaled to 100.
data = self.split[key]
if self.__scale_mode == 2:
n = None
for val in data:
if val == 0:
continue
else:
n = val
break
modifier = 100 / n # self.split[key][0]
data = [i * modifier for i in data]
self.axes.plot(data, color=color, label=label)
if self.draw_legend:
if not self.__initiated_box:
self.fig.tight_layout(pad=0.5)
box = self.axes.get_position()
self.axes.set_position(
[box.x0, box.y0, box.width * 0.9, box.height])
self.__initiated_box = True
handles, labels = self.axes.get_legend_handles_labels()
leg = self.axes.legend(handles,
labels,
loc=3,
bbox_to_anchor=(1, 0),
borderaxespad=0,
prop={'size': 12})
for handle in leg.legendHandles:
handle.set_linewidth(3.0)
# Scale based on values
x_min, x_max = self.axes.get_xlim()
y_min, y_max = self.axes.get_ylim()
# Y-axis scaling option, 0 = 0-max, 1 = min-max
if self.y_scale == 0:
y_min = 0
# Set limits accordingly
self.axes.set_ylim([y_min, y_max])
self.axes.set_xlim([x_min, x_max])
# Scale for log
if self.__scale_mode == 1:
self.axes.set_yscale('symlog')
else:
self.axes.set_yscale('linear')
# Set axes names
if self.__scale_mode == 2:
self.axes.set_ylabel("Scaled count")
else:
self.axes.set_ylabel("Count")
self.axes.set_xlabel("Split")
# Remove axis ticks
self.remove_axes_ticks()
self.canvas.draw()