def test_get_rbs_selections(self):
with tempfile.TemporaryDirectory() as tmp_dir:
path = Path(tmp_dir, self.rel_dir)
self._generate_cut_files(path)
files = [Path(entry.path) for entry in os.scandir(path)]
rbs = cut_file.get_rbs_selections(files)
self.assertEqual(
{
"1He.RBS_He.0.cut": mo.get_element(symbol="He"),
"He.RBS_Cl.0.cut": mo.get_element(symbol="Cl"),
"He.RBS_Cl.1.cut": mo.get_element(symbol="Cl"),
}, rbs)
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 __init__(self, parent, measurement: Measurement,
reference_cut_file: Path, checked_cuts: List[Path],
partition_count: int, y_scale: int, statusbar=None,
progress=None):
"""Inits widget.
Args:
parent: A MeasurementTabWidget.
reference_cut_file: absolute path to cut file.
checked_cuts: list of absolute paths to cut files.
partition_count: Integer representing how many splits cut files
are divided to.
y_scale: Integer flag representing how Y axis is scaled.
progress: a ProgressReporter object
"""
try:
super().__init__()
uic.loadUi(gutils.get_ui_dir() / "ui_element_losses.ui", self)
self.parent = parent
self.icon_manager = parent.icon_manager
self.measurement = measurement
self.reference_cut_file = reference_cut_file
self.checked_cuts = checked_cuts
self.partition_count = partition_count
self.y_scale = y_scale
self.statusbar = statusbar
title = "{0} - Reference cut: {1}".format(
self.windowTitle(),
self.reference_cut_file.name)
self.setWindowTitle(title)
# Calculate elemental losses
self.losses = ElementLosses(
self.measurement.get_cuts_dir(),
self.measurement.get_composition_changes_dir(),
self.reference_cut_file,
self.checked_cuts,
self.partition_count)
if progress is not None:
sub_progress = progress.get_sub_reporter(
lambda x: 0.9 * x
)
else:
sub_progress = None
self.split_counts = self.losses.count_element_cuts(
progress=sub_progress
)
# Check for RBS selections.
rbs_list = cut_file.get_rbs_selections(self.checked_cuts)
# Connect buttons
self.splitSaveButton.clicked.connect(self.__save_splits)
self.matplotlib = MatplotlibElementLossesWidget(
self, self.split_counts, legend=True, y_scale=y_scale,
rbs_list=rbs_list, reference_cut_file=reference_cut_file)
except Exception as e:
msg = f"Could not create Elemental Losses graph: {e}"
self.measurement.log_error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
finally:
if progress is not None:
progress.report(100)
def __init__(self,
parent: BaseTab,
spectrum_type: str = MEASUREMENT,
use_cuts=None,
bin_width=0.025,
use_efficiency=False,
save_file_int=0,
statusbar=None,
spectra_changed=None):
"""Inits widget.
Args:
parent: A TabWidget.
use_cuts: A string list representing Cut files.
bin_width: A float representing Energy Spectrum histogram's bin
width.
use_efficiency: whether efficiency is taken into account when
measured spectra is calculated
save_file_int: n integer to have unique save file names for
simulation energy spectra combinations.
spectra_changed: pyqtSignal that indicates a change in energy
spectra.
"""
sbh = None
super().__init__()
uic.loadUi(gutils.get_ui_dir() / "ui_energy_spectrum.ui", self)
try:
self.parent = parent
self.icon_manager = parent.icon_manager
self.progress_bar = None
if use_cuts is None:
use_cuts = []
self.use_cuts = use_cuts
self.bin_width = bin_width
self.energy_spectrum_data = {}
self.spectrum_type = spectrum_type
rbs_list = {}
title = f"{self.windowTitle()} - Bin Width: {bin_width}"
self.setWindowTitle(title)
if isinstance(self.parent.obj, Measurement):
self.measurement = self.parent.obj
# Removal is done in the finally block so autoremove
# is set to False
sbh = StatusBarHandler(statusbar, autoremove=False)
# Do energy spectrum stuff on this
self.energy_spectrum_data = \
EnergySpectrum.calculate_measured_spectra(
self.measurement, use_cuts, bin_width,
progress=sbh.reporter, use_efficiency=use_efficiency
)
# Check for RBS selections.
rbs_list = cut_file.get_rbs_selections(self.use_cuts)
else:
self.simulation = self.parent.obj
self.save_file_int = save_file_int
self.save_file = f"widget_energy_spectrum_{save_file_int}.save"
for file in use_cuts:
self.energy_spectrum_data[file] = GetEspe.read_espe_file(
file)
# Graph in matplotlib widget and add to window
self.matplotlib = MatplotlibEnergySpectrumWidget(
self,
self.energy_spectrum_data,
rbs_list,
spectrum_type,
spectra_changed=spectra_changed,
channel_width=bin_width)
except (PermissionError, IsADirectoryError, FileNotFoundError) as e:
# If the file path points to directory, this will either raise
# PermissionError (Windows) or IsADirectoryError (Mac)
msg = f"Could not create Energy Spectrum graph: {e}"
self.parent.obj.log_error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
self.matplotlib = None
finally:
if sbh is not None:
sbh.remove_progress_bar()