class DetectorsPresenterTest(unittest.TestCase):
def setUp(self):
self.mock_view = mock.Mock()
self.mock_view.widgets = {
'name1': 'GE1',
'name2': 'GE2',
'name3': 'GE3'
}
self.detector_presenter = DetectorsPresenter(self.mock_view)
def test_that_all_view_widgets_are_appended_to_detector_list(self):
self.assertEqual(self.detector_presenter.detectors,
list(self.mock_view.widgets.values()))
def test_that_setStateQuietly_calls_view_setStateQuietly(self):
name = 'name'
state = 3
self.detector_presenter.setStateQuietly(name, state)
self.mock_view.setStateQuietly.assert_called_with(name, state)
self.assertEqual(self.mock_view.setStateQuietly.call_count, 1)
def test_that_get_names_gives_correct_list_of_names(self):
self.assertEqual(self.detector_presenter.getNames(),
self.mock_view.widgets.keys())
def setUp(self):
self.mock_view = mock.Mock()
self.mock_view.widgets = {
'name1': 'GE1',
'name2': 'GE2',
'name3': 'GE3'
}
self.detector_presenter = DetectorsPresenter(self.mock_view)
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
self.ptable = PeriodicTablePresenter(PeriodicTableView(),
PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
self.load_widget = LoadPresenter(LoadView(), LoadModel(),
CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
self.widget_list = QtGui.QVBoxLayout()
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
self.plotting = PlotPresenter(PlotView())
self.plotting.view.setMinimumSize(self.plotting.view.sizeHint())
self.box = QtGui.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtGui.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_data = {}
self.element_lines = {}
self.gamma_lines = []
self.gamma_peaks = self.ptable.peak_data["Gammas"]
self.electron_peaks = self._get_electron_peaks()
self.electron_lines = []
self._generate_element_widgets()
self._generate_element_data()
self.line_colours = cycle(["r", "g", "b", "c", "m", "y"])
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
# set menu
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
# periodic table stuff
self.ptable = PeriodicTablePresenter(PeriodicTableView(),
PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
# load stuff
self.load_widget = LoadPresenter(LoadView(), LoadModel(),
CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
# detectors
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
# peaks boxes
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.setChecked(True)
self.peaks.major.on_checkbox_checked(self.major_peaks_changed)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_changed)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_changed)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_changed)
self.peaks.gamma.on_checkbox_checked(self.gammas_changed)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_changed)
self.peaks.electron.on_checkbox_checked(self.electrons_changed)
self.peaks.electron.on_checkbox_unchecked(self.electrons_changed)
self.peaks.set_deselect_elements_slot(self.deselect_elements)
# Line type boxes
self.lines = LineSelectorPresenter(LineSelectorView())
self.lines.total.setChecked(True)
self.lines.total.on_checkbox_checked(self.line_total_changed)
self.lines.total.on_checkbox_unchecked(self.line_total_changed)
self.lines.prompt.on_checkbox_checked(self.line_prompt_changed)
self.lines.prompt.on_checkbox_unchecked(self.line_prompt_changed)
self.lines.delayed.on_checkbox_checked(self.line_delayed_changed)
self.lines.delayed.on_checkbox_unchecked(self.line_delayed_changed)
# set up
self.widget_list = QtWidgets.QVBoxLayout()
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.lines.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
# plotting
self.plot_window = None
self.num_colors = len(mpl.rcParams['axes.prop_cycle'])
self.used_colors = {}
# layout
self.box = QtWidgets.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtWidgets.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_lines = {}
self.electron_peaks = {}
self._generate_element_widgets()
class ElementalAnalysisGui(QtWidgets.QMainWindow):
BLUE = 'C0'
ORANGE = 'C1'
GREEN = 'C2'
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
# set menu
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
# periodic table stuff
self.ptable = PeriodicTablePresenter(PeriodicTableView(),
PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
# load stuff
self.load_widget = LoadPresenter(LoadView(), LoadModel(),
CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
# detectors
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
# peaks boxes
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.setChecked(True)
self.peaks.major.on_checkbox_checked(self.major_peaks_changed)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_changed)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_changed)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_changed)
self.peaks.gamma.on_checkbox_checked(self.gammas_changed)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_changed)
self.peaks.electron.on_checkbox_checked(self.electrons_changed)
self.peaks.electron.on_checkbox_unchecked(self.electrons_changed)
self.peaks.set_deselect_elements_slot(self.deselect_elements)
# Line type boxes
self.lines = LineSelectorPresenter(LineSelectorView())
self.lines.total.setChecked(True)
self.lines.total.on_checkbox_checked(self.line_total_changed)
self.lines.total.on_checkbox_unchecked(self.line_total_changed)
self.lines.prompt.on_checkbox_checked(self.line_prompt_changed)
self.lines.prompt.on_checkbox_unchecked(self.line_prompt_changed)
self.lines.delayed.on_checkbox_checked(self.line_delayed_changed)
self.lines.delayed.on_checkbox_unchecked(self.line_delayed_changed)
# set up
self.widget_list = QtWidgets.QVBoxLayout()
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.lines.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
# plotting
self.plot_window = None
self.num_colors = len(mpl.rcParams['axes.prop_cycle'])
self.used_colors = {}
# layout
self.box = QtWidgets.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtWidgets.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_lines = {}
self.electron_peaks = {}
self._generate_element_widgets()
def get_color(self, element):
"""
When requesting the colour for a new element, return the first unused colour of the matplotlib
default colour cycle (i.e. mpl.rcParams['axes.prop_cycle']).
If all colours are used, return the first among the least used ones.
That is if C0-4 are all used twice and C5-9 are used once, C5 will be returned.
When requesting the colour for an element that is already plotted return the colour of that element.
This prevents the same element from being displayed in different colours in separate plots
:param element: Chemical symbol of the element that one wants the colour of
:return: Matplotlib colour string: C0, C1, ..., C9 to be used as plt.plot(..., color='C3')
"""
if element in self.used_colors:
return self.used_colors[element]
occurrences = [
list(self.used_colors.values()).count('C{}'.format(i))
for i in range(self.num_colors)
]
color_index = occurrences.index(min(occurrences))
color = "C{}".format(color_index)
self.used_colors[element] = color
return color
def closeEvent(self, event):
if self.plot_window is not None:
self.plot_window.closeEvent(event)
super(ElementalAnalysisGui, self).closeEvent(event)
# general functions
def _gen_label(self, name, x_value_in, element=None):
if element is None:
return
# check x value is a float
try:
x_value = float(x_value_in)
except:
return
if name not in self.element_lines[element]:
self.element_lines[element].append(name)
# make sure the names are strings and x values are numbers
return Label(str(name),
x_value,
False,
offset,
True,
rotation=-90,
protected=True)
def _plot_line(self, name, x_value_in, color, element=None):
label = self._gen_label(name, x_value_in, element)
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self._plot_line_once(subplot, x_value_in, label, color)
def _plot_line_once(self, subplot, x_value, label, color):
self.plotting.add_vline_and_annotate(subplot, x_value, label, color)
def _rm_line(self, name):
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self.plotting.rm_vline_and_annotate(subplot, name)
# setup element pop up
def _generate_element_widgets(self):
self.element_widgets = {}
for element in self.ptable.peak_data:
data = self.ptable.element_data(element)
widget = PeakSelectorPresenter(PeakSelectorView(data, element))
widget.on_finished(self._update_peak_data)
self.element_widgets[element] = widget
# interact with periodic table
def table_right_clicked(self, item):
self.element_widgets[item.symbol].view.show()
def table_left_clicked(self, item):
if self.ptable.is_selected(item.symbol):
self._add_element_lines(item.symbol)
else:
self._remove_element_lines(item.symbol)
def _add_element_lines(self, element, data=None):
if data is None:
data = self.element_widgets[element].get_checked()
if element not in self.element_lines:
self.element_lines[element] = []
# Select a different color, if all used then use the first
color = self.get_color(element)
for name, x_value in data.items():
try:
x_value = float(x_value)
except ValueError:
continue
full_name = gen_name(element, name)
if full_name not in self.element_lines[element]:
self.element_lines[element].append(full_name)
self._plot_line(full_name, x_value, color, element)
def _remove_element_lines(self, element):
if element not in self.element_lines:
return
names = deepcopy(self.element_lines[element])
for name in names:
try:
self.element_lines[element].remove(name)
self._rm_line(name)
if not self.element_lines[element]:
del self.element_lines[element]
if element in self.used_colors:
del self.used_colors[element]
except:
continue
if element in self.element_lines and not self.element_lines[element]:
del self.element_lines[element]
# loading
def load_run(self, detector, run):
name = "{}; Detector {}".format(run, detector[-1])
if self.plot_window is None:
self.plot_window = MultiPlotWindow(str(run))
self.plotting = self.plot_window.multi_plot
self.add_detector_to_plot(detector, name)
self.plotting.set_all_values()
self.plotting.remove_subplot_connection(self.subplot_removed)
self.plotting.remove_line_connection(self.uncheck_on_removed)
self.plot_window.show()
# untick detectors if plot window is closed
self.plot_window.windowClosedSignal.connect(self._unset_detectors)
else:
self.add_detector_to_plot(detector, name)
self.plot_window.show()
self.plot_window.raise_()
def loading_finished(self):
last_run = self.load_widget.last_loaded_run()
if last_run is None:
return
# check all detectors are loaded
num_detectors = self.load_widget.get_run_num_loaded_detectors(last_run)
for j, detector in enumerate(self.detectors.getNames()):
if j < num_detectors:
self.detectors.enableDetector(detector)
else:
# disable checkbox and uncheck box
self.detectors.disableDetector(detector)
self.detectors.setStateQuietly(detector, False)
to_plot = deepcopy(
[det.isChecked() for det in self.detectors.detectors])
if self.plot_window is None and any(to_plot) is False:
return
# generate plots - if new run clear old plot(s) and replace it
if self.plot_window is None:
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
else:
for plot in self.plotting.get_subplots():
self.plotting.remove_subplot(plot)
for j in range(len(to_plot)):
if to_plot[j]:
self.detectors.detectors[j].setChecked(True)
# detectors
def add_detector_to_plot(self, detector, name):
self.plotting.add_subplot(detector)
ws = mantid.mtd[name]
ws.setYUnit('Counts')
# find correct detector number from the workspace group run
if self.lines.total.isChecked():
self.plotting.plot(detector,
ws.name(),
spec_num=spectrum_index["Total"],
color=self.BLUE)
if self.lines.prompt.isChecked():
self.plotting.plot(detector,
ws.name(),
spec_num=spectrum_index["Prompt"],
color=self.ORANGE)
if self.lines.delayed.isChecked():
self.plotting.plot(detector,
ws.name(),
spec_num=spectrum_index["Delayed"],
color=self.GREEN)
# add current selection of lines
for element in self.ptable.selection:
self.add_peak_data(element.symbol, detector)
def _unset_detectors(self):
self.plot_window.windowClosedSignal.disconnect()
self.plot_window = None
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
self.uncheck_detectors_if_no_line_plotted()
# plotting
def add_peak_data(self, element, subplot, data=None):
# if already selected add to just new plot
if data is None:
data = self.element_widgets[element].get_checked()
color = self.get_color(element)
for name, x_value in data.items():
if isinstance(x_value, float):
full_name = gen_name(element, name)
label = self._gen_label(full_name, x_value, element)
self._plot_line_once(subplot, x_value, label, color)
def _update_peak_data(self, element):
if self.ptable.is_selected(element):
# remove all of the lines for the element
self._remove_element_lines(element)
# add the ticked lines to the plot
self._add_element_lines(element)
else:
self._remove_element_lines(element)
def add_plot(self, checkbox):
detector = checkbox.name
last_run = self.load_widget.last_loaded_run()
# not using load_last_run prevents two calls to last_loaded_run()
if last_run is not None:
self.load_run(detector, last_run)
def del_plot(self, checkbox):
if self.load_widget.last_loaded_run() is not None:
self.plotting.remove_subplot(checkbox.name)
if not self.plotting.get_subplots(
) and self.plot_window is not None:
self.plot_window.close()
self.plot_window = None
def subplot_removed(self, name):
# need to change the state without sending signal
# as the plot has already been removed
self.detectors.setStateQuietly(name, False)
if not self.plotting.get_subplots():
self.plot_window.close()
self.plot_window = None
# sets data file for periodic table
def select_data_file(self):
old_lines = deepcopy(list(self.element_lines.keys()))
filename = QtWidgets.QFileDialog.getOpenFileName()
if isinstance(filename, tuple):
filename = filename[0]
filename = str(filename)
if filename:
self.ptable.set_peak_datafile(filename)
try:
self._generate_element_widgets()
except ValueError:
message_box.warning(
'The file does not contain correctly formatted data, resetting to default data file.'
'See "https://docs.mantidproject.org/nightly/interfaces/'
'Muon%20Elemental%20Analysis.html" for more information.')
self.ptable.set_peak_datafile(None)
self._generate_element_widgets()
for element in old_lines:
if element in self.element_widgets.keys():
self.ptable.select_element(element)
else:
self._remove_element_lines(element)
self._update_checked_data()
def _update_checked_data(self):
self.major_peaks_changed(self.peaks.major)
self.minor_peaks_changed(self.peaks.minor)
self.gammas_changed(self.peaks.gamma)
self.electrons_changed(self.peaks.electron)
# general checked data
def checked_data(self, element, selection, state):
for checkbox in selection:
checkbox.setChecked(state)
self._update_peak_data(element)
def electrons_changed(self, electron_peaks):
for element, selector in self.element_widgets.items():
self.checked_data(element, selector.electron_checkboxes,
electron_peaks.isChecked())
def gammas_changed(self, gamma_peaks):
for element, selector in self.element_widgets.items():
self.checked_data(element, selector.gamma_checkboxes,
gamma_peaks.isChecked())
def major_peaks_changed(self, major_peaks):
for element, selector in self.element_widgets.items():
self.checked_data(element, selector.primary_checkboxes,
major_peaks.isChecked())
def minor_peaks_changed(self, minor_peaks):
for element, selector in self.element_widgets.items():
self.checked_data(element, selector.secondary_checkboxes,
minor_peaks.isChecked())
def deselect_elements(self):
self.peaks.disable_deselect_elements_btn()
for element in self.element_widgets.keys():
self.ptable.deselect_element(element)
self._remove_element_lines(element)
self.peaks.enable_deselect_elements_btn()
def add_line_by_type(self, run, _type):
# Ensure all detectors are enabled
last_run = self.load_widget.last_loaded_run()
for i, detector in enumerate(self.detectors.detectors):
if i < self.load_widget.get_run_num_loaded_detectors(last_run):
if not detector.isEnabled():
detector.setEnabled(True)
if self.plot_window is None:
return
# Plot the correct line type on all open subplots
if _type == 'Total':
color = self.BLUE
elif _type == 'Prompt':
color = self.ORANGE
else:
color = self.GREEN
for subplot in self.plotting.get_subplots():
name = '{}; Detector {}'.format(run, subplot[-1])
ws = mantid.mtd[name]
self.plotting.plot(subplot,
ws.name(),
spec_num=spectrum_index[_type],
color=color)
def remove_line_type(self, run, _type):
if self.plot_window is None:
self.uncheck_detectors_if_no_line_plotted()
return
# Remove the correct line type on all open subplots
for subplot in self.plotting.get_subplots():
name = '{}; Detector {}'.format(run, subplot[-1])
ws = mantid.mtd[name]
self.plotting.remove_line(subplot,
ws.name(),
spec=spectrum_index[_type])
# If no line type is selected do not allow plotting
self.uncheck_detectors_if_no_line_plotted()
def uncheck_detectors_if_no_line_plotted(self):
last_run = self.load_widget.last_loaded_run()
if not any([
self.lines.total.isChecked(),
self.lines.prompt.isChecked(),
self.lines.delayed.isChecked()
]):
for i, detector in enumerate(self.detectors.detectors):
if i < self.load_widget.get_run_num_loaded_detectors(last_run):
detector.setEnabled(False)
# When removing a line with the remove window uncheck the line here
def uncheck_on_removed(self, removed_lines):
if sum([
1 if detector.isChecked() else 0
for detector in self.detectors.detectors
]) > 1:
return
for line in removed_lines:
if 'Total' in line:
self.lines.total.blockSignals(True)
self.lines.total.setChecked(False)
self.lines.total.blockSignals(False)
if 'Prompt' in line:
self.lines.prompt.blockSignals(True)
self.lines.prompt.setChecked(False)
self.lines.prompt.blockSignals(False)
if 'Delayed' in line:
self.lines.delayed.blockSignals(True)
self.lines.delayed.setChecked(False)
self.lines.delayed.blockSignals(False)
self.uncheck_detectors_if_no_line_plotted()
# Line total
def line_total_changed(self, line_total):
self.lines.total.setChecked(line_total.isChecked())
if line_total.isChecked():
self.add_line_by_type(self.load_widget.last_loaded_run(), 'Total')
else:
self.remove_line_type(self.load_widget.last_loaded_run(), 'Total')
# Line prompt
def line_prompt_changed(self, line_prompt):
self.lines.prompt.setChecked(line_prompt.isChecked())
if line_prompt.isChecked():
self.add_line_by_type(self.load_widget.last_loaded_run(), 'Prompt')
else:
self.remove_line_type(self.load_widget.last_loaded_run(), 'Prompt')
# Line delayed
def line_delayed_changed(self, line_delayed):
self.lines.delayed.setChecked(line_delayed.isChecked())
if line_delayed.isChecked():
self.add_line_by_type(self.load_widget.last_loaded_run(),
'Delayed')
else:
self.remove_line_type(self.load_widget.last_loaded_run(),
'Delayed')
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
self.ptable = PeriodicTablePresenter(
PeriodicTableView(), PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
self.load_widget = LoadPresenter(
LoadView(), LoadModel(), CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
self.widget_list = QtGui.QVBoxLayout()
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
self.plotting = PlotPresenter(PlotView())
self.plotting.view.setMinimumSize(self.plotting.view.sizeHint())
self.plotting.removeSubplotConnection(self.subplotRemoved)
self.box = QtGui.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtGui.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_data = {}
self.element_lines = {}
self.gamma_lines = []
self.gamma_peaks = self.ptable.peak_data["Gammas"]
self.electron_peaks = self._get_electron_peaks()
self.electron_lines = []
self._generate_element_widgets()
self._generate_element_data()
self.line_colours = cycle(["r", "g", "b", "c", "m", "y"])
class ElementalAnalysisGui(QtGui.QMainWindow):
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
self.ptable = PeriodicTablePresenter(
PeriodicTableView(), PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
self.load_widget = LoadPresenter(
LoadView(), LoadModel(), CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
self.widget_list = QtGui.QVBoxLayout()
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
self.plotting = PlotPresenter(PlotView())
self.plotting.view.setMinimumSize(self.plotting.view.sizeHint())
self.plotting.removeSubplotConnection(self.subplotRemoved)
self.box = QtGui.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtGui.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_data = {}
self.element_lines = {}
self.gamma_lines = []
self.gamma_peaks = self.ptable.peak_data["Gammas"]
self.electron_peaks = self._get_electron_peaks()
self.electron_lines = []
self._generate_element_widgets()
self._generate_element_data()
self.line_colours = cycle(["r", "g", "b", "c", "m", "y"])
def iterate_over_selectors(self, check_state, primary_checkboxes=True):
"""
Iterates over element popups.
:param check_state: True or False - i.e. check boxes or not
:param primary_checkboxes: True if Primary, False if Secondary
"""
for element, selector in iteritems(self.element_widgets):
for checkbox in selector.primary_checkboxes if primary_checkboxes else selector.secondary_checkboxes:
checkbox.setChecked(check_state)
selector.finish_selection()
def major_peaks_checked(self):
self.iterate_over_selectors(True, primary_checkboxes=True)
def major_peaks_unchecked(self):
self.iterate_over_selectors(False, primary_checkboxes=True)
self.plotting.update_canvas()
def minor_peaks_checked(self):
self.iterate_over_selectors(True, primary_checkboxes=False)
def minor_peaks_unchecked(self):
self.iterate_over_selectors(False, primary_checkboxes=False)
self.plotting.update_canvas()
def _plot_gammas(self, subplot, colour=None):
if colour is None:
colour = self.line_colours.next()
for element, peaks in iteritems(self.gamma_peaks):
for peak_type, peak in iteritems(peaks):
if peak is None:
continue
self.gamma_lines.append(
subplot.axvline(
peak, 0, 1, color=colour))
self.plotting.update_canvas()
def _iterate_over_gamma_selectors(self, check_state):
for element, selector in iteritems(self.element_widgets):
for checkbox in selector.gamma_checkboxes:
checkbox.setChecked(check_state)
selector.finish_selection()
def gammas_checked(self):
self._iterate_over_gamma_selectors(True)
def gammas_unchecked(self):
self._iterate_over_gamma_selectors(False)
for line in self.gamma_lines:
line.remove()
del line
self.gamma_lines = []
self.plotting.update_canvas()
def _get_electron_peaks(self):
return self.ptable.peak_data["Electrons"].copy()
def _plot_electrons(self, subplot, colour=None):
if colour is None:
colour = self.line_colours.next()
for peak, intensity in iteritems(self.electron_peaks):
# intensity will be used in the future for labelling lines
self.electron_lines.append(
subplot.axvline(
float(peak), 0, 1, color=colour))
self.plotting.update_canvas()
def electrons_checked(self):
colour = self.line_colours.next()
for subplot_name, subplot in iteritems(self.plotting.get_subplots()):
self._plot_electrons(subplot, colour=colour)
def electrons_unchecked(self):
for line in self.electron_lines:
line.remove()
del line
self.electron_lines = []
self.plotting.update_canvas()
def load_run(self, detector, run):
name = "{}; Detector {}".format(run, detector[-1])
subplot = self.plotting.add_subplot(detector)
subplot.set_title(detector)
for plot in mantid.mtd[name]:
self.plotting.plot(detector, plot)
if self.plotting.view.isHidden():
self.plotting.view.show()
if self.peaks.gamma.isChecked():
self._plot_gammas(subplot)
if self.peaks.electron.isChecked():
self._plot_electrons(subplot)
self.plotting.update_canvas()
def load_last_run(self, detector):
self.load_run(detector, self.load_widget.last_loaded_run())
def loading_finished(self):
last_run = self.load_widget.last_loaded_run()
if last_run is None:
return
self.plotting.view.setWindowTitle(str(last_run))
for plot in self.plotting.get_subplots():
self.plotting.remove_subplot(plot)
for detector in self.detectors.detectors:
if detector.isChecked():
self.load_run(detector.name, last_run)
for item in self.ptable.selection:
self._add_element_lines(
item.symbol, self.element_data[item.symbol])
def _generate_element_data(self):
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
try:
self.element_data[element] = self.ptable.peak_data[element]["Primary"].copy(
)
except KeyError:
continue
def _add_element_line(self, x_value, element, colour="b"):
if x_value is None:
return
for plot_name in self.plotting.get_subplots():
line = self.plotting.get_subplot(
plot_name).axvline(x_value, 0, 1, color=colour)
try:
self.element_lines[element][x_value].append(line)
except KeyError:
self.element_lines[element][x_value] = [line]
self.plotting.update_canvas()
def _add_element_lines(self, element, data):
self.element_lines[element] = {}
colour = self.line_colours.next()
for label, x_value in iteritems(data):
# label will be used in the future for labelling lines
self._add_element_line(x_value, element, colour=colour)
def _remove_element_lines(self, element):
for x_value, lines in iteritems(self.element_lines[element]):
for line in lines:
line.remove()
del line
self.plotting.update_canvas()
self.element_lines[element] = {}
def _update_element_lines(self, element, current_dict, new_dict):
# can be split up: this section removes lines
if len(current_dict) > len(new_dict): # i.e. item removed
dict_difference = {k: current_dict[k]
for k in set(current_dict) - set(new_dict)}
for label, x_value in iteritems(dict_difference):
# label will be used in the future for labelling lines
for line in self.element_lines[element][x_value]:
line.remove()
del line
self.element_lines[element][x_value] = []
del current_dict[label]
self.plotting.update_canvas()
# can be split up: this section adds lines
elif current_dict != new_dict: # i.e. item added or not closed without changes
colour = self.line_colours.next()
dict_difference = {k: new_dict[k]
for k in set(new_dict) - set(current_dict)}
for label, x_value in iteritems(dict_difference):
# label will be used in the future for labelling lines
self._add_element_line(x_value, element, colour)
current_dict.update(dict_difference)
def _update_peak_data(self, element, data):
if self.ptable.is_selected(element):
self._update_element_lines(
element, self.element_data[element], data)
else:
self.element_data[element] = data.copy()
def _generate_element_widgets(self):
self.element_widgets = {}
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
data = self.ptable.element_data(element)
try:
data["Gammas"] = self.ptable.peak_data["Gammas"][element]
except KeyError:
pass
widget = PeakSelectorPresenter(PeakSelectorView(data, element))
widget.on_finished(self._update_peak_data)
self.element_widgets[element] = widget
def table_left_clicked(self, item):
if self.ptable.is_selected(item.symbol):
self._add_element_lines(
item.symbol, self.element_data[item.symbol])
else:
self._remove_element_lines(item.symbol)
def table_right_clicked(self, item):
self.element_widgets[item.symbol].view.show()
def _clear_lines(self, lines):
for line in lines:
line.remove()
del line
return []
def _clear_lines_after_data_file_selected(self):
for element in self.element_lines.keys():
self._remove_element_lines(element)
self.electron_lines = self._clear_lines(self.electron_lines)
self.gamma_lines = self._clear_lines(self.gamma_lines)
for checkbox in self.peaks.peak_checkboxes:
checkbox.setChecked(False)
def select_data_file(self):
filename = QtGui.QFileDialog.getOpenFileName()
if isinstance(filename, tuple):
filename = filename[0]
filename = str(filename)
if filename:
self.ptable.set_peak_datafile(filename)
self._clear_lines_after_data_file_selected()
self._generate_element_widgets()
self._generate_element_data()
def add_plot(self, checkbox):
detector = checkbox.name
last_run = self.load_widget.last_loaded_run()
# not using load_last_run prevents two calls to last_loaded_run()
if last_run is not None:
self.load_run(detector, last_run)
colour = self.line_colours.next()
for element in self.ptable.selection:
for label, x_value in iteritems(self.element_data[element.symbol]):
# label will be used in the future for labelling lines
line = self.plotting.get_subplot(detector).axvline(
x_value, 1, 0, color=colour)
try:
self.element_lines[element.symbol][x_value].append(line)
except KeyError:
self.element_lines[element.symbol][x_value] = [line]
self.plotting.update_canvas()
def del_plot(self, checkbox):
if self.load_widget.last_loaded_run() is not None:
self.plotting.remove_subplot(checkbox.name)
if not self.plotting.get_subplots():
self.plotting.view.close()
def subplotRemoved(self, name):
# need to change the state without sending signal
# as the plot has already been removed
self.detectors.setStateQuietly(name, False)
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
# set menu
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
# periodic table stuff
self.ptable = PeriodicTablePresenter(
PeriodicTableView(), PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
# load stuff
self.load_widget = LoadPresenter(
LoadView(), LoadModel(), CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
# detectors
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
# peaks boxes
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.setChecked(True)
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
# set up
self.widget_list = QtWidgets.QVBoxLayout()
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
# plotting
self.plot_window = None
# layout
self.box = QtWidgets.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtWidgets.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_lines = {}
self.electron_peaks = self._get_electron_peaks()
self._generate_element_widgets()
class ElementalAnalysisGui(QtWidgets.QMainWindow):
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
# set menu
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
# periodic table stuff
self.ptable = PeriodicTablePresenter(
PeriodicTableView(), PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
# load stuff
self.load_widget = LoadPresenter(
LoadView(), LoadModel(), CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
# detectors
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
# peaks boxes
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.setChecked(True)
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
# set up
self.widget_list = QtWidgets.QVBoxLayout()
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
# plotting
self.plot_window = None
# layout
self.box = QtWidgets.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtWidgets.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_lines = {}
self.electron_peaks = self._get_electron_peaks()
self._generate_element_widgets()
def closeEvent(self, event):
if self.plot_window is not None:
self.plot_window.closeEvent(event)
super(ElementalAnalysisGui, self).closeEvent(event)
# general functions
def _gen_label(self, name, x_value_in, element=None):
if element is None:
return
# check x value is a float
x_value = 0.0
try:
x_value = float(x_value_in)
except:
return
if name not in self.element_lines[element]:
self.element_lines[element].append(name)
# make sure the names are strings and x values are numbers
return Label(str(name), float(x_value), False, offset, True, rotation=-90, protected=True)
def _plot_line(self, name, x_value_in, element=None):
label = self._gen_label(name, x_value_in, element)
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self.plotting.add_vline_and_annotate(
subplot, float(x_value_in), label)
def _plot_line_once(self, subplot, x_value, label):
self.plotting.add_vline_and_annotate(subplot, float(x_value), label)
def _rm_line(self, name):
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self.plotting.rm_vline_and_annotate(subplot, name)
# setup element pop up
def _generate_element_widgets(self):
self.element_widgets = {}
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
data = self.ptable.element_data(element)
try:
data["Gammas"] = self.ptable.peak_data["Gammas"][element]
except KeyError:
pass
widget = PeakSelectorPresenter(PeakSelectorView(data, element))
widget.on_finished(self._update_peak_data)
self.element_widgets[element] = widget
# interact with periodic table
def table_right_clicked(self, item):
self.element_widgets[item.symbol].view.show()
def table_left_clicked(self, item):
if self.ptable.is_selected(item.symbol):
self._add_element_lines(
item.symbol)
else:
self._remove_element_lines(item.symbol)
def _add_element_lines(self, element, data=None):
if data is None:
data = self.element_widgets[element].get_checked()
if element not in self.element_lines:
self.element_lines[element] = []
for name, x_value in iteritems(data):
full_name = gen_name(element, name)
self._plot_line(full_name, x_value, element)
def _remove_element_lines(self, element):
if element not in self.element_lines:
return
names = deepcopy(self.element_lines[element])
for name in names:
try:
self.element_lines[element].remove(name)
self._rm_line(name)
except:
continue
# loading
def load_run(self, detector, run):
name = "{}; Detector {}".format(run, detector[-1])
if self.plot_window is None:
self.plot_window = MultiPlotWindow(str(run))
self.plotting = self.plot_window.multi_plot
self.add_detector_to_plot(detector, name)
self.plotting.set_all_values()
self.plotting.removeSubplotConnection(self.subplotRemoved)
self.plot_window.show()
# untick detectors if plot window is closed
self.plot_window.windowClosedSignal.connect(self._unset_detectors)
else:
self.add_detector_to_plot(detector, name)
self.plot_window.show()
self.plot_window.raise_()
def loading_finished(self):
last_run = self.load_widget.last_loaded_run()
if last_run is None:
return
to_plot = deepcopy([det.isChecked()
for det in self.detectors.detectors])
if self.plot_window is None and any(to_plot) is False:
return
# generate plots - if new run clear old plot(s) and replace it
if self.plot_window is None:
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
else:
for plot in self.plotting.get_subplots():
self.plotting.remove_subplot(plot)
for j in range(len(to_plot)):
if to_plot[j]:
self.detectors.detectors[j].setChecked(True)
# detectors
def add_detector_to_plot(self, detector, name):
self.plotting.add_subplot(detector)
for ws in mantid.mtd[name]:
self.plotting.plot(detector, ws.getName())
# add current selection of lines
for element in self.ptable.selection:
self.add_peak_data(element.symbol, detector)
def _unset_detectors(self):
self.plot_window.windowClosedSignal.disconnect()
self.plot_window = None
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
# plotting
def add_peak_data(self, element, subplot, data=None):
# if already selected add to just new plot
if data is None:
data = self.element_widgets[element].get_checked()
for name, x_value in iteritems(data):
full_name = gen_name(element, name)
label = self._gen_label(full_name, x_value, element)
self._plot_line_once(subplot, float(x_value), label)
def _update_peak_data(self, element, data=None):
if self.ptable.is_selected(element):
# remove all of the lines for the element
self._remove_element_lines(element)
# add the ticked lines to the plot
self._add_element_lines(element)
else:
self._remove_element_lines(element)
def add_plot(self, checkbox):
detector = checkbox.name
last_run = self.load_widget.last_loaded_run()
# not using load_last_run prevents two calls to last_loaded_run()
if last_run is not None:
self.load_run(detector, last_run)
if self.peaks.electron.isChecked():
self.add_peak_data("e-", detector, data=self.electron_peaks)
def del_plot(self, checkbox):
if self.load_widget.last_loaded_run() is not None:
self.plotting.remove_subplot(checkbox.name)
if not self.plotting.get_subplots() and self.plot_window is not None:
self.plot_window.close()
self.plot_window = None
def subplotRemoved(self, name):
# need to change the state without sending signal
# as the plot has already been removed
self.detectors.setStateQuietly(name, False)
if not self.plotting.get_subplots():
self.plot_window.close()
self.plot_window = None
# sets data file for periodic table
def select_data_file(self):
filename = QtWidgets.QFileDialog.getOpenFileName()
if isinstance(filename, tuple):
filename = filename[0]
filename = str(filename)
if filename:
self.ptable.set_peak_datafile(filename)
# these are commneted out as they are a bug
# see issue 25326
#self._clear_lines_after_data_file_selected()
self._generate_element_widgets()
#self._generate_element_data()
# general checked data
def checked_data(self, element, selection, state):
for checkbox in selection:
checkbox.setChecked(state)
self._update_peak_data(
element,
self.element_widgets[element].get_checked())
# electron Peaks
def _get_electron_peaks(self):
# make a dict so we can label the peaks
electron_dict = {}
electron_peaks = self.ptable.peak_data["Electrons"].copy()
for peak, intensity in iteritems(electron_peaks):
electron_dict[str(peak)] = peak
return electron_dict
def electrons_checked(self):
self._add_element_lines("e-", self.electron_peaks)
def electrons_unchecked(self):
self._remove_element_lines("e-")
# gamma Peaks
def gammas_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.gamma_checkboxes, True)
def gammas_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.gamma_checkboxes, False)
# major peaks
def major_peaks_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.primary_checkboxes, True)
def major_peaks_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.primary_checkboxes, False)
# minor peaks
def minor_peaks_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.secondary_checkboxes, True)
def minor_peaks_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.secondary_checkboxes, False)
class ElementalAnalysisGui(QtWidgets.QMainWindow):
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
# set menu
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
# periodic table stuff
self.ptable = PeriodicTablePresenter(PeriodicTableView(),
PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
# load stuff
self.load_widget = LoadPresenter(LoadView(), LoadModel(),
CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
# detectors
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
# peaks boxes
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.setChecked(True)
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
# set up
self.widget_list = QtWidgets.QVBoxLayout()
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
# plotting
self.plot_window = None
self.colors = ['b', 'g', 'r', 'y', 'c', 'm', 'b']
self.color_index = 0
# layout
self.box = QtWidgets.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtWidgets.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_lines = {}
self.electron_peaks = self._get_electron_peaks()
self._generate_element_widgets()
# Return an unused colour, if all used then start with the first one
def get_color(self):
color = self.colors[self.color_index]
self.color_index = (self.color_index + 1) % len(self.colors)
return color
def closeEvent(self, event):
if self.plot_window is not None:
self.plot_window.closeEvent(event)
super(ElementalAnalysisGui, self).closeEvent(event)
# general functions
def _gen_label(self, name, x_value_in, element=None):
if element is None:
return
# check x value is a float
x_value = 0.0
try:
x_value = float(x_value_in)
except:
return
if name not in self.element_lines[element]:
self.element_lines[element].append(name)
# make sure the names are strings and x values are numbers
return Label(str(name),
float(x_value),
False,
offset,
True,
rotation=-90,
protected=True)
def _plot_line(self, name, x_value_in, color, element=None):
label = self._gen_label(name, x_value_in, element)
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self._plot_line_once(subplot, float(x_value_in), label, color)
def _plot_line_once(self, subplot, x_value, label, color):
self.plotting.add_vline_and_annotate(subplot, float(x_value), label,
color)
def _rm_line(self, name):
if self.plot_window is None:
return
for subplot in self.plotting.get_subplots():
self.plotting.rm_vline_and_annotate(subplot, name)
# setup element pop up
def _generate_element_widgets(self):
self.element_widgets = {}
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
data = self.ptable.element_data(element)
try:
data["Gammas"] = self.ptable.peak_data["Gammas"][element]
except KeyError:
pass
widget = PeakSelectorPresenter(PeakSelectorView(data, element))
widget.on_finished(self._update_peak_data)
self.element_widgets[element] = widget
# interact with periodic table
def table_right_clicked(self, item):
self.element_widgets[item.symbol].view.show()
def table_left_clicked(self, item):
if self.ptable.is_selected(item.symbol):
self._add_element_lines(item.symbol)
else:
self._remove_element_lines(item.symbol)
def _add_element_lines(self, element, data=None):
if data is None:
data = self.element_widgets[element].get_checked()
if element not in self.element_lines:
self.element_lines[element] = []
# Select a different color, if all used then use the first
color = self.get_color()
for name, x_value in iteritems(data):
full_name = gen_name(element, name)
self._plot_line(full_name, x_value, color, element)
def _remove_element_lines(self, element):
if element not in self.element_lines:
return
names = deepcopy(self.element_lines[element])
for name in names:
try:
self.element_lines[element].remove(name)
self._rm_line(name)
except:
continue
# loading
def load_run(self, detector, run):
name = "{}; Detector {}".format(run, detector[-1])
if self.plot_window is None:
self.plot_window = MultiPlotWindow(str(run))
self.plotting = self.plot_window.multi_plot
self.add_detector_to_plot(detector, name)
self.plotting.set_all_values()
self.plotting.removeSubplotConnection(self.subplotRemoved)
self.plot_window.show()
# untick detectors if plot window is closed
self.plot_window.windowClosedSignal.connect(self._unset_detectors)
else:
self.add_detector_to_plot(detector, name)
self.plot_window.show()
self.plot_window.raise_()
def loading_finished(self):
last_run = self.load_widget.last_loaded_run()
if last_run is None:
return
to_plot = deepcopy(
[det.isChecked() for det in self.detectors.detectors])
if self.plot_window is None and any(to_plot) is False:
return
# generate plots - if new run clear old plot(s) and replace it
if self.plot_window is None:
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
else:
for plot in self.plotting.get_subplots():
self.plotting.remove_subplot(plot)
for j in range(len(to_plot)):
if to_plot[j]:
self.detectors.detectors[j].setChecked(True)
# detectors
def add_detector_to_plot(self, detector, name):
self.plotting.add_subplot(detector)
for ws in mantid.mtd[name]:
self.plotting.plot(detector, ws.getName())
# add current selection of lines
for element in self.ptable.selection:
self.add_peak_data(element.symbol, detector)
def _unset_detectors(self):
self.plot_window.windowClosedSignal.disconnect()
self.plot_window = None
for name in self.detectors.getNames():
self.detectors.setStateQuietly(name, False)
# plotting
def add_peak_data(self, element, subplot, data=None):
# if already selected add to just new plot
if data is None:
data = self.element_widgets[element].get_checked()
color = self.get_color()
for name, x_value in iteritems(data):
full_name = gen_name(element, name)
label = self._gen_label(full_name, x_value, element)
self._plot_line_once(subplot, float(x_value), label, color)
def _update_peak_data(self, element, data=None):
if self.ptable.is_selected(element):
# remove all of the lines for the element
self._remove_element_lines(element)
# add the ticked lines to the plot
self._add_element_lines(element)
else:
self._remove_element_lines(element)
def add_plot(self, checkbox):
detector = checkbox.name
last_run = self.load_widget.last_loaded_run()
# not using load_last_run prevents two calls to last_loaded_run()
if last_run is not None:
self.load_run(detector, last_run)
if self.peaks.electron.isChecked():
self.add_peak_data("e-", detector, data=self.electron_peaks)
def del_plot(self, checkbox):
if self.load_widget.last_loaded_run() is not None:
self.plotting.remove_subplot(checkbox.name)
if not self.plotting.get_subplots(
) and self.plot_window is not None:
self.plot_window.close()
self.plot_window = None
def subplotRemoved(self, name):
# need to change the state without sending signal
# as the plot has already been removed
self.detectors.setStateQuietly(name, False)
if not self.plotting.get_subplots():
self.plot_window.close()
self.plot_window = None
# sets data file for periodic table
def select_data_file(self):
filename = QtWidgets.QFileDialog.getOpenFileName()
if isinstance(filename, tuple):
filename = filename[0]
filename = str(filename)
if filename:
self.ptable.set_peak_datafile(filename)
# these are commneted out as they are a bug
# see issue 25326
#self._clear_lines_after_data_file_selected()
self._generate_element_widgets()
#self._generate_element_data()
# general checked data
def checked_data(self, element, selection, state):
for checkbox in selection:
checkbox.setChecked(state)
self._update_peak_data(element,
self.element_widgets[element].get_checked())
# electron Peaks
def _get_electron_peaks(self):
# make a dict so we can label the peaks
electron_dict = {}
electron_peaks = self.ptable.peak_data["Electrons"].copy()
for peak, intensity in iteritems(electron_peaks):
electron_dict[str(peak)] = peak
return electron_dict
def electrons_checked(self):
self._add_element_lines("e-", self.electron_peaks)
def electrons_unchecked(self):
self._remove_element_lines("e-")
# gamma Peaks
def gammas_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.gamma_checkboxes, True)
def gammas_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.gamma_checkboxes, False)
# major peaks
def major_peaks_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.primary_checkboxes, True)
def major_peaks_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.primary_checkboxes, False)
# minor peaks
def minor_peaks_checked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.secondary_checkboxes, True)
def minor_peaks_unchecked(self):
for element, selector in iteritems(self.element_widgets):
self.checked_data(element, selector.secondary_checkboxes, False)
class ElementalAnalysisGui(QtGui.QMainWindow):
def __init__(self, parent=None):
super(ElementalAnalysisGui, self).__init__(parent)
self.menu = self.menuBar()
self.menu.addAction("File")
edit_menu = self.menu.addMenu("Edit")
edit_menu.addAction("Change Peak Data file", self.select_data_file)
self.menu.addAction("Binning")
self.menu.addAction("Normalise")
self.ptable = PeriodicTablePresenter(PeriodicTableView(),
PeriodicTableModel())
self.ptable.register_table_lclicked(self.table_left_clicked)
self.ptable.register_table_rclicked(self.table_right_clicked)
self.load_widget = LoadPresenter(LoadView(), LoadModel(),
CoLoadModel())
self.load_widget.on_loading_finished(self.loading_finished)
self.widget_list = QtGui.QVBoxLayout()
self.detectors = DetectorsPresenter(DetectorsView())
for detector in self.detectors.detectors:
detector.on_checkbox_checked(self.add_plot)
detector.on_checkbox_unchecked(self.del_plot)
self.peaks = PeaksPresenter(PeaksView())
self.peaks.major.on_checkbox_checked(self.major_peaks_checked)
self.peaks.major.on_checkbox_unchecked(self.major_peaks_unchecked)
self.peaks.minor.on_checkbox_checked(self.minor_peaks_checked)
self.peaks.minor.on_checkbox_unchecked(self.minor_peaks_unchecked)
self.peaks.gamma.on_checkbox_checked(self.gammas_checked)
self.peaks.gamma.on_checkbox_unchecked(self.gammas_unchecked)
self.peaks.electron.on_checkbox_checked(self.electrons_checked)
self.peaks.electron.on_checkbox_unchecked(self.electrons_unchecked)
self.widget_list.addWidget(self.peaks.view)
self.widget_list.addWidget(self.detectors.view)
self.widget_list.addWidget(self.load_widget.view)
self.plotting = PlotPresenter(PlotView())
self.plotting.view.setMinimumSize(self.plotting.view.sizeHint())
self.plotting.removeSubplotConnection(self.subplotRemoved)
self.box = QtGui.QHBoxLayout()
self.box.addWidget(self.ptable.view)
self.box.addLayout(self.widget_list)
self.setCentralWidget(QtGui.QWidget(self))
self.centralWidget().setLayout(self.box)
self.setWindowTitle("Elemental Analysis")
self.element_widgets = {}
self.element_data = {}
self.element_lines = {}
self.gamma_lines = []
self.gamma_peaks = self.ptable.peak_data["Gammas"]
self.electron_peaks = self._get_electron_peaks()
self.electron_lines = []
self._generate_element_widgets()
self._generate_element_data()
self.line_colours = cycle(["r", "g", "b", "c", "m", "y"])
def iterate_over_selectors(self, check_state, primary_checkboxes=True):
"""
Iterates over element popups.
:param check_state: True or False - i.e. check boxes or not
:param primary_checkboxes: True if Primary, False if Secondary
"""
for element, selector in iteritems(self.element_widgets):
for checkbox in selector.primary_checkboxes if primary_checkboxes else selector.secondary_checkboxes:
checkbox.setChecked(check_state)
selector.finish_selection()
def major_peaks_checked(self):
self.iterate_over_selectors(True, primary_checkboxes=True)
def major_peaks_unchecked(self):
self.iterate_over_selectors(False, primary_checkboxes=True)
self.plotting.update_canvas()
def minor_peaks_checked(self):
self.iterate_over_selectors(True, primary_checkboxes=False)
def minor_peaks_unchecked(self):
self.iterate_over_selectors(False, primary_checkboxes=False)
self.plotting.update_canvas()
def _plot_gammas(self, subplot, colour=None):
if colour is None:
colour = self.line_colours.next()
for element, peaks in iteritems(self.gamma_peaks):
for peak_type, peak in iteritems(peaks):
if peak is None:
continue
self.gamma_lines.append(
subplot.axvline(peak, 0, 1, color=colour))
self.plotting.update_canvas()
def _iterate_over_gamma_selectors(self, check_state):
for element, selector in iteritems(self.element_widgets):
for checkbox in selector.gamma_checkboxes:
checkbox.setChecked(check_state)
selector.finish_selection()
def gammas_checked(self):
self._iterate_over_gamma_selectors(True)
def gammas_unchecked(self):
self._iterate_over_gamma_selectors(False)
for line in self.gamma_lines:
line.remove()
del line
self.gamma_lines = []
self.plotting.update_canvas()
def _get_electron_peaks(self):
return self.ptable.peak_data["Electrons"].copy()
def _plot_electrons(self, subplot, colour=None):
if colour is None:
colour = self.line_colours.next()
for peak, intensity in iteritems(self.electron_peaks):
# intensity will be used in the future for labelling lines
self.electron_lines.append(
subplot.axvline(float(peak), 0, 1, color=colour))
self.plotting.update_canvas()
def electrons_checked(self):
colour = self.line_colours.next()
for subplot_name, subplot in iteritems(self.plotting.get_subplots()):
self._plot_electrons(subplot, colour=colour)
def electrons_unchecked(self):
for line in self.electron_lines:
line.remove()
del line
self.electron_lines = []
self.plotting.update_canvas()
def load_run(self, detector, run):
name = "{}; Detector {}".format(run, detector[-1])
subplot = self.plotting.add_subplot(detector)
subplot.set_title(detector)
for plot in mantid.mtd[name]:
self.plotting.plot(detector, plot)
if self.plotting.view.isHidden():
self.plotting.view.show()
if self.peaks.gamma.isChecked():
self._plot_gammas(subplot)
if self.peaks.electron.isChecked():
self._plot_electrons(subplot)
self.plotting.update_canvas()
def load_last_run(self, detector):
self.load_run(detector, self.load_widget.last_loaded_run())
def loading_finished(self):
last_run = self.load_widget.last_loaded_run()
if last_run is None:
return
self.plotting.view.setWindowTitle(str(last_run))
for plot in self.plotting.get_subplots():
self.plotting.remove_subplot(plot)
for detector in self.detectors.detectors:
if detector.isChecked():
self.load_run(detector.name, last_run)
for item in self.ptable.selection:
self._add_element_lines(item.symbol,
self.element_data[item.symbol])
def _generate_element_data(self):
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
try:
self.element_data[element] = self.ptable.peak_data[element][
"Primary"].copy()
except KeyError:
continue
def _add_element_line(self, x_value, element, colour="b"):
if x_value is None:
return
for plot_name in self.plotting.get_subplots():
line = self.plotting.get_subplot(plot_name).axvline(x_value,
0,
1,
color=colour)
try:
self.element_lines[element][x_value].append(line)
except KeyError:
self.element_lines[element][x_value] = [line]
self.plotting.update_canvas()
def _add_element_lines(self, element, data):
self.element_lines[element] = {}
colour = self.line_colours.next()
for label, x_value in iteritems(data):
# label will be used in the future for labelling lines
self._add_element_line(x_value, element, colour=colour)
def _remove_element_lines(self, element):
for x_value, lines in iteritems(self.element_lines[element]):
for line in lines:
line.remove()
del line
self.plotting.update_canvas()
self.element_lines[element] = {}
def _update_element_lines(self, element, current_dict, new_dict):
# can be split up: this section removes lines
if len(current_dict) > len(new_dict): # i.e. item removed
dict_difference = {
k: current_dict[k]
for k in set(current_dict) - set(new_dict)
}
for label, x_value in iteritems(dict_difference):
# label will be used in the future for labelling lines
for line in self.element_lines[element][x_value]:
line.remove()
del line
self.element_lines[element][x_value] = []
del current_dict[label]
self.plotting.update_canvas()
# can be split up: this section adds lines
elif current_dict != new_dict: # i.e. item added or not closed without changes
colour = self.line_colours.next()
dict_difference = {
k: new_dict[k]
for k in set(new_dict) - set(current_dict)
}
for label, x_value in iteritems(dict_difference):
# label will be used in the future for labelling lines
self._add_element_line(x_value, element, colour)
current_dict.update(dict_difference)
def _update_peak_data(self, element, data):
if self.ptable.is_selected(element):
self._update_element_lines(element, self.element_data[element],
data)
else:
self.element_data[element] = data.copy()
def _generate_element_widgets(self):
self.element_widgets = {}
for element in self.ptable.peak_data:
if element in ["Gammas", "Electrons"]:
continue
data = self.ptable.element_data(element)
try:
data["Gammas"] = self.ptable.peak_data["Gammas"][element]
except KeyError:
pass
widget = PeakSelectorPresenter(PeakSelectorView(data, element))
widget.on_finished(self._update_peak_data)
self.element_widgets[element] = widget
def table_left_clicked(self, item):
if self.ptable.is_selected(item.symbol):
self._add_element_lines(item.symbol,
self.element_data[item.symbol])
else:
self._remove_element_lines(item.symbol)
def table_right_clicked(self, item):
self.element_widgets[item.symbol].view.show()
def _clear_lines(self, lines):
for line in lines:
line.remove()
del line
return []
def _clear_lines_after_data_file_selected(self):
for element in self.element_lines.keys():
self._remove_element_lines(element)
self.electron_lines = self._clear_lines(self.electron_lines)
self.gamma_lines = self._clear_lines(self.gamma_lines)
for checkbox in self.peaks.peak_checkboxes:
checkbox.setChecked(False)
def select_data_file(self):
filename = str(QtGui.QFileDialog.getOpenFileName())
if filename:
self.ptable.set_peak_datafile(filename)
self._clear_lines_after_data_file_selected()
self._generate_element_widgets()
self._generate_element_data()
def add_plot(self, checkbox):
detector = checkbox.name
last_run = self.load_widget.last_loaded_run()
# not using load_last_run prevents two calls to last_loaded_run()
if last_run is not None:
self.load_run(detector, last_run)
colour = self.line_colours.next()
for element in self.ptable.selection:
for label, x_value in iteritems(self.element_data[element.symbol]):
# label will be used in the future for labelling lines
line = self.plotting.get_subplot(detector).axvline(
x_value, 1, 0, color=colour)
try:
self.element_lines[element.symbol][x_value].append(line)
except KeyError:
self.element_lines[element.symbol][x_value] = [line]
self.plotting.update_canvas()
def del_plot(self, checkbox):
if self.load_widget.last_loaded_run() is not None:
self.plotting.remove_subplot(checkbox.name)
if not self.plotting.get_subplots():
self.plotting.view.close()
def subplotRemoved(self, name):
# need to change the state without sending signal
# as the plot has already been removed
self.detectors.setStateQuietly(name, False)