def render_measurement(self):
self.measurement.clear()
option = self.test_measurement.currentText()
if option == 'gradient':
self.signal, self.grad_from, self.grad_to = self.measurement.addWidgets([
DropDown('Gradient of:', data_manager.get_growth_variables()),
TextEntry('Between:', placeholder='Y = '),
TextEntry('And:', placeholder='Y = ')])
elif option == 'time to':
self.signal, self.time_to = self.measurement.addWidgets([
DropDown('Time for:', data_manager.get_growth_variables()),
TextEntry('To reach:', placeholder='Y = ')])
elif option == 'fit parameter':
model = get_model(config.fit_options[0])
self.fit, self.signal, self.param, self.fit_from, self.fit_to = self.measurement.addWidgets([
DropDown('Fit:', config.fit_options,
change_action=self.update_param_list),
DropDown('Of:', data_manager.get_growth_variables()),
DropDown('Parameter:', model.params),
TextEntry('From:', placeholder=config.xvar),
TextEntry('To:', placeholder=config.xvar)])
else:
self.measurement.hide()
return
self.measurement.show()
return
def initUI(self):
self.line_style, self.line_colour, self.marker_style, _ = self.window.addWidgets(
[
DropDown('Line style:', config.line_style_options),
TextEntry('Line colour:'),
DropDown('Marker style:',
list(config.marker_style_options.keys())),
Button("Apply", clicked=self.apply_changes)
])
def initUI(self):
# Dropdown list of available file types
file_types = config.replicate_types
if self.row == -1:
file_types = config.file_types
self.file_type = self.window.addWidget(
DropDown('File type:',
file_types,
change_action=self.update_options))
# Button for selecting files to import
self.window.addWidget(
Button("Select data file(s)", clicked=self.select_data))
# List of files to import
self.file_list = self.window.addWidget(List())
self.file_list.setSpacing(-5 * config.wr)
self.file_list.setStyleSheet(styles.default_font)
# Button and list for Algem conditions files
self.select_conditions_button = self.window.addWidget(
Button("Select conditions file(s)",
clicked=self.select_conditions))
self.select_conditions_button.hide()
self.conditions_file_list = self.window.addWidget(
List(spacing=-5 * config.wr, style=styles.default_font))
self.conditions_file_list.hide()
# Button and list for HT24 details file
self.select_details_button = self.window.addWidget(
Button("Select details file", clicked=self.select_details))
self.select_details_button.hide()
self.details_file_list = self.window.addWidget(
List(spacing=-5 * config.wr, style=styles.default_font))
self.details_file_list.hide()
# Option to downsample conditions data
self.downsample = self.window.addWidget(
TextEntry('Downsample conditions:',
default=config.downsample,
tooltip='Only read in every X data points'))
self.downsample.hide()
# Checkbox for merging replicates in HT24 data
self.merge_replicates = self.window.addWidget(
CheckBox('Merge replicates'))
self.merge_replicates.hide()
# Button to load the data
self.window.addWidget(Button("Load", clicked=self.load))
self.update_options()
def initUI(self):
fit_config = LayoutWidget(QVBoxLayout)
# List of row options
self.curve_option, self.fit_option, self.fit_from, self.fit_to, self.set_bounds, _ = fit_config.addWidgets(
[
DropDown('Data:', data_manager.get_growth_data_labels()),
DropDown('Fit:', config.fit_options),
TextEntry('From:', default=config.fit_from),
TextEntry('To:', default=config.fit_to),
CheckBox('Set parameter bounds',
change_action=self.render_bounds),
Button("Fit", clicked=self.fit)
])
self.window.addWidget(fit_config.widget)
self.bound_input = LayoutWidget(QVBoxLayout)
self.param_bounds = self.bound_input.addWidget(ParameterBounds("p"))
self.window.addWidget(self.bound_input.widget)
self.bound_input.hide()
def __init__(self, text, parent=None):
self.item = QListWidgetItem()
self.type = text
# Horizontal box layout
layout = LayoutWidget(QHBoxLayout)
spacer = layout.addWidget(QWidget())
spacer.setFixedWidth(10 * config.wr)
# Add a delete button
layout.addWidget(DeleteButton(clicked=parent.remove_item))
# Add a label with row type
if (text == 'profile'):
layout.addWidget(RoundLabel('Profile'))
if (text == 'reactor'):
layout.addWidget(RoundLabel('Reactor'))
# Add other options based on type
# Gradient needs a start and end measurement point in Y
if (text == 'gradient'):
self.data, self.grad_from, self.grad_to = layout.addWidgets([
DropDown('Gradient of:', data_manager.get_growth_variables()),
TextEntry('Between:', default=-1, placeholder='Y = '),
TextEntry('And:', default=-1, placeholder='Y = ')
])
# Time to needs a Y point to reach
if (text == 'time to'):
self.data, self.time_to = layout.addWidgets([
DropDown('Time for:', data_manager.get_growth_variables()),
TextEntry('To reach:', default=-1, placeholder='Y = ')
])
# Average of a condition needs condition and start and end time
if (text == 'average of condition'):
self.condition, self.start_t, self.end_t = layout.addWidgets([
DropDown('Average of:',
data_manager.get_condition_variables()),
TextEntry('Between:', default=-1, placeholder=config.xvar),
TextEntry('And:', default=-1, placeholder=config.xvar)
])
# Condition at time needs condition and time
if (text == 'condition at time'):
self.condition, self.time = layout.addWidgets([
DropDown('Value of:', data_manager.get_condition_variables()),
TextEntry('At:', default=-1, placeholder=config.xvar)
])
# Value of fit parameter needs fit and parameter
if (text == 'fit parameter'):
model = get_model(config.fit_options[0], '', '')
self.fit, self.data, self.param, self.fit_from, self.fit_to, self.show_error = layout.addWidgets(
[
DropDown('Fit:',
config.fit_options,
change_action=self.update_param_list),
DropDown('Data:', data_manager.get_growth_variables()),
DropDown('Parameter:', model.params),
TextEntry('From:', default=-1, placeholder=config.xvar),
TextEntry('To:', default=-1, placeholder=config.xvar),
CheckBox("Show error")
])
# Pad out the row
layout.layout.addStretch()
layout.layout.setSpacing(5)
layout.layout.setContentsMargins(10, 10, 50, 5)
self.widget = layout.widget
self.item.setSizeHint(self.widget.sizeHint())
def initUI(self):
self.setGeometry(self.left, self.top, self.width, self.height)
# Configuration tab
corr_config = LayoutWidget(QVBoxLayout, margin=5, spacing=0)
# X axis selection = condition variable
# Dropdown of condition variables OR take from main plot
self.condition = corr_config.addWidget(
DropDown('X-axis: Average of',
data_manager.get_condition_variables()))
# Y axis selection = growth related measurement
# Dropdown of y variables (OD/CD) OR take from main plot
self.data = corr_config.addWidget(
DropDown('Y-axis:', data_manager.get_growth_variables()))
# Choice of fit and fit parameter
fit_option = LayoutWidget(QHBoxLayout)
model = get_model(config.fit_options[0])
self.fit, self.param = fit_option.addWidgets([
DropDown('Fit:',
config.fit_options,
change_action=self.update_param_list),
DropDown('Parameter:', model.params)
])
corr_config.addWidget(fit_option.widget)
range_option = LayoutWidget(QHBoxLayout)
self.start_t, self.end_t = range_option.addWidgets([
TextEntry('Between:', default=-1, placeholder=config.xvar),
TextEntry('And:', default=-1, placeholder=config.xvar)
])
corr_config.addWidget(range_option.widget)
self.figure_title = corr_config.addWidget(TextEntry('Figure title:'))
title_option = LayoutWidget(QHBoxLayout)
self.x_title, self.y_title = title_option.addWidgets(
[TextEntry('X-axis title:'),
TextEntry('Y-axis title:')])
corr_config.addWidget(title_option.widget)
options = LayoutWidget(QHBoxLayout)
self.label, self.calc_correlation = options.addWidgets(
[CheckBox('Label'),
CheckBox('Calculate correlation')])
corr_config.addWidget(options.widget)
# Plot button
corr_config.addWidget(Button('Plot', clicked=self.update_plot))
self.tabs.addTab(corr_config.widget, 'Configuration')
# Plot tab
plot_view = LayoutWidget(QGridLayout, margin=5, spacing=10)
# Plot
self.plot = plot_view.addWidget(
CorrelationCanvas(self,
width=10 * config.wr,
height=4 * config.hr,
dpi=100 * config.wr), 0, 0, 4, 4)
shadow = QGraphicsDropShadowEffect(blurRadius=10 * config.wr,
xOffset=3 * config.wr,
yOffset=3 * config.hr)
self.plot.setGraphicsEffect(shadow)
self.plot.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
# Save button
plot_view.addWidget(Button('Save', clicked=self.save_plot), 4, 0, 1, 4)
self.tabs.addTab(plot_view.widget, 'Plot')
def initUI(self):
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
wr = config.wr
hr = config.wr
tabs = QTabWidget()
tabs.setStyleSheet(styles.tab_style)
# ---------------------------------------------------------------------
# PLOTTING TAB
# ---------------------------------------------------------------------
# Main plotting window
splitter = QSplitter()
plot_view = LayoutWidget(QGridLayout, margin=5, spacing=10)
# Main plot window (row, column, row extent, column extent)
self.plot = plot_view.addWidget(
PlotCanvas(self, width=10 * wr, height=4 * hr, dpi=100 * wr), 0, 1,
5, 5)
shadow = QGraphicsDropShadowEffect(blurRadius=10 * wr,
xOffset=3 * wr,
yOffset=3 * hr)
self.plot.setGraphicsEffect(shadow)
self.plot.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
toolbar = plot_view.addWidget(QToolBar("Tools", self), 0, 0, 5, 1)
toolbar.setOrientation(Qt.Vertical)
toolbar.setStyleSheet(styles.toolbar_style)
toolbar_icons = [
":measure.svg", ":fit.svg", ":table.svg", ":correlations.svg",
":template.svg", ":normal.svg"
]
toolbar_labels = [
'&Measure', '&Fit', '&To Table', '&Correlations',
'&Download Template', '&Statisitical Tests'
]
toolbar_actions = [
self.toggle_cursor, self.fit_curve, self.create_table,
self.open_correlation, self.download_template, self.open_tests
]
for i, icon in enumerate(toolbar_icons):
toolbar_action = QAction(QIcon(icon), toolbar_labels[i], self)
toolbar_action.triggered.connect(toolbar_actions[i])
toolbar.addAction(toolbar_action)
splitter.addWidget(plot_view.widget)
data_entry = LayoutWidget(QVBoxLayout, margin=5, spacing=10)
self.data_button, self.data_list, _, self.condition_data_list, _, self.calibration_file, _ = data_entry.addWidgets(
[
Button('Add Data',
tooltip='Import data for plotting',
clicked=self.open_data_files),
List(scroll=True),
TopLabel('Condition Data:'),
List(scroll=True),
Button('Add Calibration Curve',
tooltip='Set OD to CD conversion from file',
clicked=self.open_calibration_file),
DelLabel('', clicked=self.remove_calibration_file),
BigButton('Plot!',
tooltip='Plot the data!',
clicked=self.update_plot)
])
self.data_button.setContextMenuPolicy(Qt.CustomContextMenu)
self.data_button.customContextMenuRequested.connect(
self.on_context_menu)
self.clear_menu = QMenu(self)
self.clear_action = QAction('Clear all', self)
self.clear_menu.addAction(self.clear_action)
self.calibration_file.setFixedHeight(40 * hr)
splitter.addWidget(data_entry.widget)
tabs.addTab(splitter, 'Plotting')
# ---------------------------------------------------------------------
# OPTIONS TABS
# ---------------------------------------------------------------------
# --------------- AXIS CONFIGURATION
# Axis configuration
axis_options = LayoutWidget(QVBoxLayout, style=styles.white_background)
axis_h = LayoutWidget(QHBoxLayout)
self.figure_title = axis_options.addWidget(TextEntry('Figure title:'))
x_options = LayoutWidget(QVBoxLayout)
x_options.addWidget(TopLabel('X (time):'))
# X axis config
x_form = Form()
self.xaxis_dropdown, self.xaxis_name, self.xaxis_unit, self.xaxis_min, self.xaxis_max, self.xaxis_log = x_form.addRows(
[
DropDown('Variable:', config.xaxis_units, index=2),
TextEntry('Label:'),
TextEntry('Unit name:', tooltip='Enter "none" for no units'),
TextEntry('Range min:', default=config.xmin),
TextEntry('Range max:', default=config.xmax),
CheckBox('Log scale')
],
padding=[False, False, False, False, False, True])
x_options.addWidget(x_form.widget)
axis_h.addWidget(x_options.widget)
y_options = LayoutWidget(QVBoxLayout)
y_options.addWidget(TopLabel('Y (growth):'))
# Y axis config
y_form = Form()
self.yaxis_dropdown, self.yaxis_name, self.yaxis_unit, self.yaxis_min, self.yaxis_max = y_form.addRows(
[
DropDown('Variable:', []),
TextEntry('Label:'),
TextEntry('Unit name:', tooltip='Enter "none" for no units'),
TextEntry('Range min:', default=config.ymin),
TextEntry('Range max:', default=config.ymax)
])
# Y axis log scale
ylog_hbox = LayoutWidget(QHBoxLayout)
ylog_hbox.layout.setSpacing(15 * wr)
ylog_hbox.layout.setContentsMargins(0, 0, 1 * wr, 1 * hr)
self.yaxis_log, self.yaxis_normlog = ylog_hbox.addWidgets(
[CheckBox('Log scale'),
CheckBox('ln(Y/Y0)')])
y_form.addRow(ylog_hbox.widget, pad=True)
y_options.addWidget(y_form.widget)
axis_h.addWidget(Spacer())
axis_h.addWidget(y_options.widget)
z_options = LayoutWidget(QVBoxLayout)
z_options.addWidget(TopLabel('Y2 (conditions):'))
# Condition Y axis drop down menu
z_form = Form()
self.condition_yaxis_dropdown, self.condition_yaxis_name, self.condition_yaxis_unit, self.condition_yaxis_min, self.condition_yaxis_max, self.condition_yaxis_log = z_form.addRows(
[
DropDown('Variable:', []),
TextEntry('Label:'),
TextEntry('Unit name:', tooltip='Enter "none" for no units'),
TextEntry('Range min:', default=config.condition_ymin),
TextEntry('Range max:', default=config.condition_ymax),
CheckBox('Log scale')
],
padding=[False, False, False, False, False, True])
z_options.addWidget(z_form.widget)
axis_h.addWidget(Spacer())
axis_h.addWidget(z_options.widget)
axis_options.addWidget(axis_h.widget)
axis_options.addWidget(Spacer())
tabs.addTab(axis_options.widget, 'Axes')
# --------------- DATA CONFIGURATION
# Data configuration options
data_options = LayoutWidget(QHBoxLayout, style=styles.white_background)
data_form = Form()
self.smooth_data, self.align_data, self.y_alignment, self.initial_y, self.growth_average, self.condition_average, self.show_events = data_form.addRows(
[
CheckBox('Data smoothing off/on',
tooltip='Apply Savitzky-Golay to noisy data'),
CheckBox('Alignment at time = 0 on/off',
tooltip='Start growth curves at 0 time'),
TextEntry('Align at Y:',
default=config.y_alignment,
tooltip='Align all growth curves at given Y value'),
TextEntry('Set initial Y:',
default=config.initial_y,
tooltip='Start growth curves at a given Y value'),
TextEntry('Growth data time average:',
default=config.growth_average,
tooltip='Average over a given time window'),
TextEntry('Condition data time average:',
default=config.condition_average,
tooltip='Average over a given time window'),
CheckBox('Show events off/on')
],
padding=[True, True, False, False, False, False, True])
data_options.addWidget(data_form.widget)
# Remove any obvious outliers from the growth data
outlier_options = LayoutWidget(QVBoxLayout)
outlier_options.addWidget(TopLabel('Data outliers:'))
outlier_form = Form()
self.auto_remove, self.remove_above, self.remove_below = outlier_form.addRows(
[
CheckBox('Auto-remove outliers off/on'),
TextEntry('Remove above:', default=config.remove_above),
TextEntry('Remove below:', default=config.remove_below)
],
padding=[True, False, False])
outlier_options.addWidget(outlier_form.widget)
outlier_options.addWidget(Spacer())
data_options.addWidget(outlier_options.widget)
data_options.addWidget(Spacer())
tabs.addTab(data_options.widget, 'Data')
# --------------- LEGEND CONFIGURATION
# Legend configuration options
legend_options = LayoutWidget(QHBoxLayout,
style=styles.white_background)
# Legend on/off checkbox
growth_options = LayoutWidget(QVBoxLayout)
growth_options.addWidget(TopLabel('Growth Legend:'))
growth_form = Form()
self.legend_toggle, self.legend_names, self.legend_title, self.extra_info, self.only_extra = growth_form.addRows(
[
CheckBox('Legend on'),
DropDown(
'Labels:', [],
tooltip='Edit names by changing text and pressing return',
edit=True),
TextEntry(
'Heading:',
tooltip='Show extra information from the file in the legend'
),
DropDown('Extra text:', config.info_options),
CheckBox('Remove labels')
],
padding=[True, False, False, False, True])
growth_options.addWidget(growth_form.widget)
growth_options.addWidget(Spacer())
legend_options.addWidget(growth_options.widget)
# Condition legend configuration
condition_options = LayoutWidget(QVBoxLayout)
condition_options.addWidget(TopLabel('Condition legend:'))
condition_form = Form()
self.condition_legend_toggle, self.condition_legend_names, self.condition_legend_title, self.condition_extra_info, self.condition_only_extra = condition_form.addRows(
[
CheckBox('Legend on'),
DropDown(
'Labels:', [],
tooltip='Edit names by changing text and pressing return',
edit=True),
TextEntry('Heading:'),
DropDown(
'Extra text:',
config.info_options,
tooltip='Show extra information from the file in the legend'
),
CheckBox('Remove labels')
],
padding=[True, False, False, False, True])
condition_options.addWidget(condition_form.widget)
condition_options.addWidget(Spacer())
legend_options.addWidget(condition_options.widget)
legend_options.addWidget(Spacer())
tabs.addTab(legend_options.widget, 'Legend')
# --------------- STYLE CONFIGURATION
# Style configuration
style_options = LayoutWidget(QHBoxLayout,
style=styles.white_background)
# Plot style dropdown menu
style_form = Form(align=True)
self.style_dropdown, self.font_dropdown, self.axis_colour, self.grid_toggle = style_form.addRows(
[
DropDown('Style:', config.style_options),
DropDown('Font style:', config.font_options),
TextEntry('Condition axis color:'),
CheckBox('Grid on/off')
],
padding=[False, False, False, True])
style_options.addWidget(style_form.widget)
# Sized
style_numeric_form = Form(align=True)
self.title_size, self.legend_size, self.label_size, self.line_width, self.marker_size, self.capsize, self.save_dpi = style_numeric_form.addRows(
[
SpinBox('Title font size:',
start=config.title_size,
min_val=0,
max_val=100),
SpinBox('Legend font size:',
start=config.legend_size,
min_val=0,
max_val=100),
SpinBox('Label font size:',
start=config.label_size,
min_val=0,
max_val=100),
SpinBox('Line width:',
start=config.line_width,
min_val=0,
max_val=20),
SpinBox('Marker size:',
start=config.marker_size,
min_val=0,
max_val=20),
SpinBox('Error cap size:',
start=config.capsize,
min_val=0,
max_val=20),
SpinBox('Saved figure DPI:',
start=config.save_dpi,
min_val=10,
max_val=2000)
])
style_options.addWidget(style_numeric_form.widget)
tabs.addTab(style_options.widget, 'Style')
# --------------- STATS CONFIGURATION
# Stats configuration
stats_form = Form(align=True, style=styles.white_background)
self.std_err, self.sig_figs, self.show_fit_text, self.show_fit_result, self.show_fit_errors = stats_form.addRows(
[
RadioButton(
'Standard deviation',
'Standard error',
tooltip=
'Show standard deviation or the standard error on the mean in plots and measurements'
),
SpinBox('Significant figures:',
start=config.sig_figs,
min_val=0,
max_val=20),
CheckBox(
'Show fit model text',
tooltip='Checked = display equation for fitted model\n'
'Unchecked = don'
't display equation'),
CheckBox(
'Show fit parameters',
tooltip='Checked = show fitted values of model parameters\n'
'Unchecked = don'
't show fit parameters'),
CheckBox(
'Show fit errors',
tooltip='Checked = show uncertainties on fit parameters\n'
'Unchecked = don'
't show uncertainties')
],
padding=[True, False, True, True, True])
tabs.addTab(stats_form.widget, 'Stats')
# --------------- ADVANCED CONFIGURATION
# Advanced configuration
advanced_options = LayoutWidget(QHBoxLayout,
style=styles.white_background)
sg_form = Form(align=True, style=styles.white_background)
_, self.sg_window_size, self.sg_order, self.sg_deriv, self.sg_rate = sg_form.addRows(
[
TopLabel('Savitsky-Golay smoothing:'),
TextEntry('Window size', default=config.sg_window_size),
TextEntry('Order of polynomial', default=config.sg_order),
TextEntry('Order of derivative', default=config.sg_deriv),
TextEntry('Sample spacing', default=config.sg_rate)
])
adv_outlier_form = Form(align=True, style=styles.white_background)
self.outlier_threshold = adv_outlier_form.addRow(
TextEntry('Auto outlier threshold',
default=config.outlier_threshold))
advanced_options.addWidget(sg_form.widget)
advanced_options.addWidget(adv_outlier_form.widget)
tabs.addTab(advanced_options.widget, 'Advanced')
# ----------------------------------
self.setCentralWidget(tabs)
self.show()