def _on_analyze(self):
"""
Searches for events in the file that is currently highlighted in the files list.
"""
selected_items = self.file_list_widget.selectedItems()
if len(selected_items) > 0:
curr_item = selected_items[0]
else:
return
parameters = self.get_current_analysis_parameters()
if isinstance(parameters, dict) and 'error' in parameters:
self._dispatch_status_update(parameters['error'])
return
debug = self.debug_check_box.isChecked()
# Clear the current events
del self.events[:]
# self.prev_concat_time = 0.
file_names = [str(curr_item.get_file_name())]
self._dispatch_status_update("Event Count: 0 Percent Done: 0")
# Start analyzing data in new analyzethread.
self.analyzethread = AnalyzeDataThread(file_names, parameters, debug)
self.analyzethread.dataReady.connect(
self._analyze_data_thread_callback)
self.add_thread(self.analyzethread)
self.analyzethread.start()
self.stop_analyze_button.setEnabled(True)
def test_one_file_with_events(self, filename):
"""
Tests that events are found and event databases are saved.
"""
test_data_file_names = tf.get_all_file_names()
test_file = tf.get_abs_path('chimera_1event.log')
analyze_thread = AnalyzeDataThread([test_file], Parameters(), debug=True, save_file_names=[filename])
analyze_thread.start()
# wait until the thread has finished
analyze_thread.wait()
self.assertTrue(os.path.exists(filename))
def _on_analyze(self):
"""
Searches for events in the file that is currently highlighted in the files list.
"""
selected_items = self.file_list_widget.selectedItems()
if len(selected_items) > 0:
curr_item = selected_items[0]
else:
return
parameters = self.get_current_analysis_parameters()
if isinstance(parameters, dict) and 'error' in parameters:
self._dispatch_status_update(parameters['error'])
return
debug = self.debug_check_box.isChecked()
# Clear the current events
del self.events[:]
# self.prev_concat_time = 0.
file_names = [str(curr_item.get_file_name())]
self._dispatch_status_update("Event Count: 0 Percent Done: 0")
# Start analyzing data in new analyzethread.
self.analyzethread = AnalyzeDataThread(file_names, parameters, debug)
self.analyzethread.dataReady.connect(self._analyze_data_thread_callback)
self.add_thread(self.analyzethread)
self.analyzethread.start()
self.stop_analyze_button.setEnabled(True)
def test_one_file_with_events(self, filename):
"""
Tests that events are found and event databases are saved.
"""
test_data_file_names = tf.get_all_file_names()
test_file = tf.get_abs_path('chimera_1event.log')
analyze_thread = AnalyzeDataThread([test_file],
Parameters(),
debug=True,
save_file_names=[filename])
analyze_thread.start()
# wait until the thread has finished
analyze_thread.wait()
self.assertTrue(os.path.exists(filename))
class EventFindingTab(BaseQSplitterDataFile):
"""
A QtGui.QSplitter that contains event finding options on the left and a plot on the right.
"""
def __init__(self, parent=None):
"""
:param PySide.QtGui.QMainWindow parent: Parent main window (optional).
"""
# Define the instance elements
self.events = [] # holds the events from the most recent analysis run
self.plot_widget = None
self.p1 = None
self.plot_tool_bar = None
super(EventFindingTab, self).__init__(parent)
def get_current_analysis_parameters(self):
"""
Reads the current analysis parameters from the gui and returns the results in a dictionary. Returns
dictionary entry 'error' with text of the error if one exists.
:returns: DictType -- the event analysis parameters. These include:
- 'error' - Text if there was an error
OR
- 'min_event_length'
- 'max_event_length'
- 'baseline_strategy'
- 'baseline_filter_parameter'
- 'baseline_current'
etc...
"""
threshold_type = baseline_type = None
# Get Min_event length in microseconds
try:
min_event_length = float(self.min_event_length_edit.text())
except ValueError:
return {'error': 'Could not read float from Min Event Length text box. Please fix.'}
# Get Max Event Length in microseconds
try:
max_event_length = float(self.max_event_length_edit.text())
except ValueError:
return {'error': 'Could not read float from Max Event Length text box. Please fix.'}
if min_event_length >= max_event_length:
return {'error': 'Min Event Length is greater than Max Event Length. Please fix.'}
baseline_type_str = str(self.baseline_type_combo.currentText())
if baseline_type_str == 'Adaptive':
try:
baseline_filter_parameter = float(self.baseline_filter_parameter_edit.text())
except ValueError:
return {'error': 'Could not read float from Baseline Filter Parameter text box. Please fix.'}
try:
variance_filter_parameter = float(self.variance_filter_parameter_edit.text())
except ValueError:
return {'error': 'Could not read float from Variance Filter Parameter text box. Please fix.'}
baseline_type = AdaptiveBaselineStrategy(baseline_filter_parameter=baseline_filter_parameter,
variance_filter_parameter=variance_filter_parameter)
elif baseline_type_str == 'Fixed':
try:
baseline_current = float(self.baseline_current_edit.text())
baseline_type = FixedBaselineStrategy(baseline=baseline_current)
except ValueError:
return {'error': 'Could not read float from Baseline Current text box. Please fix.'}
threshold_direction_str = str(self.threshold_direction_combo.currentText())
detect_positive_events = (threshold_direction_str in ('Positive', 'Both'))
detect_negative_events = (threshold_direction_str in ('Negative', 'Both'))
threshold_type_str = str(self.threshold_type_combo.currentText())
if threshold_type_str == 'Noise Based':
try:
start_stddev = float(self.threshold_stdev_start.text())
except ValueError:
return {'error': 'Could not read float from Start StdDev text box. Please fix.'}
try:
end_stddev = float(self.threshold_stdev_end.text())
except ValueError:
return {'error': 'Could not read float from End StdDev text box. Please fix.'}
threshold_type = NoiseBasedThresholdStrategy(start_std_dev=start_stddev, end_std_dev=end_stddev)
elif threshold_type_str == 'Absolute Change':
try:
absolute_change_start = float(self.absolute_change_start_edit.text())
except ValueError:
return {'error': 'Could not read float from Absolute Change Start. Please fix.'}
try:
absolute_change_end = float(self.absolute_change_end_edit.text())
except ValueError:
return {'error': 'Could not read float from Absolute Change End. Please fix.'}
threshold_type = AbsoluteChangeThresholdStrategy(change_start=absolute_change_start,
change_end=absolute_change_end)
elif threshold_type_str == 'Percent Change':
try:
percent_change_start = float(self.percentage_change_start_edit.text())
except ValueError:
return {'error': 'Could not read float from Percent Change Start text box. Please fix.'}
try:
percent_change_end = float(self.percentage_change_end_edit.text())
except ValueError:
return {'error': 'Could not read float from Percent Change End text box. Please fix.'}
threshold_type = PercentChangeThresholdStrategy(percent_change_start=percent_change_start,
percent_change_end=percent_change_end)
parameters = Parameters(min_event_length=min_event_length, max_event_length=max_event_length,
detect_positive_events=detect_positive_events,
detect_negative_events=detect_negative_events, baseline_strategy=baseline_type,
threshold_strategy=threshold_type)
return parameters
def plot_data(self, plot_options):
"""
Plots waveform in datadict.
:param DictType plot_options: Dictionary of plot options. Must contain:
* Data at plot_options['data'][0]
* sample_rate at plot_options['sample_rate']
* plot_range at plot_options['plot_range']. This can be [start,stop], or
'all' for 0:n.
"""
# Read the first file, store data in dictionary
data = plot_options['data'][0]
sample_rate = plot_options['sample_rate']
plot_range = plot_options['plot_range']
n = len(data)
# If problem with input, just plot all the data
if plot_range == 'all' or len(plot_range) != 2 or plot_range[1] <= plot_range[0]:
plot_range = [0, n]
else: # no problems!
n = plot_range[1] - plot_range[0] + 1
ts = 1 / sample_rate
times = linspace(ts * plot_range[0], ts * plot_range[1], n)
y_data = data[plot_range[0]:(plot_range[1] + 1)]
self.plot_widget.clear_event_items()
self.p1.setData(x=times, y=y_data)
self.plot_widget.autoRange()
self._dispatch_process_events()
def _analyze_data_thread_callback(self, results):
"""
Callback for updates from the AnalyzeDataThread.
"""
if 'status_text' in results:
self._dispatch_status_update(results['status_text'])
if 'Events' in results:
single_plot = False
events = results['Events']
if len(events) < 1:
return
elif len(self.events) < 1:
# if this is our first time plotting events, include the single event plot!
single_plot = True
self.events += events
self.event_display_edit.setMaxLength(int(len(self.events) / 10) + 1)
self.event_display_edit.setValidator(QtGui.QIntValidator(1, len(self.events), self.event_display_edit))
self.eventCountText.setText('/' + str(len(self.events)))
if self.plot_tool_bar.is_plot_during_checked():
self.plotEventsOnMainPlot(events)
self.addEventsToConcatEventPlot(events)
if single_plot:
self.event_display_edit.setText('1')
self._dispatch_process_events()
self.analyzethread.readyForEvents = True
if 'done' in results:
if results['done']:
self.stop_analyze_button.setEnabled(False)
def _on_analyze(self):
"""
Searches for events in the file that is currently highlighted in the files list.
"""
selected_items = self.file_list_widget.selectedItems()
if len(selected_items) > 0:
curr_item = selected_items[0]
else:
return
parameters = self.get_current_analysis_parameters()
if isinstance(parameters, dict) and 'error' in parameters:
self._dispatch_status_update(parameters['error'])
return
debug = self.debug_check_box.isChecked()
# Clear the current events
del self.events[:]
# self.prev_concat_time = 0.
file_names = [str(curr_item.get_file_name())]
self._dispatch_status_update("Event Count: 0 Percent Done: 0")
# Start analyzing data in new analyzethread.
self.analyzethread = AnalyzeDataThread(file_names, parameters, debug)
self.analyzethread.dataReady.connect(self._analyze_data_thread_callback)
self.add_thread(self.analyzethread)
self.analyzethread.start()
self.stop_analyze_button.setEnabled(True)
def _on_analyze_stop(self):
"""
Called when the user clicks the Stop button.
"""
self.clean_threads()
self.stop_analyze_button.setEnabled(False)
self._dispatch_status_update("Analyze aborted.")
def _on_file_item_doubleclick(self, item):
"""
Called when baseline_filter_parameter file list item is double clicked.
Starts the plotting thread, which opens the file, parses data, then passes to plotData
"""
# adding by emitting signal in different thread
self._dispatch_status_update("Plotting...")
decimates = self.plot_tool_bar.is_decimate_checked()
thread = PlotThread(self.p1, filename=str(item.get_file_name()), decimate=decimates)
thread.dataReady.connect(self._on_file_item_doubleclick_callback)
self.add_thread(thread)
thread.start()
def _on_file_item_doubleclick_callback(self, results):
if 'plot_options' in results:
self.plot_data(results['plot_options'])
if 'status_text' in results:
self._dispatch_status_update(results['status_text'])
if 'thread' in results:
self.remove_thread(results['thread'])
def _on_file_item_selection_changed(self):
self.analyze_button.setEnabled(True)
def _create_right_widget(self, parent=None):
wig = pg.GraphicsLayoutWidget(parent)
# Main plot
self.plot_widget = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.plot_widget)
self.plot_widget.enableAutoRange('xy', False)
self.p1 = self.plot_widget.plot() # create an empty plot curve to be filled later
# Tool bar for main plot. Contains zoom button and different checkboxes
self.plot_tool_bar = PlotToolBar(self)
if not parent is None:
parent.addToolBar(self.plot_tool_bar)
event_finder_plots_layout = LayoutWidget()
event_finder_plots_layout.addWidget(self.plot_tool_bar, row=1, col=0, colspan=3)
event_finder_plots_layout.addWidget(wig, row=2, col=0, colspan=3)
return event_finder_plots_layout
def open_data_files(self, file_names=None):
are_files_opened = super(EventFindingTab, self).open_data_files(file_names)
if are_files_opened:
self.analyze_button.setEnabled(False)
def _create_left_widget(self, parent=None):
"""
Initializes everything in the options pane on the left side of the splitter.
"""
scroll_area = QtGui.QScrollArea()
scroll_area.setWidgetResizable(True)
list_form_layout = super(EventFindingTab, self)._create_left_widget(parent)
# Other GUI controls
#
self.analyze_button = QtGui.QPushButton("&Find Events")
self.connect(self.analyze_button, QtCore.SIGNAL('clicked()'), self._on_analyze)
self.analyze_button.setEnabled(False)
self.stop_analyze_button = QtGui.QPushButton("&Stop")
self.connect(self.stop_analyze_button, QtCore.SIGNAL('clicked()'), self._on_analyze_stop)
self.stop_analyze_button.setEnabled(False)
self.debug_check_box = QtGui.QCheckBox()
self.debug_check_box.setChecked(False)
self.debug_check_box.setText('Debug')
self.debug_check_box.setToolTip("When checked, extra data will be saved to the EventDatabase. This"
" data includes the data, baseline, and thresholds at each datapoint.")
# Analysis options
self.min_event_length_edit = QtGui.QLineEdit()
self.min_event_length_edit.setText('10.0')
self.min_event_length_edit.setValidator(QtGui.QDoubleValidator(0, 1e12, 5, self.min_event_length_edit))
self.max_event_length_edit = QtGui.QLineEdit()
self.max_event_length_edit.setText('1000.0')
self.max_event_length_edit.setValidator(QtGui.QDoubleValidator(0, 1e12, 5, self.max_event_length_edit))
fixed_analysis_options = QtGui.QFormLayout()
fixed_analysis_options.addRow('Min Event Length [us]:', self.min_event_length_edit)
fixed_analysis_options.addRow('Max Event Length [us]:', self.max_event_length_edit)
# Baseline options
baseline_options = QtGui.QStackedLayout()
self.baseline_type_combo = QtGui.QComboBox()
self.baseline_type_combo.addItems(('Adaptive', 'Fixed'))
self.baseline_type_combo.activated.connect(baseline_options.setCurrentIndex)
adaptive_options_layout = QtGui.QFormLayout()
self.baseline_filter_parameter_edit = QtGui.QLineEdit()
self.baseline_filter_parameter_edit.setValidator(QtGui.QDoubleValidator(0, 10, 5, self.baseline_filter_parameter_edit))
self.baseline_filter_parameter_edit.setText('0.93')
adaptive_options_layout.addRow('Baseline Filter Parameter:', self.baseline_filter_parameter_edit)
self.variance_filter_parameter_edit = QtGui.QLineEdit()
self.variance_filter_parameter_edit.setValidator(QtGui.QDoubleValidator(0, 10, 5, self.variance_filter_parameter_edit))
self.variance_filter_parameter_edit.setText('0.99')
adaptive_options_layout.addRow('Variance Filter Parameter:', self.variance_filter_parameter_edit)
# need to cast to widget to add to QStackedLayout
adaptive_options_widget = QtGui.QWidget()
adaptive_options_widget.setLayout(adaptive_options_layout)
choose_baseline_btn = QtGui.QPushButton('Baseline:')
choose_baseline_btn.setToolTip('Click to choose the baseline from the plot.')
fixed_options_layout = QtGui.QFormLayout()
self.baseline_current_edit = QtGui.QLineEdit()
self.baseline_current_edit.setValidator(QtGui.QDoubleValidator(-9999, 9999, 9, self.baseline_current_edit))
self.baseline_current_edit.setText('0.0')
fixed_options_layout.addRow(choose_baseline_btn, self.baseline_current_edit)
fixed_options_widget = QtGui.QWidget()
fixed_options_widget.setLayout(fixed_options_layout)
baseline_options.addWidget(adaptive_options_widget)
baseline_options.addWidget(fixed_options_widget)
baseline_form = QtGui.QFormLayout()
baseline_form.addRow('Baseline Type:', self.baseline_type_combo)
# Threshold options
threshold_options = QtGui.QStackedLayout()
self.threshold_type_combo = QtGui.QComboBox()
self.threshold_type_combo.addItem('Noise Based')
self.threshold_type_combo.addItem('Absolute Change')
self.threshold_type_combo.addItem('Percent Change')
self.threshold_type_combo.activated.connect(threshold_options.setCurrentIndex)
threshold_form = QtGui.QFormLayout()
self.threshold_direction_combo = QtGui.QComboBox()
self.threshold_direction_combo.addItems(('Both', 'Positive', 'Negative'))
threshold_form.addRow('Threshold Direction:', self.threshold_direction_combo)
threshold_form.addRow('Threshold Type:', self.threshold_type_combo)
noise_based_options_layout = QtGui.QFormLayout()
self.threshold_stdev_start = QtGui.QLineEdit()
self.threshold_stdev_start.setValidator(QtGui.QDoubleValidator(-9999, 9999, 4, self.threshold_stdev_start))
self.threshold_stdev_start.setText('5.0')
noise_based_options_layout.addRow('Start StdDev:', self.threshold_stdev_start)
self.threshold_stdev_end = QtGui.QLineEdit()
self.threshold_stdev_end.setValidator(QtGui.QDoubleValidator(-9999, 9999, 4, self.threshold_stdev_end))
self.threshold_stdev_end.setText('1.0')
noise_based_options_layout.addRow('End StdDev:', self.threshold_stdev_end)
absolute_drop_options_layout = QtGui.QFormLayout()
self.absolute_change_start_edit = QtGui.QLineEdit()
self.absolute_change_start_edit.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 9, self.absolute_change_start_edit))
self.absolute_change_start_edit.setText('0.1')
absolute_drop_options_layout.addRow('Absolute Change Start [uA]:', self.absolute_change_start_edit)
self.absolute_change_end_edit = QtGui.QLineEdit()
self.absolute_change_end_edit.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 9, self.absolute_change_end_edit))
self.absolute_change_end_edit.setText('0.0')
absolute_drop_options_layout.addRow('Absolute Change End [uA]:', self.absolute_change_end_edit)
percentage_change_options_layout = QtGui.QFormLayout()
self.percentage_change_start_edit = QtGui.QLineEdit()
self.percentage_change_start_edit.setValidator(
QtGui.QDoubleValidator(0, 9999, 5, self.percentage_change_start_edit))
self.percentage_change_start_edit.setText('10.0')
percentage_change_options_layout.addRow('Percent Change Start:', self.percentage_change_start_edit)
self.percentage_change_end_edit = QtGui.QLineEdit()
self.percentage_change_end_edit.setValidator(
QtGui.QDoubleValidator(0, 9999, 5, self.percentage_change_end_edit))
self.percentage_change_end_edit.setText('0.0')
percentage_change_options_layout.addRow('Percent Change End:', self.percentage_change_end_edit)
noise_based_options = QtGui.QWidget()
noise_based_options.setLayout(noise_based_options_layout)
absolute_drop_options = QtGui.QWidget()
absolute_drop_options.setLayout(absolute_drop_options_layout)
percentage_change_options_widget = QtGui.QWidget()
percentage_change_options_widget.setLayout(percentage_change_options_layout)
threshold_options.addWidget(noise_based_options)
threshold_options.addWidget(absolute_drop_options)
threshold_options.addWidget(percentage_change_options_widget)
hbox = QtGui.QHBoxLayout()
for w in [self.analyze_button, self.stop_analyze_button]:
hbox.addWidget(w)
hbox.setAlignment(w, QtCore.Qt.AlignVCenter)
# Left vertical layout with settings
vbox_left = QtGui.QVBoxLayout()
vbox_left.addLayout(list_form_layout)
vbox_left.addLayout(fixed_analysis_options)
vbox_left.addLayout(baseline_form)
vbox_left.addLayout(baseline_options)
vbox_left.addLayout(threshold_form)
vbox_left.addLayout(threshold_options)
vbox_left.addWidget(self.debug_check_box)
vbox_left.addLayout(hbox)
vbox_left_widget = QtGui.QWidget()
vbox_left_widget.setLayout(vbox_left)
scroll_area.setWidget(vbox_left_widget)
return scroll_area
class EventFindingTab(BaseQSplitterDataFile):
"""
A QtGui.QSplitter that contains event finding options on the left and a plot on the right.
"""
def __init__(self, parent=None):
"""
:param PySide.QtGui.QMainWindow parent: Parent main window (optional).
"""
# Define the instance elements
self.events = [] # holds the events from the most recent analysis run
self.plot_widget = None
self.p1 = None
self.plot_tool_bar = None
super(EventFindingTab, self).__init__(parent)
def get_current_analysis_parameters(self):
"""
Reads the current analysis parameters from the gui and returns the results in a dictionary. Returns
dictionary entry 'error' with text of the error if one exists.
:returns: DictType -- the event analysis parameters. These include:
- 'error' - Text if there was an error
OR
- 'min_event_length'
- 'max_event_length'
- 'baseline_strategy'
- 'baseline_filter_parameter'
- 'baseline_current'
etc...
"""
threshold_type = baseline_type = None
# Get Min_event length in microseconds
try:
min_event_length = float(self.min_event_length_edit.text())
except ValueError:
return {
'error':
'Could not read float from Min Event Length text box. Please fix.'
}
# Get Max Event Length in microseconds
try:
max_event_length = float(self.max_event_length_edit.text())
except ValueError:
return {
'error':
'Could not read float from Max Event Length text box. Please fix.'
}
if min_event_length >= max_event_length:
return {
'error':
'Min Event Length is greater than Max Event Length. Please fix.'
}
baseline_type_str = str(self.baseline_type_combo.currentText())
if baseline_type_str == 'Adaptive':
try:
baseline_filter_parameter = float(
self.baseline_filter_parameter_edit.text())
except ValueError:
return {
'error':
'Could not read float from Baseline Filter Parameter text box. Please fix.'
}
try:
variance_filter_parameter = float(
self.variance_filter_parameter_edit.text())
except ValueError:
return {
'error':
'Could not read float from Variance Filter Parameter text box. Please fix.'
}
baseline_type = AdaptiveBaselineStrategy(
baseline_filter_parameter=baseline_filter_parameter,
variance_filter_parameter=variance_filter_parameter)
elif baseline_type_str == 'Fixed':
try:
baseline_current = float(self.baseline_current_edit.text())
baseline_type = FixedBaselineStrategy(
baseline=baseline_current)
except ValueError:
return {
'error':
'Could not read float from Baseline Current text box. Please fix.'
}
threshold_direction_str = str(
self.threshold_direction_combo.currentText())
detect_positive_events = (threshold_direction_str
in ('Positive', 'Both'))
detect_negative_events = (threshold_direction_str
in ('Negative', 'Both'))
threshold_type_str = str(self.threshold_type_combo.currentText())
if threshold_type_str == 'Noise Based':
try:
start_stddev = float(self.threshold_stdev_start.text())
except ValueError:
return {
'error':
'Could not read float from Start StdDev text box. Please fix.'
}
try:
end_stddev = float(self.threshold_stdev_end.text())
except ValueError:
return {
'error':
'Could not read float from End StdDev text box. Please fix.'
}
threshold_type = NoiseBasedThresholdStrategy(
start_std_dev=start_stddev, end_std_dev=end_stddev)
elif threshold_type_str == 'Absolute Change':
try:
absolute_change_start = float(
self.absolute_change_start_edit.text())
except ValueError:
return {
'error':
'Could not read float from Absolute Change Start. Please fix.'
}
try:
absolute_change_end = float(
self.absolute_change_end_edit.text())
except ValueError:
return {
'error':
'Could not read float from Absolute Change End. Please fix.'
}
threshold_type = AbsoluteChangeThresholdStrategy(
change_start=absolute_change_start,
change_end=absolute_change_end)
elif threshold_type_str == 'Percent Change':
try:
percent_change_start = float(
self.percentage_change_start_edit.text())
except ValueError:
return {
'error':
'Could not read float from Percent Change Start text box. Please fix.'
}
try:
percent_change_end = float(
self.percentage_change_end_edit.text())
except ValueError:
return {
'error':
'Could not read float from Percent Change End text box. Please fix.'
}
threshold_type = PercentChangeThresholdStrategy(
percent_change_start=percent_change_start,
percent_change_end=percent_change_end)
parameters = Parameters(min_event_length=min_event_length,
max_event_length=max_event_length,
detect_positive_events=detect_positive_events,
detect_negative_events=detect_negative_events,
baseline_strategy=baseline_type,
threshold_strategy=threshold_type)
return parameters
def plot_data(self, plot_options):
"""
Plots waveform in datadict.
:param DictType plot_options: Dictionary of plot options. Must contain:
* Data at plot_options['data'][0]
* sample_rate at plot_options['sample_rate']
* plot_range at plot_options['plot_range']. This can be [start,stop], or
'all' for 0:n.
"""
# Read the first file, store data in dictionary
data = plot_options['data'][0]
sample_rate = plot_options['sample_rate']
plot_range = plot_options['plot_range']
n = len(data)
# If problem with input, just plot all the data
if plot_range == 'all' or len(
plot_range) != 2 or plot_range[1] <= plot_range[0]:
plot_range = [0, n]
else: # no problems!
n = plot_range[1] - plot_range[0] + 1
ts = 1 / sample_rate
times = linspace(ts * plot_range[0], ts * plot_range[1], n)
y_data = data[plot_range[0]:(plot_range[1] + 1)]
self.plot_widget.clear_event_items()
self.p1.setData(x=times, y=y_data)
self.plot_widget.autoRange()
self._dispatch_process_events()
def _analyze_data_thread_callback(self, results):
"""
Callback for updates from the AnalyzeDataThread.
"""
if 'status_text' in results:
self._dispatch_status_update(results['status_text'])
if 'Events' in results:
single_plot = False
events = results['Events']
if len(events) < 1:
return
elif len(self.events) < 1:
# if this is our first time plotting events, include the single event plot!
single_plot = True
self.events += events
self.event_display_edit.setMaxLength(
int(len(self.events) / 10) + 1)
self.event_display_edit.setValidator(
QtGui.QIntValidator(1, len(self.events),
self.event_display_edit))
self.eventCountText.setText('/' + str(len(self.events)))
if self.plot_tool_bar.is_plot_during_checked():
self.plotEventsOnMainPlot(events)
self.addEventsToConcatEventPlot(events)
if single_plot:
self.event_display_edit.setText('1')
self._dispatch_process_events()
self.analyzethread.readyForEvents = True
if 'done' in results:
if results['done']:
self.stop_analyze_button.setEnabled(False)
def _on_analyze(self):
"""
Searches for events in the file that is currently highlighted in the files list.
"""
selected_items = self.file_list_widget.selectedItems()
if len(selected_items) > 0:
curr_item = selected_items[0]
else:
return
parameters = self.get_current_analysis_parameters()
if isinstance(parameters, dict) and 'error' in parameters:
self._dispatch_status_update(parameters['error'])
return
debug = self.debug_check_box.isChecked()
# Clear the current events
del self.events[:]
# self.prev_concat_time = 0.
file_names = [str(curr_item.get_file_name())]
self._dispatch_status_update("Event Count: 0 Percent Done: 0")
# Start analyzing data in new analyzethread.
self.analyzethread = AnalyzeDataThread(file_names, parameters, debug)
self.analyzethread.dataReady.connect(
self._analyze_data_thread_callback)
self.add_thread(self.analyzethread)
self.analyzethread.start()
self.stop_analyze_button.setEnabled(True)
def _on_analyze_stop(self):
"""
Called when the user clicks the Stop button.
"""
self.clean_threads()
self.stop_analyze_button.setEnabled(False)
self._dispatch_status_update("Analyze aborted.")
def _on_file_item_doubleclick(self, item):
"""
Called when baseline_filter_parameter file list item is double clicked.
Starts the plotting thread, which opens the file, parses data, then passes to plotData
"""
# adding by emitting signal in different thread
self._dispatch_status_update("Plotting...")
decimates = self.plot_tool_bar.is_decimate_checked()
thread = PlotThread(self.p1,
filename=str(item.get_file_name()),
decimate=decimates)
thread.dataReady.connect(self._on_file_item_doubleclick_callback)
self.add_thread(thread)
thread.start()
def _on_file_item_doubleclick_callback(self, results):
if 'plot_options' in results:
self.plot_data(results['plot_options'])
if 'status_text' in results:
self._dispatch_status_update(results['status_text'])
if 'thread' in results:
self.remove_thread(results['thread'])
def _on_file_item_selection_changed(self):
self.analyze_button.setEnabled(True)
def _create_right_widget(self, parent=None):
wig = pg.GraphicsLayoutWidget(parent)
# Main plot
self.plot_widget = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.plot_widget)
self.plot_widget.enableAutoRange('xy', False)
self.p1 = self.plot_widget.plot(
) # create an empty plot curve to be filled later
# Tool bar for main plot. Contains zoom button and different checkboxes
self.plot_tool_bar = PlotToolBar(self)
if not parent is None:
parent.addToolBar(self.plot_tool_bar)
event_finder_plots_layout = LayoutWidget()
event_finder_plots_layout.addWidget(self.plot_tool_bar,
row=1,
col=0,
colspan=3)
event_finder_plots_layout.addWidget(wig, row=2, col=0, colspan=3)
return event_finder_plots_layout
def open_data_files(self, file_names=None):
are_files_opened = super(EventFindingTab,
self).open_data_files(file_names)
if are_files_opened:
self.analyze_button.setEnabled(False)
def _create_left_widget(self, parent=None):
"""
Initializes everything in the options pane on the left side of the splitter.
"""
scroll_area = QtGui.QScrollArea()
scroll_area.setWidgetResizable(True)
list_form_layout = super(EventFindingTab,
self)._create_left_widget(parent)
# Other GUI controls
#
self.analyze_button = QtGui.QPushButton("&Find Events")
self.connect(self.analyze_button, QtCore.SIGNAL('clicked()'),
self._on_analyze)
self.analyze_button.setEnabled(False)
self.stop_analyze_button = QtGui.QPushButton("&Stop")
self.connect(self.stop_analyze_button, QtCore.SIGNAL('clicked()'),
self._on_analyze_stop)
self.stop_analyze_button.setEnabled(False)
self.debug_check_box = QtGui.QCheckBox()
self.debug_check_box.setChecked(False)
self.debug_check_box.setText('Debug')
self.debug_check_box.setToolTip(
"When checked, extra data will be saved to the EventDatabase. This"
" data includes the data, baseline, and thresholds at each datapoint."
)
# Analysis options
self.min_event_length_edit = QtGui.QLineEdit()
self.min_event_length_edit.setText('10.0')
self.min_event_length_edit.setValidator(
QtGui.QDoubleValidator(0, 1e12, 5, self.min_event_length_edit))
self.max_event_length_edit = QtGui.QLineEdit()
self.max_event_length_edit.setText('1000.0')
self.max_event_length_edit.setValidator(
QtGui.QDoubleValidator(0, 1e12, 5, self.max_event_length_edit))
fixed_analysis_options = QtGui.QFormLayout()
fixed_analysis_options.addRow('Min Event Length [us]:',
self.min_event_length_edit)
fixed_analysis_options.addRow('Max Event Length [us]:',
self.max_event_length_edit)
# Baseline options
baseline_options = QtGui.QStackedLayout()
self.baseline_type_combo = QtGui.QComboBox()
self.baseline_type_combo.addItems(('Adaptive', 'Fixed'))
self.baseline_type_combo.activated.connect(
baseline_options.setCurrentIndex)
adaptive_options_layout = QtGui.QFormLayout()
self.baseline_filter_parameter_edit = QtGui.QLineEdit()
self.baseline_filter_parameter_edit.setValidator(
QtGui.QDoubleValidator(0, 10, 5,
self.baseline_filter_parameter_edit))
self.baseline_filter_parameter_edit.setText('0.93')
adaptive_options_layout.addRow('Baseline Filter Parameter:',
self.baseline_filter_parameter_edit)
self.variance_filter_parameter_edit = QtGui.QLineEdit()
self.variance_filter_parameter_edit.setValidator(
QtGui.QDoubleValidator(0, 10, 5,
self.variance_filter_parameter_edit))
self.variance_filter_parameter_edit.setText('0.99')
adaptive_options_layout.addRow('Variance Filter Parameter:',
self.variance_filter_parameter_edit)
# need to cast to widget to add to QStackedLayout
adaptive_options_widget = QtGui.QWidget()
adaptive_options_widget.setLayout(adaptive_options_layout)
choose_baseline_btn = QtGui.QPushButton('Baseline:')
choose_baseline_btn.setToolTip(
'Click to choose the baseline from the plot.')
fixed_options_layout = QtGui.QFormLayout()
self.baseline_current_edit = QtGui.QLineEdit()
self.baseline_current_edit.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 9, self.baseline_current_edit))
self.baseline_current_edit.setText('0.0')
fixed_options_layout.addRow(choose_baseline_btn,
self.baseline_current_edit)
fixed_options_widget = QtGui.QWidget()
fixed_options_widget.setLayout(fixed_options_layout)
baseline_options.addWidget(adaptive_options_widget)
baseline_options.addWidget(fixed_options_widget)
baseline_form = QtGui.QFormLayout()
baseline_form.addRow('Baseline Type:', self.baseline_type_combo)
# Threshold options
threshold_options = QtGui.QStackedLayout()
self.threshold_type_combo = QtGui.QComboBox()
self.threshold_type_combo.addItem('Noise Based')
self.threshold_type_combo.addItem('Absolute Change')
self.threshold_type_combo.addItem('Percent Change')
self.threshold_type_combo.activated.connect(
threshold_options.setCurrentIndex)
threshold_form = QtGui.QFormLayout()
self.threshold_direction_combo = QtGui.QComboBox()
self.threshold_direction_combo.addItems(
('Both', 'Positive', 'Negative'))
threshold_form.addRow('Threshold Direction:',
self.threshold_direction_combo)
threshold_form.addRow('Threshold Type:', self.threshold_type_combo)
noise_based_options_layout = QtGui.QFormLayout()
self.threshold_stdev_start = QtGui.QLineEdit()
self.threshold_stdev_start.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 4, self.threshold_stdev_start))
self.threshold_stdev_start.setText('5.0')
noise_based_options_layout.addRow('Start StdDev:',
self.threshold_stdev_start)
self.threshold_stdev_end = QtGui.QLineEdit()
self.threshold_stdev_end.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 4, self.threshold_stdev_end))
self.threshold_stdev_end.setText('1.0')
noise_based_options_layout.addRow('End StdDev:',
self.threshold_stdev_end)
absolute_drop_options_layout = QtGui.QFormLayout()
self.absolute_change_start_edit = QtGui.QLineEdit()
self.absolute_change_start_edit.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 9,
self.absolute_change_start_edit))
self.absolute_change_start_edit.setText('0.1')
absolute_drop_options_layout.addRow('Absolute Change Start [uA]:',
self.absolute_change_start_edit)
self.absolute_change_end_edit = QtGui.QLineEdit()
self.absolute_change_end_edit.setValidator(
QtGui.QDoubleValidator(-9999, 9999, 9,
self.absolute_change_end_edit))
self.absolute_change_end_edit.setText('0.0')
absolute_drop_options_layout.addRow('Absolute Change End [uA]:',
self.absolute_change_end_edit)
percentage_change_options_layout = QtGui.QFormLayout()
self.percentage_change_start_edit = QtGui.QLineEdit()
self.percentage_change_start_edit.setValidator(
QtGui.QDoubleValidator(0, 9999, 5,
self.percentage_change_start_edit))
self.percentage_change_start_edit.setText('10.0')
percentage_change_options_layout.addRow(
'Percent Change Start:', self.percentage_change_start_edit)
self.percentage_change_end_edit = QtGui.QLineEdit()
self.percentage_change_end_edit.setValidator(
QtGui.QDoubleValidator(0, 9999, 5,
self.percentage_change_end_edit))
self.percentage_change_end_edit.setText('0.0')
percentage_change_options_layout.addRow(
'Percent Change End:', self.percentage_change_end_edit)
noise_based_options = QtGui.QWidget()
noise_based_options.setLayout(noise_based_options_layout)
absolute_drop_options = QtGui.QWidget()
absolute_drop_options.setLayout(absolute_drop_options_layout)
percentage_change_options_widget = QtGui.QWidget()
percentage_change_options_widget.setLayout(
percentage_change_options_layout)
threshold_options.addWidget(noise_based_options)
threshold_options.addWidget(absolute_drop_options)
threshold_options.addWidget(percentage_change_options_widget)
hbox = QtGui.QHBoxLayout()
for w in [self.analyze_button, self.stop_analyze_button]:
hbox.addWidget(w)
hbox.setAlignment(w, QtCore.Qt.AlignVCenter)
# Left vertical layout with settings
vbox_left = QtGui.QVBoxLayout()
vbox_left.addLayout(list_form_layout)
vbox_left.addLayout(fixed_analysis_options)
vbox_left.addLayout(baseline_form)
vbox_left.addLayout(baseline_options)
vbox_left.addLayout(threshold_form)
vbox_left.addLayout(threshold_options)
vbox_left.addWidget(self.debug_check_box)
vbox_left.addLayout(hbox)
vbox_left_widget = QtGui.QWidget()
vbox_left_widget.setLayout(vbox_left)
scroll_area.setWidget(vbox_left_widget)
return scroll_area
