def test_my_plot_item_add_item(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
self.assertEqual(len(plot_item._myItemList), 1)
x = y = np.zeros(2)
plot2 = PathItem(x, y)
plot_item.addItem(plot2)
self.assertEqual(len(plot_item._myItemList), 2)
def test_clear_event_items(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
self.assertEqual(len(plot_item._myEventItemList), 1)
self.assertEqual(len(plot_item.listDataItems()), 2)
plot_item.clear_event_items()
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item.listDataItems()), 1)
def test_clear(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
x = y = np.zeros(2)
plot3 = PathItem(x, y)
plot_item.add_event_item(plot3)
plot_item.clear()
self.assertEqual(len(plot_item.listDataItems()), 0)
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item._myItemList), 0)
def test_clear_event_items(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
self.assertEqual(len(plot_item._myEventItemList), 1)
self.assertEqual(len(plot_item.listDataItems()), 2)
plot_item.clear_event_items()
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item.listDataItems()), 1)
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 test_my_plot_item_add_item(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
self.assertEqual(len(plot_item._myItemList), 1)
x = y = np.zeros(2)
plot2 = PathItem(x, y)
plot_item.addItem(plot2)
self.assertEqual(len(plot_item._myItemList), 2)
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
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
def _create_event_viewer_plot_widget(self):
wig = pg.GraphicsLayoutWidget()
wig2 = pg.GraphicsLayoutWidget()
# Main plot
self.eventview_plotwid = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.eventview_plotwid)
self.eventview_plotwid.enableAutoRange('xy', False)
wig.nextRow()
# Create Qwt plot for concatenated events
self.plot_concatevents = wig.addPlot(title='Concatenated Events', name='Concat')
self.eventviewer_plots = []
# Now add 9 plots to view events in
for i in xrange(3):
wig2.nextRow()
for j in xrange(3):
plot = wig2.addPlot(title='Event ' + str(i * 3 + j), name='Single' + str(i * 3 + j))
self.eventviewer_plots.append(plot)
# Tool bar for main plot. Contains zoom button and different checkboxes
# self.plotToolBar = PlotToolBar(self)
# self.addToolBar(self.plotToolBar)
event_select_toolbar = QtGui.QToolBar(self)
if self._parent is not None:
self._parent.addToolBar(event_select_toolbar)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Previous")
button_previous.clicked.connect(self.previous_clicked)
event_select_toolbar.addWidget(button_previous)
self.event_display_edit = QtGui.QLineEdit()
self.event_display_edit.setText('0')
self.event_display_edit.setMaxLength(1)
self.event_display_edit.setValidator(QtGui.QIntValidator(0, 0, self.event_display_edit))
self.event_display_edit.textChanged.connect(self._event_display_edit_on_change)
event_select_toolbar.addWidget(self.event_display_edit)
self.event_count_text = QtGui.QLabel()
self.event_count_text.setText('/' + str(0))
event_select_toolbar.addWidget(self.event_count_text)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Next")
button_previous.clicked.connect(self.next_clicked)
event_select_toolbar.addWidget(button_previous)
frame = QtGui.QSplitter()
frame.setOrientation(QtCore.Qt.Vertical)
frame.addWidget(wig)
frame.addWidget(wig2)
event_finder_plots_layout = LayoutWidget()
# event_finder_plots_layout.addWidget(self.plotToolBar, row=1, col=0, colspan=3)
event_finder_plots_layout.addWidget(frame, row=2, col=0, colspan=3)
event_finder_plots_layout.addWidget(event_select_toolbar, row=5, col=0, colspan=3)
return event_finder_plots_layout
class EventViewingTab(_ThreadManager, QtGui.QSplitter):
"""
A QtGui.Splitter that contains a file opener list on the left and plots on the right.
"""
def __init__(self, parent=None):
"""
:param PySide.QtGui.QMainWindow parent: Parent main window (optional).
"""
super(EventViewingTab, self).__init__(parent)
self._parent = parent
self.open_directory_changed_callback = None
options = self._create_event_viewer_options()
plots = self._create_event_viewer_plot_widget()
# Put everything in baseline_filter_parameter scroll area
scroll_plots = QtGui.QScrollArea()
scroll_plots.setWidgetResizable(True)
scroll_plots.setWidget(plots)
self.addWidget(options)
self.addWidget(scroll_plots)
def open_event_databases(self, file_names=None):
"""
Adds the files to the list widget.
:param ListType<StringType> file_names: (Optional) List of file names to be added to the list widget. If not
included, then a QtGui.QFileDialog will be opened to select files.
"""
if file_names is None:
file_names = QtGui.QFileDialog.getOpenFileNames(self, 'Open event database', '.', '*.h5')[0]
if len(file_names) > 0:
self.eventview_list_widget.clear()
else:
return
for w in file_names:
item = FileListItem(w)
self.eventview_list_widget.addItem(item)
def _create_event_viewer_options(self):
scroll_area = QtGui.QScrollArea()
scroll_area.setWidgetResizable(True)
# Create baseline_filter_parameter list for files want to analyze
self.eventview_list_widget = QtGui.QListWidget()
self.eventview_list_widget.itemDoubleClicked.connect(self._on_eventview_file_item_doubleclick)
self.eventview_list_widget.setMaximumHeight(100)
fixed_analysis_options = QtGui.QFormLayout()
fixed_analysis_options.addRow('Event Databases:', self.eventview_list_widget)
vbox_left = QtGui.QVBoxLayout()
vbox_left.addLayout(fixed_analysis_options)
vbox_left_widget = QtGui.QWidget()
vbox_left_widget.setLayout(vbox_left)
scroll_area.setWidget(vbox_left_widget)
return scroll_area
def _on_eventview_file_item_doubleclick(self, item):
"""
"""
self.event_view_item = item
h5file = eD.open_file(item.get_file_name())
event_count = h5file.get_event_count()
if h5file.is_debug():
self.plot_debug(h5file)
h5file.close()
self.event_display_edit.setMaxLength(int(event_count / 10) + 1)
self.event_display_edit.setValidator(QtGui.QIntValidator(1, event_count, self.event_display_edit))
self.event_count_text.setText('/' + str(event_count))
self.event_display_edit.setText('')
self.event_display_edit.setText('1')
def plot_debug(self, event_database):
"""
Plots the data, baseline, and thresholds of the debug group in the event_database, if they exist,
in the main plot.
:param event_database: An already open\
:class:`EventDatabase <pypore.filetypes.event_database.EventDatabase>`.
"""
if not event_database.is_debug():
return
self.eventview_plotwid.clear()
sample_rate = event_database.get_sample_rate()
# TODO remove the step_size.
step_size = 1000
data = event_database.root.debug.data[0][::step_size]
data_size = data.size
times = np.linspace(0, data_size *1.0/sample_rate, data_size)
item = PathItem(times, data)
item.setPen(pg.mkPen('w'))
self.eventview_plotwid.addItem(item)
baseline = event_database.root.debug.baseline[0][::step_size]
item = PathItem(times, baseline)
item.setPen(pg.mkPen('y'))
self.eventview_plotwid.addItem(item)
threshold_p = event_database.root.debug.threshold_positive[0][::step_size]
item = PathItem(times, threshold_p)
item.setPen(pg.mkPen('g'))
self.eventview_plotwid.addItem(item)
threshold_n = event_database.root.debug.threshold_negative[0][::step_size]
item = PathItem(times, threshold_n)
item.setPen(pg.mkPen('g'))
self.eventview_plotwid.addItem(item)
def plot_single_events(self, event):
"""
Plots the event on the plot with
"""
h5file = eD.open_file(self.event_view_item.get_file_name(), mode='r')
event_count = h5file.get_event_count()
for i in xrange(3):
for j in xrange(3):
pos = 3 * i + j
if pos + event >= event_count or pos + event < 0:
self.eventviewer_plots[pos].clear()
self.eventviewer_plots[pos].setTitle('')
else:
self.plot_single_event(h5file, event + pos, self.eventviewer_plots[pos])
self.eventviewer_plots[pos].setTitle('Event ' + str(event + pos + 1))
h5file.close()
def plot_single_event(self, h5file, position, plot):
sample_rate = h5file.get_sample_rate()
row = h5file.get_event_row(position)
array_row = row['array_row']
event_length = row['event_length']
raw_points_per_side = row['raw_points_per_side']
raw_data = h5file.get_raw_data_at(array_row)
n = len(raw_data)
times = np.linspace(0.0, 1.0 * n / sample_rate, n)
plot.clear()
plot.plot(times, raw_data)
# plot the event points in yellow
plot.plot(times[raw_points_per_side:raw_points_per_side + event_length],
raw_data[raw_points_per_side:raw_points_per_side + event_length], pen='y')
# Plot the cusum levels
n_levels = row['n_levels']
baseline = row['baseline']
# left, start-1, start,
levels = h5file.get_levels_at(array_row)
indices = h5file.get_level_lengths_at(array_row)
level_times = np.zeros(2 * n_levels + 4)
level_values = np.zeros(2 * n_levels + 4)
level_times[1] = 1.0 * (raw_points_per_side - 1) / sample_rate
level_values[0] = level_values[1] = baseline
i = 0
length = 0
for i in xrange(n_levels):
level_times[2 * i + 2] = times[raw_points_per_side] + 1.0 * length / sample_rate
level_values[2 * i + 2] = levels[i]
level_times[2 * i + 3] = times[raw_points_per_side] + 1.0 * (length + indices[i]) / sample_rate
level_values[2 * i + 3] = levels[i]
length += indices[i]
i += 1
level_times[2 * i + 2] = times[raw_points_per_side + event_length]
level_times[2 * i + 3] = times[n - 1]
level_values[2 * i + 2] = level_values[2 * i + 3] = baseline
plot.plot(level_times, level_values, pen='g')
def previous_clicked(self):
self.move_event_display_by(-1 * len(self.eventviewer_plots))
def next_clicked(self):
self.move_event_display_by(len(self.eventviewer_plots))
def move_event_display_by(self, count):
"""
Changes the event displayed on the event display plot to
current value + count
"""
h5_event_count = 0
try:
h5file = eD.open_file(self.event_view_item.get_file_name())
h5_event_count = h5file.get_event_count()
h5file.close()
except:
return
try:
event_count = int(self.event_display_edit.text())
if 0 < event_count + count <= h5_event_count:
self.event_display_edit.setText(str(event_count + count))
except ValueError:
# if we can't parse the event display text but there are events,
# just set to zero
if h5_event_count > 0:
self.event_display_edit.setText('1')
def _event_display_edit_on_change(self, text):
if len(text) < 1:
return
position = int(self.event_display_edit.text())
self.plot_single_events(position - 1)
return
def _create_event_viewer_plot_widget(self):
wig = pg.GraphicsLayoutWidget()
wig2 = pg.GraphicsLayoutWidget()
# Main plot
self.eventview_plotwid = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.eventview_plotwid)
self.eventview_plotwid.enableAutoRange('xy', False)
wig.nextRow()
# Create Qwt plot for concatenated events
self.plot_concatevents = wig.addPlot(title='Concatenated Events', name='Concat')
self.eventviewer_plots = []
# Now add 9 plots to view events in
for i in xrange(3):
wig2.nextRow()
for j in xrange(3):
plot = wig2.addPlot(title='Event ' + str(i * 3 + j), name='Single' + str(i * 3 + j))
self.eventviewer_plots.append(plot)
# Tool bar for main plot. Contains zoom button and different checkboxes
# self.plotToolBar = PlotToolBar(self)
# self.addToolBar(self.plotToolBar)
event_select_toolbar = QtGui.QToolBar(self)
if self._parent is not None:
self._parent.addToolBar(event_select_toolbar)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Previous")
button_previous.clicked.connect(self.previous_clicked)
event_select_toolbar.addWidget(button_previous)
self.event_display_edit = QtGui.QLineEdit()
self.event_display_edit.setText('0')
self.event_display_edit.setMaxLength(1)
self.event_display_edit.setValidator(QtGui.QIntValidator(0, 0, self.event_display_edit))
self.event_display_edit.textChanged.connect(self._event_display_edit_on_change)
event_select_toolbar.addWidget(self.event_display_edit)
self.event_count_text = QtGui.QLabel()
self.event_count_text.setText('/' + str(0))
event_select_toolbar.addWidget(self.event_count_text)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Next")
button_previous.clicked.connect(self.next_clicked)
event_select_toolbar.addWidget(button_previous)
frame = QtGui.QSplitter()
frame.setOrientation(QtCore.Qt.Vertical)
frame.addWidget(wig)
frame.addWidget(wig2)
event_finder_plots_layout = LayoutWidget()
# event_finder_plots_layout.addWidget(self.plotToolBar, row=1, col=0, colspan=3)
event_finder_plots_layout.addWidget(frame, row=2, col=0, colspan=3)
event_finder_plots_layout.addWidget(event_select_toolbar, row=5, col=0, colspan=3)
return event_finder_plots_layout
def test_plot_clear(self):
# tests to make sure that when the clear flag is passed
# to plots, that clear works as expected
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
plot5 = PlotCurveItem(y, x)
plot_item.addItem(plot5)
x = y = np.zeros(2)
plot3 = PathItem(x, y)
plot_item.add_event_item(plot3)
plot4 = plot_item.plot(clear=True)
# Test that all of the plots have been cleared,
# and that plot4 was added successfully
self.assertEqual(len(plot_item.listDataItems()), 1)
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item._myItemList), 1)
self.assertEqual(plot_item.listDataItems()[0], plot4)
self.assertEqual(plot_item._myItemList[0], plot4)
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
def _create_event_viewer_plot_widget(self):
wig = pg.GraphicsLayoutWidget()
wig2 = pg.GraphicsLayoutWidget()
# Main plot
self.eventview_plotwid = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.eventview_plotwid)
self.eventview_plotwid.enableAutoRange('xy', False)
wig.nextRow()
# Create Qwt plot for concatenated events
self.plot_concatevents = wig.addPlot(title='Concatenated Events',
name='Concat')
self.eventviewer_plots = []
# Now add 9 plots to view events in
for i in xrange(3):
wig2.nextRow()
for j in xrange(3):
plot = wig2.addPlot(title='Event ' + str(i * 3 + j),
name='Single' + str(i * 3 + j))
self.eventviewer_plots.append(plot)
# Tool bar for main plot. Contains zoom button and different checkboxes
# self.plotToolBar = PlotToolBar(self)
# self.addToolBar(self.plotToolBar)
event_select_toolbar = QtGui.QToolBar(self)
if self._parent is not None:
self._parent.addToolBar(event_select_toolbar)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Previous")
button_previous.clicked.connect(self.previous_clicked)
event_select_toolbar.addWidget(button_previous)
self.event_display_edit = QtGui.QLineEdit()
self.event_display_edit.setText('0')
self.event_display_edit.setMaxLength(1)
self.event_display_edit.setValidator(
QtGui.QIntValidator(0, 0, self.event_display_edit))
self.event_display_edit.textChanged.connect(
self._event_display_edit_on_change)
event_select_toolbar.addWidget(self.event_display_edit)
self.event_count_text = QtGui.QLabel()
self.event_count_text.setText('/' + str(0))
event_select_toolbar.addWidget(self.event_count_text)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Next")
button_previous.clicked.connect(self.next_clicked)
event_select_toolbar.addWidget(button_previous)
frame = QtGui.QSplitter()
frame.setOrientation(QtCore.Qt.Vertical)
frame.addWidget(wig)
frame.addWidget(wig2)
event_finder_plots_layout = LayoutWidget()
# event_finder_plots_layout.addWidget(self.plotToolBar, row=1, col=0, colspan=3)
event_finder_plots_layout.addWidget(frame, row=2, col=0, colspan=3)
event_finder_plots_layout.addWidget(event_select_toolbar,
row=5,
col=0,
colspan=3)
return event_finder_plots_layout
class EventViewingTab(_ThreadManager, QtGui.QSplitter):
"""
A QtGui.Splitter that contains a file opener list on the left and plots on the right.
"""
def __init__(self, parent=None):
"""
:param PySide.QtGui.QMainWindow parent: Parent main window (optional).
"""
super(EventViewingTab, self).__init__(parent)
self._parent = parent
self.open_directory_changed_callback = None
options = self._create_event_viewer_options()
plots = self._create_event_viewer_plot_widget()
# Put everything in baseline_filter_parameter scroll area
scroll_plots = QtGui.QScrollArea()
scroll_plots.setWidgetResizable(True)
scroll_plots.setWidget(plots)
self.addWidget(options)
self.addWidget(scroll_plots)
def open_event_databases(self, file_names=None):
"""
Adds the files to the list widget.
:param ListType<StringType> file_names: (Optional) List of file names to be added to the list widget. If not
included, then a QtGui.QFileDialog will be opened to select files.
"""
if file_names is None:
file_names = QtGui.QFileDialog.getOpenFileNames(
self, 'Open event database', '.', '*.h5')[0]
if len(file_names) > 0:
self.eventview_list_widget.clear()
else:
return
for w in file_names:
item = FileListItem(w)
self.eventview_list_widget.addItem(item)
def _create_event_viewer_options(self):
scroll_area = QtGui.QScrollArea()
scroll_area.setWidgetResizable(True)
# Create baseline_filter_parameter list for files want to analyze
self.eventview_list_widget = QtGui.QListWidget()
self.eventview_list_widget.itemDoubleClicked.connect(
self._on_eventview_file_item_doubleclick)
self.eventview_list_widget.setMaximumHeight(100)
fixed_analysis_options = QtGui.QFormLayout()
fixed_analysis_options.addRow('Event Databases:',
self.eventview_list_widget)
vbox_left = QtGui.QVBoxLayout()
vbox_left.addLayout(fixed_analysis_options)
vbox_left_widget = QtGui.QWidget()
vbox_left_widget.setLayout(vbox_left)
scroll_area.setWidget(vbox_left_widget)
return scroll_area
def _on_eventview_file_item_doubleclick(self, item):
"""
"""
self.event_view_item = item
h5file = eD.open_file(item.get_file_name())
event_count = h5file.get_event_count()
if h5file.is_debug():
self.plot_debug(h5file)
h5file.close()
self.event_display_edit.setMaxLength(int(event_count / 10) + 1)
self.event_display_edit.setValidator(
QtGui.QIntValidator(1, event_count, self.event_display_edit))
self.event_count_text.setText('/' + str(event_count))
self.event_display_edit.setText('')
self.event_display_edit.setText('1')
def plot_debug(self, event_database):
"""
Plots the data, baseline, and thresholds of the debug group in the event_database, if they exist,
in the main plot.
:param event_database: An already open\
:class:`EventDatabase <pypore.filetypes.event_database.EventDatabase>`.
"""
if not event_database.is_debug():
return
self.eventview_plotwid.clear()
sample_rate = event_database.get_sample_rate()
# TODO remove the step_size.
step_size = 1000
data = event_database.root.debug.data[0][::step_size]
data_size = data.size
times = np.linspace(0, data_size * 1.0 / sample_rate, data_size)
item = PathItem(times, data)
item.setPen(pg.mkPen('w'))
self.eventview_plotwid.addItem(item)
baseline = event_database.root.debug.baseline[0][::step_size]
item = PathItem(times, baseline)
item.setPen(pg.mkPen('y'))
self.eventview_plotwid.addItem(item)
threshold_p = event_database.root.debug.threshold_positive[
0][::step_size]
item = PathItem(times, threshold_p)
item.setPen(pg.mkPen('g'))
self.eventview_plotwid.addItem(item)
threshold_n = event_database.root.debug.threshold_negative[
0][::step_size]
item = PathItem(times, threshold_n)
item.setPen(pg.mkPen('g'))
self.eventview_plotwid.addItem(item)
def plot_single_events(self, event):
"""
Plots the event on the plot with
"""
h5file = eD.open_file(self.event_view_item.get_file_name(), mode='r')
event_count = h5file.get_event_count()
for i in xrange(3):
for j in xrange(3):
pos = 3 * i + j
if pos + event >= event_count or pos + event < 0:
self.eventviewer_plots[pos].clear()
self.eventviewer_plots[pos].setTitle('')
else:
self.plot_single_event(h5file, event + pos,
self.eventviewer_plots[pos])
self.eventviewer_plots[pos].setTitle('Event ' +
str(event + pos + 1))
h5file.close()
def plot_single_event(self, h5file, position, plot):
sample_rate = h5file.get_sample_rate()
row = h5file.get_event_row(position)
event_length = row['event_length']
raw_points_per_side = row['raw_points_per_side']
raw_data = h5file.get_raw_data_at(position)
n = len(raw_data)
times = np.linspace(0.0, 1.0 * n / sample_rate, n)
plot.clear()
plot.plot(times, raw_data)
# plot the event points in yellow
plot.plot(
times[raw_points_per_side:raw_points_per_side + event_length],
raw_data[raw_points_per_side:raw_points_per_side + event_length],
pen='y')
# Plot the cusum levels
n_levels = row['n_levels']
baseline = row['baseline']
# left, start-1, start,
levels = h5file.get_levels_at(position)
indices = h5file.get_level_lengths_at(position)
level_times = np.zeros(2 * n_levels + 4)
level_values = np.zeros(2 * n_levels + 4)
level_times[1] = 1.0 * (raw_points_per_side - 1) / sample_rate
level_values[0] = level_values[1] = baseline
i = 0
length = 0
for i in xrange(n_levels):
level_times[
2 * i +
2] = times[raw_points_per_side] + 1.0 * length / sample_rate
level_values[2 * i + 2] = levels[i]
level_times[2 * i + 3] = times[raw_points_per_side] + 1.0 * (
length + indices[i]) / sample_rate
level_values[2 * i + 3] = levels[i]
length += indices[i]
i += 1
level_times[2 * i + 2] = times[raw_points_per_side + event_length]
level_times[2 * i + 3] = times[n - 1]
level_values[2 * i + 2] = level_values[2 * i + 3] = baseline
plot.plot(level_times, level_values, pen='g')
def previous_clicked(self):
self.move_event_display_by(-1 * len(self.eventviewer_plots))
def next_clicked(self):
self.move_event_display_by(len(self.eventviewer_plots))
def move_event_display_by(self, count):
"""
Changes the event displayed on the event display plot to
current value + count
"""
h5_event_count = 0
try:
h5file = eD.open_file(self.event_view_item.get_file_name())
h5_event_count = h5file.get_event_count()
h5file.close()
except:
return
try:
event_count = int(self.event_display_edit.text())
if 0 < event_count + count <= h5_event_count:
self.event_display_edit.setText(str(event_count + count))
except ValueError:
# if we can't parse the event display text but there are events,
# just set to zero
if h5_event_count > 0:
self.event_display_edit.setText('1')
def _event_display_edit_on_change(self, text):
if len(text) < 1:
return
position = int(self.event_display_edit.text())
self.plot_single_events(position - 1)
return
def _create_event_viewer_plot_widget(self):
wig = pg.GraphicsLayoutWidget()
wig2 = pg.GraphicsLayoutWidget()
# Main plot
self.eventview_plotwid = MyPlotItem(title='Current Trace', name='Plot')
wig.addItem(self.eventview_plotwid)
self.eventview_plotwid.enableAutoRange('xy', False)
wig.nextRow()
# Create Qwt plot for concatenated events
self.plot_concatevents = wig.addPlot(title='Concatenated Events',
name='Concat')
self.eventviewer_plots = []
# Now add 9 plots to view events in
for i in xrange(3):
wig2.nextRow()
for j in xrange(3):
plot = wig2.addPlot(title='Event ' + str(i * 3 + j),
name='Single' + str(i * 3 + j))
self.eventviewer_plots.append(plot)
# Tool bar for main plot. Contains zoom button and different checkboxes
# self.plotToolBar = PlotToolBar(self)
# self.addToolBar(self.plotToolBar)
event_select_toolbar = QtGui.QToolBar(self)
if self._parent is not None:
self._parent.addToolBar(event_select_toolbar)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Previous")
button_previous.clicked.connect(self.previous_clicked)
event_select_toolbar.addWidget(button_previous)
self.event_display_edit = QtGui.QLineEdit()
self.event_display_edit.setText('0')
self.event_display_edit.setMaxLength(1)
self.event_display_edit.setValidator(
QtGui.QIntValidator(0, 0, self.event_display_edit))
self.event_display_edit.textChanged.connect(
self._event_display_edit_on_change)
event_select_toolbar.addWidget(self.event_display_edit)
self.event_count_text = QtGui.QLabel()
self.event_count_text.setText('/' + str(0))
event_select_toolbar.addWidget(self.event_count_text)
button_previous = QtGui.QPushButton(event_select_toolbar)
button_previous.setText("Next")
button_previous.clicked.connect(self.next_clicked)
event_select_toolbar.addWidget(button_previous)
frame = QtGui.QSplitter()
frame.setOrientation(QtCore.Qt.Vertical)
frame.addWidget(wig)
frame.addWidget(wig2)
event_finder_plots_layout = LayoutWidget()
# event_finder_plots_layout.addWidget(self.plotToolBar, row=1, col=0, colspan=3)
event_finder_plots_layout.addWidget(frame, row=2, col=0, colspan=3)
event_finder_plots_layout.addWidget(event_select_toolbar,
row=5,
col=0,
colspan=3)
return event_finder_plots_layout
def test_plot_clear(self):
# tests to make sure that when the clear flag is passed
# to plots, that clear works as expected
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
plot5 = PlotCurveItem(y, x)
plot_item.addItem(plot5)
x = y = np.zeros(2)
plot3 = PathItem(x, y)
plot_item.add_event_item(plot3)
plot4 = plot_item.plot(clear=True)
# Test that all of the plots have been cleared,
# and that plot4 was added successfully
self.assertEqual(len(plot_item.listDataItems()), 1)
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item._myItemList), 1)
self.assertEqual(plot_item.listDataItems()[0], plot4)
self.assertEqual(plot_item._myItemList[0], plot4)
def test_clear(self):
plot_item = MyPlotItem()
x = [1]
y = [1]
plot = PlotCurveItem(x, y)
plot_item.addItem(plot)
plot2 = PlotCurveItem(y, x)
plot_item.add_event_item(plot2)
x = y = np.zeros(2)
plot3 = PathItem(x, y)
plot_item.add_event_item(plot3)
plot_item.clear()
self.assertEqual(len(plot_item.listDataItems()), 0)
self.assertEqual(len(plot_item._myEventItemList), 0)
self.assertEqual(len(plot_item._myItemList), 0)
