def calibrate_pc(self, event): """" Perform and calibrate the PC measurement """ self.view1.show_calibration_modal() null_metadata = ExperimentSettings() null_metadata.waveform = "NullWave" pc_data = self.measurement_handler.pc_calibration_measurement( null_metadata) self.pc_calibration.update_data(pc_data)
def calibrate_pc(self, event): """" Perform and calibrate the PC measurement """ self.view1.show_calibration_modal() null_metadata = ExperimentSettings() null_metadata.waveform = "NullWave" pc_data = self.measurement_handler.pc_calibration_measurement( null_metadata ) self.pc_calibration.update_data(pc_data)
class ExperimentSettingsTest(unittest.TestCase): # np.set_printoptions(threshold='nan') def setUp(self): self.meta_data = ExperimentSettings() self.maxDiff = None def test_get_settings_as_dict(self): meta_data = { "channel": "High (2A/V)", "averaging": 1, "measurement_binning": 1, "threshold_mA": 150, "inverted_channels": {"Reference": False, "PC": False, "PL": True}, "sample_rate": 1.2e3, "output_sample_rate": 1.2e3, "input_voltage_range": 10.0, "output_voltage_range": 10.0, "waveform": "Sin", "amplitude": 0.5, "offset_before": 1, "offset_after": 10, "duration": 1, "voltage_threshold": 0.08152173913043478, "channel_name": "ao0", # "pc_calibration_mean": None, "pc_calibration_std": None, } self.assertDictEqual(self.meta_data.as_dict(), meta_data) def test_init(self): self.assertEqual(self.meta_data.voltage_threshold, 0.08152173913043478) self.assertEqual(self.meta_data.channel_name, "ao0") def test_set_amplitude(self): self.assertTrue(self.meta_data.amplitude, 0.5) def test_set_amplitude_too_high(self): self.meta_data.channel = "Low (50mA/V)" self.meta_data.amplitude = 15 self.assertEqual(self.meta_data.amplitude, 10) self.meta_data.channel = "High (2A/V)" self.meta_data.amplitude = 15 self.assertEqual(self.meta_data.amplitude, 1.5) def test_set_voltage_too_high(self): pass def test_set_sample_rate_too_high(self): self.meta_data.sample_rate = 9e90 self.assertEqual(self.meta_data.sample_rate, 1.2e6)
def test_single_measurement_with_averaging(self, mock_waveform_thread): # setup settings = ExperimentSettings() settings.averaging = 2 handler = MeasurementHandler() return_tuple = [ (np.array([2, 3, 4, 5, 6, 7]), np.array([0, 1])), (np.array([3, 4, 5, 6, 7, 8]), np.array([0, 1])), ] handler.add_to_queue(self.lp.create_waveform(), settings) with patch.object(handler, '_run_thread', side_effect=return_tuple) as method: # perform test_dataset = handler.single_measurement() # assert self.assertEqual(2, method.call_count) np.testing.assert_array_equal( test_dataset, np.array([[0, 2.5, 4.5, 6.5], [1, 3.5, 5.5, 7.5]]) ) self.assertEqual(len(handler._queue), 0)
def __init__(self, parent): # models self.metadata = ExperimentSettings() self.Data = ExperimentData(metadata=self.metadata) self.light_pulse = LightPulse(self.metadata) # setup file data self.dirname = os.getcwd() self.data_file = "untitled.dat" self.metadata_file = "untitled.inf" self.__InitUI(parent) self.__InitValidators()
def _parse_experiment_settings(self, config): measurement_list = [] experiments_list = config["experiment_settings"] for item in experiments_list: try: measurement_list.append( ExperimentSettings(waveform=item['waveform'], duration=item['duration'], amplitude=item['amplitude'], offset_before=item['offset_before'], offset_after=item['offset_after'], sample_rate=item['sample_rate'], channel=item['channel'], binning=item['binning'], averaging=item['averaging'])) except KeyError as e: raise ("Missing value in Experiment Settings: {0}".format(e)) return measurement_list
def setUp(self): self.meta_data = ExperimentSettings() self.maxDiff = None
class GUIController(FrameSkeleton): """ Controller to handle interface with wx UI Attributes ---------- MyFrame1: Fig1 Data LoadPath Path measurement_type """ def __init__(self, parent): # models self.metadata = ExperimentSettings() self.Data = ExperimentData(metadata=self.metadata) self.light_pulse = LightPulse(self.metadata) # setup file data self.dirname = os.getcwd() self.data_file = "untitled.dat" self.metadata_file = "untitled.inf" self.__InitUI(parent) self.__InitValidators() def __InitUI(self, parent): # initialize parent class FrameSkeleton.__init__(self, parent) # setup Matplotlib Canvas panel self.Fig1 = CanvasPanel(self.Figure1_Panel) # make status bars m_statusBar = wx.StatusBar(self) self.SetStatusBar(m_statusBar) # self.m_statusBar.SetStatusText("Ready to go!") self.data_panel = DataProcessingPanel(self.m_notebook1) self.m_notebook1.AddPage( self.data_panel, u"Data Processing", # True ) # Setup the Menu menu_bar = wx.MenuBar() # File Menu filem = wx.Menu() filem.Append(wx.ID_OPEN, "Open\tCtrl+O") filem.Append(wx.ID_ANY, "Run\tCtrl+R") filem.Append(wx.ID_ABOUT, "About") filem.Append(wx.ID_EXIT, "Exit\tCtrl+X") # TODO: add and bind event handlers menu_bar.Append(filem, "&File") self.SetMenuBar(menu_bar) # initialise view with model parameters self.m_voltageRange.AppendItems(INPUT_VOLTAGE_RANGE_STR) self.m_Waveform.AppendItems(WAVEFORMS) self.m_Output.AppendItems(OUTPUTS) self.setWaveformParameters() self.setCollectionParameters() def __InitValidators(self): # Waveform validators self.m_Intensity.SetValidator(NumRangeValidator(numeric_type='int')) self.m_Threshold.SetValidator(NumRangeValidator(numeric_type='int')) self.m_Period.SetValidator(NumRangeValidator(numeric_type='float')) self.m_Offset_Before.SetValidator(NumRangeValidator(numeric_type='float')) self.m_Offset_After.SetValidator(NumRangeValidator(numeric_type='float')) # Data collection validators self.m_samplingFreq.SetValidator(NumRangeValidator(numeric_type='float')) self.m_Averaging.SetValidator(NumRangeValidator(numeric_type='int')) self.m_Binning.SetValidator(NumRangeValidator(numeric_type='int')) def setPCCalibrationMean(self): self.m_pcCalibrationMean.SetValue('{0:3.3f}'.format( self.metadata.pc_calibration_mean )) def setPCCalibrationStd(self): self.m_pcCalibrationStd.SetValue('{0:3.3f}'.format( self.metadata.pc_calibration_std )) def setSampleDataPoints(self, sample_data_points): self.m_DataPoint.SetValue('{0:.2e}'.format(sample_data_points)) def setFrequency(self, frequence_val): self.m_Frequency.SetValue('{0:3.3f}'.format(frequence_val)) def setWaveformParameters(self): self.m_Intensity.SetValue(str(self.metadata.amplitude)) self.m_Period.SetValue(str(self.metadata.duration)) self.m_Offset_Before.SetValue(str(self.metadata.offset_before)) self.m_Offset_After.SetValue(str(self.metadata.offset_after)) self.setFrequency(self.metadata.get_frequency()) def setCollectionParameters(self): self.m_Binning.SetValue(str(self.metadata.binning)) self.m_Averaging.SetValue(str(self.metadata.averaging)) self.m_Threshold.SetValue(str(self.metadata.threshold)) self.m_samplingFreq.SetValue(str(self.metadata.sample_rate)) self.setSampleDataPoints(self.metadata.get_total_data_points()) ################################# # Event Handlers for Measurements def Perform_Measurement(self, event): print("GUIController: Perform_Measurement") # Using that instance we then run the lights, # and measure the outputs self.measurement_handler = MeasurementHandler() measurement_handler.add_to_queue( self.light_pulse.complete_waveform, self.metadata ) raw_data = self.measurement_handler.single_measurement() self.Data.updateRawData(raw_data) self.Data.Data = utils.bin_data(raw_data, self.metadata.binning) # We then plot the datas, this has to be changed if the plots want # to be updated on the fly. pub.sendMessage('update.plot') def fftHandler(self): channel = self.data_panel.m_fftChoice.GetStringSelection() freq_data = self.Data.fftOperator(channel, self.metadata.get_total_time()) self.PlotData(freq_data, title=['FFT of Raw data', 'Frequency (hz)', 'Voltage (V)']) def onWaveformParameters(self, event): self.metadata.A = float(self.m_Intensity.GetValue()) self.metadata.Duration = float(self.m_Period.GetValue()) self.metadata.Offset_Before = float(self.m_Offset_Before.GetValue()) self.metadata.Offset_After = float(self.m_Offset_After.GetValue()) self.metadata.Waveform = self.m_Waveform.GetStringSelection() pub.sendMessage('waveform.change') def onCollectionParameters(self, event): # TODO: refactor so it obeys DRY self.metadata.binning = int(self.m_Binning.GetValue()) self.metadata.averaging = int(self.m_Averaging.GetValue()) self.metadata.channel = self.m_Output.GetStringSelection() self.metadata.threshold = float(self.m_Threshold.GetValue()) self.metadata.sample_rate = float(self.m_samplingFreq.GetValue()) self.metadata.sample_data_points = self.metadata.get_total_data_points() pub.sendMessage('collection.change') ########################## # Plot Handlers # def plotHandler(self): self.PlotData(self.Data.Data) def PlotData(self, data, data_labels=['Reference', 'PC', 'PL'], title=['Raw Data', 'Time (s)', 'Voltage (V)'], e=None): self.Fig1.clear() labels = data_labels colours = ['b', 'r', 'g'] # this is done not to clog up the plot with many points if data.shape[0] > 1000: num = data.shape[0] // 1000 else: num = 1 # This plots the figure for i, label, colour in zip(data[:, 1:].T, labels, colours): self.Fig1.draw_points( data[::num, 0], i[::num], '.', Color=colour, Label=label ) self.Fig1.legend() self.Fig1.labels(title[0], title[1], title[2]) self.Fig1.update() if e is not None: e.skip() ################# # Helper methods: def defaultFileDialogOptions(self): """ Return a dictionary with file dialog options that can be used in both the save file dialog as well as in the open file dialog. """ return dict(message='Choose a file', defaultDir=self.dirname, wildcard='*.*') def askUserForFilename(self, **dialogOptions): dialog = wx.FileDialog(self, **dialogOptions) if dialog.ShowModal() == wx.ID_OK: userProvidedFilename = True self.data_file = dialog.GetFilename() self.dirname = dialog.GetDirectory() else: userProvidedFilename = False dialog.Destroy() return userProvidedFilename def ShowCalibrationModal(self): msg_text = ( "Please remove sample from measurement area\n" "Only one PC calibration is necessary per experimental session" ) wx.MessageBox(msg_text, 'Info', wx.OK | wx.ICON_INFORMATION) ########################## # App state Event Handlers # def onSave(self, event): """ Method to handle dialogue window and saving data to file """ dialog = wx.FileDialog( None, 'Save measurement data and metadata', self.dirname, '', r'DAT and INF files (*.dat;*.inf)|*.inf;*.dat', wx.FD_SAVE ) if dialog.ShowModal() == wx.ID_OK: dialog_path = dialog.GetPath() self.dirname = os.path.dirname(dialog_path) self.SaveName = os.path.splitext(os.path.basename(dialog_path))[0] experiment_settings = self.metadata.get_settings_as_dict() waveform_settings = self.light_pulse.get_settings_as_dict() metadata_dict = experiment_settings.copy() utils.save_data(self.Data.Data, self.SaveName, self.dirname) utils.save_metadata( metadata_dict, self.SaveName, self.dirname ) else: print('Canceled save') dialog.Destroy() event.Skip() def onSaveData(self, event): print("onSaveData") if self.askUserForFilename(style=wx.SAVE, **self.defaultFileDialogOptions()): utils.save_data(self.Data.Data, self.data_file, self.dirname) # print(filename) # fullpath = os.path.join(self.dirname, self.data_file) # self.Data.updateRawData(utils.load_data(fullpath)) def onLoad(self, event): """ Method to handle load metadata dialog window and update metadata state """ dialog = wx.FileDialog( None, 'Select a metadata file', self.dirname, '', r'*.inf', wx.FD_OPEN ) if dialog.ShowModal() == wx.ID_OK: metadata_dict = utils.load_metadata(dialog.GetPath()) metadata_stringified = dict( [a, str(x)] for a, x in metadata_dict.iteritems() ) print(metadata_stringified) # experimental data self.m_Output.SetStringSelection(metadata_stringified[u'Channel']) self.m_Averaging.SetValue(metadata_stringified[u'Averaging']) try: self.m_Binning.SetValue(metadata_stringified[u'Measurement_Binning']) except: self.m_Binning.SetValue(metadata_stringified[u'Binning']) self.m_Threshold.SetValue(metadata_stringified[u'Threshold_mA']) # waveform data self.m_Intensity.SetValue(metadata_stringified[u'Intensity_v']) self.m_Waveform.SetStringSelection(metadata_stringified[u'Waveform']) self.m_Offset_Before.SetValue(metadata_stringified[u'Offset_Before_ms']) self.m_Offset_After.SetValue(metadata_stringified[u'Offset_After_ms']) self.m_Period.SetValue(metadata_stringified[u'Peroid_s']) dialog.Destroy() event.Skip() def onLoadData(self, event): """ Handlers loading of new data set into Frame """ print("start data loading") if self.askUserForFilename(style=wx.OPEN, **self.defaultFileDialogOptions()): fullpath = os.path.join(self.dirname, self.data_file) self.Data.updateRawData(utils.load_data(fullpath)) print(self.Data.Data) pub.sendMessage('update.plot') self.onWaveformParameters(self, event) self.onCollectionParameters(self, event) def onExit(self, event): self.Close() def OnAbout(self, event): dialog = wx.MessageDialog( self, 'An PV experimental assistant in wxPython', 'About PVapp', wx.OK ) dialog.ShowModal() dialog.Destroy() def onStatusUpdate(self, status, is_error=False): self.SetStatusText(status, 0) if is_error: self.m_statusBar.SetBackgroundColour('RED') self.m_statusBar.SetStatusText(status) else: self.m_statusBar.SetStatusText(status)
def setUp(self): self.settings = ExperimentSettings() self.lp = LightPulse(self.settings)
class ExperimentSettingsTest(unittest.TestCase): # np.set_printoptions(threshold='nan') def setUp(self): self.meta_data = ExperimentSettings() self.maxDiff = None def test_get_settings_as_dict(self): meta_data = { 'channel': 'High (2A/V)', 'averaging': 1, 'measurement_binning': 1, 'threshold_mA': 150, "inverted_channels": { 'Reference': False, 'PC': False, 'PL': True }, 'sample_rate': 1.2e3, 'output_sample_rate': 1.2e3, "input_voltage_range": 10.0, "output_voltage_range": 10.0, "waveform": 'Sin', "amplitude": 0.5, "offset_before": 1, "offset_after": 10, "duration": 1, "voltage_threshold": 0.08152173913043478, "channel_name": 'ao0', # "pc_calibration_mean": None, "pc_calibration_std": None } self.assertDictEqual(self.meta_data.as_dict(), meta_data) def test_init(self): self.assertEqual( self.meta_data.voltage_threshold, 0.08152173913043478, ) self.assertEqual( self.meta_data.channel_name, 'ao0' ) def test_set_amplitude(self): self.assertTrue(self.meta_data.amplitude, 0.5) def test_set_amplitude_too_high(self): self.meta_data.channel = 'Low (50mA/V)' self.meta_data.amplitude = 15 self.assertEqual(self.meta_data.amplitude, 10) self.meta_data.channel = 'High (2A/V)' self.meta_data.amplitude = 15 self.assertEqual(self.meta_data.amplitude, 1.5) def test_set_voltage_too_high(self): pass def test_set_sample_rate_too_high(self): self.meta_data.sample_rate = 9e90 self.assertEqual(self.meta_data.sample_rate, 1.2e6)