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)
def setUp(self):
self.meta_data = ExperimentSettings()
self.maxDiff = None
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)