def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_Form_tuning_curves()
self.ui.setupUi(self)
self.dialog = QtGui.QMainWindow
self.filename = ''
self.threshold = 0
self.backup_dir = ''
self.basefname = ''
self.message_num = 0
QtCore.QObject.connect(self.ui.pushButton_browse,
QtCore.SIGNAL("clicked()"), self.browse)
QtCore.QObject.connect(
self.ui.comboBox_test_num,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_traces)
QtCore.QObject.connect(
self.ui.comboBox_test_num,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_channels)
QtCore.QObject.connect(
self.ui.comboBox_trace,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_stim_info)
QtCore.QObject.connect(self.ui.pushButton_auto_threshold,
QtCore.SIGNAL("clicked()"), self.auto_threshold)
QtCore.QObject.connect(self.ui.doubleSpinBox_threshold,
QtCore.SIGNAL("valueChanged(const QString&)"),
self.update_thresh)
QtCore.QObject.connect(
self.ui.comboBox_channel,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.generate_view)
QtCore.QObject.connect(
self.ui.comboBox_trace,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.generate_view)
self.ui.view.threshLine.sigPositionChangeFinished.connect(
self.update_thresh2)
QtCore.QObject.connect(self.ui.pushButtonGenerate,
QtCore.SIGNAL("clicked()"),
self.generate_tuning_curve)
QtCore.QObject.connect(self.ui.groupBoxWindow,
QtCore.SIGNAL("clicked()"), self.window_check)
def __init__(self, parent=None):
QtGui.QWidget.__init__(self)
self.ui = Ui_Form_tuning_curves()
self.ui.setupUi(self)
self.filename = ''
self.message_num = 0
# TODO Rename and add functionality in the future
self.ui.radioButtonOther.setEnabled(False)
QtCore.QObject.connect(self.ui.comboBox_test_num, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.populate_comments)
QtCore.QObject.connect(self.ui.pushButton_auto_threshold, QtCore.SIGNAL("clicked()"), self.auto_threshold)
QtCore.QObject.connect(self.ui.doubleSpinBox_threshold, QtCore.SIGNAL("valueChanged(const QString&)"), self.update_thresh)
QtCore.QObject.connect(self.ui.comboBox_test_num, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.load_traces)
QtCore.QObject.connect(self.ui.comboBox_trace, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.load_channels)
QtCore.QObject.connect(self.ui.comboBox_channel, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.generate_view)
# TODO When changing traces think about a way to keep from resetting channel when unnecessary
QtCore.QObject.connect(self.ui.pushButtonGenerate, QtCore.SIGNAL("clicked()"), self.generate_tuning_curve)
class TuningCurveDialog(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self)
self.ui = Ui_Form_tuning_curves()
self.ui.setupUi(self)
self.filename = ''
self.message_num = 0
# TODO Rename and add functionality in the future
self.ui.radioButtonOther.setEnabled(False)
QtCore.QObject.connect(self.ui.comboBox_test_num, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.populate_comments)
QtCore.QObject.connect(self.ui.pushButton_auto_threshold, QtCore.SIGNAL("clicked()"), self.auto_threshold)
QtCore.QObject.connect(self.ui.doubleSpinBox_threshold, QtCore.SIGNAL("valueChanged(const QString&)"), self.update_thresh)
QtCore.QObject.connect(self.ui.comboBox_test_num, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.load_traces)
QtCore.QObject.connect(self.ui.comboBox_trace, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.load_channels)
QtCore.QObject.connect(self.ui.comboBox_channel, QtCore.SIGNAL("currentIndexChanged(const QString&)"), self.generate_view)
# TODO When changing traces think about a way to keep from resetting channel when unnecessary
QtCore.QObject.connect(self.ui.pushButtonGenerate, QtCore.SIGNAL("clicked()"), self.generate_tuning_curve)
def set_threshold(self, thresh):
self.ui.doubleSpinBox_threshold.setValue(thresh)
def set_test_num(self, test_num):
self.ui.comboBox_test_num.setCurrentIndex(test_num)
def set_channel_num(self, chan_num):
self.ui.comboBox_channel.setCurrentIndex(chan_num)
def set_trace_num(self, trace_num):
self.ui.comboBox_trace.setCurrentIndex(trace_num)
def populate_boxes(self, filename):
self.filename = filename
self.ui.label_title.setText('Tuning Curve Generator - ' + str.split(str(filename), '/')[-1])
self.ui.comboBox_test_num.clear()
# If the filename is not blank, attempt to extract test numbers and place them into the combobox
if self.filename != '':
if '.hdf5' in self.filename:
try:
h_file = h5py.File(unicode(self.filename), 'r')
except IOError:
self.add_message('Error: I/O Error')
self.ui.lineEdit_comments.setEnabled(False)
self.ui.lineEdit_comments.setText('')
self.ui.comboBox_test_num.setEnabled(False)
self.ui.groupBoxPlot.setEnabled(False)
self.ui.groupBoxUnits.setEnabled(False)
return
tests = {}
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
tests[test] = int(test.replace('test_', ''))
sorted_tests = sorted(tests.items(), key=operator.itemgetter(1))
for test in sorted_tests:
self.ui.comboBox_test_num.addItem(test[0])
self.ui.lineEdit_comments.setEnabled(True)
self.ui.comboBox_test_num.setEnabled(True)
self.ui.groupBoxPlot.setEnabled(True)
self.ui.groupBoxUnits.setEnabled(True)
h_file.close()
def populate_comments(self):
# Validate filename
if self.valid_filename(self.filename):
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
# Find target segment
for segment in h_file.keys():
for test in h_file[segment].keys():
if target_test == test:
target_seg = segment
target_test = test
comment = h_file[target_seg].attrs['comment']
self.ui.lineEdit_comments.setText(comment)
# Populate stimulus info
# Makes the assumption that all of the traces are of the same type
stim_info = eval(h_file[target_seg][target_test].attrs['stim'])
self.ui.label_stim_type.setText(stim_info[1]['components'][0]['stim_type'])
h_file.close()
def load_traces(self):
self.ui.comboBox_trace.clear()
# Validate filename
if self.valid_filename(self.filename):
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
self.ui.comboBox_trace.setEnabled(False)
return
if self.ui.comboBox_test_num.currentText() == 'All' or self.ui.comboBox_test_num.currentText() == '':
self.ui.comboBox_trace.setEnabled(False)
self.ui.comboBox_trace.clear()
h_file.close()
return
else:
self.ui.comboBox_trace.setEnabled(True)
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
traces = h_file[target_seg][target_test].value.shape[0]
for i in range(traces):
self.ui.comboBox_trace.addItem('trace_' + str(i+1))
self.ui.comboBox_trace.setEnabled(True)
comment = h_file[target_seg].attrs['comment']
self.ui.lineEdit_comments.setText(comment)
h_file.close()
def load_channels(self):
self.ui.comboBox_channel.clear()
# Validate filename
if self.valid_filename(self.filename):
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
self.ui.comboBox_channel.setEnabled(False)
return
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
if self.ui.comboBox_test_num.count() == 0:
h_file.close()
self.clear_view()
return
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
if len(h_file[target_seg][target_test].value.shape) > 3:
channels = h_file[target_seg][target_test].value.shape[2]
else:
channels = 1
if channels == 1:
self.ui.comboBox_channel.addItem('channel_1')
else:
for i in range(channels):
self.ui.comboBox_channel.addItem('channel_' + str(i+1))
if self.ui.comboBox_test_num.currentText() == '' or self.ui.comboBox_channel.count() < 2:
self.ui.comboBox_channel.setEnabled(False)
self.ui.comboBox_channel.clear()
else:
self.ui.comboBox_channel.setEnabled(True)
if self.ui.comboBox_test_num.currentText() != '' and self.ui.comboBox_trace.currentText() != '' and self.ui.comboBox_channel != '':
self.generate_view()
h_file.close()
def generate_view(self):
filename = self.filename
# Validate filename
if self.valid_filename(filename):
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
# Clear view
self.clear_view()
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
# Makes the assumption that all of the traces are of the same type
stim_info = eval(h_file[target_seg][target_test].attrs['stim'])
self.ui.label_stim_type.setText(stim_info[1]['components'][0]['stim_type'])
fs = h_file[target_seg].attrs['samplerate_ad']
target_trace = []
target_chan = []
# Get the values from the combo boxes
self.ui.comboBox_test_num.currentText()
if self.ui.comboBox_trace.currentText() != '':
target_trace = int(self.ui.comboBox_trace.currentText().replace('trace_', '')) - 1
if self.ui.comboBox_channel.currentText() != '':
target_chan = int(self.ui.comboBox_channel.currentText().replace('channel_', '')) - 1
test_data = h_file[target_seg][target_test].value
# Get the presentation data depending on if there is a channel field or not
if len(test_data.shape) == 4:
presentation = test_data[target_trace, [], target_chan, :]
elif len(test_data.shape) == 3:
presentation = test_data[target_trace, [], :]
len_presentation = len(presentation)
# Get the length of the window and length of presentation depending on if all is selected or not
if len_presentation != 0:
window = len(presentation) / float(fs)
else:
if len(test_data.shape) == 4:
window = len(test_data[0, 0, 0, :]) / float(fs)
len_presentation = len(test_data[0, 0, 0, :])
elif len(test_data.shape) == 3:
window = len(test_data[0, 0, :]) / float(fs)
len_presentation = len(test_data[0, 0, :])
xlist = np.linspace(0, float(window), len_presentation)
ylist = presentation
# Set window size
if not self.ui.groupBoxWindow.isChecked():
if len(presentation) > 0:
ymin = min(presentation)
ymax = max(presentation)
else:
ymin = 0
ymax = 0
if len(test_data.shape) == 3:
rep_len = test_data.shape[1]
for i in range(rep_len):
if min(test_data[target_trace, i, :]) < ymin:
ymin = min(test_data[target_trace, i, :])
if max(test_data[target_trace, i, :]) > ymax:
ymax = max(test_data[target_trace, i, :])
else:
rep_len = test_data.shape[1]
for i in range(rep_len):
if min(test_data[target_trace, i, target_chan, :]) < ymin:
ymin = min(test_data[target_trace, i, target_chan, :])
if max(test_data[target_trace, i, target_chan, :]) > ymax:
ymax = max(test_data[target_trace, i, target_chan, :])
self.ui.view.setXRange(0, window, 0)
self.ui.view.setYRange(ymin, ymax, 0.1)
# Display all repetitions
self.ui.view.tracePlot.clear()
# Fix xlist to be the length of presentation
if len(test_data.shape) == 3:
self.ui.view.addTraces(xlist, test_data[target_trace, :, :])
else:
self.ui.view.addTraces(xlist, test_data[target_trace, :, target_chan, :])
h_file.close()
def generate_tuning_curve(self):
filename = self.filename
# Validate filename
if not self.valid_filename(filename):
return
rasters = self.generate_rasters()
tuning = []
orderedKeys, freqs, spls = self.GetFreqsAttns(rasters)
for s in range(len(orderedKeys)):
for k in orderedKeys[s]:
freq = int(k.split('_')[0])
spl = int(k.split('_')[1])
raster = rasters[k]
if self.ui.radioButtonMeanSpikes.isChecked():
res = ResponseStatsSpikes(raster)
elif self.ui.radioButtonResponseRate.isChecked():
res = ResponseStats(raster)
tuning.append({'intensity': spl, 'freq': freq / 1000, 'response': res[0], 'responseSTD': res[1]})
tuningCurves = pd.DataFrame(tuning)
if self.ui.radioButtonFreq.isChecked():
# Rainbow Tuning Curve
db = np.unique(tuningCurves['intensity'])
axes = []
for d in db:
if axes:
tuningCurves[tuningCurves['intensity'] == d].plot(x='freq', y='response', ax=axes, yerr='responseSTD', capthick=1,
label=str(d) + ' dB')
else:
axes = tuningCurves[tuningCurves['intensity'] == d].plot(x='freq', y='response', yerr='responseSTD', capthick=1,
label=str(d) + ' dB')
plt.legend(loc='upper right', fontsize=12, frameon=True)
sns.despine()
plt.grid(False)
plt.xlabel('Frequency (kHz)', size=14)
if self.ui.radioButtonMeanSpikes.isChecked():
plt.ylabel('Mean Spikes Per Presentation', size=14)
elif self.ui.radioButtonResponseRate.isChecked():
plt.ylabel('Response Rate (Hz)', size=14)
elif self.ui.radioButtonOther.isChecked():
plt.ylabel('Other ???', size=14)
plt.tick_params(axis='both', which='major', labelsize=14)
plt.title(str.split(str(filename), '/')[-1].replace('.hdf5', '') + ' '
+ str(self.ui.comboBox_test_num.currentText()).replace('test_', 'Test '))
plt.figtext(.02, .02, 'Threshold: ' + str(self.ui.doubleSpinBox_threshold.value()) + ' V')
plt.show()
title = str.split(str(filename), '/')[-1].replace('.hdf5', '') + '_' \
+ str(self.ui.comboBox_test_num.currentText())
# plt.savefig('output' + os.sep + 'tuning_curves' + os.sep + title + '_tuning_curve_1.png')
check_output_folders()
try:
out_file = open('output' + os.sep + 'tuning_curves' + os.sep + title + '_tuning_curve_1.csv', 'wb')
except IOError, e:
self.add_message('Unable to open ' + str(filename) + '\nError ' + str(e.errno) + ': ' + e.strerror + '\n')
writer = csv.writer(out_file)
writer.writerow(['File:', filename])
writer.writerow(['Test:', self.ui.comboBox_test_num.currentText()])
writer.writerow(['Threshold (V):', self.ui.doubleSpinBox_threshold.value()])
writer.writerow([])
for d in db:
tc_intensity = list(tuningCurves[tuningCurves['intensity'] == d]['intensity'])[0]
tc_freq = list(tuningCurves[tuningCurves['intensity'] == d]['freq'])
tc_response = list(tuningCurves[tuningCurves['intensity'] == d]['response'])
writer.writerow(['Intensity (dB):', tc_intensity])
writer.writerow(['Frequency (kHz):'] + tc_freq)
writer.writerow(['Response (Hz):'] + tc_response)
writer.writerow([])
out_file.close()
elif self.ui.radioButtonContour.isChecked():
# Black and White Tuning Curve
tc_plot = plt.figure()
colorRange = (-10, 10.1)
I = np.unique(np.array(tuningCurves['intensity']))
F = np.array(tuningCurves['freq'])
R = np.array(np.zeros((len(I), len(F))))
for ci, i in enumerate(I):
for cf, f in enumerate(F):
R[ci, cf] = tuningCurves['response'].where(tuningCurves['intensity'] == i).where(
tuningCurves['freq'] == f).dropna().values[0]
levelRange = np.arange(colorRange[0], colorRange[1],
(colorRange[1] - colorRange[0]) / float(25 * (colorRange[1] - colorRange[0])))
sns.set_context(rc={"figure.figsize": (7, 4)})
ax = plt.contourf(F, I, R) # , vmin=colorRange[0], vmax=colorRange[1], levels=levelRange, cmap = cm.bwr )
plt.colorbar()
# plt.title(unit, fontsize=14)
plt.xlabel('Frequency (kHz)', fontsize=14)
plt.ylabel('Intensity (dB)', fontsize=14)
plt.title(str.split(str(filename), '/')[-1].replace('.hdf5', '') + ' '
+ str(self.ui.comboBox_test_num.currentText()).replace('test_', 'Test '))
plt.figtext(.02, .02, 'Threshold: ' + str(self.ui.doubleSpinBox_threshold.value()) + ' V')
tc_plot.show()
class MyForm(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_Form_tuning_curves()
self.ui.setupUi(self)
self.dialog = QtGui.QMainWindow
self.filename = ''
self.threshold = 0
self.backup_dir = ''
self.basefname = ''
self.message_num = 0
QtCore.QObject.connect(self.ui.pushButton_browse,
QtCore.SIGNAL("clicked()"), self.browse)
QtCore.QObject.connect(
self.ui.comboBox_test_num,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_traces)
QtCore.QObject.connect(
self.ui.comboBox_test_num,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_channels)
QtCore.QObject.connect(
self.ui.comboBox_trace,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.load_stim_info)
QtCore.QObject.connect(self.ui.pushButton_auto_threshold,
QtCore.SIGNAL("clicked()"), self.auto_threshold)
QtCore.QObject.connect(self.ui.doubleSpinBox_threshold,
QtCore.SIGNAL("valueChanged(const QString&)"),
self.update_thresh)
QtCore.QObject.connect(
self.ui.comboBox_channel,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.generate_view)
QtCore.QObject.connect(
self.ui.comboBox_trace,
QtCore.SIGNAL("currentIndexChanged(const QString&)"),
self.generate_view)
self.ui.view.threshLine.sigPositionChangeFinished.connect(
self.update_thresh2)
QtCore.QObject.connect(self.ui.pushButtonGenerate,
QtCore.SIGNAL("clicked()"),
self.generate_tuning_curve)
QtCore.QObject.connect(self.ui.groupBoxWindow,
QtCore.SIGNAL("clicked()"), self.window_check)
def browse(self):
self.ui.comboBox_test_num.clear()
self.ui.comboBox_channel.clear()
self.ui.comboBox_trace.clear()
self.ui.lineEdit_comments.setEnabled(False)
self.ui.lineEdit_comments.setText('')
self.ui.comboBox_test_num.setEnabled(False)
self.ui.comboBox_channel.setEnabled(False)
self.ui.comboBox_trace.setEnabled(False)
file_dialog = QtGui.QFileDialog(self)
self.filename = QtGui.QFileDialog.getOpenFileName(
file_dialog, 'Open', '', "HDF5 files (*.hdf5)")
self.ui.lineEdit_file_name.setText(self.filename)
# If the filename is not blank, attempt to extract test numbers and place them into the combobox
if self.filename != '':
if '.hdf5' in self.filename:
try:
h_file = h5py.File(unicode(self.filename), 'r')
except IOError:
self.add_message('Error: I/O Error')
return
tests = {}
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
tests[test] = int(test.replace('test_', ''))
sorted_tests = sorted(tests.items(),
key=operator.itemgetter(1))
for test in sorted_tests:
self.ui.comboBox_test_num.addItem(test[0])
self.ui.lineEdit_comments.setEnabled(True)
self.ui.comboBox_test_num.setEnabled(True)
self.ui.comboBox_channel.setEnabled(True)
self.ui.comboBox_trace.setEnabled(True)
h_file.close()
self.generate_view()
else:
self.add_message('Error: Must select a .hdf5 file.')
return
else:
self.add_message('Error: Must select a file to open.')
return
def valid_filename(self):
filename = self.ui.lineEdit_file_name.text()
# Validate filename
if filename != '':
if '.hdf5' in filename:
try:
temp_file = h5py.File(unicode(self.filename), 'r')
temp_file.close()
except IOError:
self.add_message('Error: I/O Error')
return False
else:
self.add_message('Error: Must select a .hdf5 file.')
return False
else:
self.add_message('Error: Must select a file to open.')
return False
return True
def window_check(self):
if self.ui.groupBoxWindow.isChecked():
self.ui.label_xmax.setEnabled(True)
self.ui.label_xmin.setEnabled(True)
# self.ui.label_ymax.setEnabled(True)
# self.ui.label_ymin.setEnabled(True)
self.ui.label_zmax.setEnabled(True)
self.ui.label_zmin.setEnabled(True)
self.ui.doubleSpinBox_xmax.setEnabled(True)
self.ui.doubleSpinBox_xmin.setEnabled(True)
# self.ui.doubleSpinBox_ymax.setEnabled(True)
# self.ui.doubleSpinBox_ymin.setEnabled(True)
self.ui.doubleSpinBox_zmax.setEnabled(True)
self.ui.doubleSpinBox_zmin.setEnabled(True)
self.ui.groupBox_contourLvls.setEnabled(True)
else:
self.ui.label_xmax.setEnabled(False)
self.ui.label_xmin.setEnabled(False)
# self.ui.label_ymax.setEnabled(False)
# self.ui.label_ymin.setEnabled(False)
self.ui.label_zmax.setEnabled(False)
self.ui.label_zmin.setEnabled(False)
self.ui.doubleSpinBox_xmax.setEnabled(False)
self.ui.doubleSpinBox_xmin.setEnabled(False)
# self.ui.doubleSpinBox_ymax.setEnabled(False)
# self.ui.doubleSpinBox_ymin.setEnabled(False)
self.ui.doubleSpinBox_zmax.setEnabled(False)
self.ui.doubleSpinBox_zmin.setEnabled(False)
self.ui.groupBox_contourLvls.setEnabled(False)
def load_traces(self):
self.ui.comboBox_trace.clear()
self.ui.comboBox_trace.setEnabled(False)
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
self.ui.comboBox_trace.setEnabled(False)
return
if self.ui.comboBox_test_num.count() == 0:
self.ui.comboBox_trace.setEnabled(False)
self.ui.comboBox_trace.clear()
h_file.close()
return
target_seg = 0
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
traces = h_file[target_seg][target_test].value.shape[0]
for i in range(traces):
self.ui.comboBox_trace.addItem('trace_' + str(i + 1))
self.ui.comboBox_trace.setEnabled(True)
comment = h_file[target_seg].attrs['comment']
self.ui.lineEdit_comments.setText(comment)
h_file.close()
self.generate_view()
def load_channels(self):
self.ui.comboBox_channel.clear()
self.ui.comboBox_channel.setEnabled(False)
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
if self.ui.comboBox_test_num.count() == 0:
self.ui.comboBox_trace.setEnabled(False)
self.ui.comboBox_trace.clear()
h_file.close()
return
target_seg = 0
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
if len(h_file[target_seg][target_test].value.shape) > 3:
channels = h_file[target_seg][target_test].value.shape[2]
else:
channels = 1
if channels == 1:
self.ui.comboBox_channel.addItem('channel_1')
else:
for i in range(channels):
self.ui.comboBox_channel.addItem('channel_' + str(i + 1))
if self.ui.comboBox_channel.count() < 2:
self.ui.comboBox_channel.setEnabled(False)
else:
self.ui.comboBox_channel.setEnabled(True)
h_file.close()
self.generate_view()
def load_stim_info(self):
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
target_seg = ''
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
target_trace = 0
if self.ui.comboBox_trace.currentText() != '':
target_trace = int(self.ui.comboBox_trace.currentText().replace(
'trace_', '')) - 1
stim_info = eval(h_file[target_seg][target_test].attrs['stim'])
self.ui.label_stim_type.setText(
stim_info[target_trace]['components'][0]['stim_type'])
if stim_info[target_trace]['components'][0][
'stim_type'] == 'Pure Tone':
self.ui.label_frequency.setText(
str(
int(stim_info[target_trace]['components'][0]['frequency'] /
1000)) + ' kHz')
else:
self.ui.label_frequency.setText('')
h_file.close()
def generate_view(self):
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
target_seg = ''
for key in h_file.keys():
if 'segment' in key:
for test in h_file[key].keys():
if target_test == test:
target_seg = key
target_test = test
fs = h_file[target_seg].attrs['samplerate_ad']
target_trace = []
target_rep = []
target_chan = []
# Get the values from the combo boxes
self.ui.comboBox_test_num.currentText()
if self.ui.comboBox_trace.currentText() != '':
target_trace = int(self.ui.comboBox_trace.currentText().replace(
'trace_', '')) - 1
# if self.ui.comboBox_rep.currentText() != 'All' and self.ui.comboBox_rep.currentText() != '':
# target_rep = int(self.ui.comboBox_rep.currentText().replace('rep_', '')) - 1
if self.ui.comboBox_channel.currentText() != '':
target_chan = int(self.ui.comboBox_channel.currentText().replace(
'channel_', '')) - 1
test_data = h_file[target_seg][target_test].value
presentation = []
# Get the presentation data depending on if there is a channel field or not
if len(test_data.shape) == 4:
presentation = test_data[target_trace, target_rep, target_chan, :]
elif len(test_data.shape) == 3:
presentation = test_data[target_trace, target_rep, :]
len_presentation = len(presentation)
# Get the length of the window and length of presentation depending on if all is selected or not
if len_presentation != 0:
window = len(presentation) / float(fs)
else:
if len(test_data.shape) == 4:
window = len(test_data[0, 0, 0, :]) / float(fs)
len_presentation = len(test_data[0, 0, 0, :])
elif len(test_data.shape) == 3:
window = len(test_data[0, 0, :]) / float(fs)
len_presentation = len(test_data[0, 0, :])
xlist = np.linspace(0, float(window), len_presentation)
ylist = presentation
# TODO Set window size
if True: # not self.ui.checkBox_custom_window.checkState():
if len(presentation) > 0:
ymin = min(presentation)
ymax = max(presentation)
else:
ymin = 0
ymax = 0
if len(test_data.shape) == 3:
rep_len = test_data.shape[1]
for i in range(rep_len):
if not test_data[target_trace, i, :].any():
return
if min(test_data[target_trace, i, :]) < ymin:
ymin = min(test_data[target_trace, i, :])
if max(test_data[target_trace, i, :]) > ymax:
ymax = max(test_data[target_trace, i, :])
else:
rep_len = test_data.shape[1]
for i in range(rep_len):
if not test_data[target_trace, i,
target_chan, :].any():
return
if min(test_data[target_trace, i,
target_chan, :]) < ymin:
ymin = min(test_data[target_trace, i,
target_chan, :])
if max(test_data[target_trace, i,
target_chan, :]) > ymax:
ymax = max(test_data[target_trace, i,
target_chan, :])
self.ui.view.setXRange(0, window, 0)
self.ui.view.setYRange(ymin, ymax, 0.1)
self.ui.view.tracePlot.clear()
# Fix xlist to be the length of presentation
if len(test_data.shape) == 3:
self.ui.view.addTraces(xlist, test_data[target_trace, :, :])
else:
self.ui.view.addTraces(xlist, test_data[target_trace, :,
target_chan, :])
h_file.close()
def generate_tuning_curve(self):
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
target_seg = []
# Find target segment
for segment in h_file.keys():
for test in h_file[segment].keys():
if target_test == test:
target_seg = segment
target_test = test
trace_data = h_file[target_seg][target_test].value
fs = h_file[target_seg].attrs['samplerate_ad']
samples = trace_data.shape[-1]
traces = trace_data.shape[0]
reps = trace_data.shape[1]
if len(h_file[target_seg][target_test].value.shape) > 3:
channels = h_file[target_seg][target_test].value.shape[2]
else:
channels = 1
stim_info = eval(h_file[target_seg][target_test].attrs['stim'])
# Get the values from the combo boxes
if self.ui.comboBox_trace.currentText() != '':
target_trace = int(self.ui.comboBox_trace.currentText().replace(
'trace_', '')) - 1
if self.ui.comboBox_channel.currentText() != '':
target_chan = int(self.ui.comboBox_channel.currentText().replace(
'channel_', '')) - 1
# Get the values from the spinbox
thresh = self.ui.doubleSpinBox_threshold.value()
# print 'test:', target_test
# print 'trace:', target_trace
# print 'chan:', target_chan
# print ''
frequency = []
intensity = []
spike_count = {}
if len(trace_data.shape) == 4:
for t in range(traces):
# print 'trace:', t
# print 'stim_type:', stim_info[t]['components'][0]['stim_type']
# print 'intensity:', stim_info[t]['components'][0]['intensity']
# if stim_info[t]['components'][0]['stim_type'] != 'silence':
# print 'frequency:', stim_info[t]['components'][0]['frequency']
if stim_info[t]['components'][0]['stim_type'] != 'silence':
intensity.append(
stim_info[t]['components'][0]['intensity'])
frequency.append(
stim_info[t]['components'][0]['frequency'] / 1000)
spikes = 0
for r in range(reps):
if self.ui.groupBoxWindow.isChecked():
x_min = np.floor(
self.ui.doubleSpinBox_xmin.value() * fs)
x_max = np.floor(
self.ui.doubleSpinBox_xmax.value() * fs)
temp_trace = trace_data[t][r][target_chan]
trace = temp_trace[x_min:x_max]
pass
else:
trace = trace_data[t][r][target_chan]
spike_times = 1000 * np.array(
get_spike_times(trace, thresh, fs,
self.ui.view._abs))
spikes += len(spike_times)
spike_count[(stim_info[t]['components'][0]['frequency'] /
1000,
stim_info[t]['components'][0]['intensity']
)] = float(spikes) / float(reps)
# print 'spikes:', float(spikes)
# print 'avg_spikes:', float(spikes)/float(reps)
if len(trace_data.shape) == 3:
for t in range(traces):
if stim_info[t]['components'][0]['stim_type'] != 'silence':
intensity.append(
stim_info[t]['components'][0]['intensity'])
frequency.append(
stim_info[t]['components'][0]['frequency'] / 1000)
spikes = 0
for r in range(reps):
trace = trace_data[t][r]
spike_times = 1000 * np.array(
get_spike_times(trace, thresh, fs, self.ui.view._abs))
spikes += len(spike_times)
if stim_info[t]['components'][0]['stim_type'] != 'silence':
spike_count[(stim_info[t]['components'][0]['frequency'] /
1000,
stim_info[t]['components'][0]['intensity']
)] = float(spikes) / float(reps)
# Get only the unique values
frequency = sorted(list(set(frequency)))
intensity = sorted(list(set(intensity)))
# print 'freq', len(frequency), frequency
# print 'inten', len(intensity), intensity
xlist = np.linspace(min(frequency), max(frequency), len(frequency))
ylist = np.linspace(min(intensity), max(intensity), len(intensity))
# print 'xlist', len(xlist), xlist
# print 'ylist', len(ylist), ylist
# Initialize Z
Z = np.empty([len(intensity), len(frequency)])
X, Y = np.meshgrid(xlist, ylist)
for y in range(len(intensity)):
for x in range(len(frequency)):
Z[y][x] = spike_count[(frequency[x], intensity[y])]
# print '(y, x):', y, x
# print 'freq:', frequency[x]
# print 'inten:', intensity[y]
plt.figure()
if self.ui.groupBoxWindow.isChecked():
# Set the min, max and number of contour levels
levels = np.linspace(self.ui.doubleSpinBox_zmin.value(),
self.ui.doubleSpinBox_zmax.value(),
num=(self.ui.spinBoxContourLevels.value() +
1))
cp = plt.contourf(X, Y, Z, levels)
else:
# Auto assign contour levels
cp = plt.contourf(X, Y, Z)
plt.colorbar(cp, label='Mean Spikes Per Presentation')
# print 'X:', X
# print 'Y:', Y
# print 'Z:', Z
# plt.title('Tuning Curve')
if channels == 1:
plt.title(
str.split(str(self.filename), '/')[-1].replace('.hdf5', '') +
' ' + str(self.ui.comboBox_test_num.currentText()).replace(
'test_', 'Test '))
else:
plt.title(
str.split(str(self.filename), '/')[-1].replace('.hdf5', '') +
' ' + str(self.ui.comboBox_test_num.currentText()).replace(
'test_', 'Test ') + ' ' +
str(self.ui.comboBox_channel.currentText()).replace(
'channel_', 'Channel '))
plt.xlabel('Frequency (kHz)')
# plt.xlabel('Frequency (Hz)')
plt.ylabel('Intensity (dB)')
plt.figtext(
.02, .02, 'Threshold: ' +
str(self.ui.doubleSpinBox_threshold.value()) + ' V')
# Idea to try interpolation, didn't work as intended
# plt.imshow(Z, aspect='equal', interpolation=None, origin='lower')
plt.show()
def auto_threshold(self):
thresh_fraction = 0.7
if self.valid_filename():
h_file = h5py.File(unicode(self.filename), 'r')
target_test = self.ui.comboBox_test_num.currentText()
else:
return
# Find target segment
target_seg = []
for segment in h_file.keys():
for test in h_file[segment].keys():
if target_test == test:
target_seg = segment
target_test = test
trace_data = h_file[target_seg][target_test].value
if len(trace_data.shape) == 4:
target_chan = int(self.ui.comboBox_channel.currentText().replace(
'channel_', '')) - 1
# Compute threshold from average maximum of traces
max_trace = []
for n in range(len(trace_data[1, :, target_chan, 0])):
max_trace.append(
np.max(np.abs(trace_data[1, n, target_chan, :])))
average_max = np.array(max_trace).mean()
thresh = thresh_fraction * average_max
# self.add_message(trace_data.shape)
elif len(trace_data.shape) == 3:
# Compute threshold from average maximum of traces
max_trace = []
for n in range(len(trace_data[1, :, 0])):
max_trace.append(np.max(np.abs(trace_data[1, n, :])))
average_max = np.array(max_trace).mean()
thresh = thresh_fraction * average_max
# self.add_message(trace_data.shape)
self.ui.doubleSpinBox_threshold.setValue(thresh)
self.update_thresh()
h_file.close()
def update_thresh(self):
self.ui.view.setThreshold(self.ui.doubleSpinBox_threshold.value())
self.ui.view.update_thresh()
def update_thresh2(self):
self.ui.doubleSpinBox_threshold.setValue(self.ui.view.getThreshold())
def add_message(self, message):
self.message_num += 1
self.ui.textEdit.append('[' + str(self.message_num) + ']: ' + message +
'\n')
