def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Baseline', data, parent, liveplot)
self.liveplot_container, self.liveplot = self.liveplot
# data
self.input = {'y': None, 'object_source': None}
self.output = {'baseline': None, 'y': None}
# methods
# 1 Polynomial Fitting
self.addMethod('Polynomial Fitting', bl_polynomial_fitting_params, self.polyFit)
self.markerItems = []
# 2 Asymmetric Least Squares
self.addMethod('Asymmetric Least Squares', bl_asymmetric_ls_params, self.alsWrapper)
# 3 Top Hat
self.addMethod('Top Hat', bl_top_hat_params, self.topHatWrapper)
# 4 Moving Average
self.addMethod('Moving Average', bl_moving_average_params, self.movingAverageWrapper)
self.activateFunc = self.showMarkers
self.initMethodUI()
self.initParametersUI()
def __init__(self, name: str, description: str, count_index: int):
Feature.__init__(self,
name=name,
description=description,
count_index=count_index)
self._wavelength_count = 0
self._count = 0
def __init__(self, name: str, description: str, count_index: int):
Feature.__init__(self,
name=name,
description=description,
count_index=count_index)
self._amplitude_count = 0
self._count = 0
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Background Subtraction', data, parent,
liveplot)
# data
self.input = {
'y': None,
'roi_params': None,
'roi_image': None,
'cell': None,
'roi_ellipse_mode': None
}
self.output = {'background mean': None, 'y': None}
self.imv = self.liveplot
self.activateFunc = self.showGUI
## METHODS ##
# 1 ROI Background Subtraction
self.addMethod('ROI', bs_roi_params, self.ROIBackgroundSubtraction)
# 2 Perisomatic Background Subtraction
self.addMethod('Perisomatic', bs_perisomatic_params,
self.perisomaticBackgroundSubtraction)
self.initMethodUI()
self.initParametersUI()
self.undisplayPlots()
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Event Shape', data, parent, liveplot)
# data
self.input = {
'y': None,
'burst_time': None,
'spike_time': None,
'object_source_frequency': None
}
self.output = {
'shapes': None,
'mean shape': None,
'mean shape smoothed': None
}
## METHODS ##
# 1 Mean Amplitude
self.addMethod('Spike Shape', es_params, self.spikeShapeCalculation)
self.addMethod('Burst Shape', es_params, self.burstShapeCalculation)
self.initMethodUI()
self.initParametersUI()
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self,
'Cell Selection',
data,
parent,
liveplot,
display_name_label=False)
self.data_manager = data
self.data_manager.cell_selection = self
self.setMinimumSize(350, 450)
self.allowEditROI = True
self.disabled_roi_handles = []
self.preview_mode = True
self.show_user_roi = False
self.ellipse_mode = True
self.update_on_ellipse_mode_change = True
# data
self.input = {'source': None, 'roi_ellipse_mode': None}
self.output = {'cell': None, 'cell mean': None, 'roi': None}
# view / plot
self.imv = ImageView()
self.imv.setMinimumHeight(450)
self.layout.addWidget(self.imv)
self.imv.view.mouseClickEvent = lambda ev: self.imvViewMouseClickEvent(
self.imv.view, ev)
self.imv.view.raiseContextMenu = lambda ev: self.imvViewRaiseContextMenu(
self.imv.view, ev)
self.imv.view.getContextMenus = lambda ev=None: self.imvViewGetContextMenus(
self.imv.view, ev)
self.imv.view.preview_mode = self.imv.view.menu.addAction(
'live preview mode')
self.imv.view.preview_mode.setCheckable(True)
self.imv.view.preview_mode.setChecked(self.preview_mode)
self.imv.view.preview_mode.triggered.connect(self.switchPreviewMode)
self.imv.view.ellipse_mode = self.imv.view.menu.addAction(
'ellipse mode')
self.imv.view.ellipse_mode.setCheckable(True)
self.imv.view.ellipse_mode.setChecked(self.ellipse_mode)
self.connectEllipseMode()
# methods
self.addMethod('ROI', cs_roi_params, self.calculateROI)
self.initMethodUI()
self.initParametersUI()
self.show()
"""
the image must be displayed once such that the roicurve is created and can be shown
even if the user loads a non-TIF source before he loads a TIF source.
"""
self.imv.setImage(np.zeros((1, 10, 10)), xvals=np.arange(10))
self.imv.clear()
def __init__(self, name: str, description: str, count_index: int):
Feature.__init__(self,
name=name,
description=description,
count_index=count_index)
self._latest_complete_lvl8 = None
self._latest_complete_lvl16 = None
self._latest_answer_Q0 = None
self._latest_answer_Q2 = None
self._answer_time = None
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Spike Detection', data, parent, liveplot)
# data
self.input = {
'y': None,
'object_source_frequency': None,
'object_noise_std': None
}
self.output = {
'time': None,
'amplitude': None,
'train': None,
'spike frequency': None,
'mean amplitude': None,
'τDecay': None,
'mean τDecay': None
}
# dialog for averages
self.showBtn = QtWidgets.QPushButton('Show quantities')
self.showBtn.clicked.connect(self.showQuantities)
self.layout.addWidget(self.showBtn)
self.dialog = QtWidgets.QDialog(self,
flags=QtCore.Qt.WindowTitleHint
| QtCore.Qt.WindowCloseButtonHint)
self.dialog.setWindowTitle(self.name + ' -- Quantities')
self.dialog_table = QtWidgets.QTableWidget(self.dialog)
self.dialog_table.horizontalHeader().hide()
self.dialog_table.verticalHeader().hide()
self.dialog_table.horizontalHeader().setSectionResizeMode(
QtWidgets.QHeaderView.ResizeToContents)
self.dialog_table.setRowCount(3)
self.dialog_table.setColumnCount(2)
self.dialog_table.setItem(0, 0,
QtWidgets.QTableWidgetItem('mean amplitude'))
self.dialog_table.setItem(
1, 0, QtWidgets.QTableWidgetItem('spike frequency (#spikes / s)'))
self.dialog_table.setItem(2, 0,
QtWidgets.QTableWidgetItem('mean τDecay'))
self.dialog_layout = QtWidgets.QGridLayout(self.dialog)
self.dialog.setLayout(self.dialog_layout)
self.dialog.layout().addWidget(self.dialog_table)
## METHODS ##
self.addMethod('Threshold', sd_params, self.spikeUpdate)
self.initMethodUI()
self.initParametersUI()
def __init__(self,
data,
name,
input_data_name,
parent=None,
liveplot=None,
step_mode=False):
# Init Feature
Feature.__init__(self, name, data, parent, liveplot)
self.input_data_name = input_data_name
self.step_mode = step_mode
# data
self.output = {
'xrange': None,
'correlation': None,
'coefficient': None,
'delay': None,
'delay coefficient': None
}
self.showBtn = QtWidgets.QPushButton(
'Show Correlation Coefficients and Main Lags', self)
self.showBtn.clicked.connect(self.showCoefficients)
self.layout.addWidget(self.showBtn)
self.dialog = QtWidgets.QDialog(self,
flags=QtCore.Qt.WindowTitleHint
| QtCore.Qt.WindowCloseButtonHint)
self.dialog.setWindowTitle(
self.name + ' -- Correlation Coefficients and Main Lags')
self.dialog_table_coefficients = QtWidgets.QTableWidget(self.dialog)
self.dialog_table_delay = QtWidgets.QTableWidget(self.dialog)
self.dialog_table_delay_coefficients = QtWidgets.QTableWidget(
self.dialog)
self.dialog_layout = QtWidgets.QGridLayout(self.dialog)
self.dialog.setLayout(self.dialog_layout)
self.dialog.layout().addWidget(
QtWidgets.QLabel('Correlation Coefficients'))
self.dialog.layout().addWidget(self.dialog_table_coefficients)
self.dialog_mainlag_layout = QtWidgets.QLabel()
self.dialog.layout().addWidget(self.dialog_mainlag_layout)
self.dialog.layout().addWidget(self.dialog_table_delay)
self.dialog_table_delay_coefficients_label = QtWidgets.QLabel(
'Correlation Coefficients at Main Lags')
self.dialog.layout().addWidget(
self.dialog_table_delay_coefficients_label)
self.dialog.layout().addWidget(self.dialog_table_delay_coefficients)
def __init__(self, data, parent=None, liveplot=None):
Feature.__init__(self, 'Movement Correction', data, parent, liveplot, display_name_label=False)
self.input = {'source':None}
self.output = {'source':None}
self.addMethod('Movement Correction', mc_params, self.movementCorrection)
self.initMethodUI()
self.initParametersUI()
self.symmetric_diffeomorphic_option = 'Symmetric Diffeomorphic'
self.options = [
('None [original image]', None),
(self.symmetric_diffeomorphic_option, None),
('Translation', StackReg.TRANSLATION),
('Rigid Body', StackReg.RIGID_BODY),
('Scaled Rotation', StackReg.SCALED_ROTATION),
('Affine', StackReg.AFFINE)
]
self.calculated = []
compare_layout = QtWidgets.QGridLayout()
compare_layout.setSpacing(0)
compare_layout.setMargin(0)
compare_layout_widget = QtWidgets.QWidget()
self.layout.addWidget(compare_layout_widget)
compare_layout_widget.setLayout(compare_layout)
compare_layout.addWidget(QtWidgets.QLabel('Correction: '), 0, 0)
compare_layout.addWidget(QtWidgets.QLabel('Compare to: '), 1, 0)
self.correction_combobox = QtWidgets.QComboBox()
compare_layout.addWidget(self.correction_combobox, 0, 1)
self.compare_combobox = QtWidgets.QComboBox()
compare_layout.addWidget(self.compare_combobox, 1, 1)
for type_, _ in self.options:
self.correction_combobox.addItem(type_)
self.compare_combobox.addItem(type_)
self.calculated.append(None)
self._connectComboboxes()
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Power Spectrum', data, parent, liveplot)
# data
self.input = {'y': None, 'object_source_frequency': None}
self.output = {
'frequencies': None,
'psd': None,
'max power': None,
'max power frequency': None
}
# methods
self.addMethod('Fast Fourier Transform', fs_fft_params,
self.updateFourier)
self.initMethodUI()
self.initParametersUI()
def __init__(self, data, parent=None, liveplot=None):
# Init Feature
Feature.__init__(self, 'Smoothing', data, parent, liveplot)
# data
self.input = {'y':None, 'object_source_frequency':None}
self.output = {'y':None, 'noise_std': None}
# methods
# 1 Savitzky Golay
self.addMethod('Savitzky Golay', sg_savitzky_golay_params, self.updateSGData)
# 2 Moving Average
self.addMethod('Moving Average', sg_moving_average_params, self.movingAverageWrapper)
# 3 Butterworth
self.addMethod('Butterworth', sg_butterworth_params, self.butter_lowpass_filter_wrapper)
# 4 Scaled Window Convolution
self.addMethod('Scaled Window Convolution', sg_scaled_window_convolution_params, self.scaled_window_convolution)
self.initMethodUI()
self.initParametersUI()
def __init__(self, data, parent=None, liveplot=None):
Feature.__init__(self,
'Adjust Frequency',
data,
parent,
liveplot,
display_name_label=False)
self.input = {'y': None, 'object_source_af_params': None}
self.output = {'y': None}
self.addMethod('Nearest Neighbour', af_params,
self.nearestNeighbourWrapper)
self.addMethod('Linear', af_params, self.linearWrapper)
self.addMethod('Cubic', af_params, self.cubicWrapper)
self.initMethodUI()
self.initParametersUI()
# disconnect the usual method because we dont want updates when the method is changed, only graphic updates.
self.disconnectMethodCombo()
self.method_combo.currentIndexChanged.connect(self.updateParametersUI)
def __init__(self, name:str, description:str, count_index:int):
Feature.__init__(self, name=name, description=description, count_index=count_index)
self._answer = None
def __init__(self, name:str, description:str):
Feature.__init__(self, name=name, description=description, count_index=0)
def __init__(self, name:str, description:str, count_index:int):
Feature.__init__(self, name=name, description=description, count_index=count_index)
self._offset_count = 0
self._good_count = 0
