def __init__(self):
QtCore.QObject.__init__(self)
self.params = pt.Parameter(name='Spike detection',
type='group',
children=[
{
'name': 'gaussian sigma',
'type': 'float',
'value': 2.0
},
{
'name': 'deconv const',
'type': 'float',
'value': 0.04,
'step': 0.01
},
{
'name': 'threshold',
'type': 'float',
'value': 0.05,
'step': 0.01
},
])
self.sig_plot = None
self.deconv_plot = None
self.sig_trace = None
self.vticks = None
self.deconv_trace = None
self.threshold_line = None
self.params.sigTreeStateChanged.connect(self._parameters_changed)
self.params.child('threshold').sigValueChanged.connect(
self._threshold_param_changed)
def __init__(self):
QtCore.QObject.__init__(self)
self.params = pt.Parameter(name='Triggered Average', type='group', children=[
{'name': 'on/off', 'type': 'list', 'values': ['any', 'on', 'off']},
{'name': 'delay', 'type': 'float', 'value': -0.2, 'suffix': 's', 'siPrefix': True, 'step': 50e-3},
{'name': 'delay range', 'type': 'float', 'value': 1.0, 'limits': [0,None], 'suffix': 's', 'siPrefix': True, 'step': 50e-3},
{'name': 'blur STA', 'type': 'float', 'value': 1.0, 'limits': [0,None], 'step': 0.5},
])
self.imgview = None
self.params.sigTreeStateChanged.connect(self.parameters_changed)
def __init__(self):
QtCore.QObject.__init__(self)
self.params = pt.Parameter(name='Spike detection',
type='group',
children=[
{
'name': 'gaussian sigma',
'type': 'float',
'value': 200e-6,
'bounds': [0, None],
'suffix': 's',
'siPrefix': True,
'dec': True,
'minStep': 10e-6
},
{
'name': 'deconv const',
'type': 'float',
'value': 0.01,
'suffix': 's',
'siPrefix': True,
'dec': True,
'minStep': 1e-4
},
{
'name': 'threshold',
'type': 'float',
'value': 0.05,
'dec': True,
'minStep': 1e-12
},
])
self.sig_plot = None
self.deconv_plot = None
self.sig_trace = None
self.vticks = None
self.deconv_trace = None
self.threshold_line = None
self.params.sigTreeStateChanged.connect(self._parameters_changed)
self.params.child('threshold').sigValueChanged.connect(
self._threshold_param_changed)
def __init__(self):
QtCore.QObject.__init__(self)
self.params = pt.Parameter(name='Cell selection',
type='group',
children=[
{
'name': 'cell id',
'type': 'list',
'value': None,
'values': {
'': None
}
},
])
self.fluor_img = None
self.roi_img = None
self.cell_ids = []
self.imv = None
self.roi_img_item = None
self.params.child('cell id').sigValueChanged.connect(
self._selection_changed)
def __init__(self, boc, expt_id, cell_id):
self.boc = boc
self.data_set = boc.get_ophys_experiment_data(
ophys_experiment_id=expt_id)
self.lsn_tmp = self.data_set.get_stimulus_template(
'locally_sparse_noise')
# setup cell selector
cells = self.data_set.get_cell_specimen_ids()
self.cell_selector = CellSelector()
roi_img = (self.data_set.get_roi_mask_array() *
np.array(cells)[:, None, None]).max(axis=0)
max_img = self.data_set.get_max_projection()
self.cell_selector.set_images(max_img, roi_img)
# setup spike detector
self.spike_detector = SpikeDetector()
# setup averager
self.averager = TriggeredAverager()
# make stimulus frame locations easier to look up
self.lsn_id = None
QtGui.QWidget.__init__(self)
self.hs = pg.QtGui.QSplitter()
self.hs.setOrientation(pg.QtCore.Qt.Horizontal)
self.vs1 = pg.QtGui.QSplitter()
self.vs1.setOrientation(pg.QtCore.Qt.Vertical)
self.params = pt.Parameter(name='params',
type='group',
children=[
self.cell_selector.params,
self.spike_detector.params,
self.averager.params,
])
self.tree = pt.ParameterTree(showHeader=False)
self.tree.setParameters(self.params, showTop=False)
self.vs1.addWidget(self.tree)
self.expt_imv = pg.ImageView()
self.cell_selector.set_imageview(self.expt_imv)
self.vs1.addWidget(self.expt_imv)
self.vs2 = pg.QtGui.QSplitter()
self.vs2.setOrientation(pg.QtCore.Qt.Vertical)
self.plt1 = pg.PlotWidget()
self.plt2 = pg.PlotWidget()
self.plt2.setXLink(self.plt1)
self.spike_detector.set_plots(self.plt1, self.plt2)
self.sta_imv = pg.ImageView()
self.averager.set_imageview(self.sta_imv)
self.vs2.addWidget(self.plt1)
self.vs2.addWidget(self.plt2)
self.vs2.addWidget(self.sta_imv)
self.hs.addWidget(self.vs1)
self.hs.addWidget(self.vs2)
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.layout.addWidget(self.hs)
self.resize(1400, 800)
self.hs.setSizes([600, 600])
self.show()
self.cell_selector.cell_selection_changed.connect(self.loadCell)
self.spike_detector.parameters_changed.connect(self.updateSpikes)
self.averager.parameters_changed.connect(self.updateOutput)
self.loadCell()
