def __init__(self, canvas, analog_data, spike_data):
super().__init__()
self.canvas = canvas
self.analog_data = analog_data
self.spike_data = mea.MEASpikeDict(spike_data)
prespikes = spike_data.copy()
prespikes.electrode = prespikes.electrode.str.split('.').str.get(0)
self.condensed_spike_data = mea.MEASpikeDict(prespikes)
self._t0 = 0
self._dt = 20
self.mouse_t = 0
self.electrode = ''
self._time_window = 20 # in milliseconds
self._scale = (5, 150)
self.extra_text = ''
self._selected_electrodes = []
self.program = gloo.Program(self.VERTEX_SHADER, self.FRAGMENT_SHADER)
self.program['u_scale'] = self._scale
self.program['a_position'] = [[0, 0, 0, 0]]
self.program['a_color'] = [[0, 0, 0, 0]]
self.program['u_width'] = 100
self.program['u_rows'] = self.canvas.layout.rows
self.program['u_columns'] = self.canvas.layout.columns
self.grid = LineCollection()
self.create_grid()
self.sample_rate = 1.0 / (self.analog_data.index[1] -
self.analog_data.index[0])
self.measuring = False
self.measure_start = (0, 0)
self.measure_line = visuals.LineVisual(np.array(((0, 0), (0, 0))),
Theme.yellow,
method='agg')
self.configure_transforms()
def __init__(self, canvas, spike_data):
self.canvas = canvas
# Load data
self.spike_data = mea.MEASpikeDict(spike_data)
self.spike_data.sort()
self.program = gloo.Program(RasterPlotVisualization.VERTEX_SHADER,
RasterPlotVisualization.FRAGMENT_SHADER)
self._t0 = 0
self._dt = self.spike_data.max_time()
self.electrode = ''
self.program['u_pan'] = self._t0
self.program['u_y_scale'] = self._dt / 2
self.program['u_top_margin'] = 20.0 * 2.0 / canvas.size[1]
self._row_count = 120
self._display_selected = False
self._unselected_row_count = 120
self.selected_electrodes = []
self.row_count = len(self.spike_data)
self.resample()
self.margin = {}
self.margin['top'] = 20
self.velocity = 0
self.tick_separtion = 50
self.tick_labels = [
visuals.TextVisual('', font_size=10, color='w') for x in range(18)
]
self.tick_marks = LineCollection()
self.mouse_t = 0
self.extra_text = ''
def __init__(self, canvas, spike_data):
super().__init__()
self.canvas = canvas
if 'conductance' not in spike_data.columns:
spike_data['conductance'] = False
self.spike_data = mea.MEASpikeDict(spike_data)
self.spike_data.sort()
self.program = gloo.Program(RasterPlotVisualization.VERTEX_SHADER,
RasterPlotVisualization.FRAGMENT_SHADER)
self._t0 = 0
self._dt = self.spike_data.max_time()
self.electrode = ''
self.program['u_pan'] = self._t0
self.program['u_y_scale'] = self._dt / 2
self.program['u_top_margin'] = 20.0 * 2.0 / canvas.size[1]
self._row_count = 120
self._display_selected = False
self.selected_electrodes = []
self.row_count = len(self.spike_data)
self._unselected_row_count = self.row_count
self._dim_conductance = False
self.resample()
self.margin = {'top': 20}
self.velocity = 0
self.tick_separtion = 50
self.tick_labels = [visuals.TextVisual('', font_size=10, color='w')
for x in range(14)]
self.tick_marks = LineCollection()
self.mouse_t = 0
self.extra_text = ''
self.measuring = False
self.measure_start = (0, 0)
self.measure_line = visuals.LineVisual(np.array(((0, 0), (100, 100))),
Theme.yellow)
def __init__(self, canvas, analog_data, spike_data):
super().__init__()
self.canvas = canvas
self.analog_data = analog_data
self.raw_data = spike_data
self.spike_data = mea.MEASpikeDict(spike_data)
self.show_spikes = False
self._dim_conductance = False
self._t0 = 0
self._dt = 20
self._y_scale = 150
self._pan = 0
self._scale = 1
self.mouse_t = 0
self.electrode = ''
self.selected_electrodes = ['h11'] # l5, m5
self.strip_program = gloo.Program(self.STRIP_VERTEX_SHADER,
self.STRIP_FRAGMENT_SHADER)
self.strip_program['u_color'] = Theme.blue
self.point_program = gloo.Program(self.POINT_VERTEX_SHADER,
self.POINT_FRAGMENT_SHADER)
self.pan = self._t0
self.scale = (2.0 / self._dt, 1 / self._y_scale)
self.velocity = 0
self.measuring = False
self.measure_start = (0, 0)
self.measure_line = visuals.LineVisual(np.array(((0, 0), (100, 100))),
Theme.yellow)
self.scale_bar = visuals.LineVisual(np.array(((10, 10), (200, 10))),
Theme.black,
width=10,
method='agg')
self.scale_label = visuals.TextVisual('', font_size=8)
self.configure_transforms()
self.extra_text = ''
self._filtered = False
self._filter_cutoff = [200, 4000]
self.all_spike_colors = []
self.propagation_spike_colors = []
self.resample()
self.background_color = Theme.background
def __init__(self, canvas, analog_data, spike_data):
self.canvas = canvas
self.analog_data = analog_data
self.spike_data = mea.MEASpikeDict(spike_data)
self.show_spikes = False
self._t0 = 0
self._dt = 20
self._y_scale = 150
self._pan = 0
self._scale = 1
self.mouse_t = 0
self.electrode = ''
self.electrodes = ['h11'] # l5, m5
self.strip_program = gloo.Program(self.STRIP_VERTEX_SHADER,
self.STRIP_FRAGMENT_SHADER)
self.strip_program['u_color'] = Theme.blue
self.point_program = gloo.Program(self.POINT_VERTEX_SHADER,
self.POINT_FRAGMENT_SHADER)
self.point_program['u_color'] = Theme.yellow
self.pan = self._t0
self.scale = (2.0 / self._dt, 1 / self._y_scale)
self.velocity = 0
self.measuring = False
self.measure_start = (0, 0)
self.measure_line = visuals.LineVisual(np.array(((0, 0), (100, 100))),
Theme.grid_line)
self.extra_text = ''
self._filtered = False
self._filter_cutoff = [200, 4000]
self.resample()
self.background_color = Theme.background
def tag_cond(args):
if len(args.FILES) < 2:
print('Must specify src and dest files.')
return
src = args.FILES[-1]
if len(args.FILES) == 2:
files = [
f for f in glob.glob(args.FILES[0])
if f.endswith('.csv') and os.path.exists(f)
]
else:
files = [f for f in args.FILES[:-1] if f.endswith('.csv')]
seqs = []
with open(src, 'r') as f:
for line in f:
seqs.append([s.lower().strip() for s in line.split(',')])
import pymea as mea
for i, f in enumerate(files):
conductance_locs = []
df = pd.read_csv(f)
spikes = mea.MEASpikeDict(df)
for seq in seqs:
e_keep = seq[0]
sub_df = pd.concat([spikes[tag] for tag in seq])
cofiring = pd.concat(mea.cofiring_events(sub_df, 0.0007))
conductance_locs.extend(
list(cofiring[cofiring.electrode != e_keep].index.values))
df['conductance'] = False
df.ix[conductance_locs, 'conductance'] = True
df.to_csv(f, index=False)
print('%d of %d exported.' % (i + 1, len(files)))
