def attach_yaxis(self, axis_color=(0, 1, 1, 0.8)):
'''
Provide y axis for the population rate
'''
fg = axis_color
# text show amplitude
self.amp_text = scene.Text("",
pos=(0, 0),
italic=False,
bold=False,
anchor_x='left',
anchor_y='center',
color=axis_color,
font_size=10,
parent=self._view2)
self.amp_text.pos = (0, 20)
# x axis shows time and can be moved horizontally for clipping
self._yaxis = scene.AxisWidget(orientation='left',
text_color=fg,
axis_color=fg,
tick_color=fg)
self._yaxis.stretch = (0, 1)
self._grid.add_widget(self._yaxis, row=10, col=0, row_span=3)
self._yaxis.link_view(self._view2)
def attach_xaxis(self, axis_color=(0, 1, 1, 0.8)):
'''
Provide x axis. This method is optional for child class.
'''
fg = axis_color
# text show amplitude
self.amp_text = scene.Text("",
pos=(0, 0),
italic=False,
bold=False,
anchor_x='left',
anchor_y='center',
color=axis_color,
font_size=15,
parent=self._view)
self.amp_text.pos = (0, 12)
# x axis shows time and can be moved horizontally for clipping
self._xaxis = scene.AxisWidget(orientation='bottom',
text_color=fg,
axis_color=fg,
tick_color=fg)
self._xaxis.stretch = (0.9, 0.1)
self._grid.add_widget(self._xaxis, row=7, col=0, row_span=2)
self._xaxis.link_view(self._view)
self.x_axis_lock = True
def _add_label(self, curve_index, new_color):
new_label = scene.Text(f"{self.labels[curve_index]}",
color=new_color,
anchor_x='left',
parent=self.canvas.scene)
new_label.pos = self.LBL_POS_DEFAULTX, self.LBL_POS_DEFAULTY + self.LBL_SPACING * len(
self.hl_labels)
self.hl_labels.append((curve_index, new_label))
N = 200
pos = np.zeros((N, 2), dtype=np.float32)
pos[:, 0] = np.linspace(10, 390, N)
pos[:, 1] = np.random.normal(size=N, scale=20, loc=0)
canvas = scene.SceneCanvas(keys='interactive', size=(400, 200), show=True)
# Create a visual that updates the line with different colormaps
color = next(colormaps)
line = scene.Line(pos=pos, color=color, method='gl')
line.transform = STTransform(translate=[0, 140])
line.parent = canvas.central_widget
text = scene.Text(color,
bold=True,
font_size=24,
color='w',
pos=(200, 40),
parent=canvas.central_widget)
def on_timer(event):
global colormaps, line, text, pos
color = next(colormaps)
line.set_data(pos=pos, color=color)
text.text = color
timer = app.Timer(.5, connect=on_timer, start=True)
if __name__ == '__main__':
canvas.app.run()
def __init__(self,
data=None,
fs=25e3,
spks=None,
chs=None,
color=None,
pagesize=20000,
ncols=1,
gap_value=0.8 * 0.95,
ls='-',
time_slice=0):
scene.SceneCanvas.__init__(self, keys=None)
self.unfreeze()
assert data is not None
self.grid1 = self.central_widget.add_grid(spacing=0,
bgcolor='gray',
border_color='k')
self.view2 = self.grid1.add_view(row=0,
col=1,
col_span=36,
margin=10,
bgcolor=(0, 0, 0, 1),
border_color=(0, 1, 0))
self.view2.camera = scene.cameras.PanZoomCamera()
self.view2.camera.set_range()
self.cursor_color = '#0FB6B6'
self.cursor_text = scene.Text("",
pos=(0, 0),
italic=False,
bold=True,
anchor_x='left',
anchor_y='center',
color=self.cursor_color,
font_size=14,
parent=self.view2.scene)
self.cursor_text_ref = scene.Text("",
pos=(0, 0),
italic=True,
bold=False,
anchor_x='left',
anchor_y='center',
color=(0, 1, 1, 1),
font_size=14,
parent=self.view2.scene)
self.palette = palette
self._gap_value = gap_value
self.fs = fs
wav_visual = scene.visuals.create_visual_node(MyWaveVisual)
self.waves1 = wav_visual(ls=ls,
parent=self.view2.scene,
color=color,
gap=self._gap_value)
self.grid2 = self.view2.add_grid(spacing=0,
bgcolor=(0, 0, 0, 0),
border_color='k')
self.cross = Cross(cursor_color=self.cursor_color)
self.timer_cursor = app.Timer(connect=self.update_cursor,
interval=0.01,
start=False)
self.view1 = self.grid1.add_view(row=0,
col=0,
col_span=1,
margin=10,
bgcolor=(0, 0, 0, 1),
border_color=(1, 0, 0))
self.view1.camera = scene.cameras.PanZoomCamera()
self.view1.camera.set_range()
self._start_index = 0
self.flag = 0
self._pagesize = pagesize
self.location = ''
y_sync_cam = YSyncCamera()
self.view1.camera.link(y_sync_cam)
self.view2.camera.link(y_sync_cam)
self.ch_no_text = scene.Text('',
pos=(0, 0),
italic=False,
bold=True,
color=self.cursor_color,
font_size=12,
parent=self.view1.scene)
self.data = data
if chs is not None:
chs = np.array(chs)
if chs.ndim != 1:
chs = chs.ravel()
self.data = self.data[:, chs]
chs_labels = chs
elif self.data.shape[1] <= 32:
chs_labels = np.arange(self.data.shape[1])
else:
chs_labels = np.arange(32)
self._chs = list(zip(chs_labels, np.arange(len(chs_labels))))
self._chs_idx = sorted([j for _, j in self._chs], reverse=True)
self.spikes = self._spkarray2dist(spks)
self._render(self.data[0:self.pagesize, self._chs_idx])
self.attach_texts()
self.highlight_ch()
self.set_range()
self.cross.attach(self.grid2)
self.cross.link_view(self.view2)
self._current_time = 0.0
self._sliding_time = 1.0
# for picker
self.key_option = 0
self._picker = Picker(self.scene, self.view2.camera.transform)
self.picked_data = []
def draw_axes(self):
#First, calculate positions
self.position_axes()
#Draw x axis
self._xax=scene.Axis(
pos=[[self._xlim[0],
self._ylim[self._axpos[0,1]],
self._zlim[self._axpos[0,2]]],
[self._xlim[1],
self._ylim[self._axpos[0,1]],
self._zlim[self._axpos[0,2]]]],
domain=self._xlim,
tick_direction=(0,-1,0),
major_tick_length=10*self._cam_dist,
font_size=10*self._cam_dist,
font_face='FreeSerif',
axis_color='k',
tick_color='k',
text_color='k',
parent=self._view.scene)
self._xlabel = scene.Text("x",
pos=[(self._xlim[0]+self._xlim[1])/2,
self._ylim[self._axpos[0,1]]-self._label_dist,
self._zlim[self._axpos[0,2]]],
font_size=10*self._cam_dist,
face='FreeSerif',
color='k',
parent=self._view.scene)
#Draw y axis
self._yax=scene.Axis(
pos=[[self._xlim[self._axpos[1,0]],
self._ylim[0],
self._zlim[self._axpos[1,2]]],
[self._xlim[self._axpos[1,0]],
self._ylim[1],
self._zlim[self._axpos[1,2]]]],
domain=self._ylim,
tick_direction=(1,0,0),
major_tick_length=10*self._cam_dist,
font_size=10*self._cam_dist,
font_face='FreeSerif',
axis_color='k',
tick_color='k',
text_color='k',
parent=self._view.scene)
self._ylabel = scene.Text("y",
pos=[self._xlim[self._axpos[1,0]]-self._label_dist,
(self._ylim[0]+self._ylim[1])/2,
self._zlim[self._axpos[1,2]]],
font_size=10*self._cam_dist,
face='FreeSerif',
color='k',
parent=self._view.scene)
#Draw z axis
self._zax=scene.Axis(
pos=[[self._xlim[self._axpos[2,0]],
self._ylim[self._axpos[2,1]],
self._zlim[0]],
[self._xlim[self._axpos[2,0]],
self._ylim[self._axpos[2,1]],
self._zlim[1]]],
domain=self._zlim,
tick_direction=(0,-1,0),
major_tick_length=10*self._cam_dist,
font_face='FreeSerif',
font_size=10*self._cam_dist,
axis_color='k',
tick_color='k',
text_color='k',
parent=self._view.scene)
self._zlabel = scene.Text("z",
pos=[self._xlim[self._axpos[2,0]],
self._ylim[self._axpos[2,1]]-self._label_dist,
(self._zlim[0]+self._zlim[1])/2],
font_size=10*self._cam_dist,
face='FreeSerif',
color='k',
parent=self._view.scene)
self._xax._update_subvisuals()
self._yax._update_subvisuals()
self._zax._update_subvisuals()
#Add plot to scene
self._view.add(self._volume)
def __init__(self,
data,
color=None,
fs=25e3,
spklen=19,
ncols=1,
gap_value=0.8 * 0.95,
ls='-',
time_slice=0):
scene.SceneCanvas.__init__(self, keys=None)
self.unfreeze()
self.data = data
self.fs = fs
self.spklen = spklen
self.grid1 = self.central_widget.add_grid(spacing=0,
bgcolor='gray',
border_color='k')
self.view2 = self.grid1.add_view(row=0,
col=0,
col_span=36,
margin=10,
bgcolor=(0, 0, 0, 1),
border_color=(0, 1, 0))
self.view2.camera = scene.cameras.PanZoomCamera()
self.view2.camera.set_range()
self.cursor_color = '#0FB6B6'
self.cursor_text = scene.Text("",
pos=(0, 0),
italic=False,
bold=True,
anchor_x='left',
anchor_y='center',
color=self.cursor_color,
font_size=24,
parent=self.view2.scene)
self.cursor_text_ref = scene.Text("",
pos=(0, 0),
italic=True,
bold=False,
anchor_x='left',
anchor_y='center',
color=(0, 1, 1, 1),
font_size=24,
parent=self.view2.scene)
self.cursor_rect = scene.Rectangle(center=(0, 0, 0),
height=1.,
width=1.,
radius=[0., 0., 0., 0.],
color=(0.1, 0.3, 0.3, 0.5),
border_width=0,
border_color=(0, 0, 0, 0),
parent=self.view2.scene)
self.cursor_rect.visible = False
self.palette = palette
self._gap_value = gap_value
self._locate_buffer = 200
self._picker = Picker(self.scene, self.view2.camera.transform)
wav_visual = scene.visuals.create_visual_node(MyWaveVisual)
self.waves1 = wav_visual(ls=ls,
parent=self.view2.scene,
color=color,
gap=self._gap_value)
self.grid2 = self.view2.add_grid(spacing=0,
bgcolor=(0, 0, 0, 0),
border_color='k')
self.cross = Cross(cursor_color=self.cursor_color)
self.timer_cursor = app.Timer(connect=self.update_cursor,
interval=0.01,
start=False)
self.event = EventEmitter()
def plot_elements(elements,
overlay_deformed=False,
sel_nodes=None,
sel_elements=None,
canvas={},
hold_on=False,
view=None,
cam={},
tmat_scaling=1,
plot_tmat_ax=None,
plot_nodes=False,
node_labels=False,
element_labels=False,
element_label_settings={},
node_label_settings={},
element_settings={},
node_settings={},
sel_node_settings={},
sel_element_settings={},
sel_node_label_settings={},
sel_element_label_settings={},
tmat_settings={},
deformed_element_settings={},
title='BEEF Element plot'):
el_settings = dict(color='#008800')
el_settings.update(**element_settings)
def_el_settings = dict(color='#ff2288')
def_el_settings.update(**deformed_element_settings)
elsel_settings = dict(color='#ff0055', width=3)
elsel_settings.update(**sel_element_settings)
elsellab_settings = dict(color='#ff0055',
bold=True,
italic=False,
face='OpenSans',
font_size=10,
anchor_x='left')
elsellab_settings.update(**sel_element_label_settings)
ellab_settings = dict(color='#008800',
bold=False,
italic=False,
face='OpenSans',
font_size=10,
anchor_x='left')
ellab_settings.update(**element_label_settings)
n_settings = dict(face_color='#0000ff', edge_color=None, size=4)
n_settings.update(**node_settings)
nlab_settings = dict(color='#0000ff',
bold=False,
italic=False,
face='OpenSans',
font_size=10,
anchor_x='left')
nlab_settings.update(**node_label_settings)
nsel_settings = dict(face_color='#ff0000', edge_color='#ff0000', size=8)
nsel_settings.update(**sel_node_settings)
nsellab_settings = dict(color='#ff0000',
bold=True,
italic=False,
face='OpenSans',
font_size=10,
anchor_x='left')
nsellab_settings.update(**sel_node_label_settings)
tmat_colors = ['#0000ff', '#00ff00', '#ff0000']
tmatax_settings = dict(arrow_size=1)
tmatax_settings.update(**tmat_settings)
# Node coordinates
nodes = list(set([a for b in [el.nodes for el in elements]
for a in b])) #flat list of unique nodes
node_pos = np.vstack([node.coordinates for node in nodes])
# Selected elements
if sel_elements is None:
sel_elements = []
unsel_elements = [el for el in elements if el.label not in sel_elements]
sel_elements = [el for el in elements if el.label in sel_elements]
if view is None:
view, canvas, cam = initialize_plot(canvas=canvas,
cam=cam,
elements=elements,
title=title)
else:
canvas = view.canvas
cam = view.camera
if not hold_on:
rm_visuals(view)
# Establish element lines
if len(unsel_elements) > 0:
element_lines = [None] * len(unsel_elements)
for ix, el in enumerate(unsel_elements):
element_lines[ix] = np.vstack(
[node.coordinates for node in el.nodes])
element_visual = scene.Line(pos=np.vstack(element_lines),
connect='segments',
**el_settings)
view.add(element_visual)
# Establish selected element lines
if len(sel_elements) > 0:
element_lines = [None] * len(sel_elements)
for ix, el in enumerate(sel_elements):
element_lines[ix] = np.vstack(
[node.coordinates for node in el.nodes])
element_visual = scene.Line(pos=np.vstack(element_lines),
connect='segments',
**elsel_settings)
view.add(element_visual)
# Overlay deformed plot if
if overlay_deformed:
element_lines = [None] * len(elements)
for ix, el in enumerate(elements):
element_lines[ix] = np.vstack([node.x[:3] for node in el.nodes])
element_visual = scene.Line(pos=np.vstack(element_lines),
connect='segments',
**def_el_settings)
view.add(element_visual)
# Establish element labels
if element_labels and len(unsel_elements) > 0:
el_cog = [el.get_cog() for el in unsel_elements]
el_labels = [str(el.label) for el in unsel_elements]
element_label_visual = scene.Text(text=el_labels,
pos=el_cog,
**ellab_settings)
view.add(element_label_visual)
if len(sel_elements) > 0:
el_cog = [el.get_cog() for el in sel_elements]
el_labels = [str(el.label) for el in sel_elements]
element_label_visual = scene.Text(text=el_labels,
pos=el_cog,
**elsellab_settings)
view.add(element_label_visual)
# Node labels
if node_labels:
node_labels = [str(node.label) for node in nodes]
element_label_visual = scene.Text(text=node_labels,
pos=node_pos,
**nlab_settings)
view.add(element_label_visual)
# Nodes
if plot_nodes:
node_visual = scene.visuals.Markers(pos=node_pos, **n_settings)
view.add(node_visual)
if sel_nodes is not None:
sel_nodes = [node for node in nodes if node.label in sel_nodes]
sel_node_labels = [str(node.label) for node in sel_nodes]
if len(sel_nodes) >= 1:
node_pos = np.vstack([node.coordinates for node in sel_nodes])
sel_node_label_visual = scene.Text(text=sel_node_labels,
pos=node_pos,
**nsellab_settings)
sel_node_visual = scene.visuals.Markers(pos=node_pos,
**nsel_settings)
view.add(sel_node_label_visual)
view.add(sel_node_visual)
else:
print('Requested nodes to highlight not found.')
# Add transformation matrices
if plot_tmat_ax is not None:
for ax in plot_tmat_ax:
el_vecs = np.vstack(
[element.tmat[ax, 0:3] for element in elements]) * tmat_scaling
el_cogs = np.vstack([element.get_cog() for element in elements])
# INTERTWINE TMAT AND ELCOGS
arrow_data = np.hstack([el_cogs, el_cogs + el_vecs])
tmat_visual = scene.Arrow(pos=arrow_data.reshape(
[el_vecs.shape[0] * 2, 3]),
color=tmat_colors[ax],
arrow_color=tmat_colors[ax],
connect='segments',
arrows=arrow_data,
**tmatax_settings)
view.add(tmat_visual)
canvas.show()
axis = scene.visuals.XYZAxis(parent=view.scene)
return canvas, view
