def __init__(self, **kwargs):
"""Init."""
# Create the main window :
super(UiInit, self).__init__(None)
self.setupUi(self)
# Cameras :
grid_rect = (0, 0, 1, 1)
cb_rect = (-.05, -2, .8, 4.)
cam_signal = viscam.PanZoomCamera()
cam_grid = viscam.PanZoomCamera(rect=grid_rect)
cam_cbar = viscam.PanZoomCamera(rect=cb_rect)
# Canvas creation :
cargs = {'size': (800, 600)}
self._grid_canvas = VisbrainCanvas(axis=False,
name='Grid',
cargs=cargs,
camera=cam_grid,
**kwargs)
self._signal_canvas = VisbrainCanvas(axis=True,
name='Signal',
cargs=cargs,
add_cbar=True,
camera=cam_signal,
**kwargs)
self._signal_canvas.wc_cbar.camera = cam_cbar
# Add canvas to layout :
self._GridLayout.addWidget(self._grid_canvas.canvas.native)
self._SignalLayout.addWidget(self._signal_canvas.canvas.native)
# Initialize shortcuts :
GridShortcuts.__init__(self, self._grid_canvas.canvas)
SignalShortcuts.__init__(self, self._signal_canvas.canvas)
def __init__(self, bgcolor='black', verbose=None, **kwargs):
"""Init."""
# ====================== PyQt creation ======================
_PyQtModule.__init__(self,
verbose=verbose,
to_describe='view.wc',
icon='brain_icon.svg')
self._userobj = {}
self._gl_scale = 100. # fix appearance for small meshes
self._camera = viscam.TurntableCamera(name='MainBrainCamera')
# ====================== Canvas creation ======================
UiInit.__init__(self, bgcolor) # GUI creation + canvas
PROFILER("Canvas creation")
# ====================== App creation ======================
PROFILER("Visual elements", as_type='title')
Visuals.__init__(self, self.view.wc, **kwargs)
# ====================== Ui interactions ======================
UiElements.__init__(self) # GUI interactions
PROFILER("Ui interactions")
self._shpopup.set_shortcuts(self.sh) # shortcuts dict
# ====================== Cameras ======================
# Main camera :
self.view.wc.camera = self._camera
self._vbNode.parent = self.view.wc.scene
self.atlas.camera = self._camera
self.roi.camera = self._camera
self.atlas._csize = self.view.canvas.size
self.atlas.rotate('top')
self.atlas.camera.set_default_state()
PROFILER("Cameras creation")
# ====================== Colorbar ======================
camera = viscam.PanZoomCamera(rect=(-.2, -2.5, 1, 5))
BrainCbar.__init__(self, camera)
PROFILER("Colorbar and panzoom creation")
self.background_color(bgcolor)
# ====================== Shortcuts ======================
BrainShortcuts.__init__(self, self.cbqt.cbviz._canvas)
PROFILER("Set brain shortcuts")
self._fcn_on_load()
PROFILER("Functions on load")
def _cam_creation(self):
"""Create a set of cameras."""
# ------------------- Channels -------------------
self._chanCam = []
for k in range(len(self)):
self._chanCam.append(FixedCam()) # viscam.PanZoomCamera()
# ------------------- Spectrogram -------------------
self._speccam = FixedCam() # viscam.PanZoomCamera()
self._specCanvas.set_camera(self._speccam)
# ------------------- Hypnogram -------------------
self._hypcam = FixedCam() # viscam.PanZoomCamera()
self._hypCanvas.set_camera(self._hypcam)
# ------------------- Topoplot -------------------
self._topocam = viscam.PanZoomCamera()
self._topoCanvas.set_camera(self._topocam)
# ------------------- Time axis -------------------
self._timecam = FixedCam()
self._TimeAxis.set_camera(self._timecam)
# Keep all cams :
self._allCams = (self._chanCam, self._speccam, self._hypcam,
self._topocam, self._timecam)
def __init__(self, data, sf=1, **kwargs):
"""Init."""
# Be sure to have float arguments :
if data.dtype != np.float32:
data = data.astype(np.float32, copy=False)
warn("Data should be an array of float number. Use "
"data.astype(np.float32) before opening the interface.")
# ====================== ui Arguments ======================
# Background color (for all of the canvas) :
bgcolor = kwargs.get('ui_bgcolor', (.09, .09, .09))
nd_title = kwargs.get('nd_title', 'Nd-plot')
nd_xlabel = kwargs.get('nd_xlabel', 'X axis')
nd_ylabel = kwargs.get('nd_ylabel', 'Y axis')
nd_grid = kwargs.get('nd_grid', False)
nd_visible = kwargs.get('nd_visible', True)
od_grid = kwargs.get('od_grid', True)
od_visible = kwargs.get('od_visible', False)
od_title = kwargs.get('od_title', '1d-plot')
od_xlabel = kwargs.get('od_xlabel', 'X axis')
od_ylabel = kwargs.get('od_ylabel', 'Y axis')
# Default linewidth :
self._ndlw = kwargs.get('nd_lw', 2.)
self._1dlw = kwargs.get('od_lw', 2.)
self._oridata = np.ascontiguousarray(data)
self._sf = np.float32(sf)
# print('ID 0: ', id(self._oridata))
# Savename, extension and croping region (usefull for the screenshot) :
self._savename = kwargs.get('ui_savename', None)
self._extension = kwargs.get('ui_extension', '.png')
self._crop = kwargs.get('ui_region', None)
if self._extension not in ['png', 'tiff']:
self._extension = 'png'
# ====================== App creation ======================
# Create the app and initialize all graphical elements :
self._app = QtWidgets.QApplication(sys.argv)
uiInit.__init__(self, bgcolor, nd_title, nd_xlabel, nd_ylabel,
od_title, od_xlabel, od_ylabel)
# ====================== Objects creation ======================
visuals.__init__(self, data, self._sf, **kwargs)
# ====================== user & GUI interaction ======================
# User <-> GUI :
uiElements.__init__(self)
# ====================== Cameras ======================
# Nd-plot camera :
ndcam = viscam.PanZoomCamera(rect=(-1, -1, 2, 2))
self._ndplt.mesh.set_camera(ndcam)
self._ndCanvas.set_camera(ndcam)
# 1d-plot camera :
odcam = viscam.PanZoomCamera(rect=self._1dplt.mesh.rect)
self._1dCanvas.set_camera(odcam)
# Fixed colorbar camera :
turntable = viscam.TurntableCamera(interactive=True,
azimuth=0,
elevation=90)
self._cbCanvas.set_camera(turntable)
self._cbCanvas.wc.camera.set_range(x=(-24, 24),
y=(-0.5, 0.5),
margin=0)
# self._cbCanvas.wc.scene.children[0].parent = None
# ====================== Visibility ======================
# Nd-panel :
self._CanVisNd.setChecked(nd_visible)
self._NdVizPanel.setVisible(nd_visible)
self._ndGridTog.setChecked(nd_grid)
self._ndCanvas.visible_axis(nd_grid)
# 1d-panel :
self._CanVis1d.setChecked(od_visible)
self._1dVizPanel.setVisible(od_visible)
self._1dGridTog.setChecked(od_grid)
self._1dCanvas.visible_axis(od_grid)
# Finally, update each canvas and tab selection :
self._ndCanvas.canvas.update()
self._1dCanvas.canvas.update()
self._fcn_QuickTabSelec()
def __init__(self, *args, **kwargs):
"""Init."""
# ====================== ui Arguments ======================
# Background color (for the main and the colorbar canvas) :
bgcolor = kwargs.get('ui_bgcolor', (0., 0., 0.))
# Savename, extension and croping region (usefull for the screenshot) :
self._savename = kwargs.get('ui_savename', None)
self._crop = kwargs.get('ui_region', None)
self._autocrop = kwargs.get('ui_autocrop', True)
self._uirez = kwargs.get('ui_resolution', 3000.)
self._xyzRange = {
'turntable': {
'x': None,
'y': (-1200, 1200),
'z': None
},
'fly': {
'x': (-120, 120),
'y': (-100, 200),
'z': (-90, 90)
},
}
self._cbarexport = True
self._userobj = {}
# ====================== App creation ======================
# Create the app and initialize all graphical elements :
self._app = QtWidgets.QApplication(sys.argv)
uiInit.__init__(self, bgcolor)
# Set icon :
# pathfile = sys.modules[__name__].__file__
# path = os.path.join(*['brain', 'interface', 'gui', 'vbicon.png'])
# self.setWindowIcon(QtGui.QIcon(os.path.join(pathfile.split(
# '/vbrain')[0], path)))
# ====================== Objects creation ======================
camera = viscam.TurntableCamera(azimuth=0,
distance=1000,
name='turntable')
base.__init__(self, self.view.wc, self._csGrid, self.progressBar,
**kwargs)
# ====================== UI to visbrain ======================
# Link UI and visbrain function :
uiElements.__init__(self)
self._shpopup.set_shortcuts(self.sh)
# ====================== Cameras ======================
# Main camera :
self.view.wc.camera = camera
self.atlas.mesh.set_camera(self.view.wc.camera)
self.pic.set_camera(self.view.wc.camera)
self._vbNode.parent = self.view.wc.scene
self._rotate(fixed='axial')
self.view.wc.camera.set_default_state()
# ====================== Colorbar ======================
# Fixed colorbar camera :
camera = viscam.PanZoomCamera(rect=(-.2, -2.5, 1, 5))
# Cbar creation :
BrainCbar.__init__(self, camera)
# Add shortcuts on it :
BrainShortcuts.__init__(self, self.cbqt.cbviz._canvas)
self._fcn_on_load()
def __init__(self, bgcolor='black', verbose=None, **kwargs):
"""Init."""
# ====================== PyQt creation ======================
_PyQtModule.__init__(self,
verbose=verbose,
to_describe='view.wc',
icon='brain_icon.svg')
self._userobj = {}
self._gl_scale = 100. # fix appearance for small meshes
self._camera = viscam.TurntableCamera(name='MainEngramCamera')
# ====================== Canvas creation ======================
UiInit.__init__(self, bgcolor) # GUI creation + canvas
PROFILER("Canvas creation")
# ====================== App creation ======================
PROFILER("Visual elements", as_type='title')
Visuals.__init__(self, self.view.wc, **kwargs)
# ====================== Metadata Storage ======================
if 'metadata' in kwargs.keys():
self.metadata = kwargs['metadata']
else:
self.metadata = {}
# ====================== Rotation Kinetics ======================
if 'rotation' in kwargs.keys():
self.rotation = kwargs['rotation']
else:
self.rotation = 0
# ====================== Carousel Options ======================
self.ease_xyz = False # Between carousel options
self.ignore_streams = True
if 'carousel_metadata' in kwargs.keys():
self.carousel_metadata = kwargs['carousel_metadata']
else:
self.carousel_metadata = {}
# Carousel Display Method
if 'carousel_display_method' in kwargs.keys():
self._carousel_display_method = kwargs['carousel_display_method']
else:
self._carousel_display_method = 'text'
# Carousel Options
if 'hierarchy_lookup' in self.carousel_metadata:
options = np.asarray(self.carousel_metadata['hierarchy_lookup'])
self._carousel_options_inds = [np.asarray([0])]
for dims in (range(len(options))):
_combs = itertools.combinations(range(len(options)), dims + 1)
_combs = list(_combs)
for ll, comb in enumerate(_combs):
comb = list(comb)
if len(comb) > 1:
if ll == 0:
combs = [np.array(list(comb)) + 1]
else:
combs.append(np.array(list(comb)) + 1)
else:
if ll == 0:
combs = [np.array([comb[0] + 1])]
else:
combs.append(np.array([list(comb)[0] + 1]))
self._carousel_options_inds.append(combs)
self._carousel_options_inds[0] = [self._carousel_options_inds[0]]
options = list(options)
new_options = [np.asarray(['None'])]
for ii in np.arange(len(options)) + 1:
new_options.append(options[ii - 1])
self._carousel_options = np.asarray(new_options)
else:
self._carousel_options_inds = [np.asarray([])]
self._carousel_options = np.asarray(['None'])
# Carousel Choice
if 'carousel_choice' in kwargs.keys():
self._carousel_choice = kwargs['carousel_choice']
self._prev_carousel_choice = kwargs['carousel_choice']
else:
self._carousel_choice = [0, 0]
self._prev_carousel_choice = [0, 0]
# Display Method
self.update_carousel()
# Toggle Options
self._userdistance = [0]
self._uservelocity = 0
# ====================== Control Device ======================
if 'control_method' in kwargs.keys():
self.control_method = kwargs['control_method']
else:
self.control_method = 'keyboard'
if self.control_method is 'IR_Distance':
self.ser = serial.Serial('/dev/cu.usbmodem144101')
self.use_distance = True
else:
self.ser = None
self.prev_rotation = 0
def arduino_control(method='none'):
if self.ser is not None:
# Check Arduino inputs
try:
b = self.ser.readline() # read a byte string
string_n = b.decode() # decode byte string into Unicode
message = string_n.rstrip() # remove \n and \r
messages = message.split('|')
distance = messages[0]
command = messages[1]
except:
distance = 500
command = 'NONE'
if method == 'IR_Distance':
if self.use_distance:
THRESHOLD = 20 # cm
HEIGHT = 0
flt = float(distance)
self._userdistance = np.append(
self._userdistance, flt) # convert string to float
# Distance Selections
if flt < HEIGHT + THRESHOLD:
self._carousel_choice[0] = 0
if flt >= HEIGHT + (THRESHOLD) and flt < HEIGHT + (
2 * THRESHOLD):
self._carousel_choice[0] = 1
if flt >= HEIGHT + (2 * THRESHOLD):
self._carousel_choice[0] = 3
# Remote Option
if command != 'NONE':
print(command)
if command == 'POWER':
sys.exit()
if command == 'ST/REPT' and not self.use_distance:
if self._carousel_choice[0] < (
len(self._carousel_options_inds) - 1):
if self._carousel_choice[0] == 1:
self._carousel_choice[0] = 3
else:
self._carousel_choice[0] += 1
else:
self._carousel_choice[0] = 0
self._carousel_choice[1] = 0
if command == 'EQ':
if self.use_distance:
self.use_distance = False
else:
self.use_distance = True
if command == 'FUNC/STOP':
if self._carousel_choice[1] < (
len(self._carousel_options_inds[
self._carousel_choice[0]]) - 1):
self._carousel_choice[1] += 1
else:
self._carousel_choice[1] = 0
if command == 'VOL+' or command == 'VOL-':
if command == 'VOL+':
self.view.wc.camera.distance -= 5000
else:
self.view.wc.camera.distance += 5000
if command == 'UP':
self.rotation += .25
elif command == 'DOWN':
self.rotation -= .25
elif command == 'FAST BACK':
if np.sign(self.timescaling) == 1:
self.timescaling = -0.1
else:
self.timescaling -= 0.10
elif command == 'FAST FORWARD':
if np.sign(self.timescaling) == -1:
self.timescaling = 0.1
else:
self.timescaling += 0.10
elif command == 'PAUSE':
if self.timescaling == 0:
print('PLAY')
self.timescaling = self.default_timescaling
self.rotation = self.prev_rotation
self.displayed_time = self.time_cache
self.time_cache = None
else:
print('PAUSE')
self.prev_rotation = self.rotation
self.time_cache = self.displayed_time
self.rotation = 0
self.timescaling = 0
self.paused = True
if self.paused == True:
if command == 'FAST FORWARD':
self.time_cache += .02
elif command == 'FAST BACK':
self.time_cache -= .02
# Remote Numbers
if command == '0':
self.view.wc.camera.azimuth = 0
self.view.wc.camera.elevation = 90
elif command == '1':
self.view.wc.camera.azimuth = 0
self.view.wc.camera.elevation = -90
elif command == '2':
self.view.wc.camera.azimuth = 90
self.view.wc.camera.elevation = 0
elif command == '3':
self.view.wc.camera.azimuth = -90
self.view.wc.camera.elevation = 0
elif command == '4':
self.view.wc.camera.azimuth = 0
self.view.wc.camera.elevation = 0
elif command == '5':
self.view.wc.camera.azimuth = 180
self.view.wc.camera.elevation = 0
elif command == '6':
self.view.wc.camera.azimuth = 45
self.view.wc.camera.elevation = 30
elif command == '7':
self.view.wc.camera.azimuth = 45
self.view.wc.camera.elevation = -30
elif command == '8':
self.view.wc.camera.azimuth = -45
self.view.wc.camera.elevation = 30
elif command == '9':
self.view.wc.camera.azimuth = -45
self.view.wc.camera.elevation = -30
# ====================== Timer Creation ======================
self.loop_shift = 0
self.start_offset = 0
self.default_timescaling = 1 / 4
self.timescaling = self.default_timescaling
self.time_cache = None
self.displayed_time = 0
self.paused = False
def on_timer(*args, **kwargs):
# Change Source Radii and Connectivity Values
if self.time_cache is None:
time_inc = (args[0].dt * self.timescaling)
self.displayed_time = self.loop_shift + (
self.displayed_time + time_inc) % (
(np.shape(self.sources[0].data)[1] /
self.metadata['fs']) - self.loop_shift)
else:
self.displayed_time = self.loop_shift + (self.time_cache) % (
(np.shape(self.sources[0].data)[1] / self.metadata['fs']) -
self.loop_shift)
timepoint = int(self.displayed_time * self.metadata['fs'])
for source in self.sources:
source._update_radius(timepoint=timepoint)
for connect in self.connect:
connect._update_time(timepoint=timepoint)
arduino_control(self.control_method)
self.update_target_positions()
self.update_carousel()
self.update_visibility()
self._prev_carousel_choice = self._carousel_choice
if len(self._userdistance) > 2:
self._userdistance = [-1]
# Update Time Display
t_str = str(round(self.displayed_time, 3)) + ' s'
if not hasattr(self, '_time'):
self._time = Text(t_str,
parent=self.view.canvas.scene,
color='white')
else:
self._time.text = t_str
self._time.anchors = ('right', 'bottom')
self._time.font_size = self.view.canvas.size[1] // 200
self._time.pos = (49) * self.view.canvas.size[0] // 50, (
19) * self.view.canvas.size[1] // 20
self._time.update()
# Ease to New Positions if Triggered
if self.ease_xyz:
self.ease_xyz = False
for source in self.sources:
out = source._ease_to_target_position()
if out:
self.ease_xyz = True
for connect in self.connect:
out = connect._ease_to_target_position()
if out:
self.ease_xyz = True
# if hasattr(self.view.wc, 'camera'):
# diff_az = self.target_azimuth - self.view.wc.camera.azimuth
# diff_el = self.target_elevation - self.view.wc.camera.elevation
# # Ease scene rotation
# if (diff_az != 0.) | (diff_el != 0.):
# # Flip target and current (since I cannot find a way to update the shortcuts directly)
# if self.first_ease:
# temp_ = self.target_elevation
# self.target_elevation = self.view.wc.camera.elevation
# self.view.wc.camera.elevation = temp_
# temp_ = self.target_azimuth
# self.target_azimuth = self.view.wc.camera.azimuth
# self.view.wc.camera.azimuth = temp_
# self.first_ease = False
# if (abs(diff_az) > 0.001) | (abs(diff_el) > 0.001):
# self.view.wc.camera.azimuth += .1*(diff_az)
# self.view.wc.camera.elevation += .1*(diff_el)
# print('updating rotation')
# if self.first_ease:
# self.first_ease = False
# else:
# self.view.wc.camera.azimuth = self.target_azimuth
# self.view.wc.camera.elevation = self.target_elevation
# self.first_ease = True
#Iterate scene rotation
# else:
self.view.wc.camera.azimuth += self.rotation
self.view.wc.canvas.update()
kw = dict(connect=on_timer,
app=CONFIG['VISPY_APP'],
interval='auto',
iterations=-1)
self._app_timer = app.Timer(**kw)
self._app_timer.start()
# ====================== Ui interactions ======================
UiElements.__init__(self) # GUI interactions
PROFILER("Ui interactions")
self._shpopup.set_shortcuts(self.sh) # shortcuts dict
# ====================== Cameras ======================
# Main camera :
self.view.wc.camera = self._camera
self._vbNode.parent = self.view.wc.scene
self.atlas.camera = self._camera
self.roi.camera = self._camera
self.atlas._csize = self.view.canvas.size
self.atlas.rotate('top')
self.atlas.camera.set_default_state()
PROFILER("Cameras creation")
# Set easing
self.target_azimuth = self.view.wc.camera.azimuth
self.target_elevation = self.view.wc.camera.elevation
self.first_ease = True
# ====================== Colorbar ======================
camera = viscam.PanZoomCamera(rect=(-.2, -2.5, 1, 5))
EngramCbar.__init__(self, camera)
PROFILER("Colorbar and panzoom creation")
self.background_color(bgcolor)
# ====================== Shortcuts ======================
EngramShortcuts.__init__(self, self.cbqt.cbviz._canvas)
PROFILER("Set engram shortcuts")
self._fcn_on_load()
PROFILER("Functions on load")
def add_topoplot(self,
name,
data,
xyz=None,
channels=None,
system='cartesian',
unit='degree',
title=None,
title_color='black',
title_size=5.,
line_color='black',
line_width=2.,
chan_size=2.,
chan_offset=(0., 0., 0.),
chan_mark_color='white',
chan_mark_symbol='disc',
chan_txt_color='black',
bgcolor='white',
cbar=True,
cblabel=None,
cb_txt_size=4.,
levels=None,
level_colors='white',
cmap='viridis',
clim=None,
vmin=None,
under='gray',
vmax=None,
over='red',
row=0,
col=0,
row_span=1,
col_span=1,
margin=.05):
"""Add a subplot embedded in a subplot.
For now, there's two for using coordinates to define the subplot :
* Using the xyz input (must either be in cartesian or spherical
coordinate system)
* Using the channel input. The Topo class contains a list of
existing channel names and will try to identify those in the
channels variable.
Parameters
----------
name : string
Name of the topographic plot.
data : array_like
Array of data of shape (n_channels,).
xyz : array_like | None
Array of source's coordinates.
channels : list | None
List of channel names.
system : {'cartesian', 'spherical'}
Coordinate system.
unit : {'degree', 'rad'}
If system is 'spherical', specify if angles are in degrees or
radians.
title : string | None
Title of the topoplot.
title_color : array_like/string | 'black'
Color for the title.
title_size : float | 20.
Size of the title.
line_color : array_like/string | 'black'
Color of lines for the head, nose and eras.
line_width : float | 4.
Line width for the head, nose and eras.
chan_size : float | 12.
Size of channel names text.
chan_mark_color : array_like/string | 'white'
Color of channel markers.
chan_mark_symbol : string | 'disc'
Symbol to use for markers. Use disc, arrow, ring, clobber, square,
diamond, vbar, hbar, cross, tailed_arrow, x, triangle_up,
triangle_down, and star.
chan_txt_color : array_like/string | 'black'
Color of channel names.
bgcolor : array_like/string | 'white'
Background color.
cbar : bool | True
Attach a colorbar to the topoplot.
cblabel : string | None
Colorbar label.
cb_txt_size : float | 16.
Text size for the colorbar limits and label.
levels : array_like/int | None
The levels at which the isocurve is constructed.
level_colors : string/array_like | 'white'
The color to use when drawing the line. If a list is given, it
must be of shape (Nlev), if an array is given, it must be of
shape (Nlev, ...). and provide one color per level
(rgba, colorname). By default, all levels are whites.
cmap : string | None
Matplotlib colormap (like 'viridis', 'inferno'...).
clim : tuple/list | None
Colorbar limit. Every values under / over clim will
clip.
vmin : float | None
Every values under vmin will have the color defined
using the under parameter.
vmax : float | None
Every values over vmin will have the color defined
using the over parameter.
under : tuple/string | None
Matplotlib color under vmin.
over : tuple/string | None
Matplotlib color over vmax.
row : int | 0
The row in which to add the widget (0 is the topmost row)
col : int | 0
The column in which to add the widget (0 is the leftmost column)
row_span : int | 1
The number of rows to be occupied by the topoplot.
col_span : int | 1
The number of columns to be occupied by the topoplot.
margin : float | .05
Margin percentage between the topoplot and the edge of the subplot.
"""
# Check if name is avaible :
self._check_name_for(name, 'topoplot')
# Create the topoplot and set the data :
topo = TopoMesh(xyz, channels, system, unit, title, title_color,
title_size, line_color, line_width, chan_size,
chan_offset, chan_mark_color, chan_mark_symbol,
chan_txt_color, bgcolor, cbar, cb_txt_size, margin)
topo.set_data(data, levels, level_colors, cmap, clim, vmin, under,
vmax, over, cblabel)
self[name] = topo
# Create a PanZoom camera :
cam = viscam.PanZoomCamera(aspect=1., rect=topo.rect)
cam.set_default_state()
# Create a subplot and add the camera :
self._topoGrid[name] = self._grid.add_view(row,
col,
row_span,
col_span,
bgcolor=bgcolor,
camera=cam)
# Add the topoplot to the subplot :
self._topoGrid[name].add(self[name].node)
def add_shared_colorbar(self,
name,
cmap='viridis',
clim=(0, 1),
vmin=None,
vmax=None,
under='gray',
over='red',
cblabel='',
cbtxtsz=5.,
cbtxtsh=2.3,
txtcolor='black',
txtsz=3.,
txtsh=1.2,
width=.17,
border=True,
bw=2.,
limtxt=True,
bgcolor='white',
ndigits=2,
row=0,
col=0,
row_span=1,
col_span=1,
rect=(-1.2, -1.2, 2.4, 2.4)):
"""Add a shared colorbar across subplots.
Parameters
----------
cmap : string | None
Matplotlib colormap (like 'viridis', 'inferno'...).
clim : tuple/list | None
Colorbar limit. Every values under / over clim will
clip.
vmin : float | None
Every values under vmin will have the color defined
using the under parameter.
vmax : float | None
Every values over vmin will have the color defined
using the over parameter.
under : tuple/string | None
Matplotlib color under vmin.
over : tuple/string | None
Matplotlib color over vmax.
cblabel : string | ''
Colorbar label.
cbtxtsz : float | 5..
Text size of the colorbar label.
cbtxtsh : float | 2.3
Shift for the colorbar label.
txtcolor : string | 'white'
Text color.
txtsz : float | 3.
Text size for clim/vmin/vmax text.
txtsh : float | 1.2
Shift for clim/vmin/vmax text.
border : bool | True
Display colorbar borders.
bw : float | 2.
Border width.
limtxt : bool | True
Display vmin/vmax text.
bgcolor : tuple/string | (0., 0., 0.)
Background color of the colorbar canvas.
ndigits : int | 2
Number of digits for the text.
row : int | 0
The row in which to add the widget (0 is the topmost row)
col : int | 0
The column in which to add the widget (0 is the leftmost column)
row_span : int | 1
The number of rows to be occupied by the topoplot.
col_span : int | 1
The number of columns to be occupied by the topoplot.
rect : tuple | (-1.2, -1.2, 2.4, 2.4)
The 2-D area on the screen to display. The rect input describe
(x_start, y_start, x_width, y_height). This variable can be used
to translate or scale.
"""
# Check if name is avaible :
self._check_name_for(name, 'colorbar')
# Create a PanZoom camera :
cam = viscam.PanZoomCamera(rect=rect)
cam.set_default_state()
# Create a subplot and add the camera :
self._topoGrid[name] = self._grid.add_view(row,
col,
row_span,
col_span,
bgcolor=bgcolor,
camera=cam)
# Get if vmin and vmax exist :
isvmin, isvmax = vmin is not None, vmax is not None
# Create a colorbar object :
parent = Node(name=name)
cbar = CbarVisual(cmap=cmap,
clim=clim,
vmin=vmin,
isvmin=isvmin,
vmax=vmax,
isvmax=isvmax,
under=under,
over=over,
cblabel=cblabel,
cbtxtsz=cbtxtsz,
cbtxtsh=cbtxtsh,
txtcolor=txtcolor,
txtsz=txtsz,
txtsh=txtsh,
width=width,
border=border,
bw=bw,
limtxt=limtxt,
bgcolor=bgcolor,
ndigits=ndigits,
parent=parent)
self[name] = cbar
# Add the colorbar to the subplot :
self._topoGrid[name].add(parent)
def __init__(self,
data,
axis=-1,
time=None,
sf=1.,
enable_grid=True,
form='line',
color='black',
line_lw=1.,
line_smooth=False,
marker_symbol='disc',
marker_size=10.,
hist_nbins=10,
tf_norm=0,
tf_baseline=None,
tf_interp='gaussian',
tf_cmap='viridis',
tf_av_window=None,
tf_av_overlap=0.,
tf_clim=None,
psd_nperseg=256,
psd_noverlap=128,
display_grid=True,
display_signal=True,
annotations=None,
annot_txtsz=18.,
annot_marksz=16.,
annot_color='#2ecc71',
grid_lw=1.,
grid_smooth=False,
grid_titles=None,
grid_font_size=10.,
grid_color='random',
grid_shape=None,
grid_titles_color='black',
verbose=None,
**kwargs):
"""Init."""
dscb = ['_grid_canvas.canvas.scene', '_signal_canvas.canvas.scene']
PyQtModule.__init__(self, verbose=verbose, to_describe=dscb)
self._enable_grid = enable_grid
self._previous_form = form
display_grid = bool(display_grid * self._enable_grid)
# ==================== APP CREATION ====================
UiInit.__init__(self, **kwargs)
# ==================== DATA CHECKING ====================
if isinstance(data, (list, tuple)):
data = np.asarray(data)
if not isinstance(data, np.ndarray) or (data.ndim > 3):
raise TypeError("data must be an NumPy array with less than three "
"dimensions.")
if data.ndim == 1 or not self._enable_grid: # disable grid
display_grid = self._enable_grid = False
self.actionGrid.setEnabled(False)
toggle_enable_tab(self.QuickSettings, 'Grid', False)
self._data = data.astype(np.float32, copy=False)
self._axis = axis
# ==================== VISUALS ====================
grid_parent = self._grid_canvas.wc.scene
signal_parent = self._signal_canvas.wc.scene
Visuals.__init__(self, data, time, sf, axis, grid_titles, grid_color,
grid_shape, grid_parent, signal_parent)
# ==================== CAMERA ====================
grid_rect = (0, 0, 1, 1)
sig_rect = self._signal.rect
cb_rect = (-.05, -2, .8, 4.)
self._grid_canvas.camera = viscam.PanZoomCamera(rect=grid_rect)
self._signal_canvas.camera = viscam.PanZoomCamera(rect=sig_rect)
self._signal_canvas.wc_cbar.camera = viscam.PanZoomCamera(rect=cb_rect)
# ==================== UI INIT ====================
self._fix_elements_limits()
# ------------- Signal -------------
# Signal and axis color :
self._sig_color.setText(str(color2tuple(color, astype=float)))
ax_color = kwargs.get('axis_color', color2vb('black'))
self._axis_color.setText(str(ax_color))
# Title, labels and ticks :
self._sig_title.setText(kwargs.get('title', ''))
self._sig_title_fz.setValue(kwargs.get('title_font_size', 15.))
self._sig_xlab.setText(kwargs.get('xlabel', ''))
self._sig_ylab.setText(kwargs.get('ylabel', ''))
self._sig_lab_fz.setValue(kwargs.get('axis_font_size', 12.))
self._sig_ticks_fz.setValue(kwargs.get('tick_font_size', 8.))
# Signal properties :
safely_set_cbox(self._sig_form, form)
self._sig_lw.setValue(line_lw) # line
self._sig_smooth.setChecked(line_smooth) # line
self._sig_nbins.setValue(hist_nbins) # histogram
self._sig_size.setValue(marker_size) # marker
safely_set_cbox(self._sig_symbol, marker_symbol) # marker
self._sig_norm.setCurrentIndex(tf_norm)
safely_set_cbox(self._sig_tf_interp, tf_interp)
self._sig_tf_rev.setChecked(bool(tf_cmap.find('_r') + 1))
self._sig_tf_cmap.addItems(mpl_cmap())
safely_set_cbox(self._sig_tf_cmap, tf_cmap.replace('_r', ''))
if (tf_baseline is not None) and (len(tf_baseline) == 2):
self._sig_baseline.setChecked(True)
self._sig_base_start.setValue(tf_baseline[0])
self._sig_base_end.setValue(tf_baseline[1])
if isinstance(tf_av_window, int):
self._sig_averaging.setChecked(True)
self._sig_av_win.setValue(tf_av_window)
self._sig_av_overlap.setValue(tf_av_overlap)
if (tf_clim is not None) and (len(tf_clim) == 2):
self._sig_tf_clim.setChecked(True)
self._sig_climin.setValue(tf_clim[0])
self._sig_climax.setValue(tf_clim[1])
self._sig_nperseg.setValue(psd_nperseg)
self._sig_noverlap.setValue(psd_noverlap)
# ------------- Grid -------------
if hasattr(self, '_grid'):
n_rows, n_cols = self._grid.g_size
self._grid_nrows.setValue(n_rows)
self._grid_nrows.setMaximum(np.prod(self._grid.g_size))
self._grid_ncols.setValue(n_cols)
self._grid_ncols.setMaximum(np.prod(self._grid.g_size))
gt_st = str(color2tuple(grid_titles_color, astype=float))
self._grid_titles_fz.setValue(grid_font_size)
self._grid_titles_color.setText(gt_st)
self._grid_lw.setValue(grid_lw)
# ------------- Cbar -------------
self._signal_canvas.cbar.txtcolor = ax_color
self._signal_canvas.cbar.border = False
self._signal_canvas.cbar.cbtxtsz = 15.
self._signal_canvas.cbar.txtsz = 12.
# ------------- Settings -------------
bgcolor = kwargs.get('bgcolor', 'white')
self._set_bgcolor.setText(str(color2tuple(bgcolor, astype=float)))
self._grid_smooth.setChecked(grid_smooth)
# ------------- Annotations -------------
self._annot_txtsz.setValue(annot_txtsz)
self._annot_marksz.setValue(annot_marksz)
self._annot_color.setText(str(color2tuple(annot_color, astype=float)))
# ------------- Menu -------------
self.actionGrid.setChecked(display_grid)
self.actionSignal.setChecked(display_signal)
self._fcn_on_creation()
# ==================== USER <-> GUI ====================
UiElements.__init__(self, **kwargs)
# ==================== SHORTCUTS ====================
self._shpopup.set_shortcuts(self._sh_grid + self._sh_sig)
# ------------- Annotations -------------
if annotations is not None:
assert os.path.isfile(annotations)
self._fcn_load_annotations(filename=annotations)
def __init__(self, bgcolor='black', verbose=None, **kwargs):
"""Init."""
# ====================== PyQt creation ======================
_PyQtModule.__init__(self,
verbose=verbose,
to_describe='view.wc',
icon='brain_icon.svg')
self._userobj = {}
self._gl_scale = 100. # fix appearance for small meshes
self._camera = viscam.TurntableCamera(name='MainEngramCamera')
# ====================== Canvas creation ======================
UiInit.__init__(self, bgcolor) # GUI creation + canvas
PROFILER("Canvas creation")
# ====================== App creation ======================
PROFILER("Visual elements", as_type='title')
Visuals.__init__(self, self.view.wc, **kwargs)
# ====================== Metadata Storage ======================
if 'metadata' in kwargs.keys():
self.metadata = kwargs['metadata']
else:
self.metadata = {}
# ====================== Rotation Kinetics ======================
if 'rotation' in kwargs.keys():
self.rotation = kwargs['rotation']
else:
self.rotation = 0
# ====================== Carousel Options ======================
if 'carousel_metadata' in kwargs.keys():
self.carousel_metadata = kwargs['carousel_metadata']
else:
self.carousel_metadata = {}
# Carousel Display Method
if 'carousel_display_method' in kwargs.keys():
self._carousel_display_method = kwargs['carousel_display_method']
else:
self._carousel_display_method = 'text'
# Carousel Options
if 'hierarchy_lookup' in self.carousel_metadata:
options = np.asarray(self.carousel_metadata['hierarchy_lookup'])
self._carousel_options_inds = [np.asarray([0])]
for dims in (range(len(options))):
_combs = itertools.combinations(range(len(options)), dims + 1)
_combs = list(_combs)
for ll, comb in enumerate(_combs):
comb = list(comb)
if len(comb) > 1:
if ll == 0:
combs = [np.array(list(comb)) + 1]
else:
combs.append(np.array(list(comb)) + 1)
else:
if ll == 0:
combs = [np.array([comb[0] + 1])]
else:
combs.append(np.array([list(comb)[0] + 1]))
self._carousel_options_inds.append(combs)
self._carousel_options_inds[0] = [self._carousel_options_inds[0]]
options = list(options)
new_options = [np.asarray(['None'])]
for ii in np.arange(len(options)) + 1:
new_options.append(options[ii - 1])
self._carousel_options = np.asarray(new_options)
else:
self._carousel_options_inds = [np.asarray([])]
self._carousel_options = np.asarray(['None'])
# Carousel Choice
if 'carousel_choice' in kwargs.keys():
self._carousel_choice = kwargs['carousel_choice']
self._prev_carousel_choice = kwargs['carousel_choice']
else:
self._carousel_choice = [0, 0]
self._prev_carousel_choice = [0, 0]
# Display Method
self.update_carousel()
# ====================== Timer Creation ======================
def on_timer(*args, **kwargs):
if hasattr(self.view.wc, 'camera'):
self.view.wc.camera.azimuth += self.rotation
self.view.wc.canvas.update()
TIMESCALING = 1 / 1
SHIFT = 0
t = SHIFT + (SHIFT + (args[0].elapsed * TIMESCALING)) % (
(np.shape(self.sources[0].data)[1] / self.metadata['fs']) -
SHIFT)
timepoint = int(t * self.metadata['fs'])
for source in self.sources:
source._update_radius(timepoint=timepoint)
for connect in self.connect:
connect._update_time(timepoint=timepoint)
t_str = str(round(t, 3)) + ' s'
if not hasattr(self, '_time'):
self._time = Text(t_str,
parent=self.view.canvas.scene,
color='white')
else:
self._time.text = t_str
self._time.anchors = ('right', 'bottom')
self._time.font_size = self.view.canvas.size[1] // 200
self._time.pos = (49) * self.view.canvas.size[0] // 50, (
19) * self.view.canvas.size[1] // 20
self._time.update()
kw = dict(connect=on_timer,
app=CONFIG['VISPY_APP'],
interval='auto',
iterations=-1)
self._app_timer = app.Timer(**kw)
self._app_timer.start()
# ====================== Ui interactions ======================
UiElements.__init__(self) # GUI interactions
PROFILER("Ui interactions")
self._shpopup.set_shortcuts(self.sh) # shortcuts dict
# ====================== Cameras ======================
# Main camera :
self.view.wc.camera = self._camera
self._vbNode.parent = self.view.wc.scene
self.atlas.camera = self._camera
self.roi.camera = self._camera
self.atlas._csize = self.view.canvas.size
self.atlas.rotate('top')
self.atlas.camera.set_default_state()
PROFILER("Cameras creation")
# ====================== Colorbar ======================
camera = viscam.PanZoomCamera(rect=(-.2, -2.5, 1, 5))
EngramCbar.__init__(self, camera)
PROFILER("Colorbar and panzoom creation")
self.background_color(bgcolor)
# ====================== Shortcuts ======================
EngramShortcuts.__init__(self, self.cbqt.cbviz._canvas)
PROFILER("Set engram shortcuts")
self._fcn_on_load()
PROFILER("Functions on load")
