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EBR-35: comment connectivity notebook cell #66

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Apr 2, 2024
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EBR-35: comment connectivity notebook cell #66

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37 changes: 17 additions & 20 deletions notebooks/Connectivity.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -14,33 +14,17 @@
"tags": []
},
"outputs": [],
"source": [
"from tvbwidgets.api import ConnectivityWidgetReact\n",
"from tvb.datatypes.connectivity import Connectivity\n",
"\n",
"connectivity = Connectivity.from_file() # defaults to connectivy_76.zip\n",
"\n",
"\n",
"wid = ConnectivityWidgetReact(connectivity=connectivity)\n",
"wid"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from tvbwidgets.api import ConnectivityWidget\n",
"from tvb.datatypes.connectivity import Connectivity\n",
"import pyvista as pv\n",
"import numpy as np\n",
"pv.set_jupyter_backend('pythreejs')\n",
"pv.set_jupyter_backend(\"pythreejs\")\n",
"\n",
"conn = Connectivity.from_file() # defaults to connectivy_76.zip\n",
"conn.configure()\n",
"\n",
"wid = ConnectivityWidget(conn, default_active_tab='viewers') # default_active_tab can be any value between 'viewers'|'operations'|'both'\n",
"wid = ConnectivityWidget(conn, default_active_tab='viewers', width=500, height=500) # default_active_tab can be any value between 'viewers'|'operations'|'both'\n",
"\n",
"display(wid)"
]
Expand All @@ -63,7 +47,20 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
"source": [
"# Using the React Connectivity widget may lead to Jupyter Lab freezing or crashing.\n",
"# If you choose to use it, we recommend to run it in Mozilla Firefox web browser.\n",
"\n",
"\n",
"# from tvbwidgets.api import ConnectivityWidgetReact\n",
"# from tvb.datatypes.connectivity import Connectivity\n",
"\n",
"# connectivity = Connectivity.from_file() # defaults to connectivy_76.zip\n",
"\n",
"\n",
"# wid = ConnectivityWidgetReact(connectivity=connectivity)\n",
"# wid"
]
}
],
"metadata": {
Expand All @@ -82,7 +79,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.9.18"
}
},
"nbformat": 4,
Expand Down
22 changes: 10 additions & 12 deletions tvbwidgets/ui/connectivity_ipy/connectivity_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,8 +109,10 @@ def on_ctx_change(value):

class Connectivity3DViewer(ipywidgets.VBox):

def __init__(self, **kwargs):
def __init__(self, width, height, **kwargs):
self.output = PyVistaOutput()
self.output.plotter.window_size = [width, height]
self.output.plotter.set_background("darkgrey")

super(Connectivity3DViewer, self).__init__([self.output], *kwargs)

Expand All @@ -120,7 +122,7 @@ def __init__(self, **kwargs):
def __init_view_connectivity(self):
self.output.plotter.clear()
points, edges = self.__add_actors()
points_toggle, edges_toggle, labels_toggle = self.__init_controls()
points_toggle, edges_toggle = self.__init_controls()

def on_change_points(change):
if change['new']:
Expand All @@ -140,12 +142,10 @@ def on_change_edges(change):

edges_toggle.observe(on_change_edges, 'value')

window_controls = self.output.get_window_controls()

self.children = [
ipywidgets.HBox(children=(
points_toggle, edges_toggle, labels_toggle)),
window_controls,
points_toggle, edges_toggle)),
self.output]
self.output.display_actor(points)
self.output.display_actor(edges)
Expand All @@ -159,9 +159,7 @@ def __init_controls(self):
description='Edges',
)

labels_toggle = ipywidgets.ToggleButton(value=False,
description='Labels')
return points_toggle, edges_toggle, labels_toggle
return points_toggle, edges_toggle

def __add_actors(self):
plotter = self.output.plotter
Expand Down Expand Up @@ -197,11 +195,11 @@ def __extract_edges(self):


class ConnectivityViewers(ipywidgets.Accordion):
def __init__(self, **kwargs):
def __init__(self, width, height, **kwargs):
super().__init__(**kwargs)
self.children = [
Connectivity2DViewer(),
Connectivity3DViewer()
Connectivity3DViewer(width, height)
]
self.set_title(0, '2D Connectivity Matrix viewer')
self.set_title(1, '3D Connectivity viewer')
Expand Down Expand Up @@ -235,7 +233,7 @@ def get_connectivity(self, gid=None):
return None
return conn[0]

def __init__(self, connectivity, default_active_tab='both', **kwargs):
def __init__(self, connectivity, default_active_tab='both', width=500, height=500, **kwargs):

style = self.DEFAULT_BORDER
super().__init__(**kwargs, layout=style)
Expand All @@ -246,7 +244,7 @@ def __init__(self, connectivity, default_active_tab='both', **kwargs):
viewers_visible = default_active_tab in ['both', 'viewers']
operations_visible = default_active_tab in ['both', 'operations']

self.viewers_tab = ConnectivityViewers()
self.viewers_tab = ConnectivityViewers(width, height)
self.viewers_tab.layout.display = viewers_visible and 'inline-block' or 'none'
self.operations_tab = ConnectivityOperations()
self.operations_tab.layout.display = operations_visible and 'inline-block' or 'none'
Expand Down
35 changes: 0 additions & 35 deletions tvbwidgets/ui/connectivity_ipy/outputs_3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
#
# (c) 2022-2023, TVB Widgets Team
#
import ipywidgets

from tvbwidgets.ui.connectivity_ipy.config import ConnectivityConfig
from tvbwidgets.ui.connectivity_ipy.exceptions import UnknownOutputException
Expand Down Expand Up @@ -42,40 +41,6 @@ def update_plot(self):
self.clear_output(wait=True)
self.plotter.show()

def get_window_controls(self):
height = ipywidgets.IntSlider(
value=self.CONFIG.size[1],
min=50,
max=1500,
step=1,
orientation='horizontal',
description='Plot height',
continuous_update=False,
)
width = ipywidgets.IntSlider(
value=self.CONFIG.size[0],
min=50,
max=1500,
step=1,
orientation='horizontal',
description='Plot width',
continuous_update=False,
)

self.plotter.window_size = [width.value, height.value]

def on_change_height(value):
self.plotter.window_size = [width.value, value['new']]
self.update_plot()

def on_change_width(value):
self.plotter.window_size = [value['new'], height.value]
self.update_plot()

height.observe(on_change_height, 'value')
width.observe(on_change_width, 'value')
return ipywidgets.HBox(children=(width, height))


def output_3d_factory(output_type):
"""Factory function for a custom 3d output"""
Expand Down
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