Merge pull request #74 from peeplika/WID247

WID-247 - SpaceTimeVisualizer widget

notebooks/ConnectivitySpaceTimeWidget.ipynb

@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Connectivity SpaceTime Widget\n",
+    "Displays a large scale Connectivity split into time slices, based on the delays of passing the signals to adjacent regions.The first slice is the complete weights matrix.<br><br>\n",
+    "This work has been produced as part of GSOC 2024.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from tvb.datatypes.connectivity import Connectivity\n",
+    "from tvbwidgets.ui.spacetime_widget import SpaceTimeVisualizerWidget\n",
+    "conn = Connectivity.from_file() # defaults to connectivy_76.zip\n",
+    "conn.configure()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x = SpaceTimeVisualizerWidget(conn)\n",
+    "x.display()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "tvb-wid",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tvbwidgets/api.py

@@ -9,6 +9,7 @@
 from .ui.connectivity_react.connectivity_widget import ConnectivityWidgetReact
 from .ui.dicom_widget import DicomWidget
 from .ui.phase_plane_widget import PhasePlaneWidget
+from .ui.spacetime_widget import SpaceTimeVisualizerWidget
 from .ui.storage_widget import StorageWidget
 from .ui.head_widget import HeadBrowser, HeadWidget, HeadWidgetConfig
 from .ui.ts.mne_ts_widget import TimeSeriesWidgetMNE

tvbwidgets/tests/test_spacetime_widget.py

@@ -0,0 +1,122 @@
+import pytest
+import numpy as np
+import pythreejs as p3
+import matplotlib
+from ipywidgets import Tab, Output, BoundedFloatText, Text, HBox, HTML
+from tvbwidgets.ui.spacetime_widget import SpaceTimeVisualizerWidget
+from tvb.datatypes.connectivity import Connectivity
+
+matplotlib.use('Agg')
+
+@pytest.fixture
+def connectivity():
+    conn = Connectivity.from_file()
+    conn.configure()
+    return conn
+
+@pytest.fixture
+def wid(connectivity):
+    widget = SpaceTimeVisualizerWidget(connectivity)
+    return widget
+
+def test_display(wid):
+    wid.display()
+    assert isinstance(wid, SpaceTimeVisualizerWidget)
+
+def test_prepare_widget(wid):
+    assert isinstance(wid.hbox, HBox)
+    assert len(wid.hbox.children) == 2
+    assert isinstance(wid.hbox.children[0], Tab)
+    assert isinstance(wid.hbox.children[1], HTML)
+    assert isinstance(wid.tab, Tab)
+    assert len(wid.tab.children) == 2
+    assert isinstance(wid.tab.children[0], Output)
+    assert isinstance(wid.tab.children[1], Output)
+    assert isinstance(wid.renderer, p3.Renderer)
+    assert isinstance(wid.fig, matplotlib.figure.Figure)
+
+def test_prepare_scene(wid):
+    assert isinstance(wid.scene, p3.Scene)
+    assert isinstance(wid.camera, p3.PerspectiveCamera)
+    assert isinstance(wid.light, p3.AmbientLight)
+    assert isinstance(wid.key_light, p3.DirectionalLight)
+    assert isinstance(wid.picker, p3.Picker)
+    assert isinstance(wid.renderer, p3.Renderer)
+
+def test_prepare_slices(wid):
+    assert len(wid.graph_slices) == 7
+    assert wid.graph_slices[0].material.map is not None
+    for i in range(7):
+        assert wid.graph_slices[i] in wid.scene.children
+
+def tests_create_graph_slice(wid):
+    assert wid.graph_slices[0].geometry.height == 7.0
+    assert wid.graph_slices[0].geometry.width == 7.0
+    assert wid.graph_slices[0].geometry.depth == 0.1
+    for i in range(len(wid.graph_slices)):
+        z = -i*3 + 14 if i is 0 else -i*2 + 11 - 0.1*i*i
+        assert wid.graph_slices[i].position == (16.0, 0.0, z)
+
+def test_generate_texture(wid):
+    for i in range(7):
+        texture = wid._generate_texture(i)
+        assert texture.format == "RGBFormat"
+        assert texture.data.shape == (76, 76, 3)
+
+
+def test_generate_colors(wid):
+    colors = wid._generate_colors(wid.connectivity.weights)
+    assert colors is not None
+    assert colors.shape == (76, 76, 3)
+
+def test_prepare_grid(wid):
+    wid._prepare_grid()
+    assert isinstance(wid.grid, p3.Mesh)
+    assert wid.grid.material.map is not None
+    assert wid.grid.material.transparent == True
+    assert wid.grid.position == (0, 0, 0)
+    assert wid.grid.name == "grid"
+    assert wid.grid.scale == (4, 3, 1)
+
+def test_generate_gridlines(wid):
+    grid = wid._generate_gridlines()
+    assert grid.format == "RGBAFormat"
+    assert grid.data.shape == (76*5, 76*5, 4)
+
+def test_prepare_connectivity(wid):
+    i = 2
+    connectivity = wid._prepare_connectivity(2)
+    assert connectivity.shape == (76, 76)
+
+def test_create_matplotlib_graphs(wid):
+    assert len(wid.ims) == 7
+    assert len(wid.fig.axes) == 7
+    assert wid.fig.get_figheight() == 10.0
+    assert wid.fig.get_figwidth() == 14.0
+
+def test_add_options(wid):
+    assert len(wid.options.children) == 4
+    assert isinstance(wid.options.children[0], BoundedFloatText)
+    assert isinstance(wid.options.children[1], BoundedFloatText)
+    assert isinstance(wid.options.children[2], BoundedFloatText)
+    assert isinstance(wid.options.children[3], Text)
+
+    assert wid.options.children[1].description == "from[ms]:"
+    assert wid.options.children[2].description == "to[ms]:"
+    assert wid.options.children[3].description == "selection[ms]:"
+    assert wid.options.children[0].value == 1.0
+    assert wid.options.children[0].description == "Conduction Speed:"
+    assert wid.options.children[1].value == 0.0
+    assert wid.options.children[1].min == 0.0
+    assert wid.options.children[1].max == 153.48574
+    assert wid.options.children[2].value == 153.48574
+    assert wid.options.children[2].min == 0.0
+    assert wid.options.children[2].max == 153.48574
+    assert wid.options.children[3].value == "None"
+
+
+
+
+
+
+