Merge pull request #76 from peeplika/WID247-2

WID-247 ConnectivityMatrixEditor widget

notebooks/ConnectivityMatrixEditor.ipynb

@@ -0,0 +1,87 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Connectivity Matrix Editor Widget\n",
+    "\n",
+    "The connectivity matrix editor lets you edit the connectivity weights or tract_lengths, save the new connectivity, and view saved connectivities. Only 1 quadrant is displayed at a time.<br><br>\n",
+    "This work has been produced as part of GSOC 2024."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from tvbwidgets.ui.connectivity_matrix_editor_widget import ConnectivityMatrixEditor\n",
+    "from tvb.datatypes.connectivity import Connectivity\n",
+    "conn = Connectivity().from_file()   #defaults to connectivity_76.zip\n",
+    "conn.configure()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wid = ConnectivityMatrixEditor(conn, size = None)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wid.display()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# to get the gid of all the saved connectivities\n",
+    "wid.saved_connectivities()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# replace None in the method below with the gid of the connectivity you wish to export\n",
+    "# if no gid is provided it will export the connectivity currently viewed\n",
+    "\n",
+    "wid.get_connectivity(gid=None)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": 4
+}

requirements.txt

@@ -21,3 +21,4 @@ pyunicore>=1.0.0
 traitlets>=5.7.1
 toml
 bokeh
+ipycanvas

tvbwidgets/api.py

@@ -7,6 +7,7 @@
 
 from .ui.connectivity_ipy.connectivity_widget import ConnectivityWidget
 from .ui.connectivity_react.connectivity_widget import ConnectivityWidgetReact
+from .ui.connectivity_matrix_editor_widget import ConnectivityMatrixEditor
 from .ui.dicom_widget import DicomWidget
 from .ui.phase_plane_widget import PhasePlaneWidget
 from .ui.spacetime_widget import SpaceTimeVisualizerWidget

tvbwidgets/tests/test_connectivity_matrix_editor_widget.py

@@ -0,0 +1,130 @@
+# -*- coding: utf-8 -*-
+#
+# "TheVirtualBrain - Widgets" package
+#
+# (c) 2022-2024, TVB Widgets Team
+#
+
+import math
+import pytest
+import numpy as np
+import ipycanvas as canvas
+import ipywidgets as widgets
+from tvb.datatypes.connectivity import Connectivity
+from tvbwidgets.ui.connectivity_matrix_editor_widget import ConnectivityMatrixEditor
+
+@pytest.fixture
+def connectivity():
+    conn = Connectivity.from_file()
+    conn.configure()
+    return conn
+
+@pytest.fixture
+def wid(connectivity):
+    widget = ConnectivityMatrixEditor(connectivity)
+    return widget
+
+def test_display(wid):
+    wid.display()
+    assert isinstance(wid, ConnectivityMatrixEditor)
+
+def test_make_header(wid):
+    assert len(wid.header.children) == 5
+    assert isinstance(wid.header.children[0], widgets.Dropdown)
+    assert isinstance(wid.header.children[1], widgets.Text)
+    assert isinstance(wid.header.children[2], widgets.Button)
+    assert isinstance(wid.header.children[3], widgets.Button)
+    assert isinstance(wid.header.children[4], widgets.Dropdown)
+
+def test_get_quadrant_range(wid):
+    wid._get_quadrant_range(selection = 1)
+    assert wid.from_row == 0
+    assert wid.from_col == 0
+    wid._get_quadrant_range(selection = 2)
+    assert wid.from_row == 38
+    assert wid.from_col == 0
+    wid._get_quadrant_range(selection = 3)
+    assert wid.from_row == 0
+    assert wid.from_col == 38
+    wid._get_quadrant_range(selection = 4)
+    assert wid.from_col == 38
+    assert wid.from_row == 38
+
+def test_prepare_matrices_tab(wid):
+    assert isinstance(wid.weights_matrix, canvas.canvas.MultiCanvas)
+    assert isinstance(wid.tract_lengths_matrix, canvas.canvas.MultiCanvas)
+    assert len(wid.tab.children) == 2
+    assert wid.tab.get_title(0) == "weights"
+    assert wid.tab.get_title(1) == "tract_lengths"
+
+def test_prepare_matrix(wid):
+    assert math.isclose(wid.cell_size, 16.43, abs_tol=0.1)
+    assert math.isclose(wid.weights_matrix.width, 1140, abs_tol=1)
+    assert math.isclose(wid.weights_matrix.height, 912, abs_tol=1)
+    assert math.isclose(wid.tract_lengths_matrix.width, 1140, abs_tol=1)
+    assert math.isclose(wid.tract_lengths_matrix.height, 912, abs_tol=1)
+    assert isinstance(wid.weights_matrix[0], canvas.canvas.Canvas)
+    assert isinstance(wid.weights_matrix[1], canvas.canvas.Canvas)
+    assert isinstance(wid.weights_matrix[2], canvas.canvas.Canvas)
+    assert isinstance(wid.weights_matrix[3], canvas.canvas.Canvas)
+    assert isinstance(wid.weights_matrix[4], canvas.canvas.Canvas)
+    assert isinstance(wid.weights_matrix[5], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[0], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[1], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[2], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[3], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[4], canvas.canvas.Canvas)
+    assert isinstance(wid.tract_lengths_matrix[5], canvas.canvas.Canvas)
+
+def test_generate_color_with_indices(wid, connectivity):
+    color = wid._generate_color(connectivity, i=20, j=38, matrix_name="weights")
+    assert color == 'rgba(102, 121, 123, 1.00)'    
+    color = wid._generate_color(connectivity, i=5, j=70, matrix_name="tract_lengths")
+    assert color == 'rgba(38, 124, 105, 1.00)'
+
+def test_generate_color_with_single_value(wid, connectivity):
+    color = wid._generate_color(connectivity, value = 2, matrix_name="weights")
+    assert color == 'rgba(145, 224, 255, 1.00)' 
+    color = wid._generate_color(connectivity, value = 3, matrix_name = "tract_lengths")
+    assert color == 'rgba(97, 101, 108, 1.00)'
+
+def test_generate_color_with_array_value(wid, connectivity):
+    value = np.array([[1, 2], [2, 3]])
+    colors = wid._generate_color(connectivity, value = value, matrix_name="weights")
+    assert np.allclose(colors, [[[ 61.33333333, 170.66666667,  62.        ],
+                                        [145.        , 224.33333333, 255.        ]],
+                                        [[145.        , 224.33333333, 255.        ],
+                                        [251.        ,  82.        ,  38.        ]]])
+
+    colors = wid._generate_color(connectivity, value = value, matrix_name="tract_lengths")
+    assert np.allclose(colors, [[[101.01176471, 117.04705882, 120.09019608],
+                                  [ 99.03529412, 109.14117647, 114.27058824]],
+                                  [[ 99.03529412, 109.14117647, 114.27058824],
+                                  [ 97.05882353, 101.23529412, 108.45098039]]])
+
+def test_saved_connectivities(wid):
+    conn_list = wid.saved_connectivities()
+    assert conn_list is not None
+    assert isinstance(conn_list, list)
+    assert isinstance(conn_list[0], str)
+
+def test_get_connectivity(wid):
+    conn = wid.get_connectivity()
+    assert isinstance(conn, Connectivity)
+    assert conn == wid.connectivity
+
+def test_on_click_save(wid):
+    wid.save_button.click()
+    assert len(wid.connectivity_history_list) == 2
+
+def test_prepare_new_connectivity(wid):
+    conn = wid._prepare_new_connectivity()
+    assert isinstance(conn, Connectivity)
+    assert wid.new_connectivity.parent_connectivity == wid.connectivity.gid.hex
+    assert wid.new_connectivity.centres.all() == wid.connectivity.centres.all()
+    assert wid.new_connectivity.orientations.all() == wid.connectivity.orientations.all()
+    assert wid.new_connectivity.cortical.all() == wid.connectivity.cortical.all()
+    assert wid.new_connectivity.hemispheres.all() == wid.connectivity.hemispheres.all()
+    assert wid.new_connectivity.areas.all() == wid.connectivity.areas.all()
+    assert wid.new_connectivity.weights.all() == wid.connectivity.weights.all()
+    assert wid.new_connectivity.tract_lengths.all() == wid.connectivity.tract_lengths.all()