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AnthonyAndroulakisAnthonyAndroulakis
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feat(graph): add afni.ipynb notebook example
Add the afni.ipynb notebook example, which includes the following changes: - add `Graph` traitlet class - add `nv.graph` - change `file_serializer` to accept null - add `pairedImgData` option to volumes
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‎examples/afni.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "8ac54f8d-2d2c-4e57-a8a1-a1a1463b6451",
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"metadata": {},
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"source": [
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"# Import necessary modules"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "e57b7f74-2402-4580-a3c9-bd1dbb3b8cdc",
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"metadata": {},
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"outputs": [],
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"source": [
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"import asyncio\n",
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"import pathlib\n",
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"\n",
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"import ipywidgets as widgets\n",
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"from IPython.display import display\n",
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"\n",
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"import ipyniivue\n",
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"from ipyniivue import NiiVue, ShowRender, SliceType, download_dataset"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b000ac63-b5b8-4258-b1be-e83868675c25",
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"metadata": {},
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"source": [
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"# Download required data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "8f176e83",
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"metadata": {},
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"outputs": [],
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"source": [
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"DATA_FOLDER = pathlib.Path(ipyniivue.__file__).parent / \"images\"\n",
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"\n",
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"download_dataset(\n",
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" api_url=\"https://niivue.com/demos/images/\",\n",
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" dest_folder=DATA_FOLDER,\n",
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" files=[\n",
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" \"example4d+orig.HEAD\",\n",
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" \"example4d+orig.BRIK.gz\",\n",
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" ],\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "a3678fb5-65b1-4528-9a74-d7f27c62c8df",
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"metadata": {},
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"source": [
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"# Create the NiiVue widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a873dc99-8c09-4518-a053-c6a4720aff8d",
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"metadata": {},
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"outputs": [],
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"source": [
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"nv = NiiVue()\n",
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"\n",
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"nv.set_radiological_convention(False)\n",
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"nv.set_slice_type(SliceType.MULTIPLANAR)\n",
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"nv.opts.multiplanar_show_render = ShowRender.ALWAYS\n",
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"\n",
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"# Configure graph values\n",
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"nv.graph.auto_size_multiplanar = True\n",
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"nv.graph.normalize_values = False\n",
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"nv.graph.opacity = 1.0\n",
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"\n",
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"# Load 4D volume with paired HEAD and BRIK files\n",
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"nv.load_volumes(\n",
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" [\n",
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" {\n",
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" \"path\": DATA_FOLDER / \"example4d+orig.HEAD\",\n",
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" \"paired_img_path\": DATA_FOLDER / \"example4d+orig.BRIK.gz\",\n",
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" \"colormap\": \"gray\",\n",
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" \"opacity\": 1.0,\n",
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" \"visible\": True,\n",
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" },\n",
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" ]\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "dd0e9aee-0bdb-4eba-829c-e6e5acd68835",
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"metadata": {},
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"source": [
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"# Create other buttons/checkboxes"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "3fd88e96-ca86-4b36-92eb-1e1f2d80f8ed",
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"metadata": {},
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"outputs": [],
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"source": [
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"display_frame = widgets.Label(value=\"Volume: 0\")\n",
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"\n",
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"normalize_checkbox = widgets.Checkbox(\n",
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" value=False,\n",
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" description=\"Normalize Graph\",\n",
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")\n",
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"\n",
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"prev_button = widgets.Button(description=\"Back\")\n",
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"next_button = widgets.Button(description=\"Forward\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "111a97d2-714e-47ae-81b8-80c44f6726a9",
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"metadata": {},
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"source": [
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"# Implement the callbacks"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "167128f8-a16a-43bd-803f-da10f08c0d4d",
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"metadata": {},
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"outputs": [],
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"source": [
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"def on_normalize_change(change):\n",
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" \"\"\"Normalize graph.\"\"\"\n",
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" nv.graph.normalize_values = change[\"new\"]\n",
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"\n",
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"\n",
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"normalize_checkbox.observe(on_normalize_change, names=\"value\")\n",
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"\n",
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"\n",
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"def on_prev_button_clicked(b):\n",
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" \"\"\"Decrement the frame index.\"\"\"\n",
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" if nv.volumes:\n",
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" current_frame = nv.volumes[0].frame4D\n",
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" new_frame = max(current_frame - 1, 0)\n",
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" nv.volumes[0].frame4D = new_frame\n",
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" display_frame.value = f\"Volume: {new_frame}\"\n",
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"\n",
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"\n",
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"def on_next_button_clicked(b):\n",
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" \"\"\"Increment the frame index.\"\"\"\n",
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" if nv.volumes:\n",
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" current_frame = nv.volumes[0].frame4D\n",
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" n_frames = nv.volumes[0].n_frame4D\n",
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" new_frame = min(current_frame + 1, n_frames - 1)\n",
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" nv.volumes[0].frame4D = new_frame\n",
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" display_frame.value = f\"Volume: {new_frame}\"\n",
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"\n",
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"\n",
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"prev_button.on_click(on_prev_button_clicked)\n",
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"next_button.on_click(on_next_button_clicked)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b310d908-6f11-4d66-83fa-117af002799e",
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"metadata": {},
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"source": [
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"# Create animate button"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "24726cb0-0d09-4e98-a16c-630d3b746cd3",
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"metadata": {},
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"outputs": [],
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"source": [
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"animate_button = widgets.Button(description=\"Animate\")\n",
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"\n",
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"animation_running = False\n",
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"animation_task = None\n",
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"\n",
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"\n",
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"async def animate_frames():\n",
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" \"\"\"Animation loop.\"\"\"\n",
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" global animation_running\n",
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" if not nv.volumes:\n",
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" return\n",
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" n_frames = nv.volumes[0].n_frame4D\n",
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" try:\n",
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" while animation_running:\n",
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" current_frame = nv.volumes[0].frame4D\n",
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" current_frame = (current_frame + 1) % n_frames\n",
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" nv.volumes[0].frame4D = current_frame\n",
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" display_frame.value = f\"Volume: {current_frame}\"\n",
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" await asyncio.sleep(0.1)\n",
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" except asyncio.CancelledError:\n",
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" pass\n",
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"\n",
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"\n",
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"def on_animate_button_clicked(b):\n",
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" \"\"\"Define 'Animate' button click handler.\"\"\"\n",
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" global animation_running, animation_task\n",
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" if not animation_running:\n",
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" # Start animation\n",
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" animation_running = True\n",
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" animate_button.description = \"Stop\"\n",
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" # Schedule the animation coroutine and store the future\n",
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" animation_task = asyncio.ensure_future(animate_frames())\n",
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" else:\n",
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" # Stop animation\n",
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" animation_running = False\n",
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" animate_button.description = \"Animate\"\n",
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" # Cancel the running task if it's active\n",
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" if animation_task is not None:\n",
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" animation_task.cancel()\n",
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" animation_task = None\n",
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"\n",
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"\n",
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"animate_button.on_click(on_animate_button_clicked)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "5f6f5a15-6b36-4312-b735-10e185900c19",
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"metadata": {},
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"source": [
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"# Reset frame index on image loaded"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "71ba69a0-6fe0-48a7-a03b-29822e24d676",
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"metadata": {},
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"outputs": [],
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"source": [
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"@nv.on_image_loaded\n",
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"def update_number_of_frames(volume):\n",
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" \"\"\"Reset to first frame.\"\"\"\n",
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" nv.volumes[0].frame4D = 0\n",
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" display_frame.value = \"Volume: 0\""
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]
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},
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{
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"cell_type": "markdown",
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"id": "906aee0a-cb57-46b6-9808-a8ac5443a408",
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"metadata": {},
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"source": [
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"# Display all"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "44999f74-851a-40c7-aee1-84a65aeb69b0",
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"metadata": {},
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"outputs": [],
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"source": [
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"controls = widgets.HBox(\n",
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" [\n",
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" normalize_checkbox,\n",
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" prev_button,\n",
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" next_button,\n",
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" animate_button,\n",
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" ]\n",
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")\n",
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"\n",
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"display(widgets.VBox([controls, display_frame, nv]))"
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]
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}
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],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎js/types.ts‎

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@@ -24,9 +24,30 @@ type LUT = {
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labels?: string[];
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};
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type Graph = {
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LTWH: number[];
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opacity: number;
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vols: number[];
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autoSizeMultiplanar: boolean;
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normalizeValues: boolean;
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isRangeCalMinMax: boolean;
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plotLTWH?: number[];
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backColor?: number[];
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lineColor?: number[];
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textColor?: number[];
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lineThickness?: number;
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gridLineThickness?: number;
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lineAlpha?: number;
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lines?: number[][];
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selectedColumn?: number;
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lineRGB?: number[][];
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};
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export type VolumeModel = AnyModel<{
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path: File;
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id: string;
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paired_img_path: File;
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name: string;
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colormap: string;
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opacity: number;
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colormap_label: LUT;
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colormap_invert: boolean;
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n_frame4D: number | null;
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}>;
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export type MeshModel = AnyModel<{
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draw_lut: LUT;
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draw_opacity: number;
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draw_fill_overwrites: boolean;
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graph: Graph;
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}>;
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// Custom message datas

‎js/volume.ts‎

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@@ -103,12 +103,20 @@ async function create_volume(
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const idx = nv.getVolumeIndexByID(vmodel.get("id"));
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volume = nv.volumes[idx];
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} else {
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let pairedImgData = null;
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const pairedImg = vmodel.get("paired_img_path").data;
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if (pairedImg !== null) {
110+
pairedImgData = pairedImg.buffer as ArrayBuffer;
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}
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console.log("pairedImgData", pairedImgData);
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106114
volume = await niivue.NVImage.new(
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vmodel.get("path").data.buffer as ArrayBuffer, // dataBuffer
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vmodel.get("path").name, // name
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vmodel.get("colormap"), // colormap
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vmodel.get("opacity"), // opacity
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null, // pairedImgData
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pairedImgData, // pairedImgData
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vmodel.get("cal_min") ?? Number.NaN, // cal_min
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vmodel.get("cal_max") ?? Number.NaN, // cal_max
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true, // trustCalMinMax
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vmodel.set("id", volume.id);
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vmodel.set("name", volume.name);
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vmodel.set("n_frame4D", volume.nFrame4D ?? null);
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vmodel.save_changes();
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// Handle changes to the volume properties

‎js/widget.ts‎

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@@ -95,6 +95,15 @@ function attachModelEventHandlers(
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nv.drawFillOverwrites = model.get("draw_fill_overwrites");
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});
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model.on("change:graph", () => {
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const graphData = model.get("graph");
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for (const [key, value] of Object.entries(graphData)) {
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// biome-ignore lint/suspicious/noExplicitAny: Update graph vals, only clear out old vals when needed
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(nv.graph as any)[key] = value;
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}
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nv.updateGLVolume();
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});
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// Handle any message directions from the nv object.
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model.on(
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"msg:custom",
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model.off("change:clip_plane_depth_azi_elev");
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model.off("change:draw_lut");
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model.off("change:draw_opacity");
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model.off("change:change:draw_fill_overwrites");
588+
model.off("change:draw_fill_overwrites");
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model.off("change:graph");
580590
};
581591
},
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async render({ model, el }: { model: Model; el: HTMLElement }) {

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