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Merge pull request #176 from AnthonyAndroulakis/afni
Add afni.ipynb notebook example
2 parents 2017312 + 077b2b3 commit 00d0a48

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‎docs/source/api.rst‎

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API Documentation
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=================
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.. autoclass:: ipyniivue.widget.NiiVue
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.. autoclass:: ipyniivue.NiiVue
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: ipyniivue.widget.Volume
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.. autoclass:: ipyniivue.Volume
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: ipyniivue.widget.Mesh
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.. autoclass:: ipyniivue.Mesh
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: ipyniivue.widget.MeshLayer
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: ipyniivue.traits.ColorMap
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: ipyniivue.traits.LUT
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.. autoclass:: ipyniivue.MeshLayer
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/enums.rst‎

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Enums
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=====
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.. currentmodule:: ipyniivue.constants
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.. currentmodule:: ipyniivue
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.. autoclass:: DragMode
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:members:

‎docs/source/index.rst‎

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install
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api
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options
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traits
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enums
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contributing

‎docs/source/traits.rst‎

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Traits
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======
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.. currentmodule:: ipyniivue
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.. autoclass:: ColorMap
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: LUT
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:members:
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:undoc-members:
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:show-inheritance:
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.. autoclass:: Graph
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:members:
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:undoc-members:
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:show-inheritance:

‎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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}

‎examples/mesh.matcap.ipynb‎

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"\n",
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"# Matcaps\n",
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"download_dataset(\n",
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" api_url=\"https://api.github.com/repos/niivue/niivue/contents/packages/niivue/demos/matcaps\",\n",
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" api_url=\"https://niivue.com/demos/matcaps\",\n",
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" dest_folder=DATA_FOLDER / \"matcaps\",\n",
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" files=[\n",
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" \"Shiny.jpg\",\n",
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" \"Cortex.jpg\",\n",
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" \"Cream.jpg\",\n",
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" \"Fuzzy.jpg\",\n",
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" \"Peach.jpg\",\n",
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" \"Plastic.jpg\",\n",
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" \"Gold.jpg\",\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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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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