✨ Enhance plasma and radiation data handling with 3D visualization support

.binder/environment.yml

@@ -4,3 +4,4 @@ channels:
 dependencies:
   - cherab-imas
   - ultraplot
+  - plotly

CHANGELOG.md

@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.5.0] - Unreleased
+## [0.5.0] - 2026-06-24
 
 ### Added
 
@@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add notebook.link environment configuration for interactive notebook demos for future use in documentation.
 - Add Fourier-Bezier reconstruction module and integrate it into math utilities
 - Add JINTRAC/JOREK dataset fixtures and interpolator cache tests
+- Add radiation data loading modules and emitter initialization
+- Add JOREK-based 3D radiation emitter visualization notebook
+- Add 3D grid visualization notebook for ITER JOREK data
+- Add unit tests for `get_ids_time_slice` function with fallback handling
 
 ### Changed
 
@@ -25,11 +29,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Enhance interpolator caching behavior in grid classes and add subset validation in `load_unstruct_grid_2d_extended`
 - Update pixi channels and `doc-serve` task to support normal conda-forge settings and dynamic port arguments
 - Refactor dataset handling to make `pooch` a required dependency and simplify cache directory handling
+- Implement re-slicing of IDS via IMAS memory backend with fallback handling
+- Update `environment.yml` to include additional dependencies for binder
+- Update docstrings for interpolator cache parameters in grid classes
 
 ### Fixed
 
 - Ensure bolometer dataset cache directories are created before use
 - Fix total power calculation and exception handling in the emission notebook workflow
+- Fix charge type conversion in `load_core_plasma` function
+- Fix grid subset handling in plasma loading functions
+- Ensure coefficients array is C-contiguous in `FourierBezierConstructor`
 
 ### Removed
 

docs/notebooks/radiation/3d_radiation.ipynb

@@ -0,0 +1,356 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# 3D Radiation Emitter\n",
+    "\n",
+    "This notebook demonstrates how to create a 3D radiation emitter from IMAS radiation IDS.\n",
+    "\n",
+    "The example test data was calculated by JOREK for an ITER disruption scenario."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import ultraplot as uplt\n",
+    "from imas import DBEntry\n",
+    "from raysect.optical import World\n",
+    "from rich import print as rprint\n",
+    "from rich.table import Table\n",
+    "\n",
+    "from cherab.core.math import sample3d_grid\n",
+    "from cherab.imas.datasets import iter_jorek\n",
+    "from cherab.imas.emitter import load_radiation_emitter\n",
+    "\n",
+    "# Set dark background for plots\n",
+    "uplt.rc.style = \"dark_background\"\n",
+    "\n",
+    "TOGW = 1e-9  # [W] -> [GW]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## Retrieve ITER JOREK sample data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "path = iter_jorek()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "## Create 3D radiation emitter from IMAS IDS"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "world = World()\n",
+    "emitter = load_radiation_emitter(\n",
+    "    path,\n",
+    "    \"r\",\n",
+    "    time=0.0042853,\n",
+    "    parent=world,\n",
+    "    interpolator_cache=\"disk\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6",
+   "metadata": {},
+   "source": [
+    "## Visualize the emitter in 2D\n",
+    "\n",
+    "Sample 2D visualization of the radiation function at all toroidal angles."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "R_MIN, R_MAX = 4.0, 8.5\n",
+    "Z_MIN, Z_MAX = -4.5, 4.4\n",
+    "RES = 0.01  # resolution of grid in [m]\n",
+    "n_r = round((R_MAX - R_MIN) / RES) + 1\n",
+    "n_z = round((Z_MAX - Z_MIN) / RES) + 1\n",
+    "dr, dz = (R_MAX - R_MIN) / (n_r - 1), (Z_MAX - Z_MIN) / (n_z - 1)\n",
+    "\n",
+    "# (r, z) coordinates at phi=0\n",
+    "r_pts = np.linspace(R_MIN, R_MAX, n_r, endpoint=True)\n",
+    "z_pts = np.linspace(Z_MIN, Z_MAX, n_z, endpoint=True)\n",
+    "\n",
+    "# Toroidal angles to sample the radiation function at\n",
+    "n_phi = 64\n",
+    "d_phi = 360 / n_phi\n",
+    "eps = 1e-6  # small offset to avoid sampling at exactly 0 and 360 degrees\n",
+    "phis = np.linspace(0 + d_phi + eps, 360 + d_phi - eps, n_phi + 1, endpoint=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "n_phi = len(phis)\n",
+    "rad = np.zeros((n_r, n_z, n_phi), dtype=float)\n",
+    "for i, j, k in np.ndindex(n_r, n_z, n_phi):\n",
+    "    rad[i, j, k] = emitter.material.radiation_function(\n",
+    "        r_pts[i] * np.cos(np.deg2rad(phis[k])),\n",
+    "        r_pts[i] * np.sin(np.deg2rad(phis[k])),\n",
+    "        z_pts[j],\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9",
+   "metadata": {},
+   "source": [
+    "### Cross-sectional view of the radiation\n",
+    "\n",
+    "2D poloidal cross-sections of the radiation function at two toroidal angles."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phi_selected = [95, 330]  # toroidal angles to visualize\n",
+    "\n",
+    "# Get the maximum value\n",
+    "vmax = -np.inf\n",
+    "for phi in phi_selected:\n",
+    "    i_phi = np.argmin(np.abs(phis - phi))\n",
+    "    vmax = max(vmax, np.max(rad[:, :, i_phi] * TOGW))\n",
+    "\n",
+    "\n",
+    "fig, axs = uplt.subplots(ncols=len(phi_selected), spanx=False)\n",
+    "for i, phi in enumerate(phi_selected):\n",
+    "    i_phi = np.argmin(np.abs(phis - phi))\n",
+    "\n",
+    "    im = axs[i].pcolormesh(\n",
+    "        r_pts,\n",
+    "        z_pts,\n",
+    "        rad[:, :, i_phi].T * TOGW,\n",
+    "        shading=\"auto\",\n",
+    "        cmap=\"inferno\",\n",
+    "        discrete=False,\n",
+    "        vmax=vmax,\n",
+    "        vmin=0,\n",
+    "    )\n",
+    "    axs[i].format(\n",
+    "        axesedgecolor=f\"C{i}\",\n",
+    "        urtitle=f\"{phis[i_phi]:.1f}°\",\n",
+    "        titleborder=False,\n",
+    "        aspect=\"equal\",\n",
+    "        xlabel=\"$R$ [m]\",\n",
+    "        ylabel=\"$Z$ [m]\",\n",
+    "    )\n",
+    "\n",
+    "fig.colorbar(\n",
+    "    im,\n",
+    "    ax=axs,\n",
+    "    loc=\"b\",\n",
+    "    label=\"[GW/m³]\",\n",
+    "    shrink=0.5,\n",
+    "    tickminor=True,\n",
+    ");"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "11",
+   "metadata": {},
+   "source": [
+    "### Z-integrated X-Y projection\n",
+    "\n",
+    "The radiation distribution is integrated along the z-axis and projected onto the X-Y plane.\n",
+    "\n",
+    "Each toroidal angle at which the cross-section was plotted above is also shown as a colored line in the X-Y projection."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "12",
+   "metadata": {
+    "tags": [
+     "nbsphinx-thumbnail"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "fig, ax = uplt.subplots(\n",
+    "    proj=\"polar\",\n",
+    "    dpi=150,\n",
+    "    refwidth=4,\n",
+    ")\n",
+    "\n",
+    "im = ax.pcolormesh(\n",
+    "    np.deg2rad(phis),\n",
+    "    r_pts,\n",
+    "    rad.sum(axis=1) * TOGW * dz,\n",
+    "    shading=\"auto\",\n",
+    "    cmap=\"inferno\",\n",
+    "    discrete=False,\n",
+    "    vmin=0,\n",
+    ")\n",
+    "fig.colorbar(\n",
+    "    im,\n",
+    "    ax=ax,\n",
+    "    label=\"[GW/m²]\",\n",
+    "    loc=\"b\",\n",
+    "    shrink=0.35,\n",
+    "    ticks=2,\n",
+    "    tickminor=True,\n",
+    "    orientation=\"horizontal\",\n",
+    "    pad=-15,\n",
+    ")\n",
+    "\n",
+    "for i, phi in enumerate(phi_selected):\n",
+    "    ax.axvline(\n",
+    "        np.deg2rad(phis[np.argmin(np.abs(phis - phi))]),\n",
+    "        color=uplt.set_alpha(f\"C{i}\", 0.5),\n",
+    "        lw=4,\n",
+    "    )\n",
+    "ax.format(\n",
+    "    rmin=r_pts.min(),\n",
+    "    rmax=r_pts.max(),\n",
+    "    rformatter=\"none\",\n",
+    "    r0=r_pts.min() / r_pts.max(),\n",
+    "    thetalocator=30,\n",
+    "    rlabelpos=0,\n",
+    "    rlines=1,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "13",
+   "metadata": {},
+   "source": [
+    "## Visualize the emitter in 3D\n",
+    "\n",
+    "Resample the radiation function between the toroidal angle 270° and 360° (quarter of the torus) in (X, Y, Z) coordinates and visualize the result in 3D.\n",
+    "\n",
+    "To plot 3D data, we use the [plotly](https://plotly.com/python/) library. The 3D radiation distribution is visualized as a volume rendering."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import plotly.graph_objects as go\n",
+    "from plotly import io\n",
+    "\n",
+    "io.renderers.default = \"notebook\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dr = dz = 10e-2\n",
+    "x_pts = np.arange(0, R_MAX, dr)\n",
+    "y_pts = np.arange(0, -R_MAX, -dr)\n",
+    "z_pts = np.arange(Z_MIN, Z_MAX, dz)\n",
+    "X, Y, Z = np.meshgrid(x_pts, y_pts, z_pts)\n",
+    "\n",
+    "rad_xyz = np.zeros((len(x_pts), len(y_pts), len(z_pts)), dtype=float)\n",
+    "for i, j, k in np.ndindex(len(x_pts), len(y_pts), len(z_pts)):\n",
+    "    rad_xyz[i, j, k] = emitter.material.radiation_function(x_pts[i], y_pts[j], z_pts[k])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig = go.Figure(\n",
+    "    data=go.Volume(\n",
+    "        x=X.flatten(),\n",
+    "        y=Y.flatten(),\n",
+    "        z=Z.flatten(),\n",
+    "        value=rad_xyz.flatten(),\n",
+    "        isomin=1e8,\n",
+    "        isomax=rad_xyz.max(),\n",
+    "        opacity=0.1,  # needs to be small to see through all surfaces\n",
+    "        surface_count=21,  # needs to be a large number for good volume rendering\n",
+    "    )\n",
+    ")\n",
+    "fig.update_layout(\n",
+    "    scene=dict(\n",
+    "        xaxis_title=\"X [m]\",\n",
+    "        yaxis_title=\"Y [m]\",\n",
+    "        zaxis_title=\"Z [m]\",\n",
+    "        aspectmode=\"data\",\n",
+    "    ),\n",
+    "    margin=dict(l=0, r=0, b=0, t=0),\n",
+    "    template=\"plotly_dark\",\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "docs",
+   "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": "3.14.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}