Fix the grid_3d notebook

docs/notebooks/observer/bolometer.ipynb

@@ -41,7 +41,7 @@
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    "The list of instances :obj:`~cherab.tools.observers.bolometry.BolometerCamera` are loaded from the ``\"bolometer\"`` IDS."
+    "The list of instances :obj:`~cherab.tools.observers.bolometry.BolometerCamera` are loaded from the `bolometer IDS <https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/bolometer.html>`__."
    ]
   },
   {
@@ -157,7 +157,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.3"
+   "version": "3.14.6"
   }
  },
  "nbformat": 4,

docs/notebooks/plasma/equilibrium.ipynb → docs/notebooks/plasma/1_equilibrium.ipynb

@@ -48,7 +48,8 @@
    "metadata": {},
    "source": [
     "## Load the equilibrium data\n",
-    "The equilibrium information is loaded from the IMAS `equilibrium` IDS."
+    "\n",
+    "The equilibrium information is loaded from the IMAS [equilibrium IDS](https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/equilibrium.html)."
    ]
   },
   {

docs/notebooks/plasma/edge_plasma.ipynb → docs/notebooks/plasma/2_edge_plasma.ipynb

@@ -137,7 +137,7 @@
     "\n",
     "### Select grid subset\n",
     "\n",
-    "In \"edge_profiles\" IDS, there are multiple grid subsets defined.\n",
+    "In [edge_profiles IDS](https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/edge_profiles.html), there are multiple grid subsets defined.\n",
     "Here, we choose the `\"cells\"` subset to visualize the edge plasma profiles."
    ]
   },

docs/notebooks/plasma/full_plasma.ipynb → docs/notebooks/plasma/3_full_plasma.ipynb

@@ -191,9 +191,9 @@
     }
    },
    "source": [
-    "The instance of the :obj:`~cherab.core.Plasma` class is created by loading the ``core_profiles`` and ``edge_profiles`` IDSs from the IMAS database.\n",
+    "The instance of the :obj:`~cherab.core.Plasma` class is created by loading the `core_profiles <https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/core_profiles.html>`__ and `edge_profiles <https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/edge_profiles.html>`__ IDSs from the IMAS database.\n",
     "\n",
-    "The equilibrium information is automatically loaded from the ``equilibrium`` IDS if not already provided."
+    "The equilibrium information is automatically loaded from the `equilibrium <https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/equilibrium.html>`__ IDS if not already provided."
    ]
   },
   {

docs/notebooks/plasma/emission.ipynb → docs/notebooks/plasma/4_emission.ipynb

@@ -114,7 +114,7 @@
    "source": [
     "## Load full plasma from IMAS\n",
     "\n",
-    "The details of loading a full plasma are covered in the [Full Plasma](./full_plasma.ipynb) notebook.\n",
+    "The details of loading a full plasma are covered in the [Full Plasma](./3_full_plasma.ipynb) notebook.\n",
     "Here we simply load a plasma from an IMAS jintrac dataset."
    ]
   },

docs/notebooks/radiation/grid_3d.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# 3D Grid Visualization\n",
     "\n",
-    "This notebook demonstrates how to load and visualize a 3-D grid from Generalized Grid Description (GGD) in IMAS.\n",
+    "This notebook demonstrates how to load and visualize a 3-D grid from [Generalized Grid Description (GGD) in IMAS](https://imas-data-dictionary.readthedocs.io/en/latest/ggd_guide/doc.html).\n",
     "\n",
     "The example test data was calculated by JOREK for an ITER disruption scenario."
    ]
@@ -51,10 +51,18 @@
     "path = iter_jorek()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "Retrieve the GGD data belonging to the [radiation IDS](https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/radiation.html)."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,7 +73,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "6",
    "metadata": {},
    "source": [
     "Show the grid specification"
@@ -74,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -90,7 +98,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "8",
    "metadata": {},
    "source": [
     "## Visualize the cross-section of the grid\n",
@@ -101,7 +109,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -133,16 +141,16 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "10",
    "metadata": {},
    "source": [
-    "Plot center points of cells\n"
+    "Plot center points of cells"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "11",
    "metadata": {
     "tags": [
      "nbsphinx-thumbnail"
@@ -196,7 +204,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "12",
    "metadata": {},
    "source": [
     "## Cut out quarter of the torus"
@@ -205,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -214,7 +222,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "14",
    "metadata": {},
    "source": [
     "Visualize the 3D grid in a quarter of the torus.\n",
@@ -224,20 +232,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
     "import plotly.graph_objects as go\n",
     "from plotly import io\n",
     "\n",
-    "io.renderers.default = \"notebook\""
+    "io.renderers.default = \"png\""
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,7 +279,7 @@
     "\n",
     "# Customize edge appearance here.\n",
     "edge_color = \"black\"\n",
-    "edge_width = 2\n",
+    "edge_width = 1.5\n",
     "\n",
     "# Convert edge index pairs to line segments separated by NaN for Plotly.\n",
     "edge_xyz = verts[boundary_edges]\n",
@@ -314,13 +322,19 @@
     "\n",
     "fig.update_layout(\n",
     "    title=\"Quarter-torus tetrahedral mesh\",\n",
+    "    width=500,\n",
+    "    height=500,\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=40),\n",
+    "    margin=dict(l=0, r=0, b=0, t=30),\n",
+    "    scene_camera=dict(\n",
+    "        eye=dict(x=0.0, y=-2.0, z=0.25),\n",
+    "    ),\n",
+    "    template=\"plotly_dark\",\n",
     ")"
    ]
   }

docs/notebooks/radiation/3d_radiation.ipynb → docs/notebooks/radiation/radiation_3d.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# 3D Radiation Emitter\n",
     "\n",
-    "This notebook demonstrates how to create a 3D radiation emitter from IMAS radiation IDS.\n",
+    "This notebook demonstrates how to create a 3D radiation emitter from IMAS [radiation IDS](https://imas-data-dictionary.readthedocs.io/en/latest/generated/ids/radiation.html).\n",
     "\n",
     "The example test data was calculated by JOREK for an ITER disruption scenario."
    ]

docs/source/examples.md

@@ -9,7 +9,6 @@ Each notebook is designed to showcase specific functionalities and provide pract
 .. nbgallery::
     :name: plasma-gallery
     :glob:
-    :reversed:
 
     notebooks/plasma/*
 ```
@@ -20,7 +19,6 @@ Each notebook is designed to showcase specific functionalities and provide pract
 .. nbgallery::
     :name: radiation-gallery
     :glob:
-    :reversed:
 
     notebooks/radiation/*
 ```
@@ -31,7 +29,6 @@ Each notebook is designed to showcase specific functionalities and provide pract
 .. nbgallery::
     :name: observer-gallery
     :glob:
-    :reversed:
 
     notebooks/observer/*
 ```
@@ -42,7 +39,6 @@ Each notebook is designed to showcase specific functionalities and provide pract
 .. nbgallery::
     :name: misc-gallery
     :glob:
-    :reversed:
 
     notebooks/misc/*
 ```

src/cherab/imas/plasma/core.py

@@ -89,9 +89,6 @@ def load_core_plasma(
         Alternative ``psi_norm(rho_tor_norm)`` interpolator.
         Used only if ``psi`` is missing in the core grid. By default None.
         Obtained from the ``equilibrium`` IDS.
-    mask
-        Mask function used for blending: ``(1 - mask) * f_edge + mask * f_core``.
-        By default, uses `~cherab.tools.equilibrium.efit.EFITEquilibrium`'s `inside_lcfs`.
     time_threshold
         Maximum allowed difference between the requested time and the nearest
         available time, by default `numpy.inf`.