From 2b82fdd094dcaf68da49789caa4e19fc90e9340d Mon Sep 17 00:00:00 2001 From: munechika-koyo Date: Thu, 25 Jun 2026 10:39:23 +0200 Subject: [PATCH 1/5] =?UTF-8?q?=F0=9F=90=9B=20Remove=20unnecessary=20:reve?= =?UTF-8?q?rsed:=20option=20from=20nbgallery=20sections=20in=20examples.md?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/source/examples.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/source/examples.md b/docs/source/examples.md index d64a3e5..456db39 100644 --- a/docs/source/examples.md +++ b/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/* ``` From be05bf921aeaa7c011a0bc309b862a8278314685 Mon Sep 17 00:00:00 2001 From: munechika-koyo Date: Thu, 25 Jun 2026 10:45:09 +0200 Subject: [PATCH 2/5] =?UTF-8?q?=F0=9F=9A=9A=20Rename=20notebooks?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/notebooks/plasma/{equilibrium.ipynb => 1_equilibrium.ipynb} | 0 docs/notebooks/plasma/{edge_plasma.ipynb => 2_edge_plasma.ipynb} | 0 docs/notebooks/plasma/{full_plasma.ipynb => 3_full_plasma.ipynb} | 0 docs/notebooks/plasma/{emission.ipynb => 4_emission.ipynb} | 0 .../radiation/{3d_radiation.ipynb => radiation_3d.ipynb} | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename docs/notebooks/plasma/{equilibrium.ipynb => 1_equilibrium.ipynb} (100%) rename docs/notebooks/plasma/{edge_plasma.ipynb => 2_edge_plasma.ipynb} (100%) rename docs/notebooks/plasma/{full_plasma.ipynb => 3_full_plasma.ipynb} (100%) rename docs/notebooks/plasma/{emission.ipynb => 4_emission.ipynb} (100%) rename docs/notebooks/radiation/{3d_radiation.ipynb => radiation_3d.ipynb} (100%) diff --git a/docs/notebooks/plasma/equilibrium.ipynb b/docs/notebooks/plasma/1_equilibrium.ipynb similarity index 100% rename from docs/notebooks/plasma/equilibrium.ipynb rename to docs/notebooks/plasma/1_equilibrium.ipynb diff --git a/docs/notebooks/plasma/edge_plasma.ipynb b/docs/notebooks/plasma/2_edge_plasma.ipynb similarity index 100% rename from docs/notebooks/plasma/edge_plasma.ipynb rename to docs/notebooks/plasma/2_edge_plasma.ipynb diff --git a/docs/notebooks/plasma/full_plasma.ipynb b/docs/notebooks/plasma/3_full_plasma.ipynb similarity index 100% rename from docs/notebooks/plasma/full_plasma.ipynb rename to docs/notebooks/plasma/3_full_plasma.ipynb diff --git a/docs/notebooks/plasma/emission.ipynb b/docs/notebooks/plasma/4_emission.ipynb similarity index 100% rename from docs/notebooks/plasma/emission.ipynb rename to docs/notebooks/plasma/4_emission.ipynb diff --git a/docs/notebooks/radiation/3d_radiation.ipynb b/docs/notebooks/radiation/radiation_3d.ipynb similarity index 100% rename from docs/notebooks/radiation/3d_radiation.ipynb rename to docs/notebooks/radiation/radiation_3d.ipynb From 6d8abba994ccef68c3e6269edde32afc8518f81c Mon Sep 17 00:00:00 2001 From: munechika-koyo Date: Thu, 25 Jun 2026 10:45:26 +0200 Subject: [PATCH 3/5] =?UTF-8?q?=F0=9F=94=A5=20Remove=20obsolete=20mask=20p?= =?UTF-8?q?arameter=20from=20load=5Fcore=5Fplasma=20function?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/cherab/imas/plasma/core.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/cherab/imas/plasma/core.py b/src/cherab/imas/plasma/core.py index 616ad23..ef9c627 100644 --- a/src/cherab/imas/plasma/core.py +++ b/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`. From 5e603fd1fd4a891d551b7bb56379095bcc8bd30b Mon Sep 17 00:00:00 2001 From: munechika-koyo Date: Thu, 25 Jun 2026 14:04:56 +0200 Subject: [PATCH 4/5] =?UTF-8?q?=F0=9F=90=9B=20Fix=20plotly=20renderer=20se?= =?UTF-8?q?tting=20to=20show=20it=20exactly?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit by reducing the output size --- docs/notebooks/radiation/grid_3d.ipynb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/docs/notebooks/radiation/grid_3d.ipynb b/docs/notebooks/radiation/grid_3d.ipynb index 7e4f026..9d55bb7 100644 --- a/docs/notebooks/radiation/grid_3d.ipynb +++ b/docs/notebooks/radiation/grid_3d.ipynb @@ -136,7 +136,7 @@ "id": "9", "metadata": {}, "source": [ - "Plot center points of cells\n" + "Plot center points of cells" ] }, { @@ -231,7 +231,7 @@ "import plotly.graph_objects as go\n", "from plotly import io\n", "\n", - "io.renderers.default = \"notebook\"" + "io.renderers.default = \"png\"" ] }, { @@ -271,7 +271,7 @@ "\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 +314,19 @@ "\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", ")" ] } From fd6d22e8dcce624b16955e3b503240a0b5c81ee3 Mon Sep 17 00:00:00 2001 From: munechika-koyo Date: Thu, 25 Jun 2026 15:49:23 +0200 Subject: [PATCH 5/5] =?UTF-8?q?=F0=9F=93=9D=20Update=20links=20in=20notebo?= =?UTF-8?q?oks?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/notebooks/observer/bolometer.ipynb | 4 +-- docs/notebooks/plasma/1_equilibrium.ipynb | 3 +- docs/notebooks/plasma/2_edge_plasma.ipynb | 2 +- docs/notebooks/plasma/3_full_plasma.ipynb | 4 +-- docs/notebooks/plasma/4_emission.ipynb | 2 +- docs/notebooks/radiation/grid_3d.ipynb | 34 +++++++++++++-------- docs/notebooks/radiation/radiation_3d.ipynb | 2 +- 7 files changed, 30 insertions(+), 21 deletions(-) diff --git a/docs/notebooks/observer/bolometer.ipynb b/docs/notebooks/observer/bolometer.ipynb index 9aa74d0..dd73352 100644 --- a/docs/notebooks/observer/bolometer.ipynb +++ b/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 `__." ] }, { @@ -157,7 +157,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.14.3" + "version": "3.14.6" } }, "nbformat": 4, diff --git a/docs/notebooks/plasma/1_equilibrium.ipynb b/docs/notebooks/plasma/1_equilibrium.ipynb index 1ebd31c..75ad162 100644 --- a/docs/notebooks/plasma/1_equilibrium.ipynb +++ b/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)." ] }, { diff --git a/docs/notebooks/plasma/2_edge_plasma.ipynb b/docs/notebooks/plasma/2_edge_plasma.ipynb index 71fda6a..d79e8ba 100644 --- a/docs/notebooks/plasma/2_edge_plasma.ipynb +++ b/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." ] }, diff --git a/docs/notebooks/plasma/3_full_plasma.ipynb b/docs/notebooks/plasma/3_full_plasma.ipynb index b75882a..2fa643b 100644 --- a/docs/notebooks/plasma/3_full_plasma.ipynb +++ b/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 `__ and `edge_profiles `__ 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 `__ IDS if not already provided." ] }, { diff --git a/docs/notebooks/plasma/4_emission.ipynb b/docs/notebooks/plasma/4_emission.ipynb index 74b6ee9..3c192e7 100644 --- a/docs/notebooks/plasma/4_emission.ipynb +++ b/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." ] }, diff --git a/docs/notebooks/radiation/grid_3d.ipynb b/docs/notebooks/radiation/grid_3d.ipynb index 9d55bb7..4e8dc8a 100644 --- a/docs/notebooks/radiation/grid_3d.ipynb +++ b/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": [ @@ -133,7 +141,7 @@ }, { "cell_type": "markdown", - "id": "9", + "id": "10", "metadata": {}, "source": [ "Plot center points of cells" @@ -142,7 +150,7 @@ { "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", @@ -224,7 +232,7 @@ { "cell_type": "code", "execution_count": null, - "id": "14", + "id": "15", "metadata": {}, "outputs": [], "source": [ @@ -237,7 +245,7 @@ { "cell_type": "code", "execution_count": null, - "id": "15", + "id": "16", "metadata": {}, "outputs": [], "source": [ diff --git a/docs/notebooks/radiation/radiation_3d.ipynb b/docs/notebooks/radiation/radiation_3d.ipynb index 9b42387..ba7ec45 100644 --- a/docs/notebooks/radiation/radiation_3d.ipynb +++ b/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." ]