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   "source": [
    "# Interactive Features in cdiutils\n",
    "\n",
    "This notebook demonstrates the interactive visualisation and data exploration tools available in `cdiutils`:\n",
    "\n",
    "1. **`plot_3d_isosurface`**: Interactive 3D isosurface plotting with multiple quantities\n",
    "2. **`ThreeDViewer`**: Widget for exploring complex 3D arrays (amplitude + phase)\n",
    "3. **`TabPlotData`**: Interactive browser for exploring CDI reconstruction results\n",
    "\n",
    "## Installation\n",
    "\n",
    "These features require additional dependencies:\n",
    "```bash\n",
    "pip install cdiutils[interactive]\n",
    "```\n",
    "\n",
    "Or install individually:\n",
    "```bash\n",
    "pip install plotly scikit-image scipy ipywidgets h5glance\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "642ba5e5",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "\n",
    "import cdiutils\n",
    "from cdiutils.interactive import TabPlotData, ThreeDViewer, plot_3d_isosurface\n",
    "\n",
    "cdiutils.update_plot_params()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "194ae93a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# load reconstruction data from CXI file (here, we assume it has been generated by CDIutils pipeline)\n",
    "data_path = \"\"\n",
    "data = cdiutils.io.load_cxi(\n",
    "    data_path,\n",
    "    \"amplitude\",\n",
    "    \"phase\",\n",
    "    \"het_strain\",\n",
    "    \"lattice_parameter\",\n",
    "    \"dspacing\",\n",
    "    \"support\",\n",
    ")\n",
    "voxel_size = cdiutils.io.load_cxi(data_path, \"voxel_size\")\n",
    "\n",
    "print(f\"Data shape: {data['amplitude'].shape}\")\n",
    "print(f\"Voxel size: {voxel_size} nm\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "89cbf86f",
   "metadata": {},
   "source": [
    "## `plot_3d_isosurface`\n",
    "\n",
    "Interactive isosurface plot with multiple quantities. Features:\n",
    "- **Threshold slider**: control isosurface level\n",
    "- **Quantity dropdown**: switch between different data arrays\n",
    "- **Colormap dropdown**: choose from 20+ colormaps\n",
    "- **Colorbar controls**: auto-scale, symmetric mode, or manual limits\n",
    "- **Replace NaN checkbox**: replace NaN values with mean to avoid artefacts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e0834298",
   "metadata": {},
   "outputs": [],
   "source": [
    "plot_3d_isosurface(\n",
    "    data[\"amplitude\"],\n",
    "    data,\n",
    "    voxel_size=voxel_size,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "64e8f12e",
   "metadata": {},
   "source": [
    "## `ThreeDViewer` Class\n",
    "\n",
    "A widget for exploring complex 3D arrays (amplitude + phase). Features:\n",
    "- **Threshold slider**: control isosurface level based on amplitude\n",
    "- **Phase/Amplitude toggle**: switch between phase and amplitude display\n",
    "- **Colormap dropdown**: choose from 20+ colormaps\n",
    "- **Colorbar controls**: auto-scale, symmetric mode, or manual limits\n",
    "- **Replace NaN checkbox**: replace NaN values with mean\n",
    "- **Rotation toggle**: enable continuous rotation animation\n",
    "- **Theme toggle**: switch between light and dark themes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "47d7a5ec",
   "metadata": {},
   "outputs": [],
   "source": [
    "# create complex 3D array\n",
    "complex_3d = data[\"amplitude\"] * np.exp(1j * data[\"phase\"])\n",
    "\n",
    "# create viewer\n",
    "viewer = ThreeDViewer(complex_3d, voxel_size=voxel_size, figsize=(9, 6))\n",
    "viewer.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "abfb7c1f",
   "metadata": {},
   "source": [
    "## Notes\n",
    "\n",
    "- Try adjusting the threshold slider to explore different isosurface levels\n",
    "- Use the colormap dropdown to find the best visualisation for your data\n",
    "- Enable \"Replace NaN with mean\" if you see unusual colours (NaN artefacts)\n",
    "- For strain data, use symmetric colorbar with diverging colormaps like \"cet_CET_D13\"\n",
    "- The dark theme can be helpful when working in low-light environments"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e4c1cfee",
   "metadata": {},
   "source": [
    "## `TabPlotData` Class\n",
    "\n",
    "An interactive browser for exploring CDI reconstruction results from a folder structure. Features:\n",
    "- **Tab navigation**: browse through different scans and reconstructions\n",
    "- **Interactive plots**: 2D slices and 3D visualisations\n",
    "- **Data inspection**: view metadata and reconstruction parameters\n",
    "- **Quick comparison**: easily compare results from different scans"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6b4dc0a0",
   "metadata": {},
   "outputs": [],
   "source": [
    "path_to_results_dir = \"\"\n",
    "tab = TabPlotData(path_to_results_dir)\n",
    "tab.show()"
   ]
  }
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