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Fix issues with read the doc #5

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Merged
merged 6 commits into from
Aug 18, 2025
Merged

Fix issues with read the doc #5

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e4c4077
add missing rtd deps
KedoKudo Aug 18, 2025
8336cd9
update pixi lock file
KedoKudo Aug 18, 2025
728e949
Update pyproject.toml
KedoKudo Aug 18, 2025
97c3322
update pixi lock
KedoKudo Aug 18, 2025
4a2cc85
fix notebook issues in doc building
KedoKudo Aug 18, 2025
4146713
bypass the notebook rendering issue with sphinx
KedoKudo Aug 18, 2025
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280 changes: 280 additions & 0 deletions documentation/source/archived_notebooks_backup/tutorial_homogeneous_tiff.ipynb
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Original file line number Diff line number Diff line change
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"# Tutorial homogenous cylinder"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## import"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"import os\n",
"import sys\n",
"import numpy as np\n",
"\n",
"root_folder = os.path.dirname(os.getcwd())\n",
"sys.path.insert(0, root_folder)\n",
"from neutron_geomcorr.geometry_correction import GeometryCorrection\n",
"import glob\n",
"\n",
"import matplotlib.pyplot as plt\n",
"\n",
"\n",
"from ipywidgets import widgets, interact"
]
},
{
"cell_type": "markdown",
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"## initialize object "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"list_tiff = glob.glob('data/tiff/homogeneous*.tif')\n",
"\n",
"# initialize object\n",
"o_cgc = GeometryCorrection(list_files=list_tiff)\n",
"o_cgc.load_files(notebook=True)"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true,
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"## Display images"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"list_images = o_cgc.list_data\n",
"\n",
"fig1, (ax1, ax2) = plt.subplots(1, 2)\n",
" \n",
"def plot(index):\n",
" \n",
" ax1.clear()\n",
" ax1.imshow(list_images[index])\n",
" \n",
" ax2.clear()\n",
" ax2.plot(list_images[index][0,:])\n",
" \n",
"interact(plot,\n",
" index = widgets.IntSlider(value=0,\n",
" max=len(list_images)-1),\n",
" continuous_update=False)"
]
},
{
"cell_type": "markdown",
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"## Define parameters "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"# center of cylinder\n",
"pixel_center = 256\n",
"\n",
"# radius of cylinder\n",
"radius = 200\n",
"\n",
"# define the parameters\n",
"o_cgc.define_parameters(outer_radius=radius, pixel_center=pixel_center)"
]
},
{
"cell_type": "markdown",
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"## Run correction "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"o_cgc.correct(notebook=True)"
]
},
{
"cell_type": "markdown",
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"source": [
"## Display data corrected "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": [
"list_images_corrected = o_cgc.list_data_corrected\n",
"\n",
"fig2, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(8,3))\n",
" \n",
"def plot(index):\n",
" \n",
" ax1.clear()\n",
" ax1.imshow(list_images_corrected[index])\n",
" \n",
" ax2.clear()\n",
" max_y_value = np.nanmax(list_images_corrected[index][0, 1:])\n",
" ax2.plot(list_images_corrected[index][0,:])\n",
" ax2.set_ylim(0,max_y_value+1)\n",
" \n",
" ax3.clear()\n",
" ax3.plot(list_images_corrected[index][0,:])\n",
" \n",
" plt.tight_layout()\n",
" \n",
"interact(plot,\n",
" index = widgets.IntSlider(value=0,\n",
" max=len(list_images_corrected)-1),\n",
" continuous_update=False)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"run_control": {
"frozen": false,
"read_only": false
}
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.6.4"
},
"toc": {
"colors": {
"hover_highlight": "#DAA520",
"running_highlight": "#FF0000",
"selected_highlight": "#FFD700"
},
"moveMenuLeft": true,
"nav_menu": {
"height": "118px",
"width": "252px"
},
"navigate_menu": true,
"number_sections": true,
"sideBar": true,
"threshold": 4,
"toc_cell": false,
"toc_section_display": "block",
"toc_window_display": false
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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