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EasyScience · Nov 21, 2024 · a38629a · a38629a
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diff --git a/.doctrees/api/assemblies/gradient_layer.doctree b/.doctrees/api/assemblies/gradient_layer.doctree
diff --git a/.doctrees/api/assemblies/multilayer.doctree b/.doctrees/api/assemblies/multilayer.doctree
diff --git a/.doctrees/api/assemblies/repeating_multilayer.doctree b/.doctrees/api/assemblies/repeating_multilayer.doctree
diff --git a/.doctrees/api/assemblies/surfactant_layer.doctree b/.doctrees/api/assemblies/surfactant_layer.doctree
diff --git a/.doctrees/api/data.doctree b/.doctrees/api/data.doctree
diff --git a/.doctrees/api/model.doctree b/.doctrees/api/model.doctree
diff --git a/.doctrees/api/sample.doctree b/.doctrees/api/sample.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/nbsphinx/tutorials/fitting/repeating.ipynb b/.doctrees/nbsphinx/tutorials/fitting/repeating.ipynb
diff --git a/.doctrees/nbsphinx/tutorials/fitting/simple_fitting.ipynb b/.doctrees/nbsphinx/tutorials/fitting/simple_fitting.ipynb
diff --git a/.doctrees/nbsphinx/tutorials/magnetism.ipynb b/.doctrees/nbsphinx/tutorials/magnetism.ipynb
diff --git a/.doctrees/nbsphinx/tutorials/project.ipynb b/.doctrees/nbsphinx/tutorials/project.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Project\n",
+    "This notebook serves to demonstrate some of the functionality of the Project object.\n",
+    "\n",
+    "## Setup\n",
+    "First configure matplotlib to place figures in notebook and import needed modules."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from easyreflectometry import Project\n",
+    "from easyreflectometry.summary import Summary"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Project object\n",
+    "\n",
+    "First we will create a `Project` object. There should only be one such object. The project is follwoing set to have the current folder at its root and the we give it the name: `MyNewProject`. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project = Project()\n",
+    "project.set_path_project_parent('.')\n",
+    "project._info['name'] = 'MyNewProject'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We will then populate this `Project` with the default model."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "EasyModels:\n",
+      "- EasyModel:\n",
+      "    scale: 1.0\n",
+      "    background: 1.0e-08\n",
+      "    resolution: 5.0 %\n",
+      "    color: black\n",
+      "    sample:\n",
+      "      EasySample:\n",
+      "      - Superphase:\n",
+      "          Vacuum Layer:\n",
+      "          - Vacuum Layer:\n",
+      "              material:\n",
+      "                Air:\n",
+      "                  sld: 0.000e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 0.000 Å\n",
+      "              roughness: 0.000 Å\n",
+      "      - D2O:\n",
+      "          D2O Layer:\n",
+      "          - D2O Layer:\n",
+      "              material:\n",
+      "                D2O:\n",
+      "                  sld: 6.335e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 100.000 Å\n",
+      "              roughness: 3.000 Å\n",
+      "      - Subphase:\n",
+      "          Si Layer:\n",
+      "          - Si Layer:\n",
+      "              material:\n",
+      "                Si:\n",
+      "                  sld: 2.074e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 0.000 Å\n",
+      "              roughness: 1.200 Å\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "project.default_model()\n",
+    "print(project.models)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can also see which materials that are defined in the `Project`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "EasyMaterials:\n",
+      "- Air:\n",
+      "    sld: 0.000e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "- D2O:\n",
+      "    sld: 6.335e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "- Si:\n",
+      "    sld: 2.074e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(project._materials)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "It is possible to save a `Project` object.  It will be place in the project folder and the state will be save in the file name `project.json`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save_as_json(overwrite=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can also generate a summary of the project.  We are also going to store the PDF and HTML files with the summary in the project folder."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "WindowsPath('MyNewProject/summary.pdf')"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "summary = Summary(project)\n",
+    "summary.save_pdf_summary(str(project.path / 'summary.pdf'))\n",
+    "summary.save_html_summary(str(project.path / 'summary.html'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[Link to PDF summary](MyNewProject/summary.pdf) in `MyNewProject/summary.pdf`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can reset the project to a blank state."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "EasyModels: []\n",
+      "\n",
+      "EasyMaterials: []\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "project.reset()\n",
+    "print(project.models)\n",
+    "print(project._materials)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Then let us try to load the state we saved above."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "EasyModels:\n",
+      "- EasyModel:\n",
+      "    scale: 1.0\n",
+      "    background: 1.0e-08\n",
+      "    resolution: 5.0 %\n",
+      "    color: black\n",
+      "    sample:\n",
+      "      EasySample:\n",
+      "      - Superphase:\n",
+      "          EasyLayerCollection:\n",
+      "          - Vacuum Layer:\n",
+      "              material:\n",
+      "                Air:\n",
+      "                  sld: 0.000e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 0.000 Å\n",
+      "              roughness: 0.000 Å\n",
+      "      - D2O:\n",
+      "          EasyLayerCollection:\n",
+      "          - D2O Layer:\n",
+      "              material:\n",
+      "                D2O:\n",
+      "                  sld: 6.335e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 100.000 Å\n",
+      "              roughness: 3.000 Å\n",
+      "      - Subphase:\n",
+      "          EasyLayerCollection:\n",
+      "          - Si Layer:\n",
+      "              material:\n",
+      "                Si:\n",
+      "                  sld: 2.074e-6 1/Å^2\n",
+      "                  isld: 0.000e-6 1/Å^2\n",
+      "              thickness: 0.000 Å\n",
+      "              roughness: 1.200 Å\n",
+      "\n",
+      "EasyMaterials:\n",
+      "- Air:\n",
+      "    sld: 0.000e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "- D2O:\n",
+      "    sld: 6.335e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "- Si:\n",
+      "    sld: 2.074e-6 1/Å^2\n",
+      "    isld: 0.000e-6 1/Å^2\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "project.set_path_project_parent('.')\n",
+    "project._info['name'] = 'MyNewProject'\n",
+    "project.load_from_json()\n",
+    "print(project.models)\n",
+    "print(project._materials)"
+   ]
+  }
+ ],
+ "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": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}