|
| 1 | +{ |
| 2 | + "cells": [ |
| 3 | + { |
| 4 | + "cell_type": "markdown", |
| 5 | + "id": "7bf33a06-009a-487a-991b-715a28b1069b", |
| 6 | + "metadata": {}, |
| 7 | + "source": [ |
| 8 | + "# Scope and description" |
| 9 | + ] |
| 10 | + }, |
| 11 | + { |
| 12 | + "cell_type": "markdown", |
| 13 | + "id": "d96031b8-ee40-43ca-9001-011f4751d4c1", |
| 14 | + "metadata": {}, |
| 15 | + "source": [ |
| 16 | + "<One line description>\n", |
| 17 | + "\n", |
| 18 | + "Elements contained:\n", |
| 19 | + "- <Element>\n", |
| 20 | + "- <Another element>\n", |
| 21 | + "\n", |
| 22 | + "Annotations contained:\n", |
| 23 | + "- <table annotating...>\n", |
| 24 | + "\n", |
| 25 | + "<Additional notes>" |
| 26 | + ] |
| 27 | + }, |
| 28 | + { |
| 29 | + "cell_type": "markdown", |
| 30 | + "id": "5a4c6566-882a-48d4-a4cd-0777332a5a99", |
| 31 | + "metadata": {}, |
| 32 | + "source": [ |
| 33 | + "# Prepare the data" |
| 34 | + ] |
| 35 | + }, |
| 36 | + { |
| 37 | + "cell_type": "code", |
| 38 | + "execution_count": null, |
| 39 | + "id": "094509a1-86fb-4aa6-b920-11e34ed43e1c", |
| 40 | + "metadata": {}, |
| 41 | + "outputs": [], |
| 42 | + "source": [ |
| 43 | + "NAME = \"name_of_the_notebook\"" |
| 44 | + ] |
| 45 | + }, |
| 46 | + { |
| 47 | + "cell_type": "code", |
| 48 | + "execution_count": null, |
| 49 | + "id": "332c9c62-7451-4d8e-ba9e-13c12131c312", |
| 50 | + "metadata": {}, |
| 51 | + "outputs": [], |
| 52 | + "source": [ |
| 53 | + "import spatialdata as sd\n", |
| 54 | + "import spatialdata_plot\n", |
| 55 | + "from spatialdata.datasets import blobs\n", |
| 56 | + "from io_utils import delete_old_data, write_sdata_and_check_consistency\n", |
| 57 | + "\n", |
| 58 | + "delete_old_data(name=NAME)\n", |
| 59 | + "sdata = <create sdata here>\n", |
| 60 | + "sdata" |
| 61 | + ] |
| 62 | + }, |
| 63 | + { |
| 64 | + "cell_type": "markdown", |
| 65 | + "id": "800a540b-2906-46c9-8245-99def219692f", |
| 66 | + "metadata": {}, |
| 67 | + "source": [ |
| 68 | + "# Read-write and IO validation" |
| 69 | + ] |
| 70 | + }, |
| 71 | + { |
| 72 | + "cell_type": "code", |
| 73 | + "execution_count": null, |
| 74 | + "id": "b6c01345-27de-42f3-af07-75a43e84808a", |
| 75 | + "metadata": {}, |
| 76 | + "outputs": [], |
| 77 | + "source": [ |
| 78 | + "write_sdata_and_check_consistency(sdata=sdata, name=NAME)" |
| 79 | + ] |
| 80 | + }, |
| 81 | + { |
| 82 | + "cell_type": "markdown", |
| 83 | + "id": "06806f13-f346-410f-ab04-fdd61fd77a10", |
| 84 | + "metadata": {}, |
| 85 | + "source": [ |
| 86 | + "# Plot the data" |
| 87 | + ] |
| 88 | + }, |
| 89 | + { |
| 90 | + "cell_type": "code", |
| 91 | + "execution_count": null, |
| 92 | + "id": "af8d7108-8b7c-461e-871e-77d82de82af6", |
| 93 | + "metadata": {}, |
| 94 | + "outputs": [], |
| 95 | + "source": [ |
| 96 | + "<plot teh data>" |
| 97 | + ] |
| 98 | + } |
| 99 | + ], |
| 100 | + "metadata": { |
| 101 | + "kernelspec": { |
| 102 | + "display_name": "Python 3 (ipykernel)", |
| 103 | + "language": "python", |
| 104 | + "name": "python3" |
| 105 | + }, |
| 106 | + "language_info": { |
| 107 | + "codemirror_mode": { |
| 108 | + "name": "ipython", |
| 109 | + "version": 3 |
| 110 | + }, |
| 111 | + "file_extension": ".py", |
| 112 | + "mimetype": "text/x-python", |
| 113 | + "name": "python", |
| 114 | + "nbconvert_exporter": "python", |
| 115 | + "pygments_lexer": "ipython3", |
| 116 | + "version": "3.10.12" |
| 117 | + } |
| 118 | + }, |
| 119 | + "nbformat": 4, |
| 120 | + "nbformat_minor": 5 |
| 121 | +} |
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