Merge pull request #16 from davidbrochart/notebook

Add notebook explore_hierarchy.ipynb

examples/explore_hierarchy.ipynb

@@ -0,0 +1,296 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Zarr (v3) store API"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this notebook we make use of the Zarr (v3) store API to access a hierarchy in C++."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Download development source code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">bash\n",
+    "rm -rf zarrita *.tar.gz*\n",
+    "mkdir -p zarrita\n",
+    "\n",
+    "wget https://github.com/alimanfoo/zarrita/archive/master.tar.gz -O zarrita.tar.gz -q\n",
+    "tar zxf zarrita.tar.gz -C zarrita --strip-components 1\n",
+    "mv zarrita/zarrita.py ."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "#pragma cling add_include_path(\"../include\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "#pragma cling add_library_path(\"$CONDA_PREFIX/lib\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "#pragma cling load(\"storage_client\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "#include \"xtensor/xio.hpp\"\n",
+    "#include \"xtensor/xview.hpp\"\n",
+    "#include \"xtensor/xchunked_array.hpp\"\n",
+    "#include \"xtensor-io/xio_gzip.hpp\"\n",
+    "#include \"xtensor-io/xchunk_store_manager.hpp\"\n",
+    "#include \"xtensor-zarr/xzarr_hierarchy.hpp\"\n",
+    "#include \"xtensor-zarr/xzarr_file_system_store.hpp\"\n",
+    "#include \"xtensor-zarr/xzarr_gcs_store.hpp\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create a Zarr hierarchy in Python"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">bash\n",
+    "rm -rf test.zr3"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import zarrita\n",
+    "h = zarrita.create_hierarchy('test.zr3')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h.create_group('marvin')\n",
+    "h['marvin'].create_group('paranoid')\n",
+    "attrs = {'age': 42, 'gender': 'male'}\n",
+    "h.create_group('/tricia/mcmillan', attrs=attrs)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">bash\n",
+    "find test.zr3"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Open the Zarr hierarchy in C++"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "xt::xzarr_file_system_store s1(\"test.zr3\");\n",
+    "auto h1 = xt::get_zarr_hierarchy(s1);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Explore the hierarchy in C++"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Explore the hierarchy top-down:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "std::string children1 = h1.get_children(\"/\").dump();\n",
+    "children1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "std::string children2 = h1.get_children(\"/marvin\").dump();\n",
+    "children2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "std::string children3 = h1.get_children(\"/tricia\").dump();\n",
+    "children3"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "std::string attrs1 = h1[\"/tricia/mcmillan\"].get_group().attrs().dump();\n",
+    "attrs1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "View the whole hierarchy in one go:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "std::string nodes = h1.get_nodes().dump();\n",
+    "nodes"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create groups in C++"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    ">xcpp14\n",
+    "nlohmann::json attrs2 = {{\"heart\", \"gold\"}, {\"improbability\", \"infinite\"}};\n",
+    "auto g1 = h1.create_group(\"/foo/bar\", attrs2);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Explore the hierarchy in Python"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h = zarrita.get_hierarchy('test.zr3')\n",
+    "h.get_children('/')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h.get_children('foo')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h['foo/bar'].attrs"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "All the Kernels",
+   "language": "",
+   "name": "atk"
+  },
+  "language_info": {
+   "mimetype": "text/plain",
+   "name": "all-of-them"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}