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Merge pull request #8 from davidbrochart/leftover
zarray is now separate from xtensor
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,273 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Zarr (v2) store reading with xtensor-zarr" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "In this notebook we use [zarr-python](https://github.com/zarr-developers/zarr-python) to chunk an array and store it in a store (in Zarr v2 format). We then read it with [xtensor-zarr](https://github.com/xtensor-stack/xtensor-zarr), which supports reading Zarr v2 stores." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import matplotlib.pyplot as plt\n", | ||
| "from matplotlib.image import imread\n", | ||
| "import zarr" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "a = imread('marie_curie.jpg')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "a" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "plt.imshow(a, cmap='Greys_r')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "a.shape" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Store the array in Zarr v2" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "!rm -rf marie_curie.zarr" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "z = zarr.open('marie_curie.zarr', mode='w', shape=a.shape, chunks=(30, 20), dtype=a.dtype)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "z[:] = a" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "!ls marie_curie.zarr" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The array consists of about 100 chunks." | ||
| ] | ||
| }, | ||
| { | ||
| "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(\"blosc\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "#include \"xtensor/xio.hpp\"\n", | ||
| "#include \"xtensor/xview.hpp\"\n", | ||
| "#include \"xwidgets/ximage.hpp\"\n", | ||
| "#include \"xtensor/xchunked_array.hpp\"\n", | ||
| "#include \"xtensor-io/xio_blosc.hpp\"\n", | ||
| "#include \"xtensor-io/xchunk_store_manager.hpp\"\n", | ||
| "#include \"xtensor-io/ximage.hpp\"\n", | ||
| "#include \"xtensor-zarr/xzarr_hierarchy.hpp\"\n", | ||
| "#include \"xtensor-zarr/xzarr_file_system_store.hpp\"\n", | ||
| "#include \"xtl/xbase64.hpp\"\n", | ||
| "#include \"xcpp/xdisplay.hpp\"" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Read the Zarr store (v2) with xtensor-zarr" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "xt::xzarr_register_compressor<xt::xzarr_file_system_store, xt::xio_blosc_config>();\n", | ||
| "xt::xzarr_file_system_store s(\"marie_curie.zarr\");\n", | ||
| "auto h = xt::get_zarr_hierarchy(s, \"2\");\n", | ||
| "auto z = h.get_array(\"\");" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "auto a = z.get_array<uint8_t>();\n", | ||
| "a" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "std::vector<char> read_file(const char* filename)\n", | ||
| "{\n", | ||
| " std::basic_ifstream<char> file(filename, std::ios::binary);\n", | ||
| " return std::vector<char>((std::istreambuf_iterator<char>(file)), std::istreambuf_iterator<char>());\n", | ||
| "}" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "template <class E>\n", | ||
| "std::vector<char> to_png_buffer(const xt::xexpression<E>& e)\n", | ||
| "{\n", | ||
| " const char* temp_filename = \"/tmp/xio_image.png\";\n", | ||
| " xt::dump_image(temp_filename, e);\n", | ||
| " return read_file(temp_filename);\n", | ||
| "}" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| ">xcpp14\n", | ||
| "xw::image img;\n", | ||
| "img.value = to_png_buffer(a);\n", | ||
| "img" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The original image has been reconstructed." | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "All the Kernels", | ||
| "language": "", | ||
| "name": "atk" | ||
| }, | ||
| "language_info": { | ||
| "mimetype": "text/plain", | ||
| "name": "all-of-them" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |
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