Created
September 4, 2024 14:05
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "id": "eca0ba22-85fe-4668-acbb-065c0a618a86", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import numpy as np\n", | |
| "import zarr" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 51, | |
| "id": "b5ba2eef-9199-4473-995a-88b2c60f4cfe", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Make some data\n", | |
| "chunk_size = 64\n", | |
| "data_shape = [chunk_size * 2, chunk_size * 2, chunk_size * 2]\n", | |
| "data = np.arange(np.prod(data_shape)).reshape(data_shape).astype(np.uint64)\n", | |
| "# Coordinate transform translation (we will use this later)\n", | |
| "translation = [512, 4050, 324]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 52, | |
| "id": "530b4be7-9418-478e-8d0b-0ea3ced4afba", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "ome_zarr_root = zarr.open_group(\"test.ome.zarr\", mode='w')\n", | |
| "array_path = \"0\"\n", | |
| "zarr_array = ome_zarr_root.create_dataset(array_path, shape=data_shape, dtype=np.uint64, dimension_separator='/')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 53, | |
| "id": "5a9f5f8c-9842-411e-b30b-a0ebbb0ea8da", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "zarr_array[:] = data" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 54, | |
| "id": "ab42909f-e29a-465a-bd84-46ab68469c86", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "ome_zarr_root.attrs['multiscales'] = [{\n", | |
| " 'version': '0.4',\n", | |
| " 'axes': [\n", | |
| " {\"name\": \"x\", \"type\": \"space\", \"unit\": \"micrometer\"},\n", | |
| " {\"name\": \"y\", \"type\": \"space\", \"unit\": \"micrometer\"},\n", | |
| " {\"name\": \"z\", \"type\": \"space\", \"unit\": \"micrometer\"},\n", | |
| " ],\n", | |
| " 'name': '',\n", | |
| " 'datasets': [\n", | |
| " {\n", | |
| " 'path': array_path,\n", | |
| " 'coordinateTransformations': [{\n", | |
| " 'type': 'translation',\n", | |
| " 'translation': translation,\n", | |
| " }]\n", | |
| " },\n", | |
| " ]\n", | |
| "}]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "id": "8493a89e-bd87-4513-9a61-71de502363ad", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "Python 3 (ipykernel)", | |
| "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": "3.10.14" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 5 | |
| } |
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