From 160a8d81260b84c363e40d525616d46c5581b06c Mon Sep 17 00:00:00 2001 From: Eli Holmes Date: Tue, 20 Aug 2024 23:02:53 +0000 Subject: [PATCH] update the visualization notebook --- book/notebooks/IO_Zarr_visualizations.ipynb | 14271 ++++++++++-------- notebooks/CHL_prediction_ConvLSTM_.ipynb | 2132 +-- 2 files changed, 8340 insertions(+), 8063 deletions(-) diff --git a/book/notebooks/IO_Zarr_visualizations.ipynb b/book/notebooks/IO_Zarr_visualizations.ipynb index a7d30a1..78fe8a8 100644 --- a/book/notebooks/IO_Zarr_visualizations.ipynb +++ b/book/notebooks/IO_Zarr_visualizations.ipynb @@ -33,569 +33,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 20, "id": "70b6ea85-0a62-4f1f-a4ae-cd1e063ef24b", "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "application/javascript": [ - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = true;\n", - " var py_version = '3.2.2'.replace('rc', 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else if (typeof google != 'undefined' && google.colab.kernel != null) {\n google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n console.log(message)\n var content = {data: message.data, comm_id};\n var buffers = []\n for (var buffer of message.buffers || []) {\n buffers.push(new DataView(buffer))\n }\n var metadata = message.metadata || {};\n var msg = {content, buffers, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n })\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || 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handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "import xarray as xr\n", "import numpy as np\n", @@ -623,36 +66,7 @@ "metadata": { "tags": [] }, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "No such file or directory: '/home/jovyan/shared-public/mind_the_chl_gap/IO.zarr'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:1307\u001b[0m, in \u001b[0;36m_get_open_params\u001b[0;34m(store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, stacklevel, zarr_version)\u001b[0m\n\u001b[1;32m 1306\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1307\u001b[0m zarr_group \u001b[38;5;241m=\u001b[39m \u001b[43mzarr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_consolidated\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstore\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mopen_kwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1308\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/zarr/convenience.py:1360\u001b[0m, in \u001b[0;36mopen_consolidated\u001b[0;34m(store, metadata_key, mode, **kwargs)\u001b[0m\n\u001b[1;32m 1359\u001b[0m \u001b[38;5;66;03m# setup metadata store\u001b[39;00m\n\u001b[0;32m-> 1360\u001b[0m meta_store \u001b[38;5;241m=\u001b[39m \u001b[43mConsolidatedStoreClass\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstore\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmetadata_key\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmetadata_key\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1362\u001b[0m \u001b[38;5;66;03m# pass through\u001b[39;00m\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/zarr/storage.py:3046\u001b[0m, in \u001b[0;36mConsolidatedMetadataStore.__init__\u001b[0;34m(self, store, metadata_key)\u001b[0m\n\u001b[1;32m 3045\u001b[0m \u001b[38;5;66;03m# retrieve consolidated metadata\u001b[39;00m\n\u001b[0;32m-> 3046\u001b[0m meta \u001b[38;5;241m=\u001b[39m json_loads(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstore\u001b[49m\u001b[43m[\u001b[49m\u001b[43mmetadata_key\u001b[49m\u001b[43m]\u001b[49m)\n\u001b[1;32m 3048\u001b[0m \u001b[38;5;66;03m# check format of consolidated metadata\u001b[39;00m\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/zarr/storage.py:1120\u001b[0m, in \u001b[0;36mDirectoryStore.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 1119\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1120\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key)\n", - "\u001b[0;31mKeyError\u001b[0m: '.zmetadata'", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mGroupNotFoundError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:1310\u001b[0m, in \u001b[0;36m_get_open_params\u001b[0;34m(store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, stacklevel, zarr_version)\u001b[0m\n\u001b[1;32m 1309\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1310\u001b[0m zarr_group \u001b[38;5;241m=\u001b[39m \u001b[43mzarr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_group\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstore\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mopen_kwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1311\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 1312\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFailed to open Zarr store with consolidated metadata, \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1313\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mbut successfully read with non-consolidated metadata. \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1324\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39mstacklevel,\n\u001b[1;32m 1325\u001b[0m )\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/zarr/hierarchy.py:1578\u001b[0m, in \u001b[0;36mopen_group\u001b[0;34m(store, mode, cache_attrs, synchronizer, path, chunk_store, storage_options, zarr_version, meta_array)\u001b[0m\n\u001b[1;32m 1577\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m ContainsArrayError(path)\n\u001b[0;32m-> 1578\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m GroupNotFoundError(path)\n\u001b[1;32m 1580\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m mode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n", - "\u001b[0;31mGroupNotFoundError\u001b[0m: group not found at path ''", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[2], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m ds \u001b[38;5;241m=\u001b[39m ds \u001b[38;5;241m=\u001b[39m \u001b[43mxr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_zarr\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m~/shared-public/mind_the_chl_gap/IO.zarr\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:1097\u001b[0m, in \u001b[0;36mopen_zarr\u001b[0;34m(store, group, synchronizer, chunks, decode_cf, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, consolidated, overwrite_encoded_chunks, chunk_store, storage_options, decode_timedelta, use_cftime, zarr_version, chunked_array_type, from_array_kwargs, **kwargs)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mopen_zarr() got unexpected keyword arguments \u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m,\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(kwargs\u001b[38;5;241m.\u001b[39mkeys())\n\u001b[1;32m 1085\u001b[0m )\n\u001b[1;32m 1087\u001b[0m backend_kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msynchronizer\u001b[39m\u001b[38;5;124m\"\u001b[39m: synchronizer,\n\u001b[1;32m 1089\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mconsolidated\u001b[39m\u001b[38;5;124m\"\u001b[39m: consolidated,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1094\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mzarr_version\u001b[39m\u001b[38;5;124m\"\u001b[39m: zarr_version,\n\u001b[1;32m 1095\u001b[0m }\n\u001b[0;32m-> 1097\u001b[0m ds \u001b[38;5;241m=\u001b[39m \u001b[43mopen_dataset\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1098\u001b[0m \u001b[43m \u001b[49m\u001b[43mfilename_or_obj\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstore\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1099\u001b[0m \u001b[43m \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgroup\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1100\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_cf\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_cf\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1101\u001b[0m \u001b[43m \u001b[49m\u001b[43mmask_and_scale\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmask_and_scale\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1102\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_times\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_times\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1103\u001b[0m \u001b[43m \u001b[49m\u001b[43mconcat_characters\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconcat_characters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1104\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_coords\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_coords\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1105\u001b[0m \u001b[43m \u001b[49m\u001b[43mengine\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mzarr\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1106\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunks\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunks\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1107\u001b[0m \u001b[43m \u001b[49m\u001b[43mdrop_variables\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdrop_variables\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1108\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked_array_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked_array_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1109\u001b[0m \u001b[43m \u001b[49m\u001b[43mfrom_array_kwargs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfrom_array_kwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1110\u001b[0m \u001b[43m \u001b[49m\u001b[43mbackend_kwargs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbackend_kwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1111\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_timedelta\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_timedelta\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1112\u001b[0m \u001b[43m \u001b[49m\u001b[43muse_cftime\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muse_cftime\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1113\u001b[0m \u001b[43m \u001b[49m\u001b[43mzarr_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mzarr_version\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1114\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ds\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/api.py:571\u001b[0m, in \u001b[0;36mopen_dataset\u001b[0;34m(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)\u001b[0m\n\u001b[1;32m 559\u001b[0m decoders \u001b[38;5;241m=\u001b[39m _resolve_decoders_kwargs(\n\u001b[1;32m 560\u001b[0m decode_cf,\n\u001b[1;32m 561\u001b[0m open_backend_dataset_parameters\u001b[38;5;241m=\u001b[39mbackend\u001b[38;5;241m.\u001b[39mopen_dataset_parameters,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 567\u001b[0m decode_coords\u001b[38;5;241m=\u001b[39mdecode_coords,\n\u001b[1;32m 568\u001b[0m )\n\u001b[1;32m 570\u001b[0m overwrite_encoded_chunks \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124moverwrite_encoded_chunks\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m)\n\u001b[0;32m--> 571\u001b[0m backend_ds \u001b[38;5;241m=\u001b[39m \u001b[43mbackend\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_dataset\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 572\u001b[0m \u001b[43m \u001b[49m\u001b[43mfilename_or_obj\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 573\u001b[0m \u001b[43m \u001b[49m\u001b[43mdrop_variables\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdrop_variables\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 574\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mdecoders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 575\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 576\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 577\u001b[0m ds \u001b[38;5;241m=\u001b[39m _dataset_from_backend_dataset(\n\u001b[1;32m 578\u001b[0m backend_ds,\n\u001b[1;32m 579\u001b[0m filename_or_obj,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 589\u001b[0m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[1;32m 590\u001b[0m )\n\u001b[1;32m 591\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ds\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:1167\u001b[0m, in \u001b[0;36mZarrBackendEntrypoint.open_dataset\u001b[0;34m(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, synchronizer, consolidated, chunk_store, storage_options, stacklevel, zarr_version, store, engine)\u001b[0m\n\u001b[1;32m 1165\u001b[0m filename_or_obj \u001b[38;5;241m=\u001b[39m _normalize_path(filename_or_obj)\n\u001b[1;32m 1166\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m store:\n\u001b[0;32m-> 1167\u001b[0m store \u001b[38;5;241m=\u001b[39m \u001b[43mZarrStore\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_group\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1168\u001b[0m \u001b[43m \u001b[49m\u001b[43mfilename_or_obj\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1169\u001b[0m \u001b[43m \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgroup\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1170\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1171\u001b[0m \u001b[43m \u001b[49m\u001b[43msynchronizer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msynchronizer\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1172\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsolidated\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconsolidated\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1173\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsolidate_on_close\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 1174\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunk_store\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunk_store\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1175\u001b[0m \u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstorage_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1176\u001b[0m \u001b[43m \u001b[49m\u001b[43mstacklevel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstacklevel\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1177\u001b[0m \u001b[43m \u001b[49m\u001b[43mzarr_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mzarr_version\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1178\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1180\u001b[0m store_entrypoint \u001b[38;5;241m=\u001b[39m StoreBackendEntrypoint()\n\u001b[1;32m 1181\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m close_on_error(store):\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:483\u001b[0m, in \u001b[0;36mZarrStore.open_group\u001b[0;34m(cls, store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, append_dim, write_region, safe_chunks, stacklevel, zarr_version, write_empty)\u001b[0m\n\u001b[1;32m 464\u001b[0m \u001b[38;5;129m@classmethod\u001b[39m\n\u001b[1;32m 465\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_group\u001b[39m(\n\u001b[1;32m 466\u001b[0m \u001b[38;5;28mcls\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 480\u001b[0m write_empty: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 481\u001b[0m ):\n\u001b[0;32m--> 483\u001b[0m zarr_group, consolidate_on_close, close_store_on_close \u001b[38;5;241m=\u001b[39m \u001b[43m_get_open_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 484\u001b[0m \u001b[43m \u001b[49m\u001b[43mstore\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstore\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 485\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 486\u001b[0m \u001b[43m \u001b[49m\u001b[43msynchronizer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msynchronizer\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 487\u001b[0m \u001b[43m \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgroup\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsolidated\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconsolidated\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsolidate_on_close\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconsolidate_on_close\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 490\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunk_store\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunk_store\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 491\u001b[0m \u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstorage_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 492\u001b[0m \u001b[43m \u001b[49m\u001b[43mstacklevel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstacklevel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 493\u001b[0m \u001b[43m \u001b[49m\u001b[43mzarr_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mzarr_version\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 494\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 496\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mcls\u001b[39m(\n\u001b[1;32m 497\u001b[0m zarr_group,\n\u001b[1;32m 498\u001b[0m mode,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 504\u001b[0m close_store_on_close,\n\u001b[1;32m 505\u001b[0m )\n", - "File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/backends/zarr.py:1327\u001b[0m, in \u001b[0;36m_get_open_params\u001b[0;34m(store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, stacklevel, zarr_version)\u001b[0m\n\u001b[1;32m 1311\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 1312\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFailed to open Zarr store with consolidated metadata, \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1313\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mbut successfully read with non-consolidated metadata. \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1324\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39mstacklevel,\n\u001b[1;32m 1325\u001b[0m )\n\u001b[1;32m 1326\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m zarr\u001b[38;5;241m.\u001b[39merrors\u001b[38;5;241m.\u001b[39mGroupNotFoundError:\n\u001b[0;32m-> 1327\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo such file or directory: \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mstore\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1328\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m consolidated:\n\u001b[1;32m 1329\u001b[0m \u001b[38;5;66;03m# TODO: an option to pass the metadata_key keyword\u001b[39;00m\n\u001b[1;32m 1330\u001b[0m zarr_group \u001b[38;5;241m=\u001b[39m zarr\u001b[38;5;241m.\u001b[39mopen_consolidated(store, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mopen_kwargs)\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: No such file or directory: '/home/jovyan/shared-public/mind_the_chl_gap/IO.zarr'" - ] - } - ], + "outputs": [], "source": [ "ds = ds = xr.open_zarr(\"~/shared-public/mind_the_chl_gap/IO.zarr\")" ] @@ -699,6 +113,7 @@ "}\n", "\n", "html[theme=dark],\n", + "html[data-theme=dark],\n", "body[data-theme=dark],\n", "body.vscode-dark {\n", " --xr-font-color0: rgba(255, 255, 255, 1);\n", @@ -1031,40 +446,40 @@ " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", - "
<xarray.Dataset>\n",
-       "Dimensions:          (time: 16071, lat: 177, lon: 241)\n",
+       "
<xarray.Dataset> Size: 66GB\n",
+       "Dimensions:                       (time: 16071, lat: 177, lon: 241)\n",
        "Coordinates:\n",
-       "  * lat              (lat) float32 32.0 31.75 31.5 31.25 ... -11.5 -11.75 -12.0\n",
-       "  * lon              (lon) float32 42.0 42.25 42.5 42.75 ... 101.5 101.8 102.0\n",
-       "  * time             (time) datetime64[ns] 1979-01-01 1979-01-02 ... 2022-12-31\n",
-       "Data variables: (12/19)\n",
-       "    CHL              (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    CHL_uncertainty  (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    adt              (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    air_temp         (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    curr_dir         (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    curr_speed       (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    ...               ...\n",
-       "    ug_curr          (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    v_curr           (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    v_wind           (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    vg_curr          (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    wind_dir         (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "    wind_speed       (time, lat, lon) float32 dask.array<chunksize=(100, 177, 241), meta=np.ndarray>\n",
-       "Attributes: (12/17)\n",
-       "    creator_email:              minhphan@uw.edu\n",
-       "    creator_name:               Minh Phan\n",
-       "    creator_type:               person\n",
-       "    date_created:               2023-07-19\n",
-       "    geospatial_lat_max:         32.0\n",
-       "    geospatial_lat_min:         -12.0\n",
-       "    ...                         ...\n",
-       "    geospatial_lon_units:       degrees_east\n",
-       "    source:                     Earth & Space Research (ESR), Copernicus Clim...\n",
-       "    summary:                    Daily mean of 0.25 x 0.25 degrees gridded dat...\n",
-       "    time_coverage_end:          2022-12-31T23:59:59\n",
-       "    time_coverage_start:        1979-01-01T00:00:00\n",
-       "    title:                      Climate Data for Coastal Upwelling Machine Le...