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Created February 22, 2022 17:27
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Pangeo-Coiled-Demo.ipynb
{
"cells": [
{
"cell_type": "markdown",
"id": "81fe39ba-ff68-40e3-adf8-01f6dabb8a19",
"metadata": {},
"source": [
"# Pangeo - Coiled Webinar Demo"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b1b3698c-cb35-47b4-a486-43b77d5afb8a",
"metadata": {},
"outputs": [],
"source": [
"import intake\n",
"import hvplot.xarray\n",
"import holoviews as hv\n",
"from xhistogram.xarray import histogram\n",
"import numpy as np"
]
},
{
"cell_type": "markdown",
"id": "be8da7c3-eb15-4887-95bd-81dd4edca108",
"metadata": {},
"source": [
"## Open data from Intake catalog\n",
"\n",
"Zarr in Google Cloud Storage, opened with Xarray"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "38a27799-ee7e-46b4-a1b4-5bb616617322",
"metadata": {},
"outputs": [],
"source": [
"cat = intake.open_catalog(\"https://raw.githubusercontent.com/pangeo-data/pangeo-datastore/master/intake-catalogs/ocean/CESM_POP.yaml\")\n",
"ds = cat['CESM_POP_hires_control'](chunks=None).to_dask().reset_coords()\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "de04e337-1c62-43e1-a5d9-7e375a40a815",
"metadata": {},
"outputs": [],
"source": [
"ds.nbytes/1e12"
]
},
{
"cell_type": "markdown",
"id": "126b2166-dbe6-4b44-bc15-15656eb2c73e",
"metadata": {},
"source": [
"## Interactive exploration with Holoviews"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "519d567d-5b1a-4e84-b77d-d90597beca24",
"metadata": {},
"outputs": [],
"source": [
"hv.output(widget_location='bottom', widget_type='scrubber')\n",
"opts = dict(kind='image', x='nlon', y='nlat', rasterize=True, width=800, height=400)\n",
"\n",
"(ds.SST.hvplot(cmap='magma', label='Temperature', **opts).opts(bgcolor='lightgray') +\n",
" ds.SSS.hvplot(cmap='viridis', label='Salinity', **opts).opts(bgcolor='lightgray'))"
]
},
{
"cell_type": "markdown",
"id": "af7c85d5-a851-40e9-9796-7431f2b16c7b",
"metadata": {},
"source": [
"## Compute some Joint Histograms of Temperature and Salinity"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "cca53eb7-be8e-4327-96e9-1336586006a3",
"metadata": {},
"outputs": [],
"source": [
"t_bins = np.linspace(-2, 30, 500)\n",
"s_bins = np.linspace(30, 40, 500)\n",
"\n",
"dsc = ds.chunk({\"time\": \"auto\"})\n",
"ts_hist = histogram(dsc.SSS, dsc.SST, bins=[s_bins, t_bins], dim=('nlon', 'nlat'))\n",
"ts_hist"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "22729d53-7939-4820-bd81-2a3acf08a86f",
"metadata": {},
"outputs": [],
"source": [
"from matplotlib.colors import LogNorm\n",
"test_plot = ts_hist[0]\n",
"test_plot = test_plot.where(test_plot > 0)\n",
"test_plot.plot(x='SSS_bin', norm=LogNorm(), figsize=(12, 8))"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "474657fd-a963-4e13-9441-a15019e58707",
"metadata": {},
"outputs": [],
"source": [
"cluster"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0a89de9b-15ed-492e-949b-689dc6242594",
"metadata": {},
"outputs": [],
"source": [
"with cluster.get_client():\n",
" ts_mean = ts_hist.mean('time').compute()\n",
"ts_mean"
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "23740d48-2c42-4273-8bba-ddca8bef582f",
"metadata": {},
"outputs": [
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"</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;histogram_SSS_SST&#x27; (SSS_bin: 499, SST_bin: 499)&gt;\n",
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" * SST_bin (SST_bin) float64 -1.968 -1.904 -1.84 -1.776 ... 29.84 29.9 29.97</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'histogram_SSS_SST'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>SSS_bin</span>: 499</li><li><span class='xr-has-index'>SST_bin</span>: 499</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-89a1d425-7d31-4d93-9777-3ae8fe1a5ab9' class='xr-array-in' type='checkbox' checked><label for='section-89a1d425-7d31-4d93-9777-3ae8fe1a5ab9' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(499, 499), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>\n",
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" </td>\n",
" </tr>\n",
"</table></div></div></li><li class='xr-section-item'><input id='section-90976568-43cc-463e-81b7-d0db4840dd87' class='xr-section-summary-in' type='checkbox' checked><label for='section-90976568-43cc-463e-81b7-d0db4840dd87' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>SSS_bin</span></div><div class='xr-var-dims'>(SSS_bin)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>30.01 30.03 30.05 ... 39.97 39.99</div><input id='attrs-661f5b00-4bf9-431b-a60a-f7652a2b719c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-661f5b00-4bf9-431b-a60a-f7652a2b719c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1b6266ca-74e0-406a-bc6b-ce948f104442' class='xr-var-data-in' type='checkbox'><label for='data-1b6266ca-74e0-406a-bc6b-ce948f104442' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>cell_methods :</span></dt><dd>time: mean</dd><dt><span>grid_loc :</span></dt><dd>2110</dd><dt><span>long_name :</span></dt><dd>Surface Salinity</dd><dt><span>units :</span></dt><dd>gram/kilogram</dd></dl></div><div class='xr-var-data'><pre>array([30.01002, 30.03006, 30.0501 , ..., 39.9499 , 39.96994, 39.98998])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>SST_bin</span></div><div class='xr-var-dims'>(SST_bin)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>-1.968 -1.904 -1.84 ... 29.9 29.97</div><input id='attrs-7d377057-08c2-4cb0-868a-a07d21b2b077' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7d377057-08c2-4cb0-868a-a07d21b2b077' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ab0ee77d-74b3-4d81-8427-a0a3947e7c70' class='xr-var-data-in' type='checkbox'><label for='data-ab0ee77d-74b3-4d81-8427-a0a3947e7c70' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>cell_methods :</span></dt><dd>time: mean</dd><dt><span>grid_loc :</span></dt><dd>2110</dd><dt><span>long_name :</span></dt><dd>Surface Potential Temperature</dd><dt><span>units :</span></dt><dd>degC</dd></dl></div><div class='xr-var-data'><pre>array([-1.967936, -1.903808, -1.839679, ..., 29.839679, 29.903808, 29.967936])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-65d8a295-b8f2-46ab-a7b0-3434ef6fab45' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-65d8a295-b8f2-46ab-a7b0-3434ef6fab45' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
],
"text/plain": [
"<xarray.DataArray 'histogram_SSS_SST' (SSS_bin: 499, SST_bin: 499)>\n",
"dask.array<mean_agg-aggregate, shape=(499, 499), dtype=float64, chunksize=(499, 499), chunktype=numpy.ndarray>\n",
"Coordinates:\n",
" * SSS_bin (SSS_bin) float64 30.01 30.03 30.05 30.07 ... 39.95 39.97 39.99\n",
" * SST_bin (SST_bin) float64 -1.968 -1.904 -1.84 -1.776 ... 29.84 29.9 29.97"
]
},
"execution_count": 42,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ts_mean.plot(x='SSS_bin', norm=LogNorm(), figsize=(12, 8))"
]
},
{
"cell_type": "markdown",
"id": "c80e1f40-dd60-46ae-a9ec-c5493e095c7e",
"metadata": {},
"source": [
"&nbsp;\n",
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]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "8989cad3-841c-4cb8-8cfc-941ef557239e",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/srv/conda/envs/notebook/lib/python3.9/site-packages/dask_gateway/client.py:21: FutureWarning: format_bytes is deprecated and will be removed in a future release. Please use dask.utils.format_bytes instead.\n",
" from distributed.utils import LoopRunner, format_bytes\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "c3c9e68f02a145c1905820893bac753a",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"VBox(children=(HTML(value='<h2>GatewayCluster</h2>'), HBox(children=(HTML(value='\\n<div>\\n<style scoped>\\n …"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from dask_gateway import Gateway\n",
"gateway = Gateway()\n",
"cluster = gateway.new_cluster(worker_cores=1, worker_memory=10)\n",
"cluster.scale(30)\n",
"cluster"
]
},
{
"cell_type": "code",
"execution_count": 45,
"id": "5f280c95-715c-47d9-9f2b-dc2a610957f7",
"metadata": {},
"outputs": [],
"source": [
"cluster.scale(0)\n",
"cluster.close()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e4aa93b7-2abb-4196-8e3f-2126d42cce46",
"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": "3.9.7"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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