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add an xarray example
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@sjdaines
sjdaines committed Dec 22, 2024
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{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"id": "68667024",
"metadata": {},
"source": [
"# Example reading netcdf output using python xarray\n",
"\n",
"Generate file 'test.nc' with:\n",
"\n",
" julia> include(\"MITgcm_2deg8_PO4MMcarbSCH4.jl\")\n",
" julia> PALEOmodel.OutputWriters.save_netcdf(paleorun.output, \"MITgcm_PO4MMcarbSCH42deg8.nc\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d640c5a0",
"metadata": {},
"outputs": [],
"source": [
"import os"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c9a1bd15",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"import xarray as xr"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a5ddcd9d",
"metadata": {},
"outputs": [],
"source": [
"os.getcwd()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "401e5aef",
"metadata": {},
"outputs": [],
"source": [
"# read top-level dataset\n",
"ds = xr.open_dataset(\"MITgcm_PO4MMcarbSCH42deg8.nc\")\n",
"ds.attrs"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4b80a015",
"metadata": {},
"outputs": [],
"source": [
"# read ocean group (= PALEO Domain ocean) from netcdf file\n",
"ds_ocean = xr.open_dataset(\"MITgcm_PO4MMcarbSCH42deg8.nc\", group=\"ocean\")\n",
"\n",
"# attach z coordinates (this is not automatic!)\n",
"ds_ocean = ds_ocean.set_coords([\"zmid\", \"zlower\", \"zupper\"])"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8ef1c0ef",
"metadata": {
"scrolled": false
},
"outputs": [],
"source": [
"ds_ocean"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "11dcd1af",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"# timeseries for a scalar variable\n",
"print(ds_ocean[\"O2_total\"])\n",
"ds_ocean[\"O2_total\"].plot()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1c315b33",
"metadata": {},
"outputs": [],
"source": [
"# surface P_conc at last timestep\n",
"P_conc = ds_ocean.P_conc\n",
"P_conc"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2d8967e3",
"metadata": {},
"outputs": [],
"source": [
"# P_conc at last timestep\n",
"P_conc_last = ds_ocean.P_conc.isel(tmodel=6) # NB: zero-based !\n",
"P_conc_last"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f96a43bd",
"metadata": {},
"outputs": [],
"source": [
"# surface P_conc at last timestep\n",
"P_conc_last_surface = ds_ocean.P_conc.isel(tmodel=6).isel(zt=0) # NB: zero-based !\n",
"P_conc_last_surface"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "937c6815",
"metadata": {},
"outputs": [],
"source": [
"P_conc_last_surface.plot()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "245e512c",
"metadata": {},
"outputs": [],
"source": [
"# section P_conc at last timestep\n",
"P_conc_last_section = ds_ocean.P_conc.isel(tmodel=6).sel(lon=200.0, method=\"nearest\") # NB: zero-based !\n",
"P_conc_last_section"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ecb644c7",
"metadata": {},
"outputs": [],
"source": [
"P_conc_last_section.plot()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b70a2ee3",
"metadata": {},
"outputs": [],
"source": [
"# sections by faceting\n",
"\n",
"P_conc_last_3sections = ds_ocean.P_conc.isel(tmodel=6).sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"P_conc_last_3sections"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6a4ddf13",
"metadata": {},
"outputs": [],
"source": [
"P_conc_last_3sections.plot(col=\"lon\", col_wrap=3)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "3c910a6d",
"metadata": {},
"outputs": [],
"source": [
"# O_conc at last timestep\n",
"O2_conc_last_3sections = ds_ocean.O2_conc.isel(tmodel=6).sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"O2_conc_last_3sections.plot(col=\"lon\", col_wrap=3, vmin=0)\n",
"\n",
"# H2S_conc at last timestep\n",
"H2S_conc_last_3sections = ds_ocean.H2S_conc.isel(tmodel=6).sel(isotopelinear=\"total\").sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"H2S_conc_last_3sections.plot(col=\"lon\", col_wrap=3, vmin=0)\n",
"\n",
"# H2S d34S at last timestep\n",
"H2S_d34S_last_3sections = ds_ocean.H2S_conc.isel(tmodel=6).sel(isotopelinear=\"delta\").sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"H2S_d34S_last_3sections.plot(col=\"lon\", col_wrap=3)\n",
"\n",
"# CH4_conc at last timestep\n",
"CH4_conc_last_3sections = ds_ocean.CH4_conc.isel(tmodel=6).sel(isotopelinear=\"total\").sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"CH4_conc_last_3sections.plot(col=\"lon\", col_wrap=3, vmin=0)\n",
"\n",
"# CH4 d13C at last timestep\n",
"CH4_d13C_last_3sections = ds_ocean.CH4_conc.isel(tmodel=6).sel(isotopelinear=\"delta\").sel(lon=[70.0, 200.0, 340.0], method=\"nearest\") # NB: zero-based !\n",
"CH4_d13C_last_3sections.plot(col=\"lon\", col_wrap=3)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "80eef703",
"metadata": {},
"outputs": [],
"source": [
"# column at ~Pacific OMZ\n",
"\n",
"H2S_conc_PacOMZ = ds_ocean.H2S_conc.isel(tmodel=6).sel(isotopelinear=\"total\").sel(lon=260, lat=0, method=\"nearest\") # NB: zero-based !\n",
"\n",
"H2S_conc_PacOMZ"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d3f24850",
"metadata": {},
"outputs": [],
"source": [
"# columns from 3 lon sections at lat = 0\n",
"H2S_conc_depth_3lon = ds_ocean.H2S_conc.isel(tmodel=6).sel(isotopelinear=\"total\").sel(lon=[70.0, 200.0, 260.0, 340.0], lat=0, method=\"nearest\") \n",
"H2S_conc_depth_3lon.plot.line(y=\"zmid\", hue=\"lon\")\n",
"# TODO - use zlower, zupper to create a stepped plot"
]
}
],
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"file_extension": ".py",
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