EOF analysis on model data

notebooks/.virtual_documents/cesmLME.ipynb

@@ -0,0 +1,83 @@
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+import s3fs
+import fsspec
+import xarray as xr
+import glob
+
+
+
+
+
+URL = 'https://js2.jetstream-cloud.org:8001/'
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+path = f'pythia/cesmLME'
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+fs = fsspec.filesystem("s3", anon=True, client_kwargs=dict(endpoint_url=URL))
+
+
+pattern = f's3://{path}/*.nc'
+
+
+files = sorted(fs.glob(pattern))
+
+
+
+
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+files[0:2]
+
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+fileset = [fs.open(file) for file in files[0:2]]
+
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+data = xr.open_dataset(fileset[0])
+
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+data
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+
+
+# This works
+dataMul = xr.open_mfdataset(fileset[:3], combine='by_coords')
+
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+dataMul
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notebooks/.virtual_documents/notebook-template.ipynb

@@ -19,17 +19,134 @@
 
 
 
-import sys
+#To deal with model data
+import s3fs
+import fsspec
+import xarray as xr
+import glob
 
+#To deal with proxy data
+import pandas as pd
+import numpy as np
 
+#To deal with analysis
+import pyleoclim as pyleo
+from eofs.xarray import Eof
 
+#Plotting and mapping
+import cartopy.crs as ccrs
+import matplotlib.pyplot as plt
 
 
 
 
 
-# as well as any and all of your code cells
-print("Hello world!")
+
+
+
+URL = 'https://js2.jetstream-cloud.org:8001/' #Locate and read a file
+
+
+path = f'pythia/cesmLME' # specify data location
+
+
+fs = fsspec.filesystem("s3", anon=True, client_kwargs=dict(endpoint_url=URL)) 
+pattern = f's3://{path}/*.nc'
+files = sorted(fs.glob(pattern))
+
+
+
+
+
+base_name = 'pythia/cesmLME/b.ie12.B1850C5CN.f19_g16.LME.002.cam.h0.'
+time_period =  '085001-184912'
+
+names = [name for name in files if base_name in name and time_period in name]
+
+names
+
+
+fileset = [fs.open(file) for file in names]
+
+
+
+
+
+%%time
+for idx,item in enumerate(fileset):
+    ds_u = xr.open_dataset(item)
+    var_name = names[idx].split('.')[-3]
+    da = ds_u[var_name]
+    try:
+        ds[var_name]= da
+    except:
+        ds = da.to_dataset()
+        ds.attrs = ds_u.attrs 
+    ds_u.close()
+    da.close()
+
+
+ds
+
+
+
+
+
+ds_geo = ds.sel(lat=slice(-27,27), lon=slice(250,330))
+
+
+
+
+
+#ds_geo.to_netcdf(path='../data/LME.002.cam.h0.precip_iso.085001-184912.nc')
+
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+ds_geo
+
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+
+
+
+%%time
+p16O = ds_geo['PRECRC_H216Or'] + ds_geo['PRECSC_H216Os'] + ds_geo['PRECRL_H216OR'] + ds_geo['PRECSL_H216OS']
+p18O = ds_geo['PRECRC_H218Or'] + ds_geo['PRECSC_H218Os'] + ds_geo['PRECRL_H218OR'] + ds_geo['PRECSL_H218OS']
+
+p16O = p16O.where(p16O > 1e-18, 1e-18)
+p18O = p18O.where(p18O > 1e-18, 1e-18)
+
+d18Op = (p18O / p16O - 1)*1000
+
+
+
+
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+d18Oa = d18Op - d18Op.mean(dim='time')
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+
+
+solver = Eof(d18Oa, weights=None)
+
+
+
+
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+eof1 = solver.eofsAsCovariance(neofs=1)
+
+
+
+
+
+clevs = np.linspace(-2, 5, 20)
+proj = ccrs.PlateCarree(central_longitude=290)
+ax = plt.axes(projection=proj)
+ax.coastlines()
+#ax.set_global()
+eof1[0].plot.contourf(ax=ax, levels = clevs, cmap=plt.cm.RdBu_r,
+                         transform=ccrs.PlateCarree(), add_colorbar=True)
+ax.set_title('EOF1 expressed as covariance', fontsize=16)
+plt.show()
 
 
 

notebooks/cesmLME.ipynb

@@ -26,10 +26,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "f7604cb4-59ec-4068-adeb-b79aadb50db7",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 's3fs'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01ms3fs\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mxarray\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mxr\u001b[39;00m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 's3fs'"
+     ]
+    }
+   ],
    "source": [
     "import s3fs\n",
     "import fsspec\n",