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andrewdelmanandrewdelman
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some more tutorial updates for ecco_access
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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Example_MHT.ipynb‎

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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Example_OSNAP.ipynb‎

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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Example_calculations_with_scalar_quantities.ipynb‎

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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Gradient_calc_on_native_grid.ipynb‎

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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Heat_budget_closure.ipynb‎

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@@ -7,7 +7,7 @@
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"# Global Heat Budget Closure\n",
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"*Contributors*: [Jan-Erik Tesdal](https://github.com/jetesdal), [Ryan Abernathey](https://github.com/rabernat), [Ian Fenty](https://github.com/ifenty), and [Andrew Delman](https://github.com/andrewdelman)\n",
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"\n",
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"Updated 2024-10-16\n",
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"Updated 2024-10-17\n",
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"\n",
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"A major part of this tutorial is based on \"*A Note on Practical Evaluation of Budgets in ECCO Version 4 Release 3\"* by Christopher G. Piecuch (https://ecco.jpl.nasa.gov/drive/files/Version4/Release3/doc/v4r3_budgets_howto.pdf). Calculation steps and Python code presented here are converted from the MATLAB code presented in the above reference."
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]
@@ -220,8 +220,7 @@
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"## Set top-level file directory for the ECCO NetCDF files\n",
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"## =================================================================\n",
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"\n",
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"## currently set to /efs_ecco/ECCO_V4r4_PODAAC, \n",
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"## the default if ecco_podaac_download was used to download dataset granules\n",
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"## currently set to ~/Downloads/ECCO_V4r4_PODAAC\n",
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"ECCO_dir = join(user_home_dir,'ECCO_V4r4_PODAAC')\n",
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"\n",
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"# # for access_mode = 's3_open_fsspec', need to specify the root directory \n",

‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Interpolating_Fields_to_LatLon_Grid.ipynb‎

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‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Plotting_Tiles.ipynb‎

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@@ -53,7 +53,9 @@
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"\n",
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"## Plotting single tiles using ``imshow``, ``pcolormesh``, and ``contourf``\n",
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"\n",
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"First, let's load the all 13 tiles for sea surface height and the model grid parameters."
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"First, let's load the all 13 tiles for sea surface height and the model grid parameters.\n",
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"\n",
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"> **Note:** The notebook uses the `ecco_access` library to download (or direct access in the AWS Cloud) the ECCO output. It is recommended to set up `ecco_access` [in your Python path](https://ecco-v4-python-tutorial.readthedocs.io/ECCO_access_intro.html#Setting-up-ecco_access), if you haven't already."
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]
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},
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{
@@ -71,9 +73,20 @@
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"import warnings\n",
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"warnings.filterwarnings('ignore')\n",
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"\n",
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"\n",
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"# indicate whether you are working in a cloud instance (True if yes, False otherwise)\n",
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"incloud_access = False"
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"import ecco_access as ea\n",
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"\n",
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"# indicate mode of access\n",
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"# options are:\n",
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"# 'download': direct download from internet to your local machine\n",
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"# 'download_ifspace': like download, but only proceeds \n",
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"# if your machine have sufficient storage\n",
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"# 's3_open': access datasets in-cloud from an AWS instance\n",
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"# 's3_open_fsspec': use jsons generated with fsspec and \n",
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"# kerchunk libraries to speed up in-cloud access\n",
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"# 's3_get': direct download from S3 in-cloud to an AWS instance\n",
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"# 's3_get_ifspace': like s3_get, but only proceeds if your instance \n",
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"# has sufficient storage\n",
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"access_mode = 'download_ifspace'"
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]
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},
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{
@@ -121,9 +134,12 @@
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"## Set top-level file directory for the ECCO NetCDF files\n",
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"## =================================================================\n",
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"\n",
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"## currently set to ~/Downloads/ECCO_V4r4_PODAAC, \n",
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"## the default if ecco_podaac_download was used to download dataset granules\n",
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"ECCO_dir = join(user_home_dir,'Downloads','ECCO_V4r4_PODAAC')"
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"## currently set to /Downloads/ECCO_V4r4_PODAAC\n",
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"ECCO_dir = join(user_home_dir,'Downloads','ECCO_V4r4_PODAAC')\n",
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"\n",
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"# # for access_mode = 's3_open_fsspec', need to specify the root directory \n",
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"# # containing the jsons\n",
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"# jsons_root_dir = join('/efs_ecco','mzz-jsons')"
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]
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},
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{
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"ShortNames_list = [\"ECCO_L4_GEOMETRY_LLC0090GRID_V4R4\",\\\n",
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" \"ECCO_L4_SSH_LLC0090GRID_MONTHLY_V4R4\",\\\n",
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" \"ECCO_L4_TEMP_SALINITY_LLC0090GRID_MONTHLY_V4R4\"]\n",
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"if incloud_access == True:\n",
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" from ecco_s3_retrieve import ecco_podaac_s3_get_diskaware\n",
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" files_dict = ecco_podaac_s3_get_diskaware(ShortNames=ShortNames_list,\\\n",
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"\n",
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"ds_dict = ea.ecco_podaac_access(ShortNames_list,\\\n",
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" StartDate='2000-01',EndDate='2000-12',\\\n",
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" max_avail_frac=0.5,\\\n",
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" download_root_dir=ECCO_dir)\n",
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" ecco_grid = xr.open_dataset(files_dict[ShortNames_list[0]])\n",
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" ds_SSH = xr.open_mfdataset(files_dict[ShortNames_list[1]],\\\n",
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" compat='override',data_vars='minimal',coords='minimal')\n",
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" ds_temp_sal = xr.open_mfdataset(files_dict[ShortNames_list[2]],\\\n",
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" compat='override',data_vars='minimal',coords='minimal')\n",
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"else:\n",
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" ecco_grid = xr.open_dataset(glob.glob(join(ECCO_dir,ShortNames_list[0],'*.nc'))[0])\n",
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" ds_SSH = xr.open_mfdataset(glob.glob(join(ECCO_dir,ShortNames_list[1],'*2000-*.nc')),\\\n",
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" compat='override',data_vars='minimal',coords='minimal')\n",
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" ds_temp_sal = xr.open_mfdataset(glob.glob(join(ECCO_dir,ShortNames_list[2],'*2000-*.nc')),\\\n",
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" compat='override',data_vars='minimal',coords='minimal')\n",
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" download_root_dir=ECCO_dir,\\\n",
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" max_avail_frac=0.5)\n",
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"\n",
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"ecco_grid = ds_dict[ShortNames_list[0]]\n",
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"ds_SSH = ds_dict[ShortNames_list[1]]\n",
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"ds_temp_sal = ds_dict[ShortNames_list[2]]\n",
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"\n",
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"## select only *surface* temperature and salinity (SST and SSS)\n",
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"ds_SST_SSS = ds_temp_sal.isel(k=0)\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.8"
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"version": "3.11.9"
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}
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},
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"nbformat": 4,

‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Salt_and_salinity_budget.ipynb‎

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"# Salt, Salinity and Freshwater Budgets\n",
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"*Contributors*: [Jan-Erik Tesdal](https://github.com/jetesdal), [Ryan Abernathey](https://github.com/rabernat), [Ian Fenty](https://github.com/ifenty), [Emma Boland](https://github.com/emmomp), and [Andrew Delman](https://github.com/andrewdelman).\n",
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"\n",
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"Updated 2024-10-17\n",
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"\n",
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"A major part of this tutorial is based on \"*A Note on Practical Evaluation of Budgets in ECCO Version 4 Release 3\"* by Christopher G. Piecuch (https://dspace.mit.edu/handle/1721.1/111094?show=full). Calculation steps and Python code presented here are converted from the MATLAB code presented in the above reference."
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"## Set top-level file directory for the ECCO NetCDF files\n",
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"## =================================================================\n",
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"\n",
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"## currently set to /efs_ecco/ECCO_V4r4_PODAAC, \n",
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"## the default if ecco_podaac_download was used to download dataset granules\n",
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"## currently set to ~/Downloads/ECCO_V4r4_PODAAC\n",
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"ECCO_dir = join(user_home_dir,'ECCO_V4r4_PODAAC')\n",
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"\n",
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"# # for access_mode = 's3_open_fsspec', need to specify the root directory \n",

‎Tutorials_as_Jupyter_Notebooks/ECCO_v4_Volume_budget_closure.ipynb‎

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"## Set top-level file directory for the ECCO NetCDF files\n",
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"## =================================================================\n",
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"\n",
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"## currently set to /efs_ecco/ECCO_V4r4_PODAAC, \n",
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"## the default if ecco_podaac_download was used to download dataset granules\n",
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"## currently set to ~/Downloads/ECCO_V4r4_PODAAC\n",
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"ECCO_dir = join(user_home_dir,'ECCO_V4r4_PODAAC')\n",
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"\n",
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"# # for access_mode = 's3_open_fsspec', need to specify the root directory \n",

‎Tutorials_as_Jupyter_Notebooks/Untitled.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "ad5ec9ef-46c3-4446-b5ee-233ad7ed2283",
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"metadata": {},
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"outputs": [],
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"source": [
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"from ecco_s3_retrieve import *"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "a7b41b61-b63c-4696-b146-34f65c923aa2",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Help on function ecco_podaac_s3_open in module ecco_s3_retrieve:\n",
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"\n",
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"ecco_podaac_s3_open(ShortName, StartDate, EndDate)\n",
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" This routine searches for and opens ECCO datasets from S3 buckets in the PO.DAAC Cloud.\n",
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" It returns a list of opened file(s) on S3 that can be passed to xarray.\n",
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" This function is intended to be called from an EC2 instance running in AWS region us-west-2.\n",
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" \n",
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" Parameters\n",
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" ----------\n",
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" ShortName: str, the ShortName that identifies the dataset on PO.DAAC.\n",
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" \n",
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" StartDate,EndDate: str, in 'YYYY', 'YYYY-MM', or 'YYYY-MM-DD' format, \n",
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" define date range [StartDate,EndDate] for download.\n",
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" EndDate is included in the time range (unlike typical Python ranges).\n",
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" ECCOv4r4 date range is '1992-01-01' to '2017-12-31'.\n",
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" For 'SNAPSHOT' datasets, an additional day is added to EndDate to enable closed budgets\n",
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" within the specified date range.\n",
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" \n",
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" Returns\n",
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" -------\n",
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" open_files: str or list, opened file(s) on S3 that can be passed directly to xarray (open_dataset or open_mfdataset)\n",
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"\n"
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]
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}
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],
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"source": [
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"help(ecco_podaac_s3_open)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "5dd4f5ad-8e63-4ea1-880d-35ff89499aff",
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"import xarray as xr"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "01e934e2-f796-4314-a60c-1ded8f5297ad",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Please provide Earthdata Login credentials for access.\n"
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]
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},
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{
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"name": "stdin",
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"output_type": "stream",
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"text": [
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"Username: adelman\n"
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]
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},
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{
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"ename": "NameError",
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"evalue": "name 'getpass' is not defined",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
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"File \u001b[0;32m~/ECCO-v4-Python-Tutorial/Tutorials_as_Jupyter_Notebooks/ecco_s3_retrieve.py:63\u001b[0m, in \u001b[0;36mecco_podaac_s3_query.<locals>.setup_earthdata_login_auth\u001b[0;34m(url)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 63\u001b[0m username, _, password \u001b[38;5;241m=\u001b[39m \u001b[43mnetrc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m_netrc\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mauthenticators(url)\n\u001b[1;32m 65\u001b[0m \u001b[38;5;66;03m# if the file is not found, prompt the user for the login/password\u001b[39;00m\n",
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"File \u001b[0;32m/srv/conda/envs/notebook/lib/python3.11/netrc.py:74\u001b[0m, in \u001b[0;36mnetrc.__init__\u001b[0;34m(self, file)\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 74\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mencoding\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mutf-8\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m fp:\n\u001b[1;32m 75\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_parse(file, fp, default_netrc)\n",
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"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/home/jovyan/.netrc'",
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"\nDuring handling of the above exception, another exception occurred:\n",
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"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m files \u001b[38;5;241m=\u001b[39m \u001b[43mecco_podaac_s3_open\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mECCO_L4_SSH_LLC0090GRID_MONTHLY_V4R4\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m\\\u001b[49m\n\u001b[1;32m 2\u001b[0m \u001b[43m \u001b[49m\u001b[43mStartDate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m2000-01\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43mEndDate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m2000-12\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/ECCO-v4-Python-Tutorial/Tutorials_as_Jupyter_Notebooks/ecco_s3_retrieve.py:362\u001b[0m, in \u001b[0;36mecco_podaac_s3_open\u001b[0;34m(ShortName, StartDate, EndDate)\u001b[0m\n\u001b[1;32m 359\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m \n\u001b[1;32m 361\u001b[0m \u001b[38;5;66;03m# get list of files\u001b[39;00m\n\u001b[0;32m--> 362\u001b[0m s3_files_list \u001b[38;5;241m=\u001b[39m \u001b[43mecco_podaac_s3_query\u001b[49m\u001b[43m(\u001b[49m\u001b[43mShortName\u001b[49m\u001b[43m,\u001b[49m\u001b[43mStartDate\u001b[49m\u001b[43m,\u001b[49m\u001b[43mEndDate\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 364\u001b[0m num_grans \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlen\u001b[39m(s3_files_list)\n\u001b[1;32m 365\u001b[0m \u001b[38;5;28mprint\u001b[39m (\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124mTotal number of matching granules: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnum_grans\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n",
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"File \u001b[0;32m~/ECCO-v4-Python-Tutorial/Tutorials_as_Jupyter_Notebooks/ecco_s3_retrieve.py:169\u001b[0m, in \u001b[0;36mecco_podaac_s3_query\u001b[0;34m(ShortName, StartDate, EndDate)\u001b[0m\n\u001b[1;32m 163\u001b[0m EndDate \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mstr\u001b[39m(np\u001b[38;5;241m.\u001b[39mdatetime64(EndDate,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mD\u001b[39m\u001b[38;5;124m'\u001b[39m) \u001b[38;5;241m+\u001b[39m np\u001b[38;5;241m.\u001b[39mtimedelta64(\u001b[38;5;241m1\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mD\u001b[39m\u001b[38;5;124m'\u001b[39m))\n\u001b[1;32m 166\u001b[0m \u001b[38;5;66;03m## Log into Earthdata using your username and password\u001b[39;00m\n\u001b[1;32m 167\u001b[0m \n\u001b[1;32m 168\u001b[0m \u001b[38;5;66;03m# actually log in with this command:\u001b[39;00m\n\u001b[0;32m--> 169\u001b[0m \u001b[43msetup_earthdata_login_auth\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 171\u001b[0m \u001b[38;5;66;03m# Query the NASA Common Metadata Repository to find the URL of every granule associated with the desired \u001b[39;00m\n\u001b[1;32m 172\u001b[0m \u001b[38;5;66;03m# ECCO Dataset and date range of interest.\u001b[39;00m\n\u001b[1;32m 173\u001b[0m \n\u001b[1;32m 174\u001b[0m \u001b[38;5;66;03m# create a Python dictionary with our search criteria: `ShortName` and `temporal`\u001b[39;00m\n\u001b[1;32m 175\u001b[0m input_search_params \u001b[38;5;241m=\u001b[39m {\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mShortName\u001b[39m\u001b[38;5;124m'\u001b[39m: ShortName,\n\u001b[1;32m 176\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtemporal\u001b[39m\u001b[38;5;124m'\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([StartDate, EndDate])}\n",
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"File \u001b[0;32m~/ECCO-v4-Python-Tutorial/Tutorials_as_Jupyter_Notebooks/ecco_s3_retrieve.py:68\u001b[0m, in \u001b[0;36mecco_podaac_s3_query.<locals>.setup_earthdata_login_auth\u001b[0;34m(url)\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\u001b[38;5;167;01mFileNotFoundError\u001b[39;00m, \u001b[38;5;167;01mTypeError\u001b[39;00m):\n\u001b[1;32m 67\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPlease provide Earthdata Login credentials for access.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m---> 68\u001b[0m username, password \u001b[38;5;241m=\u001b[39m \u001b[38;5;28minput\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mUsername: \u001b[39m\u001b[38;5;124m'\u001b[39m), \u001b[43mgetpass\u001b[49m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPassword: \u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 70\u001b[0m manager \u001b[38;5;241m=\u001b[39m request\u001b[38;5;241m.\u001b[39mHTTPPasswordMgrWithDefaultRealm()\n\u001b[1;32m 71\u001b[0m manager\u001b[38;5;241m.\u001b[39madd_password(\u001b[38;5;28;01mNone\u001b[39;00m, url, username, password)\n",
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"\u001b[0;31mNameError\u001b[0m: name 'getpass' is not defined"
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]
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}
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],
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"source": [
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"files = ecco_podaac_s3_open(\"ECCO_L4_SSH_LLC0090GRID_MONTHLY_V4R4\",\\\n",
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" StartDate='2000-01',EndDate='2000-12')"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.9"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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