├── reticfox
    ├── __init__.py
    ├── api.py
    └── cli.py
├── environment.yml
├── README.md
├── setup.py
├── .gitignore
├── hpc_job_d18osw.sh
├── hpc_job_seatemps.sh
├── parse_icesm.sh
├── download_icesm.py
└── LICENSE


/reticfox/__init__.py:
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1 | 


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/environment.yml:
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 1 | name: reticfox
 2 | channels:
 3 |   - conda-forge
 4 |   - defaults
 5 | dependencies:
 6 |   - bottleneck
 7 |   - dask
 8 |   - gsw
 9 |   - netCDF4
10 |   - pip
11 |   - pyngl
12 |   - python>=3.6
13 |   - scipy
14 |   - xarray
15 |   - click
16 |   - pip:
17 |     - globus-cli


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/README.md:
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 1 | # reticfox
 2 | Scripts to parse and move iCESM LGM slices for LGM Data Assimilation.
 3 | 
 4 | # Installation
 5 | These scripts have strong dependencies. You can install these dependencies into a [`conda`](https://conda.io/en/latest/miniconda.html) environment. With `conda` installed, create the environment with:
 6 | 
 7 | ```bash
 8 | conda env create -f environment.yml
 9 | ```
10 | 
11 | Then activate the environment with:
12 | 
13 | ```bash
14 | conda activate icesm_parse
15 | ```
16 | 


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/setup.py:
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 1 | from setuptools import setup, find_packages
 2 | 
 3 | setup(
 4 |     name='reticfox',
 5 |     version='0.0.1a',
 6 |     license='GPLv3',
 7 |     description='Scripts to parse and move iCESM LGM slices for LGM Data Assimilation',
 8 | 
 9 |     author='S. Brewster Malevich',
10 |     author_email='malevich@email.arizona.edu',
11 |     url='https://github.com/brews/reticfox',
12 | 
13 |     packages=find_packages(),
14 |     install_requires=['numpy', 'scipy', 'xarray', 'click', 'Ngl', 'dask', 'gsw'],
15 | 
16 |     entry_points={
17 |         'console_scripts': [
18 |             'reticfox = reticfox.cli:reticfox_cli',
19 |         ]
20 |     },
21 | )
22 | 


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/.gitignore:
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  1 | # Byte-compiled / optimized / DLL files
  2 | __pycache__/
  3 | *.py[cod]
  4 | *$py.class
  5 | 
  6 | # C extensions
  7 | *.so
  8 | 
  9 | # Distribution / packaging
 10 | .Python
 11 | build/
 12 | develop-eggs/
 13 | dist/
 14 | downloads/
 15 | eggs/
 16 | .eggs/
 17 | lib/
 18 | lib64/
 19 | parts/
 20 | sdist/
 21 | var/
 22 | wheels/
 23 | *.egg-info/
 24 | .installed.cfg
 25 | *.egg
 26 | MANIFEST
 27 | 
 28 | # PyInstaller
 29 | #  Usually these files are written by a python script from a template
 30 | #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 31 | *.manifest
 32 | *.spec
 33 | 
 34 | # Installer logs
 35 | pip-log.txt
 36 | pip-delete-this-directory.txt
 37 | 
 38 | # Unit test / coverage reports
 39 | htmlcov/
 40 | .tox/
 41 | .coverage
 42 | .coverage.*
 43 | .cache
 44 | nosetests.xml
 45 | coverage.xml
 46 | *.cover
 47 | .hypothesis/
 48 | .pytest_cache/
 49 | 
 50 | # Translations
 51 | *.mo
 52 | *.pot
 53 | 
 54 | # Django stuff:
 55 | *.log
 56 | local_settings.py
 57 | db.sqlite3
 58 | 
 59 | # Flask stuff:
 60 | instance/
 61 | .webassets-cache
 62 | 
 63 | # Scrapy stuff:
 64 | .scrapy
 65 | 
 66 | # Sphinx documentation
 67 | docs/_build/
 68 | 
 69 | # PyBuilder
 70 | target/
 71 | 
 72 | # Jupyter Notebook
 73 | .ipynb_checkpoints
 74 | 
 75 | # pyenv
 76 | .python-version
 77 | 
 78 | # celery beat schedule file
 79 | celerybeat-schedule
 80 | 
 81 | # SageMath parsed files
 82 | *.sage.py
 83 | 
 84 | # Environments
 85 | .env
 86 | .venv
 87 | env/
 88 | venv/
 89 | ENV/
 90 | env.bak/
 91 | venv.bak/
 92 | 
 93 | # Spyder project settings
 94 | .spyderproject
 95 | .spyproject
 96 | 
 97 | # Rope project settings
 98 | .ropeproject
 99 | 
100 | # mkdocs documentation
101 | /site
102 | 
103 | # mypy
104 | .mypy_cache/
105 | 
106 | # vscode
107 | *.code-workspace
108 | .vscode/


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/hpc_job_d18osw.sh:
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 1 | #!/usr/bin/env bash
 2 | ### script to run a serial job using one core on htc using queue windfall or standard
 3 | 
 4 | ### beginning of line, three pound/cross-hatch characters indicate comment
 5 | ### beginning of line #PBS indicates an active PBS command/directive
 6 | ### use ###PBS and #PBS to deactivate and activate (respectively PBS lines without removing them from script
 7 | 
 8 | ### Refer to UA Batch System website for system and queue specific limits (max values)
 9 | ### Minimize resource requests (ncpus, mem, walltime, cputime, etc) to minimize queue wait delays
10 | 
11 | ### Set the job name
12 | #PBS -N icesm_open_pop
13 | 
14 | ### Request email when job begins and ends
15 | #PBS -m bea
16 | 
17 | ### Specify email address to use for notification.
18 | #PBS -M malevich@email.arizona.edu
19 | 
20 | ### Specify the PI group for this job
21 | ### List of PI groups available to each user can be found with "va" command
22 | #PBS -W group_list=jesst
23 | 
24 | ### Set the queue for this job as windfall or standard (adjust ### and #)
25 | #PBS -q standard
26 | ####PBS -q windfall
27 | 
28 | ### Set the number of cores (cpus) and memory that will be used for this job
29 | ### When specifying memory request slightly less than 2GB memory per ncpus for standard node
30 | ### Some memory needs to be reserved for the Linux system processes
31 | #PBS -l select=1:ncpus=28:mem=168gb
32 | 
33 | ### Important!!! Include this line for your 1p job.
34 | ### Without it, the entire node, containing 12 core, will be allocated
35 | #PBS -l place=pack:shared
36 | 
37 | ### Specify "wallclock time" required for this job, hhh:mm:ss
38 | #PBS -l walltime=06:00:00
39 | 
40 | ### Specify total cpu time required for this job, hhh:mm:ss
41 | ### total cputime = walltime * ncpus
42 | #PBS -l cput=168:00:00
43 | 
44 | ### Load required modules/libraries if needed (blas example)
45 | ### Use "module avail" command to list all available modules
46 | ### NOTE: /usr/share/Modules/init/csh -CAPITAL M in Modules
47 | #source /usr/share/Modules/init/csh
48 | 
49 | source ~/miniconda3/etc/profile.d/conda.sh
50 | conda activate icesm_parse
51 | 
52 | ### set directory for job execution, ~netid = home directory path
53 | cd /xdisk/malevich/b.e12.B1850C5.f19_g16.i21ka.03/
54 | 
55 | ### run your executable program with begin and end date and time output
56 | date
57 | 
58 | python make_d18osw.py
59 | 
60 | date
61 | 


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/hpc_job_seatemps.sh:
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 1 | #!/usr/bin/env bash
 2 | ### script to run a serial job using one core on htc using queue windfall or standard
 3 | 
 4 | ### beginning of line, three pound/cross-hatch characters indicate comment
 5 | ### beginning of line #PBS indicates an active PBS command/directive
 6 | ### use ###PBS and #PBS to deactivate and activate (respectively PBS lines without removing them from script
 7 | 
 8 | ### Refer to UA Batch System website for system and queue specific limits (max values)
 9 | ### Minimize resource requests (ncpus, mem, walltime, cputime, etc) to minimize queue wait delays
10 | 
11 | ### Set the job name
12 | #PBS -N icesm_open_pop
13 | 
14 | ### Request email when job begins and ends
15 | #PBS -m bea
16 | 
17 | ### Specify email address to use for notification.
18 | #PBS -M malevich@email.arizona.edu
19 | 
20 | ### Specify the PI group for this job
21 | ### List of PI groups available to each user can be found with "va" command
22 | #PBS -W group_list=jesst
23 | 
24 | ### Set the queue for this job as windfall or standard (adjust ### and #)
25 | #PBS -q standard
26 | ####PBS -q windfall
27 | 
28 | ### Set the number of cores (cpus) and memory that will be used for this job
29 | ### When specifying memory request slightly less than 2GB memory per ncpus for standard node
30 | ### Some memory needs to be reserved for the Linux system processes
31 | #PBS -l select=1:ncpus=28:mem=168gb
32 | 
33 | ### Important!!! Include this line for your 1p job.
34 | ### Without it, the entire node, containing 12 core, will be allocated
35 | #PBS -l place=pack:shared
36 | 
37 | ### Specify "wallclock time" required for this job, hhh:mm:ss
38 | #PBS -l walltime=06:00:00
39 | 
40 | ### Specify total cpu time required for this job, hhh:mm:ss
41 | ### total cputime = walltime * ncpus
42 | #PBS -l cput=168:00:00
43 | 
44 | ### Load required modules/libraries if needed (blas example)
45 | ### Use "module avail" command to list all available modules
46 | ### NOTE: /usr/share/Modules/init/csh -CAPITAL M in Modules
47 | #source /usr/share/Modules/init/csh
48 | 
49 | source ~/miniconda3/etc/profile.d/conda.sh
50 | conda activate icesm_parse
51 | 
52 | ### set directory for job execution, ~netid = home directory path
53 | cd /xdisk/malevich/b.e12.B1850C5.f19_g16.i21ka.03/
54 | 
55 | ### run your executable program with begin and end date and time output
56 | date
57 | 
58 | python make_tempga_sst_sss.py
59 | 
60 | date
61 | 


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/reticfox/api.py:
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 1 | import logging
 2 | import numpy as np
 3 | import scipy.stats as stats
 4 | import xarray as xr
 5 | import gsw
 6 | 
 7 | 
 8 | log = logging.getLogger(__name__)
 9 | 
10 | 
11 | def pot2insitu_temp(theta, salt, insitu_temp_name='insitu_temp'):
12 |     """Get insitu temp DataArray from potential temperature (theta) and salinity (salt) dataset
13 | 
14 |     You may need to run ``.compute()`` on the output if dask-enabled and you want numbers.
15 |     """
16 |     # Convert depth (cm) to (m) & positive up.
17 |     # sea pressure (dbar) from depth (m), note it needs latitude as input,
18 |     # unlike ferret and NCL functions.
19 |     p = xr.apply_ufunc(gsw.p_from_z, -theta.z_t * 0.01, theta.TLAT,
20 |                        output_dtypes=['float32'], dask='parallelized')
21 | 
22 |     insitu_temp = xr.apply_ufunc(gsw.pt_from_t, salt.SALT, theta.TEMP, np.array([0]), p,
23 |                                  output_dtypes=['float32'], dask='parallelized')
24 | 
25 |     # Add metadata attributes.
26 |     insitu_temp.name = str(insitu_temp_name)
27 |     insitu_temp.attrs['units'] = 'degC'
28 |     insitu_temp.attrs['long_name'] = 'Sea Temperature (In-situ Temperature)'
29 |     return insitu_temp
30 | 
31 | 
32 | def tex86_gammaavg_depth(ds, target_var='TEMP', gatemp_name='toga'):
33 |     """Return gamma-average DataArray of input temperature Dataset (ds)
34 |     """
35 |     gamma_a = 4.5
36 |     # Original spec from Tierney paper was in m, depth in CCSM and CESM is in cm, so * 100:
37 |     gamma_b = 15.0 * 100
38 | 
39 |     # # If you want to see plot of gamma weights over depth.
40 |     # ideal_depths = np.arange(0, 22510, 10)  # in cm
41 |     # gamma_pdf = stats.gamma.pdf(ideal_depths, a=GAMMA_A, scale=GAMMA_B)
42 |     # plt.plot(ideal_depths, gamma_pdf);plt.xlabel('depth (cm)');plt.show()
43 | 
44 |     # Diff of CDF between bottom of depth "bin" and top of depth "bin". - i.e.
45 |     # the gamma distribution mass within the depth "bin". We're using DataArrays
46 |     # with depth index to ensure this compares apples to apples along depth.
47 |     shallow_cdf = xr.DataArray(stats.gamma.cdf(ds.z_w_top, gamma_a, scale=gamma_b),
48 |                                coords=[ds.z_t], dims=['z_t'])
49 |     deep_cdf = xr.DataArray(stats.gamma.cdf(ds.z_w_bot, gamma_a, scale=gamma_b),
50 |                             coords=[ds.z_t], dims=['z_t'])
51 |     gamma_weights = deep_cdf - shallow_cdf
52 |     # Can see weights with `gamma_weights.plot()`
53 | 
54 |     # gamma_weights /= gamma_weights.sum()  # Normalize, no - not like this... <-
55 |     # Normalize, careful to consider grid points with missing depth values:
56 |     gamma_weights_norm = gamma_weights / \
57 |         (ds[target_var].notnull() * gamma_weights).sum('z_t')
58 |     temp_gamma_avg = (
59 |         ds[target_var] * gamma_weights_norm).sum(dim='z_t')
60 | 
61 |     # Make NA where original was NA.
62 |     temp_gamma_avg = temp_gamma_avg.where(ds[target_var].isel(z_t=0).notnull())
63 | 
64 |     # Add metadata attributes.
65 |     temp_gamma_avg.name = str(gatemp_name)
66 |     temp_gamma_avg.attrs['units'] = 'degC'
67 |     temp_gamma_avg.attrs['long_name'] = 'Sea Temperature (Gamma-average)'
68 | 
69 |     return temp_gamma_avg
70 | 


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/parse_icesm.sh:
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  1 | #! /usr/bin/env bash
  2 | # Parse iCESM POP and CAM files.
  3 | # Be sure you've run `conda activate icesm_parse` before running this script.
  4 | 
  5 | #PBS -N parse_icesm
  6 | #PBS -m bea
  7 | #PBS -M malevich@email.arizona.edu
  8 | #PBS -W group_list=jesst
  9 | #PBS -q standard
 10 | #PBS -l select=1:ncpus=28:mem=168gb
 11 | ### Consider using `pvmem` if have mem problems ^
 12 | #PBS -l place=pack:shared
 13 | #PBS -l walltime=24:00:00
 14 | ### total cputime = walltime * ncpus:
 15 | #PBS -l cput=672:00:00
 16 | 
 17 | source ~/miniconda3/etc/profile.d/conda.sh
 18 | conda activate icesm_parse
 19 | 
 20 | CASENAME="b.e12.B1850C5.f19_g16.i21ka.03"
 21 | IN_DIR="/xdisk/malevich/$CASENAME"
 22 | OUT_DIR="/rsgrps/jesst/icesm/$CASENAME"
 23 | TIMECHUNKS=5
 24 | 
 25 | date
 26 | 
 27 | mkdir -p $OUT_DIR
 28 | 
 29 | # atm output
 30 | reticfox make_ts \
 31 |     --ts_glob "$IN_DIR/*.TS.*.nc" \
 32 |     --ts_str "ts" \
 33 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.ts.nc"
 34 | 
 35 | reticfox make_tas \
 36 |     --trefht_glob "$IN_DIR/*.TREFHT.*.nc" \
 37 |     --tas_str "tas" \
 38 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.tas.nc"
 39 | 
 40 | reticfox make_pr \
 41 |     --precc_glob "$IN_DIR/*.PRECC.*.nc" \
 42 |     --precl_glob "$IN_DIR/*.PRECL.*.nc" \
 43 |     --pr_str "pr" \
 44 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.pr.nc"
 45 | 
 46 | reticfox make_d18op \
 47 |     --precrl_h216o_glob "$IN_DIR/*.PRECRL_H216OR.*.nc" \
 48 |     --precrc_h216o_glob "$IN_DIR/*.PRECRC_H216Or.*.nc" \
 49 |     --precsc_h216o_glob "$IN_DIR/*.PRECSC_H216Os.*.nc" \
 50 |     --precsl_h216o_glob "$IN_DIR/*.PRECSL_H216OS.*.nc" \
 51 |     --precrc_h218o_glob "$IN_DIR/*.PRECRC_H218Or.*.nc" \
 52 |     --precrl_h218o_glob "$IN_DIR/*.PRECRL_H218OR.*.nc" \
 53 |     --precsc_h218o_glob "$IN_DIR/*.PRECSC_H218Os.*.nc" \
 54 |     --precsl_h218o_glob "$IN_DIR/*.PRECSL_H218OS.*.nc" \
 55 |     --d18op_str "d18op" \
 56 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.d18op.nc"
 57 | 
 58 | reticfox make_omega \
 59 |     --omega_glob "$IN_DIR/*.OMEGA.*.nc" \
 60 |     --ps_glob "$IN_DIR/*.PS.*.nc" \
 61 |     --omega_str "omega" \
 62 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.omega.nc"\
 63 |     --time_chunks "$TIMECHUNKS"
 64 | 
 65 | reticfox make_ddp \
 66 |     --precrl_h2o_glob "$IN_DIR/*.PRECRL_H2OR.*.nc" \
 67 |     --precrc_h2o_glob "$IN_DIR/*.PRECRC_H2Or.*.nc" \
 68 |     --precsc_h2o_glob "$IN_DIR/*.PRECSC_H2Os.*.nc" \
 69 |     --precsl_h2o_glob "$IN_DIR/*.PRECSL_H2OS.*.nc" \
 70 |     --precrc_hdo_glob "$IN_DIR/*.PRECRC_HDOr.*.nc" \
 71 |     --precrl_hdo_glob "$IN_DIR/*.PRECRL_HDOR.*.nc" \
 72 |     --precsc_hdo_glob "$IN_DIR/*.PRECSC_HDOs.*.nc" \
 73 |     --precsl_hdo_glob "$IN_DIR/*.PRECSL_HDOS.*.nc" \
 74 |     --ddp_str "ddp" \
 75 |     --outfl "$OUT_DIR/$CASENAME.cam.h0.ddp.nc"
 76 | 
 77 | # pop output
 78 | reticfox make_sos \
 79 |     --salt_glob "$IN_DIR/*.SALT.*.nc" \
 80 |     --sos_str "sos" \
 81 |     --outfl "$OUT_DIR/$CASENAME.pop.h.sos.nc" \
 82 |     --time_chunks "$TIMECHUNKS" \
 83 |     --mask_badsalt
 84 | 
 85 | reticfox make_d18osw \
 86 |     --r18o_glob "$IN_DIR/*.R18O.*.nc" \
 87 |     --d18osw_str "d18osw" \
 88 |     --outfl "$OUT_DIR/$CASENAME.pop.h.d18osw.nc" \
 89 |     --time_chunks "$TIMECHUNKS" \
 90 |     --bad_sos_glob "$OUT_DIR/$CASENAME.pop.h.sos.nc" \
 91 |     --sos_str "sos"
 92 | 
 93 | reticfox make_tos \
 94 |     --temp_glob "$IN_DIR/$CASENAME.pop.h.TEMP.*.nc" \
 95 |     --salt_glob "$IN_DIR/$CASENAME.pop.h.SALT.*.nc" \
 96 |     --tos_str "tos" \
 97 |     --outfl "$OUT_DIR/$CASENAME.pop.h.tos.nc" \
 98 |     --time_chunks "$TIMECHUNKS" \
 99 |     --mask_badsalt
100 | 
101 | reticfox make_toga \
102 |     --temp_glob "$IN_DIR/$CASENAME.pop.h.TEMP.*.nc" \
103 |     --salt_glob "$IN_DIR/$CASENAME.pop.h.SALT.*.nc" \
104 |     --toga_str "toGA" \
105 |     --outfl "$OUT_DIR/$CASENAME.pop.h.toGA.nc" \
106 |     --time_chunks "$TIMECHUNKS" \
107 |     --mask_badsalt 
108 | 
109 | date
110 | 


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/download_icesm.py:
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  1 | # Stupid wrapper for `globus-cli` to load cesm files from NCAR server.
  2 | # Assumes you've already logged in to globus from shell with `globus login`
  3 | #
  4 | # Can run from Bash with:
  5 | #
  6 | # python download_icesm.py \
  7 | #     --casename b.e12.B1850C5.f19_g16.i21ka.03 \
  8 | #     --downloadpath /xdisk/malevich/transferstuff
  9 | #
 10 | # See help with `python download_icesm.py --help`.
 11 | 
 12 | import os
 13 | import pathlib
 14 | import subprocess
 15 | import argparse
 16 | import logging
 17 | 
 18 | 
 19 | log = logging.getLogger(__name__)
 20 | 
 21 | 
 22 | def globus_find_endpoint(searchname, owner_id):
 23 |     """Get globus endpoint ID based on name and owner_id.
 24 | 
 25 |     Parameters
 26 |     ----------
 27 |     searchname : str
 28 |         Endpoint name to search for.
 29 |     owner_id : str
 30 |         Endpoint owner name to filter results by.
 31 | 
 32 |     Returns
 33 |     -------
 34 |     String endpoint ID or `None`.
 35 |     """
 36 |     log.debug('finding globus endpoint for {} ({})'.format(searchname, owner_id))
 37 |     searchname = str(searchname)
 38 |     owner_id = str(owner_id)
 39 |     # In future might want to change `--format UNIX`, below, to something more
 40 |     # machine-readable.
 41 |     cmd_template = ["globus", "endpoint", "search", searchname,
 42 |                     "--filter-owner-id", owner_id,
 43 |                     "--jq", "DATA[0].id", "--format", "UNIX"]
 44 |     response = subprocess.run(cmd_template, check=True, stdout=subprocess.PIPE,
 45 |                               stderr=subprocess.PIPE)
 46 | 
 47 |     endpoint_id = None
 48 |     if response.returncode == 0 and response.returncode != b'None\n':
 49 |         endpoint_id = response.stdout.rstrip().decode('utf-8')
 50 | 
 51 |     log.debug('globus endpoint ID {}'.format(endpoint_id))
 52 |     return endpoint_id
 53 | 
 54 | 
 55 | def globus_transfer(from_endpoint, from_dir, to_endpoint, to_dir, task_label=None):
 56 |     """Globus transfer from 'from' endpoint and dir to 'to endpoint and dir.
 57 | 
 58 |     Assumes you've alread run `globus login`.
 59 | 
 60 |     Parameters
 61 |     ----------
 62 |     from_endpoint : str
 63 |         Globus ID of endpoint containing data to transfer.
 64 |     from_dir : str
 65 |         Path to directory on 'from' endpoint containing all the data we will 
 66 |         transfer.
 67 |     to_endpoint : str
 68 |         Globus ID of endpoint we want to transfer data to.
 69 |     to_dir : str
 70 |         Path to directory on 'to' endpoint we want to transfer data into.
 71 |     task_label : str or None
 72 |         Optional str label to give globus transfer task.
 73 | 
 74 | 
 75 |     Examples
 76 |     --------
 77 |     > # in shell before, run `globus login`
 78 |     > from_d = '/gpfs/csfs1/univ/uazn0013/jiangzhu/archive/b.e12.B1850C5.f19_g16.i21ka.03/atm/proc/tseries/monthly/PS/'
 79 |     > to_d = '/xdisk/malevich/'
 80 |     > tranfer(from_d, to_d)
 81 |     """
 82 |     from_endpoint = str(from_endpoint)
 83 |     to_endpoint = str(to_endpoint)
 84 | 
 85 |     # In future might want to change `--format UNIX`, below, to something more
 86 |     # machine-readable.
 87 |     cmd_template = ["globus", "transfer", "--recursive", "--sync-level", "mtime",
 88 |                     "{}:{}".format(from_endpoint, from_dir),
 89 |                     "{}:{}".format(to_endpoint, to_dir),
 90 |                     "--jq", "task_id", "--format", "UNIX"]
 91 | 
 92 |     if task_label is not None:
 93 |         cmd_template.append("--label")
 94 |         cmd_template.append(str(task_label))
 95 | 
 96 |     subprocess.run(cmd_template, check=True,
 97 |                    stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 98 |     log.debug('created globus transfer task from {}:{} to {}:{}'.format(
 99 |         from_endpoint, from_dir, to_endpoint, to_dir))
100 | 
101 | 
102 | def download_icesm(casename, download_path, atm_variables, ocn_variables):
103 |     """Start globus transfers of iCESM output from NCAR Campaign to UA HPC.
104 | 
105 |     You should have run `globus login` from shell terminal before using this command.
106 | 
107 |     Parameters
108 |     ----------
109 |     casename : str
110 |         iCESM experiment case name. Used to find the model run on NCAR.
111 |     download_path : str
112 |         UA HPC path we're transfering files to. Should be able to handle lots of data.
113 |         Path must already exist.
114 |     atm_variables : list of strs
115 | 
116 |     """
117 |     log.debug('begin creating globus transfers for {} to {}'.format(
118 |         casename, download_path))
119 |     ncar_endpoint = globus_find_endpoint(
120 |         searchname='NCAR Campaign Storage', owner_id='ncar@globusid.org')
121 |     uahpc_endpoint = globus_find_endpoint(
122 |         searchname='arizona#sdmz-dtn', owner_id='tmerritt@arizona.edu')
123 | 
124 |     assert ncar_endpoint is not None or uahpc_endpoint is not None, 'could not get globus endpoint IDs'
125 | 
126 |     lab = 'download_icesm_py'
127 |     # Load files from atmosphere component
128 |     from_atm_template = '/gpfs/csfs1/univ/uazn0013/jiangzhu/archive/{}/atm/proc/tseries/monthly/{}/'
129 |     for variable in atm_variables:
130 |         from_d = from_atm_template.format(casename, variable)
131 |         globus_transfer(from_endpoint=ncar_endpoint, from_dir=from_d,
132 |                         to_endpoint=uahpc_endpoint, to_dir=download_path, task_label=lab)
133 | 
134 |     # Load files from ocean component
135 |     from_ocn_template = '/gpfs/csfs1/univ/uazn0013/jiangzhu/archive/{}/ocn/proc/tseries/monthly/{}/'
136 |     for variable in ocn_variables:
137 |         from_d = from_ocn_template.format(casename, variable)
138 |         globus_transfer(from_endpoint=ncar_endpoint, from_dir=from_d,
139 |                         to_endpoint=uahpc_endpoint, to_dir=download_path, task_label=lab)
140 |     log.debug('globus transfers created')
141 | 
142 | 
143 | if __name__ == '__main__':
144 |     parser = argparse.ArgumentParser(
145 |         description='Globus transfer iCESM files from NCAR to UA HPC')
146 |     parser.add_argument('--casename', metavar='CASENAME', nargs=1,
147 |                         default=['b.e12.B1850C5.f19_g16.i21ka.03'],
148 |                         help='iCESM experiment case name')
149 |     parser.add_argument('--downloadpath', metavar='DOWNLOADPATH', nargs=1,
150 |                         default=[None],
151 |                         help='directory files will be transferred to. PWD is default. Will be created if it doesnt exist.')
152 |     parser.add_argument('--log', metavar='LOGPATH', nargs=1, default=[None],
153 |                         help='file path that log will be written to')
154 |     args = parser.parse_args()
155 | 
156 |     if args.log[0] is not None:
157 |         logging.basicConfig(level=logging.DEBUG,
158 |                             filename=args.log[0],
159 |                             format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
160 | 
161 |     dl_path = args.downloadpath[0]
162 |     if dl_path is None:
163 |         dl_path = os.getcwd()
164 | 
165 |     # Create dl path if doesn't exist.
166 |     dl_path = pathlib.Path(dl_path)
167 |     dl_path.mkdir(parents=True, exist_ok=True)
168 | 
169 |     casename = str(args.casename[0])
170 | 
171 |     atm_variables = ['PRECC',
172 |                      'PRECL',
173 |                      'TS',
174 |                      'TREFHT',
175 |                      'PRECRC_H218Or',
176 |                      'PRECRL_H218OR',
177 |                      'PRECSC_H218Os',
178 |                      'PRECSL_H218OS',
179 |                      'PRECRC_H216Or',
180 |                      'PRECRL_H216OR',
181 |                      'PRECSC_H216Os',
182 |                      'PRECSL_H216OS',
183 |                      'PRECRC_H2Or',
184 |                      'PRECRL_H2OR',
185 |                      'PRECSC_H2Os',
186 |                      'PRECSL_H2OS',
187 |                      'PRECRC_HDOr',
188 |                      'PRECRL_HDOR',
189 |                      'PRECSC_HDOs',
190 |                      'PRECSL_HDOS',
191 |                      'OMEGA',
192 |                      'PS',
193 |                      ]
194 | 
195 |     ocn_variables = ['R18O',
196 |                      'TEMP',
197 |                      'SALT',
198 |                      ]
199 | 
200 |     download_icesm(casename=casename, download_path=dl_path,
201 |                    atm_variables=atm_variables, ocn_variables=ocn_variables)
202 | 


--------------------------------------------------------------------------------
/reticfox/cli.py:
--------------------------------------------------------------------------------
  1 | import click
  2 | from glob import glob
  3 | import xarray as xr
  4 | import Ngl
  5 | import reticfox.api as api
  6 | 
  7 | 
  8 | # Main entry point
  9 | @click.group(context_settings={'help_option_names': ['-h', '--help']})
 10 | def reticfox_cli():
 11 |     """Parse LGM iCESM processed netCDF files"""
 12 | 
 13 | 
 14 | @reticfox_cli.command(help='Parse d18O (precip) from iCESM output')
 15 | @click.option('--precrc_h216o_glob', help='Glob pattern to input CAM PRECRC_H216Or NetCDF files.')
 16 | @click.option('--precrl_h216o_glob', help='Glob pattern to input CAM PRECRL_H216OR NetCDF files.')
 17 | @click.option('--precsc_h216o_glob', help='Glob pattern to input CAM PRECSC_H216Os NetCDF files.')
 18 | @click.option('--precsl_h216o_glob', help='Glob pattern to input CAM PRECSL_H216OS NetCDF files.')
 19 | @click.option('--precrc_h218o_glob', help='Glob pattern to input CAM PRECRL_H218Or NetCDF files.')
 20 | @click.option('--precrl_h218o_glob', help='Glob pattern to input CAM PRECRL_H218OR NetCDF files.')
 21 | @click.option('--precsc_h218o_glob', help='Glob pattern to input CAM PRECSC_H218Os NetCDF files.')
 22 | @click.option('--precsl_h218o_glob', help='Glob pattern to input CAM PRECSL_H218OS NetCDF files.')
 23 | @click.option('--d18op_str', default='d18op', help='Variable name in output NetCDF file.')
 24 | @click.option('--outfl', help='Path for output NetCDF file.')
 25 | def make_d18op(precrc_h216o_glob, precrl_h216o_glob, precsc_h216o_glob, precsl_h216o_glob,
 26 |                precrc_h218o_glob, precrl_h218o_glob, precsc_h218o_glob, precsl_h218o_glob,
 27 |                d18op_str, outfl=None):
 28 |     """Parse CAM PRE*_H216O* and PRE*_H218O* iCESM netCDF files and write δ18O to outfl.
 29 |     """
 30 |     ptiny = 1e-18
 31 | 
 32 |     globs = [precrc_h216o_glob, precrl_h216o_glob, precsc_h216o_glob, precsl_h216o_glob,
 33 |              precrc_h218o_glob, precrl_h218o_glob, precsc_h218o_glob, precsl_h218o_glob]
 34 |     # log.debug('working precip d18O files in globs {}'.format(globs))
 35 | 
 36 |     matched_files = []
 37 |     for g in globs:
 38 |         for match in glob(g):
 39 |             matched_files.append(match)
 40 | 
 41 |     h21xo = xr.open_mfdataset(matched_files).sortby('time')
 42 | 
 43 |     # Combine parts
 44 |     h21xo['p18o'] = h21xo.PRECRC_H218Or + h21xo.PRECRL_H218OR + \
 45 |         h21xo.PRECSC_H218Os + h21xo.PRECSL_H218OS
 46 |     h21xo['p16o'] = h21xo.PRECRC_H216Or + h21xo.PRECRL_H216OR + \
 47 |         h21xo.PRECSC_H216Os + h21xo.PRECSL_H216OS
 48 |     h21xo['p16o'] = xr.where(h21xo['p16o'] > ptiny, h21xo['p16o'], ptiny)
 49 |     h21xo[d18op_str] = (h21xo['p18o'] / h21xo['p16o'] - 1.0) * 1000.0
 50 | 
 51 |     # Metadata
 52 |     h21xo[d18op_str].attrs['long_name'] = 'precipitation d18O'
 53 |     h21xo[d18op_str].attrs['units'] = 'permil'
 54 | 
 55 |     out = h21xo[[d18op_str, 'time_bnds']]
 56 |     if outfl is not None:
 57 |         # Dump to file
 58 |         # log.debug('Writing variable {} to {}'.format(d18op_str, outfl))
 59 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
 60 |     return out
 61 | 
 62 | 
 63 | @reticfox_cli.command(help='Parse delta D (precip) from iCESM output')
 64 | @click.option('--precrc_h2o_glob', help='Glob pattern to input CAM PRECRC_H2Or NetCDF files.')
 65 | @click.option('--precrl_h2o_glob', help='Glob pattern to input CAM PRECRL_H2OR NetCDF files.')
 66 | @click.option('--precsc_h2o_glob', help='Glob pattern to input CAM PRECSC_H2Os NetCDF files.')
 67 | @click.option('--precsl_h2o_glob', help='Glob pattern to input CAM PRECSL_H2OS NetCDF files.')
 68 | @click.option('--precrc_hdo_glob', help='Glob pattern to input CAM PRECRC_HDOr NetCDF files.')
 69 | @click.option('--precrl_hdo_glob', help='Glob pattern to input CAM PRECRL_HDOR NetCDF files.')
 70 | @click.option('--precsc_hdo_glob', help='Glob pattern to input CAM PRECSC_HDOs NetCDF files.')
 71 | @click.option('--precsl_hdo_glob', help='Glob pattern to input CAM PRECSL_HDOS NetCDF files.')
 72 | @click.option('--ddp_str', default='ddp', help='Variable name in output NetCDF file.')
 73 | @click.option('--outfl', help='Path for output NetCDF file.')
 74 | def make_ddp(precrc_h2o_glob, precrl_h2o_glob, precsc_h2o_glob, precsl_h2o_glob,
 75 |              precrc_hdo_glob, precrl_hdo_glob, precsc_hdo_glob, precsl_hdo_glob,
 76 |              ddp_str, outfl=None):
 77 |     """Parse CAM PRE*_HDO* and PRE*_H2O* iCESM netCDF files and write δD to outfl.
 78 |     """
 79 |     ptiny = 1e-18
 80 | 
 81 |     globs = [precrc_h2o_glob, precrl_h2o_glob, precsc_h2o_glob, precsl_h2o_glob,
 82 |              precrc_hdo_glob, precrl_hdo_glob, precsc_hdo_glob, precsl_hdo_glob]
 83 |     # log.debug('working precip deuterium files in globs {}'.format(globs))
 84 | 
 85 |     matched_files = []
 86 |     for g in globs:
 87 |         for match in glob(g):
 88 |             matched_files.append(match)
 89 | 
 90 |     hxo = xr.open_mfdataset(matched_files).sortby('time')
 91 | 
 92 |     # Combine parts
 93 |     hxo['ph2o'] = hxo.PRECRC_H2Or + hxo.PRECRL_H2OR + \
 94 |         hxo.PRECSC_H2Os + hxo.PRECSL_H2OS
 95 |     hxo['phdo'] = hxo.PRECRC_HDOr + hxo.PRECRL_HDOR + \
 96 |         hxo.PRECSC_HDOs + hxo.PRECSL_HDOS
 97 |     hxo['ph2o'] = xr.where(hxo['ph2o'] > ptiny, hxo['ph2o'], ptiny)
 98 |     hxo[ddp_str] = (hxo['phdo'] / hxo['ph2o'] - 1.0) * 1000.0
 99 | 
100 |     # Metadata
101 |     hxo[ddp_str].attrs['long_name'] = 'precipitation dD'
102 |     hxo[ddp_str].attrs['units'] = 'permil'
103 | 
104 |     out = hxo[[ddp_str, 'time_bnds']]
105 |     if outfl is not None:
106 |         # Dump to file
107 |         # log.debug('Writing variable {} to {}'.format(ddp_str, outfl))
108 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
109 |     return out
110 | 
111 | 
112 | @reticfox_cli.command(help='Parse CAM OMEGA from iCESM output')
113 | @click.option('--omega_glob', help='Glob pattern to input CAM OMEGA NetCDF files.')
114 | @click.option('--ps_glob', help='Glob pattern to input CAM PS NetCDF files.')
115 | @click.option('--omega_str', default='omega', help='Variable name in output NetCDF file.')
116 | @click.option('--outfl', help='Path for output NetCDF file.')
117 | @click.option('--levels', default=None, help='Pressure levels to interpolate omega to.')
118 | @click.option('--time_chunks', default=5, help='Number of time steps in each input files chunk.')
119 | def make_omega(omega_glob, ps_glob, omega_str, outfl=None, levels=None, time_chunks=5):
120 |     """Parse CAM omega iCESM netCDF files and write to outfl.
121 |     """
122 |     # log.debug('working omega files in glob {}'.format(omega_glob))
123 |     if levels is None:
124 |         levels = [500.0]
125 | 
126 |     # ps = xr.open_mfdataset(ps_glob).sortby('time')
127 |     # omega = xr.open_mfdataset(omega_glob).sortby('time')
128 | 
129 |     omega = xr.open_mfdataset(omega_glob, chunks={'time': time_chunks},
130 |                               data_vars=['OMEGA']).sortby('time')
131 |     ps = xr.open_mfdataset(ps_glob, chunks={'time': time_chunks}).sortby('time')
132 | 
133 |     # omega500 = Ngl.vinth2p(omega.OMEGA.values, omega.hyam.values, omega.hybm.values,
134 |     #                        levels, ps.PS.values, 1, 1000.0, 1, True)
135 |     # # insitu_temp = xr.apply_ufunc(gsw.pt_from_t, salt.SALT, theta.TEMP, np.array([0]), p,
136 |     # #                             output_dtypes=['float32'], dask='parallelized')
137 | 
138 |     # omega500 = dask.delayed(Ngl.vinth2p)(omega.OMEGA, omega.hyam, omega.hybm, levels, ps.PS, 1, 1000.0, 1, True)
139 |     # omega500 = xr.apply_ufunc(Ngl.vinth2p, omega.OMEGA, omega.hyam, omega.hybm, levels, ps.PS, 1, 1000.0, 1, True, dask='allowed')
140 | 
141 |     # omega500 = xr.apply_ufunc(Ngl.vinth2p, omega['OMEGA'], omega['hyam'].values, omega['hybm'].values, levels, ps['PS'], 1, 1000.0, 1, True,
142 |     # output_sizes={'time': omega.dims['time'], 'lev': len(levels), 'lat': omega.dims['lat'], 'lon': omega.dims['lon']}, output_dtypes=['float32'], dask='parallelized')
143 | 
144 |     # omega500 = xr.apply_ufunc(Ngl.vinth2p, omega['OMEGA'], omega['hyam'], omega['hybm'], np.array([500.0]), ps['PS'], 1, 1000.0, 1, True,
145 |     #     input_core_dims=[['lev', 'lat', 'lon'], ['lev'], ['lev'], [], ['lat', 'lon'], [], [], [], []],
146 |     #     output_sizes={'time': omega.dims['time'], 'lev': len(levels), 'lat': omega.dims['lat'], 'lon': omega.dims['lon']},
147 |     #     output_dtypes=['float32'], dask='parallelized')
148 |     omega500 = Ngl.vinth2p(omega.OMEGA, omega.hyam, omega.hybm,
149 |                            [500], ps.PS, 1, 1000.0, 1, True)
150 | 
151 |     # Setup pressure coordinates
152 |     omega.coords['plev'] = ('plev', levels)
153 |     omega.coords['plev'].attrs['positive'] = 'down'
154 |     omega.coords['plev'].attrs['long_name'] = 'pressure level'
155 |     omega.coords['plev'].attrs['units'] = 'hPa'
156 | 
157 |     # Add new interpolated omega to dataset and write variable to NetCDF
158 |     omega[omega_str] = (('time', 'plev', 'lat', 'lon'), omega500)
159 |     omega[omega_str].attrs['units'] = 'Pa/s'
160 |     omega[omega_str].attrs['long_name'] = 'Vertical velocity (pressure)'
161 | 
162 |     out = omega[[omega_str, 'time_bnds']]
163 |     out[omega_str] = out[omega_str].astype('float32')
164 |     if outfl is not None:
165 |         # Dump to file
166 |         # log.debug('Writing variable {} to {}'.format(omega_str, outfl))
167 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
168 |     return out
169 | 
170 | 
171 | @reticfox_cli.command(help='Parse pr from iCESM output')
172 | @click.option('--precc_glob', help='Glob pattern to input CAM PRECRC NetCDF files.')
173 | @click.option('--precl_glob', help='Glob pattern to input CAM PRECRL NetCDF files.')
174 | @click.option('--pr_str', default='pr', help='Variable name in output NetCDF file.')
175 | @click.option('--outfl', help='Path for output NetCDF file.')
176 | def make_pr(precc_glob, precl_glob, pr_str, outfl=None):
177 |     """Parse CAM PREC* iCESM netCDF files and write to outfl.
178 |     """
179 |     globs = [precc_glob, precl_glob]
180 |     # log.debug('working precip files in glob {}'.format(globs))
181 | 
182 |     matched_files = []
183 |     for g in globs:
184 |         for match in glob(g):
185 |             matched_files.append(match)
186 | 
187 |     pre = xr.open_mfdataset(matched_files).sortby('time')
188 | 
189 |     # Combine parts
190 |     pre[pr_str] = pre['PRECC'] + pre['PRECL']
191 | 
192 |     # Metadata
193 |     pre[pr_str].attrs['long_name'] = 'total precipitation rate'
194 |     pre[pr_str].attrs['units'] = 'm/s'
195 | 
196 |     out = pre[[pr_str, 'time_bnds']]
197 |     if outfl is not None:
198 |         # log.debug('Writing variable {} to {}'.format(pr_str, outfl))
199 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
200 |     return out
201 | 
202 | 
203 | @reticfox_cli.command(help='Parse TREFHT from iCESM output')
204 | @click.option('--trefht_glob', help='Glob pattern to input CAM TREFHT NetCDF files.')
205 | @click.option('--tas_str', default='tas', help='Variable name in output NetCDF file.')
206 | @click.option('--outfl', help='Path for output NetCDF file.')
207 | def make_tas(trefht_glob, tas_str, outfl=None):
208 |     """Parse CAM tas iCESM NetCDF files and write to outfl.
209 |     """
210 |     # log.debug('working trefht files in glob {}'.format(trefht_glob))
211 |     x = xr.open_mfdataset(trefht_glob).sortby('time')
212 |     x[tas_str] = x['TREFHT']
213 | 
214 |     out = x[[tas_str, 'time_bnds']]
215 |     if outfl is not None:
216 |         # log.debug('Writing variable {} to {}'.format(tas_str, outfl))
217 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
218 |     return out
219 | 
220 | 
221 | @reticfox_cli.command(help='Parse CAM TS from iCESM output')
222 | @click.option('--ts_glob', help='Glob pattern to input CAM TS NetCDF files.')
223 | @click.option('--ts_str', default='ts', help='Variable name in output NetCDF file.')
224 | @click.option('--outfl', help='Path for output NetCDF file.')
225 | def make_ts(ts_glob, ts_str, outfl=None):
226 |     """Parse CAM TS iCESM NetCDF files and write to outfl.
227 |     """
228 |     # log.debug('working ts files in glob {}'.format(ts_glob))
229 |     x = xr.open_mfdataset(ts_glob).sortby('time')
230 |     x[ts_str] = x['TS']
231 | 
232 |     out = x[[ts_str, 'time_bnds']]
233 |     if outfl is not None:
234 |         # log.debug('Writing variable {} to {}'.format(ts_str, outfl))
235 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
236 |     return out
237 | 
238 | 
239 | @reticfox_cli.command(help='Parse POP TEMP from iCESM output')
240 | @click.option('--temp_glob', help='Glob pattern to input POP TEMP NetCDF files.')
241 | @click.option('--salt_glob', help='Glob pattern to input POP SALT NetCDF files.')
242 | @click.option('--tos_str', default='tos', help='Variable name in output NetCDF file.')
243 | @click.option('--outfl', help='Path for output NetCDF file.')
244 | @click.option('--time_chunks', default=5, help='Number of time steps in each input files chunk.')
245 | @click.option('--mask_badsalt', is_flag=True, help='Mask-out negative SALT values with NAs?')
246 | def make_tos(temp_glob, salt_glob, tos_str, outfl=None, time_chunks=5, mask_badsalt=True):
247 |     """Parse POP TEMP iCESM NetCDF files
248 |     """
249 |     top_level = 500.0  # highest ocean level in iCESM (cm)
250 |     tinsitu_str = 'tinsitu'
251 | 
252 |     theta = xr.open_mfdataset(temp_glob,  chunks={'time': time_chunks}).sel(
253 |         z_t=top_level).sortby('time')
254 |     salt = xr.open_mfdataset(salt_glob, chunks={'time': time_chunks}).sel(
255 |         z_t=top_level).sortby('time')
256 | 
257 |     if mask_badsalt:
258 |         salt['SALT'] = salt['SALT'].where(salt['SALT'] > 0)
259 | 
260 |     theta[tinsitu_str] = api.pot2insitu_temp(
261 |         theta, salt, insitu_temp_name=tinsitu_str)
262 | 
263 |     out = theta[[tinsitu_str, 'time_bound']].rename({tinsitu_str: tos_str})
264 |     if outfl is not None:
265 |         # Write ~SST file
266 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
267 |     return out
268 | 
269 | 
270 | @reticfox_cli.command(help='Make surface salinity file from iCESM SALT')
271 | @click.option('--salt_glob', help='Glob pattern to input POP SALT NetCDF files.')
272 | @click.option('--sos_str', default='sos', help='Variable name in output NetCDF file.')
273 | @click.option('--outfl', help='Path for output NetCDF file.')
274 | @click.option('--time_chunks', default=5, help='Number of time steps in each input files chunk.')
275 | @click.option('--mask_badsalt', is_flag=True, help='Mask-out negative SALT values with NAs?')
276 | def make_sos(salt_glob, sos_str, outfl=None, time_chunks=5, mask_badsalt=True):
277 |     """Parse POP SALT iCESM NetCDF files
278 |     """
279 |     top_level = 500.0  # highest ocean level in iCESM (cm)
280 |     # Note we're grabbing 500 cm depth - should be top-most ocean layer.
281 |     salt = (xr.open_mfdataset(salt_glob, chunks={'time': time_chunks})
282 |             .sel(z_t=top_level)
283 |             .sortby('time'))
284 | 
285 |     if mask_badsalt:
286 |         salt['SALT'] = salt['SALT'].where(salt['SALT'] > 0)
287 | 
288 |     out = salt[['SALT', 'time_bound']].rename({'SALT': sos_str})
289 |     if outfl is not None:
290 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
291 |     return out
292 | 
293 | 
294 | @reticfox_cli.command(help='Parse POP TEMP, SALT from iCESM output for TEX86 gamma-avg temp')
295 | @click.option('--temp_glob', help='Glob pattern to input POP TEMP NetCDF files.')
296 | @click.option('--salt_glob', help='Glob pattern to input POP SALT NetCDF files.')
297 | @click.option('--toga_str', default='toga', help='Variable name in output NetCDF file.')
298 | @click.option('--outfl', help='Path for output NetCDF file.')
299 | @click.option('--time_chunks', default=5, help='Number of time steps in each input files chunk.')
300 | @click.option('--mask_badsalt', is_flag=True, help='Mask-out negative SALT values with NAs?')
301 | def make_toga(temp_glob, salt_glob, toga_str, outfl=None, time_chunks=5,
302 |               mask_badsalt=True):
303 |     """Parse POP TEMP and SALT iCESM NetCDF files for gamma-average insitu temp
304 |     """
305 |     cutoff_z = 20000
306 |     tinsitu_str = 'tinsitu'
307 |     theta = xr.open_mfdataset(temp_glob,  chunks={'time': time_chunks}).sel(
308 |         z_t=slice(0, cutoff_z)).sortby('time')
309 |     salt = xr.open_mfdataset(salt_glob, chunks={'time': time_chunks}).sel(
310 |         z_t=slice(0, cutoff_z)).sortby('time')
311 | 
312 |     if mask_badsalt:
313 |         salt['SALT'] = salt['SALT'].where(salt['SALT'] > 0)
314 | 
315 |     theta[tinsitu_str] = api.pot2insitu_temp(
316 |         theta, salt, insitu_temp_name=tinsitu_str)
317 | 
318 |     # Because using z_t slice doesn't get z_w which has depth layers' bounds.
319 |     # We trim by z_w_bot length because we don't want the bottom of the layer to
320 |     # be deeper than `cutoff_z`.
321 |     theta = theta.sel(z_w_bot=slice(0, cutoff_z))
322 |     theta = theta.isel(z_t=slice(0, len(theta['z_w_bot'])))
323 |     theta = theta.isel(z_w_top=slice(0, len(theta['z_w_bot'])))
324 | 
325 |     # get gamma average, add to tinsitu
326 |     theta[toga_str] = api.tex86_gammaavg_depth(
327 |         theta, target_var=tinsitu_str)
328 | 
329 |     out = theta[[toga_str, 'time_bound']]
330 |     out[toga_str] = out[toga_str].astype('float32')
331 |     if outfl is not None:
332 |         # Write gamma-average file
333 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
334 |     return out
335 | 
336 | 
337 | @reticfox_cli.command(help='Parse d18Osw from iCESM output')
338 | @click.option('--r18o_glob', help='Glob pattern to input POP R18O NetCDF files.')
339 | @click.option('--d18osw_str', default='d18osw', help='Variable name in output NetCDF file.')
340 | @click.option('--outfl', help='Path for output NetCDF file.')
341 | @click.option('--time_chunks', default=5, help='Number of time steps in each input files chunk.')
342 | @click.option('--bad_sos_glob', default='NONE', help='Glob pattern to input surface NetCDF files, to mask subzero salinity.')
343 | @click.option('--sos_str', default='sos', help='Surface salinity variable name in `bad_sos_glob`s.')
344 | def make_d18osw(r18o_glob, d18osw_str, outfl=None, time_chunks=5, bad_sos_glob=None, sos_str='sos'):
345 |     """Parse POP R18O iCESM netCDF files and write to outfl.
346 |     """
347 |     if bad_sos_glob.lower() == 'none':
348 |         bad_sos_glob = None
349 | 
350 |     top_level = 500.0  # highest ocean level in iCESM (cm)
351 |     r18o = (xr.open_mfdataset(r18o_glob, chunks={'time': time_chunks})
352 |             .sel(z_t=top_level)
353 |             .sortby('time'))
354 |     r18o[d18osw_str] = (r18o['R18O'] - 1.0) * 1000.0
355 | 
356 |     if bad_sos_glob is not None:
357 |         # Read in and mask out grid points with subzero seawater salinity.
358 |         sos = (xr.open_mfdataset(bad_sos_glob, chunks={'time': time_chunks})
359 |                .sortby('time'))
360 |         r18o[d18osw_str] = r18o[d18osw_str].where(sos[sos_str] > 0)
361 | 
362 |     # Metadata
363 |     r18o[d18osw_str] = r18o[d18osw_str].astype('float32')
364 |     r18o[d18osw_str].attrs['long_name'] = 'seawater d18O'
365 |     r18o[d18osw_str].attrs['units'] = 'permil'
366 | 
367 |     out = r18o[[d18osw_str, 'time_bound']]
368 |     if outfl is not None:
369 |         # Dump to file
370 |         # log.debug('Writing variable {} to {}'.format(d18osw_str, outfl))
371 |         out.to_netcdf(outfl, format='NETCDF4', engine='netcdf4')
372 |     return out
373 | 
374 | 
375 | @reticfox_cli.command(help='Parse d18Osw from iCESM output')
376 | @click.option('--nc_glob', help='Glob pattern for NetCDF files.')
377 | @click.option('--outfl', help='Path for output NetCDF file.')
378 | @click.option('--sortby', default='time', help='Variable to sort merged files by.')
379 | def combine_netcdf_glob(nc_glob, outfl=None, sortby='time'):
380 |     """Combine a glob of NetCDF file names to a single dataset, write to disk as one file
381 |     """
382 |     ds = xr.open_mfdataset(nc_glob).sortby(sortby)
383 |     if outfl is not None:
384 |         ds.to_netcdf(outfl)
385 |     return ds
386 | 
387 | 
388 | if __name__ == '__main__':
389 |     reticfox_cli()
390 | 


--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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479 | hereafter acquired, that would be infringed by some manner, permitted
480 | by this License, of making, using, or selling its contributor version,
481 | but do not include claims that would be infringed only as a
482 | consequence of further modification of the contributor version.  For
483 | purposes of this definition, "control" includes the right to grant
484 | patent sublicenses in a manner consistent with the requirements of
485 | this License.
486 | 
487 |   Each contributor grants you a non-exclusive, worldwide, royalty-free
488 | patent license under the contributor's essential patent claims, to
489 | make, use, sell, offer for sale, import and otherwise run, modify and
490 | propagate the contents of its contributor version.
491 | 
492 |   In the following three paragraphs, a "patent license" is any express
493 | agreement or commitment, however denominated, not to enforce a patent
494 | (such as an express permission to practice a patent or covenant not to
495 | sue for patent infringement).  To "grant" such a patent license to a
496 | party means to make such an agreement or commitment not to enforce a
497 | patent against the party.
498 | 
499 |   If you convey a covered work, knowingly relying on a patent license,
500 | and the Corresponding Source of the work is not available for anyone
501 | to copy, free of charge and under the terms of this License, through a
502 | publicly available network server or other readily accessible means,
503 | then you must either (1) cause the Corresponding Source to be so
504 | available, or (2) arrange to deprive yourself of the benefit of the
505 | patent license for this particular work, or (3) arrange, in a manner
506 | consistent with the requirements of this License, to extend the patent
507 | license to downstream recipients.  "Knowingly relying" means you have
508 | actual knowledge that, but for the patent license, your conveying the
509 | covered work in a country, or your recipient's use of the covered work
510 | in a country, would infringe one or more identifiable patents in that
511 | country that you have reason to believe are valid.
512 | 
513 |   If, pursuant to or in connection with a single transaction or
514 | arrangement, you convey, or propagate by procuring conveyance of, a
515 | covered work, and grant a patent license to some of the parties
516 | receiving the covered work authorizing them to use, propagate, modify
517 | or convey a specific copy of the covered work, then the patent license
518 | you grant is automatically extended to all recipients of the covered
519 | work and works based on it.
520 | 
521 |   A patent license is "discriminatory" if it does not include within
522 | the scope of its coverage, prohibits the exercise of, or is
523 | conditioned on the non-exercise of one or more of the rights that are
524 | specifically granted under this License.  You may not convey a covered
525 | work if you are a party to an arrangement with a third party that is
526 | in the business of distributing software, under which you make payment
527 | to the third party based on the extent of your activity of conveying
528 | the work, and under which the third party grants, to any of the
529 | parties who would receive the covered work from you, a discriminatory
530 | patent license (a) in connection with copies of the covered work
531 | conveyed by you (or copies made from those copies), or (b) primarily
532 | for and in connection with specific products or compilations that
533 | contain the covered work, unless you entered into that arrangement,
534 | or that patent license was granted, prior to 28 March 2007.
535 | 
536 |   Nothing in this License shall be construed as excluding or limiting
537 | any implied license or other defenses to infringement that may
538 | otherwise be available to you under applicable patent law.
539 | 
540 |   12. No Surrender of Others' Freedom.
541 | 
542 |   If conditions are imposed on you (whether by court order, agreement or
543 | otherwise) that contradict the conditions of this License, they do not
544 | excuse you from the conditions of this License.  If you cannot convey a
545 | covered work so as to satisfy simultaneously your obligations under this
546 | License and any other pertinent obligations, then as a consequence you may
547 | not convey it at all.  For example, if you agree to terms that obligate you
548 | to collect a royalty for further conveying from those to whom you convey
549 | the Program, the only way you could satisfy both those terms and this
550 | License would be to refrain entirely from conveying the Program.
551 | 
552 |   13. Use with the GNU Affero General Public License.
553 | 
554 |   Notwithstanding any other provision of this License, you have
555 | permission to link or combine any covered work with a work licensed
556 | under version 3 of the GNU Affero General Public License into a single
557 | combined work, and to convey the resulting work.  The terms of this
558 | License will continue to apply to the part which is the covered work,
559 | but the special requirements of the GNU Affero General Public License,
560 | section 13, concerning interaction through a network will apply to the
561 | combination as such.
562 | 
563 |   14. Revised Versions of this License.
564 | 
565 |   The Free Software Foundation may publish revised and/or new versions of
566 | the GNU General Public License from time to time.  Such new versions will
567 | be similar in spirit to the present version, but may differ in detail to
568 | address new problems or concerns.
569 | 
570 |   Each version is given a distinguishing version number.  If the
571 | Program specifies that a certain numbered version of the GNU General
572 | Public License "or any later version" applies to it, you have the
573 | option of following the terms and conditions either of that numbered
574 | version or of any later version published by the Free Software
575 | Foundation.  If the Program does not specify a version number of the
576 | GNU General Public License, you may choose any version ever published
577 | by the Free Software Foundation.
578 | 
579 |   If the Program specifies that a proxy can decide which future
580 | versions of the GNU General Public License can be used, that proxy's
581 | public statement of acceptance of a version permanently authorizes you
582 | to choose that version for the Program.
583 | 
584 |   Later license versions may give you additional or different
585 | permissions.  However, no additional obligations are imposed on any
586 | author or copyright holder as a result of your choosing to follow a
587 | later version.
588 | 
589 |   15. Disclaimer of Warranty.
590 | 
591 |   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592 | APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
596 | PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
597 | IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599 | 
600 |   16. Limitation of Liability.
601 | 
602 |   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610 | SUCH DAMAGES.
611 | 
612 |   17. Interpretation of Sections 15 and 16.
613 | 
614 |   If the disclaimer of warranty and limitation of liability provided
615 | above cannot be given local legal effect according to their terms,
616 | reviewing courts shall apply local law that most closely approximates
617 | an absolute waiver of all civil liability in connection with the
618 | Program, unless a warranty or assumption of liability accompanies a
619 | copy of the Program in return for a fee.
620 | 
621 |                      END OF TERMS AND CONDITIONS
622 | 
623 |             How to Apply These Terms to Your New Programs
624 | 
625 |   If you develop a new program, and you want it to be of the greatest
626 | possible use to the public, the best way to achieve this is to make it
627 | free software which everyone can redistribute and change under these terms.
628 | 
629 |   To do so, attach the following notices to the program.  It is safest
630 | to attach them to the start of each source file to most effectively
631 | state the exclusion of warranty; and each file should have at least
632 | the "copyright" line and a pointer to where the full notice is found.
633 | 
634 |     <one line to give the program's name and a brief idea of what it does.>
635 |     Copyright (C) <year>  <name of author>
636 | 
637 |     This program is free software: you can redistribute it and/or modify
638 |     it under the terms of the GNU General Public License as published by
639 |     the Free Software Foundation, either version 3 of the License, or
640 |     (at your option) any later version.
641 | 
642 |     This program is distributed in the hope that it will be useful,
643 |     but WITHOUT ANY WARRANTY; without even the implied warranty of
644 |     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
645 |     GNU General Public License for more details.
646 | 
647 |     You should have received a copy of the GNU General Public License
648 |     along with this program.  If not, see <https://www.gnu.org/licenses/>.
649 | 
650 | Also add information on how to contact you by electronic and paper mail.
651 | 
652 |   If the program does terminal interaction, make it output a short
653 | notice like this when it starts in an interactive mode:
654 | 
655 |     <program>  Copyright (C) <year>  <name of author>
656 |     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657 |     This is free software, and you are welcome to redistribute it
658 |     under certain conditions; type `show c' for details.
659 | 
660 | The hypothetical commands `show w' and `show c' should show the appropriate
661 | parts of the General Public License.  Of course, your program's commands
662 | might be different; for a GUI interface, you would use an "about box".
663 | 
664 |   You should also get your employer (if you work as a programmer) or school,
665 | if any, to sign a "copyright disclaimer" for the program, if necessary.
666 | For more information on this, and how to apply and follow the GNU GPL, see
667 | <https://www.gnu.org/licenses/>.
668 | 
669 |   The GNU General Public License does not permit incorporating your program
670 | into proprietary programs.  If your program is a subroutine library, you
671 | may consider it more useful to permit linking proprietary applications with
672 | the library.  If this is what you want to do, use the GNU Lesser General
673 | Public License instead of this License.  But first, please read
674 | <https://www.gnu.org/licenses/why-not-lgpl.html>.
675 | 


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