import intake
import hvplot.pandas
import hvplot.xarray
import cook_inlet_catalogs as cic
import holoviews as hv
Underway CTD (NOAA PMEL): Towed on ferry¶
An oceanographic monitoring system aboard the Alaska Marine Highway System ferry Tustumena operated for four years in the Alaska Coastal Current (ACC) with funding from the Exxon Valdez Oil Spill Trustee Council’s Gulf Ecosystem Monitoring Program, the North Pacific Research Board and the National Oceanic and Atmospheric Administration. An electronic public display aboard the ferry educated passengers about the local oceanography and mapped the ferry’s progress. Sampling water at 4 m, the underway system measured: (1) temperature and salinity (used in the present report), and (2) nitrate, (3) chlorophyll fluorescence, (4) colored dissolved organic matter fluorescence, and (5) optical beam transmittance (not used in report).
Nominal 4 meter depth.
NORTH PACIFIC RESEARCH BOARD PROJECT FINAL REPORT Alaskan Ferry Oceanographic Monitoring in the Gulf of Alaska NPRB Project 707 Final Report Edward D. Cokelet and Calvin W. Mordy. https://www.nodc.noaa.gov/archive/arc0031/0070122/1.1/data/0-data/Final_Report_NPRB_0707.pdf
Exxon Valdez Oil Spill Gulf Ecosystem Monitoring and Research Project Final Report Biophysical Observations Aboard Alaska Marine Highway System Ferries Gulf Ecosystem Monitoring and Research Project 040699 Final Report Edward D. Cokelet, Calvin W. Mordy, Antonio J. Jenkins, W. Scott Pegau https://www.nodc.noaa.gov/archive/arc0031/0070122/1.1/data/0-data/Final_Report_GEM_040699.pdf
Archive: https://www.ncei.noaa.gov/metadata/geoportal/rest/metadata/item/gov.noaa.nodc%3A0070122/html
cat = intake.open_catalog(cic.utils.cat_path("ctd_towed_ferry_noaa_pmel"))
Plot all datasets in catalog¶
dd, ddlabels = cic.utils.combine_datasets_for_map(cat)
dd.hvplot(**cat.metadata["map"]) * ddlabels.hvplot(**cat.metadata["maplabels"])
List available datasets in the catalog¶
dataset_ids = list(cat)
dataset_ids
['2004-10',
'2004-11',
'2004-12',
'2004-9',
'2005-1',
'2005-10',
'2005-11',
'2005-2',
'2005-3',
'2005-4',
'2005-5',
'2005-6',
'2005-7',
'2005-8',
'2005-9',
'2006-10',
'2006-11',
'2006-12',
'2006-5',
'2006-6',
'2006-7',
'2006-8',
'2006-9',
'2007-1',
'2007-10',
'2007-2',
'2007-3',
'2007-4',
'2007-5',
'2007-6',
'2007-7',
'2007-8',
'2007-9',
'2008-10',
'2008-11',
'2008-3',
'2008-4',
'2008-5',
'2008-6',
'2008-7',
'2008-8',
'2008-9']
Select one dataset to investigate¶
try:
dataset_id = dataset_ids[2]
except:
dataset_id = dataset_ids[0]
print(dataset_id)
dd = cat[dataset_id].read()
dd
2004-12
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
Cell In[5], line 7
4 dataset_id = dataset_ids[0]
5 print(dataset_id)
----> 7 dd = cat[dataset_id].read()
8 dd
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/intake/readers/readers.py:121, in BaseReader.read(self, *args, **kwargs)
119 kw.update(kwargs)
120 args = kw.pop("args", ()) or args
--> 121 return self._read(*args, **kw)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/intake/readers/convert.py:631, in Pipeline._read(self, discover, **kwargs)
629 data = self._read_stage_n(i, data=data, **kw)
630 else:
--> 631 data = self._read_stage_n(i, discover=discover, **kw)
632 return data
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/intake/readers/convert.py:620, in Pipeline._read_stage_n(self, stage, discover, **kwargs)
618 return func.discover(*arg, **kw2)
619 else:
--> 620 return func.read(*arg, **kw2)
621 else:
622 return func(*arg, **kw2)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/intake/readers/readers.py:121, in BaseReader.read(self, *args, **kwargs)
119 kw.update(kwargs)
120 args = kw.pop("args", ()) or args
--> 121 return self._read(*args, **kw)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/intake/readers/readers.py:1331, in XArrayDatasetReader._read(self, data, open_local, **kw)
1329 return open_dataset(f, **kw)
1330 else:
-> 1331 f = fsspec.open(data.url, **(data.storage_options or {})).open()
1332 return open_dataset(f, **kw)
1333 return open_dataset(data.url, **kw)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/core.py:491, in open(urlpath, mode, compression, encoding, errors, protocol, newline, expand, **kwargs)
433 """Given a path or paths, return one ``OpenFile`` object.
434
435 Parameters
(...) 488 https://filesystem-spec.readthedocs.io/en/latest/api.html#other-known-implementations
489 """
490 expand = DEFAULT_EXPAND if expand is None else expand
--> 491 out = open_files(
492 urlpath=[urlpath],
493 mode=mode,
494 compression=compression,
495 encoding=encoding,
496 errors=errors,
497 protocol=protocol,
498 newline=newline,
499 expand=expand,
500 **kwargs,
501 )
502 if not out:
503 raise FileNotFoundError(urlpath)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/core.py:295, in open_files(urlpath, mode, compression, encoding, errors, name_function, num, protocol, newline, auto_mkdir, expand, **kwargs)
216 def open_files(
217 urlpath,
218 mode="rb",
(...) 228 **kwargs,
229 ):
230 """Given a path or paths, return a list of ``OpenFile`` objects.
231
232 For writing, a str path must contain the "*" character, which will be filled
(...) 293 https://filesystem-spec.readthedocs.io/en/latest/api.html#other-known-implementations
294 """
--> 295 fs, fs_token, paths = get_fs_token_paths(
296 urlpath,
297 mode,
298 num=num,
299 name_function=name_function,
300 storage_options=kwargs,
301 protocol=protocol,
302 expand=expand,
303 )
304 if fs.protocol == "file":
305 fs.auto_mkdir = auto_mkdir
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/core.py:667, in get_fs_token_paths(urlpath, mode, num, name_function, storage_options, protocol, expand)
665 inkwargs["fo"] = urls
666 paths, protocol, _ = chain[0]
--> 667 fs = filesystem(protocol, **inkwargs)
668 if isinstance(urlpath, (list, tuple, set)):
669 pchains = [
670 _un_chain(stringify_path(u), storage_options or {})[0] for u in urlpath
671 ]
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/registry.py:322, in filesystem(protocol, **storage_options)
315 warnings.warn(
316 "The 'arrow_hdfs' protocol has been deprecated and will be "
317 "removed in the future. Specify it as 'hdfs'.",
318 DeprecationWarning,
319 )
321 cls = get_filesystem_class(protocol)
--> 322 return cls(**storage_options)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/spec.py:81, in _Cached.__call__(cls, *args, **kwargs)
79 return cls._cache[token]
80 else:
---> 81 obj = super().__call__(*args, **kwargs)
82 # Setting _fs_token here causes some static linters to complain.
83 obj._fs_token_ = token
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/implementations/cached.py:762, in SimpleCacheFileSystem.__init__(self, **kwargs)
760 for key in ["cache_check", "expiry_time", "check_files"]:
761 kw[key] = False
--> 762 super().__init__(**kw)
763 for storage in self.storage:
764 if not os.path.exists(storage):
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/fsspec/implementations/cached.py:137, in CachingFileSystem.__init__(self, target_protocol, cache_storage, cache_check, check_files, expiry_time, target_options, fs, same_names, compression, cache_mapper, **kwargs)
135 else:
136 storage = cache_storage
--> 137 os.makedirs(storage[-1], exist_ok=True)
138 self.storage = storage
139 self.kwargs = target_options or {}
File <frozen os>:215, in makedirs(name, mode, exist_ok)
File <frozen os>:215, in makedirs(name, mode, exist_ok)
File <frozen os>:225, in makedirs(name, mode, exist_ok)
PermissionError: [Errno 13] Permission denied: '/home/kristen'
Plot one dataset¶
keys = list(cat[dataset_id].metadata["plots"].keys())
print(keys)
plots = []
for key in keys:
plot_kwargs = cat[dataset_id].metadata["plots"][key]
if "clim" in plot_kwargs and isinstance(plot_kwargs["clim"], list):
plot_kwargs["clim"] = tuple(plot_kwargs["clim"])
if "dynamic" in plot_kwargs:
plot_kwargs["dynamic"] = False
plots.append(cat[dataset_id].ToHvPlot(**plot_kwargs).read())
hv.Layout(plots).cols(1)