import intake
import hvplot.pandas
import hvplot.xarray
import cook_inlet_catalogs as cic
import holoviews as hv
CTD Transect (OTF KBNERR): Repeated from Anchor Point¶
CTD Transect Across Anchor Point, for GEM Project 030670.
This project used a vessel of opportunity to collect physical oceanographic and fisheries data at six stations along a transect across lower Cook Inlet from Anchor Point (AP) to the Red River delta each day during July. Logistical support for the field sampling was provided in part by the Alaska Department of Fish and Game which has chartered a drift gillnet vessel annually to fish along this transect providing inseason projections of the size of sockeye salmon runs entering Cook Inlet. This project funded collection of physical oceanographic data on board the chartered vessel to help identify intrusions of the Alaska Coastal Current (ACC) into Cook Inlet and test six hypotheses regarding effects of changing oceanographic conditions on migratory behavior and catchability of sockeye salmon entering Cook Inlet. In 2003-2007, a conductivity-temperature-depth profiler was deployed at each station. In 2003-2005, current velocities were estimated along the transect using a towed acoustic Doppler current profiler, and salmon relative abundance and vertical distribution was estimated using towed fisheries acoustic equipment.
Willette, T.M., W.S. Pegau, and R.D. DeCino. 2010. Monitoring dynamics of the Alaska coastal current and development of applications for management of Cook Inlet salmon - a pilot study. Exxon Valdez Oil Spill Gulf Ecosystem Monitoring and Research Project Final Report (GEM Project 030670), Alaska Department of Fish and Game, Commercial Fisheries Division, Soldotna, Alaska.
Report: https://evostc.state.ak.us/media/2176/2004-040670-final.pdf Project description: https://evostc.state.ak.us/restoration-projects/project-search/monitoring-dynamics-of-the-alaska-coastal-current-and-development-of-applications-for-management-of-cook-inlet-salmon-040670/
cat = intake.open_catalog(cic.utils.cat_path("ctd_transects_otf_kbnerr"))
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
['2003-07-01',
'2003-07-02',
'2003-07-04',
'2003-07-05',
'2003-07-06',
'2003-07-07',
'2003-07-08',
'2003-07-09',
'2003-07-10',
'2003-07-11',
'2003-07-12',
'2003-07-13',
'2003-07-14',
'2003-07-15',
'2003-07-16',
'2003-07-17',
'2003-07-18',
'2003-07-19',
'2003-07-21',
'2003-07-22',
'2003-07-23',
'2003-07-24',
'2003-07-25',
'2003-07-26',
'2003-07-28',
'2003-07-29',
'2003-07-30',
'2004-07-01',
'2004-07-02',
'2004-07-03',
'2004-07-04',
'2004-07-05',
'2004-07-06',
'2004-07-07',
'2004-07-08',
'2004-07-09',
'2004-07-10',
'2004-07-11',
'2004-07-12',
'2004-07-13',
'2004-07-14',
'2004-07-15',
'2004-07-16',
'2004-07-17',
'2004-07-18',
'2004-07-19',
'2004-07-20',
'2004-07-21',
'2004-07-22',
'2004-07-23',
'2004-07-24',
'2004-07-25',
'2004-07-27',
'2004-07-28',
'2004-07-29',
'2004-07-30',
'2005-07-01',
'2005-07-02',
'2005-07-03',
'2005-07-04',
'2005-07-05',
'2005-07-06',
'2005-07-07',
'2005-07-08',
'2005-07-09',
'2005-07-10',
'2005-07-11',
'2005-07-12',
'2005-07-13',
'2005-07-14',
'2005-07-15',
'2005-07-16',
'2005-07-17',
'2005-07-18',
'2005-07-19',
'2005-07-20',
'2005-07-21',
'2005-07-22',
'2005-07-23',
'2005-07-24',
'2005-07-25',
'2005-07-26',
'2005-07-27',
'2005-07-28',
'2005-07-29',
'2005-07-30',
'2006-07-01',
'2006-07-02',
'2006-07-03',
'2006-07-04',
'2006-07-05',
'2006-07-06',
'2006-07-07',
'2006-07-09',
'2006-07-10',
'2006-07-11',
'2006-07-12',
'2006-07-13',
'2006-07-15',
'2006-07-16',
'2006-07-17',
'2006-07-18',
'2006-07-19',
'2006-07-21',
'2006-07-23',
'2006-07-25',
'2006-07-26',
'2006-07-27',
'2006-07-28']
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
2003-07-04
---------------------------------------------------------------------------
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:176, in FileReader._read(self, data, **kw)
174 if self.storage_options and data.storage_options:
175 kw["storage_options"] = data.storage_options
--> 176 return self._func(**kw)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1026, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)
1013 kwds_defaults = _refine_defaults_read(
1014 dialect,
1015 delimiter,
(...) 1022 dtype_backend=dtype_backend,
1023 )
1024 kwds.update(kwds_defaults)
-> 1026 return _read(filepath_or_buffer, kwds)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/parsers/readers.py:620, in _read(filepath_or_buffer, kwds)
617 _validate_names(kwds.get("names", None))
619 # Create the parser.
--> 620 parser = TextFileReader(filepath_or_buffer, **kwds)
622 if chunksize or iterator:
623 return parser
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1620, in TextFileReader.__init__(self, f, engine, **kwds)
1617 self.options["has_index_names"] = kwds["has_index_names"]
1619 self.handles: IOHandles | None = None
-> 1620 self._engine = self._make_engine(f, self.engine)
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1880, in TextFileReader._make_engine(self, f, engine)
1878 if "b" not in mode:
1879 mode += "b"
-> 1880 self.handles = get_handle(
1881 f,
1882 mode,
1883 encoding=self.options.get("encoding", None),
1884 compression=self.options.get("compression", None),
1885 memory_map=self.options.get("memory_map", False),
1886 is_text=is_text,
1887 errors=self.options.get("encoding_errors", "strict"),
1888 storage_options=self.options.get("storage_options", None),
1889 )
1890 assert self.handles is not None
1891 f = self.handles.handle
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/common.py:728, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
725 codecs.lookup_error(errors)
727 # open URLs
--> 728 ioargs = _get_filepath_or_buffer(
729 path_or_buf,
730 encoding=encoding,
731 compression=compression,
732 mode=mode,
733 storage_options=storage_options,
734 )
736 handle = ioargs.filepath_or_buffer
737 handles: list[BaseBuffer]
File ~/checkouts/readthedocs.org/user_builds/cook-inlet-catalogs/conda/stable/lib/python3.11/site-packages/pandas/io/common.py:430, in _get_filepath_or_buffer(filepath_or_buffer, encoding, compression, mode, storage_options)
427 pass
429 try:
--> 430 file_obj = fsspec.open(
431 filepath_or_buffer, mode=fsspec_mode, **(storage_options or {})
432 ).open()
433 # GH 34626 Reads from Public Buckets without Credentials needs anon=True
434 except tuple(err_types_to_retry_with_anon):
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)