# This software is open source software available under the BSD-3 license.
#
# Copyright (c) 2022 Triad National Security, LLC. All rights reserved.
# Copyright (c) 2022 Lawrence Livermore National Security, LLC. All rights
# reserved.
# Copyright (c) 2022 UT-Battelle, LLC. All rights reserved.
#
# Additional copyright and license information can be found in the LICENSE file
# distributed with this code, or at
# https://raw.githubusercontent.com/MPAS-Dev/MPAS-Analysis/main/LICENSE
from mpas_analysis.shared import AnalysisTask
from mpas_analysis.shared.plot import timeseries_analysis_plot, savefig
from mpas_analysis.shared.time_series import combine_time_series_with_ncrcat
from mpas_analysis.shared.io import open_mpas_dataset
from mpas_analysis.shared.timekeeping.utility import date_to_days, \
days_to_datetime
from mpas_analysis.shared.io.utility import build_config_full_path, \
make_directories, check_path_exists
from mpas_analysis.shared.html import write_image_xml
from mpas_analysis.ocean.utility import (
add_standard_regions_and_subset,
get_standard_region_names
)
[docs]
class TimeSeriesSST(AnalysisTask):
"""
Performs analysis of the time-series output of sea-surface temperature
(SST).
Attributes
----------
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
controlconfig : tranche.Tranche
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis, Milena Veneziani
[docs]
def __init__(self, config, mpasTimeSeriesTask, controlConfig=None):
"""
Construct the analysis task.
Parameters
----------
config : tranche.Tranche
Configuration options
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
controlconfig : tranche.Tranche, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
# first, call the constructor from the base class (AnalysisTask)
super(TimeSeriesSST, self).__init__(
config=config,
taskName='timeSeriesSST',
componentName='ocean',
tags=['timeSeries', 'sst', 'publicObs'])
self.mpasTimeSeriesTask = mpasTimeSeriesTask
self.controlConfig = controlConfig
self.run_after(mpasTimeSeriesTask)
def setup_and_check(self):
"""
Perform steps to set up the analysis and check for errors in the setup.
Raises
------
OSError
If files are not present
"""
# Authors
# -------
# Xylar Asay-Davis
# first, call setup_and_check from the base class (AnalysisTask),
# which will perform some common setup, including storing:
# self.inDirectory, self.plotsDirectory, self.namelist, self.streams
# self.calendar
super(TimeSeriesSST, self).setup_and_check()
config = self.config
self.startDate = self.config.get('timeSeries', 'startDate')
self.endDate = self.config.get('timeSeries', 'endDate')
self.variableList = \
['timeMonthly_avg_avgValueWithinOceanRegion_avgSurfaceTemperature']
self.mpasTimeSeriesTask.add_variables(variableList=self.variableList)
if config.get('runs', 'preprocessedReferenceRunName') != 'None':
check_path_exists(config.get('oceanPreprocessedReference',
'baseDirectory'))
self.inputFile = self.mpasTimeSeriesTask.outputFile
mainRunName = config.get('runs', 'mainRunName')
regionShortNames = config.getexpression('timeSeriesSST',
'regionShortNames')
self.xmlFileNames = []
self.filePrefixes = {}
regions = get_standard_region_names(config, regionShortNames)
for region in regions:
regionSuffix = region.replace(' ', '_')
filePrefix = 'sst_{}_{}'.format(regionSuffix, mainRunName)
self.xmlFileNames.append('{}/{}.xml'.format(self.plotsDirectory,
filePrefix))
self.filePrefixes[region] = filePrefix
return
def run_task(self):
"""
Performs analysis of the time-series output of sea-surface temperature
(SST).
"""
# Authors
# -------
# Xylar Asay-Davis, Milena Veneziani
self.logger.info("\nPlotting SST time series...")
self.logger.info(' Load SST data...')
config = self.config
calendar = self.calendar
mainRunName = config.get('runs', 'mainRunName')
preprocessedReferenceRunName = \
config.get('runs', 'preprocessedReferenceRunName')
preprocessedInputDirectory = config.get('oceanPreprocessedReference',
'baseDirectory')
movingAveragePoints = config.getint('timeSeriesSST',
'movingAveragePoints')
regionShortNames = config.getexpression('timeSeriesSST',
'regionShortNames')
outputDirectory = build_config_full_path(config, 'output',
'timeseriesSubdirectory')
make_directories(outputDirectory)
dsSST = open_mpas_dataset(fileName=self.inputFile,
calendar=calendar,
variableList=self.variableList,
startDate=self.startDate,
endDate=self.endDate)
dsSST = add_standard_regions_and_subset(
dsSST, config, regionShortNames=regionShortNames)
yearStart = days_to_datetime(dsSST.Time.min(), calendar=calendar).year
yearEnd = days_to_datetime(dsSST.Time.max(), calendar=calendar).year
timeStart = date_to_days(year=yearStart, month=1, day=1,
calendar=calendar)
timeEnd = date_to_days(year=yearEnd, month=12, day=31,
calendar=calendar)
if self.controlConfig is not None:
baseDirectory = build_config_full_path(
self.controlConfig, 'output', 'timeSeriesSubdirectory')
controlFileName = '{}/{}.nc'.format(
baseDirectory, self.mpasTimeSeriesTask.fullTaskName)
controlStartYear = self.controlConfig.getint(
'timeSeries', 'startYear')
controlEndYear = self.controlConfig.getint('timeSeries', 'endYear')
controlStartDate = '{:04d}-01-01_00:00:00'.format(controlStartYear)
controlEndDate = '{:04d}-12-31_23:59:59'.format(controlEndYear)
dsRefSST = open_mpas_dataset(
fileName=controlFileName,
calendar=calendar,
variableList=self.variableList,
startDate=controlStartDate,
endDate=controlEndDate)
dsRefSST = add_standard_regions_and_subset(
dsRefSST, self.controlConfig,
regionShortNames=regionShortNames)
else:
dsRefSST = None
if preprocessedReferenceRunName != 'None':
self.logger.info(' Load in SST for a preprocesses reference '
'run...')
inFilesPreprocessed = '{}/SST.{}.year*.nc'.format(
preprocessedInputDirectory, preprocessedReferenceRunName)
outFolder = '{}/preprocessed'.format(outputDirectory)
make_directories(outFolder)
outFileName = '{}/sst.nc'.format(outFolder)
combine_time_series_with_ncrcat(inFilesPreprocessed,
outFileName, logger=self.logger)
dsPreprocessed = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
yearEndPreprocessed = days_to_datetime(dsPreprocessed.Time.max(),
calendar=calendar).year
if yearStart <= yearEndPreprocessed:
dsPreprocessedTimeSlice = \
dsPreprocessed.sel(Time=slice(timeStart, timeEnd))
else:
self.logger.warning('Preprocessed time series ends before the '
'timeSeries startYear and will not be '
'plotted.')
preprocessedReferenceRunName = 'None'
self.logger.info(' Make plots...')
for regionName in dsSST.regionNames.values:
title = f'{regionName} SST'
xLabel = 'Time [years]'
yLabel = r'[$\degree$C]'
varName = self.variableList[0]
dsSST = dsSST.set_xindex('regionNames')
SST = dsSST[varName].sel(regionNames=regionName)
filePrefix = self.filePrefixes[regionName]
outFileName = '{}/{}.png'.format(self.plotsDirectory, filePrefix)
lineColors = [config.get('timeSeries', 'mainColor')]
lineWidths = [3]
fields = [SST]
legendText = [mainRunName]
if dsRefSST is not None:
dsRefSST = dsRefSST.set_xindex('regionNames')
refSST = dsRefSST[varName].sel(regionNames=regionName)
fields.append(refSST)
lineColors.append(config.get('timeSeries', 'controlColor'))
lineWidths.append(1.5)
controlRunName = self.controlConfig.get('runs', 'mainRunName')
legendText.append(controlRunName)
if preprocessedReferenceRunName != 'None':
SST_v0 = dsPreprocessedTimeSlice.SST
fields.append(SST_v0)
lineColors.append('purple')
lineWidths.append(1.5)
legendText.append(preprocessedReferenceRunName)
if config.has_option(self.taskName, 'firstYearXTicks'):
firstYearXTicks = config.getint(self.taskName,
'firstYearXTicks')
else:
firstYearXTicks = None
if config.has_option(self.taskName, 'yearStrideXTicks'):
yearStrideXTicks = config.getint(self.taskName,
'yearStrideXTicks')
else:
yearStrideXTicks = None
timeseries_analysis_plot(config, fields, calendar=calendar,
title=title, xlabel=xLabel, ylabel=yLabel,
movingAveragePoints=movingAveragePoints,
lineColors=lineColors,
lineWidths=lineWidths,
legendText=legendText,
firstYearXTicks=firstYearXTicks,
yearStrideXTicks=yearStrideXTicks)
savefig(outFileName, config)
caption = f'Running Mean of {regionName} Sea Surface Temperature'
write_image_xml(
config=config,
filePrefix=filePrefix,
componentName='Ocean',
componentSubdirectory='ocean',
galleryGroup='Time Series',
groupLink='timeseries',
thumbnailDescription=f'{regionName} SST',
imageDescription=caption,
imageCaption=caption)
# }}}