# This software is open source software available under the BSD-3 license.
#
# Copyright (c) 2020 Triad National Security, LLC. All rights reserved.
# Copyright (c) 2020 Lawrence Livermore National Security, LLC. All rights
# reserved.
# Copyright (c) 2020 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/master/LICENSE
from __future__ import absolute_import, division, print_function, \
unicode_literals
import xarray as xr
from mpas_analysis.shared import AnalysisTask
from mpas_analysis.shared.plot import timeseries_analysis_plot, \
timeseries_analysis_plot_polar, savefig
from mpas_analysis.shared.io.utility import build_config_full_path, \
check_path_exists, make_directories, build_obs_path
from mpas_analysis.shared.timekeeping.utility import date_to_days, \
days_to_datetime, datetime_to_days, get_simulation_start_time
from mpas_analysis.shared.timekeeping.MpasRelativeDelta import \
MpasRelativeDelta
from mpas_analysis.shared.time_series import combine_time_series_with_ncrcat
from mpas_analysis.shared.io import open_mpas_dataset, write_netcdf
from mpas_analysis.shared.html import write_image_xml
[docs]class TimeSeriesSeaIce(AnalysisTask):
"""
Performs analysis of time series of sea-ice properties.
Attributes
----------
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
controlConfig : ``MpasAnalysisConfigParser``
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 : ``MpasAnalysisConfigParser``
Configuration options
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
# first, call the constructor from the base class (AnalysisTask)
super(TimeSeriesSeaIce, self).__init__(
config=config,
taskName='timeSeriesSeaIceAreaVol',
componentName='seaIce',
tags=['timeSeries', 'publicObs', 'arctic', 'antarctic'])
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.runDirectory , self.historyDirectory, self.plotsDirectory,
# self.namelist, self.runStreams, self.historyStreams,
# self.calendar
super(TimeSeriesSeaIce, 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_iceAreaCell',
'timeMonthly_avg_iceVolumeCell']
self.mpasTimeSeriesTask.add_variables(variableList=self.variableList)
self.inputFile = self.mpasTimeSeriesTask.outputFile
if config.get('runs', 'preprocessedReferenceRunName') != 'None':
check_path_exists(config.get('seaIcePreprocessedReference',
'baseDirectory'))
# get a list of timeSeriesStatsMonthly output files from the streams
# file, reading only those that are between the start and end dates
streamName = 'timeSeriesStatsMonthlyOutput'
self.startDate = config.get('timeSeries', 'startDate')
self.endDate = config.get('timeSeries', 'endDate')
self.inputFiles = \
self.historyStreams.readpath(streamName,
startDate=self.startDate,
endDate=self.endDate,
calendar=self.calendar)
if len(self.inputFiles) == 0:
raise IOError('No files were found in stream {} between {} and '
'{}.'.format(streamName, self.startDate,
self.endDate))
self.simulationStartTime = get_simulation_start_time(self.runStreams)
try:
self.restartFileName = self.runStreams.readpath('restart')[0]
except ValueError:
raise IOError('No MPAS-SeaIce restart file found: need at least '
'one restart file to perform remapping of '
'climatologies.')
# these are redundant for now. Later cleanup is needed where these
# file names are reused in run()
self.xmlFileNames = []
polarPlot = config.getboolean('timeSeriesSeaIceAreaVol', 'polarPlot')
mainRunName = config.get('runs', 'mainRunName')
preprocessedReferenceRunName = \
config.get('runs', 'preprocessedReferenceRunName')
compareWithObservations = config.getboolean('timeSeriesSeaIceAreaVol',
'compareWithObservations')
polarXMLFileNames = []
if (not compareWithObservations and
preprocessedReferenceRunName == 'None'):
for variableName in ['iceArea', 'iceVolume']:
filePrefix = '{}.{}'.format(mainRunName,
variableName)
self.xmlFileNames.append('{}/{}.xml'.format(
self.plotsDirectory, filePrefix))
polarXMLFileNames.append('{}/{}_polar.xml'.format(
self.plotsDirectory, filePrefix))
else:
for hemisphere in ['NH', 'SH']:
for variableName in ['iceArea', 'iceVolume']:
filePrefix = '{}{}_{}'.format(variableName,
hemisphere,
mainRunName)
self.xmlFileNames.append('{}/{}.xml'.format(
self.plotsDirectory, filePrefix))
polarXMLFileNames.append('{}/{}_polar.xml'.format(
self.plotsDirectory, filePrefix))
if polarPlot:
self.xmlFileNames.extend(polarXMLFileNames)
return # }}}
def run_task(self): # {{{
"""
Performs analysis of time series of sea-ice properties.
"""
# Authors
# -------
# Xylar Asay-Davis, Milena Veneziani
self.logger.info("\nPlotting sea-ice area and volume time series...")
config = self.config
calendar = self.calendar
sectionName = self.taskName
plotTitles = {'iceArea': 'Sea-ice area',
'iceVolume': 'Sea-ice volume',
'iceThickness': 'Sea-ice mean thickness'}
units = {'iceArea': '[km$^2$]',
'iceVolume': '[10$^3$ km$^3$]',
'iceThickness': '[m]'}
obsFileNames = {
'iceArea': {'NH': build_obs_path(
config, 'seaIce',
relativePathOption='areaNH',
relativePathSection=sectionName),
'SH': build_obs_path(
config, 'seaIce',
relativePathOption='areaSH',
relativePathSection=sectionName)},
'iceVolume': {'NH': build_obs_path(
config, 'seaIce',
relativePathOption='volNH',
relativePathSection=sectionName),
'SH': build_obs_path(
config, 'seaIce',
relativePathOption='volSH',
relativePathSection=sectionName)}}
# Some plotting rules
titleFontSize = config.get('timeSeriesSeaIceAreaVol', 'titleFontSize')
mainRunName = config.get('runs', 'mainRunName')
preprocessedReferenceRunName = \
config.get('runs', 'preprocessedReferenceRunName')
preprocessedReferenceDirectory = \
config.get('seaIcePreprocessedReference', 'baseDirectory')
compareWithObservations = config.getboolean('timeSeriesSeaIceAreaVol',
'compareWithObservations')
movingAveragePoints = config.getint('timeSeriesSeaIceAreaVol',
'movingAveragePoints')
polarPlot = config.getboolean('timeSeriesSeaIceAreaVol', 'polarPlot')
outputDirectory = build_config_full_path(config, 'output',
'timeseriesSubdirectory')
make_directories(outputDirectory)
self.logger.info(' Load sea-ice data...')
# Load mesh
dsTimeSeries = self._compute_area_vol()
yearStart = days_to_datetime(dsTimeSeries['NH'].Time.min(),
calendar=calendar).year
yearEnd = days_to_datetime(dsTimeSeries['NH'].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 preprocessedReferenceRunName != 'None':
# determine if we're beyond the end of the preprocessed data
# (and go ahead and cache the data set while we're checking)
outFolder = '{}/preprocessed'.format(outputDirectory)
make_directories(outFolder)
inFilesPreprocessed = '{}/icevol.{}.year*.nc'.format(
preprocessedReferenceDirectory, preprocessedReferenceRunName)
outFileName = '{}/iceVolume.nc'.format(outFolder)
combine_time_series_with_ncrcat(inFilesPreprocessed,
outFileName,
logger=self.logger)
dsPreprocessed = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
preprocessedYearEnd = days_to_datetime(dsPreprocessed.Time.max(),
calendar=calendar).year
if yearStart <= preprocessedYearEnd:
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'
if self.controlConfig is not None:
dsTimeSeriesRef = {}
baseDirectory = build_config_full_path(
self.controlConfig, 'output', 'timeSeriesSubdirectory')
controlRunName = self.controlConfig.get('runs', 'mainRunName')
for hemisphere in ['NH', 'SH']:
inFileName = '{}/seaIceAreaVol{}.nc'.format(baseDirectory,
hemisphere)
dsTimeSeriesRef[hemisphere] = xr.open_dataset(inFileName)
norm = {'iceArea': 1e-6, # m^2 to km^2
'iceVolume': 1e-12, # m^3 to 10^3 km^3
'iceThickness': 1.}
xLabel = 'Time [years]'
galleryGroup = 'Time Series'
groupLink = 'timeseries'
obs = {}
preprocessed = {}
figureNameStd = {}
figureNamePolar = {}
title = {}
plotVars = {}
obsLegend = {}
plotVarsRef = {}
for hemisphere in ['NH', 'SH']:
self.logger.info(' Make {} plots...'.format(hemisphere))
for variableName in ['iceArea', 'iceVolume']:
key = (hemisphere, variableName)
# apply the norm to each variable
plotVars[key] = (norm[variableName] *
dsTimeSeries[hemisphere][variableName])
if self.controlConfig is not None:
plotVarsRef[key] = norm[variableName] * \
dsTimeSeriesRef[hemisphere][variableName]
prefix = '{}/{}{}_{}'.format(self.plotsDirectory,
variableName,
hemisphere,
mainRunName)
figureNameStd[key] = '{}.png'.format(prefix)
figureNamePolar[key] = '{}_polar.png'.format(prefix)
title[key] = '{} ({})'.format(plotTitles[variableName],
hemisphere)
if compareWithObservations:
key = (hemisphere, 'iceArea')
obsLegend[key] = 'SSM/I observations, annual cycle '
if hemisphere == 'NH':
key = (hemisphere, 'iceVolume')
obsLegend[key] = 'PIOMAS, annual cycle (blue)'
if preprocessedReferenceRunName != 'None':
for variableName in ['iceArea', 'iceVolume']:
key = (hemisphere, variableName)
if compareWithObservations:
outFolder = '{}/obs'.format(outputDirectory)
make_directories(outFolder)
outFileName = '{}/iceArea{}.nc'.format(outFolder, hemisphere)
combine_time_series_with_ncrcat(
obsFileNames['iceArea'][hemisphere],
outFileName, logger=self.logger)
dsObs = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
key = (hemisphere, 'iceArea')
obs[key] = self._replicate_cycle(plotVars[key], dsObs.IceArea,
calendar)
key = (hemisphere, 'iceVolume')
if hemisphere == 'NH':
outFileName = '{}/iceVolume{}.nc'.format(outFolder,
hemisphere)
combine_time_series_with_ncrcat(
obsFileNames['iceVolume'][hemisphere],
outFileName, logger=self.logger)
dsObs = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
obs[key] = self._replicate_cycle(plotVars[key],
dsObs.IceVol,
calendar)
else:
obs[key] = None
if preprocessedReferenceRunName != 'None':
outFolder = '{}/preprocessed'.format(outputDirectory)
inFilesPreprocessed = '{}/icearea.{}.year*.nc'.format(
preprocessedReferenceDirectory,
preprocessedReferenceRunName)
outFileName = '{}/iceArea.nc'.format(outFolder)
combine_time_series_with_ncrcat(inFilesPreprocessed,
outFileName,
logger=self.logger)
dsPreprocessed = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
dsPreprocessedTimeSlice = dsPreprocessed.sel(
Time=slice(timeStart, timeEnd))
key = (hemisphere, 'iceArea')
preprocessed[key] = dsPreprocessedTimeSlice[
'icearea_{}'.format(hemisphere.lower())]
inFilesPreprocessed = '{}/icevol.{}.year*.nc'.format(
preprocessedReferenceDirectory,
preprocessedReferenceRunName)
outFileName = '{}/iceVolume.nc'.format(outFolder)
combine_time_series_with_ncrcat(inFilesPreprocessed,
outFileName,
logger=self.logger)
dsPreprocessed = open_mpas_dataset(fileName=outFileName,
calendar=calendar,
timeVariableNames='xtime')
dsPreprocessedTimeSlice = dsPreprocessed.sel(
Time=slice(timeStart, timeEnd))
key = (hemisphere, 'iceVolume')
preprocessed[key] = dsPreprocessedTimeSlice[
'icevolume_{}'.format(hemisphere.lower())]
for variableName in ['iceArea', 'iceVolume']:
key = (hemisphere, variableName)
dsvalues = [plotVars[key]]
legendText = [mainRunName]
lineColors = ['k']
lineWidths = [3]
if compareWithObservations and key in obsLegend.keys():
dsvalues.append(obs[key])
legendText.append(obsLegend[key])
lineColors.append('b')
lineWidths.append(1.2)
if preprocessedReferenceRunName != 'None':
dsvalues.append(preprocessed[key])
legendText.append(preprocessedReferenceRunName)
lineColors.append('purple')
lineWidths.append(1.2)
if self.controlConfig is not None:
dsvalues.append(plotVarsRef[key])
legendText.append(controlRunName)
lineColors.append('r')
lineWidths.append(1.2)
if config.has_option(sectionName, 'firstYearXTicks'):
firstYearXTicks = config.getint(sectionName,
'firstYearXTicks')
else:
firstYearXTicks = None
if config.has_option(sectionName, 'yearStrideXTicks'):
yearStrideXTicks = config.getint(sectionName,
'yearStrideXTicks')
else:
yearStrideXTicks = None
# separate plots for nothern and southern hemispheres
timeseries_analysis_plot(
config, dsvalues, calendar=calendar, title=title[key],
xlabel=xLabel, ylabel=units[variableName],
movingAveragePoints=movingAveragePoints,
lineColors=lineColors, lineWidths=lineWidths,
legendText=legendText, titleFontSize=titleFontSize,
firstYearXTicks=firstYearXTicks,
yearStrideXTicks=yearStrideXTicks)
savefig(figureNameStd[key])
filePrefix = '{}{}_{}'.format(variableName,
hemisphere,
mainRunName)
thumbnailDescription = '{} {}'.format(
hemisphere, plotTitles[variableName])
caption = 'Running mean of {}'.format(
thumbnailDescription)
write_image_xml(
config,
filePrefix,
componentName='Sea Ice',
componentSubdirectory='sea_ice',
galleryGroup=galleryGroup,
groupLink=groupLink,
thumbnailDescription=thumbnailDescription,
imageDescription=caption,
imageCaption=caption)
if (polarPlot):
timeseries_analysis_plot_polar(config, dsvalues, title[key],
movingAveragePoints,
lineColors=lineColors,
lineWidths=lineWidths,
legendText=legendText,
titleFontSize=titleFontSize)
savefig(figureNamePolar[key])
filePrefix = '{}{}_{}_polar'.format(variableName,
hemisphere,
mainRunName)
write_image_xml(
config,
filePrefix,
componentName='Sea Ice',
componentSubdirectory='sea_ice',
galleryGroup=galleryGroup,
groupLink=groupLink,
thumbnailDescription=thumbnailDescription,
imageDescription=caption,
imageCaption=caption)
# }}}
def _replicate_cycle(self, ds, dsToReplicate, calendar): # {{{
"""
Replicates a periodic time series `dsToReplicate` to cover the
timeframe of the dataset `ds`.
Parameters
----------
ds : dataset used to find the start and end time of the replicated
cycle
dsToReplicate : dataset to replicate. The period of the cycle is the
length of dsToReplicate plus the time between the first two time
values (typically one year total).
calendar : {'gregorian', 'gregorian_noleap'}
The name of one of the calendars supported by MPAS cores
Returns:
--------
dsShift : a cyclicly repeated version of `dsToReplicte` covering the
range of time of `ds`.
"""
# Authors
# -------
# Xylar Asay-Davis, Milena Veneziani
dsStartTime = days_to_datetime(ds.Time.min(), calendar=calendar)
dsEndTime = days_to_datetime(ds.Time.max(), calendar=calendar)
repStartTime = days_to_datetime(dsToReplicate.Time.min(),
calendar=calendar)
repEndTime = days_to_datetime(dsToReplicate.Time.max(),
calendar=calendar)
repSecondTime = days_to_datetime(dsToReplicate.Time.isel(Time=1),
calendar=calendar)
period = (MpasRelativeDelta(repEndTime, repStartTime) +
MpasRelativeDelta(repSecondTime, repStartTime))
startIndex = 0
while(dsStartTime > repStartTime + (startIndex + 1) * period):
startIndex += 1
endIndex = 0
while(dsEndTime > repEndTime + endIndex * period):
endIndex += 1
dsShift = dsToReplicate.copy()
times = days_to_datetime(dsShift.Time, calendar=calendar)
dsShift.coords['Time'] = ('Time',
datetime_to_days(times + startIndex * period,
calendar=calendar))
# replicate cycle:
for cycleIndex in range(startIndex, endIndex):
dsNew = dsToReplicate.copy()
dsNew.coords['Time'] = \
('Time', datetime_to_days(times + (cycleIndex + 1) * period,
calendar=calendar))
dsShift = xr.concat([dsShift, dsNew], dim='Time')
# clip dsShift to the range of ds
dsStartTime = dsShift.Time.sel(Time=ds.Time.min(),
method=str('nearest')).values
dsEndTime = dsShift.Time.sel(Time=ds.Time.max(),
method=str('nearest')).values
dsShift = dsShift.sel(Time=slice(dsStartTime, dsEndTime))
return dsShift # }}}
def _compute_area_vol(self): # {{{
'''
Compute part of the time series of sea ice volume and area, given time
indices to process.
'''
outFileNames = {}
for hemisphere in ['NH', 'SH']:
baseDirectory = build_config_full_path(
self.config, 'output', 'timeSeriesSubdirectory')
make_directories(baseDirectory)
outFileName = '{}/seaIceAreaVol{}.nc'.format(baseDirectory,
hemisphere)
outFileNames[hemisphere] = outFileName
dsTimeSeries = {}
dsMesh = xr.open_dataset(self.restartFileName)
dsMesh = dsMesh[['latCell', 'areaCell']]
# Load data
ds = open_mpas_dataset(
fileName=self.inputFile,
calendar=self.calendar,
variableList=self.variableList,
startDate=self.startDate,
endDate=self.endDate)
for hemisphere in ['NH', 'SH']:
if hemisphere == 'NH':
mask = dsMesh.latCell > 0
else:
mask = dsMesh.latCell < 0
dsAreaSum = (ds.where(mask) * dsMesh.areaCell).sum('nCells')
dsAreaSum = dsAreaSum.rename(
{'timeMonthly_avg_iceAreaCell': 'iceArea',
'timeMonthly_avg_iceVolumeCell': 'iceVolume'})
dsAreaSum['iceThickness'] = (dsAreaSum.iceVolume /
dsMesh.areaCell.sum('nCells'))
dsAreaSum['iceArea'].attrs['units'] = 'm$^2$'
dsAreaSum['iceArea'].attrs['description'] = \
'Total {} sea ice area'.format(hemisphere)
dsAreaSum['iceVolume'].attrs['units'] = 'm$^3$'
dsAreaSum['iceVolume'].attrs['description'] = \
'Total {} sea ice volume'.format(hemisphere)
dsAreaSum['iceThickness'].attrs['units'] = 'm'
dsAreaSum['iceThickness'].attrs['description'] = \
'Mean {} sea ice volume'.format(hemisphere)
dsTimeSeries[hemisphere] = dsAreaSum
write_netcdf(dsAreaSum, outFileNames[hemisphere])
return dsTimeSeries # }}}
# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python