# 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 os
import xarray
import numpy
import csv
import matplotlib.pyplot as plt
from geometric_features import FeatureCollection, read_feature_collection
from mpas_analysis.shared.analysis_task import AnalysisTask
from mpas_analysis.shared.constants import constants
from mpas_analysis.shared.plot import timeseries_analysis_plot, savefig, \
add_inset
from mpas_analysis.shared.io import open_mpas_dataset, write_netcdf
from mpas_analysis.shared.io.utility import build_config_full_path, \
make_directories, build_obs_path, decode_strings
from mpas_analysis.shared.html import write_image_xml
[docs]class TimeSeriesAntarcticMelt(AnalysisTask): # {{{
"""
Performs analysis of the time-series output of Antarctic sub-ice-shelf
melt rates.
"""
# Authors
# -------
# Xylar Asay-Davis, Stephen Price
[docs] def __init__(self, config, mpasTimeSeriesTask, regionMasksTask,
controlConfig=None):
# {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
regionMasksTask : ``ComputeRegionMasks``
A task for computing region masks
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(TimeSeriesAntarcticMelt, self).__init__(
config=config,
taskName='timeSeriesAntarcticMelt',
componentName='ocean',
tags=['timeSeries', 'melt', 'landIceCavities', 'antarctic'])
regionGroup = 'Ice Shelves'
iceShelvesToPlot = config.getExpression('timeSeriesAntarcticMelt',
'iceShelvesToPlot')
if len(iceShelvesToPlot) == 0:
# nothing else to do
return
masksSubtask = regionMasksTask.add_mask_subtask(regionGroup=regionGroup)
self.iceShelfMasksFile = masksSubtask.geojsonFileName
iceShelvesToPlot = masksSubtask.expand_region_names(iceShelvesToPlot)
startYear = config.getint('timeSeries', 'startYear')
endYear = config.get('timeSeries', 'endYear')
if endYear == 'end':
# a valid end year wasn't found, so likely the run was not found,
# perhaps because we're just listing analysis tasks
endYear = startYear
else:
endYear = int(endYear)
years = list(range(startYear, endYear + 1))
# in the end, we'll combine all the time series into one, but we
# create this task first so it's easier to tell it to run after all
# the compute tasks
combineSubtask = CombineMeltSubtask(
self, startYears=years, endYears=years)
# run one subtask per year
for year in years:
computeSubtask = ComputeMeltSubtask(
self, startYear=year, endYear=year,
mpasTimeSeriesTask=mpasTimeSeriesTask,
masksSubtask=masksSubtask,
iceShelvesToPlot=iceShelvesToPlot)
self.add_subtask(computeSubtask)
computeSubtask.run_after(masksSubtask)
combineSubtask.run_after(computeSubtask)
self.add_subtask(combineSubtask)
for index, iceShelf in enumerate(iceShelvesToPlot):
plotMeltSubtask = PlotMeltSubtask(self, iceShelf, index,
controlConfig)
plotMeltSubtask.run_after(combineSubtask)
self.add_subtask(plotMeltSubtask)
# }}}
# }}}
class ComputeMeltSubtask(AnalysisTask): # {{{
"""
Computes time-series of Antarctic sub-ice-shelf melt rates.
Attributes
----------
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
masksSubtask : ``ComputeRegionMasksSubtask``
A task for creating mask files for each ice shelf to plot
iceShelvesToPlot : list of str
A list of ice shelves to plot
"""
# Authors
# -------
# Xylar Asay-Davis, Stephen Price
def __init__(self, parentTask, startYear, endYear, mpasTimeSeriesTask,
masksSubtask, iceShelvesToPlot): # {{{
"""
Construct the analysis task.
Parameters
----------
parentTask : TimeSeriesAntarcticMelt
The parent task, used to get the ``taskName``, ``config`` and
``componentName``
mpasTimeSeriesTask : ``MpasTimeSeriesTask``
The task that extracts the time series from MPAS monthly output
masksSubtask : ``ComputeRegionMasksSubtask``
A task for creating mask files for each ice shelf to plot
iceShelvesToPlot : list of str
A list of ice shelves to plot
"""
# Authors
# -------
# Xylar Asay-Davis
# first, call the constructor from the base class (AnalysisTask)
super(ComputeMeltSubtask, self).__init__(
config=parentTask.config,
taskName=parentTask.taskName,
componentName=parentTask.componentName,
tags=parentTask.tags,
subtaskName='computeMeltRates_{:04d}-{:04d}'.format(startYear,
endYear))
self.mpasTimeSeriesTask = mpasTimeSeriesTask
self.run_after(mpasTimeSeriesTask)
self.masksSubtask = masksSubtask
self.run_after(masksSubtask)
self.iceShelvesToPlot = iceShelvesToPlot
self.restartFileName = None
self.startYear = startYear
self.endYear = endYear
self.startDate = '{:04d}-01-01_00:00:00'.format(self.startYear)
self.endDate = '{:04d}-12-31_23:59:59'.format(self.endYear)
self.variableList = \
['timeMonthly_avg_landIceFreshwaterFlux']
# }}}
def setup_and_check(self): # {{{
"""
Perform steps to set up the analysis and check for errors in the setup.
Raises
------
IOError
If a restart file is not present
ValueError
If ``config_land_ice_flux_mode`` is not one of ``standalone`` or
``coupled``
"""
# 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(ComputeMeltSubtask, self).setup_and_check()
self.check_analysis_enabled(
analysisOptionName='config_am_timeseriesstatsmonthly_enable',
raiseException=True)
landIceFluxMode = self.namelist.get('config_land_ice_flux_mode')
if landIceFluxMode not in ['standalone', 'coupled']:
raise ValueError('*** timeSeriesAntarcticMelt requires '
'config_land_ice_flux_mode \n'
' to be standalone or coupled. Otherwise, no '
'melt rates are available \n'
' for plotting.')
# Load mesh related variables
try:
self.restartFileName = self.runStreams.readpath('restart')[0]
except ValueError:
raise IOError('No MPAS-O restart file found: need at least one '
'restart file for Antarctic melt calculations')
self.mpasTimeSeriesTask.add_variables(variableList=self.variableList)
return # }}}
def run_task(self): # {{{
"""
Computes time-series of Antarctic sub-ice-shelf melt rates.
"""
# Authors
# -------
# Xylar Asay-Davis, Stephen Price
self.logger.info("Computing Antarctic melt rate time series...")
mpasTimeSeriesTask = self.mpasTimeSeriesTask
config = self.config
outputDirectory = '{}/iceShelfFluxes/'.format(
build_config_full_path(config, 'output', 'timeseriesSubdirectory'))
try:
os.makedirs(outputDirectory)
except OSError:
pass
outFileName = '{}/iceShelfFluxes_{:04d}-{:04d}.nc'.format(
outputDirectory, self.startYear, self.endYear)
# Load data:
inputFile = mpasTimeSeriesTask.outputFile
dsIn = open_mpas_dataset(fileName=inputFile,
calendar=self.calendar,
variableList=self.variableList,
startDate=self.startDate,
endDate=self.endDate)
try:
if os.path.exists(outFileName):
# The file already exists so load it
dsOut = xarray.open_dataset(outFileName)
if numpy.all(dsOut.Time.values == dsIn.Time.values):
return
else:
self.logger.warning('File {} is incomplete. Deleting '
'it.'.format(outFileName))
os.remove(outFileName)
except OSError:
# something is potentially wrong with the file, so let's delete
# it and try again
self.logger.warning('Problems reading file {}. Deleting '
'it.'.format(outFileName))
os.remove(outFileName)
restartFileName = \
mpasTimeSeriesTask.runStreams.readpath('restart')[0]
dsRestart = xarray.open_dataset(restartFileName)
areaCell = \
dsRestart.landIceFraction.isel(Time=0) * dsRestart.areaCell
regionMaskFileName = self.masksSubtask.maskFileName
dsRegionMask = xarray.open_dataset(regionMaskFileName)
# figure out the indices of the regions to plot
regionNames = decode_strings(dsRegionMask.regionNames)
regionIndices = []
for iceShelf in self.iceShelvesToPlot:
for index, regionName in enumerate(regionNames):
if iceShelf == regionName:
regionIndices.append(index)
break
# select only those regions we want to plot
dsRegionMask = dsRegionMask.isel(nRegions=regionIndices)
regionNames = decode_strings(dsRegionMask.regionNames)
datasets = []
nTime = dsIn.sizes['Time']
for tIndex in range(nTime):
self.logger.info(' {}/{}'.format(tIndex+1, nTime))
freshwaterFlux = \
dsIn.timeMonthly_avg_landIceFreshwaterFlux.isel(Time=tIndex)
nRegions = dsRegionMask.sizes['nRegions']
meltRates = numpy.zeros((nRegions,))
totalMeltFluxes = numpy.zeros((nRegions,))
for regionIndex in range(nRegions):
self.logger.info(' {}'.format(regionNames[regionIndex]))
cellMask = \
dsRegionMask.regionCellMasks.isel(nRegions=regionIndex)
# convert from kg/s to kg/yr
totalMeltFlux = constants.sec_per_year * \
(cellMask * areaCell * freshwaterFlux).sum(dim='nCells')
totalArea = (cellMask * areaCell).sum(dim='nCells')
# from kg/m^2/yr to m/yr
meltRates[regionIndex] = ((1. / constants.rho_fw) *
(totalMeltFlux / totalArea))
# convert from kg/yr to GT/yr
totalMeltFlux /= constants.kg_per_GT
totalMeltFluxes[regionIndex] = totalMeltFlux
dsOut = xarray.Dataset()
dsOut.coords['Time'] = dsIn.Time.isel(Time=tIndex)
dsOut['totalMeltFlux'] = (('nRegions',), totalMeltFluxes)
dsOut['meltRates'] = (('nRegions',), meltRates)
datasets.append(dsOut)
dsOut = xarray.concat(objs=datasets, dim='Time')
dsOut['regionNames'] = dsRegionMask.regionNames
dsOut.totalMeltFlux.attrs['units'] = 'GT a$^{-1}$'
dsOut.totalMeltFlux.attrs['description'] = \
'Total melt flux summed over each ice shelf or region'
dsOut.meltRates.attrs['units'] = 'm a$^{-1}$'
dsOut.meltRates.attrs['description'] = \
'Melt rate averaged over each ice shelf or region'
write_netcdf(dsOut, outFileName)
# }}}
# }}}
class CombineMeltSubtask(AnalysisTask): # {{{
"""
Combine individual time series into a single data set
"""
# Authors
# -------
# Xylar Asay-Davis
def __init__(self, parentTask, startYears, endYears): # {{{
"""
Construct the analysis task.
Parameters
----------
parentTask : TimeSeriesAntarcticMelt
The main task of which this is a subtask
startYears, endYears : list
The beginning and end of each time series to combine
"""
# Authors
# -------
# Xylar Asay-Davis
subtaskName = 'combineAntarcticMeltTimeSeries'
# first, call the constructor from the base class (AnalysisTask)
super(CombineMeltSubtask, self).__init__(
config=parentTask.config,
taskName=parentTask.taskName,
componentName=parentTask.componentName,
tags=parentTask.tags,
subtaskName=subtaskName)
self.startYears = startYears
self.endYears = endYears
# }}}
def run_task(self): # {{{
"""
Combine the time series
"""
# Authors
# -------
# Xylar Asay-Davis
outputDirectory = '{}/iceShelfFluxes/'.format(
build_config_full_path(self.config, 'output',
'timeseriesSubdirectory'))
outFileName = '{}/iceShelfFluxes_{:04d}-{:04d}.nc'.format(
outputDirectory, self.startYears[0], self.endYears[-1])
if not os.path.exists(outFileName):
inFileNames = []
for startYear, endYear in zip(self.startYears, self.endYears):
inFileName = '{}/iceShelfFluxes_{:04d}-{:04d}.nc'.format(
outputDirectory, startYear, endYear)
inFileNames.append(inFileName)
ds = xarray.open_mfdataset(inFileNames, combine='nested',
concat_dim='Time', decode_times=False)
ds.load()
write_netcdf(ds, outFileName)
# }}}
# }}}
class PlotMeltSubtask(AnalysisTask):
"""
Plots time-series output of Antarctic sub-ice-shelf melt rates.
Attributes
----------
iceShelf : str
Name of the ice shelf to plot
regionIndex : int
The index into the dimension ``nRegions`` of the ice shelf to plot
controlConfig : ``MpasAnalysisConfigParser``
The configuration options for the control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis, Stephen Price
def __init__(self, parentTask, iceShelf, regionIndex, controlConfig):
# {{{
"""
Construct the analysis task.
Parameters
----------
parentTask : TimeSeriesAntarcticMelt
The parent task, used to get the ``taskName``, ``config`` and
``componentName``
iceShelf : str
Name of the ice shelf to plot
regionIndex : int
The index into the dimension ``nRegions`` of the ice shelf to plot
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(PlotMeltSubtask, self).__init__(
config=parentTask.config,
taskName=parentTask.taskName,
componentName=parentTask.componentName,
tags=parentTask.tags,
subtaskName='plotMeltRates_{}'.format(iceShelf.replace(' ', '_')))
self.iceShelfMasksFile = parentTask.iceShelfMasksFile
self.iceShelf = iceShelf
self.regionIndex = regionIndex
self.controlConfig = controlConfig
# }}}
def setup_and_check(self): # {{{
"""
Perform steps to set up the analysis and check for errors in the setup.
Raises
------
IOError
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(PlotMeltSubtask, self).setup_and_check()
self.xmlFileNames = []
for prefix in ['melt_flux', 'melt_rate']:
self.xmlFileNames.append(
'{}/{}_{}.xml'.format(self.plotsDirectory, prefix,
self.iceShelf.replace(' ', '_')))
return # }}}
def run_task(self): # {{{
"""
Plots time-series output of Antarctic sub-ice-shelf melt rates.
"""
# Authors
# -------
# Xylar Asay-Davis, Stephen Price
self.logger.info("\nPlotting Antarctic melt rate time series for "
"{}...".format(self.iceShelf))
self.logger.info(' Load melt rate data...')
config = self.config
calendar = self.calendar
iceShelfMasksFile = self.iceShelfMasksFile
fcAll = read_feature_collection(iceShelfMasksFile)
fc = FeatureCollection()
for feature in fcAll.features:
if feature['properties']['name'] == self.iceShelf:
fc.add_feature(feature)
break
totalMeltFlux, meltRates = self._load_ice_shelf_fluxes(config)
plotControl = self.controlConfig is not None
if plotControl:
controlRunName = self.controlConfig.get('runs', 'mainRunName')
refTotalMeltFlux, refMeltRates = \
self._load_ice_shelf_fluxes(self.controlConfig)
# Load observations from multiple files and put in dictionary based
# on shelf key name
observationsDirectory = build_obs_path(config, 'ocean',
'meltSubdirectory')
obsFileNameDict = {'Rignot et al. (2013)':
'Rignot_2013_melt_rates_20201117.csv',
'Rignot et al. (2013) SS':
'Rignot_2013_melt_rates_SS_20201117.csv'}
obsDict = {} # dict for storing dict of obs data
for obsName in obsFileNameDict:
obsFileName = '{}/{}'.format(observationsDirectory,
obsFileNameDict[obsName])
obsDict[obsName] = {}
obsFile = csv.reader(open(obsFileName, 'rU'))
next(obsFile, None) # skip the header line
for line in obsFile: # some later useful values commented out
shelfName = line[0]
if shelfName != self.iceShelf:
continue
# surveyArea = line[1]
meltFlux = float(line[2])
meltFluxUncertainty = float(line[3])
meltRate = float(line[4])
meltRateUncertainty = float(line[5])
# actualArea = float( line[6] ) # actual area here is in sq km
# build dict of obs. keyed to filename description
# (which will be used for plotting)
obsDict[obsName] = {
'meltFlux': meltFlux,
'meltFluxUncertainty': meltFluxUncertainty,
'meltRate': meltRate,
'meltRateUncertainty': meltRateUncertainty}
break
# If areas from obs file used need to be converted from sq km to sq m
mainRunName = config.get('runs', 'mainRunName')
movingAverageMonths = config.getint('timeSeriesAntarcticMelt',
'movingAverageMonths')
outputDirectory = build_config_full_path(config, 'output',
'timeseriesSubdirectory')
make_directories(outputDirectory)
self.logger.info(' Make plots...')
# get obs melt flux and unc. for shelf (similar for rates)
obsMeltFlux = []
obsMeltFluxUnc = []
obsMeltRate = []
obsMeltRateUnc = []
for obsName in obsDict:
if len(obsDict[obsName]) > 0:
obsMeltFlux.append(
obsDict[obsName]['meltFlux'])
obsMeltFluxUnc.append(
obsDict[obsName]['meltFluxUncertainty'])
obsMeltRate.append(
obsDict[obsName]['meltRate'])
obsMeltRateUnc.append(
obsDict[obsName]['meltRateUncertainty'])
else:
# append NaN so this particular obs won't plot
self.logger.warning('{} observations not available for '
'{}'.format(obsName, self.iceShelf))
obsMeltFlux.append(None)
obsMeltFluxUnc.append(None)
obsMeltRate.append(None)
obsMeltRateUnc.append(None)
title = self.iceShelf.replace('_', ' ')
xLabel = 'Time (yr)'
yLabel = 'Melt Flux (GT/yr)'
timeSeries = totalMeltFlux.isel(nRegions=self.regionIndex)
filePrefix = 'melt_flux_{}'.format(self.iceShelf.replace(' ', '_'))
outFileName = '{}/{}.png'.format(self.plotsDirectory, filePrefix)
fields = [timeSeries]
lineColors = ['k']
lineWidths = [2.5]
legendText = [mainRunName]
if plotControl:
fields.append(refTotalMeltFlux.isel(nRegions=self.regionIndex))
lineColors.append('r')
lineWidths.append(1.2)
legendText.append(controlRunName)
fig = timeseries_analysis_plot(config, fields, calendar=calendar,
title=title, xlabel=xLabel,
ylabel=yLabel,
movingAveragePoints=movingAverageMonths,
lineColors=lineColors,
lineWidths=lineWidths,
legendText=legendText,
obsMean=obsMeltFlux,
obsUncertainty=obsMeltFluxUnc,
obsLegend=list(obsDict.keys()))
# do this before the inset because otherwise it moves the inset
# and cartopy doesn't play too well with tight_layout anyway
plt.tight_layout()
add_inset(fig, fc, width=2.0, height=2.0)
savefig(outFileName)
caption = 'Running Mean of Total Melt Flux under Ice ' \
'Shelves in the {} Region'.format(title)
write_image_xml(
config=config,
filePrefix=filePrefix,
componentName='Ocean',
componentSubdirectory='ocean',
galleryGroup='Antarctic Melt Time Series',
groupLink='antmelttime',
gallery='Total Melt Flux',
thumbnailDescription=title,
imageDescription=caption,
imageCaption=caption)
xLabel = 'Time (yr)'
yLabel = 'Melt Rate (m/yr)'
timeSeries = meltRates.isel(nRegions=self.regionIndex)
filePrefix = 'melt_rate_{}'.format(self.iceShelf.replace(' ', '_'))
outFileName = '{}/{}.png'.format(self.plotsDirectory, filePrefix)
fields = [timeSeries]
lineColors = ['k']
lineWidths = [2.5]
legendText = [mainRunName]
if plotControl:
fields.append(refMeltRates.isel(nRegions=self.regionIndex))
lineColors.append('r')
lineWidths.append(1.2)
legendText.append(controlRunName)
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
fig = timeseries_analysis_plot(config, fields, calendar=calendar,
title=title, xlabel=xLabel,
ylabel=yLabel,
movingAveragePoints=movingAverageMonths,
lineColors=lineColors,
lineWidths=lineWidths,
legendText=legendText,
firstYearXTicks=firstYearXTicks,
yearStrideXTicks=yearStrideXTicks,
obsMean=obsMeltRate,
obsUncertainty=obsMeltRateUnc,
obsLegend=list(obsDict.keys()))
# do this before the inset because otherwise it moves the inset
# and cartopy doesn't play too well with tight_layout anyway
plt.tight_layout()
add_inset(fig, fc, width=2.0, height=2.0)
savefig(outFileName)
caption = 'Running Mean of Area-averaged Melt Rate under Ice ' \
'Shelves in the {} Region'.format(title)
write_image_xml(
config=config,
filePrefix=filePrefix,
componentName='Ocean',
componentSubdirectory='ocean',
galleryGroup='Antarctic Melt Time Series',
groupLink='antmelttime',
gallery='Area-averaged Melt Rate',
thumbnailDescription=title,
imageDescription=caption,
imageCaption=caption)
# }}}
def _load_ice_shelf_fluxes(self, config): # {{{
"""
Reads melt flux time series and computes regional total melt flux and
mean melt rate.
"""
# Authors
# -------
# Xylar Asay-Davis
outputDirectory = '{}/iceShelfFluxes/'.format(
build_config_full_path(config, 'output', 'timeseriesSubdirectory'))
startYear = config.getint('timeSeries', 'startYear')
endYear = config.getint('timeSeries', 'endYear')
outFileName = '{}/iceShelfFluxes_{:04d}-{:04d}.nc'.format(
outputDirectory, startYear, endYear)
dsOut = xarray.open_dataset(outFileName)
return dsOut.totalMeltFlux, dsOut.meltRates
# }}}
# }}}
# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python