def run_task(self): # {{{
'''
Computes NINO34 index and plots the time series and power spectrum with
95 and 99% confidence bounds
'''
# Authors
# -------
# Luke Van Roekel, Xylar Asay-Davis
config = self.config
calendar = self.calendar
regionToPlot = config.get('indexNino34', 'region')
ninoIndexNumber = regionToPlot[4:]
self.logger.info("\nPlotting El Nino {} Index time series and power "
"spectrum....".format(ninoIndexNumber))
self.logger.info(' Load SST data...')
fieldName = 'nino'
startDate = self.config.get('index', 'startDate')
endDate = self.config.get('index', 'endDate')
startYear = self.config.getint('index', 'startYear')
endYear = self.config.getint('index', 'endYear')
dataSource = config.get('indexNino34', 'observationData')
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
# specify obsTitle based on data path
# These are the only data sets supported
if dataSource == 'HADIsst':
dataPath = "{}/HADIsst_nino34_20180710.nc".format(
observationsDirectory)
obsTitle = 'HADSST'
refDate = '1870-01-01'
elif dataSource == 'ERS_SSTv4':
dataPath = "{}/ERS_SSTv4_nino34_20180710.nc".format(
observationsDirectory)
obsTitle = 'ERS SSTv4'
refDate = '1800-01-01'
else:
raise ValueError('Bad value for config option observationData {} '
'in [indexNino34] section.'.format(dataSource))
mainRunName = config.get('runs', 'mainRunName')
# regionIndex should correspond to NINO34 in surface weighted Average
# AM
regions = config.getExpression('regions', 'regions')
regionToPlot = config.get('indexNino34', 'region')
regionIndex = regions.index(regionToPlot)
# Load data:
ds = open_mpas_dataset(fileName=self.inputFile,
calendar=calendar,
variableList=self.variableList,
startDate=startDate,
endDate=endDate)
# Observations have been processed to the nino34Index prior to reading
dsObs = xr.open_dataset(dataPath, decode_cf=False, decode_times=False)
# add the days between 0001-01-01 and the refDate so we have a new
# reference date of 0001-01-01 (like for the model Time)
dsObs["Time"] = dsObs.Time + \
string_to_days_since_date(dateString=refDate, calendar=calendar)
nino34Obs = dsObs.sst
self.logger.info(
' Compute El Nino {} Index...'.format(ninoIndexNumber))
varName = self.variableList[0]
regionSST = ds[varName].isel(nOceanRegions=regionIndex)
nino34Main = self._compute_nino34_index(regionSST, calendar)
# Compute the observational index over the entire time range
# nino34Obs = compute_nino34_index(dsObs.sst, calendar)
self.logger.info(
' Computing El Nino {} power spectra...'.format(ninoIndexNumber))
spectraMain = self._compute_nino34_spectra(nino34Main)
# Compute the observational spectra over the whole record
spectraObs = self._compute_nino34_spectra(nino34Obs)
# Compute the observational spectra over the last 30 years for
# comparison. Only saving the spectra
subsetEndYear = 2016
if self.controlConfig is None:
subsetStartYear = 1976
else:
# make the subset the same length as the input data set
subsetStartYear = subsetEndYear - (endYear - startYear)
time_start = datetime_to_days(datetime.datetime(subsetStartYear, 1, 1),
calendar=calendar)
time_end = datetime_to_days(datetime.datetime(subsetEndYear, 12, 31),
calendar=calendar)
nino34Subset = nino34Obs.sel(Time=slice(time_start, time_end))
spectraSubset = self._compute_nino34_spectra(nino34Subset)
if self.controlConfig is None:
nino34s = [nino34Obs[2:-3], nino34Subset, nino34Main[2:-3]]
titles = [
'{} (Full Record)'.format(obsTitle),
'{} ({} - {})'.format(obsTitle, subsetStartYear,
subsetEndYear), mainRunName
]
spectra = [spectraObs, spectraSubset, spectraMain]
else:
baseDirectory = build_config_full_path(self.controlConfig,
'output',
'timeSeriesSubdirectory')
refFileName = '{}/{}.nc'.format(
baseDirectory, self.mpasTimeSeriesTask.fullTaskName)
dsRef = open_mpas_dataset(fileName=refFileName,
calendar=calendar,
variableList=self.variableList)
regionSSTRef = dsRef[varName].isel(nOceanRegions=regionIndex)
nino34Ref = self._compute_nino34_index(regionSSTRef, calendar)
nino34s = [nino34Subset, nino34Main[2:-3], nino34Ref[2:-3]]
controlRunName = self.controlConfig.get('runs', 'mainRunName')
spectraRef = self._compute_nino34_spectra(nino34Ref)
titles = [
'{} ({} - {})'.format(obsTitle, subsetStartYear,
subsetEndYear), mainRunName,
'Control: {}'.format(controlRunName)
]
spectra = [spectraSubset, spectraMain, spectraRef]
# Convert frequencies to period in years
for s in spectra:
s['period'] = \
1.0 / (constants.eps + s['f'] * constants.sec_per_year)
self.logger.info(
' Plot El Nino {} index and spectra...'.format(ninoIndexNumber))
outFileName = '{}/nino{}_{}.png'.format(self.plotsDirectory,
ninoIndexNumber, mainRunName)
self._nino34_timeseries_plot(
nino34s=nino34s,
title=u'El Niño {} Index'.format(ninoIndexNumber),
panelTitles=titles,
outFileName=outFileName)
self._write_xml(filePrefix='nino{}_{}'.format(ninoIndexNumber,
mainRunName),
plotType='Time Series',
ninoIndexNumber=ninoIndexNumber)
outFileName = '{}/nino{}_spectra_{}.png'.format(
self.plotsDirectory, ninoIndexNumber, mainRunName)
self._nino34_spectra_plot(
spectra=spectra,
title=u'El Niño {} power spectrum'.format(ninoIndexNumber),
panelTitles=titles,
outFileName=outFileName)
self._write_xml(filePrefix='nino{}_spectra_{}'.format(
ninoIndexNumber, mainRunName),
plotType='Spectra',
ninoIndexNumber=ninoIndexNumber)
def run_task(self): # {{{
"""
Compute time-series output of properties in an ocean region.
"""
# Authors
# -------
# Xylar Asay-Davis
self.logger.info("\nAveraging T and S for {}...".format(
self.regionName))
obsDict = self.obsDict
config = self.config
regionGroup = self.regionGroup
timeSeriesName = regionGroup[0].lower() + \
regionGroup[1:].replace(' ', '')
sectionSuffix = regionGroup[0].upper() + \
regionGroup[1:].replace(' ', '')
sectionName = 'timeSeries{}'.format(sectionSuffix)
outputDirectory = '{}/{}/'.format(
build_config_full_path(self.config, 'output',
'timeseriesSubdirectory'), timeSeriesName)
try:
os.makedirs(outputDirectory)
except OSError:
pass
outFileName = '{}/TS_{}_{}.nc'.format(outputDirectory,
obsDict['suffix'], self.prefix)
if os.path.exists(outFileName):
return
regionMaskFileName = obsDict['maskTask'].maskFileName
print(regionMaskFileName)
print(xarray.open_dataset(regionMaskFileName))
dsRegionMask = \
xarray.open_dataset(regionMaskFileName).stack(
nCells=(obsDict['latVar'], obsDict['lonVar']))
dsRegionMask = dsRegionMask.reset_index('nCells').drop_vars(
[obsDict['latVar'], obsDict['lonVar']])
maskRegionNames = decode_strings(dsRegionMask.regionNames)
regionIndex = maskRegionNames.index(self.regionName)
dsMask = dsRegionMask.isel(nRegions=regionIndex)
cellMask = dsMask.regionCellMasks == 1
if config.has_option(sectionName, 'zmin'):
zmin = config.getfloat(sectionName, 'zmin')
else:
zmin = dsMask.zminRegions.values
if config.has_option(sectionName, 'zmax'):
zmax = config.getfloat(sectionName, 'zmax')
else:
zmax = dsMask.zmaxRegions.values
TVarName = obsDict['TVar']
SVarName = obsDict['SVar']
zVarName = obsDict['zVar']
lonVarName = obsDict['lonVar']
latVarName = obsDict['latVar']
volVarName = obsDict['volVar']
tDim = obsDict['tDim']
obsFileName = build_obs_path(config,
component=self.componentName,
relativePath=obsDict['TFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
ds = xarray.open_dataset(obsFileName)
if obsDict['SFileName'] != obsDict['TFileName']:
obsFileName = build_obs_path(config,
component=self.componentName,
relativePath=obsDict['SFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
dsS = xarray.open_dataset(obsFileName)
ds[SVarName] = dsS[SVarName]
if obsDict['volFileName'] is None:
# compute volume from lat, lon, depth bounds
self.logger.info(' Computing volume...'.format(obsFileName))
latBndsName = ds[latVarName].attrs['bounds']
lonBndsName = ds[lonVarName].attrs['bounds']
zBndsName = ds[zVarName].attrs['bounds']
latBnds = ds[latBndsName]
lonBnds = ds[lonBndsName]
zBnds = ds[zBndsName]
dLat = numpy.deg2rad(latBnds[:, 1] - latBnds[:, 0])
dLon = numpy.deg2rad(lonBnds[:, 1] - lonBnds[:, 0])
lat = numpy.deg2rad(ds[latVarName])
dz = zBnds[:, 1] - zBnds[:, 0]
radius = 6378137.0
area = radius**2 * numpy.cos(lat) * dLat * dLon
volume = dz * area
ds[volVarName] = volume
elif obsDict['volFileName'] != obsDict['TFileName']:
obsFileName = build_obs_path(config,
component=self.componentName,
relativePath=obsDict['volFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
dsVol = xarray.open_dataset(obsFileName)
ds[volVarName] = dsVol[volVarName]
if 'positive' in ds[zVarName].attrs and \
ds[zVarName].attrs['positive'] == 'down':
attrs = ds[zVarName].attrs
ds[zVarName] = -ds[zVarName]
ds[zVarName].attrs = attrs
ds[zVarName].attrs['positive'] = 'up'
TMean = numpy.zeros(ds.sizes[tDim])
SMean = numpy.zeros(ds.sizes[tDim])
depthMask = numpy.logical_and(ds[zVarName] >= zmin,
ds[zVarName] <= zmax)
for tIndex in range(ds.sizes[tDim]):
dsMonth = ds.isel({tDim: tIndex})
dsMonth = dsMonth.stack(nCells=(obsDict['latVar'],
obsDict['lonVar']))
dsMonth = dsMonth.reset_index('nCells').drop_vars(
[obsDict['latVar'], obsDict['lonVar']])
dsMonth = dsMonth.where(cellMask, drop=True)
dsMonth = dsMonth.where(depthMask)
mask = dsMonth[TVarName].notnull()
TSum = (dsMonth[TVarName] *
dsMonth[volVarName]).sum(dim=('nCells', zVarName))
volSum = (mask * dsMonth[volVarName]).sum(dim=('nCells', zVarName))
TMean[tIndex] = TSum / volSum
mask = dsMonth[SVarName].notnull()
SSum = (dsMonth[SVarName] *
dsMonth[volVarName]).sum(dim=('nCells', zVarName))
volSum = (mask * dsMonth[volVarName]).sum(dim=('nCells', zVarName))
SMean[tIndex] = SSum / volSum
dsOut = xarray.Dataset()
dsOut['temperature'] = ('Time', TMean)
dsOut['salinity'] = ('Time', SMean)
dsOut['zbounds'] = ('nBounds', [zmin, zmax])
dsOut['month'] = ('Time', numpy.array(ds.month.values, dtype=float))
dsOut['year'] = ('Time', numpy.ones(ds.sizes[tDim]))
write_netcdf(dsOut, outFileName)
def __init__(self, config, mpasClimatologyTask,
controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fieldName = 'meltRate'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapAntarcticMelt, self).__init__(
config=config, taskName='climatologyMapAntarcticMelt',
componentName='ocean',
tags=['climatology', 'horizontalMap', fieldName,
'landIceCavities', 'antarctic'])
sectionName = self.taskName
mpasFieldName = 'timeMonthly_avg_landIceFreshwaterFlux'
iselValues = None
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variable 'timeMonthly_avg_landIceFreshwaterFlux' will be added to
# mpasClimatologyTask along with the seasons.
remapClimatologySubtask = RemapMpasAntarcticMeltClimatology(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=[mpasFieldName],
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
if controlConfig is None:
refTitleLabel = \
'Observations (Rignot et al, 2013)'
observationsDirectory = build_obs_path(
config, 'ocean', 'meltSubdirectory')
obsFileName = \
'{}/Rignot_2013_melt_rates_6000.0x6000.0km_10.0km_' \
'Antarctic_stereo.nc'.format(observationsDirectory)
refFieldName = 'meltRate'
outFileLabel = 'meltRignot'
galleryName = 'Observations: Rignot et al. (2013)'
remapObservationsSubtask = RemapObservedAntarcticMeltClimatology(
parentTask=self, seasons=seasons, fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
diffTitleLabel = 'Model - Observations'
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = 'melt'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self, season, comparisonGridName, remapClimatologySubtask,
remapObservationsSubtask, controlConfig=controlConfig)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle='Melt Rate',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'm a$^{-1}$',
imageCaption='Antarctic Melt Rate',
galleryGroup='Melt Rate',
groupSubtitle=None,
groupLink='antarctic_melt',
galleryName=galleryName)
self.add_subtask(subtask)
def _add_obs_tasks(self, seasons, comparisonGridNames, hemisphere,
hemisphereLong, remapClimatologySubtask,
mpasFieldName): # {{{
config = self.config
obsFieldName = 'seaIceConc'
sectionName = self.taskName
observationPrefixes = config.getExpression(sectionName,
'observationPrefixes')
for prefix in observationPrefixes:
for season in seasons:
observationTitleLabel = \
'Observations (SSM/I {})'.format(prefix)
obsFileName = build_obs_path(
config,
'seaIce',
relativePathOption='concentration{}{}_{}'.format(
prefix, hemisphere, season),
relativePathSection=sectionName)
remapObservationsSubtask = RemapObservedConcClimatology(
parentTask=self,
seasons=[season],
fileName=obsFileName,
outFilePrefix='{}{}{}_{}'.format(obsFieldName, prefix,
hemisphere, season),
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservations_{}{}'.format(
prefix, season))
self.add_subtask(remapObservationsSubtask)
for comparisonGridName in comparisonGridNames:
imageDescription = \
'{} Climatology Map of {}-Hemisphere Sea-Ice ' \
'Concentration'.format(season, hemisphereLong)
imageCaption = \
'{}. <br> Observations: SSM/I {}'.format(
imageDescription, prefix)
galleryGroup = \
'{}-Hemisphere Sea-Ice Concentration'.format(
hemisphereLong)
# make a new subtask for this season and comparison
# grid
subtask = PlotClimatologyMapSubtask(
self,
hemisphere,
season,
comparisonGridName,
remapClimatologySubtask,
remapObsClimatologySubtask=remapObservationsSubtask,
subtaskSuffix=prefix)
subtask.set_plot_info(
outFileLabel='iceconc{}{}'.format(prefix, hemisphere),
fieldNameInTitle='Sea ice concentration',
mpasFieldName=mpasFieldName,
refFieldName=obsFieldName,
refTitleLabel=observationTitleLabel,
diffTitleLabel='Model - Observations',
unitsLabel=r'fraction',
imageDescription=imageDescription,
imageCaption=imageCaption,
galleryGroup=galleryGroup,
groupSubtitle=None,
groupLink='{}_conc'.format(hemisphere.lower()),
galleryName='Observations: SSM/I {}'.format(prefix))
self.add_subtask(subtask)
def __init__(self, config, regionMasksTask, controlConfig=None):
# {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
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(TimeSeriesOceanRegions,
self).__init__(config=config,
taskName='timeSeriesOceanRegions',
componentName='ocean',
tags=['timeSeries', 'regions', 'antarctic'])
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)
regionGroups = config.getExpression(self.taskName, 'regionGroups')
obsDicts = {
'SOSE': {
'suffix': 'SOSE',
'gridName': 'SouthernOcean_0.167x0.167degree',
'gridFileName': 'SOSE/SOSE_2005-2010_monthly_pot_temp_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'TFileName': 'SOSE/SOSE_2005-2010_monthly_pot_temp_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'SFileName': 'SOSE/SOSE_2005-2010_monthly_salinity_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'volFileName': 'SOSE/SOSE_volume_'
'SouthernOcean_0.167x0.167degree_20190815.nc',
'lonVar': 'lon',
'latVar': 'lat',
'TVar': 'theta',
'SVar': 'salinity',
'volVar': 'volume',
'zVar': 'z',
'tDim': 'Time',
'legend': 'SOSE 2005-2010 ANN mean'
},
'WOA18': {
'suffix': 'WOA18',
'gridName': 'Global_0.25x0.25degree',
'gridFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'TFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'SFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'volFileName': None,
'lonVar': 'lon',
'latVar': 'lat',
'TVar': 't_an',
'SVar': 's_an',
'volVar': 'volume',
'zVar': 'depth',
'tDim': 'month',
'legend': 'WOA18 1955-2017 ANN mean'
}
}
for regionGroup in regionGroups:
sectionSuffix = regionGroup[0].upper() + \
regionGroup[1:].replace(' ', '')
sectionName = 'timeSeries{}'.format(sectionSuffix)
regionNames = config.getExpression(sectionName, 'regionNames')
if len(regionNames) == 0:
# no regions in this group were requested
continue
masksSubtask = regionMasksTask.add_mask_subtask(
regionGroup=regionGroup)
regionNames = masksSubtask.expand_region_names(regionNames)
years = list(range(startYear, endYear + 1))
obsList = config.getExpression(sectionName, 'obs')
groupObsDicts = {}
for obsName in obsList:
localObsDict = dict(obsDicts[obsName])
obsFileName = build_obs_path(
config,
component=self.componentName,
relativePath=localObsDict['gridFileName'])
obsMasksSubtask = regionMasksTask.add_mask_subtask(
regionGroup=regionGroup,
obsFileName=obsFileName,
lonVar=localObsDict['lonVar'],
latVar=localObsDict['latVar'],
meshName=localObsDict['gridName'])
obsDicts[obsName]['maskTask'] = obsMasksSubtask
localObsDict['maskTask'] = obsMasksSubtask
groupObsDicts[obsName] = localObsDict
# 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 = CombineRegionalProfileTimeSeriesSubtask(
self,
startYears=years,
endYears=years,
regionGroup=regionGroup)
depthMasksSubtask = ComputeRegionDepthMasksSubtask(
self,
masksSubtask=masksSubtask,
regionGroup=regionGroup,
regionNames=regionNames)
depthMasksSubtask.run_after(masksSubtask)
# run one subtask per year
for year in years:
computeSubtask = ComputeRegionTimeSeriesSubtask(
self,
startYear=year,
endYear=year,
masksSubtask=masksSubtask,
regionGroup=regionGroup,
regionNames=regionNames)
self.add_subtask(computeSubtask)
computeSubtask.run_after(depthMasksSubtask)
computeSubtask.run_after(masksSubtask)
combineSubtask.run_after(computeSubtask)
self.add_subtask(combineSubtask)
for index, regionName in enumerate(regionNames):
fullSuffix = sectionSuffix + '_' + regionName[0].lower() + \
regionName[1:].replace(' ', '')
obsSubtasks = {}
for obsName in obsList:
localObsDict = dict(groupObsDicts[obsName])
obsSubtask = ComputeObsRegionalTimeSeriesSubtask(
self, regionGroup, regionName, fullSuffix,
localObsDict)
obsSubtasks[obsName] = obsSubtask
plotRegionSubtask = PlotRegionTimeSeriesSubtask(
self, regionGroup, regionName, index, controlConfig,
sectionName, fullSuffix, obsSubtasks,
masksSubtask.geojsonFileName)
plotRegionSubtask.run_after(combineSubtask)
self.add_subtask(plotRegionSubtask)
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
Authors
-------
Phillip J. Wolfram, Riley X. Brady, Xylar Asay-Davis
"""
# call the constructor from the base class (AnalysisTask)
bgcVars = config.getExpression('climatologyMapBGC', 'variables')
super(ClimatologyMapBGC, self).__init__(
config=config,
taskName='climatologyMapBGC',
componentName='ocean',
tags=['climatology', 'horizontalMap', 'BGC'] + bgcVars)
sectionName = 'climatologyMapBGC'
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
preindustrial = config.getboolean(sectionName, 'preindustrial')
obsFileDict = {
'Chl': 'Chl_SeaWIFS_20180702.nc',
'CO2_gas_flux': 'CO2_gas_flux_1.0x1.0degree_20180628.nc',
'SiO3': 'SiO3_1.0x1.0degree_20180628.nc',
'PO4': 'PO4_1.0x1.0degree_20180628.nc',
'ALK': 'ALK_1.0x1.0degree_20180629.nc',
'NO3': 'NO3_1.0x1.0degree_20180628.nc',
'pCO2surface': 'pCO2surface_1.0x1.0degree_20180629.nc',
'O2': 'O2_1.0x1.0degree_20180628.nc',
'pH_3D': 'pH_3D_1.0x1.0degree_20180629.nc'
}
# If user wants to compare to preindustrial data, make sure
# that we load in the right DIC field.
if preindustrial:
obsFileDict['DIC'] = 'PI_DIC_1.0x1.0degree_20180629.nc'
else:
obsFileDict['DIC'] = 'DIC_1.0x1.0degree_20180629.nc'
for fieldName in bgcVars:
fieldSectionName = '{}_{}'.format(sectionName, fieldName)
prefix = config.get(fieldSectionName, 'filePrefix')
mpasFieldName = '{}{}'.format(prefix, fieldName)
# CO2 flux and pCO2 has no vertical levels, throws error if you try
# to select any. Can add any other flux-like variables to this
# list.
if fieldName not in ['CO2_gas_flux', 'pCO2surface']:
iselValues = {'nVertLevels': 0}
else:
iselValues = None
# Read in units (since BGC units are variable)
units = config.get(fieldSectionName, 'units')
# Pass multiple variables if working with Chlorophyll to sum
# them to total chlorophyll
if fieldName == 'Chl':
prefix = 'timeMonthly_avg_ecosysTracers_'
variableList = [
prefix + 'spChl', prefix + 'diatChl', prefix + 'diazChl',
prefix + 'phaeoChl'
]
plotField = 'Chl'
else:
variableList = [mpasFieldName]
plotField = mpasFieldName
remapClimatologySubtask = RemapBGCClimatology(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=variableList,
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues,
subtaskName='remapMpasClimatology_{}'.format(fieldName))
if controlConfig is None:
refTitleLabel = 'Observations'
if preindustrial and 'DIC' in fieldName:
refTitleLabel += ' (Preindustrial)'
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
obsFileName = "{}/{}".format(observationsDirectory,
obsFileDict[fieldName])
observationsLabel = config.get(fieldSectionName,
'observationsLabel')
refFieldName = fieldName
outFileLabel = fieldName + observationsLabel
galleryLabel = config.get(fieldSectionName, 'galleryLabel')
galleryName = '{} (Compared to {})'.format(
galleryLabel, observationsLabel)
remapObservationsSubtask = RemapObservedBGCClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservations_{}'.format(fieldName))
self.add_subtask(remapObservationsSubtask)
diffTitleLabel = 'Model - Observations'
# Certain BGC observations are only available at annual
# resolution. Need to ensure that the user is aware that their
# seasonal or monthly climatology is being compared to ANN.
# Currently, this is just with GLODAP.
if observationsLabel == 'GLODAPv2':
diffTitleLabel += ' (Compared to ANN)'
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = fieldName
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self,
season,
comparisonGridName,
remapClimatologySubtask,
remapObservationsSubtask,
controlConfig=controlConfig,
subtaskName='plot{}_{}_{}'.format(
fieldName, season, comparisonGridName))
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle=fieldName,
mpasFieldName=plotField,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
unitsLabel=units,
imageCaption='Mean ' + fieldName,
galleryGroup='Sea Surface Biogeochemistry',
groupSubtitle=None,
groupLink=fieldName,
galleryName=galleryName,
diffTitleLabel=diffTitleLabel,
configSectionName=fieldSectionName)
self.add_subtask(subtask)
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fieldName = 'mld'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapMLD, self).__init__(
config=config,
taskName='climatologyMapMLD',
componentName='ocean',
tags=['climatology', 'horizontalMap', fieldName, 'publicObs'])
sectionName = self.taskName
mpasFieldName = 'timeMonthly_avg_dThreshMLD'
iselValues = None
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variable 'timeMonthly_avg_dThreshMLD' will be added to
# mpasClimatologyTask along with the seasons.
remapClimatologySubtask = RemapMpasClimatologySubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=[mpasFieldName],
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
if controlConfig is None:
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
obsFileName = "{}/holtetalley_mld_climatology_20180710.nc".format(
observationsDirectory)
refFieldName = 'mld'
outFileLabel = 'mldHolteTalleyARGO'
remapObservationsSubtask = RemapObservedMLDClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
galleryName = 'Observations: Holte-Talley ARGO'
refTitleLabel = \
'Observations (HolteTalley density threshold MLD)'
diffTitleLabel = 'Model - Observations'
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = 'mld'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self,
season,
comparisonGridName,
remapClimatologySubtask,
remapObservationsSubtask,
controlConfig=controlConfig)
subtask.set_plot_info(outFileLabel=outFileLabel,
fieldNameInTitle='MLD',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'm',
imageCaption='Mean Mixed-Layer Depth',
galleryGroup='Mixed-Layer Depth',
groupSubtitle=None,
groupLink='mld',
galleryName=galleryName)
self.add_subtask(subtask)
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,
movingAveragePoints,
title[key], xLabel,
units[variableName],
calendar=calendar,
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,
movingAveragePoints,
title[key],
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 __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fieldName = 'sst'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapSST, self).__init__(
config=config,
taskName='climatologyMapSST',
componentName='ocean',
tags=['climatology', 'horizontalMap', fieldName, 'publicObs'])
mpasFieldName = 'timeMonthly_avg_activeTracers_temperature'
iselValues = {'nVertLevels': 0}
sectionName = self.taskName
climStartYear = config.getint(sectionName, 'obsStartYear')
climEndYear = config.getint(sectionName, 'obsEndYear')
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variable mpasFieldName will be added to mpasClimatologyTask
# along with the seasons.
remapClimatologySubtask = RemapMpasClimatologySubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=[mpasFieldName],
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
if controlConfig is None:
if climStartYear < 1925:
period = 'pre-industrial'
else:
period = 'present-day'
refTitleLabel = \
'Observations (Hadley/OI, {} {:04d}-{:04d})'.format(
period, climStartYear, climEndYear)
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
obsFileName = \
"{}/MODEL.SST.HAD187001-198110.OI198111-201203_" \
"20180710.nc".format(observationsDirectory)
refFieldName = 'sst'
outFileLabel = 'sstHADOI'
galleryName = 'Observations: Hadley-NOAA-OI'
remapObservationsSubtask = RemapObservedSSTClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
diffTitleLabel = 'Model - Observations'
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = 'sst'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self,
season,
comparisonGridName,
remapClimatologySubtask,
remapObservationsSubtask,
controlConfig=controlConfig)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle='SST',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'$^o$C',
imageCaption='Mean Sea Surface Temperature',
galleryGroup='Sea Surface Temperature',
groupSubtitle=None,
groupLink='sst',
galleryName=galleryName)
self.add_subtask(subtask)
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fields = \
[{'prefix': 'temperature',
'mpas': '******',
'units': r'$\degree$C',
'obs': 'botTheta',
'title': 'Potential Temperature'},
{'prefix': 'salinity',
'mpas': '******',
'units': r'PSU',
'obs': 'botSalinity',
'title': 'Salinity'},
{'prefix': 'potentialDensity',
'mpas': '******',
'units': r'kg m$^{-3}$',
'obs': 'botPotentialDensity',
'title': 'Potential Density'}]
tags = ['climatology', 'horizontalMap', 'antarctic'] \
+ [field['prefix'] for field in fields]
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapSchmidtko,
self).__init__(config=config,
taskName='climatologyMapSchmidtko',
componentName='ocean',
tags=tags)
sectionName = self.taskName
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
observationsDirectory = build_obs_path(config, 'ocean',
'schmidtkoSubdirectory')
obsFileName = '{}/Schmidtko_et_al_2014_bottom_PT_S_PD_' \
'6000.0x6000.0km_10.0km_Antarctic_stereo.nc' \
''.format(observationsDirectory)
# the variable 'timeMonthly_avg_landIceFreshwaterFlux' will be added to
# mpasClimatologyTask along with the seasons.
remapClimatologySubtask = RemapDepthSlicesSubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='schmidtko',
variableList=[field['mpas'] for field in fields],
seasons=seasons,
depths=['bot'],
comparisonGridNames=comparisonGridNames)
if controlConfig is None:
refTitleLabel = 'Observations: Schmidtko et al. (2014)'
diffTitleLabel = 'Model - Observations'
groupSubtitle = refTitleLabel
else:
controlRunName = controlConfig.get('runs', 'mainRunName')
refTitleLabel = 'Control: {}'.format(controlRunName)
diffTitleLabel = 'Main - Control'
groupSubtitle = None
for field in fields:
fieldPrefix = field['prefix']
upperFieldPrefix = fieldPrefix[0].upper() + fieldPrefix[1:]
if controlConfig is None:
refFieldName = field['obs']
outFileLabel = '{}Schmidtko'.format(fieldPrefix)
remapObservationsSubtask = RemapSchmidtko(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix='{}Schmidtko'.format(fieldPrefix),
fieldName=refFieldName,
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservations{}'.format(upperFieldPrefix))
self.add_subtask(remapObservationsSubtask)
else:
remapObservationsSubtask = None
refFieldName = field['mpas']
outFileLabel = '{}Bottom'.format(fieldPrefix)
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
subtask = PlotClimatologyMapSubtask(
parentTask=self,
season=season,
comparisonGridName=comparisonGridName,
remapMpasClimatologySubtask=remapClimatologySubtask,
remapObsClimatologySubtask=remapObservationsSubtask,
controlConfig=controlConfig,
depth='bot',
subtaskName='plot{}_{}_{}'.format(
upperFieldPrefix, season, comparisonGridName))
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle=field['title'],
mpasFieldName=field['mpas'],
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=field['units'],
imageCaption=field['title'],
galleryGroup='Seafloor Maps',
groupSubtitle=groupSubtitle,
groupLink='seafloor',
galleryName=field['title'],
configSectionName='climatologyMapSchmidtko{}'.format(
upperFieldPrefix))
self.add_subtask(subtask)
def setup_and_check(self): # {{{
'''
Perform steps to set up the analysis and check for errors in the setup.
'''
# Authors
# -------
# Mark Petersen, Milena Veneziani, 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(MeridionalHeatTransport, self).setup_and_check()
self.startYear = self.mpasClimatologyTask.startYear
self.startDate = self.mpasClimatologyTask.startDate
self.endYear = self.mpasClimatologyTask.endYear
self.endDate = self.mpasClimatologyTask.endDate
config = self.config
self.check_analysis_enabled(
analysisOptionName='config_am_meridionalheattransport_enable',
raiseException=True)
self.sectionName = 'meridionalHeatTransport'
# Read in obs file information
compareWithObs = config.getboolean(self.sectionName,
'compareWithObservations')
self.observationsFile = None
if compareWithObs:
observationsDirectory = build_obs_path(config, 'ocean',
'mhtSubdirectory')
observationsFile = config.get(self.sectionName, 'observationData')
observationsFile = '{}/{}'.format(observationsDirectory,
observationsFile)
if os.path.exists(observationsFile):
self.observationsFile = observationsFile
else:
print('Warning: No MHT observations file found: skip plotting '
'obs')
mainRunName = self.config.get('runs', 'mainRunName')
variableList = [
'timeMonthly_avg_meridionalHeatTransportLat',
'timeMonthly_avg_meridionalHeatTransportLatZ'
]
self.mpasClimatologyTask.add_variables(variableList=variableList,
seasons=['ANN'])
self.xmlFileNames = []
self.filePrefixes = {}
prefixes = ['mht']
if config.getboolean(self.sectionName, 'plotVerticalSection'):
prefixes.append('mhtZ')
for prefix in prefixes:
filePrefix = '{}_{}_years{:04d}-{:04d}'.format(
prefix, mainRunName, self.startYear, self.endYear)
self.xmlFileNames.append('{}/{}.xml'.format(
self.plotsDirectory, filePrefix))
self.filePrefixes[prefix] = filePrefix
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Milena Veneziani
fields = \
[{'prefix': 'temperature',
'mpas': '******',
'units': r'$\degree$C',
'titleName': 'Potential Temperature',
'obsFieldName': 't_an'},
{'prefix': 'salinity',
'mpas': '******',
'units': r'PSU',
'titleName': 'Salinity',
'obsFieldName': 's_an'}]
tags = ['climatology', 'horizontalMap', 'woa', 'publicObs'] + \
[field['prefix'] for field in fields]
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapWoa, self).__init__(config=config,
taskName='climatologyMapWoa',
componentName='ocean',
tags=tags)
sectionName = self.taskName
fieldList = config.getExpression(sectionName, 'fieldList')
fields = [field for field in fields if field['prefix'] in fieldList]
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
depths = config.getExpression(sectionName, 'depths')
if len(depths) == 0:
raise ValueError('config section {} does not contain valid '
'list of depths'.format(sectionName))
variableList = [field['mpas'] for field in fields]
shallowVsDeepColormapDepth = config.getfloat(
sectionName, 'shallowVsDeepColormapDepth')
shallow = []
for depth in depths:
if depth == 'top':
shallow.append(True)
elif depth == 'bot':
shallow.append(False)
else:
shallow.append(depth >= shallowVsDeepColormapDepth)
remapMpasSubtask = RemapDepthSlicesSubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='WOA',
variableList=variableList,
seasons=seasons,
depths=depths,
comparisonGridNames=comparisonGridNames,
iselValues=None)
remapAnnObsSubtask = None
remapMonObsSubtask = None
if controlConfig is None:
# Since we have a WOA18 annual climatology file and
# another file containing the 12 WOA18 monthly climatologies,
# do the remapping for each season separately
observationsDirectory = build_obs_path(config, 'ocean',
'woa18Subdirectory')
refFieldNames = [field['obsFieldName'] for field in fields]
if 'ANN' in seasons:
obsFileName = \
'{}/woa18_decav_04_TS_ann_20190829.nc'.format(
observationsDirectory)
remapAnnObsSubtask = RemapWoaClimatology(
parentTask=self,
seasons=['ANN'],
fileName=obsFileName,
outFilePrefix='woa18_ann',
fieldNames=refFieldNames,
depths=depths,
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservationsAnn')
self.add_subtask(remapAnnObsSubtask)
seasonsMinusAnn = list(seasons)
if 'ANN' in seasonsMinusAnn:
seasonsMinusAnn.remove('ANN')
if len(seasonsMinusAnn) > 0:
obsFileName = \
'{}/woa18_decav_04_TS_mon_20190829.nc'.format(
observationsDirectory)
remapMonObsSubtask = RemapWoaClimatology(
parentTask=self,
seasons=seasonsMinusAnn,
fileName=obsFileName,
outFilePrefix='woa18_mon',
fieldNames=refFieldNames,
depths=depths,
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservationsMon')
self.add_subtask(remapMonObsSubtask)
for field in fields:
fieldPrefix = field['prefix']
upperFieldPrefix = fieldPrefix[0].upper() + fieldPrefix[1:]
sectionName = '{}{}'.format(self.taskName, upperFieldPrefix)
if controlConfig is None:
refTitleLabel = 'WOA18 Climatology'
refFieldName = field['obsFieldName']
outFileLabel = '{}WOA18'.format(fieldPrefix)
galleryName = 'WOA18 Climatology'
diffTitleLabel = 'Model - Climatology'
else:
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = 'Control: {}'.format(controlRunName)
refTitleLabel = galleryName
refFieldName = field['mpas']
outFileLabel = '{}WOA18'.format(fieldPrefix)
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for depthIndex, depth in enumerate(depths):
for season in seasons:
if season == 'ANN':
remapObsSubtask = remapAnnObsSubtask
else:
remapObsSubtask = remapMonObsSubtask
subtaskName = 'plot{}_{}_{}_depth_{}'.format(
upperFieldPrefix, season, comparisonGridName,
depth)
subtask = PlotClimatologyMapSubtask(
parentTask=self,
season=season,
comparisonGridName=comparisonGridName,
remapMpasClimatologySubtask=remapMpasSubtask,
remapObsClimatologySubtask=remapObsSubtask,
controlConfig=controlConfig,
depth=depth,
subtaskName=subtaskName)
configSectionName = 'climatologyMapWoa{}'.format(
upperFieldPrefix)
# if available, use a separate color map for shallow
# and deep
if depth is not None:
if shallow[depthIndex]:
suffix = 'Shallow'
else:
suffix = 'Deep'
testSectionName = '{}{}'.format(
configSectionName, suffix)
if config.has_section(testSectionName):
configSectionName = testSectionName
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle=field['titleName'],
mpasFieldName=field['mpas'],
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=field['units'],
imageCaption=field['titleName'],
galleryGroup=field['titleName'],
groupSubtitle=None,
groupLink='{}_woa'.format(fieldPrefix),
galleryName=galleryName,
configSectionName=configSectionName)
self.add_subtask(subtask)
def __init__(self, config, mpasClimatologyTask,
controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis, Kevin Rosa
fieldName = 'eke'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapEKE, self).__init__(
config=config, taskName='climatologyMapEKE',
componentName='ocean',
tags=['climatology', 'horizontalMap', fieldName, 'publicObs'])
mpasFieldName = 'eke'
iselValues = {'nVertLevels': 0}
sectionName = self.taskName
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
# EKE observations are annual climatology so only accept annual
# climatology **should move this to setup_and_check()
if seasons != ['ANN']:
raise ValueError('config section {} does not contain valid list '
'of seasons. For EKE, may only request annual '
'climatology'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variables in variableList will be added to mpasClimatologyTask
# along with the seasons.
variableList = ['timeMonthly_avg_velocityZonal',
'timeMonthly_avg_velocityMeridional',
'timeMonthly_avg_velocityZonalSquared',
'timeMonthly_avg_velocityMeridionalSquared']
remapClimatologySubtask = RemapMpasEKEClimatology(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=variableList,
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
# to compare to observations:
if controlConfig is None:
refTitleLabel = \
'Observations (Surface EKE from Drifter Data)'
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
obsFileName = \
"{}/drifter_variance_20180804.nc".format(
observationsDirectory)
refFieldName = 'eke'
outFileLabel = 'ekeDRIFTER'
galleryName = 'Observations: EKE from Drifters'
remapObservationsSubtask = RemapObservedEKEClimatology(
parentTask=self, seasons=seasons, fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
diffTitleLabel = 'Model - Observations'
# compare with previous run:
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = 'eke'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self, season, comparisonGridName, remapClimatologySubtask,
remapObservationsSubtask, controlConfig=controlConfig)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle='EKE',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'cm$^2$/s$^2$',
imageCaption='Mean Surface Eddy Kinetic Energy',
galleryGroup='Eddy Kinetic Energy',
groupSubtitle=None,
groupLink='eke',
galleryName=galleryName)
self.add_subtask(subtask)
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Luke Van Roekel, Xylar Asay-Davis
fieldName = 'temperatureArgo'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapArgoTemperature,
self).__init__(config=config,
taskName='climatologyMapArgoTemperature',
componentName='ocean',
tags=[
'climatology', 'horizontalMap', 'argo',
'temperature', 'publicObs'
])
sectionName = self.taskName
mpasFieldName = 'timeMonthly_avg_activeTracers_temperature'
iselValues = None
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
depths = config.getExpression(sectionName, 'depths')
if len(depths) == 0:
raise ValueError('config section {} does not contain valid '
'list of depths'.format(sectionName))
# the variable 'timeMonthly_avg_landIceFreshwaterFlux' will be added to
# mpasClimatologyTask along with the seasons.
remapClimatologySubtask = RemapDepthSlicesSubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=[mpasFieldName],
seasons=seasons,
depths=depths,
comparisonGridNames=comparisonGridNames,
iselValues=iselValues)
if controlConfig is None:
refTitleLabel = 'Roemmich-Gilson Argo Climatology: Potential ' \
'Temperature'
observationsDirectory = build_obs_path(config, 'ocean',
'argoSubdirectory')
obsFileName = \
'{}/ArgoClimatology_TS_20180710.nc'.format(
observationsDirectory)
refFieldName = 'theta'
outFileLabel = 'tempArgo'
galleryName = 'Roemmich-Gilson Climatology: Argo'
diffTitleLabel = 'Model - Argo'
remapObservationsSubtask = RemapArgoClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix='{}Argo'.format(refFieldName),
fieldName=refFieldName,
depths=depths,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = 'Control: {}'.format(controlRunName)
refTitleLabel = galleryName
refFieldName = mpasFieldName
outFileLabel = 'temp'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
for depth in depths:
subtask = PlotClimatologyMapSubtask(
parentTask=self,
season=season,
comparisonGridName=comparisonGridName,
remapMpasClimatologySubtask=remapClimatologySubtask,
remapObsClimatologySubtask=remapObservationsSubtask,
controlConfig=controlConfig,
depth=depth)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle='Potential Temperature',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'$\degree$C',
imageCaption='Model potential temperature compared '
'with Argo observations',
galleryGroup='Argo Potential Temperature',
groupSubtitle=None,
groupLink='tempArgo',
galleryName=galleryName)
self.add_subtask(subtask)
def run_task(self): # {{{
"""
Plots time-series output of properties in an ocean region.
"""
# Authors
# -------
# Xylar Asay-Davis
if os.path.exists(self.fileName):
return
config = self.config
obsDict = self.obsDict
season = self.season
obsFileName = build_obs_path(
config,
component=self.componentName,
relativePath=obsDict['preprocessedFileTemplate'].format(season))
if os.path.exists(obsFileName):
# we already pre-processed this data so no need to redo it!
os.symlink(obsFileName, self.fileName)
return
with dask.config.set(schedular='threads',
pool=ThreadPool(self.daskThreads)):
self.logger.info("\n computing T S climatogy for {}...".format(
self.obsName))
chunk = {obsDict['tVar']: 6}
TVarName = obsDict['TVar']
SVarName = obsDict['SVar']
zVarName = obsDict['zVar']
lonVarName = obsDict['lonVar']
latVarName = obsDict['latVar']
volVarName = obsDict['volVar']
obsFileName = build_obs_path(config,
component=self.componentName,
relativePath=obsDict['TFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
ds = xarray.open_dataset(obsFileName, chunks=chunk)
if obsDict['SFileName'] != obsDict['TFileName']:
obsFileName = build_obs_path(config,
component=self.componentName,
relativePath=obsDict['SFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
dsS = xarray.open_dataset(obsFileName, chunks=chunk)
ds[SVarName] = dsS[SVarName]
if obsDict['volFileName'] is None:
# compute volume from lat, lon, depth bounds
self.logger.info(' Computing volume...'.format(obsFileName))
latBndsName = ds[latVarName].attrs['bounds']
lonBndsName = ds[lonVarName].attrs['bounds']
zBndsName = ds[zVarName].attrs['bounds']
latBnds = ds[latBndsName]
lonBnds = ds[lonBndsName]
zBnds = ds[zBndsName]
dLat = numpy.deg2rad(latBnds[:, 1] - latBnds[:, 0])
dLon = numpy.deg2rad(lonBnds[:, 1] - lonBnds[:, 0])
lat = numpy.deg2rad(ds[latVarName])
dz = zBnds[:, 1] - zBnds[:, 0]
radius = 6378137.0
area = radius**2 * numpy.cos(lat) * dLat * dLon
ds[volVarName] = dz * area
elif obsDict['volFileName'] != obsDict['TFileName']:
obsFileName = build_obs_path(
config,
component=self.componentName,
relativePath=obsDict['volFileName'])
self.logger.info(' Reading from {}...'.format(obsFileName))
dsVol = xarray.open_dataset(obsFileName)
ds[volVarName] = dsVol[volVarName]
temp_file_name = self._get_file_name(obsDict, suffix='_combined')
temp_files = [temp_file_name]
self.logger.info(' computing the dataset')
ds.compute()
self.logger.info(
' writing temp file {}...'.format(temp_file_name))
write_netcdf(ds, temp_file_name)
chunk = {obsDict['latVar']: 400, obsDict['lonVar']: 400}
self.logger.info(
' Reading back from {}...'.format(temp_file_name))
ds = xarray.open_dataset(temp_file_name, chunks=chunk)
if obsDict['tVar'] in ds.dims:
if obsDict['tVar'] != 'Time':
if obsDict['tVar'] == 'month':
ds = ds.rename({obsDict['tVar']: 'Time'})
ds.coords['month'] = ds['Time']
else:
ds = ds.rename({obsDict['tVar']: 'Time'})
if 'year' not in ds:
ds.coords['year'] = numpy.ones(ds.sizes['Time'], int)
monthValues = constants.monthDictionary[season]
self.logger.info(' Computing climatology...')
ds = compute_climatology(ds, monthValues, maskVaries=True)
temp_file_name = self._get_file_name(obsDict, suffix='_clim')
temp_files.append(temp_file_name)
self.logger.info(' computing the dataset')
ds.compute()
self.logger.info(
' writing temp file {}...'.format(temp_file_name))
write_netcdf(ds, temp_file_name)
self.logger.info(
' Reading back from {}...'.format(temp_file_name))
ds = xarray.open_dataset(temp_file_name, chunks=chunk)
self.logger.info(' Broadcasting z coordinate...')
if 'positive' in ds[zVarName].attrs and \
ds[zVarName].attrs['positive'] == 'down':
attrs = ds[zVarName].attrs
ds[zVarName] = -ds[zVarName]
ds[zVarName].attrs = attrs
ds[zVarName].attrs['positive'] = 'up'
T, S, z = xarray.broadcast(ds[TVarName], ds[SVarName],
ds[zVarName])
ds['zBroadcast'] = z
self.logger.info(' computing the dataset')
ds.compute()
self.logger.info(' writing {}...'.format(self.fileName))
write_netcdf(ds, self.fileName)
for file_name in temp_files:
self.logger.info(' Deleting temp file {}'.format(file_name))
os.remove(file_name)
self.logger.info(' Done!')
def __init__(self, config, mpasClimatologyTask, controlConfig=None):
# {{{
'''
Construct the analysis task and adds it as a subtask of the
``parentTask``.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
as a transect
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
'''
# Authors
# -------
# Xylar Asay-Davis
tags = ['climatology', 'transect', 'woce']
# call the constructor from the base class (AnalysisTask)
super(WoceTransects, self).__init__(config=config,
taskName='woceTransects',
componentName='ocean',
tags=tags)
sectionName = self.taskName
seasons = config.getExpression(sectionName, 'seasons')
horizontalResolution = config.get(sectionName, 'horizontalResolution')
verticalComparisonGridName = config.get(sectionName,
'verticalComparisonGridName')
if verticalComparisonGridName in ['mpas', 'obs']:
verticalComparisonGrid = None
else:
verticalComparisonGrid = config.getExpression(
sectionName, 'verticalComparisonGrid', usenumpyfunc=True)
horizontalBounds = config.getExpression(sectionName,
'horizontalBounds')
observationsDirectory = build_obs_path(config, 'ocean',
'woceSubdirectory')
obsFileNames = OrderedDict()
obsFileNames['WOCE_A21'] = \
'WOCE_A21_Drake_Passage_20181126.nc'
obsFileNames['WOCE_A23'] = \
'WOCE_A23_South_Atlantic_20181126.nc'
obsFileNames['WOCE_A12'] = \
'WOCE_A12_Prime_Meridian_20181126.nc'
for transectName in obsFileNames:
fileName = '{}/{}'.format(observationsDirectory,
obsFileNames[transectName])
obsFileNames[transectName] = fileName
fields = \
{'temperature':
{'mpas': '******',
'obs': 'potentialTemperature',
'titleName': 'Potential Temperature',
'units': r'$\degree$C'},
'salinity':
{'mpas': '******',
'obs': 'salinity',
'titleName': 'Salinity',
'units': r'PSU'},
'potentialDensity':
{'mpas': '******',
'obs': 'potentialDensity',
'titleName': 'Potential Density',
'units': r'kg m$^{-3}$'}}
transectCollectionName = 'WOCE_transects'
if horizontalResolution != 'obs':
transectCollectionName = '{}_{}km'.format(transectCollectionName,
horizontalResolution)
transectsObservations = TransectsObservations(config, obsFileNames,
horizontalResolution,
transectCollectionName)
computeTransectsSubtask = ComputeTransectsSubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='WOCE',
transectCollectionName=transectCollectionName,
variableList=[field['mpas'] for field in fields.values()],
seasons=seasons,
obsDatasets=transectsObservations,
verticalComparisonGridName=verticalComparisonGridName,
verticalComparisonGrid=verticalComparisonGrid)
plotObs = controlConfig is None
if plotObs:
refTitleLabel = 'Observations (WOCE)'
diffTitleLabel = 'Model - Observations'
else:
controlRunName = controlConfig.get('runs', 'mainRunName')
refTitleLabel = 'Control: {}'.format(controlRunName)
diffTitleLabel = 'Main - Control'
fieldNameDict = {
'temperature': 'temperatureTransect',
'salinity': 'salinityTransect',
'potentialDensity': 'potentialDensityTransect'
}
for fieldName in fields:
for transectName in obsFileNames:
for season in seasons:
outFileLabel = fieldNameDict[fieldName]
if plotObs:
refFieldName = fields[fieldName]['obs']
else:
refFieldName = fields[fieldName]['mpas']
fieldNameUpper = fieldName[0].upper() + fieldName[1:]
titleName = fields[fieldName]['titleName']
fieldNameInTytle = '{} from {}'.format(
titleName, transectName.replace('_', ' '))
# make a new subtask for this season and comparison grid
subtask = PlotTransectSubtask(
self, season, transectName, fieldName,
computeTransectsSubtask, plotObs, controlConfig,
horizontalBounds[transectName])
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle=fieldNameInTytle,
mpasFieldName=fields[fieldName]['mpas'],
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=fields[fieldName]['units'],
imageCaption='{} {}'.format(fieldNameInTytle, season),
galleryGroup='WOCE Transects',
groupSubtitle=None,
groupLink='woce',
galleryName=titleName,
configSectionName='woce{}Transects'.format(
fieldNameUpper))
self.add_subtask(subtask)
def __init__(self,
config,
mpasClimatologyTask,
regionMasksTask,
controlConfig=None):
# {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
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(RegionalTSDiagrams,
self).__init__(config=config,
taskName='regionalTSDiagrams',
componentName='ocean',
tags=['climatology', 'regions', 'publicObs'])
self.run_after(mpasClimatologyTask)
self.mpasClimatologyTask = mpasClimatologyTask
regionGroups = config.getExpression(self.taskName, 'regionGroups')
self.seasons = config.getExpression(self.taskName, 'seasons')
obsDicts = {
'SOSE': {
'suffix': 'SOSE',
'gridName': 'SouthernOcean_0.167x0.167degree',
'gridFileName': 'SOSE/SOSE_2005-2010_monthly_pot_temp_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'TFileName': 'SOSE/SOSE_2005-2010_monthly_pot_temp_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'SFileName': 'SOSE/SOSE_2005-2010_monthly_salinity_'
'SouthernOcean_0.167x0.167degree_20180710.nc',
'volFileName': 'SOSE/SOSE_volume_'
'SouthernOcean_0.167x0.167degree_20190815.nc',
'preprocessedFileTemplate': 'SOSE/SOSE_{}_T_S_z_vol_'
'SouthernOcean_0.167x0.167degree_20200514.nc',
'lonVar': 'lon',
'latVar': 'lat',
'TVar': 'theta',
'SVar': 'salinity',
'volVar': 'volume',
'zVar': 'z',
'tVar': 'Time'
},
'WOA18': {
'suffix': 'WOA18',
'gridName': 'Global_0.25x0.25degree',
'gridFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'TFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'SFileName': 'WOA18/woa18_decav_04_TS_mon_20190829.nc',
'volFileName': None,
'preprocessedFileTemplate':
'WOA18/woa18_{}_T_S_z_vol_20200514.nc',
'lonVar': 'lon',
'latVar': 'lat',
'TVar': 't_an',
'SVar': 's_an',
'volVar': 'volume',
'zVar': 'depth',
'tVar': 'month'
}
}
allObsUsed = []
for regionGroup in regionGroups:
sectionSuffix = regionGroup[0].upper() + \
regionGroup[1:].replace(' ', '')
sectionName = 'TSDiagramsFor{}'.format(sectionSuffix)
obsList = config.getExpression(sectionName, 'obs')
allObsUsed = allObsUsed + obsList
allObsUsed = set(allObsUsed)
for obsName in allObsUsed:
obsDict = obsDicts[obsName]
obsDicts[obsName]['climatologyTask'] = {}
for season in self.seasons:
climatologySubtask = ComputeObsTSClimatology(self,
obsName,
obsDict,
season=season)
obsDicts[obsName]['climatologyTask'][season] = \
climatologySubtask
self.add_subtask(climatologySubtask)
for regionGroup in regionGroups:
sectionSuffix = regionGroup[0].upper() + \
regionGroup[1:].replace(' ', '')
sectionName = 'TSDiagramsFor{}'.format(sectionSuffix)
regionMaskSuffix = config.getExpression(sectionName,
'regionMaskSuffix')
regionMaskFile = get_region_mask(
config, '{}.geojson'.format(regionMaskSuffix))
regionNames = config.getExpression(sectionName, 'regionNames')
if 'all' in regionNames and os.path.exists(regionMaskFile):
regionNames = get_feature_list(regionMaskFile)
mpasMasksSubtask = regionMasksTask.add_mask_subtask(
regionMaskFile, outFileSuffix=regionMaskSuffix)
obsList = config.getExpression(sectionName, 'obs')
groupObsDicts = {}
for obsName in obsList:
localObsDict = dict(obsDicts[obsName])
obsFileName = build_obs_path(
config,
component=self.componentName,
relativePath=localObsDict['gridFileName'])
obsMasksSubtask = regionMasksTask.add_mask_subtask(
regionMaskFile,
outFileSuffix=regionMaskSuffix,
obsFileName=obsFileName,
lonVar=localObsDict['lonVar'],
latVar=localObsDict['latVar'],
meshName=localObsDict['gridName'])
obsDicts[obsName]['maskTask'] = obsMasksSubtask
localObsDict['maskTask'] = obsMasksSubtask
groupObsDicts[obsName] = localObsDict
for regionName in regionNames:
fullSuffix = sectionSuffix + '_' + \
regionName[0].lower() + \
regionName[1:].replace(' ', '')
for season in self.seasons:
computeRegionSubtask = ComputeRegionTSSubtask(
self, regionGroup, regionName, controlConfig,
sectionName, fullSuffix, mpasClimatologyTask,
mpasMasksSubtask, groupObsDicts, season)
computeRegionSubtask.run_after(mpasMasksSubtask)
for obsName in obsList:
task = \
obsDicts[obsName]['climatologyTask'][season]
computeRegionSubtask.run_after(task)
task = obsDicts[obsName]['maskTask']
computeRegionSubtask.run_after(task)
self.add_subtask(computeRegionSubtask)
plotRegionSubtask = PlotRegionTSDiagramSubtask(
self, regionGroup, regionName, controlConfig,
sectionName, fullSuffix, mpasClimatologyTask,
mpasMasksSubtask, groupObsDicts, season)
plotRegionSubtask.run_after(computeRegionSubtask)
self.add_subtask(plotRegionSubtask)
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 keyname
observationsDirectory = build_obs_path(config, 'ocean',
'meltSubdirectory')
obsFileNameDict = {'Rignot et al. (2013)':
'Rignot_2013_melt_rates_20200623.csv',
'Rignot et al. (2013) SS':
'Rignot_2013_melt_rates_SS_20200623.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 combine_observations(self): # {{{
'''
Combine SOSE oservations into a single file
'''
# Authors
# -------
# Xylar Asay-Davis
config = self.config
longitudes = sorted(
config.getExpression('soseTransects',
'longitudes',
usenumpyfunc=True))
observationsDirectory = build_obs_path(config, 'ocean',
'soseSubdirectory')
outObsDirectory = build_config_full_path(
config=config,
section='output',
relativePathOption='climatologySubdirectory',
relativePathSection='oceanObservations')
make_directories(outObsDirectory)
combinedFileName = '{}/{}.nc'.format(outObsDirectory,
self.transectCollectionName)
obsFileNames = OrderedDict()
for lon in longitudes:
transectName = 'lon_{}'.format(lon)
obsFileNames[transectName] = combinedFileName
self.obsFileNames = obsFileNames
if os.path.exists(combinedFileName):
return
print('Preprocessing SOSE transect data...')
minLat = config.getfloat('soseTransects', 'minLat')
maxLat = config.getfloat('soseTransects', 'maxLat')
dsObs = None
for field in self.fields:
prefix = field['obsFilePrefix']
fieldName = field['obsFieldName']
if prefix is None:
continue
print(' {}'.format(field['prefix']))
fileName = '{}/SOSE_2005-2010_monthly_{}_SouthernOcean' \
'_0.167x0.167degree_20180710.nc'.format(
observationsDirectory, prefix)
dsLocal = xr.open_dataset(fileName)
lat = dsLocal.lat.values
mask = numpy.logical_and(lat >= minLat, lat <= maxLat)
indices = numpy.argwhere(mask)
dsLocal = dsLocal.isel(lat=slice(indices[0][0], indices[-1][0]))
dsLocal.load()
if fieldName == 'zonalVel':
# need to average in longitude
nLon = dsLocal.sizes['lon']
lonIndicesP1 = numpy.mod(numpy.arange(nLon) + 1, nLon)
dsLocal = 0.5 * (dsLocal + dsLocal.isel(lon=lonIndicesP1))
if fieldName == 'meridVel':
# need to average in latitude
nLat = dsLocal.sizes['lat']
latIndicesP1 = numpy.mod(numpy.arange(nLat) + 1, nLat)
dsLocal = 0.5 * (dsLocal + dsLocal.isel(lat=latIndicesP1))
dsLocal = dsLocal.sel(lon=longitudes, method=str('nearest'))
if dsObs is None:
dsObs = dsLocal
else:
dsLocal['lon'] = dsObs.lon
dsLocal['lat'] = dsObs.lat
dsObs[fieldName] = dsLocal[fieldName]
dsLocal.close()
if 'zonalVel' in dsObs and 'meridVel' in dsObs:
# compute the velocity magnitude
print(' velMag')
description = 'Monthly velocity magnitude climatologies ' \
'from 2005-2010 average of the Southern Ocean ' \
'State Estimate (SOSE)'
dsObs['velMag'] = numpy.sqrt(dsObs.zonalVel**2 + dsObs.meridVel**2)
dsObs.velMag.attrs['units'] = 'm s$^{-1}$'
dsObs.velMag.attrs['description'] = description
write_netcdf(dsObs, combinedFileName)
print(' Done.')
def __init__(self, config, mpasClimatologyTask,
controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fieldName = 'sss'
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapSSS, self).__init__(
config=config, taskName='climatologyMapSSS',
componentName='ocean',
tags=['climatology', 'horizontalMap', fieldName, 'publicObs'])
mpasFieldName = 'timeMonthly_avg_activeTracers_salinity'
iselValues = {'nVertLevels': 0}
sectionName = self.taskName
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variable self.mpasFieldName will be added to mpasClimatologyTask
# along with the seasons.
remapClimatologySubtask = RemapMpasClimatologySubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName=fieldName,
variableList=[mpasFieldName],
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
if controlConfig is None:
refTitleLabel = \
'Observations (Aquarius, 2011-2014)'
observationsDirectory = build_obs_path(
config, 'ocean', '{}Subdirectory'.format(fieldName))
obsFileName = \
"{}/Aquarius_V3_SSS_Monthly_20180710.nc".format(
observationsDirectory)
refFieldName = 'sss'
outFileLabel = 'sssAquarius'
galleryName = 'Observations: Aquarius'
remapObservationsSubtask = RemapObservedSSSClimatology(
parentTask=self, seasons=seasons, fileName=obsFileName,
outFilePrefix=refFieldName,
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
diffTitleLabel = 'Model - Observations'
else:
remapObservationsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
outFileLabel = 'sss'
diffTitleLabel = 'Main - Control'
for comparisonGridName in comparisonGridNames:
for season in seasons:
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(
self, season, comparisonGridName, remapClimatologySubtask,
remapObservationsSubtask, controlConfig=controlConfig)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle='SSS',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'PSU',
imageCaption='Mean Sea Surface Salinity',
galleryGroup='Sea Surface Salinity',
groupSubtitle=None,
groupLink='sss',
galleryName=galleryName)
self.add_subtask(subtask)
def __init__(self,
config,
mpasClimatologyTask,
hemisphere,
controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
hemisphere : {'NH', 'SH'}
The hemisphere to plot
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Darin Comeau, Xylar Asay-Davis
taskName = 'climatologyMapIcebergConc{}'.format(hemisphere)
fieldName = 'IcebergConc'
tags = ['icebergs', 'climatology', 'horizontalMap', fieldName]
if hemisphere == 'NH':
tags = tags + ['arctic']
else:
tags = tags + ['antarctic']
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapIcebergConc, self).__init__(config=config,
taskName=taskName,
componentName='seaIce',
tags=tags)
mpasFieldName = 'timeMonthly_avg_bergAreaCell'
iselValues = None
sectionName = taskName
if hemisphere == 'NH':
hemisphereLong = 'Northern'
else:
hemisphereLong = 'Southern'
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid list '
'of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid list '
'of comparison grids'.format(sectionName))
# the variable self.mpasFieldName will be added to mpasClimatologyTask
# along with the seasons.
remapClimatologySubtask = RemapMpasClimatologySubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='{}{}'.format(fieldName, hemisphere),
variableList=[mpasFieldName],
comparisonGridNames=comparisonGridNames,
seasons=seasons,
iselValues=iselValues)
if controlConfig is None:
refTitleLabel = 'Observations (Altiberg)'
galleryName = 'Observations: Altiberg'
diffTitleLabel = 'Model - Observations'
refFieldName = 'icebergConc'
obsFileName = build_obs_path(
config, 'iceberg',
'concentrationAltiberg{}'.format(hemisphere))
remapObservationsSubtask = RemapAltibergConcClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix='{}{}'.format(refFieldName, hemisphere),
comparisonGridNames=comparisonGridNames)
self.add_subtask(remapObservationsSubtask)
else:
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = None
refTitleLabel = 'Control: {}'.format(controlRunName)
refFieldName = mpasFieldName
diffTitleLabel = 'Main - Control'
remapObservationsSubtask = None
for season in seasons:
for comparisonGridName in comparisonGridNames:
imageDescription = \
'{} Climatology Map of {}-Hemisphere Iceberg ' \
'Concentration.'.format(season, hemisphereLong)
imageCaption = imageDescription
galleryGroup = \
'{}-Hemisphere Iceberg Concentration'.format(
hemisphereLong)
# make a new subtask for this season and comparison grid
subtask = PlotClimatologyMapSubtask(self, hemisphere, season,
comparisonGridName,
remapClimatologySubtask,
remapObservationsSubtask,
controlConfig)
subtask.set_plot_info(
outFileLabel='bergconc{}'.format(hemisphere),
fieldNameInTitle='Iceberg concentration',
mpasFieldName=mpasFieldName,
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=r'fraction',
imageDescription=imageDescription,
imageCaption=imageCaption,
galleryGroup=galleryGroup,
groupSubtitle=None,
groupLink='{}_conc'.format(hemisphere.lower()),
galleryName=galleryName,
maskValue=None)
self.add_subtask(subtask)
def __init__(self, config, mpasClimatologyTask, controlConfig=None): # {{{
"""
Construct the analysis task.
Parameters
----------
config : ``MpasAnalysisConfigParser``
Configuration options
mpasClimatologyTask : ``MpasClimatologyTask``
The task that produced the climatology to be remapped and plotted
controlConfig : ``MpasAnalysisConfigParser``, optional
Configuration options for a control run (if any)
"""
# Authors
# -------
# Xylar Asay-Davis
fields = \
[{'prefix': 'temperature',
'mpas': '******',
'units': r'$\degree$C',
'titleName': 'Potential Temperature',
'3D': True,
'obsFilePrefix': 'pot_temp',
'obsFieldName': 'theta',
'obsBotFieldName': 'botTheta'},
{'prefix': 'salinity',
'mpas': '******',
'units': r'PSU',
'titleName': 'Salinity',
'3D': True,
'obsFilePrefix': 'salinity',
'obsFieldName': 'salinity',
'obsBotFieldName': 'botSalinity'},
{'prefix': 'potentialDensity',
'mpas': '******',
'units': r'kg m$^{-3}$',
'titleName': 'Potential Density',
'3D': True,
'obsFilePrefix': 'pot_den',
'obsFieldName': 'potentialDensity',
'obsBotFieldName': 'botPotentialDensity'},
{'prefix': 'mixedLayerDepth',
'mpas': '******',
'units': r'm',
'titleName': 'Mixed Layer Depth',
'3D': False,
'obsFilePrefix': 'mld',
'obsFieldName': 'mld',
'obsBotFieldName': None},
{'prefix': 'zonalVelocity',
'mpas': '******',
'units': r'm s$^{-1}$',
'titleName': 'Zonal Velocity',
'3D': True,
'obsFilePrefix': 'zonal_vel',
'obsFieldName': 'zonalVel',
'obsBotFieldName': 'botZonalVel'},
{'prefix': 'meridionalVelocity',
'mpas': '******',
'units': r'm s$^{-1}$',
'titleName': 'Meridional Velocity',
'3D': True,
'obsFilePrefix': 'merid_vel',
'obsFieldName': 'meridVel',
'obsBotFieldName': 'botMeridVel'},
{'prefix': 'velocityMagnitude',
'mpas': '******',
'units': r'm s$^{-1}$',
'titleName': 'Velocity Magnitude',
'3D': True,
'obsFilePrefix': 'vel_mag',
'obsFieldName': 'velMag',
'obsBotFieldName': 'botVelMag'}]
tags = ['climatology', 'horizontalMap', 'sose', 'publicObs'] \
+ [field['prefix'] for field in fields]
# call the constructor from the base class (AnalysisTask)
super(ClimatologyMapSose, self).__init__(config=config,
taskName='climatologyMapSose',
componentName='ocean',
tags=tags)
sectionName = self.taskName
fileSuffix = config.get(sectionName, 'fileSuffix')
if fileSuffix.endswith('.nc'):
fileSuffix = fileSuffix.strip('.nc')
fieldList = config.getExpression(sectionName, 'fieldList')
fields = [field for field in fields if field['prefix'] in fieldList]
# read in what seasons we want to plot
seasons = config.getExpression(sectionName, 'seasons')
if len(seasons) == 0:
raise ValueError('config section {} does not contain valid '
'list of seasons'.format(sectionName))
comparisonGridNames = config.getExpression(sectionName,
'comparisonGrids')
if len(comparisonGridNames) == 0:
raise ValueError('config section {} does not contain valid '
'list of comparison grids'.format(sectionName))
if not numpy.any([field['3D'] for field in fields]):
depths = None
else:
depths = config.getExpression(sectionName, 'depths')
if len(depths) == 0:
raise ValueError('config section {} does not contain valid '
'list of depths'.format(sectionName))
variableList = [
field['mpas'] for field in fields if field['mpas'] != 'velMag'
]
if depths is None:
remapMpasSubtask = RemapMpasClimatologySubtask(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='SOSE',
variableList=variableList,
seasons=seasons,
comparisonGridNames=comparisonGridNames,
iselValues=None)
else:
remapMpasSubtask = RemapMpasVelMagClimatology(
mpasClimatologyTask=mpasClimatologyTask,
parentTask=self,
climatologyName='SOSE',
variableList=variableList,
seasons=seasons,
depths=depths,
comparisonGridNames=comparisonGridNames,
iselValues=None)
for field in fields:
fieldPrefix = field['prefix']
upperFieldPrefix = fieldPrefix[0].upper() + fieldPrefix[1:]
sectionName = '{}{}'.format(self.taskName, upperFieldPrefix)
if field['3D']:
fieldDepths = depths
else:
fieldDepths = None
if controlConfig is None:
refTitleLabel = 'State Estimate (SOSE)'
observationsDirectory = build_obs_path(config, 'ocean',
'soseSubdirectory')
obsFileName = '{}/SOSE_2005-2010_monthly_{}_{}.nc'.format(
observationsDirectory, field['obsFilePrefix'], fileSuffix)
refFieldName = field['obsFieldName']
outFileLabel = '{}SOSE'.format(fieldPrefix)
galleryName = 'State Estimate: SOSE'
diffTitleLabel = 'Model - State Estimate'
remapObsSubtask = RemapSoseClimatology(
parentTask=self,
seasons=seasons,
fileName=obsFileName,
outFilePrefix='{}SOSE'.format(refFieldName),
fieldName=refFieldName,
botFieldName=field['obsBotFieldName'],
depths=fieldDepths,
comparisonGridNames=comparisonGridNames,
subtaskName='remapObservations{}'.format(upperFieldPrefix))
self.add_subtask(remapObsSubtask)
else:
remapObsSubtask = None
controlRunName = controlConfig.get('runs', 'mainRunName')
galleryName = 'Control: {}'.format(controlRunName)
refTitleLabel = galleryName
refFieldName = field['mpas']
outFileLabel = fieldPrefix
diffTitleLabel = 'Main - Control'
if field['3D']:
fieldDepths = depths
else:
fieldDepths = [None]
for comparisonGridName in comparisonGridNames:
for season in seasons:
for depth in fieldDepths:
subtaskName = 'plot{}_{}_{}'.format(
upperFieldPrefix, season, comparisonGridName)
if depth is not None:
subtaskName = '{}_depth_{}'.format(
subtaskName, depth)
subtask = PlotClimatologyMapSubtask(
parentTask=self,
season=season,
comparisonGridName=comparisonGridName,
remapMpasClimatologySubtask=remapMpasSubtask,
remapObsClimatologySubtask=remapObsSubtask,
controlConfig=controlConfig,
depth=depth,
subtaskName=subtaskName)
subtask.set_plot_info(
outFileLabel=outFileLabel,
fieldNameInTitle=field['titleName'],
mpasFieldName=field['mpas'],
refFieldName=refFieldName,
refTitleLabel=refTitleLabel,
diffTitleLabel=diffTitleLabel,
unitsLabel=field['units'],
imageCaption=field['titleName'],
galleryGroup=field['titleName'],
groupSubtitle=None,
groupLink='{}Sose'.format(fieldPrefix),
galleryName=galleryName,
configSectionName='climatologyMapSose{}'.format(
upperFieldPrefix))
self.add_subtask(subtask)