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Merged
merged 2 commits into from
Feb 10, 2017
Merged

A reorganization of timekeeping to work with general calendars #102

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00a30d2
Add timekeeping utility functions
xylar Feb 6, 2017
f5382cd
Add MpasRelativeDelta class
xylar Feb 9, 2017
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9 changes: 7 additions & 2 deletions mpas_analysis/ocean/ocean_modelvsobs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
from ..shared.interpolation.interpolate import interp_fields, init_tree
from ..shared.constants import constants

from ..shared.io import StreamsFile
from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath


Expand Down Expand Up @@ -50,16 +50,21 @@ def ocn_modelvsobs(config, field, streamMap=None, variableMap=None):
# read parameters from config file
inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'oceanNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'oceanStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

calendar = namelist.get('config_calendar_type')

# get a list of timeSeriesStats output files from the streams file,
# reading only those that are between the start and end dates
startDate = config.get('climatology', 'startDate')
endDate = config.get('climatology', 'endDate')
streamName = streams.find_stream(streamMap['timeSeriesStats'])
inputFiles = streams.readpath(streamName, startDate=startDate,
endDate=endDate)
endDate=endDate, calendar=calendar)
print 'Reading files {} through {}'.format(inputFiles[0], inputFiles[-1])

plotsDirectory = buildConfigFullPath(config, 'output', 'plotsSubdirectory')
Expand Down
38 changes: 20 additions & 18 deletions mpas_analysis/ocean/ohc_timeseries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@
from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath

from ..shared.timekeeping.Date import Date
from ..shared.timekeeping.utility import stringToDatetime, \
clampToNumpyDatetime64


def ohc_timeseries(config, streamMap=None, variableMap=None):
Expand All @@ -35,6 +36,16 @@ def ohc_timeseries(config, streamMap=None, variableMap=None):
Last Modified: 02/02/2017
"""

inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'oceanNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'oceanStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

calendar = namelist.get('config_calendar_type')

# read parameters from config file
mainRunName = config.get('runs', 'mainRunName')
preprocessedReferenceRunName = config.get('runs',
Expand All @@ -56,14 +67,6 @@ def ohc_timeseries(config, streamMap=None, variableMap=None):
regionIndicesToPlot = config.getExpression('timeSeriesOHC',
'regionIndicesToPlot')

inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'oceanNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'oceanStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

# Note: input file, not a mesh file because we need dycore specific fields
# such as refBottomDepth and namelist fields such as config_density0, as
# well as simulationStartTime, that are not guaranteed to be in the mesh
Expand All @@ -80,7 +83,7 @@ def ohc_timeseries(config, streamMap=None, variableMap=None):
endDate = config.get('timeSeries', 'endDate')
streamName = streams.find_stream(streamMap['timeSeriesStats'])
inFiles = streams.readpath(streamName, startDate=startDate,
endDate=endDate)
endDate=endDate, calendar=calendar)
print 'Reading files {} through {}'.format(inFiles[0], inFiles[-1])

# Define/read in general variables
Expand All @@ -91,7 +94,7 @@ def ohc_timeseries(config, streamMap=None, variableMap=None):
# simulation start time
simulationStartTime = netCDF4.chartostring(
ncFile.variables['simulationStartTime'][:])
simulationStartTime = str(simulationStartTime)
simulationStartTime = str(simulationStartTime).strip()
ncFile.close()
# specific heat [J/(kg*degC)]
cp = namelist.getfloat('config_specific_heat_sea_water')
Expand Down Expand Up @@ -120,22 +123,21 @@ def ohc_timeseries(config, streamMap=None, variableMap=None):

ds = remove_repeated_time_index(ds)

# convert the start and end dates to datetime objects using
# the Date class, which ensures the results are within the
# supported range
timeStart = Date(startDate).to_datetime(yearOffset)
timeEnd = Date(endDate).to_datetime(yearOffset)
timeStart = clampToNumpyDatetime64(stringToDatetime(startDate), yearOffset)
timeEnd = clampToNumpyDatetime64(stringToDatetime(endDate), yearOffset)
# select only the data in the specified range of years
ds = ds.sel(Time=slice(timeStart, timeEnd))

# Select year-1 data and average it (for later computing anomalies)
timeStartFirstYear = Date(simulationStartTime).to_datetime(yearOffset)
timeStartFirstYear = clampToNumpyDatetime64(
stringToDatetime(simulationStartTime), yearOffset)
if timeStartFirstYear < timeStart:
startDateFirstYear = simulationStartTime
endDateFirstYear = '{}-12-31_23:59:59'.format(startDateFirstYear[0:4])
filesFirstYear = streams.readpath(streamName,
startDate=startDateFirstYear,
endDate=endDateFirstYear)
endDate=endDateFirstYear,
calendar=calendar)
dsFirstYear = xr.open_mfdataset(
filesFirstYear,
preprocess=lambda x: preprocess_mpas(x,
Expand Down
19 changes: 11 additions & 8 deletions mpas_analysis/ocean/sst_timeseries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,11 @@

from ..shared.plot.plotting import timeseries_analysis_plot

from ..shared.io import StreamsFile
from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath

from ..shared.timekeeping.Date import Date
from ..shared.timekeeping.utility import stringToDatetime, \
clampToNumpyDatetime64


def sst_timeseries(config, streamMap=None, variableMap=None):
Expand Down Expand Up @@ -39,13 +40,18 @@ def sst_timeseries(config, streamMap=None, variableMap=None):
streamsFileName = config.get('input', 'oceanStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

namelistFileName = config.get('input', 'oceanNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

calendar = namelist.get('config_calendar_type')

# get a list of timeSeriesStats output files from the streams file,
# reading only those that are between the start and end dates
startDate = config.get('timeSeries', 'startDate')
endDate = config.get('timeSeries', 'endDate')
streamName = streams.find_stream(streamMap['timeSeriesStats'])
inFiles = streams.readpath(streamName, startDate=startDate,
endDate=endDate)
endDate=endDate, calendar=calendar)
print 'Reading files {} through {}'.format(inFiles[0], inFiles[-1])

mainRunName = config.get('runs', 'mainRunName')
Expand Down Expand Up @@ -75,11 +81,8 @@ def sst_timeseries(config, streamMap=None, variableMap=None):
varmap=variableMap))
ds = remove_repeated_time_index(ds)

# convert the start and end dates to datetime objects using
# the Date class, which ensures the results are within the
# supported range
timeStart = Date(startDate).to_datetime(yearOffset)
timeEnd = Date(endDate).to_datetime(yearOffset)
timeStart = clampToNumpyDatetime64(stringToDatetime(startDate), yearOffset)
timeEnd = clampToNumpyDatetime64(stringToDatetime(endDate), yearOffset)
# select only the data in the specified range of years
ds = ds.sel(Time=slice(timeStart, timeEnd))

Expand Down
9 changes: 7 additions & 2 deletions mpas_analysis/sea_ice/modelvsobs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
remove_repeated_time_index
from ..shared.plot.plotting import plot_polar_comparison

from ..shared.io import StreamsFile
from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath


Expand All @@ -40,16 +40,21 @@ def seaice_modelvsobs(config, streamMap=None, variableMap=None):
# read parameters from config file
inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'seaIceNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'seaIceStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

calendar = namelist.get('config_calendar_type')

# get a list of timeSeriesStatsMonthly output files from the streams file,
# reading only those that are between the start and end dates
startDate = config.get('climatology', 'startDate')
endDate = config.get('climatology', 'endDate')
streamName = streams.find_stream(streamMap['timeSeriesStats'])
infiles = streams.readpath(streamName, startDate=startDate,
endDate=endDate)
endDate=endDate, calendar=calendar)
print 'Reading files {} through {}'.format(infiles[0], infiles[-1])

plotsDirectory = buildConfigFullPath(config, 'output', 'plotsSubdirectory')
Expand Down
19 changes: 11 additions & 8 deletions mpas_analysis/sea_ice/timeseries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,11 @@

from ..shared.plot.plotting import timeseries_analysis_plot

from ..shared.io import StreamsFile
from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath

from ..shared.timekeeping.Date import Date
from ..shared.timekeeping.utility import stringToDatetime, \
clampToNumpyDatetime64


def seaice_timeseries(config, streamMap=None, variableMap=None):
Expand All @@ -34,16 +35,21 @@ def seaice_timeseries(config, streamMap=None, variableMap=None):
# read parameters from config file
inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'seaIceNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'seaIceStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)

calendar = namelist.get('config_calendar_type')

# get a list of timeSeriesStatsMonthly output files from the streams file,
# reading only those that are between the start and end dates
startDate = config.get('timeSeries', 'startDate')
endDate = config.get('timeSeries', 'endDate')
streamName = streams.find_stream(streamMap['timeSeriesStats'])
inFiles = streams.readpath(streamName, startDate=startDate,
endDate=endDate)
endDate=endDate, calendar=calendar)
print 'Reading files {} through {}'.format(inFiles[0], inFiles[-1])

variableNames = ['iceAreaCell', 'iceVolumeCell']
Expand Down Expand Up @@ -113,11 +119,8 @@ def seaice_timeseries(config, streamMap=None, variableMap=None):
varmap=variableMap))
ds = remove_repeated_time_index(ds)

# convert the start and end dates to datetime objects using
# the Date class, which ensures the results are within the
# supported range
timeStart = Date(startDate).to_datetime(yearOffset)
timeEnd = Date(endDate).to_datetime(yearOffset)
timeStart = clampToNumpyDatetime64(stringToDatetime(startDate), yearOffset)
timeEnd = clampToNumpyDatetime64(stringToDatetime(endDate), yearOffset)
# select only the data in the specified range of years
ds = ds.sel(Time=slice(timeStart, timeEnd))

Expand Down
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