def setup_config(self, autocloseFileLimitFraction=0.5, maxChunkSize=10000):
config = MpasAnalysisConfigParser()
config.add_section('input')
config.set('input', 'autocloseFileLimitFraction',
str(autocloseFileLimitFraction))
config.set('input', 'maxChunkSize', str(maxChunkSize))
return config
def setup_config(self):
configPath = self.datadir.join('config.QU240')
config = MpasAnalysisConfigParser()
config.read(str(configPath))
config.set('input', 'baseDirectory', str(self.datadir))
config.set('output', 'baseDirectory', str(self.test_dir))
return config
def doTest(generate, expectedResults):
config = MpasAnalysisConfigParser()
config.add_section('output')
config.set('output', 'generate', generate)
for taskName in expectedResults:
genericTask = AnalysisTask(config=config,
taskName=taskName,
componentName=cores[taskName],
tags=tags[taskName])
expectedResult = expectedResults[taskName]
result = genericTask.check_generate()
self.assertEqual(result, expectedResult)
def setup_config(self):
configPath = self.datadir.join('config.remap_obs')
config = MpasAnalysisConfigParser()
config.read(str(configPath))
config.set('input', 'baseDirectory', str(self.datadir))
config.set('diagnostics', 'baseDirectory', str(self.datadir))
config.set('oceanObservations', 'obsSubdirectory', '.')
config.set('output', 'baseDirectory', str(self.test_dir))
return config
def main():
"""
Entry point for the main script ``mpas_analysis``
"""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-v',
'--version',
action='version',
version='mpas_analysis {}'.format(
mpas_analysis.__version__),
help="Show version number and exit")
parser.add_argument("--setup_only",
dest="setup_only",
action='store_true',
help="If only the setup phase, not the run or HTML "
"generation phases, should be executed.")
parser.add_argument("--html_only",
dest="html_only",
action='store_true',
help="If only the setup and HTML generation phases, "
"not the run phase, should be executed.")
parser.add_argument("-g",
"--generate",
dest="generate",
help="A list of analysis modules to generate "
"(nearly identical generate option in config file).",
metavar="ANALYSIS1[,ANALYSIS2,ANALYSIS3,...]")
parser.add_argument("-l",
"--list",
dest="list",
action='store_true',
help="List the available analysis tasks")
parser.add_argument("-p",
"--purge",
dest="purge",
action='store_true',
help="Purge the analysis by deleting the output"
"directory before running")
parser.add_argument('configFiles',
metavar='CONFIG',
type=str,
nargs='*',
help='config file')
parser.add_argument("--plot_colormaps",
dest="plot_colormaps",
action='store_true',
help="Make a plot displaying all available colormaps")
parser.add_argument("--verbose",
dest="verbose",
action='store_true',
help="Verbose error reporting during setup-and-check "
"phase")
args = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
for configFile in args.configFiles:
if not os.path.exists(configFile):
raise OSError('Config file {} not found.'.format(configFile))
# add config.default to cover default not included in the config files
# provided on the command line
if pkg_resources.resource_exists('mpas_analysis', 'config.default'):
defaultConfig = pkg_resources.resource_filename(
'mpas_analysis', 'config.default')
configFiles = [defaultConfig] + args.configFiles
else:
print('WARNING: Did not find config.default. Assuming other config '
'file(s) contain a\n'
'full set of configuration options.')
defaultConfig = None
configFiles = args.configFiles
config = MpasAnalysisConfigParser()
config.read(configFiles)
if args.list:
analyses = build_analysis_list(config, controlConfig=None)
for analysisTask in analyses:
print('task: {}'.format(analysisTask.taskName))
print(' component: {}'.format(analysisTask.componentName)),
print(' tags: {}'.format(', '.join(analysisTask.tags)))
sys.exit(0)
if args.plot_colormaps:
_register_custom_colormaps()
_plot_color_gradients()
sys.exit(0)
if config.has_option('runs', 'controlRunConfigFile'):
controlConfigFile = config.get('runs', 'controlRunConfigFile')
if not os.path.exists(controlConfigFile):
raise OSError('A control config file {} was specified but the '
'file does not exist'.format(controlConfigFile))
controlConfigFiles = [controlConfigFile]
if defaultConfig is not None:
controlConfigFiles = [defaultConfig] + controlConfigFiles
controlConfig = MpasAnalysisConfigParser()
controlConfig.read(controlConfigFiles)
# replace the log directory so log files get written to this run's
# log directory, not the control run's
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
controlConfig.set('output', 'logsSubdirectory', logsDirectory)
print('Comparing to control run {} rather than observations. \n'
'Make sure that MPAS-Analysis has been run previously with the '
'control config file.'.format(
controlConfig.get('runs', 'mainRunName')))
else:
controlConfig = None
if args.purge:
purge_output(config)
if config.has_option('runs', 'mainRunConfigFile'):
symlink_main_run(config, defaultConfig)
if args.generate:
update_generate(config, args.generate)
if controlConfig is not None:
# we want to use the "generate" option from the current run, not
# the control config file
controlConfig.set('output', 'generate',
config.get('output', 'generate'))
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
make_directories(logsDirectory)
update_time_bounds_in_config(config)
file_cache_maxsize = config.getint('input', 'file_cache_maxsize')
try:
xarray.set_options(file_cache_maxsize=file_cache_maxsize)
except ValueError:
# xarray version doesn't support file_cache_maxsize yet...
pass
startTime = time.time()
analyses = build_analysis_list(config, controlConfig)
analyses = determine_analyses_to_generate(analyses, args.verbose)
setupDuration = time.time() - startTime
if not args.setup_only and not args.html_only:
run_analysis(config, analyses)
runDuration = time.time() - startTime
m, s = divmod(setupDuration, 60)
h, m = divmod(int(m), 60)
print('Total setup time: {}:{:02d}:{:05.2f}'.format(h, m, s))
m, s = divmod(runDuration, 60)
h, m = divmod(int(m), 60)
print('Total run time: {}:{:02d}:{:05.2f}'.format(h, m, s))
if not args.setup_only:
generate_html(config, analyses, controlConfig)
def setup_config(self, maxChunkSize=10000):
config = MpasAnalysisConfigParser()
config.add_section('input')
config.set('input', 'maxChunkSize', str(maxChunkSize))
return config
def main():
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument("-i",
"--inDir",
dest="inDir",
required=True,
help="Directory where intermediate files used in "
"processing should be downloaded")
parser.add_argument("-o",
"--outDir",
dest="outDir",
required=True,
help="Directory where final preprocessed observation "
"are stored")
args = parser.parse_args()
date = '20190603'
inGridName = 'SouthernOcean_0.167x0.167degree_{}'.format(date)
inTPrefix = 'THETA_mnthlyBar.0000000100'
inSPrefix = 'SALT_mnthlyBar.0000000100'
inMLDPrefix = 'MLD_mnthlyBar.0000000100'
inUPrefix = 'UVEL_mnthlyBar.0000000100'
inVPrefix = 'VVEL_mnthlyBar.0000000100'
inGammaNPrefix = 'GAMMA_mnthlyBar.0000000100'
# size in km of the polar stereographic grid
antarcticStereoWidth = 10000
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
config.set('climatology', 'comparisonAntarcticStereoWidth',
'{}'.format(antarcticStereoWidth))
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = '{}_{}'.format(outDescriptor.meshName, date)
inPrefixes = [
inTPrefix, inSPrefix, inMLDPrefix, inUPrefix, inVPrefix, inGammaNPrefix
]
inGridFileName = '{}/grid.mat'.format(args.inDir)
try:
os.makedirs(args.inDir)
except OSError:
pass
try:
os.makedirs(args.outDir)
except OSError:
pass
# dowload the desired file
download_files(['GRID_README.txt'],
urlBase='http://sose.ucsd.edu/DATA',
outDir=args.inDir)
urlBase = 'http://sose.ucsd.edu/DATA/SO6_V2'
fileList = ['grid.mat']
for prefix in inPrefixes:
fileList.append('{}.data.gz'.format(prefix))
fileList.append('{}.meta'.format(prefix))
download_files(fileList, urlBase, args.inDir)
unzip_sose_data(inPrefixes, args.inDir)
prefix = '{}/SOSE'.format(args.outDir)
sose_volume_to_nc(prefix, inGridName, inGridFileName, args.inDir)
prefix = '{}/SOSE_2005-2010_monthly'.format(args.outDir)
remap_pt_s(prefix, inGridName, inGridFileName, args.inDir, inTPrefix,
inSPrefix, inGammaNPrefix, outDescriptor, outGridName)
remap_mld(prefix, inGridName, inGridFileName, args.inDir, inMLDPrefix,
outDescriptor, outGridName)
remap_u(prefix, inGridName, inGridFileName, args.inDir, inUPrefix,
outDescriptor, outGridName)
remap_v(prefix, inGridName, inGridFileName, args.inDir, inVPrefix,
outDescriptor, outGridName)
compute_vel_mag(prefix, inGridName, args.inDir, outGridName)
compute_pot_density(prefix, inGridName, args.inDir, outGridName)
resolution.
'''
from mpas_analysis.shared.interpolation import Remapper
from mpas_analysis.shared.grid import MpasMeshDescriptor
from mpas_analysis.shared.climatology import get_comparison_descriptor
from mpas_analysis.configuration import MpasAnalysisConfigParser
# replace with the MPAS mesh name
inGridName = 'oQU240'
# replace with the path to the desired mesh or restart file
inGridFileName = '/media/xylar/extra_data/analysis/edison/G-QU240-master-intel/run/mpaso.rst.0001-01-06_00000.nc'
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
# replace 1.0 with the desired resolution of the output mesh
config.set('climatology', 'comparisonLatResolution', '1.0')
config.set('climatology', 'comparisonLonResolution', '1.0')
inDescriptor = MpasMeshDescriptor(inGridFileName, inGridName)
outDescriptor = get_comparison_descriptor(config, 'latlon')
outGridName = outDescriptor.meshName
mappingFileName = 'map_{}_to_{}.nc'.format(inGridName, outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
def setup_config(self, autocloseFileLimitFraction=0.5, maxChunkSize=10000):
config = MpasAnalysisConfigParser()
config.add_section('input')
config.set('input', 'autocloseFileLimitFraction',
str(autocloseFileLimitFraction))
config.set('input', 'maxChunkSize', str(maxChunkSize))
config.set('input', 'mpasMeshName', 'QU240')
config.add_section('output')
config.set('output', 'baseDirectory', self.test_dir)
config.set('output', 'mappingSubdirectory', '.')
config.set('output', 'mpasClimatologySubdirectory', 'clim/mpas')
config.add_section('climatology')
config.set('climatology', 'startYear', '2')
config.set('climatology', 'endYear', '2')
config.set('climatology', 'comparisonLatResolution', '0.5')
config.set('climatology', 'comparisonLonResolution', '0.5')
config.set('climatology', 'mpasInterpolationMethod', 'bilinear')
config.add_section('oceanObservations')
config.set('oceanObservations', 'interpolationMethod', 'bilinear')
config.set('oceanObservations', 'climatologySubdirectory', 'clim/obs')
config.set('oceanObservations', 'remappedClimSubdirectory',
'clim/obs/remap')
return config
'''
from mpas_analysis.shared.interpolation import Remapper
from mpas_analysis.shared.grid import MpasMeshDescriptor
from mpas_analysis.shared.climatology import get_comparison_descriptor
from mpas_analysis.configuration import MpasAnalysisConfigParser
# replace with the MPAS mesh name
inGridName = 'oQU240'
# replace with the path to the desired mesh or restart file
inGridFileName = '/media/xylar/extra_data/analysis/edison/G-QU240-master-intel/run/mpaso.rst.0001-01-06_00000.nc'
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
# replace these numbers with the desired size and resolution of the output mesh
config.set('climatology', 'comparisonAntarcticStereoWidth', '6000.0')
config.set('climatology', 'comparisonAntarcticStereoResolution', '10.0')
inDescriptor = MpasMeshDescriptor(inGridFileName, inGridName)
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = outDescriptor.meshName
mappingFileName = 'map_{}_to_{}.nc'.format(inGridName, outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
