RunLAIRead Namespace Reference

Run lairead utility to initializes vegetation carbon stores. More...

Variables
tuple	parser
string	help = 'The configuration file. Must define section "GRASS" and option "GISBASE"'
tuple	args = parser.parse_args()
tuple	cmdline = RHESSysMetadata.getCommandLine()
	configFile = None
tuple	context = Context(args.projectDir, configFile)
tuple	grassMetadata = RHESSysMetadata.readGRASSEntries(context)
tuple	metadata = RHESSysMetadata.readRHESSysEntries(context)
list	rhessysDir = metadata['rhessys_dir']
tuple	paths = RHESSysPaths(args.projectDir, rhessysDir)
list	worldfileZero = metadata['worldfile_zero']
string	headerZero = "%s.hdr"
tuple	worldfileZeroPath = os.path.join(context.projectDir, worldfileZero)
tuple	worldfileDir = os.path.dirname(worldfileZeroPath)
tuple	modulePath = context.config.get('GRASS', 'MODULE_PATH')
tuple	grassDbase = os.path.join(context.projectDir, metadata['grass_dbase'])
tuple	grassConfig = GRASSConfig(context, grassDbase, metadata['grass_location'], metadata['grass_mapset'])
tuple	grassLib = GRASSLib(grassConfig=grassConfig)
list	demRast = grassMetadata['dem_rast']
	Make sure mask and region are properly set. More...
tuple	result = grassLib.script.run_command('g.region', rast=demRast)
list	basinRast = grassMetadata['basin_rast']
tuple	headerZeroPath = os.path.join(context.projectDir, headerZero)
tuple	stations = getClimateBaseStationFilenames(headerZeroPath)
tuple	firstStationPath = os.path.normpath( os.path.join(paths.RHESSYS_DIR, stations[0]) )
tuple	fourDays = datetime.timedelta(days=4)
tuple	tecDurRedef = datetime.timedelta(days=1)
	tecRedef = startDate+tecDurRedef
tuple	laireadPath = os.path.join(context.projectDir, metadata['lairead_bin'])
tuple	oldWorldPath = os.path.join(context.projectDir, worldfileZero)
string	redefWorldName = "%s.Y%dM%dD%dH%d"
tuple	redefWorldPath = os.path.join(context.projectDir, redefWorldName)
tuple	allomPath = os.path.join(context.projectDir, metadata['allometric_table'])
tuple	p
string	tecName = 'tec.lairead'
tuple	tecPath = os.path.join(paths.RHESSYS_TEC, tecName)
tuple	tecDurOutput = datetime.timedelta(days=2)
	tecOutput = startDate+tecDurOutput
tuple	f = open(tecPath, 'w')
	rhessysStart = startDate
tuple	rhessysDur = datetime.timedelta(days=3)
	rhessysEnd = startDate+rhessysDur
tuple	surfaceFlowtablePath = os.path.join(context.projectDir, metadata['surface_flowtable'])
tuple	subSurfaceFlowtablePath = os.path.join(context.projectDir, metadata['subsurface_flowtable'])
tuple	rhessysBinPath = os.path.join(context.projectDir, metadata['rhessys_bin'])
tuple	rhessysCmd
tuple	cmdArgs = rhessysCmd.split()
tuple	process = Popen(cmdArgs, cwd=paths.RHESSYS_DIR, stdout=PIPE, stderr=PIPE)
string	outputWorldName = "%s.Y%dM%dD%dH%d.state"
tuple	outputWorldPath = os.path.join(context.projectDir, outputWorldName)
string	newWorldName = 'world'
tuple	newWorldPath = os.path.join(paths.RHESSYS_WORLD, newWorldName)
string	header = "%s.hdr"
tuple	headerPath = os.path.join(paths.RHESSYS_WORLD, header)

Detailed Description

Run lairead utility to initializes vegetation carbon stores.

Will: (1) run lairead to produce a redefine worldfile; (2) run RHESSys simulation for 3-days to generate base worldfile

This software is provided free of charge under the New BSD License. Please see the following license information:

Copyright (c) 2013, University of North Carolina at Chapel Hill All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of the University of North Carolina at Chapel Hill nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Author

Brian Miles brian.nosp@m._mil.nosp@m.es@un.nosp@m.c.ed.nosp@m.u

Pre conditions

1. The following metadata entry(ies) must be present in the RHESSys section of the metadata associated with the project directory: grass_dbase grass_location grass_mapset rhessys_dir rhessys_bin lairead_bin worldfile_zero surface_flowtable subsurface_flowtable allometric_table
2. The following metadata entry(ies) must be present in the GRASS section of the metadata associated with the project directory: basin_rast dem_rast hillslope_rast zone_rast patch_rast stratum_rast lai_rast

Post conditions

1. Worldfile with initialized vegetation carbon stores will be saved to the appropriate location of the project directory
2. Will write the following entry(ies) to the RHESSys section of metadata associated with the project directory: worldfile tec_lairead

Usage:

RunLAIRead.py -p /path/to/project_dir

Note

EcoHydroWorkflowLib configuration file must be specified by environmental variable 'ECOHYDROWORKFLOW_CFG', or -i option must be specified.

Variable Documentation

tuple RunLAIRead.allomPath = os.path.join(context.projectDir, metadata['allometric_table'])

tuple RunLAIRead.args = parser.parse_args()

list RunLAIRead.basinRast = grassMetadata['basin_rast']

tuple RunLAIRead.cmdArgs = rhessysCmd.split()

tuple RunLAIRead.cmdline = RHESSysMetadata.getCommandLine()

RunLAIRead.configFile = None

tuple RunLAIRead.context = Context(args.projectDir, configFile)

list RunLAIRead.demRast = grassMetadata['dem_rast']

Make sure mask and region are properly set.

tuple RunLAIRead.f = open(tecPath, 'w')

tuple RunLAIRead.firstStationPath = os.path.normpath( os.path.join(paths.RHESSYS_DIR, stations[0]) )

tuple RunLAIRead.fourDays = datetime.timedelta(days=4)

tuple RunLAIRead.grassConfig = GRASSConfig(context, grassDbase, metadata['grass_location'], metadata['grass_mapset'])

tuple RunLAIRead.grassDbase = os.path.join(context.projectDir, metadata['grass_dbase'])

tuple RunLAIRead.grassLib = GRASSLib(grassConfig=grassConfig)

tuple RunLAIRead.grassMetadata = RHESSysMetadata.readGRASSEntries(context)

string RunLAIRead.header = "%s.hdr"

tuple RunLAIRead.headerPath = os.path.join(paths.RHESSYS_WORLD, header)

string RunLAIRead.headerZero = "%s.hdr"

tuple RunLAIRead.headerZeroPath = os.path.join(context.projectDir, headerZero)

1. Determine legal simulation start and date from climate data Read first climate station from worldfile

string RunLAIRead.help = 'The configuration file. Must define section "GRASS" and option "GISBASE"'

tuple RunLAIRead.laireadPath = os.path.join(context.projectDir, metadata['lairead_bin'])

tuple RunLAIRead.metadata = RHESSysMetadata.readRHESSysEntries(context)

tuple RunLAIRead.modulePath = context.config.get('GRASS', 'MODULE_PATH')

string RunLAIRead.newWorldName = 'world'

tuple RunLAIRead.newWorldPath = os.path.join(paths.RHESSYS_WORLD, newWorldName)

tuple RunLAIRead.oldWorldPath = os.path.join(context.projectDir, worldfileZero)

string RunLAIRead.outputWorldName = "%s.Y%dM%dD%dH%d.state"

1. Rename redefine worldfile, write to metadata

tuple RunLAIRead.outputWorldPath = os.path.join(context.projectDir, outputWorldName)

tuple RunLAIRead.p

Initial value:

= grassLib.script.pipe_command(laireadPath, old=oldWorldPath, redef=redefWorldPath,
                                      allom=allomPath, lai=grassMetadata['lai_rast'],
                                      vegid=grassMetadata['stratum_rast'],
                                      zone=grassMetadata['zone_rast'],
                                      hill=grassMetadata['hillslope_rast'],
                                      patch=grassMetadata['patch_rast'],
                                      mask=grassMetadata['basin_rast'])

tuple RunLAIRead.parser

Initial value:

= argparse.ArgumentParser(description='Run lairead utility to initializes vegetation carbon stores. Will: (1) run lairead to ' +
                                             'produce a redefine worldfile; (2) run RHESSys simulation for 3-days to generate base worldfile')

tuple RunLAIRead.paths = RHESSysPaths(args.projectDir, rhessysDir)

tuple RunLAIRead.process = Popen(cmdArgs, cwd=paths.RHESSYS_DIR, stdout=PIPE, stderr=PIPE)

string RunLAIRead.redefWorldName = "%s.Y%dM%dD%dH%d"

tuple RunLAIRead.redefWorldPath = os.path.join(context.projectDir, redefWorldName)

tuple RunLAIRead.result = grassLib.script.run_command('g.region', rast=demRast)

tuple RunLAIRead.rhessysBinPath = os.path.join(context.projectDir, metadata['rhessys_bin'])

tuple RunLAIRead.rhessysCmd

Initial value:

= generateCommandString(rhessysBinPath, None,
                                   rhessysStart, rhessysEnd,
                                   tecPath, oldWorldPath,
                                   subSurfaceFlowtablePath, surfaceFlowtablePath)

list RunLAIRead.rhessysDir = metadata['rhessys_dir']

tuple RunLAIRead.rhessysDur = datetime.timedelta(days=3)

RunLAIRead.rhessysEnd = startDate+rhessysDur

RunLAIRead.rhessysStart = startDate

1. Run RHESSys for the first 4 legal days with redefine TEC

tuple RunLAIRead.stations = getClimateBaseStationFilenames(headerZeroPath)

tuple RunLAIRead.subSurfaceFlowtablePath = os.path.join(context.projectDir, metadata['subsurface_flowtable'])

tuple RunLAIRead.surfaceFlowtablePath = os.path.join(context.projectDir, metadata['surface_flowtable'])

tuple RunLAIRead.tecDurOutput = datetime.timedelta(days=2)

tuple RunLAIRead.tecDurRedef = datetime.timedelta(days=1)

1. Run LAI read to generate redefine worldfile

string RunLAIRead.tecName = 'tec.lairead'

1. Write TEC file for redefining the initial world file Redefine on the second day of the simulation, write output on the third day

RunLAIRead.tecOutput = startDate+tecDurOutput

tuple RunLAIRead.tecPath = os.path.join(paths.RHESSYS_TEC, tecName)

RunLAIRead.tecRedef = startDate+tecDurRedef

tuple RunLAIRead.worldfileDir = os.path.dirname(worldfileZeroPath)

list RunLAIRead.worldfileZero = metadata['worldfile_zero']

tuple RunLAIRead.worldfileZeroPath = os.path.join(context.projectDir, worldfileZero)