PatchZonalStats Namespace Reference

Tool for calculating zonal statistics for patch-scale RHESSys output variables. More...

Functions
def	line_legend
	Use proxy objects to force lines in legend display. More...
def	simple_axis
def	plot_cdf

Variables
list	LINE_TYPES = ['solid', 'dashed', 'dashdot', 'dotted']
tuple	NUM_LINE_TYPES = len(LINE_TYPES)
int	INT_RESCALE = 100
tuple	VARIABLE_EXPR_RE = re.compile(r'\b([a-zA-z][a-zA-Z0-9_\.]+)\b')
tuple	RANDOM = random.randint(100000, 999999)
string	RECLASS_MAP_TMP = "patchzonalstats_cover_{0}"
string	STATS_MAP_TMP = "patchzonalstats_output_{0}"
list	methods
tuple	parser = argparse.ArgumentParser(description='Generate cummulative map of patch-scale RHESSys output variables')
string	help = 'The configuration file.'
list	choices = ['ultralight','light','normal','regular','book','medium','roman','semibold','demibold','demi','bold','heavy','extra bold','black']
string	default = 'regular'
tuple	args = parser.parse_args()
	configFile = None
tuple	context = Context(args.projectDir, configFile)
	linestyles = None
	outputFileNames = args.legend
tuple	metadata = RHESSysMetadata.readRHESSysEntries(context)
list	patchFilepaths = []
tuple	outputDir = os.path.abspath(args.outputDir)
string	outputFile = "{0}.pdf"
tuple	outputFilePath = os.path.join(outputDir, outputFile)
	variableLabels = args.variableName
list	variables = ['patchID']
tuple	m = VARIABLE_EXPR_RE.findall(args.outputVariable)
tuple	tmpDir = tempfile.mkdtemp()
tuple	reclassRule = os.path.join(tmpDir, 'reclass.rule')
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)
tuple	result
list	variablesList = []
tuple	data = np.genfromtxt(patchFilepath, names=True)
list	patchIDs = [ int(p) for p in data['patchID'] ]
tuple	expr = VARIABLE_EXPR_RE.sub(r'data["\1"]', args.outputVariable)
tuple	var = eval(expr)
	zones = args.zones
tuple	maps_to_delete = set()
string	reclass_map = "{0}_{1}"
	variable_scaled = variable*INT_RESCALE
tuple	variable_int = variable_scaled.astype(int)
tuple	reclass = open(reclassRule, 'w')
string	permrast = "{0}_{1}_{2}"
string	rMapcalcExpr = '$permrast=@$tmprast/float($scale)'
	scale = True)
tuple	pipe = grassLib.script.pipe_command('r.stats', flags='ln', input=STATS_MAP_TMP)
list	stats_scaled = []
tuple	stats = np.array(stats_scaled)
list	tmp_data = data[zone]
int	min_x = 0
tuple	max_x = max(np.max(datum), max_x)
int	fig_width = 4
tuple	fig = plt.figure(figsize=(fig_width, 3), dpi=80, tight_layout=True)
tuple	num_zones = len(zones)
list	var_label = variableLabels[i]
int	fig_num = i+1
tuple	ax = fig.add_subplot(1, num_zones, fig_num)
	linetype = linestyles,
	linewidth = args.linewidth,
	legend_fontsize = args.legendfontsize,
	fontweight = args.fontweight,
	axes_fontsize = args.axesfontsize,
	ticklabel_fontsize = args.ticklabelfontsize,
tuple	range = (min_x, max_x)

Detailed Description

Tool for calculating zonal statistics for patch-scale RHESSys output variables.

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

Copyright (c) 2014, 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. Configuration file must define the following sections and values: 'GRASS', 'GISBASE'
2. 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

Post conditions

None

Function Documentation

def PatchZonalStats.line_legend	(		ax,
			loc = 'lower right',
			fontsize = 6,
			fontweight = 'normal',
			frameon = False
	)

Use proxy objects to force lines in legend display.

def PatchZonalStats.plot_cdf	(		ax,
			data,
			legend_items,
			legend_loc = 'lower right',
			numbins = 1000,
			xlabel = None,
			ylabel = None,
			title = None,
			linetype = None,
			linewidth = None,
			range = None,
			fontweight = 'normal',
			legend_fontsize = 6,
			axes_fontsize = 8,
			ticklabel_fontsize = 6,
			fig_num = 1,
			log = False
	)

def PatchZonalStats.simple_axis	(		ax,
			noy = False
	)

Variable Documentation

tuple PatchZonalStats.args = parser.parse_args()

tuple PatchZonalStats.ax = fig.add_subplot(1, num_zones, fig_num)

PatchZonalStats.axes_fontsize = args.axesfontsize,

list PatchZonalStats.choices = ['ultralight','light','normal','regular','book','medium','roman','semibold','demibold','demi','bold','heavy','extra bold','black']

PatchZonalStats.configFile = None

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

dictionary PatchZonalStats.data = np.genfromtxt(patchFilepath, names=True)

int PatchZonalStats.default = 'regular'

tuple PatchZonalStats.expr = VARIABLE_EXPR_RE.sub(r'data["\1"]', args.outputVariable)

tuple PatchZonalStats.fig = plt.figure(figsize=(fig_width, 3), dpi=80, tight_layout=True)

int PatchZonalStats.fig_num = i+1

int PatchZonalStats.fig_width = 4

PatchZonalStats.fontweight = args.fontweight,

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

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

tuple PatchZonalStats.grassLib = GRASSLib(grassConfig=grassConfig)

string PatchZonalStats.help = 'The configuration file.'

int PatchZonalStats.INT_RESCALE = 100

PatchZonalStats.legend_fontsize = args.legendfontsize,

list PatchZonalStats.LINE_TYPES = ['solid', 'dashed', 'dashdot', 'dotted']

list PatchZonalStats.linestyles = None

PatchZonalStats.linetype = linestyles,

PatchZonalStats.linewidth = args.linewidth,

tuple PatchZonalStats.m = VARIABLE_EXPR_RE.findall(args.outputVariable)

tuple PatchZonalStats.maps_to_delete = set()

tuple PatchZonalStats.max_x = max(np.max(datum), max_x)

tuple PatchZonalStats.metadata = RHESSysMetadata.readRHESSysEntries(context)

list PatchZonalStats.methods

Initial value:

= ['average', 'mode', 'median', 'avedev', 'stddev', 'variance',
           'skewness', 'kurtosis', 'min', 'max', 'sum']

tuple PatchZonalStats.min_x = 0

tuple PatchZonalStats.NUM_LINE_TYPES = len(LINE_TYPES)

tuple PatchZonalStats.num_zones = len(zones)

tuple PatchZonalStats.outputDir = os.path.abspath(args.outputDir)

string PatchZonalStats.outputFile = "{0}.pdf"

PatchZonalStats.outputFileNames = args.legend

tuple PatchZonalStats.outputFilePath = os.path.join(outputDir, outputFile)

tuple PatchZonalStats.parser = argparse.ArgumentParser(description='Generate cummulative map of patch-scale RHESSys output variables')

list PatchZonalStats.patchFilepaths = []

list PatchZonalStats.patchIDs = [ int(p) for p in data['patchID'] ]

string PatchZonalStats.permrast = "{0}_{1}_{2}"

tuple PatchZonalStats.pipe = grassLib.script.pipe_command('r.stats', flags='ln', input=STATS_MAP_TMP)

tuple PatchZonalStats.RANDOM = random.randint(100000, 999999)

tuple PatchZonalStats.range = (min_x, max_x)

tuple PatchZonalStats.reclass = open(reclassRule, 'w')

string PatchZonalStats.reclass_map = "{0}_{1}"

string PatchZonalStats.RECLASS_MAP_TMP = "patchzonalstats_cover_{0}"

tuple PatchZonalStats.reclassRule = os.path.join(tmpDir, 'reclass.rule')

tuple PatchZonalStats.result

Initial value:

= grassLib.script.run_command('r.mask',
                                         input=args.mask,
                                         maskcats="1",
                                         flags="o")

string PatchZonalStats.rMapcalcExpr = '$permrast=@$tmprast/float($scale)'

PatchZonalStats.scale = True)

tuple PatchZonalStats.stats = np.array(stats_scaled)

string PatchZonalStats.STATS_MAP_TMP = "patchzonalstats_output_{0}"

list PatchZonalStats.stats_scaled = []

PatchZonalStats.ticklabel_fontsize = args.ticklabelfontsize,

list PatchZonalStats.tmp_data = data[zone]

tuple PatchZonalStats.tmpDir = tempfile.mkdtemp()

tuple PatchZonalStats.var = eval(expr)

list PatchZonalStats.var_label = variableLabels[i]

tuple PatchZonalStats.VARIABLE_EXPR_RE = re.compile(r'\b([a-zA-z][a-zA-Z0-9_\.]+)\b')

tuple PatchZonalStats.variable_int = variable_scaled.astype(int)

PatchZonalStats.variable_scaled = variable*INT_RESCALE

list PatchZonalStats.variableLabels = args.variableName

list PatchZonalStats.variables = ['patchID']

list PatchZonalStats.variablesList = []

PatchZonalStats.zones = args.zones