Tool for calculating zonal statistics for normalized 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}"

tuple	reclass = open(reclassRule, 'w')

string	rMapcalcExpr = '$reclass=int(($reclass/$norm)*$scale)'

	scale = True)

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

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)

	xlimit = args.xlimit)

Detailed Description

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

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

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

Configuration file must define the following sections and values: 'GRASS', 'GISBASE'
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 PatchZonalStatsNormalize.line_legend	(	ax,
		loc = `'lower right'`,
		fontsize = `6`,
		fontweight = `'normal'`,
		frameon = `False`
	)

Use proxy objects to force lines in legend display.

def PatchZonalStatsNormalize.plot_cdf	(	ax,
		data,
		legend_items,
		legend_loc = `'lower right'`,
		numbins = `1000`,
		xlimit = `None`,
		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 PatchZonalStatsNormalize.simple_axis	(	ax,
		noy = `False`
	)

Variable Documentation

tuple PatchZonalStatsNormalize.args = parser.parse_args()

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

PatchZonalStatsNormalize.axes_fontsize = args.axesfontsize,

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

PatchZonalStatsNormalize.configFile = None

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

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

int PatchZonalStatsNormalize.default = 'regular'

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

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

int PatchZonalStatsNormalize.fig_num = i+1

int PatchZonalStatsNormalize.fig_width = 4

PatchZonalStatsNormalize.fontweight = args.fontweight,

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

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

tuple PatchZonalStatsNormalize.grassLib = GRASSLib(grassConfig=grassConfig)

string PatchZonalStatsNormalize.help = 'The configuration file.'

int PatchZonalStatsNormalize.INT_RESCALE = 100

PatchZonalStatsNormalize.legend_fontsize = args.legendfontsize,

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

list PatchZonalStatsNormalize.linestyles = None

PatchZonalStatsNormalize.linetype = linestyles,

PatchZonalStatsNormalize.linewidth = args.linewidth,

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

tuple PatchZonalStatsNormalize.maps_to_delete = set()

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

tuple PatchZonalStatsNormalize.metadata = RHESSysMetadata.readRHESSysEntries(context)

list PatchZonalStatsNormalize.methods

Initial value:

1 = ['average', 'mode', 'median', 'avedev', 'stddev', 'variance',

2 'skewness', 'kurtosis', 'min', 'max', 'sum']

tuple PatchZonalStatsNormalize.min_x = 0

tuple PatchZonalStatsNormalize.NUM_LINE_TYPES = len(LINE_TYPES)

tuple PatchZonalStatsNormalize.num_zones = len(zones)

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

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

PatchZonalStatsNormalize.outputFileNames = args.legend

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

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

list PatchZonalStatsNormalize.patchFilepaths = []

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

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

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

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

tuple PatchZonalStatsNormalize.range = (min_x, max_x)

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

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

string PatchZonalStatsNormalize.RECLASS_MAP_TMP = "patchzonalstats_cover_{0}"

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

tuple PatchZonalStatsNormalize.result

Initial value:

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

string PatchZonalStatsNormalize.rMapcalcExpr = '$reclass=int(($reclass/$norm)*$scale)'

PatchZonalStatsNormalize.scale = True)

tuple PatchZonalStatsNormalize.stats = np.array(stats_scaled)

string PatchZonalStatsNormalize.STATS_MAP_TMP = "patchzonalstats_output_{0}"

list PatchZonalStatsNormalize.stats_scaled = []

PatchZonalStatsNormalize.ticklabel_fontsize = args.ticklabelfontsize,

list PatchZonalStatsNormalize.tmp_data = data[zone]

tuple PatchZonalStatsNormalize.tmpDir = tempfile.mkdtemp()

tuple PatchZonalStatsNormalize.var = eval(expr)

list PatchZonalStatsNormalize.var_label = variableLabels[i]

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

list PatchZonalStatsNormalize.variableLabels = args.variableName

list PatchZonalStatsNormalize.variables = ['patchID']

list PatchZonalStatsNormalize.variablesList = []

PatchZonalStatsNormalize.xlimit = args.xlimit)

PatchZonalStatsNormalize.zones = args.zones

Functions

Variables

Detailed Description

Pre conditions

Post conditions

Function Documentation

Variable Documentation