def main():
"""
Compute cell areas
"""
projinfo = grass.parse_command('g.proj', flags='g')
options, flags = grass.parser()
output = options['output']
units = options['units']
# First check if output exists
if len(grass.parse_command('g.list', type='rast',
pattern=options['output'])):
if not grass.overwrite():
grass.fatal("Raster map '" + options['output'] +
"' already exists. Use '--o' to overwrite.")
# Then compute
if projinfo['units'] == 'meters':
if units == 'm2':
grass.mapcalc(output+' = nsres() * ewres()')
elif units == 'km2':
grass.mapcalc(output+' = nsres() * ewres() / 10.^6')
elif projinfo['units'] == 'degrees':
if units == 'm2':
grass.mapcalc(output+' = ( 111195. * nsres() ) * \
( ewres() * '+str(np.pi/180.)+' * 6371000. * cos(y()) )')
elif units == 'km2':
grass.mapcalc(output+' = ( 111.195 * nsres() ) * \
( ewres() * '+str(np.pi/180.)+' * 6371. * cos(y()) )')
else:
print 'Units: ', + projinfo['units'] + ' not currently supported'
def getValOnPolys(inmap,poly,elev,dist,output):
n = getAreasNum(inmap)
for i in range(n-1):
# extract one feature from points set with cat value.
g.run_command("v.extract",input=poly,output="tmp",type="area",layer=1,new=-1,list=i+1,quiet=True,overwrite=True)
# Add a new column for storing a new value.
g.run_command("v.db.addcol",map="tmp",columns="val int")
# set default value as 1.
g.run_command("v.db.update",map="tmp",column="val",value=1,quiet=True)
# Redefine geographic region for procedure.
g.run_command("g.region",vect="tmp",quiet=True)
# convert vector map buffer to raster map buffer.
g.run_command("v.to.rast",input="tmp",output="tmprast",use="val",overwrite=True,quiet=True)
# get elevation on the raster buffer.
g.run_command("r.mapcalculator",amap="tmprast",bmap=elev,formula="A*B",outfile="tmprast2",overwrite=True,quiet=True)
pix = g.parse_command("r.stats",flags="1",input="tmprast2",nv="",fs=",",quiet=True)
res = "ID_" + str(i+1)
for j in pix.keys():
res = str(res) + str(j) + ","
# Write the result to text file
file = open(output + str(i+1) + ".txt", "w")
file.write(res)
file.write("\n")
file.close()
# Remove temporal features
g.parse_command("g.remove",vect="tmp",rast="tmprast,tmprast2",quiet=True)
# Set region with DEM.
g.parse_command("g.region",rast=elv,quiet=True)
def main(iters,bounds,padding,sampres,sampint,repeats,sampdist,prefix):
'''Main set of code for the sampling simulation'''
#set the sample universe size to the maximum boundaries, and set the resolution to match the sample size
grass.run_command("g.region", quiet = True, n=(bounds + padding + padding), s=0, e=(bounds + padding + padding), w=0, res=sampres)
# calculate the real binary presence/absence map for the input distribution (to compare with the sampled presabs)
realpresab = "%s_real_presab" % prefix
grass.mapcalc("${realpresab}=if(${sampdist} > 0, 1, 0)", overwrite = True, quiet = True, sampdist = sampdist, realpresab = realpresab)
#extract the number of squares that have at least one artifact
truepres = int(grass.parse_command("r.stats", quiet = True, flags="cn", input=realpresab, separator="=")["1"])
#set up statsfile
f = open('%s%s%s_stats.csv' % (os.getcwd(), os.sep, prefix), 'w+')
f.write("Iteration,Positives,True Positives,Difference,Pcnt Difference,R,R2\n")
f.flush()
#initiate the outer loop, which will randomly rotate/move the sampling grid within the sampling universe
pad = len(str(repeats)) # set the zfill pad to match the number of repeats
for x in range(repeats):
grass.message("Iteration: %s" % (x + 1))
jitt1 = random.randint(0,sampint) # get a random seed for the Y offset
jitt2 = random.randint(0,sampint) # get a random seed for the X offset
rot = random.randint(0,360) # get a random seed for the grid rotation
#reset the sample universe size and resolution
grass.run_command("g.region", quiet = True, n=(bounds + padding - jitt1), s=padding - jitt1, e=(bounds + padding - jitt2), w=padding - jitt2, res=sampres)
#make the sampling frame from the sampling interval, the current jitter, and the current rotation
init_grid = "%s_%s_vgridpts" % (prefix,str(x + 1).zfill(pad))
init_sqrs = "%s_%s_gridpts" % (prefix,str(x + 1).zfill(pad))
grass.run_command("v.mkgrid", quiet = True, overwrite = True, map=init_grid, box="%s,%s" % (sampint,sampint), angle=rot, type="point")
grass.run_command("v.to.rast", quiet = True, overwrite = True, input=init_grid, type="point", output=init_sqrs, use="val")
# zoom out to the padding distance
grass.run_command("g.region", quiet = True, n=(bounds + padding + padding), s=0, e=(bounds + padding + padding), w=0, res=sampres)
grass.run_command("r.null", quiet = True, map=init_sqrs, null=0)
#initiate and start inner loop for the additive sammpling regime
for i in range(iters):
if i + 1 == 1:
old_sqrs = init_sqrs
else:
old_sqrs = new_sqrs
new_sqrs = "%s_itr%s" % (prefix, str(i + 1).zfill(2))
grass.mapcalc("${new_sqrs}=eval(a=if(${old_sqrs} > 0 && ${sampdist} > 0, 1, 0), b=if(${old_sqrs}[1,0] == 1 || ${old_sqrs}[0,1] == 1 || ${old_sqrs}[-1,0] == 1 || ${old_sqrs}[0,-1] == 1, 1, 0), c=if(b > 0 && ${sampdist} > 0, 1, a), if(isnull(c),0,c))", quiet = True, overwrite = True, old_sqrs = old_sqrs, new_sqrs = new_sqrs, sampdist = sampdist)
# rename last map to save it
outmap = "%s_%s" % (prefix,str(x + 1).zfill(pad))
grass.run_command("g.rename", quiet = True, raster="%s,%s" % (new_sqrs,outmap))
# pull some stats
presab = grass.parse_command("r.stats", quiet = True,flags="cn", input=outmap, separator="=")
try:
pres = int(presab['1'])
except:
pres = 0
R = grass.parse_command('r.regression.line', flags='g', mapx=realpresab, mapy=outmap)["R"]
f.write("%s,%s,%s,%s,%s,%s,%s\n" % (x + 1,pres,truepres,truepres - pres,(truepres - pres)/float(truepres),R, float(R) * float(R)))
f.flush()
#clean up
f.close()
grass.run_command("g.remove", quiet = True, flags = 'f', type = 'raster', pattern = "*_itr*")
def ImportMap(self, map, column):
""" Imports GRASS map as SpatialPointsDataFrame and adds x/y columns to attribute table.
Checks for NULL values in the provided column and exits if they are present."""
#@NOTE: new way with R - as it doesn't alter original data
Rpointmap = robjects.r.readVECT(map, type='point')
# checks if x,y columns are present in dataframe. If they do are present, but with different names,
# they'll be duplicated.
if "x" not in robjects.r.names(Rpointmap):
# extract coordinates with S4 method
coordinatesPreDF = robjects.r['as.data.frame'](robjects.r.coordinates(Rpointmap))
coordinatesDF = robjects.r['data.frame'](x=coordinatesPreDF.rx('coords.x1')[0],
y=coordinatesPreDF.rx('coords.x2')[0])
# match coordinates with data slot of SpatialPointsDataFrame - maptools function
# match is done on row.names
Rpointmap = robjects.r.spCbind(Rpointmap, coordinatesDF)
# GRASS checks for null values in the chosen column. R can hardly handle column as a variable,
# looks for a hardcoded string.
cols = grass.vector_columns(map=map, layer=1)
nulls = int(grass.parse_command('v.univar',
map=map,
column=column,
type='point',
parse=(grass.parse_key_val,
{'sep': ': '}
)
)['number of NULL attributes'])
if nulls > 0:
grass.fatal(
_("%d NULL value(s) in the selected column - unable to perform kriging.") %
nulls)
return Rpointmap
def get_time_steps():
indexmaps = grass.parse_command('g.list', type='vect', patt='drainage_basins_??????').keys()
indexmaps = sorted(indexmaps)[::-1]
ages = []
for indexmap in indexmaps:
ages.append( str(indexmap.split('_')[-1]) )
return ages
def CompositionMetrics(self):
'''Overlay landcover with viewshed, calculate visible cover,
and return percentage of landcover classes in viewshed
'''
## Compute statistics ##
stat = gscript.parse_command('r.stats',
input=self.out_landuse,
flags='apn',
separator='comma',
overwrite=True)
cleanDic = {}
areaList = []
totarea = 0
for item in stat.keys():
cat = int(item.split(",")[0])
area = item.split(",")[1]
percent = item.split(",")[2]
cleanDic[cat] = percent.strip("%").strip("u")
totarea += float(area)
print totarea
areaList = []
for item in sorted(self.landuse.keys()):
if item in cleanDic.keys():
percent = cleanDic[item]
areaList.append(str(percent))
else:
areaList.append("0")
areaList.append(str(totarea))
return areaList
def set_region_from_timeseries(self, timeseries):
"""Sets computational region for rendering.
This function sets the computation region from the extent of
a space-time dataset by using its bounding box and resolution.
If user specified the name of saved region during object's initialization,
the provided region is used. If it's not specified
and use_region=True, current region is used.
"""
if self._saved_region:
self._env["GRASS_REGION"] = gs.region_env(
region=self._saved_region, env=self._env)
return
if self._use_region:
# use current
return
# Get extent, resolution from space time dataset
info = gs.parse_command("t.info",
input=timeseries,
flags="g",
env=self._env)
# Set grass region from extent
self._env["GRASS_REGION"] = gs.region_env(
n=info["north"],
s=info["south"],
e=info["east"],
w=info["west"],
nsres=info["nsres_min"],
ewres=info["ewres_min"],
)
def get_variance(mapname, raster):
"""Calculate intra-segment variance of the values of the given raster"""
# current_process name contains '-' which can cause problems so we replace
# with '_'
temp_map = "isegmentuspo_temp_variance_map_%d_%s" % (
os.getpid(),
current_process().name.replace("-", "_"),
)
gscript.run_command(
"r.stats.zonal",
base=mapname,
cover=raster,
method="variance",
output=temp_map,
overwrite=True,
quiet=True,
)
univar = gscript.parse_command("r.univar",
map_=temp_map,
flags="g",
quiet=True)
var = float(univar["mean"])
gscript.run_command("g.remove",
type_="raster",
name=temp_map,
flags="f",
quiet=True)
return var
def citation_for_module(name, add_grass=False):
"""Provide dictionary of citation values for a module"""
path = documentation_filename(name)
# derive core strings from lhmpom:
# NAME / AUTHOR / LAST CHANGED / COPYRIGHT: Years + Entity
text = open(path).read()
g_version = gs.parse_command("g.version", flags="g")
# using default empty value, this way we use just if d['k']
# to check presence and non-emptiness at the same time
citation = defaultdict(str)
citation["module"] = name
citation["grass-version"] = g_version["version"]
citation["grass-build-date"] = g_version["build_date"]
citation["authors"] = get_authors_from_documentation(text)
citation["year"] = get_year_from_documentation(text)
code_url, code_history_url = get_code_urls_from_documentation(text)
citation["code-url"] = code_url
citation["url-code-history"] = code_history_url
if add_grass:
scope = "Use the following to cite the whole GRASS GIS"
citation["references"] = [grass_cff_reference(g_version, scope=scope)]
return citation
def Analyze(self):
gscript.run_command('i.segment',
group=self.group,
output=self.segment,
threshold=0.3,
minsize=50,
env=self.env)
gscript.run_command('r.clump',
input=self.segment,
output=self.segment_clump,
env=self.env)
gscript.run_command('i.smap',
group=self.group,
subgroup=self.group,
signaturefile=self.signature,
output=self.classification,
goodness=self.reject,
env=self.env)
percentile = float(
gscript.parse_command('r.univar',
flags='ge',
map=self.reject,
env=self.env)['percentile_90'])
gscript.mapcalc(
'{new} = if({classif} < {thres}, {classif}, null())'.format(
new=self.filtered_classification,
classif=self.classification,
thres=percentile),
env=self.env)
gscript.run_command('r.stats.quantile',
base=self.segment_clump,
cover=self.filtered_classification,
output=self.output,
env=self.env)
def OnRegression(self, event):
"""Displays regression information in messagebox
"""
message = []
title = _('Regression Statistics for Scatterplot(s)')
for rpair in self.rasterList:
if isinstance(rpair, tuple) == False: continue
rast1, rast2 = rpair
rast1 = rast1.split('@')[0]
rast2 = rast2.split('@')[0]
ret = grass.parse_command('r.regression.line',
mapx = rast1,
mapy = rast2,
flags = 'g', quiet = True,
parse = (grass.parse_key_val, { 'sep' : '=' }))
eqtitle = _('Regression equation for raster map <%(rast1)s> vs. <%(rast2)s>:\n\n') % \
{ 'rast1' : rast1,
'rast2' : rast2 }
eq = ' %s = %s + %s(%s)\n\n' % (rast2, ret['a'], ret['b'], rast1)
num = 'N = %s\n' % ret['N']
rval = 'R = %s\n' % ret['R']
rsq = 'R-squared = %f\n' % pow(float(ret['R']), 2)
ftest = 'F = %s\n' % ret['F']
str = eqtitle + eq + num + rval + rsq + ftest
message.append(str)
stats = PlotStatsFrame(self, id = wx.ID_ANY, message = message,
title = title)
if stats.Show() == wx.ID_CLOSE:
stats.Destroy()
def main():
# process command options
input = options['input']
if not gs.find_file(input)['file']:
gs.fatal(_("Raster map <%s> not found") % input)
output = options['output']
if gs.find_file(output)['file'] and not gs.overwrite():
gs.fatal(_("Output map <%s> already exists") % output)
# set aside region for internal use
gs.use_temp_region()
# subset input if desired
region = options.get('region')
if region:
if not gs.find_file(region)['file']:
gs.fatal(_("Raster map <%s> not found") % region)
gs.message("Setting region to %s" % region, flag='i')
gs.run_command('g.region', rast=region, align=input)
else:
gs.message("Using existing GRASS region", flag='i')
gs.debug('='*50)
gs.debug('\n'.join(gs.parse_command('g.region', 'p').keys()))
gs.debug('='*50)
calculate_noise(input, output)
# restore original region
gs.del_temp_region()
return None
def import_raster(filename, module, args):
mapname = _map_name(filename)
gs.message(_("Processing <{}>...").format(mapname))
if module == "r.import":
kv = gs.parse_command("g.proj", flags="j")
if kv["+proj"] == "longlat":
args["resolution"] = "estimated"
else:
args["resolution"] = "value"
args["resolution_value"] = _raster_resolution(filename)
try:
gs.run_command(module, input=filename, output=mapname, **args)
if gs.raster_info(mapname)["datatype"] in ("FCELL", "DCELL"):
gs.message("Rounding to integer after reprojection")
gs.use_temp_region()
gs.run_command("g.region", raster=mapname)
gs.run_command(
"r.mapcalc",
quiet=True,
expression="tmp_%s = round(%s)" % (mapname, mapname),
)
gs.run_command(
"g.rename",
quiet=True,
overwrite=True,
raster="tmp_%s,%s" % (mapname, mapname),
)
gs.del_temp_region()
gs.raster_history(mapname)
except CalledModuleError as e:
pass # error already printed
def create_heatmaps(vectors, background_ortho, radius, width, height):
os.environ['GRASS_FONT'] = '/usr/share/fonts/truetype/freefont/FreeSansBold.ttf'
names = []
for vector in vectors:
gscript.run_command('v.kernel', input=vector, output=vector + '_kernel', radius=radius, overwrite=True, quiet=True)
names.append(vector + '_kernel')
gscript.write_command('r.colors', map=names, rules='-', stdin='0% white\n10% yellow\n40% red\n100% magenta')
maxdens = float(gscript.parse_command('r.univar', map=names, flags='g')['max'])
for vector in vectors:
gscript.run_command('d.mon', start='cairo', output='foreground_' + vector + '_kernel' + '.png',
width=width, height=height, overwrite=True)
gscript.run_command('d.rast', map=vector + '_kernel')
gscript.run_command('d.mon', stop='cairo')
# background
gscript.run_command('d.mon', start='cairo', output='background_' + vector + '_kernel' + '.png',
width=width, height=height, overwrite=True)
gscript.run_command('d.rast', map=background_ortho)
gscript.run_command('d.legend', flags='t', raster=vector + '_kernel', label_step=0.5, digits=1, range=[0, maxdens], at=[3,40,3,6], color='white')
gscript.run_command('d.mon', stop='cairo')
# put together with transparency
foreground = Image.open('foreground_' + vector + '_kernel' + '.png')
background = Image.open('background_' + vector + '_kernel' + '.png')
foreground = foreground.convert("RGBA")
datas = foreground.getdata()
newData = []
for item in datas:
intens = item[0] + item[1] + item[2]
newData.append((item[0], item[1], item[2], min(765-intens, 200)))
foreground.putdata(newData)
background.paste(foreground, (0, 0), foreground)
background.save('heatmap_{v}.png'.format(v=vector), "PNG")
gscript.try_remove('foreground_' + vector + '_kernel' + '.png')
gscript.try_remove('background_' + vector + '_kernel' + '.png')
def main(out,maps,ms,keepdtype,ndv,createopts):
# set mapset
set_mapset(ms)
# turn categorical names into dummy names
maps=parse_feature_names(maps)
# make desired output_mask
# slopes above 55 degrees masked and points on top of water or snow masked
make_output_mask('(slope < 55) && (lcc == 2 || lcc == 3)','buffered_basin_border')
# run separately for each map
for m in maps:
dtype = gscript.parse_command('r.info',flags='g',map=m)['datatype']
if dtype == 'CELL':
export_maps([m],out,'Byte',keepdtype,ndv,createopts)
else:
export_maps([m],out,'Float32',keepdtype,ndv,createopts)
# remove group and mask
gscript.run_command('g.remove',
type='group',
name='to_export',
quiet=True,
flags='f')
drop_mask()
def mkContours(self):
"""Make a contour map of the given DEM, in the given catchment"""
# check what breaks to take, if int find nice breaks, if list take as breaks
if type(self.contours) is int:
interval = self.contours
# get stats of DEM for nice breaks
stats=grass.parse_command('r.univar',map=self.elevation,flags='g')
# make nice breaks
minelev = int(float(stats['min'])/interval+1)*interval
maxelev = int(float(stats['max'])/interval)*interval
breaks = range(minelev,maxelev+1,interval)
else:
breaks = self.contours
if len(breaks)<2:
grass.fatal('Need at least 2 contour breaks: %s \nRange of elevation: %s - %s' %(breaks,stats['min'],stats['max']))
grass.message(('Contour breaks:',str(breaks)))
# form mapcalc expression and execute
exp = self.contourrast+'= if(%s<%s,1)' %(self.elevation, breaks[0]) # for the first, smaller than
for b in breaks: exp+='+ if(%s>=%s,1)' %(self.elevation,b) # for all greater eq than
grass.mapcalc(exp, overwrite=True)
grass.message(('Calculated contourmap: %s' %self.contourrast))
return
def main():
infile = options['input']
value = options['value']
mode = options['mode']
outfile = options['output']
global method
method = options['method']
clumped = flags['c']
diagonal = flags['d']
# check for unsupported locations
in_proj = grass.parse_command('g.proj', flags='g')
if in_proj['unit'].lower() == 'degree':
grass.fatal(_("Latitude-longitude locations are not supported"))
if in_proj['name'].lower() == 'xy_location_unprojected':
grass.fatal(_("xy-locations are not supported"))
# check lesser and greater parameters
limit = float(value)
if mode == 'greater' and method == 'rmarea':
grass.fatal(_("You have to specify mode='lesser' with method='rmarea'"))
if not grass.find_file(infile)['name']:
grass.fatal(_("Raster map <%s> not found") % infile)
if method == 'reclass':
reclass(infile, outfile, limit, clumped, diagonal, mode == 'lesser')
elif method == 'rmarea':
rmarea(infile, outfile, limit, in_proj['meters'])
grass.message(_("Generating output raster map <%s>...") % outfile)
def main():
"""
RichDEM flat resolution: give a gentle slope
"""
# lazy import RICHDEM
try:
import richdem as rd
except:
g.message(
flags="e",
message=("RichDEM not detected. Install pip3 and " +
"then type at the command prompt: " +
'"pip3 install richdem".'),
)
_input = options["input"]
_output = options["output"]
# Check for overwrite
_rasters = np.array(gscript.parse_command("g.list", type="raster").keys())
if (_rasters == _output).any():
g.message(flags="e", message="output would overwrite " + _output)
dem = garray.array(_input, null=np.nan)
rd_input = rd.rdarray(dem, no_data=np.nan)
rd_output = rd.ResolveFlats(rd_input)
dem[:] = rd_output[:]
dem.write(_output, overwrite=gscript.overwrite())
def get_size(vector):
tmpvector = "tmp_getsize_%s" % str(os.getpid())
rm_vectors.append(tmpvector)
grass.run_command("g.copy",
vector="%s,%s" % (vector, tmpvector),
overwrite=True,
quiet=True)
if len(grass.vector_db(tmpvector)) == 0:
grass.run_command("v.db.addtable", map=tmpvector, quiet=True)
grass.run_command("v.db.addcolumn",
map=tmpvector,
columns="tmparea DOUBLE PRECISION",
quiet=True)
grass.run_command(
"v.to.db",
map=tmpvector,
columns="tmparea",
option="area",
units="meters",
quiet=True,
overwrite=True,
)
sizeselected = grass.parse_command("v.db.select", map=tmpvector, flags="v")
sizesstr = [
x.split("|")[1:] for x in sizeselected if x.startswith("tmparea|")
][0]
sizes = [float(x) for x in sizesstr]
return sum(sizes)
def get_size(vector):
tmpvector = 'tmp_getsize_%s' % str(os.getpid())
rm_vectors.append(tmpvector)
grass.run_command('g.copy',
vector="%s,%s" % (vector, tmpvector),
quiet=True)
if len(grass.vector_db(tmpvector)) == 0:
grass.run_command('v.db.addtable', map=tmpvector, quiet=True)
grass.run_command('v.db.addcolumn',
map=tmpvector,
columns="tmparea DOUBLE PRECISION",
quiet=True)
grass.run_command('v.to.db',
map=tmpvector,
columns='tmparea',
option='area',
units='meters',
quiet=True,
overwrite=True)
sizeselected = grass.parse_command('v.db.select', map=tmpvector, flags="v")
sizesstr = [
x.split('|')[1:] for x in sizeselected if x.startswith('tmparea|')
][0]
sizes = [float(x) for x in sizesstr]
return sum(sizes)
def preprocess(reflbandnames, panbandnames, dataset, outputraster, scene):
options, flags = grass.parser()
pansuffix = ['red', 'green', 'blue']
print os.environ
importregex = re.compile('.*[.]TIF')
counter = 1
for file in os.listdir(dataset):
if re.search(importregex, file):
if len(file) == 29:
num = file[23] + file[24]
else:
num = file[23]
read2_command('r.external', input=dataset + '/' + file, output='B' + num, overwrite=True, flags='e')
counter = counter + 1
for file in os.listdir(dataset):
if fnmatch.fnmatch(file, '*.txt'):
mtl = file
metfile = os.path.join(dataset, mtl)
read2_command('i.landsat.toar', input='B', output='B_refl', metfile=metfile, sensor='oli8', overwrite=True)
print('reflectance calculated')
read2_command('r.colors', map=reflbandnames, flags='e', color='grey')
print('histograms equalized')
read2_command('i.colors.enhance', red=reflbandnames[0], green=reflbandnames[1], blue=reflbandnames[2])
print('colors enhanced')
# pansharpen
read2_command('i.fusion.brovey', ms3=reflbandnames[0], ms2=reflbandnames[1], ms1=reflbandnames[2],
pan=panbandnames[3], overwrite=True, flags='l', output_prefix='brov')
pannames = ['brov.' + s for s in pansuffix]
pannames255 = [s + '_255' for s in pannames]
print('pansharpening and composition achieved')
read2_command('g.region', raster=pannames)
read2_command('r.colors', map=pannames, flags='e', color='grey')
for raster in pannames:
minmax = grass.parse_command('r.info', map=raster, flags='r')
print(minmax)
newrast = raster + '_255'
grass.write_command('r.recode', input=raster, output=newrast, rules='-',
stdin=minmax[u'min'] + ':' + minmax[u'max'] + ':0:255',
overwrite=True)
print('rasters recoded to CELL type')
# equalize colors once again
read2_command('r.colors', map=[pannames255[0], pannames255[1], pannames255[2]], flags='e', color='grey')
read2_command('i.colors.enhance', red=pannames255[0], green=pannames255[1], blue=pannames255[2])
#read2_command('r.composite', red=pannames[0], green=pannames[1], blue=pannames[2], output='comp',
# overwrite=True)
# create imagery group
read2_command('i.group', group='pangroup876', subgroup='pangroup876', input=pannames255)
print('created imagery group')
read2_command('r.out.gdal', input='pangroup876', output=outputraster,
overwrite=True, format='GTiff', type='Int32', flags='f')
def main():
vector = options['input']
output = options['output']
# JL Handling Invalid transect_spacing parameter
try:
transect_spacing = float(options['transect_spacing'])
except:
grass.fatal(_("Invalid transect_spacing value."))
if transect_spacing == 0.0:
grass.fatal(_("Zero invalid transect_spacing value."))
dleft = options['dleft']
dright = options['dright']
shape = options['type']
print dleft, transect_spacing
if not dleft:
dleft = transect_spacing
else:
# JL Handling Invalid dleft parameter
try:
dleft = float(dleft)
except:
grass.fatal(_("Invalid dleft value."))
if not dright:
dright = transect_spacing
else:
# JL Handling Invalid dright parameter
try:
dright = float(dright)
except:
grass.fatal(_("Invalid dright value."))
# check if input file does not exists
if not grass.find_file(vector, element='vector')['file']:
grass.fatal(_("<%s> does not exist.") % vector)
# check if output file exists
if grass.find_file(output,
element='vector')['mapset'] == grass.gisenv()['MAPSET']:
if not grass.overwrite():
grass.fatal(_("output map <%s> exists") % output)
#JL Is the vector a line and does if have at least one feature?
info = grass.parse_command('v.info', flags='t', map=vector)
if info['lines'] == '0':
grass.fatal(_("vector <%s> does not contain lines") % vector)
#################################
v = loadVector(vector)
transect_locs = get_transects_locs(v, transect_spacing)
temp_map = tempmap()
if shape == 'line' or not shape:
transect_ends = get_transect_ends(transect_locs, dleft, dright)
writeTransects(transect_ends, temp_map)
elif shape == 'area':
transect_ends = get_transect_ends(transect_locs, dleft, dright)
writeQuads(transect_ends, temp_map)
else:
writePoints(transect_locs, temp_map)
grass.run_command('v.category', input=temp_map, output=output, type=shape)
grass.run_command('g.remove', vect=temp_map)
def get_time_steps():
indexmaps = grass.parse_command('g.list', type='vect', patt='drainage_basins_??????').keys()
indexmaps = sorted(indexmaps)[::-1]
ages = []
for indexmap in indexmaps:
ages.append( str(indexmap.split('_')[-1]) )
#ages = ages[-25:] # TEMPORARY HACK-EY TO FINISH G12
return ages
def main():
"""
Compute cell areas
"""
projinfo = grass.parse_command("g.proj", flags="g")
options, flags = grass.parser()
output = options["output"]
units = options["units"]
# First check if output exists
if len(grass.parse_command("g.list", type="rast", pattern=options["output"])):
if not grass.overwrite():
grass.fatal(
"Raster map '"
+ options["output"]
+ "' already exists. Use '--o' to overwrite."
)
projunits = str(projinfo["units"]) # Unicode to str
# Then compute
if (projunits == "meters") or (projunits == "Meters"):
if units == "m2":
grass.mapcalc(output + " = nsres() * ewres()")
elif units == "km2":
grass.mapcalc(output + " = nsres() * ewres() / 10.^6")
elif (projunits == "degrees") or (projunits == "Degrees"):
if units == "m2":
grass.mapcalc(
output
+ " = ( 111195. * nsres() ) * \
( ewres() * "
+ str(np.pi / 180.0)
+ " * 6371000. * cos(y()) )"
)
elif units == "km2":
grass.mapcalc(
output
+ " = ( 111.195 * nsres() ) * \
( ewres() * "
+ str(np.pi / 180.0)
+ " * 6371. * cos(y()) )"
)
else:
print("Units: ", projunits, " not currently supported")
def render_2d(envs):
# set rendering parameters
brighten = 0 # percent brightness of shaded relief
render_multiplier = 1 # multiplier for rendering size
whitespace = 1.5
fontsize = 36 * render_multiplier # legend font size
legend_coord = (10, 50, 1, 4) # legend display coordinates
zscale = 1
# create rendering directory
render = os.path.join(gisdbase, location, 'rendering')
if not os.path.exists(render):
os.makedirs(render)
for mapset in simulations:
# change mapset
gscript.read_command('g.mapset', mapset=mapset, location=location)
info = gscript.parse_command('r.info', map='elevation', flags='g')
width = int(info.cols) * render_multiplier * whitespace
height = int(info.rows) * render_multiplier
# render net difference
gscript.run_command('d.mon',
start=driver,
width=width,
height=height,
output=os.path.join(
render,
mapset + '_' + 'net_difference' + '.png'),
overwrite=1)
gscript.write_command('r.colors',
map='net_difference',
rules='-',
stdin=difference_colors)
gscript.run_command('r.relief',
input='elevation',
output='relief',
altitude=90,
azimuth=45,
zscale=zscale,
env=envs[mapset])
gscript.run_command('d.shade',
shade='relief',
color='net_difference',
brighten=brighten)
gscript.run_command('d.legend',
raster='net_difference',
fontsize=fontsize,
at=legend_coord)
gscript.run_command('d.mon', stop=driver)
try:
# stop cairo monitor
gscript.run_command('d.mon', stop=driver)
except CalledModuleError:
pass
def get_autocorrelation(mapname, raster, neighbordict, method):
"""Calculate either Moran's I or Geary's C for values of the given raster"""
raster_vars = gscript.parse_command("r.univar",
map_=raster,
flags="g",
quiet=True)
global_mean = float(raster_vars["mean"])
univar_res = gscript.read_command(
"r.univar",
flags="t",
map_=raster,
zones=mapname,
out="-",
sep="comma",
quiet=True,
)
means = {}
mean_diffs = {}
firstline = True
for line in univar_res.splitlines():
l = line.split(",")
if firstline:
i = l.index("mean")
firstline = False
else:
means[l[0]] = float(l[i])
mean_diffs[l[0]] = float(l[i]) - global_mean
sum_sq_mean_diffs = sum(x**2 for x in mean_diffs.values())
total_nb_neighbors = 0
for region in neighbordict:
total_nb_neighbors += len(neighbordict[region])
N = len(means)
sum_products = 0
sum_squared_differences = 0
for region in neighbordict:
region_value = means[region] - global_mean
neighbors = neighbordict[region]
nb_neighbors = len(neighbors)
for neighbor in neighbors:
neighbor_value = means[neighbor] - global_mean
sum_products += region_value * neighbor_value
sum_squared_differences = (means[region] - means[neighbor])**2
if method == "moran":
autocor = (float(N) / total_nb_neighbors) * (float(sum_products) /
sum_sq_mean_diffs)
elif method == "geary":
autocor = (float(N - 1) / (2 * total_nb_neighbors)) * (
float(sum_squared_differences) / sum_sq_mean_diffs)
return autocor
def comp_rasters(directory, cleanup=False, png=False):
for item in os.listdir(directory):
path = os.path.join(directory, item)
if not os.path.isdir(path) or path.endswith('gdb'):
continue
ds = gdal.Open(path)
if ds is None:
continue
# blacklist
if item in ['fl_dir']:
continue
# link arcgis raster to GRASS
arcgis = '{}_arcgis'.format(item)
gs.run_command('r.external',
input=path, output=arcgis, flags='o'
)
gs.run_command('r.colors',
map=arcgis, raster=item
)
gs.run_command('g.region',
raster=item
)
diff = '{}_diff'.format(item)
gs.run_command('r.mapcalc',
expression='{} = {} - {}'.format(diff, arcgis, item)
)
gs.run_command('r.colors',
map=diff, color='diff'
)
if png:
gs.run_command('d.mon',
start='cairo', output=os.path.join(OUTPUT, '{}.png'.format(item))
)
gs.run_command('d.rast.leg',
map=diff
)
gs.run_command('d.mon',
stop='cairo'
)
print('{sep}{nl}{map}{nl}{sep}{nl}'.format(sep='-' * 80, nl=os.linesep, map=item))
stats = gs.parse_command('r.univar',
flags='g',
map=diff
)
for key in ('min', 'max', 'range', 'mean'):
print ('{}={}'.format(key, stats[key]))
if abs(float(stats['mean'])) < 1e-4:
print ("-> OK")
else:
print ("-> KO")
if cleanup:
gs.run_command('g.remove',
type='raster', name=','.join(arcgis, diff), flags='f'
)
def get_maxim_value(self):
'''
Getting the maximum patch size of the map
This is not working for some reason, but the overall script is working
'''
stats = grass.parse_command('r.univar', map=self.patch_map, flags='g')
self.raster_max = int(stats['max'])
def reg_2deg(input = '', size = 2):
# get region center
reg = grass.parse_command('g.region', input = input, flags = 'c')
lat = float()
lon = float()
g.region(n = lat + size/2, s = lat - size/2, w = lon - size/2, e = lon + size/2,
align = input, flags = 'ap')
def main():
# Get the options
_input = options["input"]
output = options["output"]
expression = options["expression"]
base = options["basename"]
method = options["method"]
nprocs = int(options["nprocs"])
register_null = flags["n"]
spatial = flags["s"]
new_flags = ""
if register_null:
new_flags = "n"
if spatial:
new_flags = new_flags + "s"
# get list of bands available in the input strds
t_info = grass.parse_command('t.info', input=_input, flags='g')
input_bands = t_info["semantic_labels"].split(',')
nbands = len(input_bands)
# find needed bands in formula: if "data[0]" in formula:
# go through the list of bands and replace (str.replace(old, new)
# in the formula e.g. data[0] with (input_strds + '.' + bandref[0])
counter = 0
new_inputs = []
band_used = [False for i in range(nbands)]
while counter < nbands:
fstr = "data[" + str(counter) + "]"
bandname = input_bands[counter]
data_band = ("data.%s") % (bandname)
if fstr in expression:
band_used[counter] = True
newstr = ("%s.%s") % (_input, bandname)
new_inputs.append(newstr)
expression = expression.replace(fstr, newstr)
elif data_band in expression:
band_used[counter] = True
newstr = ("%s.%s") % (_input, bandname)
new_inputs.append(newstr)
expression = expression.replace(data_band, newstr)
else:
band_used[counter] = False
counter = counter + 1
# print(expression)
grass.run_command('t.rast.mapcalc',
inputs=(',').join(new_inputs),
expression=expression,
method=method,
output=output,
basename=base,
nprocs=nprocs,
flags=new_flags)
def run_view(scanned_elev, blender_path, env, **kwargs):
# regression
group = 'color'
before = 'scan_saved'
elev_threshold = 20
color_threshold = 150
dist_threshold = 30
change = 'change'
arrow = 'arrow'
arrow3d = 'arrow3d'
arrow_final = 'arrow_final'
ff = gscript.find_file(name=arrow_final, element='vector')
old_points = []
if ff and ff['fullname']:
old_p = gscript.read_command('v.out.ascii', input=ff['fullname'], format='standard', type='line', env=env).strip().splitlines()
for op in old_p:
line = op.strip().split()
if line == ['1', '1']:
continue
try:
x = float(line[0])
y = float(line[1])
z = float(line[2])
old_points.append((x, y, z))
except ValueError:
continue
except IndexError as e:
print (line)
print (e)
continue
reg_params = gscript.parse_command('r.regression.line', flags='g', mapx=before, mapy=scanned_elev, env=env)
gscript.mapcalc(exp='{new} = if(({a} + {b} * {after}) - {before} > {thr}, 1, null())'.format(a=reg_params['a'],
b=reg_params['b'], after=scanned_elev, before=before, thr=elev_threshold, new=change), env=env)
#gscript.parse_command('r.univar', map=[group + '_r', group + '_g', group + '_b'], output=, flags='t', zones=, env=env)
gscript.mapcalc(exp='{new} = if({change} && ({r} + {g} + {b}) / 3. >= {th}, 1, 2)'.format(new=arrow, change=change, th=color_threshold,
r=group + '_r', g=group + '_g', b=group + '_b'), env=env)
gscript.run_command('r.volume', input=arrow, clump=arrow, centroids=arrow, env=env)
gscript.run_command('v.drape', input=arrow, output=arrow3d, elevation=before, method='bilinear', env=env)
points = gscript.read_command('v.out.ascii', input=arrow3d, env=env).strip()
if points:
new_points = []
linetext = 'L 2 1\n'
for p in points.splitlines():
x, y, z, c = p.split('|')
new_points.append((float(x), float(y), float(z)))
linetext += '{} {} {}\n'.format(x, y, z)
linetext += '1 1\n'
# compare old and new
if not old_points or (dist(old_points[0], new_points[0]) > dist_threshold or dist(old_points[1], new_points[1]) > dist_threshold):
print ('write')
gscript.write_command('v.in.ascii', stdin=linetext, input='-', output=arrow_final, format='standard', flags='zn', env=env)
blender_export_vector(vector=arrow_final, name='vantage', z=True, vtype='line', path=blender_path, time_suffix=False, env=env)
def total_light_index(ntl_image):
"""
Evaluation index (TLI) which represents the sum of grey values in an area.
"""
univar = grass.parse_command("r.univar",
map=ntl_image,
flags='g',
parse=(grass.parse_key_val,
{'sep': '='}))
return float(univar['sum'])
def epsg_location(request, response):
"""Check whether the EPSG of a mapset corresponds the specified one."""
from grass.script import parse_command
g_proj = parse_command('g.proj', flags='g')
assert g_proj['epsg'] == '5514', \
'Error in creating a GRASS location based on an EPSG code'
return response
def file_location(request, response):
"""Check whether the datum of a mapset corresponds the file one."""
from grass.script import parse_command
g_proj = parse_command('g.proj', flags='g')
assert g_proj['datum'] == 'wgs84', \
'Error in creating a GRASS location based on a file'
return response
def isExists(FeatNam,FeatType):
# 'Delete temporal objects.'
result = False
vlist = dict.keys(g.parse_command('db.tables',flags='p'))
for i in range(len(vlist)):
# Delete the final result if exists.
if vlist[i] == 'public.'+ str(FeatNam):
result = True
print(result)
return(result)
def Calibrate(self, event):
res = gscript.parse_command('r.in.kinect', flags='c', overwrite=True)
if not (res['calib_matrix'] and len(res['calib_matrix'].split(',')) == 9):
gscript.message(_("Failed to calibrate"))
return
self.settings['tangible']['calibration']['matrix'] = res['calib_matrix']
UserSettings.SaveToFile(self.settings)
# update
self.calib_matrix = res['calib_matrix']
def rusle(self):
"""!main method in rusle_base
controlling the whole process, once called by main()
@return soillossbare name of output raster map
"""
flowacc = outprefix + "flowacc"
slope = outprefix + "slope"
lsfactor = outprefix + "lsfactor"
self.tmp_rast.append(flowacc)
self.tmp_rast.append(slope)
self.tmp_rast.append(lsfactor)
global fieldblock
if not fieldblock:
if fieldblockvect:
fieldblock = outprefix + "fieldblock"
g.run_command(
"v.to.rast",
input=fieldblockvect,
output=fieldblock,
use="val",
value="1",
quiet=quiet,
)
if fieldblock:
g.verbose('Raster map fieldblock is in "%s"' % fieldblock)
else:
fieldblock = ""
if not options["flowacc"]:
self._getFlowacc(elevation, flowacc, fieldblock)
g.verbose('Raster map flowacc is in "%s".' % flowacc)
else:
g.verbose('Raster map flowacc taken from "%s".' % flowacc)
self._getSlope(elevation, slope)
g.verbose('Raster map slope is in "%s"' % slope)
self._getLsfac(flowacc, slope, lsfactor)
g.verbose('Raster map lsfactor is in "%s"' % lsfactor)
self._getSoillossbare(lsfactor, kfactor, rfactor, soillossbare)
g.message('Soilloss for bare soil in map "%s".' % soillossbare)
stats = g.parse_command("r.univar",
flags="g",
map=soillossbare,
delimiter="=")
g.message("mean = %s \n stddev = %s \n min = %s \n max = %s" %
(stats["mean"], stats["stddev"], stats["min"], stats["max"]))
return soillossbare
def get_autocorrelation(mapname, raster, neighbordict, indicator):
""" Calculate either Moran's I or Geary's C for values of the given raster """
raster_vars = gscript.parse_command('r.univar',
map_=raster,
flags='g',
quiet=True)
global_mean = float(raster_vars['mean'])
univar_res = gscript.read_command('r.univar',
flags='t',
map_=raster,
zones=mapname,
out='-',
sep='comma',
quiet=True)
means = {}
mean_diffs = {}
firstline = True
for line in univar_res.splitlines():
l = line.split(',')
if firstline:
i = l.index('mean')
firstline = False
else:
means[l[0]] = float(l[i])
mean_diffs[l[0]] = float(l[i]) - global_mean
sum_sq_mean_diffs = sum(x**2 for x in mean_diffs.values())
total_nb_neighbors = 0
for region in neighbordict:
total_nb_neighbors += len(neighbordict[region])
N = len(means)
sum_products = 0
sum_squared_differences = 0
for region in neighbordict:
region_value = means[region] - global_mean
neighbors = neighbordict[region]
nb_neighbors = len(neighbors)
for neighbor in neighbors:
neighbor_value = means[neighbor] - global_mean
sum_products += region_value * neighbor_value
sum_squared_differences = (means[region] - means[neighbor])**2
if indicator == 'morans':
autocor = ((float(N) / total_nb_neighbors) *
(float(sum_products) / sum_sq_mean_diffs))
elif indicator == 'geary':
autocor = (float(N - 1) / (2 * total_nb_neighbors)) * \
(float(sum_squared_differences) / sum_sq_mean_diffs)
return autocor
def get_aoi(vector=None):
args = {}
if vector:
args['input'] = vector
if gs.vector_info_topo(vector)['areas'] <= 0:
gs.fatal(_("No areas found in AOI map <{}>...").format(vector))
elif gs.vector_info_topo(vector)['areas'] > 1:
gs.warning(_("More than one area found in AOI map <{}>. \
Using only the first area...").format(vector))
# are we in LatLong location?
s = gs.read_command("g.proj", flags='j')
kv = gs.parse_key_val(s)
if '+proj' not in kv:
gs.fatal(_("Unable to get AOI: unprojected location not supported"))
geom_dict = gs.parse_command('v.out.ascii', format='wkt', **args)
num_vertices = len(str(geom_dict.keys()).split(','))
geom = [key for key in geom_dict][0]
if kv['+proj'] != 'longlat':
gs.message(_("Generating WKT from AOI map ({} vertices)...").format(num_vertices))
if num_vertices > 500:
gs.fatal(_("AOI map has too many vertices to be sent via HTTP GET (sentinelsat). \
Use 'v.generalize' to simplify the boundaries"))
coords = geom.replace('POLYGON((', '').replace('))', '').split(', ')
poly = 'POLYGON(('
poly_coords = []
for coord in coords:
coord_latlon = gs.parse_command(
'm.proj', coordinates=coord.replace(' ', ','), flags='od')
for key in coord_latlon:
poly_coords.append((' ').join(key.split('|')[0:2]))
poly += (', ').join(poly_coords) + '))'
# Note: poly must be < 2000 chars incl. sentinelsat request (see RFC 2616 HTTP/1.1)
if len(poly) > 1850:
gs.fatal(_("AOI map has too many vertices to be sent via HTTP GET (sentinelsat). \
Use 'v.generalize' to simplify the boundaries"))
else:
gs.message(_("Sending WKT from AOI map to ESA..."))
return poly
else:
return geom
def test_patching_backend(tmp_path, patch_backend):
"""Check patching backend works"""
location = "test"
gs.core._create_location_xy(tmp_path, location) # pylint: disable=protected-access
with grass_setup.init(tmp_path / location):
gs.run_command("g.region", s=0, n=50, w=0, e=50, res=1)
points = "points"
reference = "reference"
gs.run_command("v.random", output=points, npoints=100)
gs.run_command("v.to.rast",
input=points,
output=reference,
type="point",
use="cat")
def run_grid_module():
# modules/shortcuts calls get_commands which requires GISBASE.
# pylint: disable=import-outside-toplevel
from grass.pygrass.modules.grid import GridModule
grid = GridModule(
"v.to.rast",
width=10,
height=5,
overlap=0,
patch_backend=patch_backend,
processes=max_processes(),
input=points,
output="output",
type="point",
use="cat",
)
grid.run()
run_in_subprocess(run_grid_module)
mean_ref = float(
gs.parse_command("r.univar", map=reference, flags="g")["mean"])
mean = float(
gs.parse_command("r.univar", map="output", flags="g")["mean"])
assert abs(mean - mean_ref) < 0.0001
def getValOnBuffer(inmap,elev,dist,output,user="",password=""):
# get number of points
n = getPointsNum(inmap)
g.run_command('v.db.addcol', map=outmap, columns='pix_vals double array', quiet=True)
#g.run_command('v.db.addcol', map=outmap, columns='fft_real double array', quiet=True)
#g.run_command('v.db.addcol', map=outmap, columns='fft_imgn double array', quiet=True)
# Connect to db server
dbinfo = getDbInfo()
dbname=dbinfo['dbname']
driver=dbinfo['driver']
conn = ppg.connect("dbname='"+str(dbname)+"' user='******' host='"+str(host)+"' password='******'")
cur = conn.cursor()
for i in range(n-1):
print "Now processing:" + str(i+1) +":" + nams.keys()[i]
# extract one feature from points set with cat value.
g.run_command("v.extract",input=inmap,output="tmp",type="point",new=-1,list=i+1,quiet=True,overwrite=True)
# create buffer of the extracted point
g.run_command("v.buffer",input="tmp",output="tmp2",type="point",distance=dist,quiet=True,overwrite=True)
# add attributes table and new a column storing value for the buffer object.
g.run_command("v.db.addtable",map="tmp2",columns="val double precision",quiet=True)
# set default value as 1.
g.run_command("v.db.update",map="tmp2",column="val",value=1,quiet=True)
# Redefine geographic region for procedure.
g.run_command("g.region",vect="tmp2",quiet=True)
# convert vector map buffer to raster map buffer.
g.run_command("v.to.rast",input="tmp2",output="tmprast",col="val",overwrite=True,quiet=True)
# get elevation on the raster buffer.
g.run_command("r.mapcalculator",amap="tmprast",bmap=elev,formula="A*B",outfile="tmprast2",overwrite=True,quiet=True)
nam = i+1
pix = g.parse_command("r.stats",flags="1",input="tmprast2",nv="",fs=",",quiet=True)
res = 'ARRAY['
for j in pix.keys():
res = res + str(j) + ','
res = res + ']'
# Update the column
sql='UPDATE '+str(inmap)+' SET pix_vals = '+str(pix_vals)+' WHERE cat = '+str(i+1)
cur.execute(sql)
# Remove temporal features
g.parse_command("g.remove",vect="tmp,tmp2",rast="tmprast,tmprast2",quiet=True)
# Set region with DEM.
g.parse_command("g.region",rast=elv,quiet=True)
conn.close()
def Data_prep(Land_cover):
'''
Function that extracts informations from the Land Cover : resolution and classes
'''
info = gscript.raster_info(Land_cover)
nsres = info.nsres
ewres = info.ewres
L = []
L = [cl for cl in gscript.parse_command('r.category', map=Land_cover)]
return nsres, ewres, L
def D_index(n1, n2, v1, v2, txtf):
"""Calculate D (Schoener's 1968)"""
tmpf0 = tmpname("rniche")
gs.mapcalc("$tmpf0 = abs(double($n1)/$v1 - double($n2)/$v2)",
tmpf0=tmpf0, n1=n1, v1=v1, n2=n2, v2=v2, quiet=True)
NO = float(gs.parse_command("r.univar", quiet=True, flags="g",
map=tmpf0)['sum'])
NOV = 1 - (0.5 * NO)
gs.info(_("Niche overlap (D) of {} and {} {}").format(n1.split('@')[0],
n2.split('@')[0], round(NOV, 3)))
return ['Niche overlap (D)', n1, n2, NOV]
def mkstreams(self):
'''Create minimal stream network reaching all subbasins and with nice main streams'''
# get max accumulation and cell count for each subbasin
rsmaxaccum = gread('r.stats', input='maxaccum__', flags='lcn')
rsmaxaccum = np.array(rsmaxaccum.split(), dtype=float).reshape((-1, 3)).astype(int)
subbasinIDs = rsmaxaccum[:, 0]
maxaccum = rsmaxaccum[:, 1]
# cellcounts must not be larger than maxaccum (may happen in subbasins with more than 1 outlet)
cellcounts = np.min([rsmaxaccum[:, 2], maxaccum], axis=0)
# calculate optima accumulation for nice headwater mainstreams
accr = grass.parse_command('r.info', map=self.accumulation, flags='g')
minaccum = np.int32(round(float(self.minmainstreams)*1e6 /
(float(accr['nsres'])*float(accr['ewres']))))
minaccum = np.ones_like(maxaccum) * minaccum
optiaccum = np.min([maxaccum-np.int32(cellcounts*0.1), minaccum], axis=0)
# check incoming subbasins maxaccum and take the smallest accumulation to update optiaccum
subnext = readSubNxtID(self.outlets)
optiaccum = dict(zip(subbasinIDs,optiaccum))
maxaccum = dict(zip(subbasinIDs,maxaccum))
for sn in np.unique(subnext['nextID']):
if sn < 0: continue
for sb in subnext[subnext['nextID']==sn]['subbasinID']:
optiaccum[sn] = min(optiaccum[sn],maxaccum[sb]-1)
# make raster
tempf = grass.tempfile()
np.savetxt(tempf,optiaccum.items(),fmt='%i=%i')
grass.run_command('r.reclass',input='maxaccum__',output='optiaccum__',
rules=tempf,quiet=True)
# get accumulation and make lines
grass.mapcalc("{0}__unthin=if({1} > {2},{1},null())".format(self.mainstreams,
self.accumulation,'optiaccum__'),overwrite=True)
# make sure all pixels between outlets and inlets are included
#grun('v.to.rast',input=self.outletinletlines,output='routingnet__rast',
# use='val',type='line',quiet=True)
#grass.mapcalc("{0}=if(isnull({0})&~isnull({1}),{2},{0})".format(self.mainstreams,
# 'routingnet__rast',self.accumulation),overwrite=True)
grun('r.thin', input=self.mainstreams+'__unthin', output=self.mainstreams, overwrite=True, quiet=True) # may exclude outlet/inlet points
# use predefined streams for subbasins that have them
if 'streams' in self.options:
grun('v.to.rast',input=self.streams,output='stream__rast',
use='val',type='line',val=1,quiet=True)
grun('r.thin', input='stream__rast', output='stream__rast__thin',
overwrite=True, quiet=True)
grun('r.stats.zonal',base=self.subbasinrast,cover='stream__rast__thin',
method='sum',output='n__streams__subbasins',quiet=True,overwrite=True)
# get subbasins that have at least x cells of streams
grass.mapcalc('{0}=if(n__streams__subbasins>10,{1},{0})'.format(self.mainstreams,'stream__rast__thin'),
overwrite=True)
# make final vector
grun('r.to.vect', input=self.mainstreams, output=self.mainstreams,
type='line',quiet=True)
return
def header(fd):
import grass.script.core as grass
fd.write('<?xml version="1.0" encoding="UTF-8"?>\n')
fd.write('<!DOCTYPE task SYSTEM "grass-addons.dtd">\n') # TODO
# doesn't work in GRASS 6
# vInfo = grass.version()
vInfo = grass.parse_command('g.version', flags='g')
fd.write('<addons version="%s" revision="%s" date="%s">\n' % \
(vInfo['version'].split('.')[0],
vInfo['revision'],
datetime.now()))
def getQu(FeatNam,colname):
# get Calculated Values from the Feature table.
dt = g.parse_command('v.db.select',flags='c', map=FeatNam ,columns=colname)
dist = []
n=len(dt)
for i in range(n-1):
dist=dist + [float(dict.keys(dt)[i])]
# calculate quantile of distance to the nearest point.
r_dist = ro.FloatVector(dist)
r_summ = r_base.summary(r_dist)
return(r_summ)
dt = g.parse_command('v.db.select',flags='c', map=FeatNam ,columns=colname)
dist = []
n=len(dt)
for i in range(n-1):
dist=dist + [float(dict.keys(dt)[i])]
# calculate quantile of distance to the nearest point.
r_dist = ro.FloatVector(dist)
r_summ = r_base.summary(r_dist)
return(r_summ)
def render_2d(envs):
brighten = 0 # percent brightness of shaded relief
render_multiplier = 1 # multiplier for rendering size
whitespace = 1.5 # canvas width relative to map for legend
fontsize = 36 * render_multiplier # legend font size
legend_coord = (5, 45, 2, 5) # legend display coordinates
zscale = 1 # vertical exaggeration
# create rendering directory
render = os.path.join(gisdbase, location, 'rendering')
if not os.path.exists(render):
os.makedirs(render)
for mapset in simulations:
# change mapset
gscript.read_command('g.mapset',
mapset=mapset,
location=location)
# set region
gscript.run_command('g.region', rast=region, res=res)
# set render size
info = gscript.parse_command('r.info',
map='elevation',
flags='g')
width = int(info.cols)*render_multiplier*whitespace
height = int(info.rows)*render_multiplier
# render net difference
gscript.run_command('d.mon',
start=driver,
width=width,
height=height,
output=os.path.join(render, mapset+'_'+'net_difference'+'.png'),
overwrite=1)
gscript.run_command('r.relief',
input='elevation',
output='relief',
altitude=90,
azimuth=45,
zscale=zscale,
env=envs[mapset])
gscript.run_command('d.shade',
shade='relief',
color='net_difference',
brighten=brighten)
gscript.run_command('d.legend',
raster='net_difference',
fontsize=fontsize,
at=legend_coord)
gscript.run_command('d.mon', stop=driver)
def parse_feature_names(maps):
"""Expand all categorical variable raster names into dummy variable raster names"""
# take the dummy variable maps, not the categorical
result = maps
for i in ['lcc','feature']:
if i in maps:
dummies = gscript.parse_command('g.list',
type='rast',
pattern='{}_*'.format(i)).keys()
result.remove(i)
result += dummies
return result
def rusle(self):
"""!main method in rusle_base
controlling the whole process, once called by main()
@return soillossbare name of output raster map
"""
flowacc = outprefix + 'flowacc'
slope = outprefix + 'slope'
lsfactor = outprefix+ 'lsfactor'
#self.tmp_rast.append(flowacc)
#self.tmp_rast.append(slope)
#self.tmp_rast.append(lsfactor)
global fieldblock
if not fieldblock:
if fieldblockvect:
fieldblock = outprefix + "fieldblock"
gscript.run_command("v.to.rast",
input=fieldblockvect,
output= fieldblock,
use="val",
value="1",
quiet=quiet
)
if fieldblock:
gscript.verbose('Raster map fieldblock is in "%s"'%fieldblock)
else: fieldblock = ""
if not options['flowacc']:
self._getFlowacc(elevation,flowacc,fieldblock)
gscript.verbose('Raster map flowacc is in "%s".'%flowacc)
else:
gscript.verbose('Raster map flowacc taken from "%s".'%flowacc)
self._getSlope(elevation,slope)
gscript.verbose('Raster map slope is in "%s"'%slope)
self._getLsfac(flowacc,slope,lsfactor)
gscript.verbose('Raster map lsfactor is in "%s"'%lsfactor)
self._getSoillossbare(lsfactor,kfactor,rfactor,soillossbare)
gscript.message('Soilloss for bare soil in map "%s".' %soillossbare)
stats = gscript.parse_command('r.univar', flags="g", map=soillossbare, delimiter = '=')
gscript.message('mean = %s \n stddev = %s \n min = %s \n max = %s' % (stats['mean'],stats['stddev'], stats['min'], stats['max']))
return soillossbare
def Analyze(self):
if self.hasSuperpixels:
gscript.run_command('i.superpixels.slic', group=self.group, output=self.segment, compactness=2,
minsize=50, env=self.env)
else:
gscript.run_command('i.segment', group=self.group, output=self.segment, threshold=0.3, minsize=50, env=self.env)
gscript.run_command('r.clump', input=self.segment, output=self.segment_clump, env=self.env)
gscript.run_command('i.smap', group=self.group, subgroup=self.group, signaturefile=self.signature,
output=self.classification, goodness=self.reject, env=self.env)
percentile = float(gscript.parse_command('r.univar', flags='ge', map=self.reject, env=self.env)['percentile_90'])
gscript.mapcalc('{new} = if({classif} < {thres}, {classif}, null())'.format(new=self.filtered_classification,
classif=self.classification, thres=percentile), env=self.env)
segments = self.segment if self.hasSuperpixels else self.segment_clump
gscript.run_command('r.stats.quantile', base=segments, cover=self.filtered_classification, output=self.output, env=self.env)
def map_info(landscape):
info = grass.parse_command('r.info', map=landscape, flags='g')
# aqui deveriamos checar se a resolucao eh inteira... como fazer isso?
dim = [int(info['rows']), int(info['cols'])]
x_west = int(info['west'])
x_east = int(info['east'])
y_south = int(info['south'])
y_north = int(info['north'])
res_x = int(info['ewres'])
res_y = int(info['nsres'])
print 'dims = %d, %d; limits W-E: %d - %d, S-N: %d - %d; res = %d, %d' % (dim[0], dim[1], x_west, x_east, y_south, y_north, res_x, res_y)
return dim, x_west, x_east, y_south, y_north, res_x, res_y
def __init__(self,**optionsandflags):
'''Process all arguments and prepare processing'''
# add all options and flags as attributes (only nonempty ones)
self.options = {}
for o in optionsandflags:
if optionsandflags[o]!='': self.options[o] = optionsandflags[o]
self.__dict__.update(self.options)
# get some location infos
self.env=grass.gisenv()
self.region=grass.region()
self.proj=grass.parse_command('g.proj',flags='g')
# convert res
self.res = float(self.res)
return
def map_info(landscape, usegrid = False, x_center = '', y_center = '', dims = ''):
'''
This function extracts information (extent, resolutin/grain, number of rows and columns) from the landscape,
directly from the GRASS GIS DataBase
Input:
- landscape: name of the landscape (it may the HABMAT landscape - binary)
Output:
- dim: (nrows, ncols) - number of rows and columns of the landscape
- x_west: western limit of the map
- x_east: eastern limit of the map
- y_south: southern limit of the map
- y_north: northern limit of the map
- res_x: resolution/grain (size of the pixel), in the west-east direction
- res_y: resolution/grain (size of the pixel), in the south-north direction
'''
#landscape='lndscp_0002_Mapa0002_tif_HABMAT_HABMAT'
#if usegrid:
#set_region(x_col=x_center, y_row=y_center, dims=dims)
#else:
#grass.run_command('g.region', raster=landscape)
info = grass.parse_command('r.info', map=landscape, flags='g')
# aqui deveriamos checar se a resolucao eh inteira... como fazer isso?
res_x = int(info['ewres'])
res_y = int(info['nsres'])
if usegrid:
dim = [dims[0]/res_y, dims[1]/res_x] # dims (y,x): in y/rows (meters), in x/cols (meters)
x_west = x_center-(dims[1]/2)
x_east = x_center+(dims[1]/2)
y_south = y_center-(dims[0]/2)
y_north = y_center+(dims[0]/2)
else:
dim = [int(info['rows']), int(info['cols'])]
x_west = int(float(info['west']))
x_east = int(float(info['east']))
y_south = int(float(info['south']))
y_north = int(float(info['north']))
#print 'dims = %d, %d; limits W-E: %d - %d, S-N: %d - %d; res = %d, %d' % (dim[0], dim[1], x_west, x_east, y_south, y_north, res_x, res_y)
return dim, x_west, x_east, y_south, y_north, res_x, res_y
#landscape_name = 'simulation_000001_p029_h059_HABMAT'
#dim, x_west, x_east, y_south, y_north, res_x, res_y = map_info(landscape=landscape_name)
#print 'dims = %d, %d; limits W-E: %d - %d, S-N: %d - %d; res = %d, %d' % (dim[0], dim[1], x_west, x_east, y_south, y_north, res_x, res_y)
def main():
# process command options
input = options['input']
if not gs.find_file(input)['file']:
gs.fatal(_("Raster map <%s> not found") % input)
smooth = options['output']
if gs.find_file(smooth)['file'] and not gs.overwrite():
gs.fatal(_("Output map <%s> already exists") % smooth)
sd = options['sd']
try:
sd = float(sd)
except ValueError:
if not gs.find_file(sd)['file']:
gs.fatal(_("Raster map <%s> not found") % sd)
alpha = float(options['alpha'])
# set aside region for internal use
gs.use_temp_region()
# subset input if desired
region = options.get('region')
if region:
if not gs.find_file(region)['file']:
gs.fatal(_("Raster map <%s> not found") % region)
gs.message("Setting region to %s" % region, flag='i')
gs.run_command('g.region', rast=region, align=input)
else:
gs.message("Using existing GRASS region", flag='i')
gs.debug('='*50)
gs.debug('\n'.join(gs.parse_command('g.region', 'p').keys()))
gs.debug('='*50)
multiscalesmooth(input, smooth, sd, alpha)
# restore original region
gs.del_temp_region()
return None
def main():
infile = options['input']
lesser = options['lesser']
greater = options['greater']
outfile = options['output']
global METHOD
METHOD = options['method']
clumped = flags['c']
diagonal = flags['d']
islesser = False
in_proj = grass.parse_command('g.proj', flags='g')
# check non supported location
if in_proj['unit'].lower() == 'degree':
grass.fatal(_("Latitude-Longitude locations are not supported"))
if in_proj['name'].lower() == 'xy_location_unprojected':
grass.fatal(_("xy-locations are not supported"))
grass.fatal(_("Need projected data with grids in metric units"))
# check lesser and greater parameters
if not lesser and not greater:
grass.fatal(_("You have to specify one of lesser= or greater="))
if lesser and greater:
grass.fatal(_("lesser= and greater= are mutually exclusive"))
if lesser:
limit = float(lesser)
islesser = True
if greater and METHOD == 'rmarea':
grass.fatal(_("You have to specify lesser= with method='rmarea'"))
elif greater:
limit = float(greater)
if not grass.find_file(infile)['name']:
grass.fatal(_("Raster map <%s> not found") % infile)
if METHOD == 'reclass':
reclass(infile, outfile, limit, clumped, diagonal, islesser)
elif METHOD == 'rmarea':
rmarea(infile, outfile, limit, in_proj['meters'])
grass.message(_("Generating output raster map <%s>...") % outfile)
def getDbInfo():
dbinfo = g.parse_command('db.connect',flags="p")
dbstat = {}
for i in range(len(dbinfo)):
info = dict.keys(dbinfo)[i].split(":")[0]
if info == "driver":
e_key = dict.keys(dbinfo)[i].split(":")[0]
e_val = dict.keys(dbinfo)[i].split(":")[1]
driver=None
if e_val == "pg":
driver="postgres"
dbstat[e_key] = driver
for i in range(len(dbinfo)):
if not dict.values(dbinfo)[i] == None:
elems = dict.values(dbinfo)[i].split(",")
for elem in elems:
if len(elem.split('=')) > 1:
e_key = elem.split('=')[0]
e_val = elem.split('=')[1]
dbstat[e_key] = e_val
return(dbstat)
def CalibrateModelBBox(self, event):
if self.IsScanning():
dlg = wx.MessageDialog(self, 'In order to calibrate, please stop scanning process first.',
'Stop scanning',
wx.OK | wx.ICON_WARNING)
dlg.ShowModal()
dlg.Destroy()
return
params = {}
if self.calib_matrix:
params['calib_matrix'] = self.calib_matrix
params['rotate'] = self.scan['rotation_angle']
zrange = ','.join(self.scan['trim_nsewtb'].split(',')[4:])
params['zrange'] = zrange
res = gscript.parse_command('r.in.kinect', flags='m', overwrite=True, **params)
if not res['bbox']:
gscript.message(_("Failed to find model extent"))
offsetcm = 2
n, s, e, w = [int(round(float(each))) for each in res['bbox'].split(',')]
self.scanning_panel.trim['n'].SetValue(str(n + offsetcm))
self.scanning_panel.trim['s'].SetValue(str(abs(s) + offsetcm))
self.scanning_panel.trim['e'].SetValue(str(e + offsetcm))
self.scanning_panel.trim['w'].SetValue(str(abs(w) + offsetcm))
def OnRegression(self, event):
"""Displays regression information in messagebox
"""
message = []
title = _("Regression Statistics for Scatterplot(s)")
for rpair in self.rasterList:
if isinstance(rpair, tuple) == False:
continue
rast1, rast2 = rpair
rast1 = rast1.split("@")[0]
rast2 = rast2.split("@")[0]
ret = grass.parse_command(
"r.regression.line",
mapx=rast1,
mapy=rast2,
flags="g",
quiet=True,
parse=(grass.parse_key_val, {"sep": "="}),
)
eqtitle = _("Regression equation for raster map <%(rast1)s> vs. <%(rast2)s>:\n\n") % {
"rast1": rast1,
"rast2": rast2,
}
eq = " %s = %s + %s(%s)\n\n" % (rast2, ret["a"], ret["b"], rast1)
num = "N = %s\n" % ret["N"]
rval = "R = %s\n" % ret["R"]
rsq = "R-squared = %f\n" % pow(float(ret["R"]), 2)
ftest = "F = %s\n" % ret["F"]
str = eqtitle + eq + num + rval + rsq + ftest
message.append(str)
stats = PlotStatsFrame(self, id=wx.ID_ANY, message=message, title=title)
if stats.Show() == wx.ID_CLOSE:
stats.Destroy()