def __init__(self,
cmd,
width=None,
height=None,
overlap=0,
processes=None,
split=False,
debug=False,
region=None,
move=None,
log=False,
start_row=0,
start_col=0,
out_prefix='',
*args,
**kargs):
kargs['run_'] = False
self.mset = Mapset()
self.module = Module(cmd, *args, **kargs)
self.width = width
self.height = height
self.overlap = overlap
self.processes = processes
self.region = region if region else Region()
self.start_row = start_row
self.start_col = start_col
self.out_prefix = out_prefix
self.log = log
self.move = move
self.gisrc_src = os.environ['GISRC']
self.n_mset, self.gisrc_dst = None, None
if self.move:
self.n_mset = copy_mapset(self.mset, self.move)
self.gisrc_dst = write_gisrc(self.n_mset.gisdbase,
self.n_mset.location,
self.n_mset.name)
rasters = [r for r in select(self.module.inputs, 'raster')]
if rasters:
copy_rasters(rasters,
self.gisrc_src,
self.gisrc_dst,
region=self.region)
vectors = [v for v in select(self.module.inputs, 'vector')]
if vectors:
copy_vectors(vectors, self.gisrc_src, self.gisrc_dst)
groups = [g for g in select(self.module.inputs, 'group')]
if groups:
copy_groups(groups,
self.gisrc_src,
self.gisrc_dst,
region=self.region)
self.bboxes = split_region_tiles(region=region,
width=width,
height=height,
overlap=overlap)
self.msetstr = cmd.replace('.', '') + "_%03d_%03d"
self.inlist = None
if split:
self.split()
self.debug = debug
def find_in_location(type, pattern, location):
res = []
for msetname in location.mapsets():
mset = Mapset(msetname, location.name, location.gisdbase)
res.extend([(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)])
return res
def main():
mapset = Mapset()
mapset.current()
with open(options['output'], 'w') as fd:
for rast in mapset.glist('raster', pattern='*_B04_10m'):
items = rast.split('_')
d = datetime.strptime(items[2], '%Y%m%dT%H%M%S')
## workaround
dd = d + timedelta(seconds=1)
vect = '{}_{}_MSK_CLOUDS'.format(items[1], items[2])
mask_vect = '{}_{}'.format(vect, options['map'].split('@')[0])
if Vector(vect).exist():
Module('v.overlay',
ainput=options['map'],
binput=vect,
operator='not',
output=mask_vect)
else:
copy(options['map'], mask_vect, 'vector')
Module('r.mask', vector=mask_vect, overwrite=True)
Module('g.remove', flags='f', type='vector', name=mask_vect)
Module('g.rename', raster=['MASK', mask_vect])
fd.write("{0}|{1}|{2}{3}".format(mask_vect,
d.strftime('%Y-%m-%d %H:%M:%S'),
dd.strftime('%Y-%m-%d %H:%M:%S'),
os.linesep))
return 0
def setUpClass(cls):
cls.org_mapset = Mapset()
cls.tmp_mapset_name = tempname(10)
make_mapset(mapset=cls.tmp_mapset_name)
cls.tmp_mapset = Mapset(mapset=cls.tmp_mapset_name)
cls.tmp_mapset.current()
cls.tmp_mapset_path = cls.tmp_mapset.path()
def find_in_location(type, pattern, location):
res = []
for msetname in location.mapsets():
mset = Mapset(msetname, location.name, location.gisdbase)
res.extend([(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)])
return res
def main():
"""
Delete all raster files which the name begin by "vshed"
"""
gscript.run_command('g.region', flags='p')
m = Mapset()
liste_viewshed = m.glist('raster', pattern='vshed*')
print(liste_viewshed)
for viewshed_layer in liste_viewshed:
run_command("g.remove", flags="f", type="raster", name=viewshed_layer)
def in_mapset(m, dtype, pattern=None):
"""Checks if a map with the same name already exists in the mapset"""
mset = Mapset()
maps = mset.glist(dtype, pattern=pattern)
if m in maps:
return True
else:
return False
def cleanup():
"""Restore old mask if it existed"""
if RasterRow("{}_MASK".format(TMP_NAME), Mapset().name).exist():
gscript.verbose("Restoring old mask...")
if RasterRow("MASK", Mapset().name).exist():
gscript.run_command("r.mask", flags="r")
gscript.run_command(
"g.rename", rast="{}_MASK,MASK".format(TMP_NAME), quiet=True
)
if RasterRow("MASK", Mapset().name).exist():
gscript.run_command("r.mask", flags="r")
def setUpClass(cls):
cls.map = tempname(10)
cls.mapset = Mapset().name
cls.bandref = "The_Doors"
cls.use_temp_region()
cls.runModule("g.region", n=1, s=0, e=1, w=0, res=1)
cls.runModule("r.mapcalc", expression="{} = 1".format(cls.map))
def get_path(path, vect_name=None):
"""Return the full path to the database; replacing environment variable
with real values
:param path: The path with substitutional parameter
:param vect_name: The name of the vector map
>>> from grass.script.core import gisenv
>>> import os
>>> path = '$GISDBASE/$LOCATION_NAME/$MAPSET/sqlite/sqlite.db'
>>> new_path = get_path(path)
>>> new_path2 = os.path.join(gisenv()['GISDBASE'], gisenv()['LOCATION_NAME'],
... gisenv()['MAPSET'], 'sqlite', 'sqlite.db')
>>> new_path.replace("//","/") == new_path2.replace("//","/")
True
>>> path = '$GISDBASE/$LOCATION_NAME/$MAPSET/vector/$MAP/sqlite.db'
>>> new_path = get_path(path, "test")
>>> new_path2 = os.path.join(gisenv()['GISDBASE'], gisenv()['LOCATION_NAME'],
... gisenv()['MAPSET'], 'vector', 'test', 'sqlite.db')
>>> new_path.replace("//","/") == new_path2.replace("//","/")
True
"""
if "$" not in path:
return path
else:
mapset = Mapset()
path = path.replace('$GISDBASE', mapset.gisdbase)
path = path.replace('$LOCATION_NAME', mapset.location)
path = path.replace('$MAPSET', mapset.name)
if vect_name is not None:
path = path.replace('$MAP', vect_name)
return path
def setUpClass(cls):
cls.mpath = utils.decode(G_mapset_path())
cls.mapset_name = Mapset().name
cls.sigdirs = []
# As signatures are created directly not via signature creation
# tools, we must ensure signature directories exist
os.makedirs(f"{cls.mpath}/signatures/sig/", exist_ok=True)
os.makedirs(f"{cls.mpath}/signatures/sigset/", exist_ok=True)
# A mapset with a random name
cls.src_mapset_name = tempname(10)
G_make_mapset(None, None, cls.src_mapset_name)
cls.src_mapset_path = (cls.mpath.rsplit("/", maxsplit=1)[0] + "/" +
cls.src_mapset_name)
# Create fake signature files
os.makedirs(f"{cls.src_mapset_path}/signatures/sig/")
cls.src_sig = tempname(10)
cls.src_sig_dir = f"{cls.src_mapset_path}/signatures/sig/{cls.src_sig}"
os.makedirs(cls.src_sig_dir)
cls.sigdirs.append(cls.src_sig_dir)
f = open(f"{cls.src_sig_dir}/sig", "w")
f.write("A sig file")
f.close()
os.makedirs(f"{cls.src_mapset_path}/signatures/sigset/")
cls.src_sigset = tempname(10)
cls.src_sigset_dir = f"{cls.src_mapset_path}/signatures/sigset/{cls.src_sigset}"
os.makedirs(cls.src_sigset_dir)
cls.sigdirs.append(cls.src_sigset_dir)
f = open(f"{cls.src_sigset_dir}/sig", "w")
f.write("A sigset file")
f.close()
def setUpClass(cls):
cls.mpath = utils.decode(G_mapset_path())
cls.mapset_name = Mapset().name
cls.sigdirs = []
# As signatures are created directly not via signature creation
# tools, we must ensure signature directories exist
os.makedirs(f"{cls.mpath}/signatures/sig/", exist_ok=True)
os.makedirs(f"{cls.mpath}/signatures/sigset/", exist_ok=True)
def main():
mapset = Mapset()
mapset.current()
with open(options['output'], 'w') as fd:
for rast in mapset.glist('raster'):
items = rast.split('_')
d = datetime.strptime(items[2], '%Y%m%dT%H%M%S')
#fd.write("{0}|{1}{2}".format(rast, iso_date, os.linesep))
## workaround
dd = d + timedelta(seconds=1)
fd.write("{0}|{1}|{2}{3}".format(rast,
d.strftime('%Y-%m-%d %H:%M:%S'),
dd.strftime('%Y-%m-%d %H:%M:%S'),
os.linesep))
return 0
def findmaps(type, pattern=None, mapset='', location='', gisdbase=''):
"""Return a list of tuple contining the names of the:
* map
* mapset,
* location,
* gisdbase
"""
from grass.pygrass.gis import Gisdbase, Location, Mapset
def find_in_location(type, pattern, location):
res = []
for msetname in location.mapsets():
mset = Mapset(msetname, location.name, location.gisdbase)
res.extend([(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)])
return res
def find_in_gisdbase(type, pattern, gisdbase):
res = []
for loc in gisdbase.locations():
res.extend(find_in_location(type, pattern,
Location(loc, gisdbase.name)))
return res
if gisdbase and location and mapset:
mset = Mapset(mapset, location, gisdbase)
return [(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)]
elif gisdbase and location:
loc = Location(location, gisdbase)
return find_in_location(type, pattern, loc)
elif gisdbase:
gis = Gisdbase(gisdbase)
return find_in_gisdbase(type, pattern, gis)
elif location:
loc = Location(location)
return find_in_location(type, pattern, loc)
elif mapset:
mset = Mapset(mapset)
return [(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)]
else:
gis = Gisdbase()
return find_in_gisdbase(type, pattern, gis)
def main():
m1 = Mapset() #Getting data tree
liste_viewshed = m1.glist('raster', pattern='vshed*') #Getting all viewshed created
for map in liste_viewshed:
output_string = options["output"] + "\\" + map + ".tif"
run_command("r.out.gdal",
input = map,
output = output_string,
format = "GTiff",
overviews = 0)
return 0
def main():
mapset = Mapset()
mapset.current()
with open(options['output'], 'w') as fd:
for vect in mapset.glist('vector', pattern='*MSK_CLOUDS'):
items = vect.split('_')
d = datetime.strptime(items[1], '%Y%m%dT%H%M%S')
## workaround
dd = d + timedelta(seconds=1)
Module('r.mask', vector=vect, flags='i')
Module('g.rename', raster=['MASK', vect])
fd.write("{0}|{1}|{2}{3}".format(vect,
d.strftime('%Y-%m-%d %H:%M:%S'),
dd.strftime('%Y-%m-%d %H:%M:%S'),
os.linesep))
return 0
def prepare_horizon(elevation, step, bufferzone, maxdistance, resolution,
prefix):
g_region(raster="{}_elev".format(prefix), res=resolution)
mset = Mapset()
maps = mset.glist("raster")
hors = [h for h in maps if "{}_horizon".format(prefix) in h]
if len(hors) == int(360 / float(step)):
pass
else:
r_horizon(elevation="{}_elev".format(prefix),
step=step,
bufferzone=bufferzone,
maxdistance=maxdistance,
output="{}_horizon".format(prefix),
overwrite=True)
def set_default(self):
"""Set the Region object to the default GRASS region.
It works only in PERMANENT mapset"""
from grass.pygrass.gis import Mapset
mapset = Mapset()
if mapset.name != 'PERMANENT':
raise GrassError("ERROR: Unable to change default region. The " \
"current mapset is not <PERMANENT>.")
self.adjust()
if libgis.G_put_window(self.c_region) < 0:
raise GrassError("Cannot change region (DEFAUL_WIND file).")
def get_mapset(gisrc_src, gisrc_dst):
"""Get mapset from a GISRC source to a GISRC destination.
:param gisrc_src: path to the GISRC source
:type gisrc_src: str
:param gisrc_dst: path to the GISRC destination
:type gisrc_dst: str
:returns: a tuple with Mapset(src), Mapset(dst)
"""
msrc, lsrc, gsrc = read_gisrc(gisrc_src)
mdst, ldst, gdst = read_gisrc(gisrc_dst)
path_src = os.path.join(gsrc, lsrc, msrc)
path_dst = os.path.join(gdst, ldst, mdst)
if not os.path.isdir(path_dst):
os.makedirs(path_dst)
copy_special_mapset_files(path_src, path_dst)
src = Mapset(msrc, lsrc, gsrc)
dst = Mapset(mdst, ldst, gdst)
visible = [m for m in src.visible]
visible.append(src.name)
dst.visible.extend(visible)
return src, dst
def cleanup():
"""Remove temporary data
"""
#remove temporary region file
grass.del_temp_region()
try:
grass.run_command('g.remove', flags='f', name=TMP_MAPS,
quiet=True, type=['vector', 'raster'],
stderr=os.devnull, stdout_=os.devnull)
except:
pass
if RasterRow("MASK", Mapset().name).exist():
grass.run_command("r.mask", flags="r", quiet=True)
reset_mask()
def setUpClass(cls):
cls.libc = ctypes.cdll.LoadLibrary(ctypes.util.find_library("c"))
cls.mapset = Mapset().name
cls.map1 = tempname(10)
cls.semantic_label1 = "The_Doors"
cls.map2 = tempname(10)
cls.semantic_label2 = "The_Who"
cls.map3 = tempname(10)
cls.use_temp_region()
cls.runModule("g.region", n=1, s=0, e=1, w=0, res=1)
cls.runModule("r.mapcalc", expression=f"{cls.map1} = 1")
cls.runModule("r.mapcalc", expression=f"{cls.map2} = 1")
cls.runModule("r.mapcalc", expression=f"{cls.map3} = 1")
Rast_write_semantic_label(cls.map1, cls.semantic_label1)
Rast_write_semantic_label(cls.map2, cls.semantic_label2)
def setUpClass(cls):
cls.list_ptr = ctypes.POINTER(ctypes.c_char_p)
cls.mpath = utils.decode(G_mapset_path())
cls.mapset_name = Mapset().name
cls.sigdirs = []
# As signatures are created directly not via signature creation
# tools, we must ensure signature directories exist
os.makedirs(f"{cls.mpath}/signatures/sig/", exist_ok=True)
os.makedirs(f"{cls.mpath}/signatures/sigset/", exist_ok=True)
# A mapset with a random name
cls.rnd_mapset_name = tempname(10)
G_make_mapset(None, None, cls.rnd_mapset_name)
cls.rnd_mapset_path = (cls.mpath.rsplit("/", maxsplit=1)[0] + "/" +
cls.rnd_mapset_name)
os.makedirs(f"{cls.rnd_mapset_path}/signatures/sig/")
os.makedirs(f"{cls.rnd_mapset_path}/signatures/sigset/")
def clean_location(self, location=None):
"""Remove all created mapsets.
:param location: a Location instance where we are running the analysis
:type location: Location object
"""
if location is None:
if self.n_mset:
self.n_mset.current()
location = Location()
mapsets = location.mapsets(self.msetstr.split('_')[0] + '_*')
for mset in mapsets:
Mapset(mset).delete()
if self.n_mset and self.n_mset.is_current():
self.mset.current()
def __init__(self, cmd, width=None, height=None, overlap=0, processes=None,
split=False, debug=False, region=None, move=None, log=False,
start_row=0, start_col=0, out_prefix='', mapset_prefix=None,
*args, **kargs):
kargs['run_'] = False
self.mset = Mapset()
self.module = Module(cmd, *args, **kargs)
self.width = width
self.height = height
self.overlap = overlap
self.processes = processes
self.region = region if region else Region()
self.start_row = start_row
self.start_col = start_col
self.out_prefix = out_prefix
self.log = log
self.move = move
self.gisrc_src = os.environ['GISRC']
self.n_mset, self.gisrc_dst = None, None
if self.move:
self.n_mset = copy_mapset(self.mset, self.move)
self.gisrc_dst = write_gisrc(self.n_mset.gisdbase,
self.n_mset.location,
self.n_mset.name)
rasters = [r for r in select(self.module.inputs, 'raster')]
if rasters:
copy_rasters(rasters, self.gisrc_src, self.gisrc_dst,
region=self.region)
vectors = [v for v in select(self.module.inputs, 'vector')]
if vectors:
copy_vectors(vectors, self.gisrc_src, self.gisrc_dst)
groups = [g for g in select(self.module.inputs, 'group')]
if groups:
copy_groups(groups, self.gisrc_src, self.gisrc_dst,
region=self.region)
self.bboxes = split_region_tiles(region=region,
width=width, height=height,
overlap=overlap)
if mapset_prefix:
self.msetstr = mapset_prefix + "_%03d_%03d"
else:
self.msetstr = cmd.replace('.', '') + "_%03d_%03d"
self.inlist = None
if split:
self.split()
self.debug = debug
def cleanup():
"""Remove raster and vector maps stored in a list"""
grass.run_command(
"g.remove",
flags="f",
type="raster,vector",
pattern="{}_*".format(TEMPNAME),
quiet=True,
stderr=subprocess.PIPE,
)
# Reset mask if user MASK was present
if (RasterRow("MASK",
Mapset().name).exist()
and RasterRow("MASK_{}".format(TEMPNAME)).exist()):
grass.run_command("r.mask", flags="r", quiet=True)
reset_mask()
def findmaps(type, pattern=None, mapset="", location="", gisdbase=""):
"""Return a list of tuple contining the names of the:
* map
* mapset,
* location,
* gisdbase
"""
from grass.pygrass.gis import Gisdbase, Location, Mapset
def find_in_location(type, pattern, location):
res = []
for msetname in location.mapsets():
mset = Mapset(msetname, location.name, location.gisdbase)
res.extend(
[
(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)
]
)
return res
def find_in_gisdbase(type, pattern, gisdbase):
res = []
for loc in gisdbase.locations():
res.extend(find_in_location(type, pattern, Location(loc, gisdbase.name)))
return res
if gisdbase and location and mapset:
mset = Mapset(mapset, location, gisdbase)
return [
(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)
]
elif gisdbase and location:
loc = Location(location, gisdbase)
return find_in_location(type, pattern, loc)
elif gisdbase:
gis = Gisdbase(gisdbase)
return find_in_gisdbase(type, pattern, gis)
elif location:
loc = Location(location)
return find_in_location(type, pattern, loc)
elif mapset:
mset = Mapset(mapset)
return [
(m, mset.name, mset.location, mset.gisdbase)
for m in mset.glist(type, pattern)
]
else:
gis = Gisdbase()
return find_in_gisdbase(type, pattern, gis)
def setUpClass(cls):
cls.mpath = utils.decode(G_mapset_path())
cls.mapset_name = Mapset().name
cls.sigdirs = []
# As signatures are created directly not via signature creation
# tools, we must ensure signature directories exist
os.makedirs(f"{cls.mpath}/signatures/sig/", exist_ok=True)
os.makedirs(f"{cls.mpath}/signatures/sigset/", exist_ok=True)
cls.sig_name1 = tempname(10)
cls.sig_dir1 = f"{cls.mpath}/signatures/sigset/{cls.sig_name1}"
os.makedirs(cls.sig_dir1)
cls.sigdirs.append(cls.sig_dir1)
open(f"{cls.sig_dir1}/sig", "a").close()
cls.sig_name2 = tempname(10)
cls.sig_dir2 = f"{cls.mpath}/signatures/sig/{cls.sig_name2}"
os.makedirs(cls.sig_dir2)
cls.sigdirs.append(cls.sig_dir2)
open(f"{cls.sig_dir2}/sig", "a").close()
def unset_mask():
"""Deactivate user mask"""
if RasterRow("MASK", Mapset().name).exist():
grass.run_command(
"g.copy",
quiet=True,
raster="MASK,MASK_{}".format(TEMPNAME),
stderr=subprocess.DEVNULL,
errors="ignore",
)
grass.run_command(
"g.remove",
quiet=True,
type="raster",
name="MASK",
stderr=subprocess.DEVNULL,
flags="f",
errors="ignore",
)
def copy_mapset(mapset, path):
"""Copy mapset to another place without copying raster and vector data.
:param mapset: a Mapset instance to copy
:type mapset: Mapset object
:param path: path where the new mapset must be copied
:type path: str
:returns: the instance of the new Mapset.
>>> from grass.script.core import gisenv
>>> mname = gisenv()['MAPSET']
>>> mset = Mapset()
>>> mset.name == mname
True
>>> import tempfile as tmp
>>> import os
>>> path = os.path.join(tmp.gettempdir(), 'my_loc', 'my_mset')
>>> copy_mapset(mset, path) # doctest: +ELLIPSIS
Mapset(...)
>>> sorted(os.listdir(path)) # doctest: +ELLIPSIS
[...'PERMANENT'...]
>>> sorted(os.listdir(os.path.join(path, 'PERMANENT')))
[u'DEFAULT_WIND', u'PROJ_EPSG', u'PROJ_INFO', u'PROJ_UNITS', u'VAR', u'WIND']
>>> sorted(os.listdir(os.path.join(path, mname))) # doctest: +ELLIPSIS
[...u'SEARCH_PATH',...u'WIND']
>>> import shutil
>>> shutil.rmtree(path)
"""
per_old = os.path.join(mapset.gisdbase, mapset.location, 'PERMANENT')
per_new = os.path.join(path, 'PERMANENT')
map_old = mapset.path()
map_new = os.path.join(path, mapset.name)
if not os.path.isdir(per_new):
os.makedirs(per_new)
if not os.path.isdir(map_new):
os.mkdir(map_new)
copy_special_mapset_files(per_old, per_new)
copy_special_mapset_files(map_old, map_new)
gisdbase, location = os.path.split(path)
return Mapset(mapset.name, location, gisdbase)
def get_path(path):
"""Return the full path to the database; replacing environment variable
with real values
>>> path = '$GISDBASE/$LOCATION_NAME/$MAPSET/sqlite/sqlite.db'
>>> new_path = get_path(path)
>>> from grass.script.core import gisenv
>>> import os
>>> new_path2 = os.path.join(gisenv()['GISDBASE'], gisenv()['LOCATION_NAME'],
... gisenv()['MAPSET'], 'sqlite', 'sqlite.db')
>>> new_path == new_path2
True
"""
if "$" not in path:
return path
else:
mapset = Mapset()
path = path.replace('$GISDBASE', mapset.gisdbase)
path = path.replace('$LOCATION_NAME', mapset.location)
path = path.replace('$MAPSET', mapset.name)
return path
def main():
mapset = Mapset()
mapset.current() # set mapset to current mapset
with open(options['output_ras'], 'w') as fd:
for rast in mapset.glist('raster'): # get all available raster data
items = rast.split('_')
d = datetime.strptime(
items[0],
'%Y%m%dT%H%M%S') # retrieve sensing date from file name
# workaround to create timespan
dd = d + timedelta(seconds=1)
fd.write("{0}|{1}|{2}{3}".format( # write to timestamps text file
rast, d.strftime('%Y-%m-%d %H:%M:%S'),
dd.strftime('%Y-%m-%d %H:%M:%S'), os.linesep))
with open(options['output_vec'], 'w') as fd:
for rast in mapset.glist(
'raster', pattern='*_B02.tif'
): # retrieve sensing date only for one band per date
items = rast.split('_')
d = datetime.strptime(items[0], '%Y%m%dT%H%M%S')
# workaround to create timespan
dd = d + timedelta(seconds=1)
vect = 'cloudmask_{}_mergedvector'.format(
items[0]) # pattern of cloud mask file names
Module('r.mask', vector=vect,
overwrite=True) # create a mask out of cloud vector file
Module('g.remove', flags='f', type='vector',
name=vect) # remove original vector data
Module('g.rename',
raster=['MASK', vect]) # rename mask to vector file name
fd.write("{0}|{1}|{2}{3}".format( # write to timestamps text file
vect, d.strftime('%Y-%m-%d %H:%M:%S'),
dd.strftime('%Y-%m-%d %H:%M:%S'), os.linesep))
return 0
from mower import GrassSession
DEM = "/home/mperry/projects/shortcreek/dem/dem.img"
with GrassSession(DEM) as gs:
from grass.pygrass.modules.shortcuts import raster
# Import/Link to External GDAL data
raster.external(input=DEM, output="dem")
# Perform calculations
raster.mapcalc(expression="demft=dem*3.28084")
raster.slope_aspect(elevation="demft", slope="slope", aspect="aspect")
# Export from GRASS to GDAL
from grass.pygrass.gis import Mapset
m = Mapset()
for r in m.glist('rast'):
if r == "dem":
# don't save the original
continue
raster.out_gdal(r, format="GTiff", output="/tmp/{}.tif".format(r), overwrite=True)
def add_color_table(self, cbrew=False, color=None, column=None, attr=None, layer='1',
nk=5, s=None, cramp=('Diverging','RdYlBu'), method='Equal_Interval',
invert_ramp=False, *args, **kwargs):
"""
Add/replace color table
Keyword Description
---------- ----------------------------------------------------------------------
nk number of classes
column layer column to color classify, If s is not provided, column is needed.
Default=None
s pandas series or numpy array. If column is not provided, s is needed.
Default=None
ccramp Boolean. If true, color scheme and color ramp use Color Brewer
(http://colorbrewer2.org/)
method pysal.mapclassify methods. Options: Map_Classifier, Box_Plot,
Equal_Interval, Fisher_Jenks, Jenks_Caspall, Jenks_Caspall_Forced,
Jenks_Caspall_Sampled, Max_P_Classifier, Maximum_Breaks,
Natural_Breaks, Quantiles, Percentiles, Std_Mean, User_Defined.
Default User_Defined. See PySal documentation for valid parameters
in each case (http://pysal.org/1.2/library/esda/mapclassify.html).
invert_ramp Boolean. Default False.
layer Grass layer where rgb column will be added
*args Additional arguments for v.colors
**kwargs Additional arguments for rgb_classify. For example, if method='User_Defined'
then the arguments bins is required.
---------- ----------------------------------------------------------------------
"""
#todo: allow editing if current mapset and mapset are PERMANENT
#assert self.mapset is not 'PERMANENT',\
# '%r is in PERMANENT and is not writable by user' % self.name
assert int(layer) <= self.dblinks.num_dblinks(), 'layer %r does not exist' % layer
if cbrew:
table_name = self.dblinks.by_layer(int(layer)).name
sqlfilter = gtable.Table(name=table_name, connection=self._con)
assert sqlfilter.exist(), 'table %r not found in mapset %r. Verify dblinks.'\
% (sqlfilter.name, self.mapset)
if hasattr(s, '__len__'):
dtype = s.dtype.type
assert (np.issubdtype(dtype, np.integer) or np.issubdtype(dtype, np.float)),\
'Numpy array dtype must be integer or float'
sqlfilter.filters.select(sqlfilter.key)
cur = sqlfilter.execute()
cat = cur.fetchall()
cat = np.array(cat)
cat = cat.flatten()
assert s.shape == cat.shape, 'Series does not match map key shape'
if column:
assert column in sqlfilter.columns.names(),\
'%r has not column %r' % (table_name, column)
sqlfilter.filters.select(sqlfilter.key, column)
cur = sqlfilter.execute()
col = cur.fetchall()
col = np.array(col).T
s = col[1]
cat = col[0]
dtype = s.dtype.type
if not (np.issubdtype(dtype, np.integer) or np.issubdtype(dtype, np.float)):
nulls = np.where(s == '')[0]
if nulls.any:
s[s == ''] = np.nan
s = s.astype(float)
s = pd.Series(s)
s_rgb = rgb_classify(s, nk, cramp=cramp, method=method, invert_ramp=invert_ramp,
**kwargs)
#TODO convert this into a save_colr_file function
# Write color table
mapset = Mapset()
mapset.current()
if self.mapset is mapset.name:
filename = os.path.join('$GISDBASE','$LOCATION_NAME', self.mapset,
'vector', self.name, 'colr')
else:
filename = os.path.join('$GISDBASE','$LOCATION_NAME', mapset.name,
'vcolr2', self.mapset, self.name)
filename = gtable.get_path(filename)
directory = os.path.dirname(filename)
if not os.path.exists(directory):
os.makedirs(directory)
with open(filename,'w') as f:
f.write('% ' + '%r %r' % (int(min(cat)), self.table.n_rows()) + '\n')
for i,item in enumerate(s_rgb):
f.write(str(cat[i]) + ':' + item + '\n')
else:
assert color, 'color attribute is required'
if column:
v.colors(map=self.full_name, layer=layer, column=column, color=color, *args)
else:
v.colors(map=self.full_name, color=color, *args)
class GridModule(object):
# TODO maybe also i.* could be supported easily
"""Run GRASS raster commands in a multiprocessing mode.
:param cmd: raster GRASS command, only command staring with r.* are valid.
:type cmd: str
:param width: width of the tile, in pixel
:type width: int
:param height: height of the tile, in pixel.
:type height: int
:param overlap: overlap between tiles, in pixel.
:type overlap: int
:param processes: number of threads, default value is equal to the number
of processor available.
:param split: if True use r.tile to split all the inputs.
:type split: bool
:param run_: if False only instantiate the object
:type run_: bool
:param args: give all the parameters to the command
:param kargs: give all the parameters to the command
>>> grd = GridModule('r.slope.aspect',
... width=500, height=500, overlap=2,
... processes=None, split=False,
... elevation='elevation',
... slope='slope', aspect='aspect', overwrite=True)
>>> grd.run()
"""
def __init__(self, cmd, width=None, height=None, overlap=0, processes=None,
split=False, debug=False, region=None, move=None, log=False,
start_row=0, start_col=0, out_prefix='',
*args, **kargs):
kargs['run_'] = False
self.mset = Mapset()
self.module = Module(cmd, *args, **kargs)
self.width = width
self.height = height
self.overlap = overlap
self.processes = processes
self.region = region if region else Region()
self.start_row = start_row
self.start_col = start_col
self.out_prefix = out_prefix
self.log = log
self.move = move
self.gisrc_src = os.environ['GISRC']
self.n_mset, self.gisrc_dst = None, None
if self.move:
self.n_mset = copy_mapset(self.mset, self.move)
self.gisrc_dst = write_gisrc(self.n_mset.gisdbase,
self.n_mset.location,
self.n_mset.name)
rasters = [r for r in select(self.module.inputs, 'raster')]
if rasters:
copy_rasters(rasters, self.gisrc_src, self.gisrc_dst,
region=self.region)
vectors = [v for v in select(self.module.inputs, 'vector')]
if vectors:
copy_vectors(vectors, self.gisrc_src, self.gisrc_dst)
groups = [g for g in select(self.module.inputs, 'group')]
if groups:
copy_groups(groups, self.gisrc_src, self.gisrc_dst,
region=self.region)
self.bboxes = split_region_tiles(region=region,
width=width, height=height,
overlap=overlap)
self.msetstr = cmd.replace('.', '') + "_%03d_%03d"
self.inlist = None
if split:
self.split()
self.debug = debug
def __del__(self):
if self.gisrc_dst:
# remove GISRC file
os.remove(self.gisrc_dst)
def clean_location(self, location=None):
"""Remove all created mapsets.
:param location: a Location instance where we are running the analysis
:type location: Location object
"""
if location is None:
if self.n_mset:
self.n_mset.current()
location = Location()
mapsets = location.mapsets(self.msetstr.split('_')[0] + '_*')
for mset in mapsets:
Mapset(mset).delete()
if self.n_mset and self.n_mset.is_current():
self.mset.current()
def split(self):
"""Split all the raster inputs using r.tile"""
rtile = Module('r.tile')
inlist = {}
for inm in select(self.module.inputs, 'raster'):
rtile(input=inm.value, output=inm.value,
width=self.width, height=self.height,
overlap=self.overlap)
patt = '%s-*' % inm.value
inlist[inm.value] = sorted(self.mset.glist(type='rast',
pattern=patt))
self.inlist = inlist
def get_works(self):
"""Return a list of tuble with the parameters for cmd_exe function"""
works = []
reg = Region()
if self.move:
mdst, ldst, gdst = read_gisrc(self.gisrc_dst)
else:
ldst, gdst = self.mset.location, self.mset.gisdbase
cmd = self.module.get_dict()
groups = [g for g in select(self.module.inputs, 'group')]
for row, box_row in enumerate(self.bboxes):
for col, box in enumerate(box_row):
inms = None
if self.inlist:
inms = {}
cols = len(box_row)
for key in self.inlist:
indx = row * cols + col
inms[key] = "%s@%s" % (self.inlist[key][indx],
self.mset.name)
# set the computational region, prepare the region parameters
bbox = dict([(k[0], str(v)) for k, v in box.items()[:-2]])
bbox['nsres'] = '%f' % reg.nsres
bbox['ewres'] = '%f' % reg.ewres
new_mset = self.msetstr % (self.start_row + row,
self.start_col + col),
works.append((bbox, inms,
self.gisrc_src,
write_gisrc(gdst, ldst, new_mset),
cmd, groups))
return works
def define_mapset_inputs(self):
"""Add the mapset information to the input maps
"""
for inmap in self.module.inputs:
inm = self.module.inputs[inmap]
if inm.type in ('raster', 'vector') and inm.value:
if '@' not in inm.value:
mset = get_mapset_raster(inm.value)
inm.value = inm.value + '@%s' % mset
def run(self, patch=True, clean=True):
"""Run the GRASS command
:param patch: set False if you does not want to patch the results
:type patch: bool
:param clean: set False if you does not want to remove all the stuff
created by GridModule
:type clean: bool
"""
self.module.flags.overwrite = True
self.define_mapset_inputs()
if self.debug:
for wrk in self.get_works():
cmd_exe(wrk)
else:
pool = mltp.Pool(processes=self.processes)
result = pool.map_async(cmd_exe, self.get_works())
result.wait()
if not result.successful():
raise RuntimeError(_("Execution of subprocesses was not successful"))
if patch:
if self.move:
os.environ['GISRC'] = self.gisrc_dst
self.n_mset.current()
self.patch()
os.environ['GISRC'] = self.gisrc_src
self.mset.current()
# copy the outputs from dst => src
routputs = [self.out_prefix + o
for o in select(self.module.outputs, 'raster')]
copy_rasters(routputs, self.gisrc_dst, self.gisrc_src)
else:
self.patch()
if self.log:
# record in the temp directory
from grass.lib.gis import G_tempfile
tmp, dummy = os.path.split(G_tempfile())
tmpdir = os.path.join(tmp, self.module.name)
for k in self.module.outputs:
par = self.module.outputs[k]
if par.typedesc == 'raster' and par.value:
dirpath = os.path.join(tmpdir, par.name)
if not os.path.isdir(dirpath):
os.makedirs(dirpath)
fil = open(os.path.join(dirpath,
self.out_prefix + par.value), 'w+')
fil.close()
if clean:
self.clean_location()
self.rm_tiles()
if self.n_mset:
gisdbase, location = os.path.split(self.move)
self.clean_location(Location(location, gisdbase))
# rm temporary gis_rc
os.remove(self.gisrc_dst)
self.gisrc_dst = None
sht.rmtree(os.path.join(self.move, 'PERMANENT'))
sht.rmtree(os.path.join(self.move, self.mset.name))
def patch(self):
"""Patch the final results."""
bboxes = split_region_tiles(width=self.width, height=self.height)
loc = Location()
mset = loc[self.mset.name]
mset.visible.extend(loc.mapsets())
for otmap in self.module.outputs:
otm = self.module.outputs[otmap]
if otm.typedesc == 'raster' and otm.value:
rpatch_map(otm.value,
self.mset.name, self.msetstr, bboxes,
self.module.flags.overwrite,
self.start_row, self.start_col, self.out_prefix)
def rm_tiles(self):
"""Remove all the tiles."""
# if split, remove tiles
if self.inlist:
grm = Module('g.remove')
for key in self.inlist:
grm(flags='f', type='rast', pattern=self.inlist[key])
def main():
in_vector = options["input"].split("@")[0]
if len(options["input"].split("@")) > 1:
in_mapset = options["input"].split("@")[1]
else:
in_mapset = None
raster_maps = options["raster"].split(
",") # raster file(s) to extract from
output = options["output"]
methods = tuple(options["methods"].split(","))
percentile = (None if options["percentile"] == "" else map(
float, options["percentile"].split(",")))
column_prefix = tuple(options["column_prefix"].split(","))
buffers = options["buffers"].split(",")
types = options["type"].split(",")
layer = options["layer"]
sep = options["separator"]
update = flags["u"]
tabulate = flags["t"]
percent = flags["p"]
remove = flags["r"]
use_label = flags["l"]
empty_buffer_warning = (
"No data in raster map {} within buffer {} around geometry {}")
# Do checks using pygrass
for rmap in raster_maps:
r_map = RasterAbstractBase(rmap)
if not r_map.exist():
grass.fatal("Could not find raster map {}.".format(rmap))
user_mask = False
m_map = RasterAbstractBase("MASK", Mapset().name)
if m_map.exist():
grass.warning("Current MASK is temporarily renamed.")
user_mask = True
unset_mask()
invect = VectorTopo(in_vector)
if not invect.exist():
grass.fatal("Vector file {} does not exist".format(in_vector))
if output:
if output == "-":
out = None
else:
out = open(output, "w")
# Check if input map is in current mapset (and thus editable)
if in_mapset and unicode(in_mapset) != unicode(Mapset()):
grass.fatal(
"Input vector map is not in current mapset and cannot be modified. \
Please consider copying it to current mapset.".format(
output))
buffers = []
for buf in options["buffers"].split(","):
try:
b = float(buf)
if b.is_integer():
buffers.append(int(b))
else:
buffers.append(b)
except:
grass.fatal("")
if b < 0:
grass.fatal("Negative buffer distance not supported!")
### Define column types depenting on statistic, map type and
### DB backend (SQLite supports only double and not real)
# int: statistic produces allways integer precision
# double: statistic produces allways floating point precision
# map_type: precision f statistic depends on map type
int_dict = {
"number": (0, "int", "n"),
"number_null": (1, "int", "null_cells"),
"minimum": (3, "map_type", "min"),
"maximum": (4, "map_type", "max"),
"range": (5, "map_type", "range"),
"average": (6, "double", "mean"),
"average_abs": (7, "double", "mean_of_abs"),
"stddev": (8, "double", "stddev"),
"variance": (9, "double", "variance"),
"coeff_var": (10, "double", "coeff_var"),
"sum": (11, "map_type", "sum"),
"first_quartile": (12, "map_type", "first_quartile"),
"median": (13, "map_type", "median"),
"third_quartile": (14, "map_type", "third_quartile"),
"percentile": (15, "map_type", "percentile"),
}
if len(raster_maps) != len(column_prefix):
grass.fatal(
"Number of maps and number of column prefixes has to be equal!")
# Generate list of required column names and types
col_names = []
valid_labels = []
col_types = []
for p in column_prefix:
rmaptype, val_lab, rcats = raster_type(
raster_maps[column_prefix.index(p)], tabulate, use_label)
valid_labels.append(val_lab)
for b in buffers:
b_str = str(b).replace(".", "_")
if tabulate:
if rmaptype == "double precision":
grass.fatal(
"{} has floating point precision. Can only tabulate integer maps"
.format(raster_maps[column_prefix.index(p)]))
col_names.append("{}_{}_b{}".format(p, "ncats", b_str))
col_types.append("int")
col_names.append("{}_{}_b{}".format(p, "mode", b_str))
col_types.append("int")
col_names.append("{}_{}_b{}".format(p, "null", b_str))
col_types.append("double precision")
col_names.append("{}_{}_b{}".format(p, "area_tot", b_str))
col_types.append("double precision")
for rcat in rcats:
if use_label and valid_labels:
rcat = rcat[0].replace(" ", "_")
else:
rcat = rcat[1]
col_names.append("{}_{}_b{}".format(p, rcat, b_str))
col_types.append("double precision")
else:
for m in methods:
col_names.append("{}_{}_b{}".format(
p, int_dict[m][2], b_str))
col_types.append(rmaptype if int_dict[m][1] ==
"map_type" else int_dict[m][1])
if percentile:
for perc in percentile:
col_names.append("{}_percentile_{}_b{}".format(
p,
int(perc) if (perc).is_integer() else perc, b_str))
col_types.append(rmaptype if int_dict[m][1] ==
"map_type" else int_dict[m][1])
# Open input vector map
in_vect = VectorTopo(in_vector, layer=layer)
in_vect.open(mode="r")
# Get name for temporary map
global TMP_MAPS
TMP_MAPS.append(tmp_map)
# Setup stats collectors
if tabulate:
# Collector for raster category statistics
stats = Module("r.stats", run_=False, stdout_=PIPE)
stats.inputs.sort = "desc"
stats.inputs.null_value = "null"
stats.flags.quiet = True
stats.flags.l = True
if percent:
stats.flags.p = True
stats.flags.n = True
else:
stats.flags.a = True
else:
# Collector for univariat statistics
univar = Module("r.univar", run_=False, stdout_=PIPE)
univar.inputs.separator = sep
univar.flags.g = True
univar.flags.quiet = True
# Add extended statistics if requested
if set(methods).intersection(
set(["first_quartile", "median", "third_quartile"])):
univar.flags.e = True
if percentile is not None:
univar.flags.e = True
univar.inputs.percentile = percentile
# Check if attribute table exists
if not output:
if not in_vect.table:
grass.fatal(
"No attribute table found for vector map {}".format(in_vect))
# Modify table as needed
tab = in_vect.table
tab_name = tab.name
tab_cols = tab.columns
# Add required columns
existing_cols = list(set(tab_cols.names()).intersection(col_names))
if len(existing_cols) > 0:
if not update:
in_vect.close()
grass.fatal(
"Column(s) {} already exist! Please use the u-flag \
if you want to update values in those columns".
format(",".join(existing_cols)))
else:
grass.warning("Column(s) {} already exist!".format(
",".join(existing_cols)))
for e in existing_cols:
idx = col_names.index(e)
del col_names[idx]
del col_types[idx]
tab_cols.add(col_names, col_types)
conn = tab.conn
cur = conn.cursor()
sql_str_start = "UPDATE {} SET ".format(tab_name)
elif output == "-":
print("cat{0}raster_map{0}buffer{0}statistic{0}value".format(sep))
else:
out.write("cat{0}raster_map{0}buffer{0}statistic{0}value{1}".format(
sep, os.linesep))
# Get computational region
grass.use_temp_region()
r = Region()
r.read()
# Adjust region extent to buffer around geometry
# reg = deepcopy(r)
# Create iterator for geometries of all selected types
geoms = chain()
geoms_n = 0
n_geom = 1
for geom_type in types:
geoms_n += in_vect.number_of(geom_type)
if in_vect.number_of(geom_type) > 0:
geoms = chain(in_vect.viter(geom_type))
# Loop over geometries
for geom in geoms:
# Get cat
cat = geom.cat
# Add where clause to UPDATE statement
sql_str_end = " WHERE cat = {};".format(cat)
# Loop over ser provided buffer distances
for buf in buffers:
b_str = str(buf).replace(".", "_")
# Buffer geometry
if buf <= 0:
buffer_geom = geom
else:
buffer_geom = geom.buffer(buf)
# Create temporary vector map with buffered geometry
tmp_vect = VectorTopo(tmp_map, quiet=True)
tmp_vect.open(mode="w")
tmp_vect.write(Boundary(points=buffer_geom[0].to_list()))
# , c_cats=int(cat), set_cats=True
if callable(buffer_geom[1]):
tmp_vect.write(Centroid(x=buffer_geom[1]().x,
y=buffer_geom[1]().y),
cat=int(cat))
else:
tmp_vect.write(Centroid(x=buffer_geom[1].x,
y=buffer_geom[1].y),
cat=int(cat))
#################################################
# How to silence VectorTopo???
#################################################
# Save current stdout
# original = sys.stdout
# f = open(os.devnull, 'w')
# with open('output.txt', 'w') as f:
# sys.stdout = io.BytesIO()
# sys.stdout.fileno() = os.devnull
# sys.stderr = f
# os.environ.update(dict(GRASS_VERBOSE='0'))
tmp_vect.close(build=False)
grass.run_command("v.build", map=tmp_map, quiet=True)
# os.environ.update(dict(GRASS_VERBOSE='1'))
# reg = Region()
# reg.read()
# r.from_vect(tmp_map)
r = align_current(r, buffer_geom[0].bbox())
r.write()
# Check if the following is needed
# needed specially with r.stats -p
# grass.run_command('g.region', vector=tmp_map, flags='a')
# Create a MASK from buffered geometry
if user_mask:
grass.run_command(
"v.to.rast",
input=tmp_map,
output=tmp_map,
use="val",
value=int(cat),
quiet=True,
)
mc_expression = (
"MASK=if(!isnull({0}) && !isnull({0}_MASK), {1}, null())".
format(tmp_map, cat))
grass.run_command("r.mapcalc",
expression=mc_expression,
quiet=True)
else:
grass.run_command(
"v.to.rast",
input=tmp_map,
output="MASK",
use="val",
value=int(cat),
quiet=True,
)
# reg.write()
updates = []
# Compute statistics for every raster map
for rm, rmap in enumerate(raster_maps):
# rmap = raster_maps[rm]
prefix = column_prefix[rm]
if tabulate:
# Get statistics on occurrence of raster categories within buffer
stats.inputs.input = rmap
stats.run()
t_stats = (stats.outputs["stdout"].value.rstrip(
os.linesep).replace(" ", " ").replace(
"no data", "no_data").replace(
" ",
"_b{} = ".format(b_str)).split(os.linesep))
if t_stats == [""]:
grass.warning(
empty_buffer_warning.format(rmap, buf, cat))
continue
if (t_stats[0].split(
"_b{} = ".format(b_str))[0].split("_")[-1] !=
"null"):
mode = (t_stats[0].split(
"_b{} = ".format(b_str))[0].split("_")[-1])
elif len(t_stats) == 1:
mode = "NULL"
else:
mode = (t_stats[1].split(
"_b{} = ".format(b_str))[0].split("_")[-1])
if not output:
updates.append("\t{}_{}_b{} = {}".format(
prefix, "ncats", b_str, len(t_stats)))
updates.append("\t{}_{}_b{} = {}".format(
prefix, "mode", b_str, mode))
area_tot = 0
for l in t_stats:
# check if raster maps has category or not
if len(l.split("=")) == 2:
updates.append("\t{}_{}".format(
prefix, l.rstrip("%")))
elif not l.startswith("null"):
vals = l.split("=")
updates.append("\t{}_{} = {}".format(
prefix,
vals[-2].strip()
if valid_labels[rm] else vals[0].strip(),
vals[-1].strip().rstrip("%"),
))
if not l.startswith("null"):
area_tot += float(
l.rstrip("%").split("= ")[-1])
if not percent:
updates.append("\t{}_{}_b{} = {}".format(
prefix, "area_tot", b_str, area_tot))
else:
out_str = "{1}{0}{2}{0}{3}{0}{4}{0}{5}{6}".format(
sep, cat, prefix, buf, "ncats", len(t_stats),
os.linesep)
out_str += "{1}{0}{2}{0}{3}{0}{4}{0}{5}{6}".format(
sep, cat, prefix, buf, "mode", mode, os.linesep)
area_tot = 0
for l in t_stats:
rcat = (l.split("= ")[1].rstrip(
"_b{} = ".format(b_str))
if valid_labels[rm] else l.split("_")[0])
area = l.split("= ")[-1]
out_str += "{1}{0}{2}{0}{3}{0}{4}{0}{5}{6}".format(
sep,
cat,
prefix,
buf,
"area {}".format(rcat),
area,
os.linesep,
)
if rcat != "null":
area_tot = area_tot + float(
l.rstrip("%").split("= ")[-1])
if not percent:
out_str += "{1}{0}{2}{0}{3}{0}{4}{0}{5}{6}".format(
sep,
cat,
prefix,
buf,
"area total",
area_tot,
os.linesep,
)
if output == "-":
print(out_str.rstrip(os.linesep))
else:
out.write(out_str)
else:
# Get univariate statistics within buffer
univar.inputs.map = rmap
univar.run()
u_stats = (univar.outputs["stdout"].value.rstrip(
os.linesep).replace(
"=", "_b{} = ".format(b_str)).split(os.linesep))
# Test if u_stats is empty and give warning
# Needs to be adjusted to number of requested stats?
if ((percentile and len(u_stats) < 14)
or (univar.flags.e and len(u_stats) < 13)
or len(u_stats) < 12):
grass.warning(
empty_buffer_warning.format(rmap, buf, cat))
break
# Extract statistics for selected methods
for m in methods:
if not output:
# Add to list of UPDATE statements
updates.append("\t{}_{}".format(
prefix,
u_stats[int_dict[m][0]] if is_number(
u_stats[int_dict[m][0]].split(" = ")[1])
else " = ".join([
u_stats[int_dict[m][0]].split(" = ")[0],
"NULL",
]),
))
else:
out_str = "{1}{0}{2}{0}{3}{0}{4}{0}{5}".format(
sep,
cat,
prefix,
buf,
m,
u_stats[int_dict[m][0]].split("= ")[1],
)
if output == "-":
print(out_str)
else:
out.write("{}{}".format(out_str, os.linesep))
if percentile:
perc_count = 0
for perc in percentile:
if not output:
updates.append(
"{}_percentile_{}_b{} = {}".format(
p,
int(perc) if
(perc).is_integer() else perc,
b_str,
u_stats[15 +
perc_count].split("= ")[1],
))
else:
out_str = "{1}{0}{2}{0}{3}{0}{4}{0}{5}".format(
sep,
cat,
prefix,
buf,
"percentile_{}".format(
int(perc) if (
perc).is_integer() else perc),
u_stats[15 + perc_count].split("= ")[1],
)
if output == "-":
print(out_str)
else:
out.write(out_str)
perc_count = perc_count + 1
if not output and len(updates) > 0:
cur.execute("{}{}{}".format(sql_str_start, ",\n".join(updates),
sql_str_end))
# Remove temporary maps
# , stderr=os.devnull, stdout_=os.devnull)
grass.run_command("g.remove",
flags="f",
type="raster",
name="MASK",
quiet=True)
grass.run_command("g.remove",
flags="f",
type="vector",
name=tmp_map,
quiet=True)
# Give progress information
grass.percent(n_geom, geoms_n, 1)
n_geom = n_geom + 1
if not output:
conn.commit()
# Close cursor and DB connection
if not output and not output == "-":
cur.close()
conn.close()
# Update history
grass.vector.vector_history(in_vector)
elif output != "-":
# write results to file
out.close()
if remove and not output:
dropcols = []
selectnum = "select count({}) from {}"
for i in col_names:
thisrow = grass.read_command("db.select",
flags="c",
sql=selectnum.format(i, in_vector))
if int(thisrow) == 0:
dropcols.append(i)
grass.debug("Columns to delete: {}".format(", ".join(dropcols)),
debug=2)
if dropcols:
grass.run_command("v.db.dropcolumn",
map=in_vector,
columns=dropcols)
def unset_mask():
"""Deactivate user mask"""
if RasterRow("MASK", Mapset().name).exist():
grass.run_command("g.rename",
quiet=True,
raster="MASK,{}_MASK".format(tmp_map))
def export_png_in_projection(src_mapset_name, map_name, output_file,
epsg_code,
routpng_flags, compression, wgs84_file,
use_region=True):
"""
:param use_region: use computation region and not map extent
"""
if use_region:
src_region = get_region()
src_proj_string = get_location_proj_string()
# TODO: change only location and not gisdbase?
# we rely on the tmp dir having enough space for our map
tgt_gisdbase = tempfile.mkdtemp()
# this is not needed if we use mkdtemp but why not
tgt_location = 'r.out.png.proj_location_%s' % epsg_code
# because we are using PERMANENT we don't have to create mapset explicitly
tgt_mapset_name = 'PERMANENT'
src_mapset = Mapset(src_mapset_name)
# get source (old) and set target (new) GISRC enviromental variable
# TODO: set environ only for child processes could be enough and it would
# enable (?) parallel runs
src_gisrc = os.environ['GISRC']
tgt_gisrc = gsetup.write_gisrc(tgt_gisdbase,
tgt_location, tgt_mapset_name)
os.environ['GISRC'] = tgt_gisrc
if os.environ.get('WIND_OVERRIDE'):
old_temp_region = os.environ['WIND_OVERRIDE']
del os.environ['WIND_OVERRIDE']
else:
old_temp_region = None
# these lines looks good but anyway when developing the module
# switching location seemed fragile and on some errors (while running
# unfinished module) location was switched in the command line
try:
# the function itself is not safe for other (backgroud) processes
# (e.g. GUI), however we already switched GISRC for us
# and child processes, so we don't influece others
gcore.create_location(dbase=tgt_gisdbase,
location=tgt_location,
epsg=epsg_code,
datum=None,
datum_trans=None)
# Mapset object cannot be created if the real mapset does not exists
tgt_mapset = Mapset(gisdbase=tgt_gisdbase, location=tgt_location,
mapset=tgt_mapset_name)
# set the current mapset in the library
# we actually don't need to switch when only calling modules
# (right GISRC is enough for them)
tgt_mapset.current()
# setting region
if use_region:
# respecting computation region of the src location
# by previous use g.region in src location
# and m.proj and g.region now
# respecting MASK of the src location would be hard
# null values in map are usually enough
tgt_proj_string = get_location_proj_string()
tgt_region = reproject_region(src_region,
from_proj=src_proj_string,
to_proj=tgt_proj_string)
# uses g.region thus and sets region only for child processes
# which is enough now
set_region(tgt_region)
else:
# find out map extent to import everything
# using only classic API because of some problems with pygrass
# on ms windows
rproj_out = gcore.read_command('r.proj', input=map_name,
dbase=src_mapset.gisdbase,
location=src_mapset.location,
mapset=src_mapset.name,
output=map_name, flags='g')
a = gcore.parse_key_val(rproj_out, sep='=', vsep=' ')
gcore.run_command('g.region', **a)
# map import
gcore.run_command('r.proj', input=map_name, dbase=src_mapset.gisdbase,
location=src_mapset.location, mapset=src_mapset.name,
output=map_name)
# actual export
gcore.run_command('r.out.png', input=map_name, output=output_file,
compression=compression, flags=routpng_flags)
# outputting file with WGS84 coordinates
if wgs84_file:
gcore.message("Projecting coordinates to LL WGS 84...")
with open(wgs84_file, 'w') as data_file:
if use_region:
# map which is smaller than region is imported in its own
# small extent, but we export image in region, so we need
# bounds to be for region, not map
# hopefully this is consistent with r.out.png behavior
data_file.write(
map_extent_to_file_content(
proj_to_wgs84(get_region())) + '\n')
else:
# use map to get extent
# the result is actually the same as using map
# if region is the same as map (use_region == False)
data_file.write(
map_extent_to_file_content(
get_map_extent_for_location(map_name))
+ '\n')
finally:
# juts in case we need to do something in the old location
# our callers probably do
os.environ['GISRC'] = src_gisrc
if old_temp_region:
os.environ['WIND_OVERRIDE'] = old_temp_region
# set current in library
src_mapset.current()
# delete the whole gisdbase
# delete file by file to ensure that we are deleting only our things
# exception will be raised when removing non-empty directory
tgt_location_path = Location(gisdbase=tgt_gisdbase,
location=tgt_location).path()
tgt_mapset.delete()
os.rmdir(tgt_location_path)
# dir created by tempfile.mkdtemp() needs to be romved manually
os.rmdir(tgt_gisdbase)
# we have to remove file created by tempfile.mkstemp function
# in write_gisrc function
os.remove(tgt_gisrc)