def p_buffer_operation(self, t):
"""
expression : buff_function LPAREN name COMMA number RPAREN
| buff_function LPAREN expression COMMA number RPAREN
"""
# Generate an intermediate name
name = self.generate_vector_map_name()
# Assign ids to expressions, names and operators.
mapid = 3
operatorid = 5
if t[1] == "buff_p":
if self.debug:
print("v.buffer input=%s type=point distance=%g output=%s" %
(t[mapid], t[operatorid], name))
if self.run:
m = mod.Module(
"v.buffer",
type="point",
input=t[mapid],
distance=float(t[operatorid]),
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[1] == "buff_l":
if self.debug:
print("v.buffer input=%s type=line distance=%g output=%s" %
(t[mapid], t[operatorid], name))
if self.run:
m = mod.Module(
"v.buffer",
type="line",
input=t[mapid],
distance=float(t[operatorid]),
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[1] == "buff_a":
if self.debug:
print("v.buffer input=%s type=area distance=%g output=%s" %
(t[mapid], t[operatorid], name))
if self.run:
m = mod.Module(
"v.buffer",
type="area",
input=t[mapid],
distance=float(t[operatorid]),
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
def __init__(
self,
pid=None,
run=False,
debug=True,
spatial=False,
register_null=False,
dry_run=False,
nprocs=1,
time_suffix=None,
):
TemporalRasterBaseAlgebraParser.__init__(
self,
pid=pid,
run=run,
debug=debug,
spatial=spatial,
register_null=register_null,
dry_run=dry_run,
nprocs=nprocs,
time_suffix=time_suffix,
)
if spatial is True:
self.m_mapcalc = pymod.Module("r.mapcalc", region="union", run_=False)
else:
self.m_mapcalc = pymod.Module("r.mapcalc")
self.m_mremove = pymod.Module("g.remove")
def __init__(self, pid=None, run=False, debug=True, spatial=False):
TemporalAlgebraParser.__init__(self, pid, run, debug, spatial)
self.m_overlay = pygrass.Module("v.overlay", quiet=True, run_=False)
self.m_rename = pygrass.Module("g.rename", quiet=True, run_=False)
self.m_patch = pygrass.Module("v.patch", quiet=True, run_=False)
self.m_mremove = pygrass.Module("g.remove", quiet=True, run_=False)
self.m_buffer = pygrass.Module("v.buffer", quiet=True, run_=False)
def remove_intermediate_vector_maps(self):
if self.debug:
for name in self.names:
print("g.remove type=vector name=%s -f" % (name))
if self.run:
for name in self.names:
m = mod.Module('g.remove', type='vector', name=name,
flags='f', run_=False)
self.cmdlist.add_cmd(m)
def g_region(self):
"""" To Validate the Output """
# Configure a g.region raster='elevation' test
module = gmodules.Module("g.region", raster="elevation")
self.run_module(module=module)
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def __init__(self,
pid=None,
run=False,
debug=True,
spatial=False,
register_null=False,
dry_run=False,
nprocs=1):
TemporalRasterBaseAlgebraParser.__init__(self,
pid=pid,
run=run,
debug=debug,
spatial=spatial,
register_null=register_null,
dry_run=dry_run,
nprocs=nprocs)
self.m_mapcalc = pymod.Module('r3.mapcalc')
self.m_mremove = pymod.Module('g.remove')
def test_flag_ui(self):
"""Test to validate the output of r.flip using flag "g"
"""
# Configure a r.flip flag="ui" test
# Force launching GUI dialog
module = gmodules.Module("r.flip",
input='test',
output='test',
flags="ui")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_overwrite(self):
"""Test to validate the output of r.flip using flag "g"
"""
# Configure a r.flip flag= "overwrite" test
# Allow output files to overwrite existing files
module = gmodules.Module("r.flip",
input='test',
output='test',
flags="overwrite")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_g(self):
"""Test to validate the output of r.flip using flag "g"
"""
# Configure a r.flip flag= "help" test
# Print usage summary
module = gmodules.Module("r.flip",
input='test',
output='test',
flags="help")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_verbose(self):
# Configure a r.gradient flag= "verbose" test
# North_South Direction
module = gmodules.Module("r.gradient",
output='test',
direction='N-S',
range='10, 20',
flags="verbose")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_verbose(self):
# Configure a r.stream.slope flag= "verbose" test
module = gmodules.Module("r.stream.slope",
direction='dir',
elevation="elevation",
gradient='downstream_gradient',
maxcurv='downstream_maxcurv',
mincurv='downstream_mincurv',
flags="verbose")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_ui(self):
"""" To Validate the Output """
# Configure a r.gradient flag= "Overwrite" test
# North-East_South-West Direction
module = gmodules.Module("r.gradient",
output='test',
direction='NE-SW',
range='10, 20',
flags="ui")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def test_flag_help(self):
"""" To Validate the Output """
# Configure a r.gradient flag= "help" test
# South_North Direction
module = gmodules.Module("r.gradient",
output='test',
direction='S-N',
range='10, 20',
flags="help")
self.run_module(module=module)
# it is not clear where to store stdout and stderr
self.assertStdout(actual=module.stdout, reference="r_info_g.ref")
def p_statement_assign(self, t):
"""
statement : NAME EQUALS expression
| NAME EQUALS name
| NAME EQUALS paren_name
"""
# We remove the invalid vector name from the list
if t[3] in self.names:
self.names.pop(t[3])
# We rename the resulting vector map
if self.debug:
print("g.rename vector=%s,%s" % (t[3], t[1]))
if self.run:
m = mod.Module('g.rename', vector=(t[3], t[1]),
overwrite=grass.overwrite(), run_=False)
self.cmdlist.add_cmd(m)
self.remove_intermediate_vector_maps()
def main():
strds = options["input"]
where = options["where"]
nprocs = int(options["nprocs"])
nullmod = pymod.Module("r.null")
nullmod.flags.quiet = True
if options["null"]:
nullmod.inputs.null = options["null"]
elif options["setnull"]:
nullmod.inputs.setnull = options["setnull"]
else:
gscript.fatal(_("Please set 'null' or 'setnull' option"))
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
sp = tgis.open_old_stds(strds, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where, "start_time", None)
if maps is None:
gscript.fatal(
_("Space time raster dataset {st} seems to be "
"empty".format(st=strds)))
return 1
# module queue for parallel execution
process_queue = pymod.ParallelModuleQueue(int(nprocs))
count = 0
num_maps = len(maps)
for mapp in maps:
count += 1
mod = copy.deepcopy(nullmod)
mod.inputs.map = mapp.get_id()
process_queue.put(mod)
if count % 10 == 0:
gscript.percent(count, num_maps, 1)
# Wait for unfinished processes
process_queue.wait()
def p_bool_and_operation(self, t):
"""
expression : name AND name
| expression AND name
| name AND expression
| expression AND expression
| name OR name
| expression OR name
| name OR expression
| expression OR expression
| name XOR name
| expression XOR name
| name XOR expression
| expression XOR expression
| name NOT name
| expression NOT name
| name NOT expression
| expression NOT expression
| name DISOR name
| expression DISOR name
| name DISOR expression
| expression DISOR expression
"""
# Generate an intermediate name
name = self.generate_vector_map_name()
# Assign ids to expressions, names and operators.
firstid = 1
secondid = 3
operatorid = 2
# Define operation commands.
if t[operatorid] == "&":
if self.debug:
print("v.overlay operator=and ainput=%s binput=%s output=%s" %
(t[firstid], t[secondid], name))
if self.run:
m = mod.Module(
"v.overlay",
operator="and",
ainput=t[firstid],
binput=t[secondid],
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[operatorid] == "|":
if self.debug:
print("v.overlay operator=or ainput=%s binput=%s output=%s" %
(t[firstid], t[secondid], name))
if self.run:
m = mod.Module(
"v.overlay",
operator="or",
ainput=t[firstid],
binput=t[secondid],
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[operatorid] == "^":
if self.debug:
print("v.overlay operator=xor ainput=%s binput=%s output=%s" %
(t[firstid], t[secondid], name))
if self.run:
m = mod.Module(
"v.overlay",
operator="xor",
ainput=t[firstid],
binput=t[secondid],
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[operatorid] == "~":
if self.debug:
print("v.overlay operator=not ainput=%s binput=%s output=%s" %
(t[firstid], t[secondid], name))
if self.run:
m = mod.Module(
"v.overlay",
operator="not",
ainput=t[firstid],
binput=t[secondid],
output=name,
run_=False,
)
self.cmdlist.add_cmd(m)
t[0] = name
elif t[operatorid] == "+":
patchinput = t[firstid] + "," + t[secondid]
if self.debug:
print("v.patch input=%s output=%s" % (patchinput, name))
if self.run:
m = mod.Module("v.patch",
input=patchinput,
output=name,
run_=False)
self.cmdlist.add_cmd(m)
t[0] = name
def main():
# Get the options
input = options["input"]
output = options["output"]
where = options["where"]
size = options["size"]
base = options["basename"]
register_null = flags["n"]
method = options["method"]
nprocs = options["nprocs"]
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
overwrite = grass.overwrite()
sp = tgis.open_old_stds(input, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where=where, dbif=dbif)
if not maps:
dbif.close()
grass.warning(
_("Space time raster dataset <%s> is empty") % sp.get_id())
return
new_sp = tgis.check_new_stds(output,
"strds",
dbif=dbif,
overwrite=overwrite)
# Configure the r.neighbor module
neighbor_module = pymod.Module("r.neighbors",
input="dummy",
output="dummy",
run_=False,
finish_=False,
size=int(size),
method=method,
overwrite=overwrite,
quiet=True)
# The module queue for parallel execution
process_queue = pymod.ParallelModuleQueue(int(nprocs))
count = 0
num_maps = len(maps)
new_maps = []
# run r.neighbors all selected maps
for map in maps:
count += 1
map_name = "%s_%i" % (base, count)
new_map = tgis.open_new_map_dataset(
map_name,
None,
type="raster",
temporal_extent=map.get_temporal_extent(),
overwrite=overwrite,
dbif=dbif)
new_maps.append(new_map)
mod = copy.deepcopy(neighbor_module)
mod(input=map.get_id(), output=new_map.get_id())
print(mod.get_bash())
process_queue.put(mod)
# Wait for unfinished processes
process_queue.wait()
# Open the new space time raster dataset
ttype, stype, title, descr = sp.get_initial_values()
new_sp = tgis.open_new_stds(output, "strds", ttype, title, descr, stype,
dbif, overwrite)
num_maps = len(new_maps)
# collect empty maps to remove them
empty_maps = []
# Register the maps in the database
count = 0
for map in new_maps:
count += 1
if count % 10 == 0:
grass.percent(count, num_maps, 1)
# Do not register empty maps
map.load()
if map.metadata.get_min() is None and \
map.metadata.get_max() is None:
if not register_null:
empty_maps.append(map)
continue
# Insert map in temporal database
map.insert(dbif)
new_sp.register_map(map, dbif)
# Update the spatio-temporal extent and the metadata table entries
new_sp.update_from_registered_maps(dbif)
grass.percent(1, 1, 1)
# Remove empty maps
if len(empty_maps) > 0:
names = ""
count = 0
for map in empty_maps:
if count == 0:
count += 1
names += "%s" % (map.get_name())
else:
names += ",%s" % (map.get_name())
grass.run_command("g.remove",
flags='f',
type='raster',
name=names,
quiet=True)
dbif.close()
def main(options, flags):
import grass.pygrass.modules as pymod
import grass.temporal as tgis
from grass.pygrass.vector import VectorTopo
invect = options["input"]
if invect.find("@") != -1:
invect = invect.split("@")[0]
incol = options["date_column"]
indate = options["date"]
endcol = options["final_date_column"]
enddate = options["final_date"]
strds = options["strds"]
nprocs = options["nprocs"]
if strds.find("@") != -1:
strds_name = strds.split("@")[0]
else:
strds_name = strds
output = options["output"]
if options["columns"]:
cols = options["columns"].split(",")
else:
cols = []
mets = options["method"].split(",")
gran = options["granularity"]
dateformat = options["date_format"]
separator = gscript.separator(options["separator"])
update = flags["u"]
create = flags["c"]
stdout = False
if output != "-" and update:
gscript.fatal(_("Cannot combine 'output' option and 'u' flag"))
elif output != "-" and create:
gscript.fatal(_("Cannot combine 'output' option and 'c' flag"))
elif output == "-" and (update or create):
if update and not cols:
gscript.fatal(_("Please set 'columns' option"))
output = invect
else:
stdout = True
if create:
cols = []
for m in mets:
colname = "{st}_{me}".format(st=strds_name, me=m)
cols.append(colname)
try:
pymod.Module(
"v.db.addcolumn",
map=invect,
columns="{col} "
"double precision".format(col=colname),
)
except CalledModuleError:
gscript.fatal(
_("Not possible to create column "
"{col}".format(col=colname)))
gscript.warning(
_("Attribute table of vector {name} will be updated"
"...").format(name=invect))
elif update:
colexist = pymod.Module("db.columns", table=invect,
stdout_=PI).outputs.stdout.splitlines()
for col in cols:
if col not in colexist:
gscript.fatal(
_("Column '{}' does not exist, please create it first".
format(col)))
gscript.warning(
_("Attribute table of vector {name} will be updated"
"...").format(name=invect))
if output != "-" and len(cols) != len(mets):
gscript.fatal(
_("'columns' and 'method' options must have the same "
"number of elements"))
tgis.init()
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
sp = tgis.open_old_stds(strds, "strds", dbif)
if sp.get_temporal_type() == "absolute":
if gran:
delta = int(tgis.gran_to_gran(gran, sp.get_granularity(), True))
if tgis.gran_singular_unit(gran) in ["year", "month"]:
delta = int(tgis.gran_to_gran(gran, "1 day", True))
td = timedelta(delta)
elif tgis.gran_singular_unit(gran) == "day":
delta = tgis.gran_to_gran(gran, sp.get_granularity(), True)
td = timedelta(delta)
elif tgis.gran_singular_unit(gran) == "hour":
td = timedelta(hours=delta)
elif tgis.gran_singular_unit(gran) == "minute":
td = timedelta(minutes=delta)
elif tgis.gran_singular_unit(gran) == "second":
td = timedelta(seconds=delta)
else:
td = None
else:
if sp.get_granularity() >= int(gran):
gscript.fatal(
_("Input granularity is smaller or equal to the {iv}"
" STRDS granularity".format(iv=strds)))
td = int(gran)
if incol and indate:
gscript.fatal(_("Cannot combine 'date_column' and 'date' options"))
elif not incol and not indate:
gscript.fatal(_("You have to fill 'date_column' or 'date' option"))
if incol:
if endcol:
mysql = "SELECT DISTINCT {dc},{ec} from {vmap} order by " "{dc}".format(
vmap=invect, dc=incol, ec=endcol)
else:
mysql = "SELECT DISTINCT {dc} from {vmap} order by " "{dc}".format(
vmap=invect, dc=incol)
try:
dates = pymod.Module("db.select",
flags="c",
stdout_=PI,
stderr_=PI,
sql=mysql)
mydates = dates.outputs["stdout"].value.splitlines()
except CalledModuleError:
gscript.fatal(_("db.select return an error"))
elif indate:
if enddate:
mydates = ["{ida}|{eda}".format(ida=indate, eda=enddate)]
else:
mydates = [indate]
mydates = [indate]
pymap = VectorTopo(invect)
pymap.open("r")
if len(pymap.dblinks) == 0:
try:
pymap.close()
pymod.Module("v.db.addtable", map=invect)
except CalledModuleError:
dbif.close()
gscript.fatal(
_("Unable to add table <%s> to vector map "
"<%s>" % invect))
if pymap.is_open():
pymap.close()
qfeat = pymod.Module("v.category",
stdout_=PI,
stderr_=PI,
input=invect,
option="print")
myfeats = qfeat.outputs["stdout"].value.splitlines()
if stdout:
outtxt = ""
for data in mydates:
try:
start, final = data.split("|")
except ValueError:
start = data
final = None
if sp.get_temporal_type() == "absolute":
fdata = datetime.strptime(start, dateformat)
else:
fdata = int(start)
if final:
sdata = datetime.strptime(final, dateformat)
elif flags["a"]:
sdata = fdata + td
else:
sdata = fdata
fdata = sdata - td
mwhere = "start_time >= '{inn}' and start_time < " "'{out}'".format(
inn=fdata, out=sdata)
lines = None
try:
r_what = pymod.Module(
"t.rast.what",
points=invect,
strds=strds,
layout="timerow",
separator=separator,
flags="v",
where=mwhere,
quiet=True,
stdout_=PI,
stderr_=PI,
nprocs=nprocs,
)
lines = r_what.outputs["stdout"].value.splitlines()
except CalledModuleError:
gscript.warning("t.rast.what faild with where='{}'".format(mwhere))
pass
if incol:
if endcol:
mysql = ("SELECT DISTINCT cat from {vmap} where {dc}='{da}' "
"AND {ec}='{ed}' order by cat".format(vmap=invect,
da=start,
dc=incol,
ed=final,
ec=endcol))
else:
mysql = ("SELECT DISTINCT cat from {vmap} where {dc}='{da}' "
"order by cat".format(vmap=invect, da=start,
dc=incol))
try:
qfeat = pymod.Module("db.select",
flags="c",
stdout_=PI,
stderr_=PI,
sql=mysql)
myfeats = qfeat.outputs["stdout"].value.splitlines()
except CalledModuleError:
gscript.fatal(
_("db.select returned an error for date "
"{da}".format(da=start)))
if not lines and stdout:
for feat in myfeats:
outtxt += "{di}{sep}{da}".format(di=feat,
da=start,
sep=separator)
for n in range(len(mets)):
outtxt += "{sep}{val}".format(val="*", sep=separator)
outtxt += "\n"
if not lines:
continue
x = 0
for line in lines:
vals = line.split(separator)
if vals[0] in myfeats:
try:
nvals = np.array(vals[3:]).astype(float)
except ValueError:
if stdout:
outtxt += "{di}{sep}{da}".format(di=vals[0],
da=start,
sep=separator)
for n in range(len(mets)):
outtxt += "{sep}{val}".format(val="*",
sep=separator)
outtxt += "\n"
continue
if stdout:
outtxt += "{di}{sep}{da}".format(di=vals[0],
da=start,
sep=separator)
for n in range(len(mets)):
result = None
if len(nvals) == 1:
result = nvals[0]
elif len(nvals) > 1:
result = return_value(nvals, mets[n])
if stdout:
if not result:
result = "*"
outtxt += "{sep}{val}".format(val=result,
sep=separator)
else:
try:
if incol:
mywhe = "{dc}='{da}' AND ".format(da=start,
dc=incol)
if endcol:
mywhe += "{dc}='{da}' AND ".format(
da=final, dc=endcol)
mywhe += "cat={ca}".format(ca=vals[0])
pymod.Module(
"v.db.update",
map=output,
column=cols[n],
value=str(result),
where=mywhe,
)
else:
pymod.Module(
"v.db.update",
map=output,
column=cols[n],
value=str(result),
where="cat={ca}".format(ca=vals[0]),
)
except CalledModuleError:
gscript.fatal(_("v.db.update return an error"))
if stdout:
outtxt += "\n"
if x == len(myfeats):
break
else:
x += 1
if stdout:
print(outtxt)
def main(options, flags):
# Get the options
points = options["points"]
coordinates = options["coordinates"]
strds = options["strds"]
output = options["output"]
where = options["where"]
order = options["order"]
layout = options["layout"]
null_value = options["null_value"]
separator = options["separator"]
nprocs = int(options["nprocs"])
write_header = flags["n"]
use_stdin = flags["i"]
#output_cat_label = flags["f"]
#output_color = flags["r"]
#output_cat = flags["i"]
overwrite = gscript.overwrite()
if coordinates and points:
gscript.fatal(_("Options coordinates and points are mutually exclusive"))
if not coordinates and not points and not use_stdin:
gscript.fatal(_("Please specify the coordinates, the points option or use the 's' option to pipe coordinate positions to t.rast.what from stdin, to provide the sampling coordinates"))
if use_stdin:
coordinates_stdin = str(sys.__stdin__.read())
# Check if coordinates are given with site names or IDs
stdin_length = len(coordinates_stdin.split('\n')[0].split())
if stdin_length <= 2:
site_input = False
elif stdin_length >= 3:
site_input = True
else:
site_input = False
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
sp = tgis.open_old_stds(strds, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where=where, order=order,
dbif=dbif)
dbif.close()
if not maps:
gscript.fatal(_("Space time raster dataset <%s> is empty") % sp.get_id())
# Setup separator
if separator == "pipe":
separator = "|"
if separator == "comma":
separator = ","
if separator == "space":
separator = " "
if separator == "tab":
separator = "\t"
if separator == "newline":
separator = "\n"
# Setup flags are disabled due to test issues
flags = ""
#if output_cat_label is True:
# flags += "f"
#if output_color is True:
# flags += "r"
#if output_cat is True:
# flags += "i"
# Configure the r.what module
if points:
r_what = pymod.Module("r.what", map="dummy",
output="dummy", run_=False,
separator=separator, points=points,
overwrite=overwrite, flags=flags,
quiet=True)
elif coordinates:
# Create a list of values
coord_list = coordinates.split(",")
r_what = pymod.Module("r.what", map="dummy",
output="dummy", run_=False,
separator=separator,
coordinates=coord_list,
overwrite=overwrite, flags=flags,
quiet=True)
elif use_stdin:
r_what = pymod.Module("r.what", map="dummy",
output="dummy", run_=False,
separator=separator,
stdin_=coordinates_stdin,
overwrite=overwrite, flags=flags,
quiet=True)
else:
grass.error(_("Please specify points or coordinates"))
if len(maps) < nprocs:
nprocs = len(maps)
# The module queue for parallel execution
process_queue = pymod.ParallelModuleQueue(int(nprocs))
num_maps = len(maps)
# 400 Maps is the absolute maximum in r.what
# We need to determie the number of maps that can be processed
# in parallel
# First estimate the number of maps per process. We use 400 maps
# simultaniously as maximum for a single process
num_loops = int(num_maps / (400 * nprocs))
remaining_maps = num_maps % (400 * nprocs)
if num_loops == 0:
num_loops = 1
remaining_maps = 0
# Compute the number of maps for each process
maps_per_loop = int((num_maps - remaining_maps) / num_loops)
maps_per_process = int(maps_per_loop / nprocs)
remaining_maps_per_loop = maps_per_loop % nprocs
# We put the output files in an ordered list
output_files = []
output_time_list = []
count = 0
for loop in range(num_loops):
file_name = gscript.tempfile() + "_%i"%(loop)
count = process_loop(nprocs, maps, file_name, count, maps_per_process,
remaining_maps_per_loop, output_files,
output_time_list, r_what, process_queue)
process_queue.wait()
gscript.verbose("Number of raster map layers remaining for sampling %i"%(remaining_maps))
if remaining_maps > 0:
# Use a single process if less then 100 maps
if remaining_maps <= 100:
mod = copy.deepcopy(r_what)
mod(map=map_names, output=file_name)
process_queue.put(mod)
else:
maps_per_process = int(remaining_maps / nprocs)
remaining_maps_per_loop = remaining_maps % nprocs
file_name = "out_remain"
process_loop(nprocs, maps, file_name, count, maps_per_process,
remaining_maps_per_loop, output_files,
output_time_list, r_what, process_queue)
# Wait for unfinished processes
process_queue.wait()
# Out the output files in the correct order together
if layout == "row":
one_point_per_row_output(separator, output_files, output_time_list,
output, write_header, site_input)
elif layout == "col":
one_point_per_col_output(separator, output_files, output_time_list,
output, write_header, site_input)
else:
one_point_per_timerow_output(separator, output_files, output_time_list,
output, write_header, site_input)
def main():
# lazy imports
import grass.temporal as tgis
import grass.pygrass.modules as pymod
# Get the options
input = options["input"]
output = options["output"]
where = options["where"]
size = options["size"]
base = options["basename"]
register_null = flags["n"]
use_raster_region = flags["r"]
method = options["method"]
nprocs = options["nprocs"]
time_suffix = options["suffix"]
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
overwrite = grass.overwrite()
sp = tgis.open_old_stds(input, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where=where, dbif=dbif)
if not maps:
dbif.close()
grass.warning(
_("Space time raster dataset <%s> is empty") % sp.get_id())
return
new_sp = tgis.check_new_stds(output,
"strds",
dbif=dbif,
overwrite=overwrite)
# Configure the r.neighbor module
neighbor_module = pymod.Module("r.neighbors",
input="dummy",
output="dummy",
run_=False,
finish_=False,
size=int(size),
method=method,
overwrite=overwrite,
quiet=True)
gregion_module = pymod.Module(
"g.region",
raster="dummy",
run_=False,
finish_=False,
)
# The module queue for parallel execution
process_queue = pymod.ParallelModuleQueue(int(nprocs))
count = 0
num_maps = len(maps)
new_maps = []
# run r.neighbors all selected maps
for map in maps:
count += 1
if sp.get_temporal_type() == 'absolute' and time_suffix == 'gran':
suffix = tgis.create_suffix_from_datetime(
map.temporal_extent.get_start_time(), sp.get_granularity())
map_name = "{ba}_{su}".format(ba=base, su=suffix)
elif sp.get_temporal_type() == 'absolute' and time_suffix == 'time':
suffix = tgis.create_time_suffix(map)
map_name = "{ba}_{su}".format(ba=base, su=suffix)
else:
map_name = tgis.create_numeric_suffix(base, count, time_suffix)
new_map = tgis.open_new_map_dataset(
map_name,
None,
type="raster",
temporal_extent=map.get_temporal_extent(),
overwrite=overwrite,
dbif=dbif)
new_maps.append(new_map)
mod = copy.deepcopy(neighbor_module)
mod(input=map.get_id(), output=new_map.get_id())
if use_raster_region is True:
reg = copy.deepcopy(gregion_module)
reg(raster=map.get_id())
print(reg.get_bash())
print(mod.get_bash())
mm = pymod.MultiModule([reg, mod],
sync=False,
set_temp_region=True)
process_queue.put(mm)
else:
print(mod.get_bash())
process_queue.put(mod)
# Wait for unfinished processes
process_queue.wait()
proc_list = process_queue.get_finished_modules()
# Check return status of all finished modules
error = 0
for proc in proc_list:
if proc.popen.returncode != 0:
grass.error(
_("Error running module: %\n stderr: %s") %
(proc.get_bash(), proc.outputs.stderr))
error += 1
if error > 0:
grass.fatal(_("Error running modules."))
# Open the new space time raster dataset
ttype, stype, title, descr = sp.get_initial_values()
new_sp = tgis.open_new_stds(output, "strds", ttype, title, descr, stype,
dbif, overwrite)
num_maps = len(new_maps)
# collect empty maps to remove them
empty_maps = []
# Register the maps in the database
count = 0
for map in new_maps:
count += 1
if count % 10 == 0:
grass.percent(count, num_maps, 1)
# Do not register empty maps
map.load()
if map.metadata.get_min() is None and \
map.metadata.get_max() is None:
if not register_null:
empty_maps.append(map)
continue
# Insert map in temporal database
map.insert(dbif)
new_sp.register_map(map, dbif)
# Update the spatio-temporal extent and the metadata table entries
new_sp.update_from_registered_maps(dbif)
grass.percent(1, 1, 1)
# Remove empty maps
if len(empty_maps) > 0:
names = ""
count = 0
for map in empty_maps:
if count == 0:
count += 1
names += "%s" % (map.get_name())
else:
names += ",%s" % (map.get_name())
grass.run_command("g.remove",
flags='f',
type='raster',
name=names,
quiet=True)
dbif.close()
def register_map_object_list(type,
map_list,
output_stds,
delete_empty=False,
unit=None,
dbif=None):
"""Register a list of AbstractMapDataset objects in the temporal database
and optional in a space time dataset.
:param type: The type of the map layer (raster, raster_3d, vector)
:param map_list: List of AbstractMapDataset objects
:param output_stds: The output stds
:param delete_empty: Set True to delete empty map layer found in the map_list
:param unit: The temporal unit of the space time dataset
:param dbif: The database interface to be used
"""
import grass.pygrass.modules as pymod
import copy
dbif, connection_state_changed = init_dbif(dbif)
filename = gscript.tempfile(True)
file = open(filename, "w")
empty_maps = []
for map_layer in map_list:
# Read the map data
map_layer.load()
# In case of a empty map continue, do not register empty maps
if delete_empty:
if type in ["raster", "raster_3d", "rast", "rast3d"]:
if (map_layer.metadata.get_min() is None
and map_layer.metadata.get_max() is None):
empty_maps.append(map_layer)
continue
if type == "vector":
if map_layer.metadata.get_number_of_primitives() == 0:
empty_maps.append(map_layer)
continue
start, end = map_layer.get_temporal_extent_as_tuple()
id = map_layer.get_id()
if not end:
end = start
string = "%s|%s|%s\n" % (id, str(start), str(end))
file.write(string)
file.close()
if output_stds:
output_stds_id = output_stds.get_id()
else:
output_stds_id = None
register_maps_in_space_time_dataset(type,
output_stds_id,
unit=unit,
file=filename,
dbif=dbif)
g_remove = pymod.Module("g.remove",
flags="f",
quiet=True,
run_=False,
finish_=True)
# Remove empty maps and unregister them from the temporal database
if len(empty_maps) > 0:
for map in empty_maps:
mod = copy.deepcopy(g_remove)
if map.get_name():
if map.get_type() == "raster":
mod(type="raster", name=map.get_name())
if map.get_type() == "raster3d":
mod(type="raster_3d", name=map.get_name())
if map.get_type() == "vector":
mod(type="vector", name=map.get_name())
mod.run()
if map.is_in_db(dbif):
map.delete(dbif)
if connection_state_changed:
dbif.close()
def aggregate_by_topology(
granularity_list,
granularity,
map_list,
topo_list,
basename,
time_suffix,
offset=0,
method="average",
nprocs=1,
spatial=None,
dbif=None,
overwrite=False,
file_limit=1000,
):
"""Aggregate a list of raster input maps with r.series
:param granularity_list: A list of AbstractMapDataset objects.
The temporal extents of the objects are used
to build the spatio-temporal topology with the
map list objects
:param granularity: The granularity of the granularity list
:param map_list: A list of RasterDataset objects that contain the raster
maps that should be aggregated
:param topo_list: A list of strings of topological relations that are
used to select the raster maps for aggregation
:param basename: The basename of the new generated raster maps
:param time_suffix: Use the granularity truncated start time of the
actual granule to create the suffix for the basename
:param offset: Use a numerical offset for suffix generation
(overwritten by time_suffix)
:param method: The aggregation method of r.series (average,min,max, ...)
:param nprocs: The number of processes used for parallel computation
:param spatial: This indicates if the spatial topology is created as
well: spatial can be None (no spatial topology), "2D"
using west, east, south, north or "3D" using west,
east, south, north, bottom, top
:param dbif: The database interface to be used
:param overwrite: Overwrite existing raster maps
:param file_limit: The maximum number of raster map layers that
should be opened at once by r.series
:return: A list of RasterDataset objects that contain the new map names
and the temporal extent for map registration
"""
import grass.pygrass.modules as pymod
import copy
msgr = get_tgis_message_interface()
dbif, connection_state_changed = init_dbif(dbif)
topo_builder = SpatioTemporalTopologyBuilder()
topo_builder.build(mapsA=granularity_list, mapsB=map_list, spatial=spatial)
# The module queue for parallel execution
process_queue = pymod.ParallelModuleQueue(int(nprocs))
# Dummy process object that will be deep copied
# and be put into the process queue
r_series = pymod.Module(
"r.series",
output="spam",
method=[method],
overwrite=overwrite,
quiet=True,
run_=False,
finish_=False,
)
g_copy = pymod.Module(
"g.copy", raster=["spam", "spamspam"], quiet=True, run_=False, finish_=False
)
output_list = []
count = 0
for granule in granularity_list:
msgr.percent(count, len(granularity_list), 1)
count += 1
aggregation_list = []
if "equal" in topo_list and granule.equal:
for map_layer in granule.equal:
aggregation_list.append(map_layer.get_name())
if "contains" in topo_list and granule.contains:
for map_layer in granule.contains:
aggregation_list.append(map_layer.get_name())
if "during" in topo_list and granule.during:
for map_layer in granule.during:
aggregation_list.append(map_layer.get_name())
if "starts" in topo_list and granule.starts:
for map_layer in granule.starts:
aggregation_list.append(map_layer.get_name())
if "started" in topo_list and granule.started:
for map_layer in granule.started:
aggregation_list.append(map_layer.get_name())
if "finishes" in topo_list and granule.finishes:
for map_layer in granule.finishes:
aggregation_list.append(map_layer.get_name())
if "finished" in topo_list and granule.finished:
for map_layer in granule.finished:
aggregation_list.append(map_layer.get_name())
if "overlaps" in topo_list and granule.overlaps:
for map_layer in granule.overlaps:
aggregation_list.append(map_layer.get_name())
if "overlapped" in topo_list and granule.overlapped:
for map_layer in granule.overlapped:
aggregation_list.append(map_layer.get_name())
if aggregation_list:
msgr.verbose(
_("Aggregating %(len)i raster maps from %(start)s to" " %(end)s")
% (
{
"len": len(aggregation_list),
"start": str(granule.temporal_extent.get_start_time()),
"end": str(granule.temporal_extent.get_end_time()),
}
)
)
if granule.is_time_absolute() is True and time_suffix == "gran":
suffix = create_suffix_from_datetime(
granule.temporal_extent.get_start_time(), granularity
)
output_name = "{ba}_{su}".format(ba=basename, su=suffix)
elif granule.is_time_absolute() is True and time_suffix == "time":
suffix = create_time_suffix(granule)
output_name = "{ba}_{su}".format(ba=basename, su=suffix)
else:
output_name = create_numeric_suffix(
basename, count + int(offset), time_suffix
)
map_layer = RasterDataset("%s@%s" % (output_name, get_current_mapset()))
map_layer.set_temporal_extent(granule.get_temporal_extent())
if map_layer.map_exists() is True and overwrite is False:
msgr.fatal(
_(
"Unable to perform aggregation. Output raster "
"map <%(name)s> exists and overwrite flag was "
"not set" % ({"name": output_name})
)
)
output_list.append(map_layer)
if len(aggregation_list) > 1:
# Create the r.series input file
filename = gscript.tempfile(True)
file = open(filename, "w")
for name in aggregation_list:
string = "%s\n" % (name)
file.write(string)
file.close()
mod = copy.deepcopy(r_series)
mod(file=filename, output=output_name)
if len(aggregation_list) > int(file_limit):
msgr.warning(
_(
"The limit of open files (%i) was "
"reached (%i). The module r.series will "
"be run with flag z, to avoid open "
"files limit exceeding."
% (int(file_limit), len(aggregation_list))
)
)
mod(flags="z")
process_queue.put(mod)
else:
mod = copy.deepcopy(g_copy)
mod(raster=[aggregation_list[0], output_name])
process_queue.put(mod)
process_queue.wait()
if connection_state_changed:
dbif.close()
msgr.percent(1, 1, 1)
return output_list
def main(options, flags):
# Get the options
input = options["input"]
output = options["output"]
where = options["where"]
base = options["basename"]
method = options["type"]
nprocs = int(options["nprocs"])
column = options["column"]
register_null = flags["n"]
t_flag = flags["t"]
s_flag = flags["s"]
v_flag = flags["v"]
b_flag = flags["b"]
z_flag = flags["z"]
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
overwrite = gscript.overwrite()
sp = tgis.open_old_stds(input, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where=where, dbif=dbif)
if not maps:
dbif.close()
gscript.warning(_("Space time raster dataset <%s> is empty") % sp.get_id())
return
# Check the new stvds
new_sp = tgis.check_new_stds(output, "stvds", dbif=dbif,
overwrite=overwrite)
# Setup the flags
flags = ""
if t_flag is True:
flags += "t"
if s_flag is True:
flags += "s"
if v_flag is True:
flags += "v"
if b_flag is True:
flags += "b"
if z_flag is True:
flags += "z"
# Configure the r.to.vect module
to_vector_module = pymod.Module("r.to.vect", input="dummy",
output="dummy", run_=False,
finish_=False, flags=flags,
type=method, overwrite=overwrite,
quiet=True)
# The module queue for parallel execution, except if attribute tables should
# be created. Then force single process use
if t_flag is False:
if nprocs > 1:
nprocs = 1
gscript.warning(_("The number of parellel r.to.vect processes was "\
"reduced to 1 because of the table attribute "\
"creation"))
process_queue = pymod.ParallelModuleQueue(int(nprocs))
count = 0
num_maps = len(maps)
new_maps = []
# run r.to.vect all selected maps
for map in maps:
count += 1
map_name = "%s_%i" % (base, count)
new_map = tgis.open_new_map_dataset(map_name, None, type="vector",
temporal_extent=map.get_temporal_extent(),
overwrite=overwrite, dbif=dbif)
new_maps.append(new_map)
mod = copy.deepcopy(to_vector_module)
mod(input=map.get_id(), output=new_map.get_id())
sys.stderr.write(mod.get_bash() + "\n")
process_queue.put(mod)
if count%10 == 0:
gscript.percent(count, num_maps, 1)
# Wait for unfinished processes
process_queue.wait()
# Open the new space time vector dataset
ttype, stype, title, descr = sp.get_initial_values()
new_sp = tgis.open_new_stds(output, "stvds", ttype, title,
descr, stype, dbif, overwrite)
# collect empty maps to remove them
num_maps = len(new_maps)
empty_maps = []
# Register the maps in the database
count = 0
for map in new_maps:
count += 1
if count%10 == 0:
gscript.percent(count, num_maps, 1)
# Do not register empty maps
map.load()
if map.metadata.get_number_of_primitives() == 0:
if not register_null:
empty_maps.append(map)
continue
# Insert map in temporal database
map.insert(dbif)
new_sp.register_map(map, dbif)
# Update the spatio-temporal extent and the metadata table entries
new_sp.update_from_registered_maps(dbif)
gscript.percent(1, 1, 1)
# Remove empty maps
if len(empty_maps) > 0:
names = ""
count = 0
for map in empty_maps:
if count == 0:
count += 1
names += "%s" % (map.get_name())
else:
names += ",%s" % (map.get_name())
gscript.run_command("g.remove", flags='f', type='vector', name=names,
quiet=True)
dbif.close()
def main(options, flags):
import grass.pygrass.modules as pymod
import grass.temporal as tgis
from grass.pygrass.vector import VectorTopo
invect = options["input"]
if invect.find('@') != -1:
invect = invect.split('@')[0]
incol = options["date_column"]
indate = options["date"]
strds = options["strds"]
if strds.find('@') != -1:
strds_name = strds.split('@')[0]
else:
strds_name = strds
output = options["output"]
cols = options["columns"].split(',')
mets = options["method"].split(',')
gran = options["granularity"]
dateformat = options["date_format"]
separator = gscript.separator(options["separator"])
stdout = False
if output != '-' and flags['u']:
gscript.fatal(_("Cannot combine 'output' option and 'u' flag"))
elif output != '-' and flags['c']:
gscript.fatal(_("Cannot combine 'output' option and 'c' flag"))
elif output == '-' and (flags['u'] or flags['c']):
output = invect
gscript.warning(_("Attribute table of vector {name} will be updated"
"...").format(name=invect))
else:
stdout = True
if flags['c']:
cols = []
for m in mets:
colname = "{st}_{me}".format(st=strds_name, me=m)
cols.append(colname)
try:
pymod.Module("v.db.addcolumn", map=invect, columns="{col} "
"double precision".format(col=colname))
except CalledModuleError:
gscript.fatal(_("Not possible to create column "
"{col}".format(col=colname)))
if output != '-' and len(cols) != len(mets):
gscript.fatal(_("'columns' and 'method' options must have the same "
"number of elements"))
tgis.init()
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
sp = tgis.open_old_stds(strds, "strds", dbif)
if sp.get_temporal_type() == 'absolute':
delta = int(tgis.gran_to_gran(gran, sp.get_granularity(), True))
if tgis.gran_singular_unit(gran) in ['year', 'month']:
delta = int(tgis.gran_to_gran(gran, '1 day', True))
td = timedelta(delta)
elif tgis.gran_singular_unit(gran) == 'day':
delta = tgis.gran_to_gran(gran, sp.get_granularity(), True)
td = timedelta(delta)
elif tgis.gran_singular_unit(gran) == 'hour':
td = timedelta(hours=delta)
elif tgis.gran_singular_unit(gran) == 'minute':
td = timedelta(minutes=delta)
elif tgis.gran_singular_unit(gran) == 'second':
td = timedelta(seconds=delta)
else:
if sp.get_granularity() >= int(gran):
gscript.fatal(_("Input granularity is smaller or equal to the {iv}"
" STRDS granularity".format(iv=strds)))
td = int(gran)
if incol and indate:
gscript.fatal(_("Cannot combine 'date_column' and 'date' options"))
elif not incol and not indate:
gscript.fatal(_("You have to fill 'date_column' or 'date' option"))
elif incol:
try:
dates = pymod.Module("db.select", flags='c', stdout_=PI,
stderr_=PI, sql="SELECT DISTINCT {dc} from "
"{vmap} order by {dc}".format(vmap=invect,
dc=incol))
mydates = dates.outputs["stdout"].value.splitlines()
except CalledModuleError:
gscript.fatal(_("db.select return an error"))
elif indate:
mydates = [indate]
pymap = VectorTopo(invect)
pymap.open('r')
if len(pymap.dblinks) == 0:
try:
pymap.close()
pymod.Module("v.db.addtable", map=invect)
except CalledModuleError:
dbif.close()
gscript.fatal(_("Unable to add table <%s> to vector map "
"<%s>" % invect))
if pymap.is_open():
pymap.close()
qfeat = pymod.Module("v.category", stdout_=PI, stderr_=PI,
input=invect, option='print')
myfeats = qfeat.outputs["stdout"].value.splitlines()
if stdout:
outtxt = ''
for data in mydates:
if sp.get_temporal_type() == 'absolute':
fdata = datetime.strptime(data, dateformat)
else:
fdata = int(data)
if flags['a']:
sdata = fdata + td
mwhere = "start_time >= '{inn}' and end_time < " \
"'{out}'".format(inn=fdata, out=sdata)
else:
sdata = fdata - td
mwhere = "start_time >= '{inn}' and end_time < " \
"'{out}'".format(inn=sdata, out=fdata)
lines = None
try:
r_what = pymod.Module("t.rast.what", points=invect, strds=strds,
layout='timerow', separator=separator,
flags="v", where=mwhere, quiet=True,
stdout_=PI, stderr_=PI)
lines = r_what.outputs["stdout"].value.splitlines()
except CalledModuleError:
pass
if incol:
try:
qfeat = pymod.Module("db.select", flags='c', stdout_=PI,
stderr_=PI, sql="SELECT DISTINCT cat from"
" {vmap} where {dc}='{da}' order by "
"cat".format(vmap=invect, da=data,
dc=incol))
myfeats = qfeat.outputs["stdout"].value.splitlines()
except CalledModuleError:
gscript.fatal(_("db.select returned an error for date "
"{da}".format(da=data)))
if not lines and stdout:
for feat in myfeats:
outtxt += "{di}{sep}{da}".format(di=feat, da=data,
sep=separator)
for n in range(len(mets)):
outtxt += "{sep}{val}".format(val='*', sep=separator)
outtxt += "\n"
if not lines:
continue
x = 0
for line in lines:
vals = line.split(separator)
if vals[0] in myfeats:
try:
nvals = np.array(vals[4:]).astype(np.float)
except ValueError:
if stdout:
outtxt += "{di}{sep}{da}".format(di=vals[0],
da=data,
sep=separator)
for n in range(len(mets)):
outtxt += "{sep}{val}".format(val='*',
sep=separator)
outtxt += "\n"
continue
if stdout:
outtxt += "{di}{sep}{da}".format(di=vals[0], da=data,
sep=separator)
for n in range(len(mets)):
result = return_value(nvals, mets[n])
if stdout:
outtxt += "{sep}{val}".format(val=result,
sep=separator)
else:
try:
if incol:
pymod.Module("v.db.update", map=output,
column=cols[n], value=str(result),
where="{dc}='{da}' AND cat="
"{ca}".format(da=data, ca=vals[0],
dc=incol))
else:
pymod.Module("v.db.update", map=output,
column=cols[n], value=str(result),
where="cat={ca}".format(ca=vals[0]))
except CalledModuleError:
gscript.fatal(_("v.db.update return an error"))
if stdout:
outtxt += "\n"
if x == len(myfeats):
break
else:
x += 1
if stdout:
print(outtxt)
def main():
# lazy imports
import grass.temporal as tgis
import grass.pygrass.modules as pymod
# Get the options
input = options["input"]
base = options["basename"]
where = options["where"]
nprocs = options["nprocs"]
tsuffix = options["suffix"]
mapset = grass.encode(grass.gisenv()["MAPSET"])
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
sp = tgis.open_old_stds(input, "strds")
maps = sp.get_registered_maps_as_objects_with_gaps(where, dbif)
num = len(maps)
# Configure the r.to.vect module
gapfill_module = pymod.Module(
"r.series.interp",
overwrite=grass.overwrite(),
quiet=True,
run_=False,
finish_=False,
)
process_queue = pymod.ParallelModuleQueue(int(nprocs))
gap_list = []
overwrite_flags = {}
# Identify all gaps and create new names
count = 0
for _map in maps:
if _map.get_id() is None:
count += 1
if sp.get_temporal_type() == 'absolute' and tsuffix in [
'gran', 'time'
]:
_id = "{ba}@{ma}".format(ba=base, ma=mapset)
else:
map_name = tgis.create_numeric_suffix(base, num + count,
tsuffix)
_id = "{name}@{ma}".format(name=map_name, ma=mapset)
_map.set_id(_id)
gap_list.append(_map)
if len(gap_list) == 0:
grass.message(_("No gaps found"))
return
# Build the temporal topology
tb = tgis.SpatioTemporalTopologyBuilder()
tb.build(maps)
# Do some checks before computation
for _map in gap_list:
if not _map.get_precedes() or not _map.get_follows():
grass.fatal(
_("Unable to determine successor "
"and predecessor of a gap."))
if len(_map.get_precedes()) > 1:
grass.warning(
_("More than one successor of the gap found. "
"Using the first found."))
if len(_map.get_follows()) > 1:
grass.warning(
_("More than one predecessor of the gap found. "
"Using the first found."))
# Interpolate the maps using parallel processing
result_list = []
for _map in gap_list:
predecessor = _map.get_follows()[0]
successor = _map.get_precedes()[0]
gran = sp.get_granularity()
tmpval, start = predecessor.get_temporal_extent_as_tuple()
end, tmpval = successor.get_temporal_extent_as_tuple()
# Now resample the gap
map_matrix = tgis.AbstractSpaceTimeDataset.resample_maplist_by_granularity(
(_map, ), start, end, gran)
map_names = []
map_positions = []
increment = 1.0 / (len(map_matrix) + 1.0)
position = increment
count = 0
for intp_list in map_matrix:
new_map = intp_list[0]
count += 1
if sp.get_temporal_type() == 'absolute' and tsuffix == 'gran':
suffix = tgis.create_suffix_from_datetime(
new_map.temporal_extent.get_start_time(),
sp.get_granularity())
new_id = "{ba}_{su}@{ma}".format(ba=new_map.get_name(),
su=suffix,
ma=mapset)
elif sp.get_temporal_type() == 'absolute' and tsuffix == 'time':
suffix = tgis.create_time_suffix(new_map)
new_id = "{ba}_{su}@{ma}".format(ba=new_map.get_name(),
su=suffix,
ma=mapset)
else:
map_name = tgis.create_numeric_suffix(new_map.get_name(),
count, tsuffix)
new_id = "{name}@{ma}".format(name=map_name, ma=mapset)
new_map.set_id(new_id)
overwrite_flags[new_id] = False
if new_map.map_exists() or new_map.is_in_db(dbif):
if not grass.overwrite():
grass.fatal(
_("Map with name <%s> already exists. "
"Please use another base name." % (_id)))
else:
if new_map.is_in_db(dbif):
overwrite_flags[new_id] = True
map_names.append(new_map.get_name())
map_positions.append(position)
position += increment
result_list.append(new_map)
mod = copy.deepcopy(gapfill_module)
mod(input=(predecessor.get_map_id(), successor.get_map_id()),
datapos=(0, 1),
output=map_names,
samplingpos=map_positions)
sys.stderr.write(mod.get_bash() + "\n")
process_queue.put(mod)
# Wait for unfinished processes
process_queue.wait()
# Insert new interpolated maps in temporal database and dataset
for _map in result_list:
id = _map.get_id()
if overwrite_flags[id] == True:
if _map.is_time_absolute():
start, end = _map.get_absolute_time()
if _map.is_in_db():
_map.delete(dbif)
_map = sp.get_new_map_instance(id)
_map.set_absolute_time(start, end)
else:
start, end, unit = _map.get_relative_time()
if _map.is_in_db():
_map.delete(dbif)
_map = sp.get_new_map_instance(id)
_map.set_relative_time(start, end, unit)
_map.load()
_map.insert(dbif)
sp.register_map(_map, dbif)
sp.update_from_registered_maps(dbif)
sp.update_command_string(dbif=dbif)
dbif.close()
def main(options, flags):
# lazy imports
import grass.temporal as tgis
import grass.pygrass.modules as pymod
# Get the options
input = options["input"]
output = options["output"]
where = options["where"]
base = options["basename"]
nprocs = int(options["nprocs"])
step = options["step"]
levels = options["levels"]
minlevel = options["minlevel"]
maxlevel = options["maxlevel"]
cut = options["cut"]
time_suffix = options["suffix"]
register_null = flags["n"]
t_flag = flags["t"]
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
overwrite = gscript.overwrite()
sp = tgis.open_old_stds(input, "strds", dbif)
maps = sp.get_registered_maps_as_objects(where=where, dbif=dbif)
if not maps:
dbif.close()
gscript.warning(
_("Space time raster dataset <%s> is empty") % sp.get_id())
return
# Check the new stvds
new_sp = tgis.check_new_stds(output,
"stvds",
dbif=dbif,
overwrite=overwrite)
# Setup the flags
flags = ""
if t_flag is True:
flags += "t"
# Configure the r.to.vect module
contour_module = pymod.Module("r.contour",
input="dummy",
output="dummy",
run_=False,
finish_=False,
flags=flags,
overwrite=overwrite,
quiet=True)
if step:
contour_module.inputs.step = float(step)
if minlevel:
contour_module.inputs.minlevel = float(minlevel)
if maxlevel:
contour_module.inputs.maxlevel = float(maxlevel)
if levels:
contour_module.inputs.levels = levels.split(",")
if cut:
contour_module.inputs.cut = int(cut)
# The module queue for parallel execution, except if attribute tables should
# be created. Then force single process use
if t_flag is False:
if nprocs > 1:
nprocs = 1
gscript.warning(
_("The number of parellel r.contour processes was "
"reduced to 1 because of the table attribute "
"creation"))
process_queue = pymod.ParallelModuleQueue(int(nprocs))
count = 0
num_maps = len(maps)
new_maps = []
# run r.to.vect all selected maps
for map in maps:
count += 1
if sp.get_temporal_type() == 'absolute' and time_suffix == 'gran':
suffix = tgis.create_suffix_from_datetime(
map.temporal_extent.get_start_time(), sp.get_granularity())
map_name = "{ba}_{su}".format(ba=base, su=suffix)
elif sp.get_temporal_type() == 'absolute' and time_suffix == 'time':
suffix = tgis.create_time_suffix(map)
map_name = "{ba}_{su}".format(ba=base, su=suffix)
else:
map_name = tgis.create_numeric_suffix(base, count, time_suffix)
new_map = tgis.open_new_map_dataset(
map_name,
None,
type="vector",
temporal_extent=map.get_temporal_extent(),
overwrite=overwrite,
dbif=dbif)
new_maps.append(new_map)
mod = copy.deepcopy(contour_module)
mod(input=map.get_id(), output=new_map.get_id())
sys.stderr.write(mod.get_bash() + "\n")
process_queue.put(mod)
if count % 10 == 0:
gscript.percent(count, num_maps, 1)
# Wait for unfinished processes
process_queue.wait()
# Open the new space time vector dataset
ttype, stype, title, descr = sp.get_initial_values()
new_sp = tgis.open_new_stds(output, "stvds", ttype, title, descr, stype,
dbif, overwrite)
# collect empty maps to remove them
num_maps = len(new_maps)
empty_maps = []
# Register the maps in the database
count = 0
for map in new_maps:
count += 1
if count % 10 == 0:
gscript.percent(count, num_maps, 1)
# Do not register empty maps
try:
if map.load() is not True:
continue
except FatalError:
continue
if map.metadata.get_number_of_primitives() == 0:
if not register_null:
empty_maps.append(map)
continue
# Insert map in temporal database
map.insert(dbif)
new_sp.register_map(map, dbif)
# Update the spatio-temporal extent and the metadata table entries
new_sp.update_from_registered_maps(dbif)
gscript.percent(1, 1, 1)
# Remove empty maps
if len(empty_maps) > 0:
names = ""
count = 0
for map in empty_maps:
if count == 0:
count += 1
names += "%s" % (map.get_name())
else:
names += ",%s" % (map.get_name())
gscript.run_command("g.remove",
flags='f',
type='vector',
name=names,
quiet=True)
dbif.close()
def main():
# Get the options
datasets = options["inputs"]
file = options["file"]
type = options["type"]
recursive = flags["r"]
force = flags["f"]
if recursive and not force:
grass.fatal(_("The recursive flag works only in conjunction with the force flag: use -rf"))
if datasets and file:
grass.fatal(_("%s= and %s= are mutually exclusive") % ("input", "file"))
# Make sure the temporal database exists
tgis.init()
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
dataset_list = []
# Dataset names as comma separated string
if datasets:
if datasets.find(",") == -1:
dataset_list = (datasets,)
else:
dataset_list = tuple(datasets.split(","))
# Read the dataset list from file
if file:
fd = open(file, "r")
line = True
while True:
line = fd.readline()
if not line:
break
line_list = line.split("\n")
dataset_name = line_list[0]
dataset_list.append(dataset_name)
statement = ""
# Create the pygrass Module object for g.remove
remove = pyg.Module("g.remove", quiet=True, flags='f', run_=False)
for name in dataset_list:
name = name.strip()
sp = tgis.open_old_stds(name, type, dbif)
if recursive and force:
grass.message(_("Removing registered maps and %s" % type))
maps = sp.get_registered_maps_as_objects(dbif=dbif)
map_statement = ""
count = 1
name_list = []
for map in maps:
map.select(dbif)
# We may have multiple layer for a single map, hence we need
# to avoid multiple deletation of the same map,
# but the database entries are still present and must be removed
if map.get_name() not in name_list:
name_list.append(str(map.get_name()))
map_statement += map.delete(dbif=dbif, execute=False)
count += 1
# Delete every 100 maps
if count%100 == 0:
dbif.execute_transaction(map_statement)
if type == "strds":
remove(type="raster", name=name_list, run_=True)
if type == "stvds":
remove(type="vector", name=name_list, run_=True)
if type == "str3ds":
remove(type="raster_3d", name=name_list, run_=True)
map_statement = ""
name_list = []
if map_statement:
dbif.execute_transaction(map_statement)
if name_list:
if type == "strds":
remove(type="raster", name=name_list, run_=True)
if type == "stvds":
remove(type="vector", name=name_list, run_=True)
if type == "str3ds":
remove(type="raster_3d", name=name_list, run_=True)
else:
grass.message(_("Note: registered maps themselves have not been removed, only the %s" % type))
statement += sp.delete(dbif=dbif, execute=False)
# Execute the collected SQL statenents
dbif.execute_transaction(statement)
dbif.close()
