def main():
"""Do the real work
"""
#Parse remaining variables
network_map = options['input']
# network_mapset = network_map.split('@')[0]
network = network_map.split('@')[1] if len(
network_map.split('@')) > 1 else None
suffix = options['suffix']
layer = options['layer']
corridor_tolerance = options['corridor_tolerance']
cores = options['cores']
where = None if options['where'] == '' else options['where']
weights = options['weights'].split(',')
s_flag = flags['s']
d_flag = flags['d']
r_flag = flags['r']
ulimit = resource.getrlimit(resource.RLIMIT_NOFILE)
net_hist_str = grass.read_command('v.info', map=network_map,
flags='h').split('\n')[0].split(': ')[1]
dist_cmd_dict = task.cmdstring_to_tuple(net_hist_str)
dist_prefix = dist_cmd_dict[1]['prefix']
#network_prefix = dist_cmd_dict[1]['prefix']
#print(where)
# in_vertices = dist_cmd_dict[1]['input']
#Check if db-connection for edge map exists
con = vect.vector_db(network_map)[int(layer)]
if not con:
grass.fatal("Database connection for map {} \
is not defined for layer {}.".format(network, layer))
#Check if required columns exist and are of required type
required_columns = ['con_id_u', 'from_p', 'to_p', 'cd_u']
if weights:
required_columns += weights
in_columns = vect.vector_columns(network_map, layer=layer)
missing_columns = np.setdiff1d(required_columns, in_columns.keys())
if missing_columns:
grass.fatal("Cannot find the following reqired/requested \
column(s) {} in vector map \
{}.".format(', '.join(missing_columns), network))
#
weight_types = []
# Check properly if column is numeric
for col in required_columns:
if in_columns[col]['type'] not in [
'INTEGER', 'DOUBLE PRECISION', 'REAL'
]:
grass.fatal("Column {} is of type {}. \
Only numeric types (integer, \
real or double precision) \
allowed!".format(col, in_columns[col]['type']))
if col in weights:
weight_types.append(in_columns[col]['type'])
# Extract necessary informartion on edges from attribute table of
# edge map
table_io = StringIO(
unicode(
grass.read_command('v.db.select',
flags='c',
map=network_map,
columns=required_columns,
separator=',',
where=where)))
try:
table_extract = np.genfromtxt(table_io,
delimiter=',',
dtype=None,
names=required_columns)
except:
grass.fatal('No edges selected to compute corridors for...')
# Output result of where-clause and exit (if requested)
if s_flag:
print(table_extract)
#grass.message("con_id_u|from_p|to_p")
#for fid in $selected_edges_ud:
# message_text = $(echo $table_extract | tr ' ' '\n' |
# tr ',' ' ' | awk -v FID=$fid '{if($1==FID) print $1 "|" $2 "|"
# $3}' | head -n 1)
# grass.message(message_text)
sys.exit(0)
#Get unique identifiers for the selected undirected edges
selected_patches = np.unique(
np.append(table_extract['from_p'], table_extract['to_p']))
selected_edges = np.unique(table_extract['con_id_u'])
# activate z-flag if more maps have to be aggregated than ulimit
z_flag = None if len(selected_edges) < ulimit else 'z'
#Check if cost distance raster maps exist
pattern = "{}_patch_*_cost_dist".format(dist_prefix)
patchmaps = grass.read_command('g.list', pattern=pattern,
type='raster').rstrip('\n').split('\n')
for patch in selected_patches:
#Check if cost distance raster maps exist
patchmap = "{}_patch_{}_cost_dist".format(dist_prefix, patch)
if not patchmap in patchmaps:
grass.fatal("Cannot find raster map {}.".format(patchmap))
#Create mapcalculator expressions for cost distance corridors,
# assigning distance values
corridormaps = {}
if d_flag:
pattern = "{}_corridor_*_cost_dist".format(dist_prefix)
corridor_base = 'dist'
else:
pattern = "{}_corridor_[0-9]+$".format(dist_prefix)
corridor_base = 'id'
corridormaps[corridor_base] = grass.read_command(
'g.list', flags='e', pattern=pattern,
type='raster').rstrip('\n').split('\n')
for weight in weights:
pattern = "{}_corridor_[0-9]+_{}".format(dist_prefix, weight)
corridormaps[weight] = grass.read_command(
'g.list', flags='e', pattern=pattern,
type='raster').rstrip('\n').split('\n')
# Setup GRASS modules for raster processing
mapcalc = Module("r.mapcalc", quiet=True, run_=False)
reclass = Module("r.reclass", rules='-', quiet=True, run_=False)
recode = Module("r.recode", rules='-', quiet=True, run_=False)
# Setup paralel module queue if parallel processing is requested
#print(weight_types)
if cores > 1:
mapcalc_queue = ParallelModuleQueue(nprocs=cores)
if 'INTEGER' in weight_types:
reclass_queue = ParallelModuleQueue(nprocs=cores)
if 'REAL' in weight_types or 'DOUBLE PRECISION' in weight_types:
recode_queue = ParallelModuleQueue(nprocs=cores)
corridor_list = []
for edge_id in selected_edges:
edge = table_extract[table_extract['con_id_u'] == edge_id][0]
#print(e.dtype.names)
if d_flag:
corridor = "{}_corridor_{}_cost_dist".format(dist_prefix, edge_id)
#corridor_list.append(corridor)
mc_expression = "{prefix}_corridor_{CON_ID}_cost_dist=if( \
({prefix}_patch_{FROM_P}_cost_dist+ \
{prefix}_patch_{TO_P}_cost_dist) - \
(({prefix}_patch_{FROM_P}_cost_dist+ \
{prefix}_patch_{TO_P}_cost_dist) * \
{cor_tolerance}/100.0)<= \
({prefix}_patch_{FROM_P}_cost_dist + \
{prefix}_patch_{TO_P}_cost_dist), \
({prefix}_patch_{FROM_P}_cost_dist+ \
{prefix}_patch_{TO_P}_cost_dist), \
null())".format(prefix=dist_prefix,
CON_ID=edge['con_id_u'],
FROM_P=edge['from_p'],
TO_P=edge['to_p'],
cor_tolerance=corridor_tolerance)
else:
corridor = "{}_corridor_{}".format(dist_prefix, edge['con_id_u'])
#corridor_list.append(corridor)
# Create mapcalculator expressions for cost distance
# corridors, assigning connection IDs for reclassification
mc_expression = "{prefix}_corridor_{CON_ID}=if( \
({prefix}_patch_{FROM_P}_cost_dist+ \
{prefix}_patch_{TO_P}_cost_dist)- \
(({prefix}_patch_{FROM_P}_cost_dist+ \
{prefix}_patch_{TO_P}_cost_dist)* \
{cor_tolerance}/100.0)<={CD}, \
{CON_ID}, null())".format(prefix=dist_prefix,
CON_ID=edge['con_id_u'],
FROM_P=edge['from_p'],
TO_P=edge['to_p'],
CD=edge['cd_u'],
cor_tolerance=corridor_tolerance)
corridor_list.append(corridor)
#print(corridor)
#print(corridormaps)
if r_flag or corridor not in corridormaps[corridor_base]:
new_mapcalc = copy.deepcopy(mapcalc)
if cores > 1:
calc = new_mapcalc(expression=mc_expression)
mapcalc_queue.put(calc)
else:
calc = new_mapcalc(expression=mc_expression,
region='intersect')
calc.run()
for weight in weights:
if r_flag or corridor not in corridormaps[weight]:
in_map = corridor
out_map = '{}_{}'.format(in_map, weight)
if in_columns[weight]['type'] == 'INTEGER':
new_reclass = copy.deepcopy(reclass)
reclass_rule = "{} = {}".format(edge['con_id_u'],
edge[weight])
rcl = new_reclass(input=in_map,
output=out_map,
stdin_=reclass_rule)
if cores > 1:
reclass_queue.put(rcl)
else:
rcl.run()
if in_columns[weight]['type'] in ['REAL', 'DOUBLE PRECISION']:
new_recode = copy.deepcopy(recode)
recode_rule = "{0}:{0}:{1}:{1}".format(
edge['con_id_u'], edge[weight])
rco = new_recode(input=in_map,
output=out_map,
stdin_=recode_rule)
if cores > 1:
recode_queue.put(rco)
else:
rco.run()
if cores > 1:
mapcalc_queue.wait()
if 'INTEGER' in weight_types:
reclass_queue.wait()
if 'REAL' in weight_types or 'DOUBLE PRECISION' in weight_types:
recode_queue.wait()
grass.verbose('Aggregating corridor maps...')
if d_flag:
grass.run_command('r.series',
flags=z_flag,
quiet=True,
input=','.join(corridor_list),
output='{}_corridors_min_cost_dist_{}'.format(
dist_prefix, suffix),
method='minimum')
else:
#Summarize corridors
if not weights:
print(','.join(corridor_list))
output_map = '{}_corridors_count_{}'.format(dist_prefix, suffix)
grass.run_command('r.series',
flags=z_flag,
quiet=True,
input=','.join(corridor_list),
output=output_map,
method='count')
write_raster_history(output_map)
else:
#Weight corridors according to user requested weights
for weight in weights:
# Generate corridor map list
corridor_map_list = (cm + '_{}'.format(weight)
for cm in corridor_list)
output_map = '{}_corridors_{}_sum_{}'.format(
dist_prefix, weight, suffix)
#Summarize corridors using r.series
grass.run_command('r.series',
flags=z_flag,
quiet=True,
input=corridor_map_list,
output=output_map,
method='sum')
write_raster_history(output_map)
('south', 's'),
('east', 'e'),
('west', 'w'),
('cols', 'cols'),
('rows', 'rows'),
('e-w resol', 'ewres'),
('n-s resol', 'nsres')]
grass_region = ''
for wkey, rkey in kwdata:
grass_region += '%s: %s;' % (wkey, region[rkey])
os.environ['GRASS_REGION'] = grass_region
if __name__ == "__main__":
cmd = gtask.cmdstring_to_tuple(sys.argv[1])
if not cmd[0] or cmd[0] == 'd.mon':
sys.exit(0)
path = os.path.dirname(os.path.abspath(__file__))
mon = os.path.split(path)[-1]
width, height = read_env_file(os.path.join(path, 'env'))
if mon.startswith('wx'):
mapfile = tempfile.NamedTemporaryFile(dir=path).name
if cmd[0] in ('d.barscale', 'd.legend', 'd.northarrow'):
mapfile += '.png'
else:
mapfile += '.ppm'
else:
mapfile = None
adjust_region(width, height)
