def main():
from dateutil.parser import parse
try:
from pygbif import occurrences
from pygbif import species
except ImportError:
grass.fatal(
_("Cannot import pygbif (https://github.com/sckott/pygbif)"
" library."
" Please install it (pip install pygbif)"
" or ensure that it is on path"
" (use PYTHONPATH variable)."))
# Parse input options
output = options["output"]
mask = options["mask"]
species_maps = flags["i"]
no_region_limit = flags["r"]
no_topo = flags["b"]
print_species = flags["p"]
print_species_table = flags["t"]
print_species_shell = flags["g"]
print_occ_number = flags["o"]
allow_no_geom = flags["n"]
hasGeoIssue = flags["s"]
taxa_list = options["taxa"].split(",")
institutionCode = options["institutioncode"]
basisofrecord = options["basisofrecord"]
recordedby = options["recordedby"].split(",")
date_from = options["date_from"]
date_to = options["date_to"]
country = options["country"]
continent = options["continent"]
rank = options["rank"]
# Define static variable
# Initialize cat
cat = 0
# Number of occurrences to fetch in one request
chunk_size = 300
# lat/lon proj string
latlon_crs = [
"+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000",
"+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0,0,0,0,0,0,0",
"+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000 +type=crs",
]
# List attributes available in Darwin Core
# not all attributes are returned in each request
# to avoid key errors when accessing the dictionary returned by pygbif
# presence of DWC keys in the returned dictionary is checked using this list
# The number of keys in this list has to be equal to the number of columns
# in the attribute table and the attributes written for each occurrence
dwc_keys = [
"key",
"taxonRank",
"taxonKey",
"taxonID",
"scientificName",
"species",
"speciesKey",
"genericName",
"genus",
"genusKey",
"family",
"familyKey",
"order",
"orderKey",
"class",
"classKey",
"phylum",
"phylumKey",
"kingdom",
"kingdomKey",
"eventDate",
"verbatimEventDate",
"startDayOfYear",
"endDayOfYear",
"year",
"month",
"day",
"occurrenceID",
"occurrenceStatus",
"occurrenceRemarks",
"Habitat",
"basisOfRecord",
"preparations",
"sex",
"type",
"locality",
"verbatimLocality",
"decimalLongitude",
"decimalLatitude",
"coordinateUncertaintyInMeters",
"geodeticDatum",
"higerGeography",
"continent",
"country",
"countryCode",
"stateProvince",
"gbifID",
"protocol",
"identifier",
"recordedBy",
"identificationID",
"identifiers",
"dateIdentified",
"modified",
"institutionCode",
"lastInterpreted",
"lastParsed",
"references",
"relations",
"catalogNumber",
"occurrenceDetails",
"datasetKey",
"datasetName",
"collectionCode",
"rights",
"rightsHolder",
"license",
"publishingOrgKey",
"publishingCountry",
"lastCrawled",
"specificEpithet",
"facts",
"issues",
"extensions",
"language",
]
# Deinfe columns for attribute table
cols = [
("cat", "INTEGER PRIMARY KEY"),
("g_search", "varchar(100)"),
("g_key", "integer"),
("g_taxonrank", "varchar(50)"),
("g_taxonkey", "integer"),
("g_taxonid", "varchar(50)"),
("g_scientificname", "varchar(255)"),
("g_species", "varchar(255)"),
("g_specieskey", "integer"),
("g_genericname", "varchar(255)"),
("g_genus", "varchar(50)"),
("g_genuskey", "integer"),
("g_family", "varchar(50)"),
("g_familykey", "integer"),
("g_order", "varchar(50)"),
("g_orderkey", "integer"),
("g_class", "varchar(50)"),
("g_classkey", "integer"),
("g_phylum", "varchar(50)"),
("g_phylumkey", "integer"),
("g_kingdom", "varchar(50)"),
("g_kingdomkey", "integer"),
("g_eventdate", "text"),
("g_verbatimeventdate", "varchar(50)"),
("g_startDayOfYear", "integer"),
("g_endDayOfYear", "integer"),
("g_year", "integer"),
("g_month", "integer"),
("g_day", "integer"),
("g_occurrenceid", "varchar(255)"),
("g_occurrenceStatus", "varchar(50)"),
("g_occurrenceRemarks", "varchar(50)"),
("g_Habitat", "varchar(50)"),
("g_basisofrecord", "varchar(50)"),
("g_preparations", "varchar(50)"),
("g_sex", "varchar(50)"),
("g_type", "varchar(50)"),
("g_locality", "varchar(255)"),
("g_verbatimlocality", "varchar(255)"),
("g_decimallongitude", "double precision"),
("g_decimallatitude", "double precision"),
("g_coordinateUncertaintyInMeters", "double precision"),
("g_geodeticdatum", "varchar(50)"),
("g_higerGeography", "varchar(255)"),
("g_continent", "varchar(50)"),
("g_country", "varchar(50)"),
("g_countryCode", "varchar(50)"),
("g_stateProvince", "varchar(50)"),
("g_gbifid", "varchar(255)"),
("g_protocol", "varchar(255)"),
("g_identifier", "varchar(50)"),
("g_recordedby", "varchar(255)"),
("g_identificationid", "varchar(255)"),
("g_identifiers", "text"),
("g_dateidentified", "text"),
("g_modified", "text"),
("g_institutioncode", "varchar(50)"),
("g_lastinterpreted", "text"),
("g_lastparsed", "text"),
("g_references", "varchar(255)"),
("g_relations", "text"),
("g_catalognumber", "varchar(50)"),
("g_occurrencedetails", "text"),
("g_datasetkey", "varchar(50)"),
("g_datasetname", "varchar(255)"),
("g_collectioncode", "varchar(50)"),
("g_rights", "varchar(255)"),
("g_rightsholder", "varchar(255)"),
("g_license", "varchar(50)"),
("g_publishingorgkey", "varchar(50)"),
("g_publishingcountry", "varchar(50)"),
("g_lastcrawled", "text"),
("g_specificepithet", "varchar(50)"),
("g_facts", "text"),
("g_issues", "text"),
("g_extensions", "text"),
("g_language", "varchar(50)"),
]
# maybe no longer required in Python3
set_output_encoding()
# Set temporal filter if requested by user
# Initialize eventDate filter
eventDate = None
# Check if date from is compatible (ISO compliant)
if date_from:
try:
parse(date_from)
except:
grass.fatal("Invalid invalid start date provided")
if date_from and not date_to:
eventDate = "{}".format(date_from)
# Check if date to is compatible (ISO compliant)
if date_to:
try:
parse(date_to)
except:
grass.fatal("Invalid invalid end date provided")
# Check if date to is after date_from
if parse(date_from) < parse(date_to):
eventDate = "{},{}".format(date_from, date_to)
else:
grass.fatal(
"Invalid date range: End date has to be after start date!")
# Set filter on basisOfRecord if requested by user
if basisofrecord == "ALL":
basisOfRecord = None
else:
basisOfRecord = basisofrecord
# Allow also occurrences with spatial issues if requested by user
hasGeospatialIssue = False
if hasGeoIssue:
hasGeospatialIssue = True
# Allow also occurrences without coordinates if requested by user
hasCoordinate = True
if allow_no_geom:
hasCoordinate = False
# Set reprojection parameters
# Set target projection of current LOCATION
proj_info = grass.parse_command("g.proj", flags="g")
target_crs = grass.read_command("g.proj", flags="fj").rstrip()
target = osr.SpatialReference()
# Prefer EPSG CRS definitions
if proj_info["epsg"]:
target.ImportFromEPSG(int(proj_info["epsg"]))
else:
target.ImportFromProj4(target_crs)
# GDAL >= 3 swaps x and y axis, see: github.com/gdal/issues/1546
if int(gdal_version[0]) >= 3:
target.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
if target_crs == "XY location (unprojected)":
grass.fatal("Sorry, XY locations are not supported!")
# Set source projection from GBIF
source = osr.SpatialReference()
source.ImportFromEPSG(4326)
# GDAL >= 3 swaps x and y axis, see: github.com/gdal/issues/1546
if int(gdal_version[0]) >= 3:
source.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
if target_crs not in latlon_crs:
transform = osr.CoordinateTransformation(source, target)
reverse_transform = osr.CoordinateTransformation(target, source)
# Generate WKT polygon to use for spatial filtering if requested
if mask:
if len(mask.split("@")) == 2:
m = VectorTopo(mask.split("@")[0], mapset=mask.split("@")[1])
else:
m = VectorTopo(mask)
if not m.exist():
grass.fatal("Could not find vector map <{}>".format(mask))
m.open("r")
if not m.is_open():
grass.fatal("Could not open vector map <{}>".format(mask))
# Use map Bbox as spatial filter if map contains <> 1 area
if m.number_of("areas") == 1:
region_pol = [area.to_wkt() for area in m.viter("areas")][0]
else:
bbox = (str(m.bbox()).replace("Bbox(", "").replace(
" ", "").rstrip(")").split(","))
region_pol = "POLYGON (({0} {1}, {0} {3}, {2} {3}, {2} {1}, {0} {1}))".format(
bbox[2], bbox[0], bbox[3], bbox[1])
m.close()
else:
# Do not limit import spatially if LOCATION is able to take global data
if no_region_limit:
if target_crs not in latlon_crs:
grass.fatal("Import of data from outside the current region is"
"only supported in a WGS84 location!")
region_pol = None
else:
# Limit import spatially to current region
# if LOCATION is !NOT! able to take global data
# to avoid pprojection ERRORS
region = grass.parse_command("g.region", flags="g")
region_pol = "POLYGON (({0} {1},{0} {3},{2} {3},{2} {1},{0} {1}))".format(
region["e"], region["n"], region["w"], region["s"])
# Do not reproject in latlon LOCATIONS
if target_crs not in latlon_crs:
pol = ogr.CreateGeometryFromWkt(region_pol)
pol.Transform(reverse_transform)
pol = pol.ExportToWkt()
else:
pol = region_pol
# Create output map if not output maps for each species are requested
if (not species_maps and not print_species and not print_species_shell
and not print_occ_number and not print_species_table):
mapname = output
new = Vector(mapname)
new.open("w", tab_name=mapname, tab_cols=cols)
cat = 1
# Import data for each species
for s in taxa_list:
# Get the taxon key if not the taxon key is provided as input
try:
key = int(s)
except:
try:
species_match = species.name_backbone(s,
rank=rank,
strict=False,
verbose=True)
key = species_match["usageKey"]
except:
grass.error(
"Data request for taxon {} failed. Are you online?".format(
s))
continue
# Return matching taxon and alternatives and exit
if print_species:
print("Matching taxon for {} is:".format(s))
print("{} {}".format(species_match["scientificName"],
species_match["status"]))
if "alternatives" in list(species_match.keys()):
print("Alternative matches might be: {}".format(s))
for m in species_match["alternatives"]:
print("{} {}".format(m["scientificName"], m["status"]))
else:
print("No alternatives found for the given taxon")
continue
if print_species_shell:
print("match={}".format(species_match["scientificName"]))
if "alternatives" in list(species_match.keys()):
alternatives = []
for m in species_match["alternatives"]:
alternatives.append(m["scientificName"])
print("alternatives={}".format(",".join(alternatives)))
continue
if print_species_table:
if "alternatives" in list(species_match.keys()):
if len(species_match["alternatives"]) == 0:
print("{0}|{1}|{2}|".format(
s, key, species_match["scientificName"]))
else:
alternatives = []
for m in species_match["alternatives"]:
alternatives.append(m["scientificName"])
print("{0}|{1}|{2}|{3}".format(
s,
key,
species_match["scientificName"],
",".join(alternatives),
))
continue
try:
returns_n = occurrences.search(
taxonKey=key,
hasGeospatialIssue=hasGeospatialIssue,
hasCoordinate=hasCoordinate,
institutionCode=institutionCode,
basisOfRecord=basisOfRecord,
recordedBy=recordedby,
eventDate=eventDate,
continent=continent,
country=country,
geometry=pol,
limit=1,
)["count"]
except:
grass.error(
"Data request for taxon {} faild. Are you online?".format(s))
returns_n = 0
# Exit if search does not give a return
# Print only number of returns for the given search and exit
if print_occ_number:
print("Found {0} occurrences for taxon {1}...".format(
returns_n, s))
continue
elif returns_n <= 0:
grass.warning(
"No occurrences for current search for taxon {0}...".format(s))
continue
elif returns_n >= 200000:
grass.warning(
"Your search for {1} returns {0} records.\n"
"Unfortunately, the GBIF search API is limited to 200,000 records per request.\n"
"The download will be incomplete. Please consider to split up your search."
.format(returns_n, s))
# Get the number of chunks to download
chunks = int(math.ceil(returns_n / float(chunk_size)))
grass.verbose("Downloading {0} occurrences for taxon {1}...".format(
returns_n, s))
# Create a map for each species if requested using map name as suffix
if species_maps:
mapname = "{}_{}".format(s.replace(" ", "_"), output)
new = Vector(mapname)
new.open("w", tab_name=mapname, tab_cols=cols)
cat = 0
# Download the data from GBIF
for c in range(chunks):
# Define offset
offset = c * chunk_size
# Adjust chunk_size to the hard limit of 200,000 records in GBIF API
# if necessary
if offset + chunk_size >= 200000:
chunk_size = 200000 - offset
# Get the returns for the next chunk
returns = occurrences.search(
taxonKey=key,
hasGeospatialIssue=hasGeospatialIssue,
hasCoordinate=hasCoordinate,
institutionCode=institutionCode,
basisOfRecord=basisOfRecord,
recordedBy=recordedby,
eventDate=eventDate,
continent=continent,
country=country,
geometry=pol,
limit=chunk_size,
offset=offset,
)
# Write the returned data to map and attribute table
for res in returns["results"]:
if target_crs not in latlon_crs:
point = ogr.CreateGeometryFromWkt("POINT ({} {})".format(
res["decimalLongitude"], res["decimalLatitude"]))
point.Transform(transform)
x = point.GetX()
y = point.GetY()
else:
x = res["decimalLongitude"]
y = res["decimalLatitude"]
point = Point(x, y)
for k in dwc_keys:
if k not in list(res.keys()):
res.update({k: None})
cat = cat + 1
new.write(
point,
cat=cat,
attrs=(
"{}".format(s),
res["key"],
res["taxonRank"],
res["taxonKey"],
res["taxonID"],
res["scientificName"],
res["species"],
res["speciesKey"],
res["genericName"],
res["genus"],
res["genusKey"],
res["family"],
res["familyKey"],
res["order"],
res["orderKey"],
res["class"],
res["classKey"],
res["phylum"],
res["phylumKey"],
res["kingdom"],
res["kingdomKey"],
"{}".format(res["eventDate"])
if res["eventDate"] else None,
"{}".format(res["verbatimEventDate"])
if res["verbatimEventDate"] else None,
res["startDayOfYear"],
res["endDayOfYear"],
res["year"],
res["month"],
res["day"],
res["occurrenceID"],
res["occurrenceStatus"],
res["occurrenceRemarks"],
res["Habitat"],
res["basisOfRecord"],
res["preparations"],
res["sex"],
res["type"],
res["locality"],
res["verbatimLocality"],
res["decimalLongitude"],
res["decimalLatitude"],
res["coordinateUncertaintyInMeters"],
res["geodeticDatum"],
res["higerGeography"],
res["continent"],
res["country"],
res["countryCode"],
res["stateProvince"],
res["gbifID"],
res["protocol"],
res["identifier"],
res["recordedBy"],
res["identificationID"],
",".join(res["identifiers"]),
"{}".format(res["dateIdentified"])
if res["dateIdentified"] else None,
"{}".format(res["modified"])
if res["modified"] else None,
res["institutionCode"],
"{}".format(res["lastInterpreted"])
if res["lastInterpreted"] else None,
"{}".format(res["lastParsed"])
if res["lastParsed"] else None,
res["references"],
",".join(res["relations"]),
res["catalogNumber"],
"{}".format(res["occurrenceDetails"])
if res["occurrenceDetails"] else None,
res["datasetKey"],
res["datasetName"],
res["collectionCode"],
res["rights"],
res["rightsHolder"],
res["license"],
res["publishingOrgKey"],
res["publishingCountry"],
"{}".format(res["lastCrawled"])
if res["lastCrawled"] else None,
res["specificEpithet"],
",".join(res["facts"]),
",".join(res["issues"]),
",".join(res["extensions"]),
res["language"],
),
)
cat = cat + 1
# Close the current map if a map for each species is requested
if species_maps:
new.table.conn.commit()
new.close()
if not no_topo:
grass.run_command("v.build", map=mapname, option="build")
# Write history to map
grass.vector_history(mapname)
# Close the output map if not a map for each species is requested
if (not species_maps and not print_species and not print_species_shell
and not print_occ_number and not print_species_table):
new.table.conn.commit()
new.close()
if not no_topo:
grass.run_command("v.build", map=mapname, option="build")
# Write history to map
grass.vector_history(mapname)
def main():
try:
import pysptools.eea as eea
except ImportError:
gs.fatal(_("Cannot import pysptools \
(https://pypi.python.org/pypi/pysptools) library."
" Please install it (pip install pysptools)"
" or ensure that it is on path"
" (use PYTHONPATH variable)."))
try:
# sklearn is a dependency of used pysptools functionality
import sklearn
except ImportError:
gs.fatal(_("Cannot import sklearn \
(https://pypi.python.org/pypi/scikit-learn) library."
" Please install it (pip install scikit-learn)"
" or ensure that it is on path"
" (use PYTHONPATH variable)."))
try:
from cvxopt import solvers, matrix
except ImportError:
gs.fatal(_("Cannot import cvxopt \
(https://pypi.python.org/pypi/cvxopt) library."
" Please install it (pip install cvxopt)"
" or ensure that it is on path"
" (use PYTHONPATH variable)."))
# Parse input options
input = options['input']
output = options['output']
prefix = options['prefix']
endmember_n = int(options['endmember_n'])
endmembers = options['endmembers']
if options['maxit']:
maxit = options['maxit']
else:
maxit = 0
extraction_method = options['extraction_method']
unmixing_method = options['unmixing_method']
atgp_init = True if not flags['n'] else False
# List maps in imagery group
try:
maps = gs.read_command('i.group', flags='g', group=input,
quiet=True).rstrip('\n').split('\n')
except:
pass
# Validate input
# q and maxit can be None according to manual, but does not work in current pysptools version
if endmember_n <= 0:
gs.fatal('Number of endmembers has to be > 0')
"""if (extraction_method == 'PPI' or
extraction_method == 'NFINDR'):
gs.fatal('Extraction methods PPI and NFINDR require endmember_n >= 2')
endmember_n = None"""
if maxit <= 0:
maxit = 3 * len(maps)
if endmember_n > len(maps) + 1:
gs.warning('More endmembers ({}) requested than bands in \
input imagery group ({})'.format(endmember_n, len(maps)))
if extraction_method != 'PPI':
gs.fatal('Only PPI method can extract more endmembers than number \
of bands in the imagery group')
if not atgp_init and extraction_method != 'NFINDR':
gs.verbose('ATGP is only taken into account in \
NFINDR extraction method...')
# Get metainformation from input bands
band_types = {}
img = None
n = 0
gs.verbose('Reading imagery group...')
for m in maps:
map = m.split('@')
# Build numpy stack from imagery group
raster = r.raster2numpy(map[0], mapset=map[1])
if raster == np.float64:
raster = float32(raster)
gs.warning('{} is of type Float64.\
Float64 is currently not supported.\
Reducing precision to Float32'.format(raster))
# Determine map type
band_types[map[0]] = get_rastertype(raster)
# Create cube and mask from GRASS internal NoData value
if n == 0:
img = raster
# Create mask from GRASS internal NoData value
mask = mask_rasternd(raster)
else:
img = np.dstack((img, raster))
mask = np.logical_and((mask_rasternd(raster)), mask)
n = n + 1
# Read a mask if present and give waringing if not
# Note that otherwise NoData is read as values
gs.verbose('Checking for MASK...')
try:
MASK = r.raster2numpy('MASK', mapset=getenv('MAPSET')) == 1
mask = np.logical_and(MASK, mask)
MASK = None
except:
pass
if extraction_method == 'NFINDR':
# Extract endmembers from valid pixels using NFINDR function from pysptools
gs.verbose('Extracting endmembers using NFINDR...')
nfindr = eea.NFINDR()
E = nfindr.extract(img, endmember_n, maxit=maxit, normalize=False,
ATGP_init=atgp_init, mask=mask)
elif extraction_method == 'PPI':
# Extract endmembers from valid pixels using PPI function from pysptools
gs.verbose('Extracting endmembers using PPI...')
ppi = eea.PPI()
E = ppi.extract(img, endmember_n, numSkewers=10000, normalize=False,
mask=mask)
elif extraction_method == 'FIPPI':
# Extract endmembers from valid pixels using FIPPI function from pysptools
gs.verbose('Extracting endmembers using FIPPI...')
fippi = eea.FIPPI()
# q and maxit can be None according to manual, but does not work
"""if not maxit and not endmember_n:
E = fippi.extract(img, q=None, normalize=False, mask=mask)
if not maxit:
E = fippi.extract(img, q=endmember_n, normalize=False, mask=mask)
if not endmember_n:
E = fippi.extract(img, q=int(), maxit=maxit, normalize=False,
mask=mask)
else:
E = fippi.extract(img, q=endmember_n, maxit=maxit, normalize=False,
mask=mask)"""
E = fippi.extract(img, q=endmember_n, maxit=maxit, normalize=False,
mask=mask)
# Write output file in format required for i.spec.unmix addon
if output:
gs.verbose('Writing spectra file...')
n = 0
with open(output, 'w') as o:
o.write('# Channels: {}\n'.format('\t'.join(band_types.keys())))
o.write('# Wrote {} spectra line wise.\n#\n'.format(endmember_n))
o.write('Matrix: {0} by {1}\n'.format(endmember_n, len(maps)))
for e in E:
o.write('row{0}: {1}\n'.format(n, '\t'.join([str(i) for i in e])))
n = n + 1
# Write vector map with endmember information if requested
if endmembers:
gs.verbose('Writing vector map with endmembers...')
from grass.pygrass import utils as u
from grass.pygrass.gis.region import Region
from grass.pygrass.vector import Vector
from grass.pygrass.vector import VectorTopo
from grass.pygrass.vector.geometry import Point
# Build attribute table
# Deinfe columns for attribute table
cols = [(u'cat', 'INTEGER PRIMARY KEY')]
for b in band_types.keys():
cols.append((b.replace('.','_'), band_types[b]))
# Get region information
reg = Region()
# Create vector map
new = Vector(endmembers)
new.open('w', tab_name=endmembers, tab_cols=cols)
cat = 1
for e in E:
# Get indices
idx = np.where((img[:,:]==e).all(-1))
# Numpy array is ordered rows, columns (y,x)
if len(idx[0]) == 0 or len(idx[1]) == 0:
gs.warning('Could not compute coordinated for endmember {}. \
Please consider rescaling your data to integer'.format(cat))
cat = cat + 1
continue
coords = u.pixel2coor((idx[1][0], idx[0][0]), reg)
point = Point(coords[1] + reg.ewres / 2.0,
coords[0] - reg.nsres / 2.0)
# Get attributes
n = 0
attr = []
for b in band_types.keys():
if band_types[b] == u'INTEGER':
attr.append(int(e[n]))
else:
attr.append(float(e[n]))
n = n + 1
# Write geometry with attributes
new.write(point, cat=cat,
attrs=tuple(attr))
cat = cat + 1
# Close vector map
new.table.conn.commit()
new.close(build=True)
if prefix:
# Run spectral unmixing
import pysptools.abundance_maps as amaps
if unmixing_method == 'FCLS':
fcls = amaps.FCLS()
result = fcls.map(img, E, normalize=False, mask=mask)
elif unmixing_method == 'NNLS':
nnls = amaps.NNLS()
result = nnls.map(img, E, normalize=False, mask=mask)
elif unmixing_method == 'UCLS':
ucls = amaps.UCLS()
result = ucls.map(img, E, normalize=False, mask=mask)
# Write results
for l in range(endmember_n):
rastname = '{0}_{1}'.format(prefix, l + 1)
r.numpy2raster(result[:,:,l], 'FCELL', rastname)
def main():
# Get the options
input = options["input"]
output = options["output"]
strds = options["strds"]
tempwhere = options["t_where"]
where = options["where"]
methods = options["method"]
percentile = options["percentile"]
overwrite = grass.overwrite()
quiet = True
if grass.verbosity() > 2:
quiet = False
if where == "" or where == " " or where == "\n":
where = None
# Check the number of sample strds and the number of columns
strds_names = strds.split(",")
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
samples = []
first_strds = tgis.open_old_stds(strds_names[0], "strds", dbif)
# Single space time raster dataset
if len(strds_names) == 1:
granu = first_strds.get_granularity()
rows = first_strds.get_registered_maps(
"name,mapset,start_time,end_time", tempwhere, "start_time", dbif)
if not rows:
dbif.close()
grass.fatal(
_("Space time raster dataset <%s> is empty") %
first_strds.get_id())
for row in rows:
start = row["start_time"]
end = row["end_time"]
raster_maps = [
row["name"] + "@" + row["mapset"],
]
s = Sample(start, end, raster_maps, first_strds.get_name(), granu)
samples.append(s)
else:
# Multiple space time raster datasets
for name in strds_names[1:]:
dataset = tgis.open_old_stds(name, "strds", dbif)
if dataset.get_temporal_type() != first_strds.get_temporal_type():
grass.fatal(
_(
"Temporal type of space time raster "
"datasets must be equal\n<%(a)s> of type "
"%(type_a)s do not match <%(b)s> of type "
"%(type_b)s" % {
"a": first_strds.get_id(),
"type_a": first_strds.get_temporal_type(),
"b": dataset.get_id(),
"type_b": dataset.get_temporal_type()
}))
mapmatrizes = tgis.sample_stds_by_stds_topology(
"strds", "strds", strds_names, strds_names[0], False, None,
"equal", False, False)
#TODO check granularity for multiple STRDS
for i in range(len(mapmatrizes[0])):
isvalid = True
mapname_list = []
for mapmatrix in mapmatrizes:
entry = mapmatrix[i]
if entry["samples"]:
sample = entry["samples"][0]
name = sample.get_id()
if name is None:
isvalid = False
break
else:
mapname_list.append(name)
if isvalid:
entry = mapmatrizes[0][i]
map = entry["granule"]
start, end = map.get_temporal_extent_as_tuple()
s = Sample(start, end, mapname_list, name)
samples.append(s)
# Get the layer and database connections of the input vector
if where:
try:
grass.run_command("v.extract",
input=input,
where=where,
output=output)
except CalledModuleError:
dbif.close()
grass.fatal(
_("Unable to run v.extract for vector map"
" <%s> and where <%s>") % (input, where))
else:
gcopy(input, output, 'vector')
msgr = Messenger()
perc_curr = 0
perc_tot = len(samples)
pymap = Vector(output)
try:
pymap.open('r')
except:
dbif.close()
grass.fatal(_("Unable to create vector map <%s>" % output))
pymap.close()
for sample in samples:
raster_names = sample.raster_names
# Call v.what.rast for each raster map
for name in raster_names:
day = sample.printDay()
column_name = "%s_%s" % (sample.strds_name, day)
try:
grass.run_command("v.rast.stats",
map=output,
raster=name,
column=column_name,
method=methods,
percentile=percentile,
quiet=quiet,
overwrite=overwrite)
except CalledModuleError:
dbif.close()
grass.fatal(
_("Unable to run v.what.rast for vector map"
" <%s> and raster map <%s>") % (output, name))
msgr.percent(perc_curr, perc_tot, 1)
perc_curr += 1
dbif.close()
def main():
# Get the options
input = options["input"]
output = options["output"]
strds = options["strds"]
where = options["where"]
tempwhere = options["t_where"]
if output and flags['u']:
grass.fatal(_("Cannot combine 'output' option and 'u' flag"))
elif not output and not flags['u']:
grass.fatal(_("'output' option or 'u' flag must be given"))
elif not output and flags['u']:
grass.warning(_("Attribute table of vector {name} will be updated...").format(name=input))
if where == "" or where == " " or where == "\n":
where = None
overwrite = grass.overwrite()
quiet = True
if grass.verbosity() > 2:
quiet = False
# Check the number of sample strds and the number of columns
strds_names = strds.split(",")
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
samples = []
first_strds = tgis.open_old_stds(strds_names[0], "strds", dbif)
# Single space time raster dataset
if len(strds_names) == 1:
rows = first_strds.get_registered_maps("name,mapset,start_time,end_time",
tempwhere, "start_time",
dbif)
if not rows:
dbif.close()
grass.fatal(_("Space time raster dataset <%s> is empty") %
first_strds.get_id())
for row in rows:
start = row["start_time"]
end = row["end_time"]
raster_maps = [row["name"] + "@" + row["mapset"], ]
s = Sample(start, end, raster_maps, first_strds.get_name())
samples.append(s)
else:
# Multiple space time raster datasets
for name in strds_names[1:]:
dataset = tgis.open_old_stds(name, "strds", dbif)
if dataset.get_temporal_type() != first_strds.get_temporal_type():
grass.fatal(_("Temporal type of space time raster "
"datasets must be equal\n<%(a)s> of type "
"%(type_a)s do not match <%(b)s> of type "
"%(type_b)s" % {"a": first_strds.get_id(),
"type_a": first_strds.get_temporal_type(),
"b": dataset.get_id(),
"type_b": dataset.get_temporal_type()}))
mapmatrizes = tgis.sample_stds_by_stds_topology("strds", "strds",
strds_names,
strds_names[0],
False, None,
"equal", False,
False)
for i in xrange(len(mapmatrizes[0])):
isvalid = True
mapname_list = []
for mapmatrix in mapmatrizes:
entry = mapmatrix[i]
if entry["samples"]:
sample = entry["samples"][0]
name = sample.get_id()
if name is None:
isvalid = False
break
else:
mapname_list.append(name)
if isvalid:
entry = mapmatrizes[0][i]
map = entry["granule"]
start, end = map.get_temporal_extent_as_tuple()
s = Sample(start, end, mapname_list, name)
samples.append(s)
# Get the layer and database connections of the input vector
if output:
gcopy(input, output, 'vector')
else:
output = input
msgr = Messenger()
perc_curr = 0
perc_tot = len(samples)
pymap = Vector(output)
try:
pymap.open('r')
except:
dbif.close()
grass.fatal(_("It is not possible to open the new map %s" % output))
if len(pymap.dblinks) == 0:
try:
grass.run_command("v.db.addtable", map=output)
except CalledModuleError:
dbif.close()
grass.fatal(_("Impossible add table to vector %s" % output))
pymap.close()
for sample in samples:
raster_names = sample.raster_names
# Call v.what.rast for each raster map
for name in raster_names:
coltype = "DOUBLE PRECISION"
# Get raster map type
raster_map = tgis.RasterDataset(name)
raster_map.load()
if raster_map.metadata.get_datatype() == "CELL":
coltype = "INT"
day = sample.printDay()
column_name = "%s_%s" % (sample.strds_name, day)
column_string = "%s %s" % (column_name, coltype)
column_string.replace('.', '_')
try:
grass.run_command("v.db.addcolumn", map=output,
column=column_string,
overwrite=overwrite)
except CalledModuleError:
dbif.close()
grass.fatal(_("Unable to add column %s to vector map "
"<%s> ") % (column_string, output))
try:
grass.run_command("v.what.rast", map=output, raster=name,
column=column_name, where=where,
quiet=quiet)
except CalledModuleError:
dbif.close()
grass.fatal(_("Unable to run v.what.rast for vector map"
" <%s> and raster map <%s>") %
(output, str(raster_names)))
msgr.percent(perc_curr, perc_tot, 1)
perc_curr += 1
dbif.close()
def main():
# lazy imports
import grass.temporal as tgis
from grass.pygrass.utils import copy as gcopy
from grass.pygrass.messages import Messenger
from grass.pygrass.vector import Vector
# Get the options
input = options["input"]
output = options["output"]
strds = options["strds"]
where = options["where"]
tempwhere = options["t_where"]
if output and flags['u']:
grass.fatal(_("Cannot combine 'output' option and 'u' flag"))
elif not output and not flags['u']:
grass.fatal(_("'output' option or 'u' flag must be given"))
elif not output and flags['u']:
grass.warning(
_("Attribute table of vector {name} will be updated...").format(
name=input))
if where == "" or where == " " or where == "\n":
where = None
overwrite = grass.overwrite()
quiet = True
if grass.verbosity() > 2:
quiet = False
# Check the number of sample strds and the number of columns
strds_names = strds.split(",")
# Make sure the temporal database exists
tgis.init()
# We need a database interface
dbif = tgis.SQLDatabaseInterfaceConnection()
dbif.connect()
samples = []
first_strds = tgis.open_old_stds(strds_names[0], "strds", dbif)
# Single space time raster dataset
if len(strds_names) == 1:
granu = first_strds.get_granularity()
rows = first_strds.get_registered_maps(
"name,mapset,start_time,end_time", tempwhere, "start_time", dbif)
if not rows:
dbif.close()
grass.fatal(
_("Space time raster dataset <%s> is empty") %
first_strds.get_id())
for row in rows:
start = row["start_time"]
end = row["end_time"]
raster_maps = [
row["name"] + "@" + row["mapset"],
]
s = Sample(start, end, raster_maps, first_strds.get_name(), granu)
samples.append(s)
else:
# Multiple space time raster datasets
for name in strds_names[1:]:
dataset = tgis.open_old_stds(name, "strds", dbif)
if dataset.get_temporal_type() != first_strds.get_temporal_type():
grass.fatal(
_(
"Temporal type of space time raster "
"datasets must be equal\n<%(a)s> of type "
"%(type_a)s do not match <%(b)s> of type "
"%(type_b)s" % {
"a": first_strds.get_id(),
"type_a": first_strds.get_temporal_type(),
"b": dataset.get_id(),
"type_b": dataset.get_temporal_type()
}))
mapmatrizes = tgis.sample_stds_by_stds_topology(
"strds", "strds", strds_names, strds_names[0], False, None,
"equal", False, False)
#TODO check granularity for multiple STRDS
for i in range(len(mapmatrizes[0])):
isvalid = True
mapname_list = []
for mapmatrix in mapmatrizes:
entry = mapmatrix[i]
if entry["samples"]:
sample = entry["samples"][0]
name = sample.get_id()
if name is None:
isvalid = False
break
else:
mapname_list.append(name)
if isvalid:
entry = mapmatrizes[0][i]
map = entry["granule"]
start, end = map.get_temporal_extent_as_tuple()
s = Sample(start, end, mapname_list, name)
samples.append(s)
# Get the layer and database connections of the input vector
if output:
gcopy(input, output, 'vector')
else:
output = input
msgr = Messenger()
perc_curr = 0
perc_tot = len(samples)
pymap = Vector(output)
try:
pymap.open('r')
except:
dbif.close()
grass.fatal(_("Unable to create vector map <%s>" % output))
if len(pymap.dblinks) == 0:
try:
pymap.close()
grass.run_command("v.db.addtable", map=output)
except CalledModuleError:
dbif.close()
grass.fatal(
_("Unable to add table <%s> to vector map <%s>" % output))
if pymap.is_open():
pymap.close()
for sample in samples:
raster_names = sample.raster_names
# Call v.what.rast for each raster map
for name in raster_names:
coltype = "DOUBLE PRECISION"
# Get raster map type
raster_map = tgis.RasterDataset(name)
raster_map.load()
if raster_map.metadata.get_datatype() == "CELL":
coltype = "INT"
day = sample.printDay()
column_name = "%s_%s" % (sample.strds_name, day)
column_string = "%s %s" % (column_name, coltype)
column_string.replace('.', '_')
try:
grass.run_command("v.db.addcolumn",
map=output,
column=column_string,
overwrite=overwrite)
except CalledModuleError:
dbif.close()
grass.fatal(
_("Unable to add column %s to vector map "
"<%s> ") % (column_string, output))
try:
grass.run_command("v.what.rast",
map=output,
raster=name,
column=column_name,
where=where,
quiet=quiet)
except CalledModuleError:
dbif.close()
grass.fatal(
_("Unable to run v.what.rast for vector map"
" <%s> and raster map <%s>") %
(output, str(raster_names)))
msgr.percent(perc_curr, perc_tot, 1)
perc_curr += 1
dbif.close()
sorted_cats_by_area = [cats_list for (area0s_list,cats_list) in sorted(zip(area0s_list,cats_list))]
from grass.pygrass.vector import Vector, VectorTopo
streams = Vector('streams')
streamsTopo = VectorTopo('streams')
# to get list of lines:
# streamsTopo.open(mode='r')
# streamsTopo.next()
streamsTopo.open()
"""
# THIS IS HOW YOU UPDATE A TABLE!!!!
v.db_addcolumn(map='streams', columns='stream_number_ascending int')
#streams.table.columns.add('stream_number_ascending','int')
streams = Vector('streams')
streams.open('rw')
cur = streams.table.conn.cursor()
for i in range(len(sorted_new_river_numbers)):
print i
cur.execute("update streams set stream_number_ascending=" +
str(river_numbers[i]) + " where cat=" + str(cats_list[i]))
streams.table.conn.commit()
streams.build()
# Should overwrite river_numbers, eventually
colNames = np.array(vector_db_select('streams')['columns'])
colValues = np.array(vector_db_select('streams')['values'].values())
river_numbers = colValues[:, colNames == 'stream_number_ascending'].astype(
int).squeeze()
# Could also just use our river_numbers vector from before
def main():
try:
from pygbif import occurrences
from pygbif import species
except ImportError:
grass.fatal(_("Cannot import pygbif (https://github.com/sckott/pygbif)"
" library."
" Please install it (pip install pygbif)"
" or ensure that it is on path"
" (use PYTHONPATH variable)."))
# Parse input options
output = options['output']
mask = options['mask']
species_maps = flags['i']
no_region_limit = flags['r']
no_topo = flags['b']
print_species = flags['p']
print_species_table = flags['t']
print_species_shell = flags['g']
print_occ_number = flags['o']
allow_no_geom = flags['n']
hasGeoIssue = flags['s']
taxa_list = options['taxa'].split(',')
institutionCode = options['institutioncode']
basisofrecord = options['basisofrecord']
recordedby = options['recordedby'].split(',')
date_from = options['date_from']
date_to = options['date_to']
country = options['country']
continent = options['continent']
rank = options['rank']
# Define static variable
#Initialize cat
cat = 0
# Number of occurrences to fetch in one request
chunk_size = 300
# lat/lon proj string
latlon_crs = ['+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000',
'+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0,0,0,0,0,0,0']
# List attributes available in Darwin Core
# not all attributes are returned in each request
# to avoid key errors when accessing the dictionary returned by pygbif
# presence of DWC keys in the returned dictionary is checked using this list
# The number of keys in this list has to be equal to the number of columns
# in the attribute table and the attributes written for each occurrence
dwc_keys = ['key', 'taxonRank', 'taxonKey', 'taxonID', 'scientificName',
'species', 'speciesKey', 'genericName', 'genus', 'genusKey',
'family', 'familyKey', 'order', 'orderKey', 'class',
'classKey', 'phylum', 'phylumKey', 'kingdom', 'kingdomKey',
'eventDate', 'verbatimEventDate', 'startDayOfYear',
'endDayOfYear', 'year', 'month', 'day', 'occurrenceID',
'occurrenceStatus', 'occurrenceRemarks', 'Habitat',
'basisOfRecord', 'preparations', 'sex', 'type', 'locality',
'verbatimLocality', 'decimalLongitude', 'decimalLatitude',
'geodeticDatum', 'higerGeography', 'continent', 'country',
'countryCode', 'stateProvince', 'gbifID', 'protocol',
'identifier', 'recordedBy', 'identificationID', 'identifiers',
'dateIdentified', 'modified', 'institutionCode',
'lastInterpreted', 'lastParsed', 'references', 'relations',
'catalogNumber', 'occurrenceDetails', 'datasetKey',
'datasetName', 'collectionCode', 'rights', 'rightsHolder',
'license', 'publishingOrgKey', 'publishingCountry',
'lastCrawled', 'specificEpithet', 'facts', 'issues',
'extensions', 'language']
# Deinfe columns for attribute table
cols = [('cat', 'INTEGER PRIMARY KEY'),
('g_search', 'varchar(100)'),
('g_key', 'integer'),
('g_taxonrank', 'varchar(50)'),
('g_taxonkey', 'integer'),
('g_taxonid', 'varchar(50)'),
('g_scientificname', 'varchar(255)'),
('g_species', 'varchar(255)'),
('g_specieskey', 'integer'),
('g_genericname', 'varchar(255)'),
('g_genus', 'varchar(50)'),
('g_genuskey', 'integer'),
('g_family', 'varchar(50)'),
('g_familykey', 'integer'),
('g_order', 'varchar(50)'),
('g_orderkey', 'integer'),
('g_class', 'varchar(50)'),
('g_classkey', 'integer'),
('g_phylum', 'varchar(50)'),
('g_phylumkey', 'integer'),
('g_kingdom', 'varchar(50)'),
('g_kingdomkey', 'integer'),
('g_eventdate', 'text'),
('g_verbatimeventdate', 'varchar(50)'),
('g_startDayOfYear', 'integer'),
('g_endDayOfYear', 'integer'),
('g_year', 'integer'),
('g_month', 'integer'),
('g_day', 'integer'),
('g_occurrenceid', 'varchar(255)'),
('g_occurrenceStatus', 'varchar(50)'),
('g_occurrenceRemarks', 'varchar(50)'),
('g_Habitat', 'varchar(50)'),
('g_basisofrecord', 'varchar(50)'),
('g_preparations', 'varchar(50)'),
('g_sex', 'varchar(50)'),
('g_type', 'varchar(50)'),
('g_locality', 'varchar(255)'),
('g_verbatimlocality', 'varchar(255)'),
('g_decimallongitude', 'double precision'),
('g_decimallatitude', 'double precision'),
('g_geodeticdatum', 'varchar(50)'),
('g_higerGeography', 'varchar(255)'),
('g_continent', 'varchar(50)'),
('g_country', 'varchar(50)'),
('g_countryCode', 'varchar(50)'),
('g_stateProvince', 'varchar(50)'),
('g_gbifid', 'varchar(255)'),
('g_protocol', 'varchar(255)'),
('g_identifier', 'varchar(50)'),
('g_recordedby', 'varchar(255)'),
('g_identificationid', 'varchar(255)'),
('g_identifiers', 'text'),
('g_dateidentified', 'text'),
('g_modified', 'text'),
('g_institutioncode', 'varchar(50)'),
('g_lastinterpreted', 'text'),
('g_lastparsed', 'text'),
('g_references', 'varchar(255)'),
('g_relations', 'text'),
('g_catalognumber', 'varchar(50)'),
('g_occurrencedetails', 'text'),
('g_datasetkey', 'varchar(50)'),
('g_datasetname', 'varchar(255)'),
('g_collectioncode', 'varchar(50)'),
('g_rights', 'varchar(255)'),
('g_rightsholder', 'varchar(255)'),
('g_license', 'varchar(50)'),
('g_publishingorgkey', 'varchar(50)'),
('g_publishingcountry', 'varchar(50)'),
('g_lastcrawled', 'text'),
('g_specificepithet', 'varchar(50)'),
('g_facts', 'text'),
('g_issues', 'text'),
('g_extensions', 'text'),
('g_language', 'varchar(50)')]
set_output_encoding()
# Set temporal filter if requested by user
# Initialize eventDate filter
eventDate = None
# Check if date from is compatible (ISO compliant)
if date_from:
try:
parse(date_from)
except:
grass.fatal("Invalid invalid start date provided")
if date_from and not date_to:
eventDate = '{}'.format(date_from)
# Check if date to is compatible (ISO compliant)
if date_to:
try:
parse(date_to)
except:
grass.fatal("Invalid invalid end date provided")
# Check if date to is after date_from
if parse(date_from) < parse(date_to):
eventDate = '{},{}'.format(date_from, date_to)
else:
grass.fatal("Invalid date range: End date has to be after start date!")
# Set filter on basisOfRecord if requested by user
if basisofrecord == 'ALL':
basisOfRecord = None
else:
basisOfRecord = basisofrecord
# Allow also occurrences with spatial issues if requested by user
hasGeospatialIssue = False
if hasGeoIssue:
hasGeospatialIssue = True
# Allow also occurrences without coordinates if requested by user
hasCoordinate = True
if allow_no_geom:
hasCoordinate = False
# Set reprojection parameters
# Set target projection of current LOCATION
target_crs = grass.read_command('g.proj', flags='fj').rstrip(os.linesep)
target = osr.SpatialReference(target_crs)
target.ImportFromProj4(target_crs)
if target == 'XY location (unprojected)':
grass.fatal("Sorry, XY locations are not supported!")
# Set source projection from GBIF
source = osr.SpatialReference()
source.ImportFromEPSG(4326)
if target_crs not in latlon_crs:
transform = osr.CoordinateTransformation(source, target)
reverse_transform = osr.CoordinateTransformation(target, source)
# Generate WKT polygon to use for spatial filtering if requested
if mask:
if len(mask.split('@')) == 2:
m = VectorTopo(mask.split('@')[0], mapset=mask.split('@')[1])
else:
m = VectorTopo(mask)
if not m.exist():
grass.fatal('Could not find vector map <{}>'.format(mask))
m.open('r')
if not m.is_open():
grass.fatal('Could not open vector map <{}>'.format(mask))
# Use map Bbox as spatial filter if map contains <> 1 area
if m.number_of('areas') == 1:
region_pol = [area.to_wkt() for area in m.viter("areas")][0]
else:
bbox = str(m.bbox()).replace('Bbox(', '').replace(' ', '').rstrip(')').split(',')
region_pol = 'POLYGON(({0} {1}, {0} {3}, {2} {3}, {2} {1}, {0} {1}))'.format(bbox[2],
bbox[0], bbox[3], bbox[1])
m.close()
else:
# Do not limit import spatially if LOCATION is able to take global data
if no_region_limit:
if target_crs not in latlon_crs:
grass.fatal('Import of data from outside the current region is'
'only supported in a WGS84 location!')
region_pol = None
else:
# Limit import spatially to current region
# if LOCATION is !NOT! able to take global data
# to avoid pprojection ERRORS
region = grass.parse_command('g.region', flags='g')
region_pol = 'POLYGON(({0} {1}, {0} {3}, {2} {3}, {2} {1}, {0} {1}))'.format(region['e'],
region['n'], region['w'], region['s'])
# Do not reproject in latlon LOCATIONS
if target_crs not in latlon_crs:
pol = ogr.CreateGeometryFromWkt(region_pol)
pol.Transform(reverse_transform)
pol = pol.ExportToWkt()
else:
pol = region_pol
# Create output map if not output maps for each species are requested
if not species_maps and not print_species and not print_species_shell and not print_occ_number and not print_species_table:
mapname = output
new = Vector(mapname)
new.open('w', tab_name=mapname, tab_cols=cols)
cat = 1
# Import data for each species
for s in taxa_list:
# Get the taxon key if not the taxon key is provided as input
try:
key = int(s)
except:
try:
species_match = species.name_backbone(s, rank=rank,
strict=False,
verbose=True)
key = species_match['usageKey']
except:
grass.error('Data request for taxon {} failed. Are you online?'.format(s))
continue
# Return matching taxon and alternatives and exit
if print_species:
print('Matching taxon for {} is:'.format(s))
print('{} {}'.format(species_match['scientificName'], species_match['status']))
if 'alternatives' in list(species_match.keys()):
print('Alternative matches might be:'.format(s))
for m in species_match['alternatives']:
print('{} {}'.format(m['scientificName'], m['status']))
else:
print('No alternatives found for the given taxon')
continue
if print_species_shell:
print('match={}'.format(species_match['scientificName']))
if 'alternatives' in list(species_match.keys()):
alternatives = []
for m in species_match['alternatives']:
alternatives.append(m['scientificName'])
print('alternatives={}'.format(','.join(alternatives)))
continue
if print_species_table:
if 'alternatives' in list(species_match.keys()):
if len(species_match['alternatives']) == 0:
print('{0}|{1}|{2}|'.format(s, key, species_match['scientificName']))
else:
alternatives = []
for m in species_match['alternatives']:
alternatives.append(m['scientificName'])
print('{0}|{1}|{2}|{3}'.format(s, key, species_match['scientificName'],
','.join(alternatives)))
continue
try:
returns_n = occurrences.search(taxonKey=key,
hasGeospatialIssue=hasGeospatialIssue,
hasCoordinate=hasCoordinate,
institutionCode=institutionCode,
basisOfRecord=basisOfRecord,
recordedBy=recordedby,
eventDate=eventDate,
continent=continent,
country=country,
geometry=pol,
limit=1)['count']
except:
grass.error('Data request for taxon {} faild. Are you online?'.format(s))
returns_n = 0
# Exit if search does not give a return
# Print only number of returns for the given search and exit
if print_occ_number:
grass.message('Found {0} occurrences for taxon {1}...'.format(returns_n, s))
continue
elif returns_n <= 0:
grass.warning('No occurrences for current search for taxon {0}...'.format(s))
continue
elif returns_n >= 200000:
grass.warning('Your search for {1} returns {0} records.\n'
'Unfortunately, the GBIF search API is limited to 200,000 records per request.\n'
'The download will be incomplete. Please consider to split up your search.'.format(returns_n, s))
# Get the number of chunks to download
chunks = int(math.ceil(returns_n / float(chunk_size)))
grass.verbose('Downloading {0} occurrences for taxon {1}...'.format(returns_n, s))
# Create a map for each species if requested using map name as suffix
if species_maps:
mapname = '{}_{}'.format(s.replace(' ', '_'), output)
new = Vector(mapname)
new.open('w', tab_name=mapname, tab_cols=cols)
cat = 0
# Download the data from GBIF
for c in range(chunks):
# Define offset
offset = c * chunk_size
# Adjust chunk_size to the hard limit of 200,000 records in GBIF API
# if necessary
if offset + chunk_size >= 200000:
chunk_size = 200000 - offset
# Get the returns for the next chunk
returns = occurrences.search(taxonKey=key,
hasGeospatialIssue=hasGeospatialIssue,
hasCoordinate=hasCoordinate,
institutionCode=institutionCode,
basisOfRecord=basisOfRecord,
recordedBy=recordedby,
eventDate=eventDate,
continent=continent,
country=country,
geometry=pol,
limit=chunk_size,
offset=offset)
# Write the returned data to map and attribute table
for res in returns['results']:
if target_crs not in latlon_crs:
point = ogr.CreateGeometryFromWkt('POINT ({} {})'.format(res['decimalLongitude'], res['decimalLatitude']))
point.Transform(transform)
x = point.GetX()
y = point.GetY()
else:
x = res['decimalLongitude']
y = res['decimalLatitude']
point = Point(x, y)
for k in dwc_keys:
if k not in list(res.keys()):
res.update({k: None})
cat = cat + 1
new.write(point, cat=cat, attrs=(
'{}'.format(s),
res['key'],
res['taxonRank'],
res['taxonKey'],
res['taxonID'],
res['scientificName'],
res['species'],
res['speciesKey'],
res['genericName'],
res['genus'],
res['genusKey'],
res['family'],
res['familyKey'],
res['order'],
res['orderKey'],
res['class'],
res['classKey'],
res['phylum'],
res['phylumKey'],
res['kingdom'],
res['kingdomKey'],
'{}'.format(res['eventDate']) if res['eventDate'] else None,
'{}'.format(res['verbatimEventDate']) if res['verbatimEventDate'] else None,
res['startDayOfYear'],
res['endDayOfYear'],
res['year'],
res['month'],
res['day'],
res['occurrenceID'],
res['occurrenceStatus'],
res['occurrenceRemarks'],
res['Habitat'],
res['basisOfRecord'],
res['preparations'],
res['sex'],
res['type'],
res['locality'],
res['verbatimLocality'],
res['decimalLongitude'],
res['decimalLatitude'],
res['geodeticDatum'],
res['higerGeography'],
res['continent'],
res['country'],
res['countryCode'],
res['stateProvince'],
res['gbifID'],
res['protocol'],
res['identifier'],
res['recordedBy'],
res['identificationID'],
','.join(res['identifiers']),
'{}'.format(res['dateIdentified']) if res['dateIdentified'] else None,
'{}'.format(res['modified']) if res['modified'] else None,
res['institutionCode'],
'{}'.format(res['lastInterpreted']) if res['lastInterpreted'] else None,
'{}'.format(res['lastParsed']) if res['lastParsed'] else None,
res['references'],
','.join(res['relations']),
res['catalogNumber'],
'{}'.format(res['occurrenceDetails']) if res['occurrenceDetails'] else None,
res['datasetKey'],
res['datasetName'],
res['collectionCode'],
res['rights'],
res['rightsHolder'],
res['license'],
res['publishingOrgKey'],
res['publishingCountry'],
'{}'.format(res['lastCrawled']) if res['lastCrawled'] else None,
res['specificEpithet'],
','.join(res['facts']),
','.join(res['issues']),
','.join(res['extensions']),
res['language'],))
cat = cat + 1
# Close the current map if a map for each species is requested
if species_maps:
new.table.conn.commit()
new.close()
if not no_topo:
grass.run_command('v.build', map=mapname, option='build')
# Close the output map if not a map for each species is requested
if not species_maps and not print_species and not print_species_shell and not print_occ_number and not print_species_table:
new.table.conn.commit()
new.close()
if not no_topo:
grass.run_command('v.build', map=mapname, option='build')
#!/usr/bin/env python
from grass.pygrass.vector import Vector
obce = Vector('obce_bod', mapset='ruian')
obce.open('r')
for prvek in obce:
print (u"{:<25}: {:.0f} {:.0f}".format(prvek.attrs['nazev'], prvek.x, prvek.y))
obce.close()
#!/usr/bin/env python3
from grass.pygrass.vector import Vector
obce = Vector('obce_bod', mapset='ruian')
obce.open('r')
for prvek in obce:
print ("{:<25}: {:.0f} {:.0f}".format(prvek.attrs['nazev'], prvek.x, prvek.y))
obce.close()