def main(locality_file):
if args.l_shape:
localities = ShapeLocalities(args, locality_file)
if args.localities:
localities = TextLocalities(args, locality_file)
from lib.result import Result
# This next part is probably redundant, sinch assigning the 'polygons' variable is now done in the main() function.
if args.p_shape:
polygons = ShapePolygons(args)
if args.polygons:
polygons = TextPolygons(args)
result = Result(polygons, args)
done = 0
# Index the geotiff files if available.
if args.tif:
from lib.readGeoTiff import indexTiffs
try:
index = indexTiffs(args.tif)
except AttributeError:
sys.exit("[ Error ] No such file \'%s\'" % args.tif[0])
# Read the locality data and test if the coordinates
# are located in any of the polygons.
# For each locality record ...
if args.localities or args.l_shape:
# localities = TextLocalities(args, locality_file)
numLoc = localities.getNrLocalities()
result.setSpeciesNames(localities)
for locality in localities.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
# locality[0] = species name, locality[1] = latitude, locality[2] = longitude
# if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
if pointInPolygon(polygon[1], locality) == True:
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon, index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
if args.gbif:
gbifData = GbifLocalities(args)
result.setSpeciesNames(gbifData)
numLoc = gbifData.getNrLocalities()
# For each GBIF locality record ...
for locality in gbifData.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
# if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
if pointInPolygon(polygon[1], locality) == True:
result.setResult(locality, polygon[0])
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon, index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
# Clean up
if args.np > 1:
try:
os.remove(locality_file)
except:
pass
sys.stderr.write("\n")
return result
def main():
from lib.result import Result
# Create list to store the geotif objects in.
polygons = Polygons()
result = Result(polygons, args)
done = 0
# Index the geotiff files if available.
if args.tif:
from lib.readGeoTiff import indexTiffs
try:
index = indexTiffs(args.tif)
except AttributeError:
sys.exit("[ Error ] No such file \'%s\'" % args.tif[0])
# Read the locality data and test if the coordinates
# are located in any of the polygons.
# For each locality record ...
if args.localities:
localities = MyLocalities()
numLoc = localities.getQuant()
result.setSpeciesNames(localities)
for locality in localities.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
if localities.getCoOrder() == "lat-long":
# locality[0] = species name, locality[1] = latitude, locality[2] = longitude
if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon, index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
else:
# locality[0] = species name, locality[1] = longitude, locality[2] = latitude
if pointInPolygon(polygon[1], locality[1], locality[2]) == True:
if args.tif:
if elevationTest(locality[2], locality[1], polygon, index) == True:
result.setResult(locality[0], polygon[0])
if args.gbif:
gbifData = GbifLocalities()
result.setSpeciesNames(gbifData)
numLoc = gbifData.getQuant()
# For each GBIF locality record ...
for locality in gbifData.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
result.setResult(locality, polygon[0])
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon, index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
sys.stderr.write("\n")
result.printNexus(args.out)
if args.plot == True:
import os
from lib.plot import prepare_plots
prepare_plots(result, polygons)
#__ GUI STUFF
dir_output = args.dir_output # Working directory
path_script = args.path_script
cmd="Rscript %s/R/graphical_output.R %s %s %s %s %s %s" \
% (path_script,path_script, "coordinates.sgc.txt", "polygons.sgc.txt", "sampletable.sgc.txt", "speciestable.sgc.txt",dir_output)
os.system(cmd)
if args.stochastic_mapping == True:
import os
import lib.stochasticMapping as stochasticMapping
# Run the stochastic mapping analysis
stochasticMapping.main(args, result)
def main():
from lib.result import Result
# Create list to store the geotif objects in.
polygons = Polygons()
result = Result(polygons, args)
done = 0
# Index the geotiff files if available.
if args.tif:
from lib.readGeoTiff import indexTiffs
try:
index = indexTiffs(args.tif)
except AttributeError:
sys.exit("[ Error ] No such file \'%s\'" % args.tif[0])
# Read the locality data and test if the coordinates
# are located in any of the polygons.
# For each locality record ...
if args.localities:
localities = MyLocalities()
numLoc = localities.getQuant()
result.setSpeciesNames(localities)
for locality in localities.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
if localities.getCoOrder() == "lat-long":
# locality[0] = species name, locality[1] = latitude, locality[2] = longitude
if pointInPolygon(polygon[1], locality[2],
locality[1]) == True:
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon,
index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
else:
# locality[0] = species name, locality[1] = longitude, locality[2] = latitude
if pointInPolygon(polygon[1], locality[1],
locality[2]) == True:
if args.tif:
if elevationTest(locality[2], locality[1], polygon,
index) == True:
result.setResult(locality[0], polygon[0])
if args.gbif:
gbifData = GbifLocalities()
result.setSpeciesNames(gbifData)
numLoc = gbifData.getQuant()
# For each GBIF locality record ...
for locality in gbifData.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
if pointInPolygon(polygon[1], locality[2],
locality[1]) == True:
result.setResult(locality, polygon[0])
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon,
index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
sys.stderr.write("\n")
result.printNexus(args.out)
if args.plot == True:
import os
from lib.plot import prepare_plots
prepare_plots(result, polygons)
#__ GUI STUFF
dir_output = args.dir_output # Working directory
path_script = args.path_script
cmd="Rscript %s/R/graphical_output.R %s %s %s %s %s %s" \
% (path_script,path_script, "coordinates.sgc.txt", "polygons.sgc.txt", "sampletable.sgc.txt", "speciestable.sgc.txt",dir_output)
os.system(cmd)
if args.stochastic_mapping == True:
import os
import lib.stochasticMapping as stochasticMapping
# Run the stochastic mapping analysis
stochasticMapping.main(args, result)
def main(locality_file):
if args.l_shape:
localities = ShapeLocalities(args, locality_file)
if args.localities:
localities = TextLocalities(args, locality_file)
from lib.result import Result
# This next part is probably redundant, sinch assigning the 'polygons' variable is now done in the main() function.
if args.p_shape:
polygons = ShapePolygons(args)
if args.polygons:
polygons = TextPolygons(args)
result = Result(polygons, args)
done = 0
# Index the geotiff files if available.
if args.tif:
from lib.readGeoTiff import indexTiffs
try:
index = indexTiffs(args.tif)
except AttributeError:
sys.exit("[ Error ] No such file \'%s\'" % args.tif[0])
# Read the locality data and test if the coordinates
# are located in any of the polygons.
# For each locality record ...
if args.localities or args.l_shape:
# localities = TextLocalities(args, locality_file)
numLoc = localities.getNrLocalities()
result.setSpeciesNames(localities)
for locality in localities.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
# locality[0] = species name, locality[1] = latitude, locality[2] = longitude
# if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
if pointInPolygon(polygon[1], locality) == True:
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon,
index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
if args.gbif:
gbifData = GbifLocalities(args)
result.setSpeciesNames(gbifData)
numLoc = gbifData.getNrLocalities()
# For each GBIF locality record ...
for locality in gbifData.getLocalities():
done = print_progress(done, numLoc)
# ... and for each polygon ...
for polygon in polygons.getPolygons():
# ... test if the locality record is found in the polygon.
# if pointInPolygon(polygon[1], locality[2], locality[1]) == True:
if pointInPolygon(polygon[1], locality) == True:
result.setResult(locality, polygon[0])
# Test if elevation files are available.
if args.tif:
if elevationTest(locality[1], locality[2], polygon,
index) == True:
# Store the result
result.setResult(locality, polygon[0])
else:
# Store the result
result.setResult(locality, polygon[0])
# Clean up
if args.np > 1:
try:
os.remove(locality_file)
except:
pass
sys.stderr.write("\n")
return result