def plottResult(result):
# polygons = TextPolygons(args)
# if args.np > 1:
# # Combine the results if multiprocessing has been used.
# finalResult = Result(polygons, args)
# joinResults(finalResult, result_objects)
###########################################
# Print the output
if args.tab == True:
result.printTab(args)
else:
result.printNexus(args)
if args.localities_in_polygon_tab:
# Print the localities found in a polygon to a tab-separated file
localities_in_polygon_tab = open(args.localities_in_polygon_tab, "w")
localities_in_polygon_tab.write(result.localitiesInPolygons())
localities_in_polygon_tab.close()
if args.localities_in_polygon_shape:
import shapefile
w = shapefile.Writer(shapefile.POINT)
# shape_outfile = args.localities_in_polygon_shape
# print shape_outfile
w.autoBalance = 1
w.field('LATITUDE')
w.field('LONGITUDE')
w.field('SPECIES', 'C', '100')
# for locality in result.localitiesInPolygons():
for locality in result.sampletable:
w.point(float(locality[2]), float(locality[3]))
# Set the field names
# Set record name and type
w.record(SPECIES=str(locality[0]), LATITUDE=float(locality[3]), LONGITUDE=float(locality[2]))
# w.record('First', 'Point')
w.save(args.localities_in_polygon_shape)
# w.save(shape_outfile)
if args.plot == True:
# Generate various plots using R
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:
# Run teh stochastic mapping analysis
import os
import lib.stochasticMapping as stochasticMapping
# Run the stochastic mapping analysis
stochasticMapping.main(args, result)
# Take uncertainty into account
if args.uncertainty == True:
print "\n"
result.sensitivityTest()
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 plottResult(result):
# polygons = TextPolygons(args)
# if args.np > 1:
# # Combine the results if multiprocessing has been used.
# finalResult = Result(polygons, args)
# joinResults(finalResult, result_objects)
###########################################
# Print the output
if args.tab == True:
result.printTab(args)
else:
result.printNexus(args)
if args.localities_in_polygon_tab:
# Print the localities found in a polygon to a tab-separated file
localities_in_polygon_tab = open(args.localities_in_polygon_tab, "w")
localities_in_polygon_tab.write(result.localitiesInPolygons())
localities_in_polygon_tab.close()
if args.localities_in_polygon_shape:
import shapefile
w = shapefile.Writer(shapefile.POINT)
# shape_outfile = args.localities_in_polygon_shape
# print shape_outfile
w.autoBalance = 1
w.field('LATITUDE')
w.field('LONGITUDE')
w.field('SPECIES', 'C', '100')
# for locality in result.localitiesInPolygons():
for locality in result.sampletable:
w.point(float(locality[2]), float(locality[3]))
# Set the field names
# Set record name and type
w.record(SPECIES=str(locality[0]),
LATITUDE=float(locality[3]),
LONGITUDE=float(locality[2]))
# w.record('First', 'Point')
w.save(args.localities_in_polygon_shape)
# w.save(shape_outfile)
if args.plot == True:
# Generate various plots using R
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:
# Run teh stochastic mapping analysis
import os
import lib.stochasticMapping as stochasticMapping
# Run the stochastic mapping analysis
stochasticMapping.main(args, result)
# Take uncertainty into account
if args.uncertainty == True:
print "\n"
result.sensitivityTest()
