def get_json(points):
"""
:param points: (long,lat)
:return: a count of species and their scientific names
"""
try:
# parse input coordinates
longa, lat = float(points.split(",")[0]), float(points.split(",")[1])
i, j = table.grid_cell.array_index(longa, lat, (1, 1))
point = r.points(longa, lat)
cell = grid_cells[i][j]
result = []
for species in cell.species:
par = k.parser(species)
if par.inside(point):
# check cached results to see if each specie's range map contains this point
now = datetime.datetime.now()
result.append({
"class": par.class_name,
"order": par.order,
"family": par.family,
"scientific_name": species,
"url": par.url,
"index_date": str(now)
})
result.sort(key=lambda x: x["scientific_name"])
return jsonify(count=len(result), species=result), 200
except:
message = """unknown error, try specieslookup.berkeley.edu/about/ for instructions on query formatting"""
return message, 400
def inside(self, query_point):
# This takes in the point object and checks to see if rangemap intersects the query point
if query_point.x < self.min_x or query_point.x > self.max_x or query_point.y < self.min_y or query_point.y > self.max_y:
return False
a = False
b = False
for good in self.outer:
ps = [r.points(dot[0], dot[1]) for dot in good]
poly = r.polygon(ps)
if poly.is_inside(query_point):
a = True
for good in self.inner:
ps = [r.points(dot[0], dot[1]) for dot in good]
poly = r.polygon(ps)
if poly.is_inside(query_point):
b = True
return a and not b
def get(points):
"""
:param points: (long,lat)
:return: a count of species and their scientific names
"""
try:
# parse input coordinates
longa, lat = float(points.split(",")[0]), float(points.split(",")[1])
i, j = table.grid_cell.array_index(longa, lat, (1, 1))
point = r.points(longa, lat)
cell = grid_cells[i][j]
result = []
for species in cell.species:
par = k.parser(species)
if par.inside(point):
# check cached results to see if each specie's range map contains this point
result.append(species)
result.append("count: " + str(len(result)))
return str(result), 200
except:
message = """unknown error, try specieslookup.berkeley.edu/about/ for instructions on query formatting"""
return message, 400
import matplotlib
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
import numpy as np
import ray_casting as r
coord = np.array([[0.2, 0.2], [0.4, 0.2], [0.2, 0.9], [0.9, 0.2]])
test = r.points(0.4, 0.9)
ps = [r.points(dot[0], dot[1]) for dot in coord]
poly = r.polygon(ps)
fig, ax = plt.subplots()
patches = []
num_polygon = 1
polygon = Polygon(coord, closed=True)
patches.append(polygon)
p = PatchCollection(patches, cmap=matplotlib.cm.jet, alpha=0.4)
ax.add_collection(p)
plt.plot([test.x], [test.y], 'ro')
plt.title("tested point (" + str(test.x) + " ," + str(test.y) +
") is contained in polygon" + str(poly.is_inside(test)))
plt.show()
# This tests the ray_casting module
import os
import time
import kmlparserclass as k
import ray_casting as r
point = r.points(-7.2, 6)
all_species = [name.split('.')[0] for name in next(os.walk('kml'))[1] if name]
accoutants = [k.parser(specie) for specie in all_species]
start = time.clock()
result = [
account.scientific_name for account in accoutants if account.inside(point)
]
stop = time.clock()
print(stop - start)
print(result)
# this is debugging for lookup_table
# need to create the class that filters request
import kmlparserclass as k
from ray_casting import points
aspecie = k.parser("Adenomera_ajurauna")
point=points(-46.5,-23.825)
aspecie.visualize(point)
print(aspecie.inside(point))
def format_vertices(arr):
return np.array([[float(arr[i][0]), float(arr[i][1])]
for i in range(len(arr))])
polys = root.findall(".//{0}Polygon".format(namespace))
for each_polygon in polys:
outer = each_polygon.findall(".//{0}outerBoundaryIs".format(namespace))
inner = each_polygon.findall(".//{0}innerBoundaryIs".format(namespace))
for each in outer:
cords = find_coordinates(each)
good = format_vertices(cords)
print(good.shape)
ps = [r.points(dot[0], dot[1]) for dot in good]
print()
poly = r.polygon(ps)
test = r.points(-2.8, 6.5)
fig, ax = plt.subplots()
patches = []
num_polygon = 1
polygon = Polygon(good, closed=True)
patches.append(polygon)
p = PatchCollection(patches, cmap=matplotlib.cm.jet, alpha=0.4)
ax.add_collection(p)
plt.plot([test.x], [test.y], 'ro')
plt.title("tested point (" + str(test.x) + " ," + str(test.y) +
all_species = [
name.split('.')[0] for name in list(os.walk('range_shapefiles'))[0][2]
if name
]
start = time.clock()
grid_cells = table.create_table()
end = time.clock()
print(end - start, " seconds for updating grid")
# print(grid_cells)
points = "-63.043301,-2.217128"
count = [[len(cell.species) for cell in row] for row in grid_cells]
print(sum([sum(row) for row in count]))
start = time.clock()
print(points)
longa, lat = float(points.split(",")[0]), float(points.split(",")[1])
i, j = table.grid_cell.array_index(longa, lat, (1, 1))
print(i, j)
point = r.points(longa, lat)
cell = grid_cells[i][j]
result = []
for species in cell.species:
par = k.parser(species)
if par.inside(point):
result.append(species)
stop = time.clock()
print(str(stop - start))
print(result)