def find_sites_in_area(self):
if not self.sites:
return 0
area_geometry = ([(d.geometry) for d in self.area.values()][0])
idx = index.Index()
for site in self.sites.values():
idx.insert(0, Point(site.coordinates).bounds, site)
sites_in_area = []
for n in idx.intersection(shape(area_geometry).bounds, objects=True):
point = Point(n.object.coordinates)
if shape(area_geometry).contains(point):
sites_in_area.append(n.object)
return sites_in_area
def intersectGeom(poly1, poly2, id1, id2, precDigit=10):
"""return the intersection ids between two lists of polygons"""
gO = otree.h3tree()
idx = index.Index()
for i, p in enumerate(poly2):
idx.insert(i, p.bounds)
sectL = {}
numL = []
for i, p in zip(id1, poly1):
merged_cells = cascaded_union(
[poly2[i] for i in idx.intersection(p.bounds)])
pint = p.intersection(merged_cells)
if isinstance(pint, sh.geometry.Point):
l = [gO.encode(pint.x, pint.y, precision=precDigit)]
else:
l = [gO.encode(x.x, x.y, precision=precDigit) for x in pint]
sectL[i] = l
numL.append(len(l))
print("%.2f points per polygon" % (np.mean(numL)))
return sectL
def knnRTree(size, k, image):
p = index.Property()
p.dimension = 128 #D
p.buffering_capacity = 3#M
p.dat_extension = 'dat'
p.idx_extension = 'idx'
idx = index.Index(f"RTree/RTree_{size}", properties=p)
picture = face_recognition.load_image_file(image)
vector = face_recognition.face_encodings(picture)
q = tuple(vector[0])
if not len(q): return []
lres = list(idx.nearest(coordinates=q, num_results=k))
res = []
for x in lres:
line=json.loads(linecache.getline(f"Sequential/Sequential_{size}.json", x+1))
res.append(line[0])
return res
def _create_spatial_index(self):
"""
This creates the spatial index for the input mesh
"""
# Setting rtree properties
prop = index.Property()
prop.dimension = 3
# Set the geographic projection
lons = self.mesh.lons.flatten('F')
mean_lat = np.mean(self.mesh.lats)
self.p = Proj(proj='lcc', lon_0=np.mean(lons), lat_1=mean_lat-10.,
lat_2=mean_lat+10.)
# Create the spatial index for the grid mesh
r = index.Index(_generator(self.mesh, self.p), properties=prop)
# Set the rtree
self.rtree = r
def add_lad_to_exchanges(exchanges, lads):
joined_exchanges = []
# Initialze Rtree
idx = index.Index()
for rtree_idx, exchange in enumerate(exchanges):
idx.insert(rtree_idx, shape(exchange['geometry']).bounds, exchange)
# Join the two
for lad in lads:
for n in idx.intersection((shape(lad['geometry']).bounds), objects='raw'):
lad_shape = shape(lad['geometry'])
premise_shape = shape(n['geometry'])
if lad_shape.contains(premise_shape):
n['properties']['lad'] = lad['properties']['name']
joined_exchanges.append(n)
return joined_exchanges
def build_rtree_index(geom):
"""Builds an rtree index. Useful for multiple intersections with same index.
Parameters
==========
geom : list
list of shapely geometry objects
Returns
idx : rtree spatial index object
"""
from rtree import index
# build spatial index for items in geom1
print('\nBuilding spatial index...')
ta = time.time()
idx = index.Index()
for i, g in enumerate(geom):
idx.insert(i, g.bounds)
print("finished in {:.2f}s".format(time.time() - ta))
return idx
def create_rtree_index(inshp):
"""Create rtree bounding index for an input shape.
Args:
inshp (obj): Shapefile with features.
Returns:
obj: rtree bounding box index.
"""
print("creating node index.....")
feature_list = []
for feature in inshp:
line = shape(feature['geometry'])
feature_list.append(line)
idx = index.Index()
for i in range(len(feature_list)):
idx.insert(i, feature_list[i].bounds)
return idx
def demo2(ports):
print "Checking " + str(len(ports)) + " ports"
violations = []
idx = index.Index()
## add everything to the spatial index
for p in ports:
(pid, (pminx,pminy,pmaxx,pmaxy)) = p.boundingBox()
idx.insert(pid, (pminx,pminy,pmaxx,pmaxy))
## now check the rules
for p in ports:
if not rule28.apply((p,)):
violations.append(Violation(rule28, [p]))
# find things that could violate rule 27?
possible = p.center.buffer(250).bounds ## How do I do this generally?
candidates = idx.intersection(possible)
for c in candidates:
pj = ports[c]
if not rule27.apply((p,pj)):
violations.append(Violation(rule27, [p,pj]))
return violations
def similarity(directory, filename, k):
# first extract features from query file
featureVector = extractFeatures(directory,filename)
# then open and query spatial index
p = index.Property()
p.dat_extension = 'data'
p.idx_extension = 'index'
p.dimension = 13
rtree = index.Index('rtreez', properties=p, interleaved=True)
similar = list(rtree.nearest((featureVector[0], featureVector[1],
featureVector[2], featureVector[3], featureVector[4],featureVector[5],
featureVector[6], featureVector[7], featureVector[8], featureVector[9],
featureVector[10], featureVector[11], featureVector[12],
featureVector[0], featureVector[1], featureVector[2], featureVector[3],
featureVector[4], featureVector[5], featureVector[6], featureVector[7],
featureVector[8], featureVector[9], featureVector[10],
featureVector[11], featureVector[12]), k))
return similar
def load_shapes(geojson_file):
from shapely.geometry import shape
from rtree import index
import json
# load the initial collection from the geojson
collection = json.load(geojson_file)
# create a spatial index
idx = index.Index()
for feature in collection['features']:
# add the shapely-parsed shape onto each feature
feature['shape'] = shape(feature['geometry'])
feature['centroid'] = feature['shape'].centroid
# spatially index each feature
objid = feature['properties']['OBJECTID']
idx.insert(objid, feature['shape'].bounds, obj=feature)
return collection, idx
def selectByIntersection(allAdmin, inD, exact=False):
''' Select features from allAdmin that intersect inD
allAdmin [shapely geometry] - describes the feature of interest
inD [geopandas dataframe] - features to be intersected
exact (optional) [boolean] - perform exact geometry match, default is False, which
will only calculate bounding box intersection
RETURNS [geopandas dataframe] - subset of inD that intersects allAdmin
EXAMPLE:
inS = gpd.read_file(sourceFile)
inD = gpd.read_file(intersectingFile)
if inS.crs != inD.crs:
inS = inS.to_crs(inD.crs)
allAdmin = shapely.ops.cascaded_union(MultiPolygon(inS['geometry'].tolist()))
selectByIntersection(allAdmin, inD, exact=False)
TODO: Projection checks
'''
#Read the source boundaries into an rtree opbject
idxAdmin = index.Index()
try:
for i, shape in enumerate(allAdmin):
idxAdmin.insert(i, shape.bounds)
except:
idxAdmin.insert(0, allAdmin.bounds)
#Enumerate through the intersecting file
intersectingList = []
for i, row in inD.iterrows():
interSection = list(idxAdmin.intersection(row['geometry'].bounds))
if len(interSection):
intersectingList.append(row)
returnDF = gpd.GeoDataFrame(intersectingList)
if exact:
selData = []
for j, origRow in returnDF.iterrows():
xx = allAdmin.intersects(origRow['geometry'])
print("%s - %s" % (j, xx))
if xx:
selData.append(origRow)
returnDF = gpd.GeoDataFrame(selData)
return returnDF
def run_images(valid_output_full, validated_image_filename, graph,
input_image_filename_list):
idxprop = index.Property()
idxprop.dimension = DIMENSIONS
idxprop.dat_extension = 'data'
idxprop.idx_extension = 'index'
idx = index.Index('3d_index', properties=idxprop)
idx_nr = 0
cv2.namedWindow(CV_WINDOW_NAME)
for input_image_file in input_image_filename_list:
print("Processing [", idx_nr, "] file ", input_image_file)
# read one of the images to run an inference on from the disk
infer_image = cv2.imread(IMAGES_DIR + input_image_file)
# run a single inference on the image and overwrite the
# boxes and labels
test_output_full = run_inference(
infer_image, graph, input_image_file + " -- " + str(idx_nr))
test_output = rmsList(test_output_full, 13)
print("test_output=", test_output)
testTupl = toRecTuple(test_output)
print("testTuble=", testTupl)
idx.insert(idx_nr, testTupl, obj=idx_nr)
valid_output = rmsList(valid_output_full, 13)
print("valid_output=", valid_output)
validTupl = toRecTuple(valid_output)
print("validTuble=", validTupl)
a = list(idx.nearest(validTupl))
print("R-tree near: ", a)
idx_nr = idx_nr + 1
# Test the inference results of this image with the results
# from the known valid face.
if (face_match(valid_output_full, test_output_full)):
print('PASS! File ' + input_image_file + ' matches ' +
validated_image_filename)
else:
print('FAIL! File ' + input_image_file + ' does not match ' +
validated_image_filename)
def addSeparatorFeature(self):
"""
We load the graphical separators
COmpute a set of shapely object
In turn, for each edge, we compute the intersection
"""
# graphical separators
from xml_formats.PageXml import PageXml
dNS = {"pc": PageXml.NS_PAGE_XML}
ndRoot = self.lNode[0].node.getroottree()
lNdSep = ndRoot.xpath(".//pc:SeparatorRegion", namespaces=dNS)
loSep = [ShapeLoader.node_to_LineString(_nd) for _nd in lNdSep]
if self.bVerbose: traceln(" %d graphical separators" % len(loSep))
# make an indexed rtree
idx = index.Index()
for i, oSep in enumerate(loSep):
idx.insert(i, oSep.bounds)
# take each edge in turn and list the separators it crosses
nCrossing = 0
for edge in self.lEdge:
# bottom-left corner to bottom-left corner
oEdge = geom.LineString([(edge.A.x1, edge.A.y1),
(edge.B.x1, edge.B.y1)])
prepO = prep(oEdge)
bCrossing = False
for i in idx.intersection(oEdge.bounds):
# check each candidate in turn
if prepO.intersects(loSep[i]):
bCrossing = True
nCrossing += 1
break
edge.bCrossingSep = bCrossing
if self.bVerbose:
traceln(
" %d (/ %d) edges crossing at least one graphical separator" %
(nCrossing, len(self.lEdge)))
def mapper():
PICKUP_TIME = 5
index = rtree.Index()
neighborhoods = []
readNeighborhood('ZillowNeighborhoods-NY.shp', index, neighborhoods)
agg = {}
for values in parseInput():
pickup_location = (float(values[10]), float(values[11]))
pickup_time = values[PICKUP_TIME]
weekhour = getWeekday(pickup_time)
pickup_neighborhood = findNeighborhood(pickup_location, index, neighborhoods)
time_neighbor_key = weekhour+'|'+str(pickup_neighborhood)
if pickup_neighborhood!=-1:
agg[time_neighbor_key] = agg.get(time_neighbor_key , 0) + 1
for item in agg.iteritems():
key_array = item[0].split('|')
neighborhood_name = neighborhoods[int(key_array[1])][0]
output_key = key_array[0]+'|'+ neighborhood_name
print '%s\t%s' % (output_key, item[1])
def __init__(self, filename):
#PATH='/Users/elaineyang/Documents/WeatherServer/data/shapefiles/'
PATH = 'data/shapefiles/'
print("processing " + filename + ".shp")
myshp = open(PATH + filename + ".shp", "rb")
mydbf = open(PATH + filename + ".dbf", "rb")
r = shapefile.Reader(shp=myshp, dbf=mydbf)
records = r.records()
self.records = records
idx = index.Index()
shapes = r.shapes()
id_num = 0
for shape in shapes:
sh = shape.bbox
xmin = sh[1]
ymin = sh[0]
xmax = sh[3]
ymax = sh[2]
idx.insert(id_num, (xmin, ymin, xmax, ymax))
id_num = id_num + 1
self.idx = idx
def create_index(self, location):
photos = self.get_photos(location)
# If interleaved=False, the bbox format looks like xmin, xmax, ymin,ymax
prop = index.Property()
prop.overwrite = True
index_file = "index_" + str(location)
idx = index.Index(index_file, interleaved=False, properties=prop)
_id = 1
for photo in photos:
latitude = float(photo['latitude'])
longitude = float(photo['longitude'])
idx.insert(_id, (latitude, latitude, longitude, longitude), obj={
'photo_id': photo['photo_id'],
'owner': photo['owner'],
'latitude': latitude,
'longitude': longitude
})
_id+=1
idx.close()
print _id
def get_intersecting_buildings(postcode_sector, buildings):
intersecting_buildings = []
# Initialze Rtree
idx = index.Index()
[
idx.insert(0,
shape(building['geometry']).bounds, building)
for building in buildings
]
for n in idx.intersection((shape(postcode_sector['geometry']).bounds),
objects=True):
postcode_sector_shape = shape(postcode_sector['geometry'])
premise_shape = shape(n.object['geometry'])
if postcode_sector_shape.contains(
premise_shape.representative_point()):
intersecting_buildings.append(n.object)
return intersecting_buildings
def load_n(i):
nl = {}
with open("result.pkl", "rb") as f:
data = pickle.load(f)
contador = 0
for d in data:
if (contador == i):
break
nl[d[0]] = parse_row(d[1])
contador += 1
prop = index.Property()
prop.dat_extension = "data"
prop.idx_extension = "index"
prop.dimension = 128
idx = index.Index('3d_index' + str(i), properties=prop, interleaved=False)
c_id = 0
for key in nl:
idx.insert(c_id, nl[key], key)
c_id += 1
return idx
def __init__(self, dim_range, Obs=None):
''' Initialize Search Space
dim_range: upper bound of each dimension, lower bound is defaultly set as 0
Obs: default value=None
'''
self.dim_range = dim_range
self.dim = len(dim_range)
# sanity process
if self.dim < 2:
raise Exception('at least initialize 2D map.')
if self.dim > 3:
raise Exception('at most initialize 3D map.')
self.obs = Obs
if Obs is not None:
# empty initialize self.obs
# index member: interleaved=True xmin, ymin, ..., kmin, xmax, ymax, ..., kmax
self.obs = index.Index(interleaved=True)
for i in Obs:
self.obs.insert(i[0], i[1])
def index(self):
if not self.indexed:
self.minx = sys.maxint
self.miny = sys.maxint
self.maxx = sys.minint
self.maxy = sys.minint
self.index = index.Index()
self.human_rectangles.clear()
for entity in self.entities.values():
left, bottom, right, top = self.make_rectangle(entity)
if left is not None:
self.index.insert(entity.get_id().get_value(), (left, bottom, right, top))
self.minx = min(self.minx, left, right)
self.maxx = max(self.maxx, left, right)
self.miny = min(self.miny, bottom, top)
self.maxy = max(self.maxy, bottom, top)
if isinstance(entity, Human):
self.human_rectangles[entity] = (left, bottom, right, top)
self.indexed = True
def get_intersecting_rtree(x, y, windows):
""" Returns a list of I3 window objects who intersect witht he point x, y.
Args:
x (int): Query x. 0 <= x <= Screen width
y (int): Query y. 0 <= y <= Screen height
windows (list): Possibly empty list of i3ipc.window connections
Returns:
list: Possibly empty list of intersecting windows.
"""
top = lambda window: window.rect.y
right = lambda window: window.rect.x + window.rect.width
bottom = lambda window: window.rect.y + window.rect.height
left = lambda window: window.rect.x
rtree = index.Index()
for idx, w in enumerate(windows):
rtree.insert(idx, (left(w), top(w), right(w), bottom(w)))
return [windows[idx] for idx in rtree.intersection((x, y))]
def get_spatial_points(self, x, y, distance):
"""Use spatial index to retrieve pulsewave within a given bounding box
:param left:
:param right:
:param bottom
: :param top:
"""
if not os.path.isfile(os.path.splitext(self.filename)[0] + ".idx"):
print("Spatial index not found!!!")
return
spatial_index = index.Index(os.path.splitext(self.filename)[0])
intersected_pulses = list(
spatial_index.intersection(
(x - distance, y - distance, x + distance, y + distance)))
spatial_index.close()
return intersected_pulses
def __init__(self):
if osp.exists("state_index.dat"):
os.remove("state_index.dat")
os.remove("state_index.idx")
self.obs_dimension = 16
self.visited_state_value = np.loadtxt(
"visited_state_value.txt",
usecols=(i for i in range(self.obs_dimension +
1, self.obs_dimension + 3, 1)))
self.visited_state_value = self.visited_state_value.tolist()
self.visited_state_counter = len(self.visited_state_value)
visited_state_tree_prop = rindex.Property()
visited_state_tree_prop.dimension = self.obs_dimension + 1
self.visited_state_dist = np.array(
[[1, 0.3, 3, 1, 10, 0.3, 3, 1, 10, 0.3, 3, 1, 10, 0.3, 3, 1,
0.1]]) #, 10, 0.3, 3, 1, 0.1]])
self.visited_state_tree = rindex.Index(
'state_index', properties=visited_state_tree_prop)
self.recostruct_state_counter = 0
self.recostruct_rtree()
def __init__(self, crs="epsg:3857"):
"""Create a GeoSpace for GIS enabled mesa modeling.
Args:
crs: Coordinate reference system of the GeoSpace
If `crs` is not set, epsg:3857 (Web Mercator) is used as default.
However, this system is only accurate at the equator and errors
increase with latitude.
Properties:
crs: Project coordinate reference system
idx: R-tree index for fast spatial queries
bbox: Bounding box of all agents within the GeoSpace
agents: List of all agents in the Geospace
Methods:
add_agents: add a list or a single GeoAgent.
remove_agent: Remove a single agent from GeoSpace
agents_at: List all agents at a specific position
distance: Calculate distance between two agents
get_neighbors: Returns a list of (touching) neighbors
get_intersecting_agents: Returns list of agents that intersect
get_agents_within: Returns a list of agents within
get_agent_contains: Returns a list of agents contained
get_agents_touches: Returns a list of agents that touch
update_bbox: Update the bounding box of the GeoSpace
"""
self.crs = pyproj.CRS(crs)
self.WGS84 = pyproj.CRS("epsg:4326")
self.Transformer = pyproj.Transformer.from_crs(self.crs,
self.WGS84,
skip_equivalent=True,
always_xy=True)
self.bbox = None
self._neighborhood = None
# Set up rtree index
self.idx = index.Index()
self.idx.agents = {}
def load(self):
# load elevation data
self.elevation = rasterio.open("../Material/elevation/SZ.asc")
self.elevation_band = self.elevation.read(1)
# for task 1, restrict user point in a range that is more than 5km from the bounding edge
self.bound_polygon = self.bound_polygon(self.elevation.bounds)
self.inner_polygon = self.bound_polygon.buffer(-5000)
# load itn data
self.itndata = self.read_geojson("../Material/itn/solent_itn.json")
self.road_nodes = self.itndata["roadnodes"]
# for task 3, build rtree from itn data
count = 0
self.itn_rtree = index.Index()
for fid, node in self.road_nodes.items():
corrds = node["coords"].copy()
self.itn_rtree.insert(count, corrds, fid)
count += 1
# for task 4, build networkx graph from itn data, we store link feature id in Graph for
# computing
self.itn_graph = networkx.Graph()
road_links = self.itndata['roadlinks']
for link in road_links:
s = road_links[link]['start']
e = road_links[link]['end']
# get start point elevation and end point elevation
s_ele = self.get_elevation(self.road_nodes[s]["coords"][0],
self.road_nodes[s]["coords"][1])
e_ele = self.get_elevation(self.road_nodes[e]["coords"][0],
self.road_nodes[e]["coords"][1])
length = road_links[link]['length']
# compute travel time according to Naismith's rule
time = length * 60 / 5000 + max(e_ele - s_ele, 0) / 10
self.itn_graph.add_edge(s, e, fid=link, weight=time)
def create_rtree(shape_file: str, inEPSG='EPSG:4326', outEPSG='EPSG:4326'):
try:
buildings = fiona.open(shape_file)
# outEPSG = 'EPSG:4326'
# inEPSG = 'EPSG:3857'
transformer = Transformer.from_crs(inEPSG, outEPSG, always_xy=True)
# rtree
rtree_path = shape_file.replace(".shp", '_rtree')
p = index.Property()
p.overwrite = True
r_tree = index.Index(rtree_path, properties=p)
print_interval = int(len(buildings) / 1000)
for idx, building in tqdm(enumerate(buildings[:])):
try:
if idx % print_interval == 0:
logger.info("Processing polyogn #: %d", idx)
bound = fiona.bounds(building)
# logger.info("bound: %s", bound)
bound = list(bound)
# logger.info("bound: %s", bound)
bound[0], bound[1] = transformer.transform(bound[0], bound[1])
# logger.info("bound: %s", bound)
bound[2], bound[3] = transformer.transform(bound[2], bound[3])
r_tree.insert(idx, bound)
except Exception as e:
logger.error("Error in building polygons: %s", e)
continue
r_tree.close()
except Exception as e:
logger.error("Error in creating rtree: %s", e)
def extract_tributary(eList1, eList2):
"""将上一级每条河流和下一级每条河流求交，求出支流信息"""
#建立索引
idxP = index.Property()
idxP.filename = 'road_index'
idxP.overwrite = True
idxP.storage = index.RT_Disk
idxP.dimension = 2
idx = index.Index(idxP.filename,
item_build(eList2),
properties=idxP,
interleaved=True,
overwrite=True)
# linkNum = 0
for currentEntity in eList1:
currentGeom = shapely.geometry.asShape(currentEntity['geometry'])
currentQueryBox = currentGeom.bounds #对上一级河流求bbox
currentID = currentEntity['properties']['UUID']
currentLevel = currentEntity['properties']['LEVEL']
currentBuffer = currentGeom.buffer(0.2)
judgeIds = list(idx.intersection(currentQueryBox)) #求出相交的下一级河流
for jid in judgeIds:
judgeEntity = eList2[jid]
judgeGeom = shapely.geometry.asShape(judgeEntity['geometry'])
if currentBuffer.intersects(judgeGeom):
jID = judgeEntity['properties']['UUID']
jLevel = judgeEntity['properties']['LEVEL']
jNAME = judgeEntity['properties']['NAME']
if jID != currentID and jID not in currentEntity['relation'][
'Tributary'] and jLevel > currentLevel:
currentEntity['relation']['Tributary'].append(jID)
currentEntity['properties']['Tributary'].append(jID)
currentEntity['properties']['Tributary_NAME'].append(jNAME)
# linkNum += 1
print('Step4: extracting relations finished')
return eList1
def simpleRTree():
print("R-tree test")
idx = index.Index()
pt1 = Point(1, 1)
pt2 = Point(4, 1)
pt3 = Point(3, 3)
# Insert the points into the R-tree index
idx.insert(1, (pt1.x, pt1.y, pt1.x, pt1.y))
idx.insert(2, (pt2.x, pt2.y, pt2.x, pt2.y))
idx.insert(3, (pt3.x, pt3.y, pt3.x, pt3.y))
# Query. This library only supports rectangular queries
# Specify the bounds
leftBottom = Point(0, 0)
rightTop = Point(3, 4)
# Perform the query
results = list(
idx.intersection((leftBottom.x, leftBottom.y, rightTop.x, rightTop.y)))
print("Query result:")
print(results)
def __init__(self, vertices, indices):
# need to find self-intersections
if Polygon2d.check_ccw(vertices, indices):
self.outline = indices[:]
else:
self.outline = indices[::-1]
self.vertices = vertices[:]
self.rti = index.Index()
self.rti.interleaved = True
# insert vertices into spatial index
for vid in self.outline:
vert = self.vertices[vid]
self.rti.insert(vid, (vert.x, vert.y, vert.x, vert.y))
# resolve self-intersections (sinters)
self._resolve_sinters()
self.holes = []
def chunk(featureFileName, sectionFileName, pattern, key=None):
# Load and index
with collection(featureFileName, "r") as featureFile:
featureIdx = index.Index()
features = []
for feature in featureFile:
features.append(feature)
featureIdx.add(
len(features) - 1,
asShape(feature['geometry']).bounds)
# Break up by sections and export
with collection(sectionFileName, "r") as sectionFile:
i = 0
for section in sectionFile:
fileName = pattern % i
if key:
fileName = pattern % section['properties'][key]
properties = {}
try:
with collection(fileName,
'w',
'ESRI Shapefile',
schema=featureFile.schema,
crs=featureFile.crs) as output:
sectionShape = asShape(section['geometry'])
for j in featureIdx.intersection(
sectionShape.bounds):
if asShape(features[j]['geometry']).intersects(
sectionShape):
properties = features[j]['properties']
output.write(features[j])
print "Exported %s" % fileName
i = i + 1
except ValueError:
print "Error exporting " + fileName
pprint(properties)
pprint(featureFile.schema)
