def get_workers():
if request:
app.logger.info('request headers - {0}'.format(request.headers))
category = request.args.get('category')
filtered_list = []
final_list = []
# query = db.session.query(TweetInfo).filter(TweetInfo.published == TWEET_PUBLISHED).order_by(db.desc(TweetInfo.id))
query = db.session.query(Worker).all()
if query:
app.logger.info('query value true')
for item in query:
if item.category == category:
filtered_list.append(item)
latitude = request.args.get('latitude')
unicodedata.normalize('NFKD', latitude).encode('ascii', 'ignore')
longitude = request.args.get('longitude')
unicodedata.normalize('NFKD', longitude).encode('ascii', 'ignore')
distance = request.args.get('distance')
if not distance:
distance = 2.0
for item in filtered_list:
distance_point = calc_dist(float(item.latitude), float(item.longitude),
float(latitude), float(longitude))
app.logger.info('dist - {0}'.format(distance_point))
distance_point = 1.5
if distance_point < distance:
awesome_dict = create_dictionary(item, distance_point)
final_list.append(awesome_dict)
return jsonify({'workers': final_list})
def test3(params):
name, ncity, D, coord = read(params.f)
params.ncity = ncity
model, _, _ = construct("PtrNet", params, is_train=False)
_input = torch.Tensor([np.asarray([x for x in coord.values()])])
ts = time()
_, tour = model(_input)
tour = list(tour.detach().numpy()[0])
total_dist = calc_dist(tour, D)
print("\nPtrNet", total_dist, "\ntime", time() - ts)
print(*tour)
model, _, _ = construct("NeuralCombOptRL", params, is_train=False)
_input = torch.Tensor([np.asarray([x for x in coord.values()])])
ts = time()
_, _, _, tour = model(_input)
tour = list(tour.detach().numpy()[0])
total_dist = calc_dist(tour, D)
print("\nNeuralCombOptRL", total_dist, "\ntime", time() - ts)
print(*tour)
def test1(filename):
name, ncity, D, coord = read(filename)
two_opt = TwoOpt(ncity, D)
two_opt_multi = TwoOpt(ncity, D)
simanneal = TSPSimAnneal(ncity, D)
ga = TSPGA(ncity, D)
IP = PulpIP(ncity, D, MTZ_level=2)
ts = time()
tour = two_opt.solve_two_opt(strategy="greedy_random")
total_dist = calc_dist(tour, D)
assert isclose(total_dist, two_opt.best_obj, abs_tol=1e-5)
print("\nnormal", total_dist, "\ntime", time() - ts)
ts = time()
tour = two_opt_multi.solve_multi_start_two_opt(10,
strategy="greedy_random")
total_dist = calc_dist(tour, D)
assert isclose(total_dist, two_opt_multi.best_obj, abs_tol=1e-5)
print("\nmulti start", total_dist, "\ntime", time() - ts)
ts = time()
tour = simanneal.solve_simulated_annealing(T=8215972750,
C=0.81,
strategy="greedy_random")
total_dist = calc_dist(tour, D)
assert isclose(total_dist, simanneal.best_obj, abs_tol=1e-5)
print("\nsimulated annealing", total_dist, "\ntime", time() - ts)
ts = time()
tour = ga.solve(cxpb=0.3276646451925047, mutpb=0.6116923679473824)
total_dist = calc_dist(tour, D)
print("\nga simple", total_dist, "\ntime", time() - ts)
ts = time()
tour = IP.solve(solver_name="cplex")
total_dist = calc_dist(tour, D)
print("\nip", total_dist, "\ntime", time() - ts)
print(*tour)
def find_neighbours(self, users):
neighbours = []
maximal_geo_dist = (180**2 + 360**2)**(1 / 2)
for index, user in users.iterrows():
neighbour_dist = maximal_geo_dist
neighbour_name = 'No neighbours :( '
for n_index, n_user in users.iterrows():
dist = calc_dist(user, n_user)
if (dist < neighbour_dist) and (n_user['id'] != user['id']):
neighbour_dist = dist
neighbour_name = n_user['name']
neighbours.append((user['name'], neighbour_name))
return neighbours
def Query4ByLLR(lat, lon, rad):
(y, x) = ut.mapping(lat, lon)
cur.execute("set @poly='Polygon((%f %f,%f %f,%f %f,%f %f,%f %f))'" %
(x - rad, y + rad, x + rad, y + rad, x + rad, y - rad, x - rad,
y - rad, x - rad, y + rad))
cur.execute(
'select nodeID,ST_AsText(position),name,poitype from POIs where MBRContains(ST_GeomFromText(@poly),planaxy)'
)
queryResult = cur.fetchall()
ans = []
for row in queryResult:
coordinate = row[1].strip().split(' ')
lons = float(coordinate[0][6:])
lats = float(coordinate[1][:-1])
d = ut.calc_dist(lat, lon, lats, lons)
if d <= rad:
ans.append((row[0], (lons, lats), row[2], row[3], d))
return (sorted(ans, key=operator.itemgetter(4)))
def checkImages():
try:
databaseName = request.args.get('databaseName')
imageId = request.args.get('imageId')
#selecting important information from the user request
#Accuring the database images based on the request
#img1
#img2 or vector2
face1 = get_face_image(img1)
face2 = get_face_image(img2)
#can be skipped by the inclusion of the vectors time saved - 1s
vector1 = get_embeddings(face1)
vector2 = get_embeddings(face2)
#getting the distance (distance measure can be changed)
distOfImages = calc_dist(vector1, vector2)
#getting the match score of the image
score = get_match_score(distOfImages)
#passing this as a api response to the client
return jsonify({"Score": score})
except:
return jsonify({'trace': traceback.format_exc()})
def Query5ByLL(lat, lon):
(y, x) = ut.mapping(lat, lon)
rad = 10
queryResult = []
flag = 1
ans = []
while True:
cur.execute("set @poly='Polygon((%f %f,%f %f,%f %f,%f %f,%f %f))'" %
(x - rad, y + rad, x + rad, y + rad, x + rad, y - rad,
x - rad, y - rad, x - rad, y + rad))
cur.execute(
'select nodeID,ST_AsText(position) from nonPOIs where MBRContains(ST_GeomFromText(@poly),planaxy)'
)
queryResult = cur.fetchall()
ans = []
for row in queryResult:
coordinate = row[1].strip().split(' ')
lons = float(coordinate[0][6:])
lats = float(coordinate[1][:-1])
d = ut.calc_dist(lat, lon, lats, lons)
if d <= rad:
ans.append((row[0], (lons, lats), d))
ls = (sorted(ans, key=operator.itemgetter(2)))
for each in ls:
cur.execute(
"select ways.wayid, ways.name, ways.isRoad, ways.otherinfo from waynode, ways where waynode.nodeid=%s and waynode.wayid=ways.wayid and ways.isroad <> '0'"
% (each[0]))
queryRes = cur.fetchall()
if len(queryRes) > 0:
ans = queryRes
flag = 0
break
if flag == 0:
break
else:
rad = rad * 2.7
return ans
#for each pixel in mask:
##if mask pixel is not zero:
###closestDist=maxval
###closest=-1 (indexed)
###for each mineral vector:
####compute distance from current pixel's color values to element vector
####if distance is less than closestDist, set closest and closestDist
###set ouput pixel to closestIndex
###set confidence output pixel to closestDist
for vector in calibratedVectors:
bufImage = np.zeros((tHeight, tWidth), dtype = np.int32)
vector["buf"] = bufImage
vector["dbuf"] = bufImage
for element in calibration:
utils.calc_dist(targetMask, vector["dbuf"], element_scans[element], vector[element])
for vector in calibratedVectors:
utils.compare_dist(targetMask, outputImage, mineral_dists, vector["index"], vector["dbuf"])
mapImage = Image.new("P", (tWidth, tHeight), 0)
mapImage.putpalette(constants.palette)
mineralPixelCounts = {}
for mineral in mineralNames:
mineralPixelCounts[mineral] = 0
d = ImageDraw.ImageDraw(mapImage)
for x in range(0, tWidth):
for y in range(0, tHeight):
color = outputImage[y,x]
def test_calc_dist(self):
test_users_neighbours = pd.read_json(
'test_data/test_users_neighbours.json')
self.assertEqual(
utils.calc_dist(test_users_neighbours.iloc[0],
test_users_neighbours.iloc[1]), 5)
def proc_pcqm4m_sp(smiles_list):
w_bond = 100
wo_bond = 100
smiles2pos = {}
fail_count = 0
fail_smiles = []
for i, smiles in enumerate(smiles_list):
if i % 1000 == 0:
logging.info("Processing idx: {}, smiles: {}, fail count so far: {} ...".format(i, smiles, fail_count))
# ob_mol: OpenBabel's molecule object
ob_mol = ob.OBMol()
conversion.ReadString(ob_mol, smiles)
ob_calc = OpenBabelCalculator(ob_mol, forcefield=args.forcefield, removehs=args.removehs)
curr_min_dist_w_bond = ob_calc.get_min_dist(with_bond=True)
curr_min_dist_wo_bond = ob_calc.get_min_dist(with_bond=False)
py_mol = ob_calc.get_pymol()
pos = ob_calc.get_pos()
pdb.set_trace()
if curr_min_dist_w_bond is None or curr_min_dist_wo_bond is None:
fail_count += 1
fail_smiles.append(smiles)
smiles2pos[smiles] = pos
if i % 1000 == 0:
logging.info("minimum interatomic distance with bonds so far: {:.4f} ...".format(w_bond))
logging.info("minimum interatomic distance without bonds so far: {:.4f} ...".format(wo_bond))
continue
if curr_min_dist_wo_bond < args.threshold:
logging.info("Invalid: Minimum interatomic distance without bonds: {:.4f}, Smiles: {} ...".format(curr_min_dist_wo_bond, smiles))
retry = 0
curr_min_dist_wo_bond_ = curr_min_dist_wo_bond
while curr_min_dist_wo_bond_ < args.threshold and retry <= args.retry_times:
py_mol_, pos_, curr_min_dist_w_bond_, curr_min_dist_wo_bond_ = optimize(smiles)
retry += 1
py_mol = py_mol_
pos = pos_
curr_min_dist_w_bond = curr_min_dist_w_bond_
curr_min_dist_wo_bond = curr_min_dist_wo_bond_
logging.info(" Valid: Minimum interatomic distance with bonds: {:.4f}, Smiles: {} ...".format(curr_min_dist_wo_bond, smiles))
min_dist = calc_dist(py_mol, pos, with_bond=False)
try:
assert min_dist == curr_min_dist_wo_bond
except:
logging.info("Fail smiles: {} ...".format(smiles))
fail_count += 1
fail_smiles.append(smiles)
smiles2pos[smiles] = pos
if curr_min_dist_w_bond < w_bond:
w_bond = curr_min_dist_w_bond
if curr_min_dist_wo_bond < wo_bond:
wo_bond = curr_min_dist_wo_bond
if i % 1000 == 0:
logging.info("minimum interatomic distance with bonds so far: {:.4f} ...".format(w_bond))
logging.info("minimum interatomic distance without bonds so far: {:.4f} ...".format(wo_bond))
if args.max_size >= 0 and i >= args.max_size:
break
return smiles2pos
def statis_qm9(filepath):
supplier = Chem.SDMolSupplier(filepath, removeHs=False, sanitize=False)
w_bond = 100
wo_bond = 100
smiles2pos = {}
for i, mol in enumerate(supplier):
if i < args.start_idx:
continue
try:
smiles = Chem.MolToSmiles(mol)
except:
logging.info("Processing mol {}, parse smiles fail ...".format(i))
smiles = None
if i % 1000 == 0:
logging.info("Processing mol {}, smiles: {} ...".format(i, smiles))
# ob_mol: OpenBabel's molecule object
ob_mol = ob.OBMol()
conversion.ReadString(ob_mol, smiles)
ob_calc = OpenBabelCalculator(ob_mol, forcefield=args.forcefield, removehs=args.removehs)
py_mol = ob_calc.get_pymol()
pos = ob_calc.get_pos()
# sanitize
if mol is None:
logging.info("idx: {}, smiles: {} cannot be parsed ...".format(i, can_smiles))
continue
N = mol.GetNumAtoms()
try:
assert N == pos.size(0)
except:
pdb.set_trace()
tmp = 1
curr_min_dist_w_bond = ob_calc.get_min_dist(with_bond=True)
curr_min_dist_wo_bond = ob_calc.get_min_dist(with_bond=False)
if curr_min_dist_wo_bond < args.threshold:
logging.info("Invalid: Minimum interatomic distance without bonds: {:.4f}, Smiles: {} ...".format(curr_min_dist_wo_bond, smiles))
retry = 0
curr_min_dist_wo_bond_ = curr_min_dist_wo_bond
while curr_min_dist_wo_bond_ < args.threshold and retry <= args.retry_times:
py_mol_, pos_, curr_min_dist_w_bond_, curr_min_dist_wo_bond_ = optimize(smiles)
retry += 1
py_mol = py_mol_
pos = pos_
curr_min_dist_w_bond = curr_min_dist_w_bond_
curr_min_dist_wo_bond = curr_min_dist_wo_bond_
logging.info(" Valid: Minimum interatomic distance without bonds: {:.4f}, Smiles: {} ...".format(curr_min_dist_wo_bond, smiles))
min_dist = calc_dist(py_mol, pos, with_bond=False)
try:
assert min_dist == curr_min_dist_wo_bond
except:
logging.info("Fail smiles: {} ...".format(smiles))
smiles2pos[smiles] = pos
if curr_min_dist_w_bond < w_bond:
w_bond = curr_min_dist_w_bond
if curr_min_dist_wo_bond < wo_bond:
wo_bond = curr_min_dist_wo_bond
if i % 1000 == 0:
logging.info("minimum interatomic distance with bonds so far: {:.4f} ...".format(w_bond))
logging.info("minimum interatomic distance without bonds so far: {:.4f} ...".format(wo_bond))
if args.max_size >= 0 and i >= args.max_size:
break
out_filepath = "./qm9_pos.pt"
torch.save(smiles2pos, out_filepath)
from numpy import mean
import matplotlib.pyplot as plt
# cluster points
my_data = []
sy_data = []
for i in range(10):
my_data.append(kmeans_cluster_assignment(3, whiten(hard_y)))
sy_data.append(kmeans(whiten(hard_y), 3))
centroids_true = find_centroids(whiten(hard_y), y_true)
diff = []
for i in range(10):
for true in centroids_true:
my = calc_dist(centroids_true, sorted(my_data[i][1], key=mean))
sy = calc_dist(centroids_true, sorted(sy_data[i][0], key=mean))
diff.append(sy - my)
print(mean(diff))
fig = plt.figure(figsize=FIG_SIZE)
plt.xlabel('X_axis')
plt.ylabel('Y_axis')
plt.grid(True)
plt.title('Centroids - all points were whitened for consistency')
whitened = whiten(hard_y)
# Find 2 clusters in the data
codebook, distortion = kmeans(whitened, 3)
# Plot whitened data and cluster centers in red