def hausdorff_distance(estimate, truth, linestring_lookup):
l_coords = curve_to_coords(estimate, linestring_lookup)
r_coords = curve_to_coords(truth, linestring_lookup)
return max(directed_hausdorff(l_coords, r_coords),
directed_hausdorff(r_coords, l_coords),
key=lambda x: x[0])[0]
def hausdorff_dist(seg_calc, seg_real, img_calc, img_real):
positions_real_fin = []
positions_calc_fin = []
space_calc = img_calc.GetSpacing()
space_real = img_real.GetSpacing()
#Calculate coordinates for predicated/calculated image
calc_slice = find_boundaries(seg_calc)
positions_calc = zip(*np.where(calc_slice > 0))
positions_calc = list(positions_calc)
positions_calc = np.array(positions_calc)
positions_calc = (positions_calc *
[space_calc[0], space_calc[1], space_calc[2]])
positions_calc = (positions_calc).tolist()
positions_calc_fin.append(positions_calc)
#Calculate coordinates for real image
real_slice = find_boundaries(seg_real)
positions_real = zip(*np.where(real_slice > 0))
positions_real = list(positions_real)
positions_real = np.array(positions_real)
positions_real = (positions_real *
[space_real[0], space_real[1], space_real[2]])
positions_real = positions_real.tolist()
positions_real_fin.append(positions_real)
#Find Hausdorff distance in both directions
dh_pc_pr = (directed_hausdorff(positions_calc, positions_real)[0])
dh_pr_pc = (directed_hausdorff(positions_real, positions_calc)[0])
dh = max(dh_pc_pr, dh_pr_pc)
return dh
def distance_between(A: traja.TrajaDataFrame,
B: traja.TrajaDataFrame,
method="dtw"):
"""Returns distance between two trajectories.
Args:
A (:class:`~traja.frame.TrajaDataFrame`) : Trajectory 1
B (:class:`~traja.frame.TrajaDataFrame`) : Trajectory 2
method (str): ``dtw`` for dynamic time warping, ``hausdorff`` for Hausdorff
Returns:
distance (float): Distance
"""
if method == "hausdorff":
dist0 = directed_hausdorff(A, B)[0]
dist1 = directed_hausdorff(B, A)[0]
symmetric_dist = max(dist0, dist1)
return symmetric_dist
elif method == "dtw":
try:
from fastdtw import fastdtw
except ImportError:
raise ImportError("""
Missing optional dependency 'fastdtw'. Install fastdtw for dynamic time warping distance with pip install
fastdtw.
""")
distance, path = fastdtw(A, B, dist=euclidean)
return distance
def test_symmetry(self):
# Ensure that the directed (asymmetric) Hausdorff distance is
# actually asymmetric
forward = directed_hausdorff(self.path_1, self.path_2)[0]
reverse = directed_hausdorff(self.path_2, self.path_1)[0]
assert_(forward != reverse)
def hausdorff_distance(input, target):
_, result = input.max(1)
result = torch.squeeze(result)
target = torch.squeeze(target)
result_np = result.data.cpu().numpy()
label_np = target.data.cpu().numpy()
output_indexes = np.where(result_np == 1.0)
sitk_output = sitk.GetImageFromArray(result_np)
label_indexes = np.where(label_np == 1.0)
sitk_label = sitk.GetImageFromArray(label_np)
if (result_np.sum()==0) or (label_np.sum()==0):
h_dist = 0
else:
# Note the reversed order of access between SimpleITK and numpy (z,y,x)
if len(output_indexes) == 3:
physical_points_output = [sitk_output.TransformIndexToPhysicalPoint([int(x), int(y), int(z)]) \
for z,y,x in zip(output_indexes[0], output_indexes[1], output_indexes[2])]
physical_points_label = [sitk_label.TransformIndexToPhysicalPoint([int(x), int(y), int(z)]) \
for z,y,x in zip(label_indexes[0], label_indexes[1], label_indexes[2])]
if len(output_indexes) == 2:
physical_points_output = [sitk_output.TransformIndexToPhysicalPoint([int(x), int(y)]) \
for y,x in zip(output_indexes[0], output_indexes[1])]
physical_points_label = [sitk_label.TransformIndexToPhysicalPoint([int(x), int(y)]) \
for y,x in zip(label_indexes[0], label_indexes[1])]
h_dist_lo, u_ind, v_ind = directed_hausdorff(u = physical_points_label, v = physical_points_output)
h_dist_ol, u_ind, v_ind = directed_hausdorff(u = physical_points_output, v = physical_points_label)
h_dist = max(h_dist_lo, h_dist_ol)
return h_dist
def set_convolution_matrix(self, gac_img, doctor_result):
from math import sqrt
from numpy import ravel, corrcoef
from scipy.spatial.distance import directed_hausdorff
import numpy as np
# Sum and subtract two images
img_sum = np.add(gac_img, doctor_result)
img_sub = np.subtract(gac_img, doctor_result)
# True (positive and negative) and False (positive and negative)
tp = np.float(np.sum((img_sum == 2).nonzero(), dtype=np.int32))
tn = np.float(np.sum((img_sum == 0).nonzero(), dtype=np.int32))
fp = np.float(np.sum((img_sub < 0).nonzero(), dtype=np.int32))
fn = np.float(np.sum((img_sub > 0).nonzero(), dtype=np.int32))
# Hausdorff equation
conf_temp = corrcoef(ravel(gac_img), ravel(doctor_result))
u = directed_hausdorff(doctor_result, gac_img)[0]
v = directed_hausdorff(gac_img, doctor_result)[0]
# Other metrics equations
self.precision = tp / (tp + fp)
self.recall = tp / (tp + fn)
self.dice = (2 * tp) / ((2 * tp) + (fp + fn))
self.sens = tp / (tp + fn)
self.spec = tn / (tn + fp)
self.jacc = tp / (fp + fn + tp)
self.accu = (tp + tn) / (tp + tn + fp + fn)
self.f1sc = 2 * ((self.precision * self.recall) /
(self.precision + self.recall))
self.matt = ((tp * tn) - (fp * fn)) / sqrt(
(tp + fp) * (tp + fn) * (tn + fp) * (tn + fn))
self.conf = conf_temp[0, 1]
self.haus = max(u, v)
def click_event(event, x, y, flags, params):
# checking for left mouse clicks
if event == cv2.EVENT_LBUTTONDOWN:
reference_image_path = "shapes_pat.png"
landscape_image_path = "shapes.jpg"
ref_image = cv2.imread(reference_image_path,0)
landscape_image = cv2.imread(landscape_image_path,0)
print(f"check for x = {x} , y = {y}")
landcape_sample = copy.deepcopy(ref_image)
n, m = ref_image.shape[:2]
RGB = False
for i in range(0, n):
for j in range(0, m):
I = int(y + i - n / 2)
J = int(x + j - m / 2)
try:
if RGB:
landcape_sample[i, j, :] = landscape_image[I, J, :]
else:
landcape_sample[i, j] = landscape_image[I, J]
except IndexError:
sys.exit(7)
result = 0
if RGB:
for k in range(0, 3):
result += max(directed_hausdorff(landcape_sample[:, :, k], ref_image[:, :, k])[0],
directed_hausdorff(ref_image[:, :, k], landcape_sample[:, :, k])[0])
else:
result = max(directed_hausdorff(landcape_sample, ref_image)[0],
directed_hausdorff(ref_image, landcape_sample)[0])
print(f"RESULT = {result}")
def Hausdorff(A, B):
"""
Calculates the Hausdorff distance between a pair of bags (videos), and returns the distance.
"""
h1 = directed_hausdorff(A, B)[0]
h2 = directed_hausdorff(B, A)[0]
return max((h1, h2))
def hausdorff_distance(x, y):
"""
Hausdorff distance between two segmentations
:param x: array
:param y: array
:return: the hausdorff distance
"""
# binarize
x = x > 0.5
y = y > 0.5
hd_0 = 0
hd_1 = 0
hd = 0
for i in range(x.shape[0]):
hd_0 += directed_hausdorff(x[i, ...], y[i, ...])[0]
hd_1 += directed_hausdorff(y[i, ...], x[i, ...])[0]
hd += max(hd_0, hd_1)
hd_0 /= x.shape[0]
hd_1 /= x.shape[0]
hd /= x.shape[0]
return hd, hd_0, hd_1
def HausdorffDist(A, B):
# D_mat = np.sqrt(inner1d(A,A)[np.newaxis].T + inner1d(B,B)-2*(np.dot(A,B.T)))
# dH = np.max(np.array([np.max(np.min(D_mat,axis=0)),np.max(np.min(D_mat,axis=1))]))
# return(dH)
d_forward = directed_hausdorff(A, B)[0]
d_backward = directed_hausdorff(B, A)[0]
return max(d_forward, d_backward)
def HausforffDistance(x1, x2):
# https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.directed_hausdorff.html
from scipy.spatial.distance import directed_hausdorff
if type(x1) == Variable:
distance = directed_hausdorff(x1.cpu().data.numpy(), x2.cpu().data.numpy())
elif type(x1) == torch.cuda.FloatTensor:
distance = directed_hausdorff(x1.cpu().numpy(), x2.cpu().numpy())
def test_symmetry(self):
# Ensure that the directed (asymmetric) Hausdorff distance is
# actually asymmetric
forward = directed_hausdorff(self.path_1, self.path_2)[0]
reverse = directed_hausdorff(self.path_2, self.path_1)[0]
assert_(forward != reverse)
def numpy_haussdorf(pred: np.ndarray, target: np.ndarray) -> float:
assert len(pred.shape) == 2
assert pred.shape == target.shape
return max(
directed_hausdorff(pred, target)[0],
directed_hausdorff(target, pred)[0])
def re_ranking(input_feature_source, input_feature, k=20, lambda_value=0.1, MemorySave=False, Minibatch=2000): ##rerank_plain
all_num_source = input_feature_source.shape[0]
all_num = input_feature.shape[0]
feat = input_feature.astype(np.float16)
print('computing source distance...')
sour_tar_dist = cdist(input_feature,input_feature_source)
source_dist_vec = np.min(sour_tar_dist, axis = 1)
source_dist_vec = source_dist_vec / np.max(source_dist_vec)
source_dist = np.zeros([all_num, all_num])
for i in range(all_num):
source_dist[i,:] = source_dist_vec + source_dist_vec[i]
del sour_tar_dist
del source_dist_vec
print('computing original distance...')
if MemorySave:
original_dist = np.zeros(shape=[all_num, all_num], dtype=np.float16)
i = 0
while True:
it = i + Minibatch
if it < np.shape(feat)[0]:
original_dist[i:it, ] = np.power(
cdist(feat[i:it, ], feat), 2).astype(np.float16)
else:
original_dist[i:, :] = np.power(
cdist(feat[i:, ], feat), 2).astype(np.float16)
break
i = it
else:
original_dist = cdist(feat, feat).astype(np.float16)
original_dist = np.power(original_dist, 2).astype(np.float16)
del feat
euclidean_dist = original_dist/np.max(original_dist)
## compute k-nn of each instance
knn_bool = np.zeros([all_num,all_num],dtype=bool)
for i in range(all_num):
tem_vec = original_dist[i,:]
kThreshold = np.partition(tem_vec,k-1,)[k-1]
knn_bool[i,:] = (tem_vec <= kThreshold)
knn_bool[i,i] = False
del tem_vec
# new added for compute hausdorff distance matrix
hausdorff_dist = np.zeros([all_num,all_num], dtype=np.float64)
for i in range(all_num):
u_set = input_feature[knn_bool[i]]
for j in range(i+1, all_num):
v_set = input_feature[knn_bool[j]]
hausdorff_dist[i,j] = max(directed_hausdorff(u_set, v_set)[0], directed_hausdorff(v_set, u_set)[0])
hausdorff_dist[j,i] = hausdorff_dist[i,j]
hausdorff_dist = hausdorff_dist/np.max(hausdorff_dist)
final_dist = hausdorff_dist*(1-lambda_value) + source_dist*lambda_value
del original_dist
del hausdorff_dist
return euclidean_dist, final_dist
def hausdorff_distance(curve1, curve2, n_sampling):
s1 = np.floor(np.linspace(0, len(curve1) - 1, n_sampling)).astype(int)
s2 = np.floor(np.linspace(0, len(curve2) - 1, n_sampling)).astype(int)
u = curve1[s1]
v = curve2[s2]
curve_dist = max(directed_hausdorff(u, v)[0], directed_hausdorff(v, u)[0])
return curve_dist
def hausdorffDistance(ptsA, ptsB):
hdAB = directed_hausdorff(ptsA, ptsB)[0]
hdBA = directed_hausdorff(ptsB, ptsA)[0]
hd = np.max([hdAB, hdBA])
return hd
def test_invalid_dimensions(self):
# Ensure that a ValueError is raised when the number of columns
# is not the same
np.random.seed(1234)
A = np.random.rand(3, 2)
B = np.random.rand(4, 5)
with pytest.raises(ValueError):
directed_hausdorff(A, B)
def compute_hausdorff_dist(self, traj1, traj2):
"""
double side hausdorff distance
"""
# import ipdb;ipdb.set_trace()
dist1 = directed_hausdorff(traj1, traj2)[0]
dist2 = directed_hausdorff(traj2, traj1)[0]
return max(dist1, dist2)
def test_invalid_dimensions(self):
# Ensure that a ValueError is raised when the number of columns
# is not the same
np.random.seed(1234)
A = np.random.rand(3, 2)
B = np.random.rand(4, 5)
with pytest.raises(ValueError):
directed_hausdorff(A, B)
def get_hausdorff(y_true, y_prediction):
'''
Here is the directed Hausdorff distance, but it computes both directions and output the larger value
'''
Hausdorff = max(
directed_hausdorff(y_true, y_prediction)[0],
directed_hausdorff(y_prediction, y_true)[0])
return Hausdorff
def post(self, request, format=None):
json_request = json.loads(request.body.decode(encoding='UTF-8'))
features = [feature['name'] for feature in json_request['features']]
target = json_request['target']['name']
sensitive_attr = json_request['sensitiveAttr']['name']
raw_df = open_dataset('./data/themis_ml_raw_sample.csv')
whole_dataset_df = open_dataset(sample_file_path)
X = whole_dataset_df[features]
X_wo_s_attr = whole_dataset_df[features]
y = whole_dataset_df[target]
s = whole_dataset_df[sensitive_attr] # male:0, female: 1
for feature in features:
X[feature] = X[feature].astype(float)
is_categorical_feature_list = []
for feature in features:
if feature in numerical_features:
is_categorical_feature_list.append(False)
else:
is_categorical_feature_list.append(True)
d = gower_distances(X,
categorical_features=is_categorical_feature_list)
df_tsne_result = pd.DataFrame(
TSNE(n_components=2, metric='precomputed',
random_state=3).fit_transform(d), X.index)
df_tsne_result['idx'] = whole_dataset_df['idx']
df_tsne_result['group'] = s
df_tsne_result['target'] = y
df_tsne_result.columns = ['dim1', 'dim2', 'idx', 'group', 'target']
df_tsne_result['dim1'] = (df_tsne_result['dim1'] - min(
df_tsne_result['dim1'])) / (max(df_tsne_result['dim1']) -
min(df_tsne_result['dim1']))
df_tsne_result['dim2'] = (df_tsne_result['dim2'] - min(
df_tsne_result['dim2'])) / (max(df_tsne_result['dim2']) -
min(df_tsne_result['dim2']))
df_group0 = df_tsne_result[df_tsne_result['group'] == 0]
df_group1 = df_tsne_result[df_tsne_result['group'] == 1]
hausdorff_distance = directed_hausdorff(df_group0[['dim1', 'dim2']],
df_group1[['dim1', 'dim2']])
hausdorff_distance2 = directed_hausdorff(df_group1[['dim1', 'dim2']],
df_group0[['dim1', 'dim2']])
return Response(
json.dumps({
'inputSpaceDist':
max(hausdorff_distance[0], hausdorff_distance2[0]),
'dimReductions':
df_tsne_result.to_json(orient='index')
}))
def test_random_state(self):
# ensure that the global random state is not modified because
# the directed Hausdorff algorithm uses randomization
rs = check_random_state(None)
old_global_state = rs.get_state()
directed_hausdorff(self.path_1, self.path_2)
rs2 = check_random_state(None)
new_global_state = rs2.get_state()
assert_equal(new_global_state, old_global_state)
def hausdorff_distance(output, label):
coor_label = np.where(label == 1)
coor_label = np.asarray(coor_label).T
coor_output = np.where(output == 1)
coor_output = np.asarray(coor_output).T
d_ab = directed_hausdorff(coor_label, coor_output)[0]
d_ba = directed_hausdorff(coor_output, coor_label)[0]
hd_ab = max(d_ab, d_ba)
return hd_ab
def test_it_correctly_computes_haussdorf_distance(input_arrays):
XA, XB = input_arrays
actual_dist = hausdorff_distance(XA, XB, distance="euclidean")
expected_dist = max(
directed_hausdorff(XA, XB)[0],
directed_hausdorff(XB, XA)[0])
np.testing.assert_almost_equal(expected_dist, actual_dist)
def test_random_state_None_int(self, seed):
# check that seed values of None or int do not alter global
# random state
rs = check_random_state(None)
old_global_state = rs.get_state()
directed_hausdorff(self.path_1, self.path_2, seed)
rs2 = check_random_state(None)
new_global_state = rs2.get_state()
assert_equal(new_global_state, old_global_state)
def test_invalid_dimensions(self):
# Ensure that a ValueError is raised when the number of columns
# is not the same
rng = np.random.default_rng(189048172503940875434364128139223470523)
A = rng.random((3, 2))
B = rng.random((3, 5))
msg = r"need to have the same number of columns"
with pytest.raises(ValueError, match=msg):
directed_hausdorff(A, B)
def calculate_hausdroff(component1,component2):
number_points = np.shape(component1)[0]
factor = 0
for i in range(0,number_points):
factor = factor + max(directed_hausdorff(u, v)[i], directed_hausdorff(v, u)[i])
factor = factor/number_points
return(factor)
def test_random_state(self):
# ensure that the global random state is not modified because
# the directed Hausdorff algorithm uses randomization
rs = check_random_state(None)
old_global_state = rs.get_state()
directed_hausdorff(self.path_1, self.path_2)
rs2 = check_random_state(None)
new_global_state = rs2.get_state()
assert_equal(new_global_state, old_global_state)
def get_Hd_distance(truth, prediction): coor_truth = np.where(truth==1) coor_truth = np.asarray(coor_truth).T coor_preds = np.where(prediction==1) coor_preds = np.asarray(coor_preds).T d_ab = directed_hausdorff(coor_truth, coor_preds)[0] d_ba = directed_hausdorff(coor_preds, coor_truth)[0] hd_ab = max(d_ab, d_ba) return hd_ab
def novelty_score(airfoil_gen, airfoils_data):
min_dist = np.inf
for airfoil in tqdm(airfoils_data):
dist_ab = directed_hausdorff(airfoil_gen, airfoil)[0]
dist_ba = directed_hausdorff(airfoil, airfoil_gen)[0]
dist = np.maximum(dist_ab, dist_ba)
if dist < min_dist:
min_dist = dist
nearest_airfoil = airfoil
return min_dist, nearest_airfoil
def test_random_state_None_int(self):
# check that seed values of None or int do not alter global
# random state
for seed in [None, 27870671]:
rs = check_random_state(None)
old_global_state = rs.get_state()
directed_hausdorff(self.path_1, self.path_2, seed)
rs2 = check_random_state(None)
new_global_state = rs2.get_state()
assert_equal(new_global_state, old_global_state)
def get_hd(outputs, labels):
'''
:param outputs: numpy array
:param labels: numpy array
:param threshold: defautl 0.5
:return:
'''
hd1 = directed_hausdorff(outputs, labels)[0]
hd2 = directed_hausdorff(outputs, labels)[0]
return max(hd1, hd2)
def mean_hausdorff_distance(seg_pred, target):
distances = np.zeros((4, ))
for channel in range(seg_pred.size(1)):
distances[channel] = max(
directed_hausdorff(
flatten(seg_pred[:, channel, ...]).cpu().detach().numpy(),
flatten(target[:, channel, ...]).cpu().detach().numpy())[0],
directed_hausdorff(
flatten(target[:, channel, ...]).cpu().detach().numpy(),
flatten(seg_pred[:, channel, ...]).cpu().detach().numpy())[0])
return distances
def __call__(self, y_true, y_pred, sample_weight=None):
"""Updates running mean of Hausdorff distances."""
y_pred = pred_to_one_hot(y_pred, self.data_format)
y_true = tf.reshape(y_true, shape=(1, -1))
y_pred = tf.reshape(y_pred, shape=(1, -1))
haus_dist = tf.maximum(
directed_hausdorff(y_true.numpy(), y_pred.numpy())[0],
directed_hausdorff(y_pred.numpy(), y_true.numpy())[0])
return super(HausdorffDistance,
self).update_state(haus_dist, sample_weight=sample_weight)
def test_indices(self):
# Ensure that correct point indices are returned -- they should
# correspond to the Hausdorff pair
path_simple_1 = np.array([[-1,-12],[0,0], [1,1], [3,7], [1,2]])
path_simple_2 = np.array([[0,0], [1,1], [4,100], [10,9]])
actual = directed_hausdorff(path_simple_2, path_simple_1)[1:]
expected = (2, 3)
assert_array_equal(actual, expected)
def test_4d_data_reverse(self):
# Ensure that 4D data is handled properly for a simple case
# relative to brute force approach.
actual = directed_hausdorff(self.path_2_4d, self.path_1_4d)[0]
# brute force over columns:
expected = max(np.amin(distance.cdist(self.path_1_4d, self.path_2_4d),
axis=0))
assert_almost_equal(actual, expected, decimal=9)
def test_2d_data_forward(self):
# Ensure that 2D data is handled properly for a simple case
# relative to brute force approach.
actual = directed_hausdorff(self.path_1[..., :2],
self.path_2[..., :2])[0]
expected = max(np.amin(distance.cdist(self.path_1[..., :2],
self.path_2[..., :2]),
axis=1))
assert_almost_equal(actual, expected, decimal=9)
def test_brute_force_comparison_reverse(self):
# Ensure that the algorithm for directed_hausdorff gives the
# same result as the simple / brute force approach in the
# reverse direction.
actual = directed_hausdorff(self.path_2, self.path_1)[0]
# brute force over columns:
expected = max(np.amin(distance.cdist(self.path_1, self.path_2),
axis=0))
assert_almost_equal(actual, expected, decimal=9)
def handwriting_recognition(imagefile1,imagefile2):
img1 = cv2.imread(imagefile1,0)
ret,thresh1=cv2.threshold(img1,0,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
contours1,hierarchy1=cv2.findContours(thresh1,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
#contours1=cv2.findContours(thresh1,1,2)
epsilon1 = 0.1*cv2.arcLength(contours1[0],True)
#epsilon1=0.2
approx1 = cv2.approxPolyDP(contours1[0],epsilon1,True)
print approx1
img2 = cv2.imread(imagefile2,0)
ret,thresh2=cv2.threshold(img2,0,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
contours2,hierarchy2=cv2.findContours(thresh2,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
#contours2=cv2.findContours(thresh2,1,2)
epsilon2 = 0.1*cv2.arcLength(contours2[0],True)
#epsilon2=0.2
approx2 = cv2.approxPolyDP(contours2[0],epsilon2,True)
print approx2
print "Distance between DP polynomials approximating two handwriting contours:", directed_hausdorff(approx1[0],approx2[0])
def time_directed_hausdorff(self, num_points):
# time directed_hausdorff code in 3 D
distance.directed_hausdorff(self.points1, self.points2)
def test_degenerate_case(self):
# The directed Hausdorff distance must be zero if both input
# data arrays match.
actual = directed_hausdorff(self.path_1, self.path_1)[0]
assert_almost_equal(actual, 0.0, decimal=9)