def dtw_score(test_trend, target_trend):
standard_test_trend = StandardScaler().fit_transform(np.array(test_trend).reshape([-1, 1]))
standard_target_trend = StandardScaler().fit_transform(np.array(target_trend).reshape([-1, 1]))
cost_matrix, _1, _2 = dtw1d(standard_test_trend.reshape([1, -1])[0], standard_target_trend.reshape([1, -1])[0])
difference = np.asarray(cost_matrix)[-1, -1]
return difference
def pathCost(a, b):
costMatrix, alignmentA, alignmentB = dtw1d(a, b)
idxs = list(zip(np.asarray(alignmentA), np.asarray(alignmentB)))
cost = 0
for idx in idxs:
cost = cost + costMatrix[idx[0], idx[1]]
return cost, costMatrix, alignmentA, alignmentB
def test_dtw1d(self):
a = np.array([0, 0, 1, 1, 2, 4, 2, 1, 2, 0], dtype=np.float64)
b = np.array([1, 1, 1, 2, 2, 2, 2, 3, 2, 0], dtype=np.float64)
cost, al_a, al_b = dtw1d(a, b)
assert (al_a == np.array([0, 1, 2, 3, 4, 4, 4, 4, 5, 6, 7, 8,
9])).all(), al_a
assert (al_b == np.array([0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 8,
9])).all(), al_b
def __reconizer_run(self, x, y):
"""
Roda o algotimo com a função de distância escolhida.
Esse método pode ser sobrescrito para utilizar implementações diferentes do DTW.
Como o AcceleratedDTW.
"""
return dtw1d(x, y).get_dist()
def dtw_similarity(test_trend, target_trend, threshold=20):
standard_test_trend = StandardScaler().fit_transform(np.array(test_trend).reshape([-1, 1]))
standard_target_trend = StandardScaler().fit_transform(np.array(target_trend).reshape([-1, 1]))
cost_matrix, _1, _2 = dtw1d(standard_test_trend.reshape([1, -1])[0], standard_target_trend.reshape([1, -1])[0])
difference = np.asarray(cost_matrix)[-1, -1]
# return difference
print(difference)
if difference < threshold:
return True,difference
else:
return False,difference
def multidtw(Seeds_B1, Seeds_B2, b1, b2, nseeds_b, n_seeds, path, **kwargs):
#SETUP OPTIONS
info = kwargs.get('info', True)
DTW_max_samp = kwargs.get('DTW_max_samp', 15)
multiprocessing = kwargs.get('multiprocessing', True)
#ALLOC VARIABLE
DTW_matrix = np.zeros((nseeds_b, nseeds_b))
#Compute the DTW distance between the seeds
if multiprocessing:
counter = Value('i', 0)
corecount = int(os.cpu_count() / 2 -
1) #half to account for virtual cores
kwargs['corecount'] = corecount
p = Pool(corecount, initializer=counterinit, initargs=(counter, ))
results = p.map(
partial(multi_DTW_process,
Seeds_B1=Seeds_B1,
Seeds_B2=Seeds_B2,
nseeds_b=nseeds_b,
corecount=corecount,
DTW_max_samp=DTW_max_samp), range(nseeds_b))
p.close()
p.join()
DTW_matrix = results
DTW_matrix = np.array(DTW_matrix)
else:
Traj1 = np.zeros((Seeds_B1.shape[2], Seeds_B1.shape[1]))
Traj2 = np.zeros((Seeds_B2.shape[2], Seeds_B2.shape[1]))
for ns1 in range(nseeds_b):
for f in range(Seeds_B1.shape[2]):
Traj1[f] = Seeds_B1[ns1, :, f]
for ns2 in range(nseeds_b):
for f in range(Seeds_B2.shape[2]):
Traj2[f] = Seeds_B2[ns2, :, f]
cost_matrix, cost, alignmend_a, alignmend_b = dtw1d(
Traj1, Traj2)
DTW_matrix_B[ns1, ns2] = cost
#SAVE OUTPUT
filename = fm.joinpath(path, 'DTW_matrix.h5')
if not os.path.isfile(filename):
with h5py.File(filename, 'w') as hf:
hf.create_dataset("DTW_matrix", (n_seeds, n_seeds), chunks=True)
hf["DTW_matrix"][b1:b1 + nseeds_b, b2:b2 + nseeds_b] = DTW_matrix
else:
with h5py.File(filename, 'a') as hf:
hf["DTW_matrix"][b1:b1 + nseeds_b, b2:b2 + nseeds_b] = DTW_matrix
def distance_fast(Traj1, Traj2, max_step):
if Traj1.ndim == 1:
cost_matrix, cost, alignmend_a, alignmend_b = dtw1d(Traj1, Traj2)
else:
Traj1 = np.ascontiguousarray(Traj1.transpose())
Traj2 = np.ascontiguousarray(Traj2.transpose())
cost_matrix, cost, alignmend_a, alignmend_b = dtw2d(Traj1, Traj2)
return cost
# def distance_fast(s1, s2, window=None, max_dist=None,
# max_step=None, max_length_diff=None, penalty=None, psi=None):
# """Fast C version of :meth:`distance`.
# Note: the series are expected to be arrays of the type ``double``.
# Thus ``numpy.array([1,2,3], dtype=numpy.double)`` or
# ``array.array('d', [1,2,3])``
# """
# if dtw_c is None:
# _print_library_missing()
# return None
# if window is None:
# window = 0
# if max_dist is None:
# max_dist = 0
# if max_step is None:
# max_step = 0
# if max_length_diff is None:
# max_length_diff = 0
# if penalty is None:
# penalty = 0
# if psi is None:
# psi = 0
# d = dtw_c.distance_nogil(s1, s2, window,
# max_dist=max_dist,
# max_step=max_step,
# max_length_diff=max_length_diff,
# penalty=penalty,
# psi=psi)
# return d
def single_DTW_process(ns1, Seeds_B_B1, Seeds_B_B2, nseeds_b, **kwargs):
#SETUP OPTIONS
info = kwargs.get('info', True)
DTW_max_samp = kwargs.get('DTW_max_samp', 15)
corecount = kwargs.get('corecount', 2)
time.sleep(.1)
with counter.get_lock():
counter.value += 1
if info:
print('\r(%i-core(s))Calculating DTW %i/%i ' %
(corecount, counter.value, nseeds_b),
end='\r')
DTW_matrix_B = np.zeros(nseeds_b)
for ns2 in range(nseeds_b):
Traj1 = Seeds_B_B1[ns1]
Traj2 = Seeds_B_B2[ns2]
cost_matrix, cost, alignmend_a, alignmend_b = dtw1d(Traj1, Traj2)
DTW_matrix[ns2] = cost
return DTW_matrix_B
def test_dtw1d(self):
a = np.array([0, 0, 1, 1, 2, 4, 2, 1, 2, 0], dtype=np.float64)
b = np.array([1, 1, 1, 2, 2, 2, 2, 3, 2, 0], dtype=np.float64)
cost, al_a, al_b = dtw1d(a, b)
assert (al_a == np.array([0, 1, 2, 3, 4, 4, 4, 4, 5, 6, 7, 8, 9])).all(), al_a
assert (al_b == np.array([0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 8, 9])).all(), al_b
if 'x' not in d.keys(): continue
us.append(d['u'])
xs.append(d['x'])
vehicle_poses.append(d['vehicle'])
solid_line_poses.append(d['solid_line'])
dash_line_poses.append(d['dash_line'])
## plot(xs)
#sys.exit()
new_xs = []
from pydtw import dtw1d
for i in xrange(1,len(xs)):
x_ref = np.array(xs[0])
x = np.array(xs[i])
_, idx1, idx2 = dtw1d(x_ref[:,0].copy(order='C'),
x[:,0].copy(order='C'))
l = []
for j in xrange(len(xs[0][-1])):
l.append(x[idx2,j])
new_xs.append(l)
## x1 = []
## x2 = []
## for i,j in zip(alignmend_a, alignmend_b):
## x1.append(a[i])
## x2.append(b[j])
print np.shape(new_xs)
# Get 3D covariance figures
def manager(tile, **kwargs):
#SETUP DEFAULT OPTIONS
info = kwargs.get('info', True)
outpath = kwargs.get('outpath', None)
savepath = fm.check_folder(outpath, tile, 'LCTraining_DTW')
blocksize = kwargs.get('blocksize', 500)
n_classes = kwargs.get('n_classes', 9)
multiprocessing = kwargs.get('multiprocessing', True)
singlefeaturedtw = kwargs.get('singlefeaturedtw', False)
featureselection = kwargs.get('featureselection', False)
multifeatureDTW = kwargs.get('multifeatureDTW', False)
similarity = kwargs.get('similarity', False)
classprototypes = kwargs.get('classprototypes', False)
DTW_max_samp = kwargs.get('DTW_max_samp',
15) # max number of samples of DTW
col_nPIXEL = 0
col_nCLASS = 1
col_nBAND = 2
col_DATA = 3
###############################
# GET INFO AND INITIALIZATION #
###############################
for rootname, _, filenames in os.walk(outpath):
for f in filenames:
if (f.endswith('.tif')):
loadpath = fm.joinpath(rootname, f)
img = fm.readGeoTIFFD(loadpath, metadata=False)
width, height, totfeature = img.shape
for rootname, _, filenames in os.walk(outpath):
for f in filenames:
if (f.endswith('ts.h5')):
loadpath = fm.joinpath(rootname)
NDI_ = fm.loadh5(loadpath, f)
#Get classes intervals
class_int = np.zeros(n_classes)
class_int_mask = np.unique(NDI_[:, col_nCLASS]).astype(int).tolist()
for n in class_int_mask:
class_int[n - 1] = n
class_int = class_int.astype(int).tolist()
#Get number of seeds
n_seeds = len(np.unique(NDI_[:, col_nPIXEL]))
#Get number of features
n_features = totfeature
#Get number of seeds per class and class seeds mask
n_seeds_c = np.zeros(n_classes)
for nc in class_int:
n_seeds_c[nc - 1] = np.size(NDI_[NDI_[:, col_nCLASS] == nc, :], axis=0)
n_seeds_c = n_seeds_c.astype(int).tolist()
seed_class_mask = NDI_[:, col_nCLASS]
#Define blocksize
nseeds_b = blocksize
#Space of analysis parameters
min_perc_samp_V = np.arange(
1, 0.64, -0.03).tolist() # minimum percentage of total used samples
min_perc_samp_mod_V = np.ones(12, dtype=float) / np.arange(
1, 13) # minimum percentage of used samples per model
min_perc_samp_mod_V = min_perc_samp_mod_V.tolist()
sepa_b_vs_b = np.zeros((12, 12, n_features))
##########################################
# SINGLE FEATURE DTW SIMILARITY MATRICES #
##########################################
if singlefeaturedtw:
for feature in range(n_features):
if info:
t_start = time.time()
print('Computing DTW feature %i/%i...' %
((feature + 1), n_features),
end='\r')
path = fm.check_folder(savepath, "Singlefeature",
'DTW_matrix_B' + str(feature + 1))
for b1 in range(0, n_seeds, nseeds_b):
Seeds_B_B1 = load_block(tile, b1, feature, col_DATA, **kwargs)
for b2 in range(0, n_seeds, nseeds_b):
Seeds_B_B2 = load_block(tile, b2, feature, col_DATA,
**kwargs)
singledtw(Seeds_B_B1, Seeds_B_B2, b1, b2, nseeds_b,
n_seeds, path, **kwargs)
if info:
t_end = time.time()
print(
'\nMODULE 3.2: calculating DTW for %ith feature..Took %i' %
(feature + 1, t_end - t_start / 60), 'min')
#Single feature DTW maximum distance
DTW_max_d_B = np.array(n_features)
for feature in range(n_features):
path = fm.check_folder(savepath, "Singlefeature",
'DTW_matrix_B' + str(feature + 1))
max_d = 0
for b1 in range(0, n_seeds, nseeds_b):
for b2 in range(0, n_seeds, nseeds_b):
with h5py.File(filename, 'r') as hf:
max_d_block = np.nanmax(
np.array(hf["DTW_matrix_B"][b1:b1 + nseeds_b,
b2:b2 + nseeds_b]))
if max_d_block > max_d:
max_d = max_d_block
DTW_max_d_B[feature] = max_d
######################################################
# FEATURE SPACE ANALYSIS AND FEATURE SPACE REDUCTION #
######################################################
if featureselection:
for feature in range(n_features):
if info:
t_start = time.time()
print('Feature %i/%i...' % ((feature + 1), n_features),
end='\r')
sepa_c_vs_c = np.zeros((12, 12))
sepa_c_vs_c_N = np.zeros((12, 12))
for i, nc in enumerate(class_int_mask):
c_r = np.delete(class_int_mask, i).tolist()
for nc1 in c_r:
simi_c_W, simi_c_C = load_block_DTW(
seed_class_mask, feature, DTW_max_d_B[feature], nc,
nc1, savepath)
for col_i, min_perc_samp in enumerate(min_perc_samp_V):
for row_i, min_perc_samp_mod in enumerate(
min_perc_samp_mod_V):
sepa_mea = np.zeros(n_seeds_c[nc - 1])
for nsc in range(n_seeds_c[nc - 1]):
simi_c_C_s = simi_c_C[:, nsc]
simi_c_C_s = simi_c_C_s[~np.isnan(simi_c_C_s)]
simi_c_C_s = sorted(simi_c_C_s, reverse=True)
simi_c_C_s = simi_c_C_s[
0:math.ceil(n_seeds_c[nc - 1] *
min_perc_samp_mod *
min_perc_samp)]
simi_c_W_s = simi_c_W[:, nsc]
simi_c_W_s = sorted(simi_c_W_s, reverse=True)
simi_c_W_s = simi_c_W_s[
0:math.ceil(n_seeds_c[nc - 1] *
min_perc_samp_mod *
min_perc_samp)]
pd_C_mu, pd_C_sigma = scipy.stats.distributions.norm.fit(
simi_c_C_s)
pd_W_mu, pd_W_sigma = scipy.stats.distributions.norm.fit(
simi_c_W_s)
if pd_C_mu <= pd_W_mu:
sepa_mea[nsc] = np.nan
else:
sepa_mea[nsc] = (pd_C_mu - pd_W_mu) / (
pd_C_sigma + pd_W_sigma)
if (sepa_mea[~np.isnan(sepa_mea)]).size / (
n_seeds_c[nc - 1]) >= min_perc_samp:
sepa_c_vs_c[row_i, col_i] = sepa_c_vs_c[
row_i, col_i] + np.mean(
sepa_mea[~np.isnan(sepa_mea)])
sepa_c_vs_c_N[row_i,
col_i] = sepa_c_vs_c_N[row_i,
col_i] + 1
sepa_b_vs_b[..., feature] = sepa_c_vs_c * sepa_c_vs_c_N
if info:
t_end = time.time()
print(
'\nMODULE 3.2: feature selection for %i th feature..Took %i'
% (feature + 1, t_end - t_start / 60), 'min')
np.save(fm.joinpath(savepath, "sepa_b_vs_b.npy"), sepa_b_vs_b)
#Search for Class Cluster Parameters
# select_bands = np.load(fm.joinpath(savepath, "select_bands.npy"))
sepa_b_vs_b = np.load(fm.joinpath(savepath, "sepa_b_vs_b.npy"))
# select_bands = select_bands.astype(int).tolist()
sepa_FS = np.zeros((12, 12))
for nb in range(n_features):
sepa_FS = sepa_FS + sepa_b_vs_b[:, :, nb]
mean_sepa_FS = np.mean(sepa_FS, axis=1)
max_sepa_pos_samp_x_mod_FS = np.argmax(mean_sepa_FS)
mean_sepa_max_v_FS = sepa_FS[max_sepa_pos_samp_x_mod_FS, :]
mean_sepa_max_v_derivate_FS = np.diff(mean_sepa_max_v_FS)
mean_sepa_max_v_derivate_FS = mean_sepa_max_v_derivate_FS / np.max(
mean_sepa_max_v_derivate_FS)
mean_sepa_max_v_derivate_FS = mean_sepa_max_v_derivate_FS * mean_sepa_max_v_FS[
1:]
max_sepa_pos_perc_samp_FS = np.argmax(mean_sepa_max_v_derivate_FS)
max_sepa_pos_perc_samp_FS = max_sepa_pos_perc_samp_FS + 1
min_perc_samp = min_perc_samp_V[max_sepa_pos_perc_samp_FS]
min_perc_samp_mod = min_perc_samp_V[
max_sepa_pos_perc_samp_FS] * min_perc_samp_mod_V[
max_sepa_pos_samp_x_mod_FS]
max_mod_class = np.round(min_perc_samp_V[max_sepa_pos_perc_samp_FS] /
min_perc_samp_mod)
#######################################
# MULTI FEATURE DTW SIMILARITY MATRIX #
#######################################
if multifeatureDTW:
if info:
t_start = time.time()
print('Computing multifeature DTW ...', end='\r')
# select_bands = np.load(fm.joinpath(savepath, "select_bands.npy"))
# select_bands = select_bands.astype(int).tolist()
path = fm.check_folder(savepath, 'Multifeature')
for b1 in range(0, n_seeds, nseeds_b):
Seeds_B1 = load_block_multifeature(tile, b1, n_features, col_DATA,
**kwargs)
for b2 in range(0, n_seeds, nseeds_b):
Seeds_B2 = load_block_multifeature(tile, b1, n_features,
col_DATA, **kwargs)
multidtw(Seeds_B1, Seeds_B2, b1, b2, nseeds_b, n_seeds, path,
**kwargs)
if info:
t_end = time.time()
print(
'\nMODULE 3.2: calculating multifeature DTW ...Took %i' %
(t_end - t_start / 60), 'min')
#Multi feature DTW maximum distance
path = fm.check_folder(savepath, 'Multifeature')
DTW_max_d = 0
for b1 in range(0, n_seeds, nseeds_b):
for b2 in range(0, n_seeds, nseeds_b):
with h5py.File(filename, 'r') as hf:
max_d_block = np.nanmax(
np.array(hf["DTW_matrix"][b1:b1 + nseeds_b,
b2:b2 + nseeds_b]))
if max_d_block > DTW_max_d:
DTW_max_d = max_d_block
#######################
# SIMILARITY ANALYSIS #
#######################
if similarity:
simi_high = kwargs.get('simi_high', 1) # high similarity measure
simi_decr = kwargs.get('simi_decr',
0.001) # decrese value of similarity measure
min_c_vs_c = np.zeros((len(class_int_mask), len(class_int_mask) - 1))
max_c_vs_c = np.zeros((len(class_int_mask), len(class_int_mask) - 1))
mean_c_vs_c = np.zeros((len(class_int_mask), len(class_int_mask) - 1))
simi_low = np.zeros((len(class_int_mask)))
for i, nc in enumerate(class_int_mask):
c_r = np.delete(class_int_mask, i).tolist()
for n, nc1 in enumerate(c_r):
simi_c_W, simi_c_C = load_block_DTW_multi(
seed_class_mask, DTW_max_d, nc, nc1, savepath)
min_c_s = np.zeros((n_seeds_c[nc - 1]))
max_c_s = np.zeros((n_seeds_c[nc - 1]))
for nsc in range(n_seeds_c[nc - 1]):
simi_c_C_s = simi_c_C[:, nsc]
simi_c_C_s = simi_c_C_s[~np.isnan(simi_c_C_s)]
simi_c_C_s = sorted(simi_c_C_s, reverse=True)
simi_c_C_s = simi_c_C_s[0:math.ceil(n_seeds_c[nc - 1] *
min_perc_samp_mod *
min_perc_samp)]
simi_c_W_s = simi_c_W[:, nsc]
simi_c_W_s = sorted(simi_c_W_s, reverse=True)
simi_c_W_s = simi_c_W_s[0:math.ceil(n_seeds_c[nc - 1] *
min_perc_samp_mod *
min_perc_samp)]
pd_C_mu, pd_C_sigma = scipy.stats.distributions.norm.fit(
simi_c_C_s)
pd_W_mu, pd_W_sigma = scipy.stats.distributions.norm.fit(
simi_c_W_s)
if pd_C_mu <= pd_W_mu:
min_c_s[nsc] = np.nan
else:
a = scipy.stats.norm(pd_C_mu, pd_C_sigma).pdf(
np.arange(0, 1, simi_decr))
b = scipy.stats.norm(pd_W_mu, pd_W_sigma).pdf(
np.arange(0, 1, simi_decr))
for int_mu in np.int64(
np.arange(np.floor(pd_W_mu * (1 / simi_decr)),
(math.ceil(pd_C_mu *
(1 / simi_decr)) + 1),
1000 * simi_decr)):
if (round(b[int_mu - 1], 1) -
round(a[int_mu - 1], 1) <= 0):
min_c_s[nsc] = int_mu * simi_decr
break
else:
min_c_s[nsc] = np.nan
for int_mu in np.flipud(
np.int64(
np.arange(
np.floor(pd_W_mu * (1 / simi_decr)),
(math.ceil(pd_C_mu *
(1 / simi_decr)) + 1),
1000 * simi_decr))):
if (round(a[int_mu - 1], 1) -
round(b[int_mu - 1], 1) <= 0):
max_c_s[nsc] = int_mu * simi_decr
break
else:
max_c_s[nsc] = np.nan
min_c_vs_c[i, n] = np.mean(min_c_s[~np.isnan(min_c_s)])
max_c_vs_c[i, n] = np.mean(max_c_s[~np.isnan(max_c_s)])
mean_c_vs_c[i, n] = min_c_vs_c[
i, n] #mean([min_c_vs_c(nc,nc1) max_c_vs_c(nc,nc1)])
simi_low[i] = np.max(mean_c_vs_c[i, :])
np.save(fm.joinpath(savepath, "simi_low.npy"), simi_low)
###############################
# CLASS PROTOTYPES GENERATION #
###############################
if classprototypes:
pass_table = np.zeros(n_classes) # array of pass/no pass
models_C = [None] * 9 # variable that contains the models seeds
used_models = np.zeros(
n_classes) # array of number of model used per class
used_samples_perc = np.zeros(
n_classes) # array of used samples per class
used_simi = np.zeros(n_classes) # array of used similarity per class
for i, nc in enumerate(class_int_mask):
max_s = 1 # set max similarity = 1
min_s = 0 #simi_low(nc); # set min similarity
while pass_table[nc - 1] == 0:
_, dist_simi_c = load_block_DTW_multi(seed_class_mask,
DTW_max_d, nc, nc,
savepath)
count_simi_c = (
dist_simi_c > max_s
) # check class seed with a similarity major then the threshold
mean_simi_c = np.empty(
(n_seeds_c[nc - 1]
)) * np.nan # initializate the similarity mean value
# compute the mean similarity value per seed for each accepted other seed
for nsc in range(n_seeds_c[nc - 1]):
mean_simi_c[nsc] = np.mean(dist_simi_c[count_simi_c[:,
nsc],
nsc])
# form a matrix with [seed ID | number of accepted seeds | mean similarity for accepted seeds]
simi_order = np.column_stack([
np.arange(0, n_seeds_c[nc - 1], 1),
np.sum(count_simi_c, axis=0), mean_simi_c
])
# order the seeds
simi_order = simi_order[np.argsort(-simi_order[:, 0])]
simi_order = np.array(
simi_order[np.argsort(-simi_order[:, 0])], dtype=int)
#simi_order = sorted(simi_order, key=lambda x : x[0], reverse=True)
models = [] # initialize the models
for nsc in range(n_seeds_c[nc - 1]):
n_mod = len(models) #number of exist models
if n_mod == 0: # if the number of models is zero, just insert the initial seed
models.append(simi_order[nsc, 0])
else: # else check if any model can accept the new seed
simi = np.zeros(
(n_mod, 3)) #initialize the similarity matrix
# for each model check if all seed can accept the new one
for nm in range(n_mod):
seed_int = models[nm] # get seed ID interval
# form a matrix with [model ID | acceptance value | mean similarity between new seed and model seeds]
simi[nm, :] = [
nm,
np.sum((dist_simi_c[simi_order[nsc, 0],
seed_int] > max_s) * 1) >=
(np.ceil(np.size(seed_int) * 1)),
np.mean(dist_simi_c[simi_order[nsc, 0],
seed_int])
]
# sort the similarity matrix to get the most similar model
simi = np.array(simi[np.argsort(-simi[:, 2])],
dtype=int)
if simi[0,
1] == 1: # if the first model can accept the new seed, insert it
models[simi[0, 0]] = list(
flatten(
[models[simi[0, 0]], simi_order[nsc, 0]]))
else: # otherwise create a new model and insert the seed
models.append(simi_order[nsc, 0])
n_mod = np.size(models, 0) # get number of models
# delete models with a percentage of seed lower than the threshold
for nm in range(n_mod):
if np.size(models[nm]) < math.ceil(
n_seeds_c[nc - 1] * min_perc_samp_mod):
models[nm] = []
models = list(filter(None, models))
u_models = len(models) # get number of used models
u_samples = np.zeros(
u_models) # initialized the percentage of used seeds
# compute the percentage of used seeds
for um in range(u_models):
u_samples[um] = np.size(models[um])
u_samples = (np.sum(u_samples)) / (n_seeds_c[nc - 1])
# if the pass condition are respected update the output matrixes
if ((u_models <= max_mod_class)
and (bool(u_samples >= min_perc_samp))):
pass_table[nc - 1] = 1
models_C[nc - 1] = models
used_models[nc - 1] = u_models
used_samples_perc[nc - 1] = u_samples
used_simi[nc - 1] = max_s
else:
if ((max_s > min_s) and (max_s > simi_decr)
): # otherwise decrease the similarity threshold
max_s = max_s - simi_decr
print(max_s)
else: # or if not possible put in the pass table a false value
pass_table[nc - 1] = 2
# class prototypes creation
models = [[[] for _ in range(len(n_features))]
for _ in range(n_classes)]
for nc in (class_int_mask):
for nb_o, nb in enumerate(n_features):
n_mod = np.size(models_C[nc - 1])
Seeds_FR, Seeds_F = load_Seeds_FR(tile, nb, col_DATA, **kwargs)
m1 = Seeds_F[:, col_nCLASS] == nc
m2 = Seeds_F[:, col_nBAND] == nb
m3 = np.logical_and(m1, m2)
TABLE_cb = Seeds_FR[m3, :]
for nm in range(n_mod):
TABLE_cbm = TABLE_cb[models_C[nc - 1][nm], :]
traj = np.mean(TABLE_cbm, 0)
models[nc - 1][nb_o].append(traj)
# prototypes vs samples
_, col = Seeds_FR.shape
Traj1 = np.zeros((len(n_features), col))
sampleVSmodels = np.zeros((n_seeds, n_classes + 3))
for ns in range(n_seeds):
for n, nb in enumerate(n_features):
Seeds_FR, Seeds_F = load_Seeds_FR(tile, nb, col_DATA, **kwargs)
Traj1[n, :] = Seeds_FR[ns, :]
sample_simi = [ns, Seeds_F[ns, col_nCLASS], 0]
for nc in (class_int):
if nc == 0:
max_simi = 0
else:
n_mod = len(models[nc - 1])
max_simi = 0
for nm in range(n_mod):
Traj2 = models[nc - 1][nm]
cost_matrix, cost, alignmend_a, alignmend_b = dtw1d(
Traj1, Traj2)
simi = ((DTW_max_d - cost) / DTW_max_d)
max_simi = np.max([max_simi, simi])
sample_simi.append(max_simi)
max_v = max(sample_simi[3:])
max_p = sample_simi[3:].index(max_v)
sample_simi[2] = max_p + 1
sampleVSmodels[ns, :] = sample_simi
#confusion matrix between training samples and prototypes
CM_S = confusion_matrix(sampleVSmodels[:, 1], sampleVSmodels[:, 2])