def persistence_image_features(X_train, pixels=[20, 20], spread=1):
start = time.time()
pim = PersImage(pixels=pixels, spread=spread)
imgs_train = pim.transform(X_train)
X_train_features = np.array([img.flatten() for img in imgs_train])
timing = time.time() - start
return timing
def subj_to_pims(sbj, sdict, px, sd, nobs):
"""
generate persistence images for all gestures for a given subject
INPUTS
sbj - subject number
sdict - dict of gestures performed by a subject
px - pixel dimension/ resolution; e.g. px=20 gives 20x20 persistence image
sd - persistence image concentration parameter (gaussian)
nobs - number of observations per subj (total num of gests they performed)
OUTPUTS
array of gestures made by subject
"""
# instantiate persistence image generator & vietoris-rips complex generators
rips = Rips(maxdim=1, verbose=False) # 1-D homology rips complex
pim = PersImage(pixels=[px, px], spread=sd)
# each vector have equal # persim pix + 2 cols for subj & gest labels
res_mat = np.zeros(px**2 * nobs + 2 * nobs).reshape(nobs, -1)
v = 0
for gnum, garray in sdict.items():
# generate rips complex on points; slice out time col and gesture label
dgms = rips.fit_transform(garray[:, 1:-1])
img = pim.transform(dgms[1]) # persistence image of 1 cycles
obs_vec = np.r_[img.flatten(), int(gnum[0]), int(sbj)]
res_mat[v, :] = obs_vec
v += 1
return res_mat
def generate_persistence_images(directory, threshold, pixel, spreadval,
rangemin, rangemax):
for file in os.listdir(directory):
dgm0 = np.squeeze(sio.loadmat(directory + file)['PD'])
# Computing Lifetimes for Thresholding of Persistence Diagrams
lifetime = np.ones(len(dgm0))
for h in range(len(dgm0)):
lifetime[h] = dgm0[h][1] - dgm0[h][0]
#Keeps only points greater than reduction value
isvalid = np.greater(lifetime, threshold)
reduced_pd = dgm0[isvalid]
print("Beginning Persistence Image Generation for " + file)
print("Length of PD: " + str(len(dgm0)) + " points")
print("Length Reduced PD: " + str(len(reduced_pd)) + " points")
pim = PersImage(pixels=[pixel, pixel],
spread=spreadval,
specs={
"minBD": rangemin,
"maxBD": rangemax
})
imgs = pim.transform(reduced_pd)
imgs = imgs / np.max(imgs)
imgs = imgs.reshape((-1))
filename = "./Persistence_Images/" + file
sio.savemat(filename, dict([('PersImg', imgs)]))
def generate_PI(PD_list, emb_dim, tau, pixels, spread):
pim = PersImage(pixels=[pixels, pixels], spread=spread)
PI_list = pim.transform(PD_list)
PI_list = np.array([img.flatten() for img in PI_list])
return np.array(PI_list)
def test_kernel_mean(self):
pim = PersImage()
kf = pim.kernel(2)
data = np.array([[0,0]])
assert kf(np.array([[0,0]]), [0,0]) >= kf(np.array([[1,1]]), [0,0]), "decreasing away"
assert kf(np.array([[0,0]]), [1,1]) == kf(np.array([[1,1]]), [0,0]), "symmetric"
def generate_persistence_image(dgm0, threshold, pixel, spreadval, rangemin,
rangemax):
# Computing Lifetimes for Thresholding of Persistence Diagrams
lifetime = np.ones(len(dgm0))
for h in range(len(dgm0)):
lifetime[h] = dgm0[h][1] - dgm0[h][0]
#Keeps only points greater than reduction value
isvalid = np.greater(lifetime, threshold)
reduced_pd = dgm0[isvalid]
print("Length of PD: " + str(len(dgm0)) + " points")
print("Length Reduced PD: " + str(len(reduced_pd)) + " points")
pim = PersImage(pixels=[pixel, pixel],
spread=spreadval,
specs={
"minBD": rangemin,
"maxBD": rangemax
})
imgs = pim.transform(reduced_pd)
imgs = imgs / np.max(imgs)
#imgs = imgs.reshape((-1))
return imgs
def test_zero_on_xaxis(self):
pim = PersImage()
wf = pim.weighting()
assert wf([1, 0]) == 0
assert wf([100, 0]) == 0
assert wf([99, 1.4]) == 1.4
def test_scales(self):
pim = PersImage()
wf = pim.weighting(np.array([[0, 1], [1, 2], [3, 4]]))
assert wf([1, 0]) == 0
assert wf([1, 4]) == 1
assert wf([1, 2]) == .5
def test_multiple_diagrams(self):
pim = PersImage(pixels=(3, 3))
diagram1 = np.array([[0, 1], [1, 1], [3, 5]])
diagram2 = np.array([[0, 1], [1, 1], [3, 6]])
imgs = pim.transform([diagram1, diagram2])
assert len(imgs) == 2
assert imgs[0].shape == imgs[1].shape
def generatePI(allPDs, segmentLength, embDim, tau, PCA_n_components, pixels,
spread, norm, savePI):
pim = PersImage(pixels=[pixels, pixels], spread=spread)
imgs = pim.transform(allPDs)
imgs_array = np.array([img.flatten() for img in imgs])
if savePI == True:
np.save(
'PI_Len%s_Dim%s_Tau%s_PCA%s_p%s_s%s_%s.npy' %
(segmentLength, embDim, tau, PCA_n_components, pixels, spread,
norm), imgs_array)
return imgs_array
def persistence(self, k_max=1, type="standard", representation="surface", shape=(16,16)):
if representation=="surface":
pi = PersImage(spread=0.025, pixels=shape, verbose=False)
result = np.array(pi.transform(diagrams[1]))
elif representation=="landscape":
raise NotImplementedError() # TODO
elif representation=="diagram":
result = diagrams
else:
raise ValueError("Representation should be 'vector', 'surface', 'landscape', or 'diagram'")
return result
def calculatePI(val = None):
global dgms, first
if not first:
r = int(sld_resolution.val)
v = sld_spread.val
else:
r = 10
v = 1
pim = PersImage(spread=v, pixels=[r,r], verbose=False)
img = pim.transform(dgms[1])
ax_1 = plt.subplot(233)
plt.title("PI for $H_1$\nspread = " + str(v)[0:4] + "\n" + str(r) + "x" + str(r))
pim.show(img, ax_1)
first = False
def test_integer_diagrams():
""" This test is inspired by gh issue #3 by gh user muszyna25.
Integer diagrams return nan values.
This does not work: dgm = [[0, 2], [0, 6], [0, 8]];
This one works fine: dgm = [[0.0, 2.0], [0.0, 6.0], [0.0, 8.0]];
"""
dgm = [[0, 2], [0, 6], [0, 8]]
dgm2 = [[0.0, 2.0], [0.0, 6.0], [0.0, 8.0]]
pim = PersImage()
res = pim.transform(dgm2)
res2 = pim.transform(dgm)
np.testing.assert_array_equal(res, res2)
def test_empyt_diagram_list(self):
dgm1 = [np.array([[2, 3]]), np.zeros((0, 2))]
pim1 = PersImage(pixels=(10, 10))
res1 = pim1.transform(dgm1)
assert np.all(res1[1] == np.zeros((10, 10)))
dgm2 = [np.zeros((0, 2)), np.array([[2, 3]])]
pim2 = PersImage(pixels=(10, 10))
res2 = pim2.transform(dgm2)
assert np.all(res2[0] == np.zeros((10, 10)))
dgm3 = [np.zeros((0, 2)), np.zeros((0, 2))]
pim3 = PersImage(pixels=(10, 10))
res3 = pim3.transform(dgm3)
assert np.all(res3[0] == np.zeros((10, 10)))
assert np.all(res3[1] == np.zeros((10, 10)))
def persistence_image_features(X_train, X_test, pixels=[20, 20], spread=1):
start = time.time()
pim = PersImage(pixels=pixels, spread=spread)
imgs_train = pim.transform(X_train)
X_train_features = np.array([img.flatten() for img in imgs_train])
pim = PersImage(pixels=pixels, spread=spread)
imgs_test = pim.transform(X_test)
X_test_features = np.array([img.flatten() for img in imgs_test])
print("Total Time (Persistence Images): ", time.time() - start)
return X_train_features, X_test_features
def fit_transform(self, data):
'''
Compute the persistence images
Params:
data: list of 1D numpy arrays, representing the surface profiles
Returns a list of persistence images
'''
Filt = [self.filtration(d) for d in data]
Diags = [
ripser(f, maxdim=0, thresh=self.thresh,
distance_matrix=True)['dgms'][0][:-1] for f in Filt
]
Imgs = PersImage(pixels=self.pixels, verbose=False).transform(Diags)
return Imgs
## Use example (see Ref)
# S2I = SurfacesProfilesToImages(thresh=20,pixels=(20,20))
# s = np.array([11, 14, 9, 7, 9, 7, 8, 10, 9])
# data = [s]
# im = S2I.fit_transform(data)
# plt.imshow(np.flip(im[0],axis=1))
def test_n_pixels(self):
pim = PersImage(pixels=(3, 3))
diagram = np.array([[0, 1], [1, 1], [3, 5]])
img = pim.transform(diagram)
assert img.shape == (3, 3)
from persim import PersImage
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split
import matplotlib.pyplot as plt
pim_df = pd.read_csv("./pim_vectors_mp20_sbst.csv")
pim_df.gest = pim_df.gest.astype("category")
pims = pim_df.values[:, :
-2] # predictor vectors: persistence images (864xpx**2)
gests = pim_df.values[:, -2].astype("int64") # data labels: gesture numbers
pimsd = 1e-5
px = 20
pim = PersImage(pixels=[px, px], spread=pimsd)
# code to load model
with open("./saved_models/log_reg_skl.sav", "rb") as fh:
log_reg = pickle.load(fh)
######## train/ test split ########
np.random.seed(1)
pims_train, pims_test, gests_train, gests_test = train_test_split(
pims, gests, test_size=0.2, random_state=1)
oos_acc = log_reg.score(pims_test, gests_test)
print(f"Accuracy: {oos_acc * 100}%")
inverse_image = np.copy(log_reg.coef_).reshape(-1, px)
for i in range(4):
def compute_single_diagram_statistics(dgm, threshold=None, dim=0):
"""
Computes stats of a single persistence diagram dgm, input as an
array with 2 columns.
"""
if dgm is None: # Return list of stat names
basenames = compute_stats(None)
stat_names = []
# Birth stats
stat_names.append(['b' + name for name in basenames])
# Death stats
stat_names.append(['d' + name for name in basenames])
# Persistence stats
stat_names.append(['p' + name for name in basenames])
# Miscllaneous stats
stat_names.append([
'bdcor', 'bdcencor', 'totalper', 'bmaxper', 'dmaxper', 'bminper',
'dminper', 'Nfeatures'
])
# Betti curve
stat_names.append(['betticurve'])
# Persistence image
stat_names.append(['PI'])
return stat_names
# Else:
Nbins = 100 # Number of betti curve bins
stats = []
dgm = clean_births_deaths(dgm, threshold, dim)
b = dgm[:, 0]
d = dgm[:, 1]
if b.size > 0:
p = d - b # persistence
stats.append(compute_stats(b))
stats.append(compute_stats(d))
stats.append(compute_stats(p))
#stats[binds0:binds1] = compute_stats(b)
#stats[dinds0:dinds1] = compute_stats(d)
#stats[pinds0:pinds1] = compute_stats(p)
bmean = stats[0][3]
dmean = stats[1][3]
#bmean = stats[binds0 + 3]
#dmean = stats[dinds0 + 3]
maxfeatind = np.argmax(p)
minfeatind = np.argmin(p)
stats.append([
np.sum(b * d),
np.sum((b - bmean) * (d - dmean)),
np.sum(p), b[maxfeatind], d[maxfeatind], b[minfeatind],
d[minfeatind], b.size
])
#stats[minds0:minds1] = [np.sum(b*d),
# np.sum((b-bmean)*(d-dmean)),
# np.sum(p),
# b[maxfeatind],
# d[maxfeatind],
# b[minfeatind],
# d[minfeatind],
# b.size]
betticurve = compute_betti_curve(dgm)
## Compute integral of Betti curve over bin
bettiints, bin_edges = integrate_binned_betti_curve(
betticurve, Nbins, threshold)
stats.append([bettiints])
#stats[betti0:betti1] = bettiints
pim = PersImage(spread=0.05, pixels=[10, 10], verbose=False)
img = pim.transform(dgm)
stats.append([img])
else:
stats = None
return stats, threshold / Nbins
def inverse(allFeatures,
classes,
nonanIndFeature=None,
cv=False,
printijScores=False):
# use only uniqueClassName with larger than 10 samples
MINCOUNT = 10
cvFolds = 10
MINCOUNTTRAINING = 5
if nonanIndFeature is not None:
classes = classes[nonanIndFeature]
allFeatures = allFeatures[nonanIndFeature]
uniqueClassName, uniqueCNameCount = np.unique(
classes, return_counts=True
) # uniqueClassName to be discriminated should be same as lr.classes_
goodClassNameInd = np.array([n >= MINCOUNT for n in uniqueCNameCount])
goodSampleInd = np.array(
[b in uniqueClassName[goodClassNameInd] for b in classes])
goodClassNameInd[np.where(uniqueClassName == 'Unknown00F')[0]] = False
#take good indices and enode the classes labels as numbers
goodClasses = classes[goodSampleInd]
goodFeatures = allFeatures[goodSampleInd]
le = preprocessing.LabelEncoder()
le.fit(goodClasses)
goodClassLabels = le.transform(goodClasses)
nGoodClass = uniqueClassName[goodClassNameInd].size
nPair = int(nGoodClass * (nGoodClass - 1) / 2)
scores = np.zeros(nPair)
pValues = np.zeros(nPair)
ncounter = 0
nhighScores = 0
nSigP = 0
lr = LogisticRegression(C=1,
class_weight=None,
dual=False,
fit_intercept=True,
intercept_scaling=1,
max_iter=100,
multi_class='ovr',
n_jobs=1,
penalty='l2',
random_state=0,
solver='liblinear',
tol=0.0001,
verbose=0,
warm_start=False)
#lt = [108, 110, 164,163,134,244,100,97,123,13,101,23,208,37]
for i in range(0): #range(nGoodClass):
for j in range(1, 2): #range(nGoodClass):
if i < j:
#if (i ==0) & (j ==14):
featureij = np.vstack(
(goodFeatures[np.where(goodClassLabels == i)[0]],
goodFeatures[np.where(goodClassLabels == j)[0]]))
classij = np.hstack(
(goodClassLabels[np.where(goodClassLabels == i)[0]],
goodClassLabels[np.where(goodClassLabels == j)[0]]))
if cv == True:
cvCount = 0
lrYes = 0
skf = StratifiedKFold(n_splits=cvFolds)
skfList = skf.split(featureij, classij)
for train, test in skfList:
# Enforce the MINCOUNT in each class for Training
trainClasses, trainCount = np.unique(
classij[train], return_counts=True)
goodIndClasses = np.array(
[n >= MINCOUNTTRAINING for n in trainCount])
goodIndTrain = np.array([
b in trainClasses[goodIndClasses]
for b in classij[train]
])
# Specity the training data set, the number of groups and priors
yTrain = classij[train[goodIndTrain]]
XrTrain = featureij[train[goodIndTrain]]
trainClasses, trainCount = np.unique(
yTrain, return_counts=True)
ntrainClasses = trainClasses.size
# Skip this cross-validation fold because of insufficient data
if ntrainClasses < 2:
continue
goodTrainInd = np.array(
[b in trainClasses for b in classij[test]])
if (goodTrainInd.size == 0):
continue
lr.fit(XrTrain, yTrain)
print(lr.coef_)
inverse_image = np.copy(lr.coef_).reshape((15, 15))
#np.save('inverseimage_0_14_p20_s0.01.npy', inverse_image)
pim = PersImage(pixels=[15, 15], spread=1)
pim.show(inverse_image)
plt.show()
lrYes += np.around(
(lr.score(featureij[test[goodTrainInd]],
classij[test[goodTrainInd]])) *
goodTrainInd.size)
cvCount += goodTrainInd.size
lrYesInt = int(lrYes)
p = 1.0 / 2
lrP = 0
for k in range(lrYesInt, cvCount + 1):
lrP += binom.pmf(k, cvCount, p)
print("LR: %.2f %% (%d/%d p=%.4f)" %
(100.0 * lrYes / cvCount, lrYes, cvCount, lrP))
#if ncounter in lt:
# print(ncounter, i, j)
scores[ncounter] = 100.0 * lrYes / cvCount
pValues[ncounter] = lrP
if scores[ncounter] >= 90.0 and pValues[ncounter] <= 0.05:
nhighScores += 1
if pValues[ncounter] <= 0.05:
nSigP += 1
else:
X_train, X_test, y_train, y_test = train_test_split(
featureij, classij, test_size=0.10, random_state=42)
lr.fit(X_train, y_train)
scores[ncounter] = lr.score(X_test, y_test)
if printijScores:
print('classes:', i, j, 'scores', scores[ncounter])
if scores[ncounter] >= .95:
nhighScores += 1
ncounter += 1
print('mean scores: ', np.mean(scores),
'nhighScores/ntotal: %s/%s' % (nhighScores, ncounter),
'nSigP/ntotal: %s/%s' % (nSigP, nPair))
return scores, pValues, nhighScores, nPair
import numpy as np
from persim import PersImage
s = (80, 100)
Persims = np.zeros(s)
import glob
#by changing Dim0 to Dim1 you can read the other Dim data
txt_files = glob.glob("Dim1-resized/*.txt")
len(txt_files)
for i in range(0, len(txt_files), 1):
print(txt_files[i])
D = np.genfromtxt(txt_files[i], skip_header=1)
D = np.array(D)
D = D[:, [1, 2]]
pim = PersImage(pixels=(10, 10))
img = pim.transform(D)
Persims[i][:] = img.flatten()
Persims
#for 8classes
#c=np.array([1,2,3,4,5,6,7,8])
#ccol=np.repeat(c,10)
#for 4 classes
c = np.array([1, 2, 3, 4])
ccol = np.repeat(c, 20)
cname = np.array(
["Apple", "Bell", "Bird", "Bottle", "Brick", "Children", "Key", "Rat"])
pixels = pixelsL[p]
spread = spreadL[s]
#if 'MidPD_Len%s_Dim%s_Tau%s_PCA%s.npy' %(segmentLength, embDim, tau, PCA_n_components)
print('processing segmentLength', segmentLength, 'embDim ', embDim, ' tau ', tau, ' PCA_n_components ', PCA_n_components, ' pixels ', pixels, ' spread ', spread, '\n\n')
# #PI0 = generatePI(allPDs, segmentLength, embDim, tau, PCA_n_components, pixels, spread, savePI, norm)
#allPIs = np.load('PI_Len%s_Dim%s_Tau%s_PCA%s_p%s_s%s_%s.npy' %(segmentLength, embDim, tau, PCA_n_components, pixels, spread, norm))
x = allSegments[:4]
allTimeDelayedSeg = timeDelayPCA(x, segmentLength, embDim, tau, PCA_n_components)
from persim import PersImage, plot_diagrams
from ripser import Rips
rips = Rips(maxdim=1, coeff=2)
diagrams_h1 = [rips.fit_transform(data)[1] for data in allTimeDelayedSeg]
pim = PersImage(pixels=[15,15], spread=1)
imgs = pim.transform(diagrams_h1)
fig = plt.figure(figsize=(5,5))
ax = fig.subplots()
ax.imshow(imgs[0], cmap=plt.get_cmap("viridis"))
ax.axis("off")
#pim.show(imgs[0], ax=ax)
#plot_diagrams(diagrams_h1[3], ax=ax, legend=False)
#ax.xaxis.set_major_locator(MultipleLocator(5000))
#ax.yaxis.set_major_locator(MultipleLocator(5000))
##MI = MI_lcmin(x, order=1, PLOT=True)
##print(MI)
import numpy as np
from sklearn import datasets
from ripser import ripser
from persim import PersImage, plot_diagrams
import scipy.misc
#generate circles
print("Generating circles")
data = None
pim = PersImage(spread=1, pixels=[10, 10], verbose=False)
for i in range(500):
if i % 10 != 0:
print(str(i), end=" ")
else:
print(str(i))
data = np.concatenate([
150 * np.random.random((150, 2)),
np.random.randint(10, 100) +
20 * datasets.make_circles(n_samples=150, factor=0.99)[0]
])
dgms = ripser(data)["dgms"]
img = pim.transform(dgms[1])
pImg = np.zeros((10, 10), dtype=np.uint8)
for idxR, r in enumerate(img):
def plot_coeff(fig, coeff, location, title):
pim = PersImage(pixels=[10, 10], spread=1)
ax = fig.add_subplot(location)
inverse_image = np.copy(coeff).reshape((10, 10))
ax.set_title(title)
pim.show(inverse_image, ax)
def do_full_run(data, quality=50, spread=0.05, kernel="gaussian", weighting="linear"):
"""
Does the full PI analysis and some training
saves the results in the results folder
:param quality: resulution (int)
:param spread: variance in smoothing (float)
:param kernel: cdf to be used for smoothing (string: gaussian, laplace, lognorm, gamma)
:param weighting: weighting to be used (string: linear, pm_linear, logistic)
:return: reports for H0 and H1
"""
pixels = quality * quality
PI_vectors_H0 = np.zeros((5 * m, pixels))
PI_vectors_H1 = np.zeros((5 * m, pixels))
PI_vectors_con = np.zeros((5 * m, 2 * pixels))
target = np.zeros(5 * m)
labels = [2, 3.5, 4.0, 4.1, 4.3]
index = 0
print("Creating the PI images for the different r's")
for i in range(5):
shape_data = data[i]
r = labels[i]
print("training for r:{}".format(r))
for j in tqdm(range(m)):
pim_0 = PersImage(spread=spread,
pixels=[quality, quality],
kernel_type=kernel,
weighting_type=weighting,
verbose=False,
specs={
"maxBD": 2,
"minBD": 0,
})
pim_1 = PersImage(spread=spread,
pixels=[quality, quality],
kernel_type=kernel,
weighting_type=weighting,
verbose=False,
specs={
"maxBD": 2,
"minBD": 0,
})
PI_data = shape_data[j, :, :]
rips = Rips(verbose=False)
dgms = rips.fit_transform(PI_data)
PI_data_H0 = pim_0.transform(dgms[0])
PI_data_H1 = pim_1.transform(dgms[1])
PI_data_H1 = PI_data_H1.reshape(pixels)
PI_data_H0 = PI_data_H0.reshape(pixels)
# PI_data_H0 = PI_data_H0[:, None]
# PI_data_H1 = PI_data_H1[:, None]
#
target[index] = int(i)
PI_vectors_H0[index, :] = PI_data_H0
PI_vectors_H1[index, :] = PI_data_H1
PI_vectors_con[index, :] = np.concatenate((PI_data_H0, PI_data_H1))
index += 1
PI_vectors_H0_train, PI_vectors_H0_test, y_train_H0, y_test_H0 = train_test_split(PI_vectors_H0,
target,
test_size=0.33)
PI_vectors_H1_train, PI_vectors_H1_test, y_train_H1, y_test_H1 = train_test_split(PI_vectors_H1,
target,
test_size=0.33)
PI_vectors_con_train, PI_vectors_con_test, y_train_con, y_test_con = train_test_split(PI_vectors_con,
target,
test_size=0.33)
y_H0_hat_ada, y_H0_hat_grad = do_training(PI_vectors_H0_train, PI_vectors_H0_test, y_train_H0)
y_H1_hat_ada, y_H1_hat_grad = do_training(PI_vectors_H1_train, PI_vectors_H1_test, y_train_H1)
y_con_hat_ada, y_con_1_hat_grad = do_training(PI_vectors_con_train, PI_vectors_con_test, y_train_con)
reports_H0_ada, reports_H0_grad = do_analysis(y_test_H0, y_H0_hat_ada, y_H0_hat_grad, labels)
reports_H1_ada, reports_H1_grad = do_analysis(y_test_H1, y_H1_hat_ada, y_H1_hat_grad, labels)
reports_con_ada, reports_con_grad = do_analysis(y_test_con, y_con_hat_ada, y_con_1_hat_grad, labels)
reports_H0_ada.to_csv("results_dynamic/{}_{}_{}_{}_H0_ada.csv".format(quality, spread, kernel, weighting))
reports_H0_grad.to_csv("results_dynamic/{}_{}_{}_{}_H0_grad.csv".format(quality, spread, kernel, weighting))
reports_H1_ada.to_csv("results_dynamic/{}_{}_{}_{}_H1_ada.csv".format(quality, spread, kernel, weighting))
reports_H1_grad.to_csv("results_dynamic/{}_{}_{}_{}_H1_grad.csv".format(quality, spread, kernel, weighting))
reports_con_ada.to_csv("results_dynamic/{}_{}_{}_{}_con_ada.csv".format(quality, spread, kernel, weighting))
reports_con_grad.to_csv("results_dynamic/{}_{}_{}_{}_con_grad.csv".format(quality, spread, kernel, weighting))
return reports_H0_ada, reports_H0_grad, reports_H1_ada, reports_H1_grad, reports_con_ada, reports_con_grad
return [h0, h1]
PI_null_images = []
PI_one_images = []
for i in range(images.shape[0]):
print(i)
f_lower_star = d.fill_freudenthal(images[i, :, :, 0].astype(float))
f_upper_star = d.fill_freudenthal(images[i, :, :, 0].astype(float),
reverse=True)
p = d.homology_persistence(f_lower_star)
dgms_temp = d.init_diagrams(p, f_lower_star)
h0_temp = homology_persistent_diagrams(dgms_temp)[0]
h1_temp = homology_persistent_diagrams(dgms_temp)[1]
pim = PersImage(pixels=[20, 20], spread=1)
PI_0_temp = pim.transform(h0_temp[1:, :])
PI_1_temp = pim.transform(h1_temp)
PI_null_images.append(PI_0_temp)
PI_one_images.append(PI_1_temp)
PI_null_images = np.array(PI_null_images, dtype=np.float32)
PI_null_images = PI_null_images.reshape((-1, 20, 20, 1)) # reshape
PI_null_images = PI_null_images / (PI_null_images.max() / 255.0) # normalize
PI_one_images = np.array(PI_one_images, dtype=np.float32)
PI_one_images = PI_one_images.reshape((-1, 20, 20, 1)) # reshape
PI_one_images = PI_one_images / (PI_one_images.max() / 255.0) # normalize
np.save('PI_null_images', PI_null_images)
np.save('PI_one_images', PI_one_images)
def test_lists_of_lists(self):
pim = PersImage(pixels=(3, 3))
diagram = [[0, 1], [1, 1], [3, 5]]
img = pim.transform(diagram)
assert img.shape == (3, 3)
def test_landscape():
bds = np.array([[1, 1], [1, 2]])
ldsp = PersImage.to_landscape(bds)
np.testing.assert_array_equal(ldsp, [[1, 0], [1, 1]])
weightings = ["linear", "logistic"]
spread = 0.05
quality = 150
pixels = [quality, quality]
fig = plt.figure()
fig.set_figwidth(9)
fig.set_figheight(6)
index = 1
for i, kern in enumerate(kernels):
for j, weighting in enumerate(weightings):
pim = PersImage(spread=spread,
pixels=pixels,
verbose=False,
kernel_type=kern,
weighting_type=weighting)
rips = Rips(verbose=False)
dgms = rips.fit_transform(PI_data)
img = pim.transform(dgms[1])
mini, maxi = np.amin(img), min(np.amax(img), 0.05)
print(mini, maxi)
X = np.arange(0, 150)
Y = np.arange(0, 150)
X, Y = np.meshgrid(X, Y)
Z = img[::-1]
ax = fig.add_subplot(2, 2, index, projection='3d')
#ax = fig.gca(projection='3d')
def test_empty_diagram(self):
dgm = np.zeros((0, 2))
pim = PersImage(pixels=(10, 10))
res = pim.transform(dgm)
assert np.all(res == np.zeros((10, 10)))