def compute_dynamic_filtration_no_inf(self,
x,
hiddens,
percentile=0,
return_nm=False):
id = 0
f = dion.Filtration()
f.append(dion.Simplex([-1], 0))
enums = []
nm = {(-1, 0, 0): -1}
params = self.params
percentiles = np.zeros((len(params)))
def collect_result(res):
nonlocal id
nonlocal f
nonlocal nm
for enum in res:
nodes = enum[0]
weight = enum[1]
if len(nodes) == 1:
if nodes[0] not in nm:
nm[nodes[0]] = id
id += 1
f.append(dion.Simplex([nm[nodes[0]]], weight))
else:
f.append(dion.Simplex([nm[nodes[0]]], weight))
f.append(dion.Simplex([nm[nodes[0]], -1], 0))
if len(nodes) == 2:
if nodes[0] not in nm:
nm[nodes[0]] = id
id += 1
if nodes[1] not in nm:
nm[nodes[1]] = id
id += 1
f.append(dion.Simplex([nm[nodes[0]], nm[nodes[1]]],
weight))
x = x.cpu().detach().numpy()
num_channels = x.shape[0]
l = 0
percentiles[l] = np.percentile(
np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
stride = 1
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
mat = conv_layer_as_matrix(p, x[c], stride)
m1, h0_births, h1_births = conv_filtration_fast2(
x[c], mat, l, c, nlc, percentile=percentiles[l])
# enums = m1
# enums += [([spec_hash((l,c,i[0]))], h0_births[i].item()) for i in np.argwhere(h0_births > percentile)]
enums = []
enums += [([spec_hash(
(l + 1, i[0] // nlc, i[0] % nlc))], h1_births[i].item())
for i in np.argwhere(h1_births > percentile)]
collect_result(enums)
h1 = hiddens[l].cpu().detach().numpy()
l = 1
percentiles[l] = np.percentile(
np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
p = params[l]
m1, h0_births, h1_births = linear_filtration_fast2(
h1, p, l, 0, percentile=percentiles[l])
enums += m1
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, c, i[0]))], h0_births[i])
for i in np.argwhere(h0_births > comp_percentile)]
h1 = hiddens[l].cpu().detach().numpy()
l = 2
percentiles[l] = np.percentile(
np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
p = params[l]
m1, h0_births, h1_births_2 = linear_filtration_fast2(
h1, p, l, 0, percentile=percentiles[l])
enums += m1
max1 = np.maximum.reduce([h0_births, h1_births])
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], max1[i])
for i in np.argwhere(max1 > comp_percentile)]
enums += [([spec_hash((l + 1, 0, i[0]))], h1_births_2[i])
for i in np.argwhere(h1_births_2 > percentiles[l])]
collect_result(enums)
# h1_id_start = x.cpu().detach().numpy().reshape(-1).shape[0]
# print('h1_id_start', h1_id_start)
# f, h1_births = conv_filtration(f, x[0], self.conv1.weight.data[:,0,:,:], 0, h1_id_start, percentile=percentile)
#
# h2_id_start = h1_id_start + hiddens[0].cpu().detach().numpy().shape[0]
# print('h2_id_start', h2_id_start)
# f, h2_births = linear_filtration(f, hiddens[0], self.fc1, h1_births, h1_id_start, h2_id_start, percentile=percentile, last=False)
#
# h3_id_start = h2_id_start + hiddens[1].cpu().detach().numpy().shape[0]
# print('h3_id_start', h3_id_start)
# f = linear_filtration(f, hiddens[1], self.fc2, h2_births, h2_id_start, h3_id_start, percentile=percentile, last=True)
print('filtration size', len(f))
f.sort(reverse=True)
if return_nm:
return f, nm
else:
return f
def compute_dynamic_filtration2(self,
x,
hiddens,
percentile=0,
return_nm=False,
absolute_value=True,
input_layer=False):
id = 0
f = dion.Filtration()
nm = {}
wm = {}
params = self.params
percentiles = np.zeros((len(params)))
for l in range(len(params)):
percentiles[l] = (1 / (l + 1)) * np.percentile(
np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
def collect_result(res):
nonlocal id
nonlocal f
nonlocal nm
nonlocal wm
for enum in res:
nodes = enum[0]
weight = enum[1][0]
if len(nodes) == 1:
if nodes[0] not in nm:
nm[nodes[0]] = id
id += 1
f.append(dion.Simplex([nm[nodes[0]]], weight))
else:
f.append(dion.Simplex([nm[nodes[0]]], weight))
if len(nodes) == 2:
act_weight = enum[1][1]
if nodes[0] not in nm:
nm[nodes[0]] = id
id += 1
if nodes[1] not in nm:
nm[nodes[1]] = id
id += 1
wm[(nodes[0], nodes[1])] = act_weight
f.append(dion.Simplex([nm[nodes[0]], nm[nodes[1]]],
weight))
x = x.cpu().detach().numpy()
num_channels = x.shape[0]
l = 0
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.shape[0]
nls = hn.shape[1] * hn.shape[2]
stride = 1
enums = []
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
mat = conv_layer_as_matrix(p, x[c], stride)
m1, h0_births, h1_births = conv_filtration_fast2(
x[c],
mat,
l,
c,
nlc,
nls,
percentile=percentiles[l],
absolute_value=absolute_value)
if input_layer:
enums += m1
enums += [([spec_hash((l, c, i[0]))], [h0_births[i].item()])
for i in np.argwhere(h0_births > percentiles[l])]
enums += [([spec_hash(
(l + 1, i[0] // nlc, i[0] % nls))], [h1_births[i].item()])
for i in np.argwhere(h1_births > percentiles[l])]
collect_result(enums)
h1 = hiddens[l].cpu().detach().numpy()
num_channels = h1.shape[0]
l = 1
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[0]
stride = 1
enums = []
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
mat = conv_layer_as_matrix(p, h1[c], stride)
m1, h0_births, h1_births = conv_filtration_fast2(
h1[c],
mat,
l,
c,
nlc,
nls,
percentile=percentiles[l],
absolute_value=absolute_value)
enums += m1
comp_percentile = percentiles[
l -
1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, c, i[0]))], [h0_births[i].item()])
for i in np.argwhere(h0_births > comp_percentile)]
enums += [([spec_hash((l + 1, 0, i[0]))], [h1_births[i].item()])
for i in np.argwhere(h1_births > percentiles[l])]
collect_result(enums)
h1 = hiddens[l].cpu().detach().numpy()
l = 2
p = params[l]
percentiles[l] = np.percentile(
np.absolute(h1 * p.weight.data.cpu().detach().numpy()), percentile)
m1, h0_births, h1_births = linear_filtration_fast2(
h1,
p,
l,
0,
percentile=percentiles[l],
absolute_value=absolute_value)
enums = m1
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], [h0_births[i]])
for i in np.argwhere(h0_births > comp_percentile)]
h1 = hiddens[l].cpu().detach().numpy()
l = 3
p = params[l]
percentiles[l] = np.percentile(
np.absolute(h1 * p.weight.data.cpu().detach().numpy()), percentile)
m1, h0_births, h1_births_2 = linear_filtration_fast2(
h1,
p,
l,
0,
percentile=percentiles[l],
absolute_value=absolute_value)
enums += m1
max1 = np.maximum.reduce([h0_births, h1_births])
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], [max1[i]])
for i in np.argwhere(max1 > comp_percentile)]
enums += [([spec_hash((l + 1, 0, i[0]))], [h1_births_2[i]])
for i in np.argwhere(h1_births_2 > percentiles[l])]
collect_result(enums)
print('filtration size', len(f))
f.sort(reverse=True)
if return_nm:
return f, nm, wm
else:
return f
def compute_induced_filtration_parallel(x,
hiddens,
params,
percentile=0,
stride=1,
return_nm=True,
absolute_value=True):
pool = mp.Pool(mp.cpu_count())
print('cpu count: {}'.format(mp.cpu_count()))
global nm
global id
global f
global wm
id = 0
nm = {}
wm = {}
f = dion.Filtration()
percentiles = np.zeros((len(params)))
for l in range(len(params)):
percentiles[l] = (1 / (l + 1)) * np.percentile(
np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
x = x.cpu().detach().numpy()
num_channels = x.shape[0]
l = 0
print('layer: {}'.format(l))
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[1] * hn.shape[2]
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
r = pool.apply_async(first_layer,
args=(x[c], p, l, c, percentiles[l], stride, nlc,
nls),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 1
percentiles[l] = np.percentile(np.absolute(h), percentile)
hn = hiddens[l].cpu().detach().numpy()
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
h1 = h[c, :, :]
hn2 = hn[c, :, :]
p = params[l]
r = pool.apply_async(max_pool_layer,
args=(h1, p, l, c, percentiles, hn2),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 2
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[1] * hn.shape[2]
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
h1 = h[c, :, :]
r = pool.apply_async(mid_conv,
args=(h1, p, l, c, percentiles, stride, nlc, nls),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 3
hn = hiddens[l].cpu().detach().numpy()
percentiles[l] = np.percentile(np.absolute(h), percentile)
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
h1 = h[c, :, :]
hn2 = hn[c, :, :]
p = params[l]
r = pool.apply_async(max_pool_layer,
args=(h1, p, l, c, percentiles, hn2),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 4
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[1] * hn.shape[2]
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
h1 = h[c, :, :]
r = pool.apply_async(mid_conv,
args=(h1, p, l, c, percentiles, stride, nlc, nls),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 5
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[1] * hn.shape[2]
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
h1 = h[c, :, :]
r = pool.apply_async(mid_conv,
args=(h1, p, l, c, percentiles, stride, nlc, nls),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 6
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
hn = hiddens[l].cpu().detach().numpy()
nlc = hn.reshape((hn.shape[0], -1)).shape[1]
nls = hn.shape[1] * hn.shape[2]
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
p = params[l].weight.data[:, c, :, :]
h1 = h[c, :, :]
r = pool.apply_async(mid_conv,
args=(h1, p, l, c, percentiles, stride, nlc, nls),
callback=collect_result)
pool.close()
pool.join()
h = hiddens[l].cpu().detach().numpy()
num_channels = h.shape[0]
l = 7
percentiles[l] = np.percentile(np.absolute(h), percentile)
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
print('layer: {}'.format(l))
pool = mp.Pool(mp.cpu_count())
for c in range(num_channels):
h1 = h[c, :, :]
p = params[l]
r = pool.apply_async(last_pool,
args=(h1, p, l, c, percentiles),
callback=collect_result)
pool.close()
pool.join()
h1 = hiddens[l].cpu().detach().numpy()
enums = [([spec_hash((l + 1, 0, i[0]))], [h1[i]])
for i in np.argwhere(h1 > percentiles[l])]
l = 8
print('layer: {}'.format(l))
p = params[l]
percentiles[l] = np.percentile(
np.absolute(h1 * p.weight.data.cpu().detach().numpy()), percentile)
m1, h0_births, h1_births = linear_filtration_fast2(
h1, p, l, 0, percentile=percentiles[l])
enums += m1
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], [h0_births[i]])
for i in np.argwhere(h0_births > comp_percentile)]
h1 = hiddens[l].cpu().detach().numpy()
l = 9
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
print('layer: {}'.format(l))
p = params[l]
percentiles[l] = np.percentile(
np.absolute(h1 * p.weight.data.cpu().detach().numpy()), percentile)
m1, h0_births, h1_births_9 = linear_filtration_fast2(
h1, p, l, 0, percentile=percentiles[l])
enums += m1
max1 = np.maximum.reduce([h0_births, h1_births])
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], [max1[i]])
for i in np.argwhere(max1 > comp_percentile)]
h1 = hiddens[l].cpu().detach().numpy()
l = 10
print('layer: {}'.format(l))
# percentiles[l] = np.percentile(np.absolute(hiddens[l].cpu().detach().numpy()), percentile)
p = params[l]
percentiles[l] = np.percentile(
np.absolute(h1 * p.weight.data.cpu().detach().numpy()), percentile)
m1, h0_births, h1_births_10 = linear_filtration_fast2(
h1, p, l, 0, percentile=percentiles[l])
enums += m1
max1 = np.maximum.reduce([h0_births, h1_births_9])
comp_percentile = percentiles[
l - 1] if percentiles[l - 1] < percentiles[l] else percentiles[l]
enums += [([spec_hash((l, 0, i[0]))], [max1[i]])
for i in np.argwhere(max1 > comp_percentile)]
enums += [([spec_hash((l + 1, 0, i[0]))], [h1_births_10[i]])
for i in np.argwhere(h1_births_10 > percentiles[l])]
collect_result(enums)
print('percentiles:', percentiles)
# with open('quick_dump.txt', 'w') as fp:
# for k, v in nm.items():
# fp.write('{}, {}\n'.format(k,v))
print('creating filtration object...')
print('filtration size', len(f))
print('Sorting filtration...')
f.sort(reverse=True)
if return_nm:
return f, nm, wm
else:
return f