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Simplify get_latents function #203

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merged 1 commit into from
Sep 25, 2023
Merged

Simplify get_latents function #203

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31 changes: 12 additions & 19 deletions vamb/aamb_encode.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@

from collections.abc import Sequence
from typing import Optional, IO, Union
from numpy.typing import NDArray


############################################################################# MODEL ###########################################################
Expand Down Expand Up @@ -425,8 +426,8 @@ def trainmodel(

########### funciton that retrieves the clusters from Y latents
def get_latents(
self, contignames: Sequence[str], data_loader, last_epoch: bool = True
):
self, contignames: Sequence[str], data_loader
) -> tuple[dict[str, set[str]], NDArray[np.float32]]:
"""Retrieve the categorical latent representation (y) and the contiouous latents (l) of the inputs

Inputs:
Expand All @@ -447,7 +448,7 @@ def get_latents(
latent = np.empty((length, self.ld), dtype=np.float32)
index_contigname = 0
row = 0
clust_y_dict = dict()
clust_y_dict: dict[str, set[str]] = dict()
Tensor = torch.cuda.FloatTensor if self.usecuda else torch.FloatTensor
with torch.no_grad():
for depths_in, tnfs_in, _ in new_data_loader:
Expand All @@ -473,23 +474,18 @@ def get_latents(
depths_in = depths_in.cuda()
tnfs_in = tnfs_in.cuda()

if last_epoch:
mu, _, _, _, y_sample = self(depths_in, tnfs_in)[0:5]
else:
y_sample = self(depths_in, tnfs_in)[4]
mu, _, _, _, y_sample = self(depths_in, tnfs_in)[0:5]

if self.usecuda:
Ys = y_sample.cpu().detach().numpy()
if last_epoch:
mu = mu.cpu().detach().numpy()
latent[row : row + len(mu)] = mu
row += len(mu)
mu = mu.cpu().detach().numpy()
latent[row : row + len(mu)] = mu
row += len(mu)
else:
Ys = y_sample.detach().numpy()
if last_epoch:
mu = mu.detach().numpy()
latent[row : row + len(mu)] = mu
row += len(mu)
mu = mu.detach().numpy()
latent[row : row + len(mu)] = mu
row += len(mu)
del y_sample

for _y in Ys:
Expand All @@ -505,7 +501,4 @@ def get_latents(
index_contigname += 1
del Ys

if last_epoch:
return clust_y_dict, latent
else:
return clust_y_dict
return clust_y_dict, latent