From 46bacfef6adf47b5007549271c65bba55c2d4f20 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Tue, 21 Apr 2020 11:22:01 +0200
Subject: [PATCH] [engine] Deploy h5py instead of bob.io.base for HDF5 I/O
---
bob/ip/binseg/engine/evaluator.py | 5 +++--
bob/ip/binseg/engine/predictor.py | 8 +++++---
2 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/bob/ip/binseg/engine/evaluator.py b/bob/ip/binseg/engine/evaluator.py
index 5b4f2a39..c3124ef9 100644
--- a/bob/ip/binseg/engine/evaluator.py
+++ b/bob/ip/binseg/engine/evaluator.py
@@ -13,7 +13,7 @@ from tqdm import tqdm
import torch
import torchvision.transforms.functional as VF
-import bob.io.base
+import h5py
from ..utils.metric import base_metrics
from ..utils.plot import precision_recall_f1iso_confintval
@@ -231,7 +231,8 @@ def run(data_loader, predictions_folder, output_folder, overlayed_folder=None,
image = sample[1].to("cpu")
gt = sample[2].to("cpu")
pred_fullpath = os.path.join(predictions_folder, stem + ".hdf5")
- pred = bob.io.base.load(pred_fullpath).astype("float32")
+ with h5py.File(pred_fullpath, "r") as f:
+ pred = f["array"][:]
pred = torch.from_numpy(pred)
if stem in data:
raise RuntimeError(f"{stem} entry already exists in data. "
diff --git a/bob/ip/binseg/engine/predictor.py b/bob/ip/binseg/engine/predictor.py
index ca22cb3e..33a91d0b 100644
--- a/bob/ip/binseg/engine/predictor.py
+++ b/bob/ip/binseg/engine/predictor.py
@@ -12,7 +12,7 @@ from tqdm import tqdm
import torch
import torchvision.transforms.functional as VF
-import bob.io.base
+import h5py
from ..utils.summary import summary
@@ -44,8 +44,10 @@ def _save_hdf5(stem, prob, output_folder):
if not os.path.exists(fulldir):
tqdm.write(f"Creating directory {fulldir}...")
os.makedirs(fulldir, exist_ok=True)
- bob.io.base.save(prob.cpu().squeeze(0).numpy(), fullpath)
-
+ with h5py.File(fullpath, 'w') as f:
+ data = prob.cpu().squeeze(0).numpy()
+ f.create_dataset("array", data=data, compression="gzip",
+ compression_opts=9)
def _save_image(stem, extension, data, output_folder):
"""Saves a PIL image into a file
--
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