From 643c74fed7da0b9feb325cdcc0fe4b72a75a1a9f Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Sat, 11 Apr 2020 10:40:10 +0200
Subject: [PATCH] Major module renaming (for consistency); DRY when possible
---
bob/ip/binseg/configs/datasets/chasedb1.py | 13 +-
.../binseg/configs/datasets/chasedb11024.py | 13 +-
.../binseg/configs/datasets/chasedb11168.py | 13 +-
bob/ip/binseg/configs/datasets/chasedb1544.py | 13 +-
bob/ip/binseg/configs/datasets/chasedb1608.py | 13 +-
.../{chasedb1test.py => chasedb1_test.py} | 15 +--
...estareiostarhrf960.py => covd_chasedb1.py} | 0
...hrf960sslchase.py => covd_chasedb1_ssl.py} | 2 +-
...echasedb1iostarhrf544.py => covd_drive.py} | 0
...tarhrf544ssldrive.py => covd_drive_ssl.py} | 2 +-
...starechasedb1iostar1168.py => covd_hrf.py} | 0
...db1iostar1168sslhrf.py => covd_hrf_ssl.py} | 4 +-
...asedb1hrf1024.py => covd_iostar_vessel.py} | 0
...ssliostar.py => covd_iostar_vessel_ssl.py} | 4 +-
...echasedb1iostarhrf608.py => covd_stare.py} | 0
...tarhrf608sslstare.py => covd_stare_ssl.py} | 2 +-
bob/ip/binseg/configs/datasets/csv.py | 15 +--
bob/ip/binseg/configs/datasets/drionsdb.py | 9 +-
.../{drionsdbtest.py => drionsdb_test.py} | 4 +-
.../{dristhigs1cup.py => dristhigs1_cup.py} | 9 +-
...higs1cuptest.py => dristhigs1_cup_test.py} | 6 +-
.../{dristhigs1od.py => dristhigs1_od.py} | 9 +-
...sthigs1odtest.py => dristhigs1_od_test.py} | 6 +-
bob/ip/binseg/configs/datasets/drive.py | 13 +-
bob/ip/binseg/configs/datasets/drive1024.py | 13 +-
bob/ip/binseg/configs/datasets/drive1168.py | 13 +-
bob/ip/binseg/configs/datasets/drive608.py | 13 +-
bob/ip/binseg/configs/datasets/drive960.py | 13 +-
.../datasets/{drivetest.py => drive_test.py} | 10 +-
bob/ip/binseg/configs/datasets/folder.py | 13 +-
bob/ip/binseg/configs/datasets/hrf.py | 13 +-
bob/ip/binseg/configs/datasets/hrf1024.py | 15 +--
bob/ip/binseg/configs/datasets/hrf544.py | 13 +-
bob/ip/binseg/configs/datasets/hrf544test.py | 29 -----
bob/ip/binseg/configs/datasets/hrf608.py | 13 +-
bob/ip/binseg/configs/datasets/hrf960.py | 15 +--
.../datasets/{hrf1168.py => hrf_1168.py} | 15 +--
.../{hrf1168test.py => hrf_1168_test.py} | 10 +-
.../datasets/{hrftest.py => hrf_test.py} | 10 +-
.../datasets/{iostarod.py => iostar_od.py} | 13 +-
.../{iostarodtest.py => iostar_od_test.py} | 8 +-
.../{iostarvessel.py => iostar_vessel.py} | 13 +-
...tarvesseltest.py => iostar_vessel_test.py} | 8 +-
.../configs/datasets/iostarvessel1168.py | 13 +-
.../configs/datasets/iostarvessel544.py | 13 +-
.../configs/datasets/iostarvessel608.py | 13 +-
.../configs/datasets/iostarvessel960.py | 13 +-
.../datasets/{refugecup.py => refuge_cup.py} | 11 +-
.../{refugecuptest.py => refuge_cup_test.py} | 15 +--
.../datasets/{refugeod.py => refuge_od.py} | 18 +--
.../{refugeodtest.py => refuge_od_test.py} | 15 +--
.../{rimoner3cup.py => rimoner3_cup.py} | 18 +--
...imoner3cuptest.py => rimoner3_cup_test.py} | 14 +-
.../{rimoner3od.py => rimoner3_od.py} | 18 +--
...{rimoner3odtest.py => rimoner3_od_test.py} | 15 +--
bob/ip/binseg/configs/datasets/stare.py | 13 +-
bob/ip/binseg/configs/datasets/stare1024.py | 11 +-
bob/ip/binseg/configs/datasets/stare1168.py | 13 +-
bob/ip/binseg/configs/datasets/stare544.py | 13 +-
bob/ip/binseg/configs/datasets/stare960.py | 11 +-
.../datasets/{staretest.py => stare_test.py} | 10 +-
.../configs/models/{driubn.py => driu_bn.py} | 0
.../models/{driubnssl.py => driu_bn_ssl.py} | 0
.../configs/models/{driuod.py => driu_od.py} | 0
.../models/{driussl.py => driu_ssl.py} | 0
.../models/{m2unetssl.py => m2unet_ssl.py} | 0
bob/ip/binseg/data/binsegdataset.py | 19 ++-
bob/ip/binseg/data/chasedb1/test.py | 27 +---
bob/ip/binseg/data/csvdataset.py | 13 +-
bob/ip/binseg/data/drive/test.py | 30 +----
bob/ip/binseg/data/folderdataset.py | 13 +-
bob/ip/binseg/data/hrf/test.py | 30 +----
bob/ip/binseg/data/iostar/test.py | 39 +-----
bob/ip/binseg/data/stare/test.py | 27 +---
bob/ip/binseg/data/utils.py | 41 ++----
bob/ip/binseg/test/test_config.py | 120 ++++++++++++++++++
bob/ip/binseg/test/utils.py | 27 ++++
doc/api.rst | 112 ++++++++--------
doc/benchmarkresults.rst | 4 +-
doc/covdresults.rst | 26 ++--
doc/models.rst | 24 ++--
doc/training.rst | 32 ++---
setup.py | 82 ++++++------
83 files changed, 566 insertions(+), 762 deletions(-)
rename bob/ip/binseg/configs/datasets/{chasedb1test.py => chasedb1_test.py} (79%)
rename bob/ip/binseg/configs/datasets/{drivestareiostarhrf960.py => covd_chasedb1.py} (100%)
rename bob/ip/binseg/configs/datasets/{drivestareiostarhrf960sslchase.py => covd_chasedb1_ssl.py} (84%)
rename bob/ip/binseg/configs/datasets/{starechasedb1iostarhrf544.py => covd_drive.py} (100%)
rename bob/ip/binseg/configs/datasets/{starechasedb1iostarhrf544ssldrive.py => covd_drive_ssl.py} (83%)
rename bob/ip/binseg/configs/datasets/{drivestarechasedb1iostar1168.py => covd_hrf.py} (100%)
rename bob/ip/binseg/configs/datasets/{drivestarechasedb1iostar1168sslhrf.py => covd_hrf_ssl.py} (69%)
rename bob/ip/binseg/configs/datasets/{drivestarechasedb1hrf1024.py => covd_iostar_vessel.py} (100%)
rename bob/ip/binseg/configs/datasets/{drivestarechasedb1hrf1024ssliostar.py => covd_iostar_vessel_ssl.py} (68%)
rename bob/ip/binseg/configs/datasets/{drivechasedb1iostarhrf608.py => covd_stare.py} (100%)
rename bob/ip/binseg/configs/datasets/{drivechasedb1iostarhrf608sslstare.py => covd_stare_ssl.py} (83%)
rename bob/ip/binseg/configs/datasets/{drionsdbtest.py => drionsdb_test.py} (89%)
rename bob/ip/binseg/configs/datasets/{dristhigs1cup.py => dristhigs1_cup.py} (90%)
rename bob/ip/binseg/configs/datasets/{dristhigs1cuptest.py => dristhigs1_cup_test.py} (85%)
rename bob/ip/binseg/configs/datasets/{dristhigs1od.py => dristhigs1_od.py} (90%)
rename bob/ip/binseg/configs/datasets/{dristhigs1odtest.py => dristhigs1_od_test.py} (85%)
rename bob/ip/binseg/configs/datasets/{drivetest.py => drive_test.py} (63%)
delete mode 100644 bob/ip/binseg/configs/datasets/hrf544test.py
rename bob/ip/binseg/configs/datasets/{hrf1168.py => hrf_1168.py} (74%)
rename bob/ip/binseg/configs/datasets/{hrf1168test.py => hrf_1168_test.py} (67%)
rename bob/ip/binseg/configs/datasets/{hrftest.py => hrf_test.py} (68%)
rename bob/ip/binseg/configs/datasets/{iostarod.py => iostar_od.py} (77%)
rename bob/ip/binseg/configs/datasets/{iostarodtest.py => iostar_od_test.py} (71%)
rename bob/ip/binseg/configs/datasets/{iostarvessel.py => iostar_vessel.py} (77%)
rename bob/ip/binseg/configs/datasets/{iostarvesseltest.py => iostar_vessel_test.py} (71%)
rename bob/ip/binseg/configs/datasets/{refugecup.py => refuge_cup.py} (88%)
rename bob/ip/binseg/configs/datasets/{refugecuptest.py => refuge_cup_test.py} (83%)
rename bob/ip/binseg/configs/datasets/{refugeod.py => refuge_od.py} (85%)
rename bob/ip/binseg/configs/datasets/{refugeodtest.py => refuge_od_test.py} (83%)
rename bob/ip/binseg/configs/datasets/{rimoner3cup.py => rimoner3_cup.py} (83%)
rename bob/ip/binseg/configs/datasets/{rimoner3cuptest.py => rimoner3_cup_test.py} (77%)
rename bob/ip/binseg/configs/datasets/{rimoner3od.py => rimoner3_od.py} (83%)
rename bob/ip/binseg/configs/datasets/{rimoner3odtest.py => rimoner3_od_test.py} (77%)
rename bob/ip/binseg/configs/datasets/{staretest.py => stare_test.py} (71%)
rename bob/ip/binseg/configs/models/{driubn.py => driu_bn.py} (100%)
rename bob/ip/binseg/configs/models/{driubnssl.py => driu_bn_ssl.py} (100%)
rename bob/ip/binseg/configs/models/{driuod.py => driu_od.py} (100%)
rename bob/ip/binseg/configs/models/{driussl.py => driu_ssl.py} (100%)
rename bob/ip/binseg/configs/models/{m2unetssl.py => m2unet_ssl.py} (100%)
create mode 100644 bob/ip/binseg/test/test_config.py
create mode 100644 bob/ip/binseg/test/utils.py
diff --git a/bob/ip/binseg/configs/datasets/chasedb1.py b/bob/ip/binseg/configs/datasets/chasedb1.py
index 2b09a757..cdf8915e 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1.py
@@ -24,18 +24,15 @@ bright strip running down the centre known as the central vessel reflex.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Crop(0, 18, 960, 960), #(upper, left, height, width)
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/chasedb11024.py b/bob/ip/binseg/configs/datasets/chasedb11024.py
index be005fd3..cc762df6 100644
--- a/bob/ip/binseg/configs/datasets/chasedb11024.py
+++ b/bob/ip/binseg/configs/datasets/chasedb11024.py
@@ -1,17 +1,14 @@
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Crop(0, 18, 960, 960),
Resize(1024),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/chasedb11168.py b/bob/ip/binseg/configs/datasets/chasedb11168.py
index 92ffccfa..e756d6ef 100644
--- a/bob/ip/binseg/configs/datasets/chasedb11168.py
+++ b/bob/ip/binseg/configs/datasets/chasedb11168.py
@@ -1,17 +1,14 @@
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Crop(140, 18, 680, 960),
Resize(1168),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/chasedb1544.py b/bob/ip/binseg/configs/datasets/chasedb1544.py
index 16639aef..d6c389e2 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1544.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1544.py
@@ -1,17 +1,14 @@
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Resize(544),
Crop(0, 12, 544, 544),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/chasedb1608.py b/bob/ip/binseg/configs/datasets/chasedb1608.py
index adfd9777..e01d939d 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1608.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1608.py
@@ -1,17 +1,14 @@
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
CenterCrop((829, 960)),
Resize(608),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/chasedb1test.py b/bob/ip/binseg/configs/datasets/chasedb1_test.py
similarity index 79%
rename from bob/ip/binseg/configs/datasets/chasedb1test.py
rename to bob/ip/binseg/configs/datasets/chasedb1_test.py
index 0504acb3..945096cf 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1test.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1_test.py
@@ -23,15 +23,10 @@ bright strip running down the centre known as the central vessel reflex.
* Split reference: [CHASEDB1-2012]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
- Crop(0, 18, 960, 960), #(upper, left, height, width)
- ToTensor(),
- ]
-)
+from bob.ip.binseg.data.transforms import Crop
+_transforms = [Crop(0, 18, 960, 960)] #(upper, left, height, width)
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.chasedb1 import dataset as chasedb1
-dataset = DelayedSample2TorchDataset(chasedb1.subsets("default")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(chasedb1.subsets("default")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py b/bob/ip/binseg/configs/datasets/covd_chasedb1.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py
rename to bob/ip/binseg/configs/datasets/covd_chasedb1.py
diff --git a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py b/bob/ip/binseg/configs/datasets/covd_chasedb1_ssl.py
similarity index 84%
rename from bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py
rename to bob/ip/binseg/configs/datasets/covd_chasedb1_ssl.py
index 2e96cecf..4d73e6a8 100644
--- a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py
+++ b/bob/ip/binseg/configs/datasets/covd_chasedb1_ssl.py
@@ -9,7 +9,7 @@ The dataset available in this file is composed of STARE, CHASE-DB1, IOSTAR
vessel and HRF (with annotated samples) and CHASE-DB1 without labels.
"""
-from bob.ip.binseg.configs.datasets.drivestareiostarhrf960 import dataset as _labelled
+from bob.ip.binseg.configs.datasets.covd_chasedb1 import dataset as _labelled
from bob.ip.binseg.configs.datasets.chasedb1 import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py b/bob/ip/binseg/configs/datasets/covd_drive.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py
rename to bob/ip/binseg/configs/datasets/covd_drive.py
diff --git a/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py b/bob/ip/binseg/configs/datasets/covd_drive_ssl.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py
rename to bob/ip/binseg/configs/datasets/covd_drive_ssl.py
index c4ce12ca..a26a81e7 100644
--- a/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py
+++ b/bob/ip/binseg/configs/datasets/covd_drive_ssl.py
@@ -9,7 +9,7 @@ The dataset available in this file is composed of STARE, CHASE-DB1, IOSTAR
vessel and HRF (with annotated samples) and DRIVE without labels.
"""
-from bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544 import dataset as _labelled
+from bob.ip.binseg.configs.datasets.covd_drive import dataset as _labelled
from bob.ip.binseg.configs.datasets.drive import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py b/bob/ip/binseg/configs/datasets/covd_hrf.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
rename to bob/ip/binseg/configs/datasets/covd_hrf.py
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py b/bob/ip/binseg/configs/datasets/covd_hrf_ssl.py
similarity index 69%
rename from bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
rename to bob/ip/binseg/configs/datasets/covd_hrf_ssl.py
index 24365196..71658d04 100644
--- a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
+++ b/bob/ip/binseg/configs/datasets/covd_hrf_ssl.py
@@ -9,7 +9,7 @@ The dataset available in this file is composed of STARE, CHASE-DB1, IOSTAR
vessel and CHASE-DB1 (with annotated samples) and HRF without labels.
"""
-from bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168 import dataset as _labelled
-from bob.ip.binseg.configs.datasets.hrf1168 import dataset as _unlabelled
+from bob.ip.binseg.configs.datasets.covd_hrf import dataset as _labelled
+from bob.ip.binseg.configs.datasets.hrf_1168 import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024.py b/bob/ip/binseg/configs/datasets/covd_iostar_vessel.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024.py
rename to bob/ip/binseg/configs/datasets/covd_iostar_vessel.py
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024ssliostar.py b/bob/ip/binseg/configs/datasets/covd_iostar_vessel_ssl.py
similarity index 68%
rename from bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024ssliostar.py
rename to bob/ip/binseg/configs/datasets/covd_iostar_vessel_ssl.py
index 5dbd5b21..6357d710 100644
--- a/bob/ip/binseg/configs/datasets/drivestarechasedb1hrf1024ssliostar.py
+++ b/bob/ip/binseg/configs/datasets/covd_iostar_vessel_ssl.py
@@ -9,7 +9,7 @@ The dataset available in this file is composed of DRIVE, STARE, CHASE-DB1, and
HRF (with annotated samples) and IOSTAR without labels.
"""
-from bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024 import dataset as _labelled
-from bob.ip.binseg.configs.datasets.iostarvessel import dataset as _unlabelled
+from bob.ip.binseg.configs.datasets.covd_iostar_vessel import dataset as _labelled
+from bob.ip.binseg.configs.datasets.iostar_vessel import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py b/bob/ip/binseg/configs/datasets/covd_stare.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py
rename to bob/ip/binseg/configs/datasets/covd_stare.py
diff --git a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py b/bob/ip/binseg/configs/datasets/covd_stare_ssl.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
rename to bob/ip/binseg/configs/datasets/covd_stare_ssl.py
index 767c0e18..ff0fce68 100644
--- a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
+++ b/bob/ip/binseg/configs/datasets/covd_stare_ssl.py
@@ -9,7 +9,7 @@ The dataset available in this file is composed of DRIVE, CHASE-DB1, IOSTAR
vessel and HRF (with annotated samples) and STARE without labels.
"""
-from bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608 import dataset as _labelled
+from bob.ip.binseg.configs.datasets.covd_stare import dataset as _labelled
from bob.ip.binseg.configs.datasets.stare import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/csv.py b/bob/ip/binseg/configs/datasets/csv.py
index 410008f8..f6aec548 100644
--- a/bob/ip/binseg/configs/datasets/csv.py
+++ b/bob/ip/binseg/configs/datasets/csv.py
@@ -66,20 +66,15 @@ See:
"""
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.csvdataset import CSVDataset
-
# add your transforms below - these are just examples
-# keep the ``ToTensor()`` transform at the end
-transforms = Compose(
- [
+from bob.ip.binseg.data.transforms import *
+_transforms = [
#CenterCrop((544, 544)),
#RandomHFlip(),
#RandomVFlip(),
#RandomRotation(),
#ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-#dataset = CSVDataset("<path.csv>", check_available=False, transform=transforms)
+from bob.ip.binseg.data.csvdataset import CSVDataset
+#dataset = CSVDataset("<path.csv>", check_available=False, transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drionsdb.py b/bob/ip/binseg/configs/datasets/drionsdb.py
index 7b1730db..fdbbac77 100644
--- a/bob/ip/binseg/configs/datasets/drionsdb.py
+++ b/bob/ip/binseg/configs/datasets/drionsdb.py
@@ -25,19 +25,16 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose(
- [
+_transforms = [
Pad((4, 8, 4, 8)), #(left, top, right, bottom)
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
# bob.db.dataset init
bobdb = DRIONS(protocol="default")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drionsdbtest.py b/bob/ip/binseg/configs/datasets/drionsdb_test.py
similarity index 89%
rename from bob/ip/binseg/configs/datasets/drionsdbtest.py
rename to bob/ip/binseg/configs/datasets/drionsdb_test.py
index 8b1a0c87..01cfccd7 100644
--- a/bob/ip/binseg/configs/datasets/drionsdbtest.py
+++ b/bob/ip/binseg/configs/datasets/drionsdb_test.py
@@ -24,10 +24,10 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose([Pad((4, 8, 4, 8)), ToTensor()])
+_transforms = [Pad((4, 8, 4, 8))]
# bob.db.dataset init
bobdb = DRIONS(protocol="default")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1cup.py b/bob/ip/binseg/configs/datasets/dristhigs1_cup.py
similarity index 90%
rename from bob/ip/binseg/configs/datasets/dristhigs1cup.py
rename to bob/ip/binseg/configs/datasets/dristhigs1_cup.py
index 485a5e68..4780d6f0 100644
--- a/bob/ip/binseg/configs/datasets/dristhigs1cup.py
+++ b/bob/ip/binseg/configs/datasets/dristhigs1_cup.py
@@ -27,19 +27,16 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose(
- [
+_transforms = [
CenterCrop((1760, 2048)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
# bob.db.dataset init
bobdb = DRISHTI(protocol="default_cup")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1cuptest.py b/bob/ip/binseg/configs/datasets/dristhigs1_cup_test.py
similarity index 85%
rename from bob/ip/binseg/configs/datasets/dristhigs1cuptest.py
rename to bob/ip/binseg/configs/datasets/dristhigs1_cup_test.py
index 511b5273..e88c988a 100644
--- a/bob/ip/binseg/configs/datasets/dristhigs1cuptest.py
+++ b/bob/ip/binseg/configs/datasets/dristhigs1_cup_test.py
@@ -22,15 +22,15 @@ and notching information.
"""
from bob.db.drishtigs1 import Database as DRISHTI
-from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.transforms import CenterCrop
from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose([CenterCrop((1760, 2048)), ToTensor()])
+_transforms = [CenterCrop((1760, 2048))]
# bob.db.dataset init
bobdb = DRISHTI(protocol="default_cup")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1od.py b/bob/ip/binseg/configs/datasets/dristhigs1_od.py
similarity index 90%
rename from bob/ip/binseg/configs/datasets/dristhigs1od.py
rename to bob/ip/binseg/configs/datasets/dristhigs1_od.py
index 5c46540a..02545418 100644
--- a/bob/ip/binseg/configs/datasets/dristhigs1od.py
+++ b/bob/ip/binseg/configs/datasets/dristhigs1_od.py
@@ -27,19 +27,16 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose(
- [
+_transforms = [
CenterCrop((1760, 2048)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
# bob.db.dataset init
bobdb = DRISHTI(protocol="default_od")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1odtest.py b/bob/ip/binseg/configs/datasets/dristhigs1_od_test.py
similarity index 85%
rename from bob/ip/binseg/configs/datasets/dristhigs1odtest.py
rename to bob/ip/binseg/configs/datasets/dristhigs1_od_test.py
index e5e5c36a..0e05f2fb 100644
--- a/bob/ip/binseg/configs/datasets/dristhigs1odtest.py
+++ b/bob/ip/binseg/configs/datasets/dristhigs1_od_test.py
@@ -22,15 +22,15 @@ and notching information.
"""
from bob.db.drishtigs1 import Database as DRISHTI
-from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.transforms import CenterCrop
from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose([CenterCrop((1760, 2048)), ToTensor()])
+_transforms = [CenterCrop((1760, 2048))]
# bob.db.dataset init
bobdb = DRISHTI(protocol="default_od")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive.py b/bob/ip/binseg/configs/datasets/drive.py
index 5e5b4986..2690b671 100644
--- a/bob/ip/binseg/configs/datasets/drive.py
+++ b/bob/ip/binseg/configs/datasets/drive.py
@@ -14,18 +14,15 @@ segmentation of blood vessels in retinal images.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
CenterCrop((544, 544)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive1024.py b/bob/ip/binseg/configs/datasets/drive1024.py
index f27ac3b7..f296c5ea 100644
--- a/bob/ip/binseg/configs/datasets/drive1024.py
+++ b/bob/ip/binseg/configs/datasets/drive1024.py
@@ -14,19 +14,16 @@ segmentation of blood vessels in retinal images.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
CenterCrop((540, 540)),
Resize(1024),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive1168.py b/bob/ip/binseg/configs/datasets/drive1168.py
index ce84af98..29328381 100644
--- a/bob/ip/binseg/configs/datasets/drive1168.py
+++ b/bob/ip/binseg/configs/datasets/drive1168.py
@@ -14,8 +14,7 @@ segmentation of blood vessels in retinal images.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Crop(75, 10, 416, 544),
Pad((21, 0, 22, 0)),
@@ -23,11 +22,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive608.py b/bob/ip/binseg/configs/datasets/drive608.py
index d5794205..efc0ae26 100644
--- a/bob/ip/binseg/configs/datasets/drive608.py
+++ b/bob/ip/binseg/configs/datasets/drive608.py
@@ -14,8 +14,7 @@ segmentation of blood vessels in retinal images.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
CenterCrop((470, 544)),
Pad((10, 9, 10, 8)),
@@ -23,11 +22,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive960.py b/bob/ip/binseg/configs/datasets/drive960.py
index a37f54b0..4a2bbe02 100644
--- a/bob/ip/binseg/configs/datasets/drive960.py
+++ b/bob/ip/binseg/configs/datasets/drive960.py
@@ -14,19 +14,16 @@ segmentation of blood vessels in retinal images.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
CenterCrop((544, 544)),
Resize(960),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drivetest.py b/bob/ip/binseg/configs/datasets/drive_test.py
similarity index 63%
rename from bob/ip/binseg/configs/datasets/drivetest.py
rename to bob/ip/binseg/configs/datasets/drive_test.py
index 9315e59a..d7f49c4b 100644
--- a/bob/ip/binseg/configs/datasets/drivetest.py
+++ b/bob/ip/binseg/configs/datasets/drive_test.py
@@ -13,10 +13,10 @@ segmentation of blood vessels in retinal images.
* Split reference: [DRIVE-2004]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([CenterCrop((544, 544)), ToTensor()])
+from bob.ip.binseg.data.transforms import CenterCrop
+_transforms = [CenterCrop((544, 544))]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.drive import dataset as drive
-dataset = DelayedSample2TorchDataset(drive.subsets("default")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(drive.subsets("default")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/folder.py b/bob/ip/binseg/configs/datasets/folder.py
index d34c2797..06e1e65a 100644
--- a/bob/ip/binseg/configs/datasets/folder.py
+++ b/bob/ip/binseg/configs/datasets/folder.py
@@ -36,16 +36,11 @@ configuration that was used to train models and try to match it as well as
possible.
"""
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.folderdataset import FolderDataset
-
# add your transforms below - these are just examples
-# keep the ``ToTensor()`` transform at the end
-transforms = Compose(
- [
+from bob.ip.binseg.data.transforms import *
+_transforms = [
#CenterCrop((544, 544)),
- ToTensor(),
]
-)
-#dataset = FolderDataset("<path.csv>", glob="*.*", transform=transforms)
+from bob.ip.binseg.data.folderdataset import FolderDataset
+#dataset = FolderDataset("<path.csv>", glob="*.*", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf.py b/bob/ip/binseg/configs/datasets/hrf.py
index 95df5b00..fb731612 100644
--- a/bob/ip/binseg/configs/datasets/hrf.py
+++ b/bob/ip/binseg/configs/datasets/hrf.py
@@ -15,18 +15,15 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Crop(0, 108, 2336, 3296),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1024.py b/bob/ip/binseg/configs/datasets/hrf1024.py
index a1d7cb36..00f79b29 100644
--- a/bob/ip/binseg/configs/datasets/hrf1024.py
+++ b/bob/ip/binseg/configs/datasets/hrf1024.py
@@ -15,19 +15,16 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Pad((0, 584, 0, 584)),
- Resize((1024)),
+ Resize(1024),
RandomRotation(),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf544.py b/bob/ip/binseg/configs/datasets/hrf544.py
index d45b4247..a1adf81b 100644
--- a/bob/ip/binseg/configs/datasets/hrf544.py
+++ b/bob/ip/binseg/configs/datasets/hrf544.py
@@ -15,19 +15,16 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Resize((363)),
Pad((0, 90, 0, 91)),
RandomRotation(),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf544test.py b/bob/ip/binseg/configs/datasets/hrf544test.py
deleted file mode 100644
index 16102bf8..00000000
--- a/bob/ip/binseg/configs/datasets/hrf544test.py
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""HRF (test set) for Vessel Segmentation
-
-The database includes 15 images of each healthy, diabetic retinopathy (DR), and
-glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
-x 2336. One set of ground-truth vessel annotations is available.
-
-* Reference: [HRF-2013]_
-* Original resolution (height x width): 2336 x 3504
-* Configuration resolution: 544 x 544 (after specific padding and rescaling)
-* Test samples: 30
-* Split reference: [ORLANDO-2017]_
-"""
-
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
- Resize((363)),
- Pad((0, 90, 0, 91)),
- ToTensor(),
- ]
-)
-
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
-from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
- transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf608.py b/bob/ip/binseg/configs/datasets/hrf608.py
index a1d4fbf9..5404a514 100644
--- a/bob/ip/binseg/configs/datasets/hrf608.py
+++ b/bob/ip/binseg/configs/datasets/hrf608.py
@@ -15,19 +15,16 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Pad((0, 345, 0, 345)),
Resize(608),
RandomRotation(),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf960.py b/bob/ip/binseg/configs/datasets/hrf960.py
index 2dd12ef6..d7c92456 100644
--- a/bob/ip/binseg/configs/datasets/hrf960.py
+++ b/bob/ip/binseg/configs/datasets/hrf960.py
@@ -15,19 +15,16 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Pad((0, 584, 0, 584)),
- Resize((960)),
+ Resize(960),
RandomRotation(),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1168.py b/bob/ip/binseg/configs/datasets/hrf_1168.py
similarity index 74%
rename from bob/ip/binseg/configs/datasets/hrf1168.py
rename to bob/ip/binseg/configs/datasets/hrf_1168.py
index 67ece23f..0d17fa20 100644
--- a/bob/ip/binseg/configs/datasets/hrf1168.py
+++ b/bob/ip/binseg/configs/datasets/hrf_1168.py
@@ -15,19 +15,16 @@ x 2336. One set of ground-truth vessel annotations is available.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Crop(0, 108, 2336, 3296), #(upper, left, height, width)
- Resize((1168)), # applies to the smaller edge
+ Resize(1168), # applies to the smaller edge
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1168test.py b/bob/ip/binseg/configs/datasets/hrf_1168_test.py
similarity index 67%
rename from bob/ip/binseg/configs/datasets/hrf1168test.py
rename to bob/ip/binseg/configs/datasets/hrf_1168_test.py
index d73da151..89b5df45 100644
--- a/bob/ip/binseg/configs/datasets/hrf1168test.py
+++ b/bob/ip/binseg/configs/datasets/hrf_1168_test.py
@@ -14,10 +14,10 @@ x 2336. One set of ground-truth vessel annotations is available.
* Split reference: [ORLANDO-2017]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([Crop(0, 108, 2336, 3296), Resize((1168)), ToTensor()])
+from bob.ip.binseg.data.transforms import Crop, Resize
+_transforms = [Crop(0, 108, 2336, 3296), Resize(1168)]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrftest.py b/bob/ip/binseg/configs/datasets/hrf_test.py
similarity index 68%
rename from bob/ip/binseg/configs/datasets/hrftest.py
rename to bob/ip/binseg/configs/datasets/hrf_test.py
index 0ae5d763..2c926af4 100644
--- a/bob/ip/binseg/configs/datasets/hrftest.py
+++ b/bob/ip/binseg/configs/datasets/hrf_test.py
@@ -14,10 +14,10 @@ x 2336. One set of ground-truth vessel annotations is available.
* Split reference: [ORLANDO-2017]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([Crop(0, 108, 2336, 3296), ToTensor()])
+from bob.ip.binseg.data.transforms import Crop
+_transforms = [Crop(0, 108, 2336, 3296)]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.hrf import dataset as hrf
-dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(hrf.subsets("default")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarod.py b/bob/ip/binseg/configs/datasets/iostar_od.py
similarity index 77%
rename from bob/ip/binseg/configs/datasets/iostarod.py
rename to bob/ip/binseg/configs/datasets/iostar_od.py
index 78a5e91c..dc4ad5d9 100644
--- a/bob/ip/binseg/configs/datasets/iostarod.py
+++ b/bob/ip/binseg/configs/datasets/iostar_od.py
@@ -16,17 +16,14 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("optic-disc")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("optic-disc")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarodtest.py b/bob/ip/binseg/configs/datasets/iostar_od_test.py
similarity index 71%
rename from bob/ip/binseg/configs/datasets/iostarodtest.py
rename to bob/ip/binseg/configs/datasets/iostar_od_test.py
index 87260044..d9503af9 100644
--- a/bob/ip/binseg/configs/datasets/iostarodtest.py
+++ b/bob/ip/binseg/configs/datasets/iostar_od_test.py
@@ -15,10 +15,6 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
* Split reference: [MEYER-2017]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([ToTensor()])
-
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("optic-disc")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("optic-disc")["test"])
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel.py b/bob/ip/binseg/configs/datasets/iostar_vessel.py
similarity index 77%
rename from bob/ip/binseg/configs/datasets/iostarvessel.py
rename to bob/ip/binseg/configs/datasets/iostar_vessel.py
index c7b44fef..e6cd47b3 100644
--- a/bob/ip/binseg/configs/datasets/iostarvessel.py
+++ b/bob/ip/binseg/configs/datasets/iostar_vessel.py
@@ -16,17 +16,14 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarvesseltest.py b/bob/ip/binseg/configs/datasets/iostar_vessel_test.py
similarity index 71%
rename from bob/ip/binseg/configs/datasets/iostarvesseltest.py
rename to bob/ip/binseg/configs/datasets/iostar_vessel_test.py
index 77051798..c05b8455 100644
--- a/bob/ip/binseg/configs/datasets/iostarvesseltest.py
+++ b/bob/ip/binseg/configs/datasets/iostar_vessel_test.py
@@ -15,10 +15,6 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
* Split reference: [MEYER-2017]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([ToTensor()])
-
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["test"])
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel1168.py b/bob/ip/binseg/configs/datasets/iostarvessel1168.py
index 6fe05ee2..13457f60 100644
--- a/bob/ip/binseg/configs/datasets/iostarvessel1168.py
+++ b/bob/ip/binseg/configs/datasets/iostarvessel1168.py
@@ -16,8 +16,7 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Crop(144, 0, 768, 1024),
Pad((30, 0, 30, 0)),
@@ -25,11 +24,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel544.py b/bob/ip/binseg/configs/datasets/iostarvessel544.py
index 2e48cfd9..d2e588e8 100644
--- a/bob/ip/binseg/configs/datasets/iostarvessel544.py
+++ b/bob/ip/binseg/configs/datasets/iostarvessel544.py
@@ -16,18 +16,15 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Resize(544),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel608.py b/bob/ip/binseg/configs/datasets/iostarvessel608.py
index e5454a9f..6b3ae8fa 100644
--- a/bob/ip/binseg/configs/datasets/iostarvessel608.py
+++ b/bob/ip/binseg/configs/datasets/iostarvessel608.py
@@ -16,19 +16,16 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Pad((81, 0, 81, 0)),
Resize(608),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel960.py b/bob/ip/binseg/configs/datasets/iostarvessel960.py
index e2206848..95ca8905 100644
--- a/bob/ip/binseg/configs/datasets/iostarvessel960.py
+++ b/bob/ip/binseg/configs/datasets/iostarvessel960.py
@@ -16,18 +16,15 @@ dataset includes annotations for the optic disc and the artery/vein ratio.
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Resize(960),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.iostar import dataset as iostar
-dataset = DelayedSample2TorchDataset(iostar.subsets("vessel")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(iostar.subsets("vessel")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refugecup.py b/bob/ip/binseg/configs/datasets/refuge_cup.py
similarity index 88%
rename from bob/ip/binseg/configs/datasets/refugecup.py
rename to bob/ip/binseg/configs/datasets/refuge_cup.py
index b90400a7..2d26cc6d 100644
--- a/bob/ip/binseg/configs/datasets/refugecup.py
+++ b/bob/ip/binseg/configs/datasets/refuge_cup.py
@@ -27,20 +27,17 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose(
- [
- Resize((1539)),
+_transforms = [
+ Resize(1539),
Pad((21, 46, 22, 47)), #(left, top, right, bottom)
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
# bob.db.dataset init
bobdb = REFUGE(protocol="default_cup")
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refugecuptest.py b/bob/ip/binseg/configs/datasets/refuge_cup_test.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/refugecuptest.py
rename to bob/ip/binseg/configs/datasets/refuge_cup_test.py
index a24ec43c..b1d839fb 100644
--- a/bob/ip/binseg/configs/datasets/refugecuptest.py
+++ b/bob/ip/binseg/configs/datasets/refuge_cup_test.py
@@ -26,16 +26,11 @@ dataset of retinal fundus images.
"""
-from bob.db.refuge import Database as REFUGE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
+from bob.ip.binseg.data.transforms import CenterCrop
+_transforms = [CenterCrop(1632)]
-transforms = Compose([CenterCrop(1632), ToTensor()])
-
-# bob.db.dataset init
+from bob.db.refuge import Database as REFUGE
bobdb = REFUGE(protocol="default_cup")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refugeod.py b/bob/ip/binseg/configs/datasets/refuge_od.py
similarity index 85%
rename from bob/ip/binseg/configs/datasets/refugeod.py
rename to bob/ip/binseg/configs/datasets/refuge_od.py
index da226c8b..d61add28 100644
--- a/bob/ip/binseg/configs/datasets/refugeod.py
+++ b/bob/ip/binseg/configs/datasets/refuge_od.py
@@ -21,26 +21,18 @@ dataset of retinal fundus images.
"""
-from bob.db.refuge import Database as REFUGE
from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
-
-transforms = Compose(
- [
+_transforms = [
Resize((1539)),
Pad((21, 46, 22, 47)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-# bob.db.dataset init
+from bob.db.refuge import Database as REFUGE
bobdb = REFUGE(protocol="default_od")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refugeodtest.py b/bob/ip/binseg/configs/datasets/refuge_od_test.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/refugeodtest.py
rename to bob/ip/binseg/configs/datasets/refuge_od_test.py
index a14ff84b..8fb2ea54 100644
--- a/bob/ip/binseg/configs/datasets/refugeodtest.py
+++ b/bob/ip/binseg/configs/datasets/refuge_od_test.py
@@ -26,16 +26,11 @@ dataset of retinal fundus images.
"""
-from bob.db.refuge import Database as REFUGE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
+from bob.ip.binseg.data.transforms import CenterCrop
+_transforms = [CenterCrop(1632)]
-transforms = Compose([CenterCrop(1632), ToTensor()])
-
-# bob.db.dataset init
+from bob.db.refuge import Database as REFUGE
bobdb = REFUGE(protocol="default_od")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/rimoner3cup.py b/bob/ip/binseg/configs/datasets/rimoner3_cup.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/rimoner3cup.py
rename to bob/ip/binseg/configs/datasets/rimoner3_cup.py
index 361e35f4..080a32f9 100644
--- a/bob/ip/binseg/configs/datasets/rimoner3cup.py
+++ b/bob/ip/binseg/configs/datasets/rimoner3_cup.py
@@ -16,25 +16,17 @@ baseline.
* Split reference: [MANINIS-2016]_
"""
-from bob.db.rimoner3 import Database as RIMONER3
from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
-
-transforms = Compose(
- [
+_transforms = [
Pad((8, 8, 8, 8)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-# bob.db.dataset init
+from bob.db.rimoner3 import Database as RIMONER3
bobdb = RIMONER3(protocol="default_cup")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/rimoner3cuptest.py b/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py
similarity index 77%
rename from bob/ip/binseg/configs/datasets/rimoner3cuptest.py
rename to bob/ip/binseg/configs/datasets/rimoner3_cup_test.py
index c897048f..6ae6c809 100644
--- a/bob/ip/binseg/configs/datasets/rimoner3cuptest.py
+++ b/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py
@@ -16,16 +16,12 @@ baseline.
* Split reference: [MANINIS-2016]_
"""
-from bob.db.rimoner3 import Database as RIMONER3
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
-transforms = Compose([Pad((8, 8, 8, 8)), ToTensor()])
+from bob.ip.binseg.data.transforms import Pad
+_transforms = [Pad((8, 8, 8, 8))]
-# bob.db.dataset init
+from bob.db.rimoner3 import Database as RIMONER3
bobdb = RIMONER3(protocol="default_cup")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/rimoner3od.py b/bob/ip/binseg/configs/datasets/rimoner3_od.py
similarity index 83%
rename from bob/ip/binseg/configs/datasets/rimoner3od.py
rename to bob/ip/binseg/configs/datasets/rimoner3_od.py
index 60e0a571..e1dd0a94 100644
--- a/bob/ip/binseg/configs/datasets/rimoner3od.py
+++ b/bob/ip/binseg/configs/datasets/rimoner3_od.py
@@ -16,25 +16,17 @@ baseline.
* Split reference: [MANINIS-2016]_
"""
-from bob.db.rimoner3 import Database as RIMONER3
from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
-
-transforms = Compose(
- [
+_transforms = [
Pad((8, 8, 8, 8)),
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-# bob.db.dataset init
+from bob.db.rimoner3 import Database as RIMONER3
bobdb = RIMONER3(protocol="default_od")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/rimoner3odtest.py b/bob/ip/binseg/configs/datasets/rimoner3_od_test.py
similarity index 77%
rename from bob/ip/binseg/configs/datasets/rimoner3odtest.py
rename to bob/ip/binseg/configs/datasets/rimoner3_od_test.py
index 0a633fd6..9fdb9a1b 100644
--- a/bob/ip/binseg/configs/datasets/rimoner3odtest.py
+++ b/bob/ip/binseg/configs/datasets/rimoner3_od_test.py
@@ -16,16 +16,11 @@ baseline.
* Split reference: [MANINIS-2016]_
"""
-from bob.db.rimoner3 import Database as RIMONER3
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
+from bob.ip.binseg.data.transforms import Pad
+_transforms = [Pad((8, 8, 8, 8))]
-transforms = Compose([Pad((8, 8, 8, 8)), ToTensor()])
-
-# bob.db.dataset init
+from bob.db.rimoner3 import Database as RIMONER3
bobdb = RIMONER3(protocol="default_od")
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/stare.py b/bob/ip/binseg/configs/datasets/stare.py
index 74adacbc..d173f846 100644
--- a/bob/ip/binseg/configs/datasets/stare.py
+++ b/bob/ip/binseg/configs/datasets/stare.py
@@ -17,18 +17,15 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
Pad((2, 1, 2, 2)), #(left, top, right, bottom)
RandomHFlip(),
RandomVFlip(),
RandomRotation(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/stare1024.py b/bob/ip/binseg/configs/datasets/stare1024.py
index ca3b3957..e68941a6 100644
--- a/bob/ip/binseg/configs/datasets/stare1024.py
+++ b/bob/ip/binseg/configs/datasets/stare1024.py
@@ -17,8 +17,7 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Pad((0, 32, 0, 32)),
Resize(1024),
@@ -26,11 +25,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
]
-)
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/stare1168.py b/bob/ip/binseg/configs/datasets/stare1168.py
index 425ac1e5..6578f86b 100644
--- a/bob/ip/binseg/configs/datasets/stare1168.py
+++ b/bob/ip/binseg/configs/datasets/stare1168.py
@@ -14,8 +14,7 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Crop(50, 0, 500, 705),
Resize(1168),
@@ -23,11 +22,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/stare544.py b/bob/ip/binseg/configs/datasets/stare544.py
index da1b8230..9301343a 100644
--- a/bob/ip/binseg/configs/datasets/stare544.py
+++ b/bob/ip/binseg/configs/datasets/stare544.py
@@ -17,19 +17,16 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Resize(471),
Pad((0, 37, 0, 36)),
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
- ]
-)
+ ]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/stare960.py b/bob/ip/binseg/configs/datasets/stare960.py
index db8b88b5..f9af017f 100644
--- a/bob/ip/binseg/configs/datasets/stare960.py
+++ b/bob/ip/binseg/configs/datasets/stare960.py
@@ -17,8 +17,7 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
"""
from bob.ip.binseg.data.transforms import *
-_transforms = Compose(
- [
+_transforms = [
RandomRotation(),
Pad((0, 32, 0, 32)),
Resize(960),
@@ -26,11 +25,9 @@ _transforms = Compose(
RandomHFlip(),
RandomVFlip(),
ColorJitter(),
- ToTensor(),
]
-)
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["train"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/staretest.py b/bob/ip/binseg/configs/datasets/stare_test.py
similarity index 71%
rename from bob/ip/binseg/configs/datasets/staretest.py
rename to bob/ip/binseg/configs/datasets/stare_test.py
index c7a69801..e8d78bcb 100644
--- a/bob/ip/binseg/configs/datasets/staretest.py
+++ b/bob/ip/binseg/configs/datasets/stare_test.py
@@ -16,10 +16,10 @@ for training and testing. The second set by Valentina Kouznetsova acts as a
* Split reference: [MANINIS-2016]_
"""
-from bob.ip.binseg.data.transforms import *
-_transforms = Compose([Pad((2, 1, 2, 2)), ToTensor()])
+from bob.ip.binseg.data.transforms import Pad
+_transforms = [Pad((2, 1, 2, 2))]
-from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
from bob.ip.binseg.data.stare import dataset as stare
-dataset = DelayedSample2TorchDataset(stare.subsets("default")["test"],
- transform=_transforms)
+dataset = SampleList2TorchDataset(stare.subsets("default")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/models/driubn.py b/bob/ip/binseg/configs/models/driu_bn.py
similarity index 100%
rename from bob/ip/binseg/configs/models/driubn.py
rename to bob/ip/binseg/configs/models/driu_bn.py
diff --git a/bob/ip/binseg/configs/models/driubnssl.py b/bob/ip/binseg/configs/models/driu_bn_ssl.py
similarity index 100%
rename from bob/ip/binseg/configs/models/driubnssl.py
rename to bob/ip/binseg/configs/models/driu_bn_ssl.py
diff --git a/bob/ip/binseg/configs/models/driuod.py b/bob/ip/binseg/configs/models/driu_od.py
similarity index 100%
rename from bob/ip/binseg/configs/models/driuod.py
rename to bob/ip/binseg/configs/models/driu_od.py
diff --git a/bob/ip/binseg/configs/models/driussl.py b/bob/ip/binseg/configs/models/driu_ssl.py
similarity index 100%
rename from bob/ip/binseg/configs/models/driussl.py
rename to bob/ip/binseg/configs/models/driu_ssl.py
diff --git a/bob/ip/binseg/configs/models/m2unetssl.py b/bob/ip/binseg/configs/models/m2unet_ssl.py
similarity index 100%
rename from bob/ip/binseg/configs/models/m2unetssl.py
rename to bob/ip/binseg/configs/models/m2unet_ssl.py
diff --git a/bob/ip/binseg/data/binsegdataset.py b/bob/ip/binseg/data/binsegdataset.py
index 9c487da3..1a94c0be 100644
--- a/bob/ip/binseg/data/binsegdataset.py
+++ b/bob/ip/binseg/data/binsegdataset.py
@@ -1,8 +1,11 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
+
from torch.utils.data import Dataset
import random
+from .transforms import Compose, ToTensor
+
class BinSegDataset(Dataset):
"""PyTorch dataset wrapper around bob.db binary segmentation datasets.
@@ -13,20 +16,28 @@ class BinSegDataset(Dataset):
----------
bobdb : :py:mod:`bob.db.base`
Binary segmentation bob database (e.g. bob.db.drive)
+
split : str
``'train'`` or ``'test'``. Defaults to ``'train'``
- transform : :py:mod:`bob.ip.binseg.data.transforms`, optional
- A transform or composition of transfroms. Defaults to ``None``.
+
+ transforms : :py:class:`list`, Optional
+ a list of transformations to be applied to **both** image and
+ ground-truth data. Notice that image changing transformations such as
+ :py:class:`.transforms.ColorJitter` are only applied to the image and
+ **not** to ground-truth. Also notice a last transform
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied.
+
mask : bool
whether dataset contains masks or not
+
"""
- def __init__(self, bobdb, split="train", transform=None, index_to=None):
+ def __init__(self, bobdb, split="train", transforms=[], index_to=None):
if index_to:
self.database = bobdb.samples(split)[:index_to]
else:
self.database = bobdb.samples(split)
- self.transform = transform
+ self.transform = Compose(transforms + [ToTensor()])
self.split = split
@property
diff --git a/bob/ip/binseg/data/chasedb1/test.py b/bob/ip/binseg/data/chasedb1/test.py
index 9fcccddf..90f196dd 100644
--- a/bob/ip/binseg/data/chasedb1/test.py
+++ b/bob/ip/binseg/data/chasedb1/test.py
@@ -7,9 +7,8 @@
import os
import nose.tools
-from ..utils import rc_variable_set, DelayedSample2TorchDataset
-from ..transforms import Compose, Crop
from . import dataset
+from ...test.utils import rc_variable_set
def test_protocol_consitency():
@@ -66,27 +65,3 @@ def test_loading():
@rc_variable_set('bob.ip.binseg.chasedb1.datadir')
def test_check():
nose.tools.eq_(dataset.check(), 0)
-
-
-@rc_variable_set('bob.ip.binseg.chasedb1.datadir')
-def test_torch_dataset():
-
- def _check_sample(s):
- nose.tools.eq_(len(s), 3)
- assert isinstance(s[0], str)
- nose.tools.eq_(s[1].size, (960, 960))
- nose.tools.eq_(s[1].mode, "RGB")
- nose.tools.eq_(s[2].size, (960, 960))
- nose.tools.eq_(s[2].mode, "1")
-
- transforms = Compose([Crop(0, 18, 960, 960)])
-
- subset = dataset.subsets("default")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 8)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 20)
- for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/csvdataset.py b/bob/ip/binseg/data/csvdataset.py
index 9e65e363..43699faf 100644
--- a/bob/ip/binseg/data/csvdataset.py
+++ b/bob/ip/binseg/data/csvdataset.py
@@ -12,6 +12,8 @@ import torchvision.transforms.functional as VF
import bob.io.base
+from .transforms import Compose, ToTensor
+
import logging
logger = logging.getLogger(__name__)
@@ -80,20 +82,21 @@ class CSVDataset(Dataset):
If set to ``True``, then checks if files in the file list are
available. Otherwise does not.
- transform : :py:class:`.transforms.Compose`, Optional
- a composition of transformations to be applied to **both** image and
+ transforms : :py:class:`list`, Optional
+ a list of transformations to be applied to **both** image and
ground-truth data. Notice that image changing transformations such as
:py:class:`.transforms.ColorJitter` are only applied to the image and
- **not** to ground-truth.
+ **not** to ground-truth. Also notice a last transform
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied.
"""
def __init__(
- self, path, root_path=None, check_available=True, transform=None
+ self, path, root_path=None, check_available=True, transforms=[]
):
self.root_path = root_path or os.path.dirname(path)
- self.transform = transform
+ self.transform = Compose(transforms + [ToTensor()])
def _make_abs_path(root, s):
retval = []
diff --git a/bob/ip/binseg/data/drive/test.py b/bob/ip/binseg/data/drive/test.py
index 2834ca41..b7b291ff 100644
--- a/bob/ip/binseg/data/drive/test.py
+++ b/bob/ip/binseg/data/drive/test.py
@@ -7,9 +7,8 @@
import os
import nose.tools
-from ..utils import rc_variable_set, DelayedSample2TorchDataset
-from ..transforms import Compose, CenterCrop
from . import dataset
+from ...test.utils import rc_variable_set
def test_protocol_consitency():
@@ -64,30 +63,3 @@ def test_loading():
@rc_variable_set('bob.ip.binseg.drive.datadir')
def test_check():
nose.tools.eq_(dataset.check(), 0)
-
-
-@rc_variable_set('bob.ip.binseg.drive.datadir')
-def test_torch_dataset():
-
- def _check_sample(s):
- nose.tools.eq_(len(s), 4)
- assert isinstance(s[0], str)
- nose.tools.eq_(s[1].size, (544, 544))
- nose.tools.eq_(s[1].mode, "RGB")
- nose.tools.eq_(s[2].size, (544, 544))
- nose.tools.eq_(s[2].mode, "1")
- nose.tools.eq_(s[3].size, (544, 544))
- nose.tools.eq_(s[3].mode, "1")
-
-
- transforms = Compose([CenterCrop((544, 544))])
-
- subset = dataset.subsets("default")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 20)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 20)
- for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/folderdataset.py b/bob/ip/binseg/data/folderdataset.py
index 19366884..2566fd77 100644
--- a/bob/ip/binseg/data/folderdataset.py
+++ b/bob/ip/binseg/data/folderdataset.py
@@ -7,6 +7,8 @@ from PIL import Image
from torch.utils.data import Dataset
+from .transforms import Compose, ToTensor
+
def _find_files(data_path, glob):
"""
@@ -42,16 +44,17 @@ class FolderDataset(Dataset):
glob that can be used to filter-down files to be loaded on the provided
path
- transform : :py:class:`.transforms.Compose`, Optional
- a composition of transformations to be applied to **both** image and
+ transforms : :py:class:`list`, Optional
+ a list of transformations to be applied to **both** image and
ground-truth data. Notice that image changing transformations such as
:py:class:`.transforms.ColorJitter` are only applied to the image and
- **not** to ground-truth.
+ **not** to ground-truth. Also notice a last transform
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied.
"""
- def __init__(self, path, glob="*", transform=None):
- self.transform = transform
+ def __init__(self, path, glob="*", transforms=[]):
+ self.transform = Compose(transforms + [ToTensor()])
self.path = path
self.data = _find_files(path, glob)
diff --git a/bob/ip/binseg/data/hrf/test.py b/bob/ip/binseg/data/hrf/test.py
index 50828041..9a463776 100644
--- a/bob/ip/binseg/data/hrf/test.py
+++ b/bob/ip/binseg/data/hrf/test.py
@@ -7,9 +7,8 @@
import os
import nose.tools
-from ..utils import rc_variable_set, DelayedSample2TorchDataset
-from ..transforms import Compose, Crop, Resize
from . import dataset
+from ...test.utils import rc_variable_set
def test_protocol_consitency():
@@ -53,30 +52,3 @@ def test_loading():
@rc_variable_set('bob.ip.binseg.hrf.datadir')
def test_check():
nose.tools.eq_(dataset.check(), 0)
-
-
-@rc_variable_set('bob.ip.binseg.hrf.datadir')
-def test_torch_dataset():
-
- def _check_sample(s):
- nose.tools.eq_(len(s), 4)
- assert isinstance(s[0], str)
- nose.tools.eq_(s[1].size, (1648, 1168))
- nose.tools.eq_(s[1].mode, "RGB")
- nose.tools.eq_(s[2].size, (1648, 1168))
- nose.tools.eq_(s[2].mode, "1")
- nose.tools.eq_(s[3].size, (1648, 1168))
- nose.tools.eq_(s[3].mode, "1")
-
-
- transforms = Compose([Crop(0, 108, 2336, 3296), Resize((1168))])
-
- subset = dataset.subsets("default")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 15)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 30)
- for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/iostar/test.py b/bob/ip/binseg/data/iostar/test.py
index b0b026db..ecedb60c 100644
--- a/bob/ip/binseg/data/iostar/test.py
+++ b/bob/ip/binseg/data/iostar/test.py
@@ -7,9 +7,8 @@
import os
import nose.tools
-from ..utils import rc_variable_set, DelayedSample2TorchDataset
-from ..transforms import Compose, Crop, Resize
from . import dataset
+from ...test.utils import rc_variable_set
def test_protocol_consitency():
@@ -70,39 +69,3 @@ def test_loading():
@rc_variable_set('bob.ip.binseg.iostar.datadir')
def test_check():
nose.tools.eq_(dataset.check(), 0)
-
-
-@rc_variable_set('bob.ip.binseg.stare.datadir')
-def test_torch_dataset():
-
- def _check_sample(s):
- nose.tools.eq_(len(s), 4)
- assert isinstance(s[0], str)
- nose.tools.eq_(s[1].size, (1024, 1024))
- nose.tools.eq_(s[1].mode, "RGB")
- nose.tools.eq_(s[2].size, (1024, 1024))
- nose.tools.eq_(s[2].mode, "1")
- nose.tools.eq_(s[3].size, (1024, 1024))
- nose.tools.eq_(s[3].mode, "1")
-
- transforms = None
-
- subset = dataset.subsets("vessel")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 20)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 10)
- for s in torch_dataset: _check_sample(s)
-
- subset = dataset.subsets("optic-disc")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 20)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 10)
- for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/stare/test.py b/bob/ip/binseg/data/stare/test.py
index b47fd4d9..0a60cd60 100644
--- a/bob/ip/binseg/data/stare/test.py
+++ b/bob/ip/binseg/data/stare/test.py
@@ -7,9 +7,8 @@
import os
import nose.tools
-from ..utils import rc_variable_set, DelayedSample2TorchDataset
-from ..transforms import Compose, Pad
from . import dataset
+from ...test.utils import rc_variable_set
def test_protocol_consitency():
@@ -66,27 +65,3 @@ def test_loading():
@rc_variable_set('bob.ip.binseg.stare.datadir')
def test_check():
nose.tools.eq_(dataset.check(), 0)
-
-
-@rc_variable_set('bob.ip.binseg.stare.datadir')
-def test_torch_dataset():
-
- def _check_sample(s):
- nose.tools.eq_(len(s), 3)
- assert isinstance(s[0], str)
- nose.tools.eq_(s[1].size, (704, 608))
- nose.tools.eq_(s[1].mode, "RGB")
- nose.tools.eq_(s[2].size, (704, 608))
- nose.tools.eq_(s[2].mode, "1")
-
- transforms = Compose([Pad((2, 1, 2, 2))])
-
- subset = dataset.subsets("default")
-
- torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
- nose.tools.eq_(len(torch_dataset), 10)
- for s in torch_dataset: _check_sample(s)
-
- torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
- nose.tools.eq_(len(torch_dataset), 10)
- for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/utils.py b/bob/ip/binseg/data/utils.py
index 6eca077a..0e1c8842 100644
--- a/bob/ip/binseg/data/utils.py
+++ b/bob/ip/binseg/data/utils.py
@@ -5,35 +5,14 @@
"""Common utilities"""
-import functools
-
-import nose.plugins.skip
-
import torch
import torch.utils.data
-import bob.extension
-
-
-def rc_variable_set(name):
- """
- Decorator that checks if a given bobrc variable is set before running
- """
-
- def wrapped_function(test):
- @functools.wraps(test)
- def wrapper(*args, **kwargs):
- if name not in bob.extension.rc:
- raise nose.plugins.skip.SkipTest("Bob's RC variable '%s' is not set" % name)
- return test(*args, **kwargs)
-
- return wrapper
-
- return wrapped_function
+from .transforms import Compose, ToTensor
-class DelayedSample2TorchDataset(torch.utils.data.Dataset):
- """PyTorch dataset wrapper around DelayedSample lists
+class SampleList2TorchDataset(torch.utils.data.Dataset):
+ """PyTorch dataset wrapper around Sample lists
A transform object can be passed that will be applied to the image, ground
truth and mask (if present).
@@ -43,17 +22,21 @@ class DelayedSample2TorchDataset(torch.utils.data.Dataset):
Parameters
----------
samples : list
- A list of :py:class:`bob.ip.binseg.data.sample.DelayedSample` objects
+ A list of :py:class:`bob.ip.binseg.data.sample.Sample` objects
- transform : :py:mod:`bob.ip.binseg.data.transforms`, optional
- A transform or composition of transfroms. Defaults to ``None``.
+ transforms : :py:class:`list`, Optional
+ a list of transformations to be applied to **both** image and
+ ground-truth data. Notice that image changing transformations such as
+ :py:class:`.transforms.ColorJitter` are only applied to the image and
+ **not** to ground-truth. Also notice a last transform
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied.
"""
- def __init__(self, samples, transform=None):
+ def __init__(self, samples, transforms=[]):
self._samples = samples
- self._transform = transform
+ self._transform = Compose(transforms + [ToTensor()])
def __len__(self):
"""
diff --git a/bob/ip/binseg/test/test_config.py b/bob/ip/binseg/test/test_config.py
new file mode 100644
index 00000000..c60bafb5
--- /dev/null
+++ b/bob/ip/binseg/test/test_config.py
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+import nose.tools
+
+import torch
+
+from .utils import rc_variable_set
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+def test_drive_default_train():
+
+ from ..configs.datasets.drive import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 4)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ nose.tools.eq_(sample[3].shape, (1, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+def test_drive_default_test():
+
+ from ..configs.datasets.drive_test import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 4)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ nose.tools.eq_(sample[3].shape, (1, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.stare.datadir")
+def test_stare_default_train():
+
+ from ..configs.datasets.stare import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 608, 704)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 608, 704)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.stare.datadir")
+def test_stare_default_test():
+
+ from ..configs.datasets.stare_test import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 608, 704)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 608, 704)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+def test_chasedb1_default_train():
+
+ from ..configs.datasets.chasedb1 import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 960, 960)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 960, 960)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+def test_chasedb1_default_test():
+
+ from ..configs.datasets.chasedb1_test import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 960, 960)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 960, 960)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+def test_hrf_default_train():
+
+ from ..configs.datasets.hrf_1168 import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 4)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ nose.tools.eq_(sample[3].shape, (1, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+def test_hrf_default_test():
+
+ from ..configs.datasets.hrf_1168_test import dataset
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 4)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ nose.tools.eq_(sample[3].shape, (1, 1168, 1648)) #planes, height, width
+ nose.tools.eq_(sample[3].dtype, torch.float32)
diff --git a/bob/ip/binseg/test/utils.py b/bob/ip/binseg/test/utils.py
new file mode 100644
index 00000000..b5739240
--- /dev/null
+++ b/bob/ip/binseg/test/utils.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+
+"""Test utilities"""
+
+
+import functools
+import nose.plugins.skip
+import bob.extension
+
+
+def rc_variable_set(name):
+ """
+ Decorator that checks if a given bobrc variable is set before running
+ """
+
+ def wrapped_function(test):
+ @functools.wraps(test)
+ def wrapper(*args, **kwargs):
+ if name not in bob.extension.rc:
+ raise nose.plugins.skip.SkipTest("Bob's RC variable '%s' is not set" % name)
+ return test(*args, **kwargs)
+
+ return wrapper
+
+ return wrapped_function
diff --git a/doc/api.rst b/doc/api.rst
index 7541a4ed..020371c8 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -109,13 +109,13 @@ Models
:template: config.rst
bob.ip.binseg.configs.models.driu
- bob.ip.binseg.configs.models.driubn
- bob.ip.binseg.configs.models.driubnssl
- bob.ip.binseg.configs.models.driuod
- bob.ip.binseg.configs.models.driussl
+ bob.ip.binseg.configs.models.driu_bn
+ bob.ip.binseg.configs.models.driu_bn_ssl
+ bob.ip.binseg.configs.models.driu_od
+ bob.ip.binseg.configs.models.driu_ssl
bob.ip.binseg.configs.models.hed
bob.ip.binseg.configs.models.m2unet
- bob.ip.binseg.configs.models.m2unetssl
+ bob.ip.binseg.configs.models.m2unet_ssl
bob.ip.binseg.configs.models.resunet
bob.ip.binseg.configs.models.unet
@@ -129,64 +129,52 @@ Datasets
:toctree: api/configs/datasets
:template: config.rst
- bob.ip.binseg.configs.datasets.chasedb1
- bob.ip.binseg.configs.datasets.chasedb11024
- bob.ip.binseg.configs.datasets.chasedb11168
- bob.ip.binseg.configs.datasets.chasedb1544
- bob.ip.binseg.configs.datasets.chasedb1608
- bob.ip.binseg.configs.datasets.chasedb1test
bob.ip.binseg.configs.datasets.csv
- bob.ip.binseg.configs.datasets.drionsdb
- bob.ip.binseg.configs.datasets.drionsdbtest
- bob.ip.binseg.configs.datasets.dristhigs1cup
- bob.ip.binseg.configs.datasets.dristhigs1cuptest
- bob.ip.binseg.configs.datasets.dristhigs1od
- bob.ip.binseg.configs.datasets.dristhigs1odtest
- bob.ip.binseg.configs.datasets.drive
- bob.ip.binseg.configs.datasets.drive1024
- bob.ip.binseg.configs.datasets.drive1168
- bob.ip.binseg.configs.datasets.drive608
- bob.ip.binseg.configs.datasets.drive960
- bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608
- bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare
- bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024
- bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar
- bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168
- bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf
- bob.ip.binseg.configs.datasets.drivestareiostarhrf960
- bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase
- bob.ip.binseg.configs.datasets.drivetest
bob.ip.binseg.configs.datasets.folder
+
+ bob.ip.binseg.configs.datasets.chasedb1
+ bob.ip.binseg.configs.datasets.chasedb1_test
+ bob.ip.binseg.configs.datasets.covd_chasedb1
+ bob.ip.binseg.configs.datasets.covd_chasedb1_ssl
+
+ bob.ip.binseg.configs.datasets.drive
+ bob.ip.binseg.configs.datasets.drive_test
+ bob.ip.binseg.configs.datasets.covd_drive
+ bob.ip.binseg.configs.datasets.covd_drive_ssl
+
bob.ip.binseg.configs.datasets.hrf
- bob.ip.binseg.configs.datasets.hrf1024
- bob.ip.binseg.configs.datasets.hrf1168
- bob.ip.binseg.configs.datasets.hrf1168test
- bob.ip.binseg.configs.datasets.hrf544
- bob.ip.binseg.configs.datasets.hrf544test
- bob.ip.binseg.configs.datasets.hrf608
- bob.ip.binseg.configs.datasets.hrf960
- bob.ip.binseg.configs.datasets.hrftest
- bob.ip.binseg.configs.datasets.iostarod
- bob.ip.binseg.configs.datasets.iostarodtest
- bob.ip.binseg.configs.datasets.iostarvessel
- bob.ip.binseg.configs.datasets.iostarvessel1168
- bob.ip.binseg.configs.datasets.iostarvessel544
- bob.ip.binseg.configs.datasets.iostarvessel608
- bob.ip.binseg.configs.datasets.iostarvessel960
- bob.ip.binseg.configs.datasets.iostarvesseltest
- bob.ip.binseg.configs.datasets.refugecup
- bob.ip.binseg.configs.datasets.refugecuptest
- bob.ip.binseg.configs.datasets.refugeod
- bob.ip.binseg.configs.datasets.refugeodtest
- bob.ip.binseg.configs.datasets.rimoner3cup
- bob.ip.binseg.configs.datasets.rimoner3cuptest
- bob.ip.binseg.configs.datasets.rimoner3od
- bob.ip.binseg.configs.datasets.rimoner3odtest
+ bob.ip.binseg.configs.datasets.hrf_1168
+ bob.ip.binseg.configs.datasets.hrf_1168_test
+ bob.ip.binseg.configs.datasets.hrf_test
+ bob.ip.binseg.configs.datasets.covd_hrf
+ bob.ip.binseg.configs.datasets.covd_hrf_ssl
+
+ bob.ip.binseg.configs.datasets.iostar_vessel
+ bob.ip.binseg.configs.datasets.iostar_vessel_test
+ bob.ip.binseg.configs.datasets.covd_iostar_vessel
+ bob.ip.binseg.configs.datasets.covd_iostar_vessel_ssl
+ bob.ip.binseg.configs.datasets.iostar_od
+ bob.ip.binseg.configs.datasets.iostar_od_test
+
bob.ip.binseg.configs.datasets.stare
- bob.ip.binseg.configs.datasets.stare1024
- bob.ip.binseg.configs.datasets.stare1168
- bob.ip.binseg.configs.datasets.stare544
- bob.ip.binseg.configs.datasets.stare960
- bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544
- bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive
- bob.ip.binseg.configs.datasets.staretest
+ bob.ip.binseg.configs.datasets.stare_test
+ bob.ip.binseg.configs.datasets.covd_stare
+ bob.ip.binseg.configs.datasets.covd_stare_ssl
+
+ bob.ip.binseg.configs.datasets.drionsdb
+ bob.ip.binseg.configs.datasets.drionsdb_test
+
+ bob.ip.binseg.configs.datasets.dristhigs1_cup
+ bob.ip.binseg.configs.datasets.dristhigs1_cup_test
+ bob.ip.binseg.configs.datasets.dristhigs1_od
+ bob.ip.binseg.configs.datasets.dristhigs1_od_test
+
+ bob.ip.binseg.configs.datasets.refuge_cup
+ bob.ip.binseg.configs.datasets.refuge_cup_test
+ bob.ip.binseg.configs.datasets.refuge_od
+ bob.ip.binseg.configs.datasets.refuge_od_test
+
+ bob.ip.binseg.configs.datasets.rimoner3_cup
+ bob.ip.binseg.configs.datasets.rimoner3_cup_test
+ bob.ip.binseg.configs.datasets.rimoner3_od
+ bob.ip.binseg.configs.datasets.rimoner3_od_test
diff --git a/doc/benchmarkresults.rst b/doc/benchmarkresults.rst
index becbf3b3..5023a3ce 100644
--- a/doc/benchmarkresults.rst
+++ b/doc/benchmarkresults.rst
@@ -39,12 +39,12 @@ F1 Scores (micro-level)
- 0.817 (0.013)
- `0.803 (0.014) <m2unet_drive.pth_>`_
- 0.822 (0.015)
- * - :py:mod:`HRF <bob.ip.binseg.configs.datasets.hrf1168>`
+ * - :py:mod:`HRF <bob.ip.binseg.configs.datasets.hrf_1168>`
- `0.783 (0.055) <driu_hrf.pth_>`_
- 0.783 (0.058)
- `0.780 (0.057) <m2unet_hrf.pth_>`_
- 0.788 (0.051)
- * - :py:mod:`IOSTAR (vessel) <bob.ip.binseg.configs.datasets.iostarvessel>`
+ * - :py:mod:`IOSTAR (vessel) <bob.ip.binseg.configs.datasets.iostar_vessel>`
- `0.825 (0.020) <driu_iostar.pth_>`_
- 0.825 (0.020)
- `0.817 (0.020) <m2unet_iostar.pth_>`_
diff --git a/doc/covdresults.rst b/doc/covdresults.rst
index 73aa7270..3abe8445 100644
--- a/doc/covdresults.rst
+++ b/doc/covdresults.rst
@@ -27,46 +27,46 @@ brackets.
:header-rows: 1
* - F1 score
- - :py:mod:`DRIU <bob.ip.binseg.configs.models.driu>`/:py:mod:`DRIU@SSL <bob.ip.binseg.configs.models.driussl>`
- - :py:mod:`DRIU+BN <bob.ip.binseg.configs.models.driubn>`/:py:mod:`DRIU+BN@SSL <bob.ip.binseg.configs.models.driubnssl>`
- - :py:mod:`M2U-Net <bob.ip.binseg.configs.models.m2unet>`/:py:mod:`M2U-Net@SSL <bob.ip.binseg.configs.models.m2unetssl>`
- * - :py:mod:`DRIVE (COVD-) <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544>`
+ - :py:mod:`DRIU <bob.ip.binseg.configs.models.driu>`/:py:mod:`DRIU@SSL <bob.ip.binseg.configs.models.driu_ssl>`
+ - :py:mod:`DRIU+BN <bob.ip.binseg.configs.models.driu_bn>`/:py:mod:`DRIU+BN@SSL <bob.ip.binseg.configs.models.driu_bn_ssl>`
+ - :py:mod:`M2U-Net <bob.ip.binseg.configs.models.m2unet>`/:py:mod:`M2U-Net@SSL <bob.ip.binseg.configs.models.m2unet_ssl>`
+ * - :py:mod:`COVD-DRIVE <bob.ip.binseg.configs.datasets.covd_drive>`
- 0.788 (0.018)
- 0.797 (0.019)
- `0.789 (0.018) <m2unet_covd-drive.pth>`_
- * - :py:mod:`DRIVE (SSL, COVD-) <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive>`
+ * - :py:mod:`COVD-DRIVE+SSL <bob.ip.binseg.configs.datasets.covd_drive_ssl>`
- 0.785 (0.018)
- 0.783 (0.019)
- `0.791 (0.014) <m2unet_covd-drive_ssl.pth>`_
- * - :py:mod:`STARE (COVD-) <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608>`
+ * - :py:mod:`COVD-STARE <bob.ip.binseg.configs.datasets.covd_stare>`
- 0.778 (0.117)
- 0.778 (0.122)
- `0.812 (0.046) <m2unet_covd-stare.pth>`_
- * - :py:mod:`STARE (SSL, COVD-) <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare>`
+ * - :py:mod:`COVD-STARE+SSL <bob.ip.binseg.configs.datasets.covd_stare_ssl>`
- 0.788 (0.102)
- 0.811 (0.074)
- `0.820 (0.044) <m2unet_covd-stare_ssl.pth>`_
- * - :py:mod:`CHASE-DB1 (COVD-) <bob.ip.binseg.configs.datasets.drivestareiostarhrf960>`
+ * - :py:mod:`COVD-CHASEDB1 <bob.ip.binseg.configs.datasets.covd_chasedb1>`
- 0.796 (0.027)
- 0.791 (0.025)
- `0.788 (0.024) <m2unet_covd-chasedb1.pth>`_
- * - :py:mod:`CHASE-DB1 (SSL, COVD-) <bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase>`
+ * - :py:mod:`COVD-CHASEDB1+SSL <bob.ip.binseg.configs.datasets.covd_chasedb1_ssl>`
- 0.796 (0.024)
- 0.798 (0.025)
- `0.799 (0.026) <m2unet_covd-chasedb1_ssl.pth>`_
- * - :py:mod:`HRF (COVD-) <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168>`
+ * - :py:mod:`COVD-HRF <bob.ip.binseg.configs.datasets.covd_hrf>`
- 0.799 (0.044)
- 0.800 (0.045)
- `0.802 (0.045) <m2unet_covd-hrf.pth>`_
- * - :py:mod:`HRF (SSL, COVD-) <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf>`
+ * - :py:mod:`COVD-HRF+SSL <bob.ip.binseg.configs.datasets.covd_hrf_ssl>`
- 0.799 (0.044)
- 0.784 (0.048)
- `0.797 (0.044) <m2unet_covd-hrf_ssl.pth>`_
- * - :py:mod:`IOSTAR (vessel, COVD-) <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024>`
+ * - :py:mod:`COVD-IOSTAR-VESSEL <bob.ip.binseg.configs.datasets.covd_iostar_vessel>`
- 0.791 (0.021)
- 0.777 (0.032)
- `0.793 (0.015) <m2unet_covd-iostar.pth>`_
- * - :py:mod:`IOSTAR (vessel, SSL, COVD-) <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar>`
+ * - :py:mod:`COVD-IOSTAR-VESSEL+SSL <bob.ip.binseg.configs.datasets.covd_iostar_vessel_ssl>`
- 0.797 (0.017)
- 0.811 (0.074)
- `0.785 (0.018) <m2unet_covd-iostar_ssl.pth>`_
diff --git a/doc/models.rst b/doc/models.rst
index 25e347f8..5f940645 100644
--- a/doc/models.rst
+++ b/doc/models.rst
@@ -19,46 +19,46 @@ weights of a subset of all evaluated models.
* - :py:mod:`drive <bob.ip.binseg.configs.datasets.drive>`
- driu_drive.pth_
- m2unet_drive.pth_
- * - :py:mod:`covd-drive <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544>`
+ * - :py:mod:`covd-drive <bob.ip.binseg.configs.datasets.covd_drive>`
-
- m2unet_covd-drive.pth_
- * - :py:mod:`covd-drive-ssl <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive>`
+ * - :py:mod:`covd-drive-ssl <bob.ip.binseg.configs.datasets.covd_drive_ssl>`
-
- m2unet_covd-drive_ssl.pth_
* - :py:mod:`stare <bob.ip.binseg.configs.datasets.stare>`
- driu_stare.pth_
- m2unet_stare.pth_
- * - :py:mod:`covd-stare <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608>`
+ * - :py:mod:`covd-stare <bob.ip.binseg.configs.datasets.covd_stare>`
-
- m2unet_covd-stare.pth_
- * - :py:mod:`covd-stare-ssl <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare>`
+ * - :py:mod:`covd-stare-ssl <bob.ip.binseg.configs.datasets.covd_stare_ssl>`
-
- m2unet_covd-stare_ssl.pth_
* - :py:mod:`chasedb1 <bob.ip.binseg.configs.datasets.chasedb1>`
- driu_chasedb1.pth_
- m2unet_chasedb1.pth_
- * - :py:mod:`covd-chasedb1 <bob.ip.binseg.configs.datasets.drivestareiostarhrf960>`
+ * - :py:mod:`covd-chasedb1 <bob.ip.binseg.configs.datasets.covd_chasedb1>`
-
- m2unet_covd-chasedb1.pth_
- * - :py:mod:`covd-chasedb1-ssl <bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase>`
+ * - :py:mod:`covd-chasedb1-ssl <bob.ip.binseg.configs.datasets.covd_chasedb1_ssl>`
-
- m2unet_covd-chasedb1_ssl.pth_
- * - :py:mod:`iostar-vessel <bob.ip.binseg.configs.datasets.iostarvessel>`
+ * - :py:mod:`iostar-vessel <bob.ip.binseg.configs.datasets.iostar_vessel>`
- driu_iostar.pth_
- m2unet_iostar.pth_
- * - :py:mod:`covd-iostar-vessel <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024>`
+ * - :py:mod:`covd-iostar-vessel <bob.ip.binseg.configs.datasets.covd_iostar_vessel>`
-
- m2unet_covd-iostar.pth_
- * - :py:mod:`covd-iostar-vessel-ssl <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar>`
+ * - :py:mod:`covd-iostar-vessel-ssl <bob.ip.binseg.configs.datasets.covd_iostar_vessel_ssl>`
-
- m2unet_covd-iostar_ssl.pth_
- * - :py:mod:`hrf <bob.ip.binseg.configs.datasets.hrf1168>`
+ * - :py:mod:`hrf <bob.ip.binseg.configs.datasets.hrf_1168>`
- driu_hrf.pth_
- m2unet_hrf.pth_
- * - :py:mod:`covd-hrf <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168>`
+ * - :py:mod:`covd-hrf <bob.ip.binseg.configs.datasets.covd_hrf>`
-
- m2unet_covd-hrf.pth_
- * - :py:mod:`covd-hrf-ssl <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf>`
+ * - :py:mod:`covd-hrf-ssl <bob.ip.binseg.configs.datasets.covd_hrf_ssl>`
-
- m2unet_covd-hrf_ssl.pth_
diff --git a/doc/training.rst b/doc/training.rst
index fe265f1e..35bf7b1d 100644
--- a/doc/training.rst
+++ b/doc/training.rst
@@ -41,8 +41,8 @@ card, for supervised training of baselines. Use it like this:
- :py:mod:`drive <bob.ip.binseg.configs.datasets.drive>`
- :py:mod:`stare <bob.ip.binseg.configs.datasets.stare>`
- :py:mod:`chasedb1 <bob.ip.binseg.configs.datasets.chasedb1>`
- - :py:mod:`iostar-vessel <bob.ip.binseg.configs.datasets.iostarvessel>`
- - :py:mod:`hrf <bob.ip.binseg.configs.datasets.hrf1168>`
+ - :py:mod:`iostar-vessel <bob.ip.binseg.configs.datasets.iostar_vessel>`
+ - :py:mod:`hrf <bob.ip.binseg.configs.datasets.hrf_1168>`
* - :py:mod:`unet <bob.ip.binseg.configs.models.unet>`
- 4
- 2
@@ -55,7 +55,7 @@ card, for supervised training of baselines. Use it like this:
- 4
- 4
- 1
- * - :py:mod:`driu <bob.ip.binseg.configs.models.driu>` / :py:mod:`driu-bn <bob.ip.binseg.configs.models.driubn>`
+ * - :py:mod:`driu <bob.ip.binseg.configs.models.driu>` / :py:mod:`driu-bn <bob.ip.binseg.configs.models.driu_bn>`
- 8
- 5
- 4
@@ -111,12 +111,12 @@ card, for supervised training of COVD- systems. Use it like this:
.. list-table::
* - **Models / Datasets**
- - :py:mod:`covd-drive <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544>`
- - :py:mod:`covd-stare <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608>`
- - :py:mod:`covd-chasedb1 <bob.ip.binseg.configs.datasets.drivestareiostarhrf960>`
- - :py:mod:`covd-iostar-vessel <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024>`
- - :py:mod:`covd-hrf <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168>`
- * - :py:mod:`driu <bob.ip.binseg.configs.models.driu>` / :py:mod:`driu-bn <bob.ip.binseg.configs.models.driubn>`
+ - :py:mod:`covd-drive <bob.ip.binseg.configs.datasets.covd_drive>`
+ - :py:mod:`covd-stare <bob.ip.binseg.configs.datasets.covd_stare>`
+ - :py:mod:`covd-chasedb1 <bob.ip.binseg.configs.datasets.covd_chasedb1>`
+ - :py:mod:`covd-iostar-vessel <bob.ip.binseg.configs.datasets.covd_iostar_vessel>`
+ - :py:mod:`covd-hrf <bob.ip.binseg.configs.datasets.covd_hrf>`
+ * - :py:mod:`driu <bob.ip.binseg.configs.models.driu>` / :py:mod:`driu-bn <bob.ip.binseg.configs.models.driu_bn>`
- 4
- 4
- 2
@@ -144,18 +144,18 @@ card, for semi-supervised learning of COVD- systems. Use it like this:
.. list-table::
* - **Models / Datasets**
- - :py:mod:`covd-drive-ssl <bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive>`
- - :py:mod:`covd-stare-ssl <bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare>`
- - :py:mod:`covd-chasedb1-ssl <bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase>`
- - :py:mod:`covd-iostar-vessel-ssl <bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar>`
- - :py:mod:`covd-hrf-ssl <bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf>`
- * - :py:mod:`driu-ssl <bob.ip.binseg.configs.models.driussl>` / :py:mod:`driu-bn-ssl <bob.ip.binseg.configs.models.driubnssl>`
+ - :py:mod:`covd-drive-ssl <bob.ip.binseg.configs.datasets.covd_drive_ssl>`
+ - :py:mod:`covd-stare-ssl <bob.ip.binseg.configs.datasets.covd_stare_ssl>`
+ - :py:mod:`covd-chasedb1-ssl <bob.ip.binseg.configs.datasets.covd_chasedb1_ssl>`
+ - :py:mod:`covd-iostar-vessel-ssl <bob.ip.binseg.configs.datasets.covd_iostar_vessel_ssl>`
+ - :py:mod:`covd-hrf-ssl <bob.ip.binseg.configs.datasets.covd_hrf_ssl>`
+ * - :py:mod:`driu-ssl <bob.ip.binseg.configs.models.driu_ssl>` / :py:mod:`driu-bn-ssl <bob.ip.binseg.configs.models.driu_bn_ssl>`
- 4
- 4
- 2
- 1
- 1
- * - :py:mod:`m2unet-ssl <bob.ip.binseg.configs.models.m2unetssl>`
+ * - :py:mod:`m2unet-ssl <bob.ip.binseg.configs.models.m2unet_ssl>`
- 4
- 4
- 2
diff --git a/setup.py b/setup.py
index 8eb42600..b8af9724 100644
--- a/setup.py
+++ b/setup.py
@@ -43,13 +43,13 @@ setup(
# models
"driu = bob.ip.binseg.configs.models.driu",
- "driu-bn = bob.ip.binseg.configs.models.driubn",
- "driu-ssl = bob.ip.binseg.configs.models.driussl",
- "driu-bn-ssl = bob.ip.binseg.configs.models.driubnssl",
- "driu-od = bob.ip.binseg.configs.models.driuod",
+ "driu-bn = bob.ip.binseg.configs.models.driu_bn",
+ "driu-ssl = bob.ip.binseg.configs.models.driu_ssl",
+ "driu-bn-ssl = bob.ip.binseg.configs.models.driu_bn_ssl",
+ "driu-od = bob.ip.binseg.configs.models.driu_od",
"hed = bob.ip.binseg.configs.models.hed",
"m2unet = bob.ip.binseg.configs.models.m2unet",
- "m2unet-ssl = bob.ip.binseg.configs.models.m2unetssl",
+ "m2unet-ssl = bob.ip.binseg.configs.models.m2unet_ssl",
"unet = bob.ip.binseg.configs.models.unet",
"resunet = bob.ip.binseg.configs.models.resunet",
@@ -57,60 +57,60 @@ setup(
"csv-dataset-example = bob.ip.binseg.configs.datasets.csv",
"folder-dataset-example = bob.ip.binseg.configs.datasets.folder",
- # drive dataset (numbers represent target resolution)
+ # drive dataset
"drive = bob.ip.binseg.configs.datasets.drive",
- "covd-drive = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544",
- "covd-drive-ssl = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive",
- "drive-test = bob.ip.binseg.configs.datasets.drivetest",
+ "covd-drive = bob.ip.binseg.configs.datasets.covd_drive",
+ "covd-drive-ssl = bob.ip.binseg.configs.datasets.covd_drive_ssl",
+ "drive-test = bob.ip.binseg.configs.datasets.drive_test",
- # stare dataset (numbers represent target resolution)
+ # stare dataset
"stare = bob.ip.binseg.configs.datasets.stare",
- "covd-stare = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608",
- "covd-stare-ssl = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare",
- "stare-test = bob.ip.binseg.configs.datasets.staretest",
+ "covd-stare = bob.ip.binseg.configs.datasets.covd_stare",
+ "covd-stare-ssl = bob.ip.binseg.configs.datasets.covd_stare_ssl",
+ "stare-test = bob.ip.binseg.configs.datasets.stare_test",
- # iostar vessel (numbers represent target resolution)
- "iostar-vessel = bob.ip.binseg.configs.datasets.iostarvessel",
- "covd-iostar-vessel = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024",
- "covd-iostar-vessel-ssl = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar",
- "iostar-vessel-test = bob.ip.binseg.configs.datasets.iostarvesseltest",
+ # iostar vessel
+ "iostar-vessel = bob.ip.binseg.configs.datasets.iostar_vessel",
+ "covd-iostar-vessel = bob.ip.binseg.configs.datasets.covd_iostar_vessel",
+ "covd-iostar-vessel-ssl = bob.ip.binseg.configs.datasets.covd_iostar_vessel_ssl",
+ "iostar-vessel-test = bob.ip.binseg.configs.datasets.iostar_vessel_test",
# iostar optic disc
- "iostarod = bob.ip.binseg.configs.datasets.iostarod",
- "iostarodtest = bob.ip.binseg.configs.datasets.iostarodtest",
+ "iostar-optic-disc = bob.ip.binseg.configs.datasets.iostar_od",
+ "iostar-optic-disc-test = bob.ip.binseg.configs.datasets.iostar_od_test",
# hrf (numbers represent target resolution)
- "hrf = bob.ip.binseg.configs.datasets.hrf1168",
- "covd-hrf = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168",
- "covd-hrf-ssl = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf",
- "hrftest-test = bob.ip.binseg.configs.datasets.hrftest",
+ "hrf = bob.ip.binseg.configs.datasets.hrf_1168",
+ "covd-hrf = bob.ip.binseg.configs.datasets.covd_hrf",
+ "covd-hrf-ssl = bob.ip.binseg.configs.datasets.covd_hrf_ssl",
+ "hrftest-test = bob.ip.binseg.configs.datasets.hrf_1168_test",
- # chase-db1 (numbers represent target resolution)
+ # chase-db1
"chasedb1 = bob.ip.binseg.configs.datasets.chasedb1",
- "covd-chasedb1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960",
- "covd-chasedb1-ssl = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase",
- "chasedb1-test = bob.ip.binseg.configs.datasets.chasedb1test",
+ "covd-chasedb1 = bob.ip.binseg.configs.datasets.covd_chasedb1",
+ "covd-chasedb1-ssl = bob.ip.binseg.configs.datasets.covd_chasedb1_ssl",
+ "chasedb1-test = bob.ip.binseg.configs.datasets.chasedb1_test",
# drionsdb
"drionsdb = bob.ip.binseg.configs.datasets.drionsdb",
- "drionsdb-test = bob.ip.binseg.configs.datasets.drionsdbtest",
+ "drionsdb-test = bob.ip.binseg.configs.datasets.drionsdb_test",
# drishtigs
- "drishtigs1-od = bob.ip.binseg.configs.datasets.dristhigs1od",
- "drishtigs1-od-test = bob.ip.binseg.configs.datasets.dristhigs1odtest",
- "drishtigs1-cup = bob.ip.binseg.configs.datasets.dristhigs1cup",
- "drishtigs1-cup-test = bob.ip.binseg.configs.datasets.dristhigs1cuptest",
+ "drishtigs1-od = bob.ip.binseg.configs.datasets.dristhigs1_od",
+ "drishtigs1-od-test = bob.ip.binseg.configs.datasets.dristhigs1_od_test",
+ "drishtigs1-cup = bob.ip.binseg.configs.datasets.dristhigs1_cup",
+ "drishtigs1-cup-test = bob.ip.binseg.configs.datasets.dristhigs1_cup_test",
# refuge
- "refuge-cup = bob.ip.binseg.configs.datasets.refugecup",
- "refuge-cup-test = bob.ip.binseg.configs.datasets.refugecuptest",
- "refuge-od = bob.ip.binseg.configs.datasets.refugeod",
- "refuge-od-test = bob.ip.binseg.configs.datasets.refugeodtest",
+ "refuge-cup = bob.ip.binseg.configs.datasets.refuge_cup",
+ "refuge-cup-test = bob.ip.binseg.configs.datasets.refuge_cup_test",
+ "refuge-od = bob.ip.binseg.configs.datasets.refuge_od",
+ "refuge-od-test = bob.ip.binseg.configs.datasets.refuge_od_test",
# rim one r3
- "rimoner3-cup = bob.ip.binseg.configs.datasets.rimoner3cup",
- "rimoner3-cup-test = bob.ip.binseg.configs.datasets.rimoner3cuptest",
- "rimoner3-od = bob.ip.binseg.configs.datasets.rimoner3od",
- "rimoner3-od-test = bob.ip.binseg.configs.datasets.rimoner3odtest",
+ "rimoner3-cup = bob.ip.binseg.configs.datasets.rimoner3_cup",
+ "rimoner3-cup-test = bob.ip.binseg.configs.datasets.rimoner3_cup_test",
+ "rimoner3-od = bob.ip.binseg.configs.datasets.rimoner3_od",
+ "rimoner3-od-test = bob.ip.binseg.configs.datasets.rimoner3_od_test",
],
},
# check classifiers, add and remove as you see fit
--
GitLab