diff --git a/bob/ip/binseg/configs/datasets/allvessel544.py b/bob/ip/binseg/configs/datasets/allvessel544.py
deleted file mode 100644
index 9044cebccd11a8ffd1873fa58d19123d7baefe43..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/allvessel544.py
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from bob.db.drive import Database as DRIVE
-from bob.db.stare import Database as STARE
-from bob.db.chasedb1 import Database as CHASEDB1
-from bob.db.iostar import Database as IOSTAR
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-# Target size: 544x544 (DRIVE)
-
-defaulttransforms = [RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()]
-
-
-# DRIVE
-transforms_drive = Compose([
- CenterCrop((544,544))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_drive = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-torch_drive = BinSegDataset(bobdb_drive, split='train', transform=transforms_drive)
-
-
-# CHASE_DB1
-transforms_chase = Compose([
- Resize(544)
- ,Crop(0,12,544,544)
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_chase = CHASEDB1(protocol = 'default')
-
-# PyTorch dataset
-torch_chase = BinSegDataset(bobdb_chase, split='train', transform=transforms_chase)
-
-
-# IOSTAR VESSEL
-transforms_iostar = Compose([
- Resize(544)
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_iostar = IOSTAR(protocol='default_vessel')
-
-# PyTorch dataset
-torch_iostar = BinSegDataset(bobdb_iostar, split='train', transform=transforms_iostar)
-
-# STARE
-transforms = Compose([
- Resize(471)
- ,Pad((0,37,0,36))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_stare = STARE(protocol = 'default')
-
-# PyTorch dataset
-torch_stare = BinSegDataset(bobdb_stare, split='train', transform=transforms)
-
-
-# HRF
-transforms_hrf = Compose([
- Resize((363))
- ,Pad((0,90,0,91))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_hrf = HRF(protocol = 'default')
-
-# PyTorch dataset
-torch_hrf = BinSegDataset(bobdb_hrf, split='train', transform=transforms_hrf)
-
-
-
-# Merge
-dataset = torch.utils.data.ConcatDataset([torch_drive,torch_stare, torch_chase, torch_iostar, torch_hrf])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/allvessel544test.py b/bob/ip/binseg/configs/datasets/allvessel544test.py
deleted file mode 100644
index 55994e9e045311db031290d63c45f6326eb4436a..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/allvessel544test.py
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from bob.db.drive import Database as DRIVE
-from bob.db.stare import Database as STARE
-from bob.db.chasedb1 import Database as CHASEDB1
-from bob.db.iostar import Database as IOSTAR
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-# Target size: 544x544 (DRIVE)
-
-defaulttransforms = [ToTensor()]
-
-
-# DRIVE
-transforms_drive = Compose([
- CenterCrop((544,544))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_drive = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-torch_drive = BinSegDataset(bobdb_drive, split='test', transform=transforms_drive)
-
-
-# CHASE_DB1
-transforms_chase = Compose([
- Resize(544)
- ,Crop(0,12,544,544)
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_chase = CHASEDB1(protocol = 'default')
-
-# PyTorch dataset
-torch_chase = BinSegDataset(bobdb_chase, split='test', transform=transforms_chase)
-
-
-# IOSTAR VESSEL
-transforms_iostar = Compose([
- Resize(544)
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_iostar = IOSTAR(protocol='default_vessel')
-
-# PyTorch dataset
-torch_iostar = BinSegDataset(bobdb_iostar, split='test', transform=transforms_iostar)
-
-# STARE
-transforms = Compose([
- Resize(471)
- ,Pad((0,37,0,36))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_stare = STARE(protocol = 'default')
-
-# PyTorch dataset
-torch_stare = BinSegDataset(bobdb_stare, split='test', transform=transforms)
-
-
-# HRF
-transforms_hrf = Compose([
- Resize((363))
- ,Pad((0,90,0,91))
- ,*defaulttransforms
- ])
-
-# bob.db.dataset init
-bobdb_hrf = HRF(protocol = 'default')
-
-# PyTorch dataset
-torch_hrf = BinSegDataset(bobdb_hrf, split='test', transform=transforms_hrf)
-
-
-
-# Merge
-dataset = torch.utils.data.ConcatDataset([torch_drive,torch_stare, torch_chase, torch_iostar, torch_hrf])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/chasedb1544.py b/bob/ip/binseg/configs/datasets/chasedb1544.py
index 9d94cd3ca6e9e1504aaba5bbb78422f547e102c2..9632d53996d343deecd0e021fb2140153df9edc0 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1544.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1544.py
@@ -8,11 +8,11 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- RandomRotation()
- ,Resize(544)
+ Resize(544)
,Crop(0,12,544,544)
,RandomHFlip()
,RandomVFlip()
+ ,RandomRotation()
,ColorJitter()
,ToTensor()
])
diff --git a/bob/ip/binseg/configs/datasets/chasedb1544test.py b/bob/ip/binseg/configs/datasets/chasedb1608.py
similarity index 50%
rename from bob/ip/binseg/configs/datasets/chasedb1544test.py
rename to bob/ip/binseg/configs/datasets/chasedb1608.py
index aa5d00a55e68bf8d025ba338cbeb59289ce3c70a..9a475cae5d7fb5be49a28ae6e479dd3fe41760ed 100644
--- a/bob/ip/binseg/configs/datasets/chasedb1544test.py
+++ b/bob/ip/binseg/configs/datasets/chasedb1608.py
@@ -7,9 +7,13 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
-transforms = Compose([
- Resize(544)
- ,Crop(0,12,544,544)
+transforms = Compose([
+ RandomRotation()
+ ,CenterCrop((829,960))
+ ,Resize(608)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
,ToTensor()
])
@@ -17,4 +21,4 @@ transforms = Compose([
bobdb = CHASEDB1(protocol = 'default')
# PyTorch dataset
-dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drive1024ssliostar.py b/bob/ip/binseg/configs/datasets/drive1024ssliostar.py
deleted file mode 100644
index 0158c4a9c4595c9baf558afa6dd97d5ee1ca64b6..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/drive1024ssliostar.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.db.iostar import Database as IOSTAR
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-#### Config ####
-
-#### Unlabeled IOSTAR TRAIN ####
-unlabeled_transforms = Compose([
- RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-sslbobdb = IOSTAR(protocol = 'default_vessel')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(sslbobdb, split='train', transform=unlabeled_transforms)
-
-
-#### Labeled ####
-labeled_transforms = Compose([
- CenterCrop((540,540))
- ,Resize(1024)
- ,RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-dataset = SSLBinSegDataset(bobdb, unlabeled_dataset, split='train', transform=labeled_transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive1168sslhrf.py b/bob/ip/binseg/configs/datasets/drive1168sslhrf.py
deleted file mode 100644
index 75f742d4a07882d979cd9a09fe498dbeaee04665..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/drive1168sslhrf.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-#### Config ####
-
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose([
- Crop(0,108,2336,3296)
- ,Resize(1168)
- ,RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-hrfbobdb = HRF(protocol = 'default')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
-
-
-#### Labeled ####
-labeled_transforms = Compose([
- Crop(75,10,416,544)
- ,Pad((21,0,22,0))
- ,Resize(1168)
- ,RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-labeled_dataset = BinSegDataset(bobdb, split='train', transform=labeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drive2336sslhrf.py b/bob/ip/binseg/configs/datasets/drive2336sslhrf.py
deleted file mode 100644
index 9b6102ffc533f0088ffba7d228a008a081922259..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/drive2336sslhrf.py
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-#### Config ####
-
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose([
- Crop(0,108,2336,3296)
- ,RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-hrfbobdb = HRF(protocol = 'default')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
-
-
-#### Labeled ####
-labeled_transforms = Compose([
- Crop(75,10,416,544)
- ,Pad((21,0,22,0))
- ,Resize(2336)
- ,RandomHFlip()
- ,RandomVFlip()
- ,RandomRotation()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-labeled_dataset = BinSegDataset(bobdb, split='train', transform=labeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drive2336test.py b/bob/ip/binseg/configs/datasets/drive2336test.py
deleted file mode 100644
index 9ce3b6491c47379abe09886bd9d904afde1ccc00..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/drive2336test.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-
-#### Config ####
-
-transforms = Compose([
- Crop(75,10,416,544)
- ,Pad((21,0,22,0))
- ,Resize(2336)
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py
new file mode 100644
index 0000000000000000000000000000000000000000..5ab57b8ad4e34d700e4667138b6111f19b4a488a
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608.py
@@ -0,0 +1,10 @@
+from bob.ip.binseg.configs.datasets.drive608 import dataset as drive
+from bob.ip.binseg.configs.datasets.chasedb1608 import dataset as chase
+from bob.ip.binseg.configs.datasets.iostarvessel608 import dataset as iostar
+from bob.ip.binseg.configs.datasets.hrf608 import dataset as hrf
+import torch
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,chase,iostar,hrf])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
new file mode 100644
index 0000000000000000000000000000000000000000..928452f4209d4526e66028457a3ababcd04fda8b
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
@@ -0,0 +1,34 @@
+from bob.ip.binseg.configs.datasets.drive608 import dataset as drive
+from bob.ip.binseg.configs.datasets.chasedb1608 import dataset as chase
+from bob.ip.binseg.configs.datasets.iostarvessel608 import dataset as iostar
+from bob.ip.binseg.configs.datasets.hrf608 import dataset as hrf
+from bob.db.stare import Database as STARE
+from bob.ip.binseg.data.transforms import *
+import torch
+from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
+
+
+#### Config ####
+
+# PyTorch dataset
+labeled_dataset = torch.utils.data.ConcatDataset([drive,chase,iostar,hrf])
+
+#### Unlabeled STARE TRAIN ####
+unlabeled_transforms = Compose([
+ Pad((2,1,2,2))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+starebobdb = STARE(protocol = 'default')
+
+# PyTorch dataset
+unlabeled_dataset = UnLabeledBinSegDataset(starebobdb, split='train', transform=unlabeled_transforms)
+
+# SSL Dataset
+
+dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1hrfl1024_all.py b/bob/ip/binseg/configs/datasets/drivestarechasedb1hrfl1024_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..5d2b345669dbc334e061780a349af69ce4fe3fe3
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb1hrfl1024_all.py
@@ -0,0 +1,14 @@
+from bob.ip.binseg.configs.datasets.drive1024all import dataset as drive
+from bob.ip.binseg.configs.datasets.stare1024all import dataset as stare
+from bob.ip.binseg.configs.datasets.hrf1024all import dataset as hrf
+from bob.ip.binseg.configs.datasets.chasedb11024all import dataset as chasedb
+from bob.db.iostar import Database as IOSTAR
+from bob.ip.binseg.data.transforms import *
+import torch
+
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,chasedb])
+
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168_all.py b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..dcf35d87f4bbe9048b82b611e2014e80cbe01d66
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168_all.py
@@ -0,0 +1,13 @@
+from bob.ip.binseg.configs.datasets.drive1168all import dataset as drive
+from bob.ip.binseg.configs.datasets.stare1168all import dataset as stare
+from bob.ip.binseg.configs.datasets.chasedb11168all import dataset as chasedb
+from bob.ip.binseg.configs.datasets.iostarvessel1168all import dataset as iostar
+from bob.db.hrf import Database as HRF
+from bob.ip.binseg.data.transforms import *
+import torch
+
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,iostar,chasedb])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py
new file mode 100644
index 0000000000000000000000000000000000000000..9343cf22c62a0cf9ad02d767b24ca576b00fd4d1
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960.py
@@ -0,0 +1,10 @@
+from bob.ip.binseg.configs.datasets.drive960 import dataset as drive
+from bob.ip.binseg.configs.datasets.stare960 import dataset as stare
+from bob.ip.binseg.configs.datasets.hrf960 import dataset as hrf
+from bob.ip.binseg.configs.datasets.iostarvessel960 import dataset as iostar
+import torch
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,iostar])
diff --git a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960_all.py b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..cedbea744f1c0843a8d010c99d2a5f7c9692928c
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960_all.py
@@ -0,0 +1,14 @@
+from bob.ip.binseg.configs.datasets.drive960all import dataset as drive
+from bob.ip.binseg.configs.datasets.stare960all import dataset as stare
+from bob.ip.binseg.configs.datasets.hrf960all import dataset as hrf
+from bob.ip.binseg.configs.datasets.iostarvessel960all import dataset as iostar
+from bob.db.chasedb1 import Database as CHASE
+from bob.db.hrf import Database as HRF
+from bob.ip.binseg.data.transforms import *
+import torch
+
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,iostar])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/hrf544.py b/bob/ip/binseg/configs/datasets/hrf544.py
new file mode 100644
index 0000000000000000000000000000000000000000..0e2cc05152aa20e4c75ffcb464cd8fd90f89e7bd
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf544.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.hrf import Database as HRF
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ Resize((363))
+ ,Pad((0,90,0,91))
+ ,RandomRotation()
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = HRF(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf608.py b/bob/ip/binseg/configs/datasets/hrf608.py
new file mode 100644
index 0000000000000000000000000000000000000000..b26e772a0793d043af6e59f18caab5943805d929
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf608.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.hrf import Database as HRF
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ Pad((0,345,0,345))
+ ,Resize(608)
+ ,RandomRotation()
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = HRF(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
diff --git a/bob/ip/binseg/configs/datasets/drive2336.py b/bob/ip/binseg/configs/datasets/iostarvessel544.py
similarity index 71%
rename from bob/ip/binseg/configs/datasets/drive2336.py
rename to bob/ip/binseg/configs/datasets/iostarvessel544.py
index 30ec9af8400daa56bece1318ca8a07a56254a8c4..aa03abe2feb64a084fb76e6f60c69afc7499961f 100644
--- a/bob/ip/binseg/configs/datasets/drive2336.py
+++ b/bob/ip/binseg/configs/datasets/iostarvessel544.py
@@ -1,16 +1,14 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-from bob.db.drive import Database as DRIVE
+from bob.db.iostar import Database as IOSTAR
from bob.ip.binseg.data.transforms import *
from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- Crop(75,10,416,544)
- ,Pad((21,0,22,0))
- ,Resize(2336)
+ Resize(544)
,RandomHFlip()
,RandomVFlip()
,RandomRotation()
@@ -19,7 +17,7 @@ transforms = Compose([
])
# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
+bobdb = IOSTAR(protocol='default_vessel')
# PyTorch dataset
dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel608.py b/bob/ip/binseg/configs/datasets/iostarvessel608.py
new file mode 100644
index 0000000000000000000000000000000000000000..7fce4507cd090555a2e0bac7f575dfd9d9f85c3d
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvessel608.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.iostar import Database as IOSTAR
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ Pad((81,0,81,0))
+ ,Resize(608)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = IOSTAR(protocol='default_vessel')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare1168sslhrf.py b/bob/ip/binseg/configs/datasets/stare1168sslhrf.py
deleted file mode 100644
index a7e3e201464c8262dc946e4ba114635299223295..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/stare1168sslhrf.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.stare import Database as STARE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-#### Config ####
-
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose([
- RandomRotation()
- ,Crop(0,108,2336,3296)
- ,Resize(1168)
- ,RandomHFlip()
- ,RandomVFlip()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-hrfbobdb = HRF(protocol = 'default')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
-
-
-#### Labeled ####
-labeled_transforms = Compose([
- RandomRotation()
- ,Crop(50,0,500,705)
- ,Resize(1168)
- ,Pad((1,0,1,0))
- ,RandomHFlip()
- ,RandomVFlip()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
-labeled_dataset = BinSegDataset(bobdb, split='train', transform=labeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare1168sslhrfrefuge.py b/bob/ip/binseg/configs/datasets/stare1168sslhrfrefuge.py
deleted file mode 100644
index a116997a8e63a3ac38e9b4fb2b43d0115fc56251..0000000000000000000000000000000000000000
--- a/bob/ip/binseg/configs/datasets/stare1168sslhrfrefuge.py
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.stare import Database as STARE
-from bob.db.refuge import Database as REFUGE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-import torch
-#### Config ####
-
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose([
- RandomRotation()
- ,Crop(0,108,2336,3296)
- ,Resize(1168)
- ,RandomHFlip()
- ,RandomVFlip()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-#### Unlabeled REFUGE Test ####
-
-unlabeled_transforms_refuge = Compose([
- RandomRotation()
- ,Crop(220,11,1150,1623)
- ,Resize(1168)
- ,RandomHFlip()
- ,RandomVFlip()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-## bob.db.dataset init
-# hrf
-hrfbobdb = HRF(protocol = 'default')
-# refuge
-refugebobdb = REFUGE()
-
-
-# PyTorch dataset
-unlabeled_dataset_1 = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
-
-unlabeled_dataset_2 = UnLabeledBinSegDataset(refugebobdb, split='test', transform=unlabeled_transforms_refuge)
-
-# Compose
-unlabeled_dataset = torch.utils.data.ConcatDataset([unlabeled_dataset_1,unlabeled_dataset_2])
-
-
-#### Labeled ####
-labeled_transforms = Compose([
- RandomRotation()
- ,Crop(50,0,500,705)
- ,Resize(1168)
- ,Pad((1,0,1,0))
- ,RandomHFlip()
- ,RandomVFlip()
- ,ColorJitter()
- ,ToTensor()
- ])
-
-# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
-labeled_dataset = BinSegDataset(bobdb, split='train', transform=labeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare544.py b/bob/ip/binseg/configs/datasets/stare544.py
index 08c2ad4fb8f4610d6213cb3357d0e4bd491a4f3f..f03fcefbe6fef80ef1e6a7ec97d2b6c1df221024 100644
--- a/bob/ip/binseg/configs/datasets/stare544.py
+++ b/bob/ip/binseg/configs/datasets/stare544.py
@@ -14,7 +14,6 @@ transforms = Compose([ RandomRotation()
,RandomVFlip()
,ColorJitter()
,ToTensor()
- ,ToTensor()
])
# bob.db.dataset init
diff --git a/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py b/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py
new file mode 100644
index 0000000000000000000000000000000000000000..72349b3bd6370c0b996edf90e96403df54ec27af
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544.py
@@ -0,0 +1,10 @@
+from bob.ip.binseg.configs.datasets.stare544 import dataset as stare
+from bob.ip.binseg.configs.datasets.chasedb1544 import dataset as chase
+from bob.ip.binseg.configs.datasets.iostarvessel544 import dataset as iostar
+from bob.ip.binseg.configs.datasets.hrf544 import dataset as hrf
+import torch
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([stare,chase,hrf,iostar])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py b/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py
new file mode 100644
index 0000000000000000000000000000000000000000..3a5e3008f73cea8d1163030783d70736fad6ef9f
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/starechasedb1iostarhrf544ssldrive.py
@@ -0,0 +1,34 @@
+from bob.ip.binseg.configs.datasets.stare544 import dataset as stare
+from bob.ip.binseg.configs.datasets.chasedb1544 import dataset as chase
+from bob.ip.binseg.configs.datasets.iostarvessel544 import dataset as iostar
+from bob.ip.binseg.configs.datasets.hrf544 import dataset as hrf
+from bob.db.drive import Database as DRIVE
+from bob.ip.binseg.data.transforms import *
+import torch
+from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
+
+
+#### Config ####
+
+# PyTorch dataset
+labeled_dataset = torch.utils.data.ConcatDataset([stare,chase,iostar,hrf])
+
+#### Unlabeled STARE TRAIN ####
+unlabeled_transforms = Compose([
+ CenterCrop((544,544))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+drivebobdb = DRIVE(protocol = 'default')
+
+# PyTorch dataset
+unlabeled_dataset = UnLabeledBinSegDataset(drivebobdb, split='train', transform=unlabeled_transforms)
+
+# SSL Dataset
+
+dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/models/m2unetssl0703.py b/bob/ip/binseg/configs/models/driussl.py
similarity index 80%
rename from bob/ip/binseg/configs/models/m2unetssl0703.py
rename to bob/ip/binseg/configs/models/driussl.py
index d5a160821deaea8436d533938c69b9f535fc763d..39afd4a03f956b24aeeb078c297fb026cdc369b5 100644
--- a/bob/ip/binseg/configs/models/m2unetssl0703.py
+++ b/bob/ip/binseg/configs/models/driussl.py
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
from torch.optim.lr_scheduler import MultiStepLR
-from bob.ip.binseg.modeling.m2u import build_m2unet
+from bob.ip.binseg.modeling.driu import build_driu
import torch.optim as optim
from torch.nn import BCEWithLogitsLoss
from bob.ip.binseg.utils.model_zoo import modelurls
@@ -23,17 +23,17 @@ scheduler_milestones = [900]
scheduler_gamma = 0.1
# model
-model = build_m2unet()
+model = build_driu()
# pretrained backbone
-pretrained_backbone = modelurls['mobilenetv2']
+pretrained_backbone = modelurls['vgg16']
# optimizer
optimizer = AdaBound(model.parameters(), lr=lr, betas=betas, final_lr=final_lr, gamma=gamma,
eps=eps, weight_decay=weight_decay, amsbound=amsbound)
-
+
# criterion
-criterion = MixJacLoss(lambda_u=0.3, jacalpha=0.7, unlabeledjacalpha=0.3)
+criterion = MixJacLoss(lambda_u=0.05, jacalpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/m2unetssl.py b/bob/ip/binseg/configs/models/m2unetssl.py
index 8280e52f8d94de8b43cc1f4da6e8afb0b4f42878..3497cea26b03c44b682cfd3beb167afce3015e43 100644
--- a/bob/ip/binseg/configs/models/m2unetssl.py
+++ b/bob/ip/binseg/configs/models/m2unetssl.py
@@ -33,7 +33,7 @@ optimizer = AdaBound(model.parameters(), lr=lr, betas=betas, final_lr=final_lr,
eps=eps, weight_decay=weight_decay, amsbound=amsbound)
# criterion
-criterion = MixJacLoss(lambda_u=0.05, jacalpha=0.7, unlabeledjacalpha=0.3)
+criterion = MixJacLoss(lambda_u=0.05, jacalpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/modeling/losses.py b/bob/ip/binseg/modeling/losses.py
index bb6578af297893252e06f7cfdafe4d950da3790a..7bcde8503fdb2334fea0a2f2ce9cc1b0c8253343 100644
--- a/bob/ip/binseg/modeling/losses.py
+++ b/bob/ip/binseg/modeling/losses.py
@@ -171,7 +171,7 @@ class MixJacLoss(_Loss):
lambda_u : int
determines the weighting of SoftJaccard and BCE.
"""
- def __init__(self, lambda_u=100, jacalpha=0.7, unlabeledjacalpha=0.3, size_average=None, reduce=None, reduction='mean', pos_weight=None):
+ def __init__(self, lambda_u=100, jacalpha=0.7, size_average=None, reduce=None, reduction='mean', pos_weight=None):
super(MixJacLoss, self).__init__(size_average, reduce, reduction)
self.lambda_u = lambda_u
self.labeled_loss = SoftJaccardBCELogitsLoss(alpha=jacalpha)
diff --git a/doc/benchmarkresults.rst b/doc/benchmarkresults.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fb30961cb203ea3f2fe1f83f96c34d99e26d2403
--- /dev/null
+++ b/doc/benchmarkresults.rst
@@ -0,0 +1,25 @@
+.. -*- coding: utf-8 -*-
+.. _bob.ip.binseg.benchmarkresults:
+
+
+==================
+Benchmark Results
+==================
+
+Dice Scores
+===========
+
+* Benchmark results for models: DRIU, HED, M2UNet and U-Net.
+* Train-Test split as indicated in :ref:`bob.ip.binseg.datasets`
+
++--------+----------+--------+---------+--------+--------+
+| | CHASEDB1 | DRIVE | HRF1168 | IOSTAR | STARE |
++--------+----------+--------+---------+--------+--------+
+| DRIU | 0.8114 | 0.8226 | 0.7865 | 0.8273 | 0.8286 |
++--------+----------+--------+---------+--------+--------+
+| HED | 0.8111 | 0.8192 | 0.7868 | 0.8275 | 0.8250 |
++--------+----------+--------+---------+--------+--------+
+| M2UNet | 0.8035 | 0.8051 | 0.7838 | 0.8194 | 0.8174 |
++--------+----------+--------+---------+--------+--------+
+| UNet | 0.8136 | 0.8237 | 0.7941 | 0.8203 | 0.8306 |
++--------+----------+--------+---------+--------+--------+
diff --git a/doc/datasets.rst b/doc/datasets.rst
index 67939144b975ed25b1b01d996b656d9aa4c2fe6e..0704149b9ca841371fa59f7b3d5c9b48a0a4ea26 100644
--- a/doc/datasets.rst
+++ b/doc/datasets.rst
@@ -1,31 +1,33 @@
.. -*- coding: utf-8 -*-
.. _bob.ip.binseg.datasets:
-
==================
-Supported Datasets
+Supported Datasets
==================
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| # | Name | H x W | # imgs | Train | Test | Mask | Vessel | OD | Cup | Ethnicity |
-+===+=============+====================+========+=======+======+======+========+====+=====+===========================+
-| 1 | DRIVE | 584 x 565 | 40 | 20 | 20 | x | x | | | Dutch (adult) |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 2 | STARE | 605 x 700 | 20 | 10 | 10 | | x | | | White American (adult) |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 3 | CHASE_DB1 | 960 x 999 | 28 | 8 | 20 | | x | | | British (child) |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 4 | HRF | 2336 x 3504 | 45 | 15 | 30 | x | x | | | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 5 | IOSTAR | 1024 x 1024 | 30 | 20 | 10 | x | x | x | | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 6 | DRIONS-DB | 400 x 600 | 110 | 60 | 50 | | | x | | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 7 | RIM-ONE r3 | 1424 x 1072 | 159 | 99 | 60 | | | x | x | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 8 | Drishti-GS1 | varying | 101 | 50 | 51 | | | x | x | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 9 | REFUGE train| 2056 x 2124 | 400 | 400 | | | | x | x | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
-| 9 | REFUGE val | 1634 x 1634 | 400 | | 400 | | | x | x | |
-+---+-------------+--------------------+--------+-------+------+------+--------+----+-----+---------------------------+
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| # | Name | H x W | # imgs | Train | Test | Mask | Vessel | OD | Cup | Train-Test split reference |
++=====+===============+=============+========+=======+======+======+========+=====+=====+============================+
+| 1 | Drive_ | 584 x 565 | 40 | 20 | 20 | x | x | | | `Staal et al. (2004)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 2 | STARE_ | 605 x 700 | 20 | 10 | 10 | | x | | | `Maninis et al. (2016)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 3 | CHASEDB1_ | 960 x 999 | 28 | 8 | 20 | | x | | | `Fraz et al. (2012)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 4 | HRF_ | 2336 x 3504 | 45 | 15 | 30 | x | x | | | `Orlando et al. (2016)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 5 | IOSTAR_ | 1024 x 1024 | 30 | 20 | 10 | x | x | x | | `Meyer et al. (2017)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 6 | DRIONS-DB_ | 400 x 600 | 110 | 60 | 50 | | | x | | `Maninis et al. (2016)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 7 | RIM-ONEr3_ | 1424 x 1072 | 159 | 99 | 60 | | | x | x | `Maninis et al. (2016)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 8 | Drishti-GS1_ | varying | 101 | 50 | 51 | | | x | x | `Sivaswamy et al. (2014)`_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 9 | REFUGE_ train | 2056 x 2124 | 400 | 400 | | | | x | x | REFUGE_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+| 9 | REFUGE_ val | 1634 x 1634 | 400 | | 400 | | | x | x | REFUGE_ |
++-----+---------------+-------------+--------+-------+------+------+--------+-----+-----+----------------------------+
+
+
+.. include:: links.rst
\ No newline at end of file
diff --git a/doc/index.rst b/doc/index.rst
index fe6cf753734f6167476572120efa5ad3283073f7..c19b48eaba56c1d134694231dded4a3c4fe34d04 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -15,6 +15,7 @@ Users Guide
:maxdepth: 2
datasets
+ benchmarkresults
api
references
diff --git a/doc/links.rst b/doc/links.rst
index d8a696c481b35c7360d2da0cf30ab2f392fada20..2398e1c87eeebc3a0e8aba0d27ee8b3a1231acfd 100644
--- a/doc/links.rst
+++ b/doc/links.rst
@@ -6,4 +6,48 @@
.. _bob: http://www.idiap.ch/software/bob
.. _installation: https://www.idiap.ch/software/bob/install
.. _mailing list: https://www.idiap.ch/software/bob/discuss
-.. _torchvision package: https://github.com/pytorch/vision
\ No newline at end of file
+.. _torchvision package: https://github.com/pytorch/vision
+
+.. DRIVE
+
+.. _drive: https://doi.org/10.1109/TMI.2004.825627
+.. _staal et al. (2004): https://doi.org/10.1109/TMI.2004.825627
+
+.. STARE
+
+.. _stare: https://doi.org/10.1109/42.845178
+.. _maninis et al. (2016): https://doi.org/10.1007/978-3-319-46723-8_17
+
+.. HRF
+
+.. _hrf: http://dx.doi.org/10.1155/2013/154860
+.. _orlando et al. (2016): https://doi.org/10.1109/TBME.2016.2535311
+
+.. IOSTAR
+
+.. _iostar: https://doi.org/10.1109/TMI.2016.2587062
+.. _meyer et al. (2017): https://doi.org/10.1007/978-3-319-59876-5_56
+
+.. CHASEDB1
+
+.. _chasedb1: https://doi.org/10.1109/TBME.2012.2205687
+.. _fraz et al. (2012): https://doi.org/10.1109/TBME.2012.2205687
+
+.. DRIONSDB
+
+.. _drions-db: http://dx.doi.org/10.1016/j.artmed.2008.04.005
+.. _maninis et al. (2016): https://doi.org/10.1007/978-3-319-46723-8_17
+
+.. RIM-ONE r3
+
+.. _rim-oner3: https://dspace5.zcu.cz/bitstream/11025/29670/1/Fumero.pdf
+.. _maninis et al. (2016): https://doi.org/10.1007/978-3-319-46723-8_17
+
+.. Drishti-GS1
+
+.. _drishti-gs1: https://doi.org/10.1109/ISBI.2014.6867807
+.. _sivaswamy et al. (2014): https://doi.org/10.1109/ISBI.2014.6867807
+
+.. REFUGE
+
+.. _refuge: http://ai.baidu.com/broad/download?dataset=gon
diff --git a/setup.py b/setup.py
index 8b82e9b20a4badd7c8af70a37dea541e41d9fb56..593a4d782a66fee45bd3f236d63340858aefacc9 100644
--- a/setup.py
+++ b/setup.py
@@ -58,6 +58,7 @@ setup(
#bob hed train configurations
'bob.ip.binseg.config': [
'DRIU = bob.ip.binseg.configs.models.driu',
+ 'DRIUSSL = bob.ip.binseg.configs.models.driussl'
'DRIUOD = bob.ip.binseg.configs.models.driuod',
'HED = bob.ip.binseg.configs.models.hed',
'M2UNet = bob.ip.binseg.configs.models.m2unet',