From 79b59ab84311edf0bf8628b81b39757aa929b9fc Mon Sep 17 00:00:00 2001
From: Tim Laibacher <tim.laibacher@idiap.ch>
Date: Wed, 19 Jun 2019 09:56:20 +0200
Subject: [PATCH] Add more ds configs
---
.../binseg/configs/datasets/chasedb11024.py | 24 +++++++
.../binseg/configs/datasets/chasedb11168.py | 24 +++++++
bob/ip/binseg/configs/datasets/chasedb1544.py | 24 +++++++
bob/ip/binseg/configs/datasets/drive1024.py | 4 +-
.../{drive608test.py => drive1168.py} | 12 ++--
.../configs/datasets/drive1168sslhrf.py | 47 +++++++++++++
.../configs/datasets/drive2336sslhrf.py | 10 +--
bob/ip/binseg/configs/datasets/drive608.py | 4 +-
bob/ip/binseg/configs/datasets/drive960.py | 4 +-
.../binseg/configs/datasets/drive960test.py | 20 ------
.../datasets/drivestarechasedb11168.py | 9 +++
.../datasets/drivestarechasedb1iostar1168.py | 10 +++
bob/ip/binseg/configs/datasets/hrf1168.py | 24 +++++++
.../{stare544test.py => hrf1168test.py} | 8 +--
.../configs/datasets/iostarvessel1168.py | 25 +++++++
.../configs/datasets/iostarvessel960.py | 23 +++++++
bob/ip/binseg/configs/datasets/stare1024.py | 25 +++++++
bob/ip/binseg/configs/datasets/stare1168.py | 25 +++++++
.../configs/datasets/stare1168sslhrf.py | 47 +++++++++++++
.../configs/datasets/stare1168sslhrfrefuge.py | 69 +++++++++++++++++++
bob/ip/binseg/configs/datasets/stare544.py | 24 +++++++
bob/ip/binseg/configs/datasets/stare960.py | 25 +++++++
bob/ip/binseg/configs/models/m2unetssl.py | 2 +-
bob/ip/binseg/configs/models/m2unetssl0703.py | 39 +++++++++++
bob/ip/binseg/engine/ssltrainer.py | 30 +++++++-
bob/ip/binseg/modeling/losses.py | 2 +-
bob/ip/binseg/script/binseg.py | 10 +++
27 files changed, 527 insertions(+), 43 deletions(-)
create mode 100644 bob/ip/binseg/configs/datasets/chasedb11024.py
create mode 100644 bob/ip/binseg/configs/datasets/chasedb11168.py
create mode 100644 bob/ip/binseg/configs/datasets/chasedb1544.py
rename bob/ip/binseg/configs/datasets/{drive608test.py => drive1168.py} (51%)
create mode 100644 bob/ip/binseg/configs/datasets/drive1168sslhrf.py
delete mode 100644 bob/ip/binseg/configs/datasets/drive960test.py
create mode 100644 bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
create mode 100644 bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
create mode 100644 bob/ip/binseg/configs/datasets/hrf1168.py
rename bob/ip/binseg/configs/datasets/{stare544test.py => hrf1168test.py} (69%)
create mode 100644 bob/ip/binseg/configs/datasets/iostarvessel1168.py
create mode 100644 bob/ip/binseg/configs/datasets/iostarvessel960.py
create mode 100644 bob/ip/binseg/configs/datasets/stare1024.py
create mode 100644 bob/ip/binseg/configs/datasets/stare1168.py
create mode 100644 bob/ip/binseg/configs/datasets/stare1168sslhrf.py
create mode 100644 bob/ip/binseg/configs/datasets/stare1168sslhrfrefuge.py
create mode 100644 bob/ip/binseg/configs/datasets/stare544.py
create mode 100644 bob/ip/binseg/configs/datasets/stare960.py
create mode 100644 bob/ip/binseg/configs/models/m2unetssl0703.py
diff --git a/bob/ip/binseg/configs/datasets/chasedb11024.py b/bob/ip/binseg/configs/datasets/chasedb11024.py
new file mode 100644
index 00000000..028f10fb
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb11024.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.chasedb1 import Database as CHASEDB1
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ RandomRotation()
+ ,Crop(0,18,960,960)
+ ,Resize(1024)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = CHASEDB1(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/chasedb11168.py b/bob/ip/binseg/configs/datasets/chasedb11168.py
new file mode 100644
index 00000000..d221ea48
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb11168.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.chasedb1 import Database as CHASEDB1
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ RandomRotation()
+ ,Crop(140,18,680,960)
+ ,Resize(1168)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = CHASEDB1(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/chasedb1544.py b/bob/ip/binseg/configs/datasets/chasedb1544.py
new file mode 100644
index 00000000..9d94cd3c
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb1544.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.chasedb1 import Database as CHASEDB1
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ RandomRotation()
+ ,Resize(544)
+ ,Crop(0,12,544,544)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = CHASEDB1(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drive1024.py b/bob/ip/binseg/configs/datasets/drive1024.py
index d5f08ff8..dae199f5 100644
--- a/bob/ip/binseg/configs/datasets/drive1024.py
+++ b/bob/ip/binseg/configs/datasets/drive1024.py
@@ -8,11 +8,11 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- CenterCrop((540,540))
+ RandomRotation()
+ ,CenterCrop((540,540))
,Resize(1024)
,RandomHFlip()
,RandomVFlip()
- ,RandomRotation()
,ColorJitter()
,ToTensor()
])
diff --git a/bob/ip/binseg/configs/datasets/drive608test.py b/bob/ip/binseg/configs/datasets/drive1168.py
similarity index 51%
rename from bob/ip/binseg/configs/datasets/drive608test.py
rename to bob/ip/binseg/configs/datasets/drive1168.py
index 7c597136..3f0f0537 100644
--- a/bob/ip/binseg/configs/datasets/drive608test.py
+++ b/bob/ip/binseg/configs/datasets/drive1168.py
@@ -8,9 +8,13 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- CenterCrop((470,544))
- ,Pad((10,9,10,8))
- ,Resize(608)
+ RandomRotation()
+ ,Crop(75,10,416,544)
+ ,Pad((21,0,22,0))
+ ,Resize(1168)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
,ToTensor()
])
@@ -18,4 +22,4 @@ transforms = Compose([
bobdb = DRIVE(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/drive1168sslhrf.py b/bob/ip/binseg/configs/datasets/drive1168sslhrf.py
new file mode 100644
index 00000000..75f742d4
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drive1168sslhrf.py
@@ -0,0 +1,47 @@
+#!/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
index 6ab1e77d..9b6102ff 100644
--- a/bob/ip/binseg/configs/datasets/drive2336sslhrf.py
+++ b/bob/ip/binseg/configs/datasets/drive2336sslhrf.py
@@ -19,10 +19,10 @@ unlabeled_transforms = Compose([
])
# bob.db.dataset init
-sslbobdb = HRF(protocol = 'default')
+hrfbobdb = HRF(protocol = 'default')
# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(sslbobdb, split='train', transform=unlabeled_transforms)
+unlabeled_dataset = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
#### Labeled ####
@@ -39,6 +39,8 @@ labeled_transforms = Compose([
# bob.db.dataset init
bobdb = DRIVE(protocol = 'default')
+labeled_dataset = BinSegDataset(bobdb, split='train', transform=labeled_transforms)
-# PyTorch dataset
-dataset = SSLBinSegDataset(bobdb, unlabeled_dataset, 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/drive608.py b/bob/ip/binseg/configs/datasets/drive608.py
index 64037a07..65bc5e65 100644
--- a/bob/ip/binseg/configs/datasets/drive608.py
+++ b/bob/ip/binseg/configs/datasets/drive608.py
@@ -8,12 +8,12 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- CenterCrop((470,544))
+ RandomRotation()
+ ,CenterCrop((470,544))
,Pad((10,9,10,8))
,Resize(608)
,RandomHFlip()
,RandomVFlip()
- ,RandomRotation()
,ColorJitter()
,ToTensor()
])
diff --git a/bob/ip/binseg/configs/datasets/drive960.py b/bob/ip/binseg/configs/datasets/drive960.py
index f0d06b78..ab3ac5a9 100644
--- a/bob/ip/binseg/configs/datasets/drive960.py
+++ b/bob/ip/binseg/configs/datasets/drive960.py
@@ -8,11 +8,11 @@ from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- CenterCrop((544,544))
+ RandomRotation()
+ ,CenterCrop((544,544))
,Resize(960)
,RandomHFlip()
,RandomVFlip()
- ,RandomRotation()
,ColorJitter()
,ToTensor()
])
diff --git a/bob/ip/binseg/configs/datasets/drive960test.py b/bob/ip/binseg/configs/datasets/drive960test.py
deleted file mode 100644
index 041fa775..00000000
--- a/bob/ip/binseg/configs/datasets/drive960test.py
+++ /dev/null
@@ -1,20 +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([
- CenterCrop((544,544))
- ,Resize(960)
- ,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/drivestarechasedb11168.py b/bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
new file mode 100644
index 00000000..0e36eff7
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
@@ -0,0 +1,9 @@
+from bob.ip.binseg.configs.datasets.drive1168 import dataset as drive
+from bob.ip.binseg.configs.datasets.stare1168 import dataset as stare
+from bob.ip.binseg.configs.datasets.chasedb11168 import dataset as chase
+import torch
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,chase])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
new file mode 100644
index 00000000..62e2972d
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
@@ -0,0 +1,10 @@
+from bob.ip.binseg.configs.datasets.drive1168 import dataset as drive
+from bob.ip.binseg.configs.datasets.stare1168 import dataset as stare
+from bob.ip.binseg.configs.datasets.chasedb11168 import dataset as chase
+from bob.ip.binseg.configs.datasets.iostarvessel1168 import dataset as iostar
+import torch
+
+#### Config ####
+
+# PyTorch dataset
+dataset = torch.utils.data.ConcatDataset([drive,stare,chase,iostar])
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/hrf1168.py b/bob/ip/binseg/configs/datasets/hrf1168.py
new file mode 100644
index 00000000..4d0c4d9e
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf1168.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([
+ Crop(0,108,2336,3296)
+ ,Resize((1168))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = HRF(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare544test.py b/bob/ip/binseg/configs/datasets/hrf1168test.py
similarity index 69%
rename from bob/ip/binseg/configs/datasets/stare544test.py
rename to bob/ip/binseg/configs/datasets/hrf1168test.py
index 09b26873..86014b75 100644
--- a/bob/ip/binseg/configs/datasets/stare544test.py
+++ b/bob/ip/binseg/configs/datasets/hrf1168test.py
@@ -1,20 +1,20 @@
#!/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
#### Config ####
transforms = Compose([
- Resize(471)
- ,Pad((0,37,0,36))
+ Crop(0,108,2336,3296)
+ ,Resize((1168))
,ToTensor()
])
# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
+bobdb = HRF(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/iostarvessel1168.py b/bob/ip/binseg/configs/datasets/iostarvessel1168.py
new file mode 100644
index 00000000..5da5ed1e
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvessel1168.py
@@ -0,0 +1,25 @@
+#!/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([
+ RandomRotation()
+ ,Crop(144,0,768,1024)
+ ,Pad((30,0,30,0))
+ ,Resize(1168)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,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/iostarvessel960.py b/bob/ip/binseg/configs/datasets/iostarvessel960.py
new file mode 100644
index 00000000..32feec85
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvessel960.py
@@ -0,0 +1,23 @@
+#!/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([
+ Resize(960)
+ ,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/stare1024.py b/bob/ip/binseg/configs/datasets/stare1024.py
new file mode 100644
index 00000000..8f6df507
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare1024.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.stare import Database as STARE
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ RandomRotation()
+ ,Pad((0,32,0,32))
+ ,Resize(1024)
+ ,CenterCrop(1024)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = STARE(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare1168.py b/bob/ip/binseg/configs/datasets/stare1168.py
new file mode 100644
index 00000000..77e934bf
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare1168.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.stare import Database as STARE
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+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')
+
+# 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
new file mode 100644
index 00000000..a7e3e201
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare1168sslhrf.py
@@ -0,0 +1,47 @@
+#!/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
new file mode 100644
index 00000000..a116997a
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare1168sslhrfrefuge.py
@@ -0,0 +1,69 @@
+#!/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
new file mode 100644
index 00000000..08c2ad4f
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare544.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.stare import Database as STARE
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([ RandomRotation()
+ ,Resize(471)
+ ,Pad((0,37,0,36))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = STARE(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare960.py b/bob/ip/binseg/configs/datasets/stare960.py
new file mode 100644
index 00000000..0d1ed788
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare960.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.stare import Database as STARE
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ RandomRotation()
+ ,Pad((0,32,0,32))
+ ,Resize(960)
+ ,CenterCrop(960)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = STARE(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/models/m2unetssl.py b/bob/ip/binseg/configs/models/m2unetssl.py
index ac8847ab..8280e52f 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=0.01, jacalpha=0.7, unlabeledjacalpha=0.7)
+criterion = MixJacLoss(lambda_u=0.05, jacalpha=0.7, unlabeledjacalpha=0.3)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/m2unetssl0703.py b/bob/ip/binseg/configs/models/m2unetssl0703.py
new file mode 100644
index 00000000..d5a16082
--- /dev/null
+++ b/bob/ip/binseg/configs/models/m2unetssl0703.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from torch.optim.lr_scheduler import MultiStepLR
+from bob.ip.binseg.modeling.m2u import build_m2unet
+import torch.optim as optim
+from torch.nn import BCEWithLogitsLoss
+from bob.ip.binseg.utils.model_zoo import modelurls
+from bob.ip.binseg.modeling.losses import MixJacLoss
+from bob.ip.binseg.engine.adabound import AdaBound
+
+##### Config #####
+lr = 0.001
+betas = (0.9, 0.999)
+eps = 1e-08
+weight_decay = 0
+final_lr = 0.1
+gamma = 1e-3
+eps = 1e-8
+amsbound = False
+
+scheduler_milestones = [900]
+scheduler_gamma = 0.1
+
+# model
+model = build_m2unet()
+
+# pretrained backbone
+pretrained_backbone = modelurls['mobilenetv2']
+
+# 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)
+
+# scheduler
+scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/engine/ssltrainer.py b/bob/ip/binseg/engine/ssltrainer.py
index 8fb6d2f1..38243117 100644
--- a/bob/ip/binseg/engine/ssltrainer.py
+++ b/bob/ip/binseg/engine/ssltrainer.py
@@ -51,6 +51,27 @@ def mix_up(alpha, input, target, unlabeled_input, unlabled_target):
return input_mixedup, target_mixedup, unlabeled_input_mixedup, unlabled_target_mixedup
+def square_rampup(current, rampup_length=16):
+ """slowly ramp-up ``lambda_u``
+
+ Parameters
+ ----------
+ current : int
+ current epoch
+ rampup_length : int, optional
+ how long to ramp up, by default 16
+
+ Returns
+ -------
+ float
+ ramp up factor
+ """
+ if rampup_length == 0:
+ return 1.0
+ else:
+ current = np.clip((current/ float(rampup_length))**2, 0.0, 1.0)
+ return float(current)
+
def linear_rampup(current, rampup_length=16):
"""slowly ramp-up ``lambda_u``
@@ -109,7 +130,8 @@ def do_ssltrain(
checkpoint_period,
device,
arguments,
- output_folder
+ output_folder,
+ rampup_length
):
"""
Train model and save to disk.
@@ -134,6 +156,8 @@ def do_ssltrain(
start end end epochs
output_folder : str
output path
+ rampup_Length : int
+ rampup epochs
"""
logger = logging.getLogger("bob.ip.binseg.engine.trainer")
logger.info("Start training")
@@ -173,7 +197,7 @@ def do_ssltrain(
unlabeled_ground_truths = guess_labels(unlabeled_images, model)
#unlabeled_ground_truths = sharpen(unlabeled_ground_truths,0.5)
#images, ground_truths, unlabeled_images, unlabeled_ground_truths = mix_up(0.75, images, ground_truths, unlabeled_images, unlabeled_ground_truths)
- ramp_up_factor = linear_rampup(epoch,rampup_length=500)
+ ramp_up_factor = square_rampup(epoch,rampup_length=rampup_length)
loss, ll, ul = criterion(outputs, ground_truths, unlabeled_outputs, unlabeled_ground_truths, ramp_up_factor)
optimizer.zero_grad()
@@ -244,7 +268,7 @@ def do_ssltrain(
))
log_plot_file = os.path.join(output_folder,"{}_trainlog.pdf".format(model.name))
- logdf = pd.read_csv(os.path.join(output_folder,"{}_trainlog.csv".format(model.name)),header=None, names=["avg. loss", "median loss","lr","max memory"])
+ logdf = pd.read_csv(os.path.join(output_folder,"{}_trainlog.csv".format(model.name)),header=None, names=["avg. loss", "median loss", "labeled loss", "unlabeled loss", "lr","max memory"])
fig = loss_curve(logdf,output_folder)
logger.info("saving {}".format(log_plot_file))
fig.savefig(log_plot_file)
diff --git a/bob/ip/binseg/modeling/losses.py b/bob/ip/binseg/modeling/losses.py
index da2b5f5e..bb6578af 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=0.7, size_average=None, reduce=None, reduction='mean', pos_weight=None):
+ def __init__(self, lambda_u=100, jacalpha=0.7, unlabeledjacalpha=0.3, 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/bob/ip/binseg/script/binseg.py b/bob/ip/binseg/script/binseg.py
index 16b59f2d..6af9d438 100644
--- a/bob/ip/binseg/script/binseg.py
+++ b/bob/ip/binseg/script/binseg.py
@@ -466,6 +466,14 @@ def visualize(dataset, output_path, **kwargs):
required=True,
default='cpu',
cls=ResourceOption)
+@click.option(
+ '--rampup',
+ '-r',
+ help='Ramp-up length in epochs',
+ show_default=True,
+ required=True,
+ default='900',
+ cls=ResourceOption)
@verbosity_option(cls=ResourceOption)
def ssltrain(model
@@ -479,6 +487,7 @@ def ssltrain(model
,dataset
,checkpoint_period
,device
+ ,rampup
,**kwargs):
""" Train a model """
@@ -513,4 +522,5 @@ def ssltrain(model
, device
, arguments
, output_path
+ , rampup
)
\ No newline at end of file
--
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