From a99b34a6f7be2a874250479b241c89769811a677 Mon Sep 17 00:00:00 2001
From: Tim Laibacher <tim.laibacher@idiap.ch>
Date: Wed, 22 May 2019 11:00:01 +0200
Subject: [PATCH] Add configs
---
.gitignore | 1 +
README.rst | 2 +-
.../binseg/configs/datasets/allvessel544.py | 90 +++++++++++++++++++
.../configs/datasets/allvessel544test.py | 86 ++++++++++++++++++
bob/ip/binseg/configs/datasets/chasedb1.py | 23 +++++
.../configs/datasets/chasedb1544test.py | 20 +++++
.../binseg/configs/datasets/chasedb1test.py | 19 ++++
bob/ip/binseg/configs/datasets/drionsdb.py | 23 +++++
.../{drivecroptest.py => drionsdbtest.py} | 6 +-
.../binseg/configs/datasets/dristhigs1cup.py | 23 +++++
.../configs/datasets/dristhigs1cuptest.py | 18 ++++
.../binseg/configs/datasets/dristhigs1od.py | 23 +++++
.../configs/datasets/dristhigs1odtest.py | 19 ++++
.../datasets/{drivecroptrain.py => drive.py} | 0
bob/ip/binseg/configs/datasets/hrf.py | 23 +++++
bob/ip/binseg/configs/datasets/hrf544test.py | 20 +++++
bob/ip/binseg/configs/datasets/hrftest.py | 19 ++++
.../datasets/{drivetrain.py => iostarod.py} | 6 +-
.../binseg/configs/datasets/iostarodtest.py | 18 ++++
.../binseg/configs/datasets/iostarvessel.py | 22 +++++
.../configs/datasets/iostarvessel544test.py | 19 ++++
.../configs/datasets/iostarvesseltest.py | 18 ++++
bob/ip/binseg/configs/datasets/refugecup.py | 24 +++++
.../binseg/configs/datasets/refugecuptest.py | 19 ++++
bob/ip/binseg/configs/datasets/refugeod.py | 24 +++++
.../binseg/configs/datasets/refugeodtest.py | 19 ++++
bob/ip/binseg/configs/datasets/rimoner3cup.py | 23 +++++
.../configs/datasets/rimoner3cuptest.py | 19 ++++
bob/ip/binseg/configs/datasets/rimoner3od.py | 23 +++++
.../binseg/configs/datasets/rimoner3odtest.py | 19 ++++
bob/ip/binseg/configs/datasets/stare.py | 23 +++++
.../binseg/configs/datasets/stare544test.py | 20 +++++
bob/ip/binseg/configs/datasets/staretest.py | 19 ++++
bob/ip/binseg/configs/models/driu.py | 7 +-
bob/ip/binseg/configs/models/driuadam.py | 33 -------
.../configs/models/{unetj01.py => driuod.py} | 9 +-
bob/ip/binseg/configs/models/hed.py | 6 +-
bob/ip/binseg/configs/models/m2unet.py | 6 +-
bob/ip/binseg/configs/models/resunet.py | 6 +-
bob/ip/binseg/configs/models/unet.py | 6 +-
bob/ip/binseg/data/binsegdataset.py | 4 +-
bob/ip/binseg/engine/inferencer.py | 6 +-
bob/ip/binseg/modeling/driupix.py | 80 +++++++++++++++++
bob/ip/binseg/script/binseg.py | 11 ++-
setup.py | 19 ++--
45 files changed, 845 insertions(+), 78 deletions(-)
create mode 100644 bob/ip/binseg/configs/datasets/allvessel544.py
create mode 100644 bob/ip/binseg/configs/datasets/allvessel544test.py
create mode 100644 bob/ip/binseg/configs/datasets/chasedb1.py
create mode 100644 bob/ip/binseg/configs/datasets/chasedb1544test.py
create mode 100644 bob/ip/binseg/configs/datasets/chasedb1test.py
create mode 100644 bob/ip/binseg/configs/datasets/drionsdb.py
rename bob/ip/binseg/configs/datasets/{drivecroptest.py => drionsdbtest.py} (74%)
create mode 100644 bob/ip/binseg/configs/datasets/dristhigs1cup.py
create mode 100644 bob/ip/binseg/configs/datasets/dristhigs1cuptest.py
create mode 100644 bob/ip/binseg/configs/datasets/dristhigs1od.py
create mode 100644 bob/ip/binseg/configs/datasets/dristhigs1odtest.py
rename bob/ip/binseg/configs/datasets/{drivecroptrain.py => drive.py} (100%)
create mode 100644 bob/ip/binseg/configs/datasets/hrf.py
create mode 100644 bob/ip/binseg/configs/datasets/hrf544test.py
create mode 100644 bob/ip/binseg/configs/datasets/hrftest.py
rename bob/ip/binseg/configs/datasets/{drivetrain.py => iostarod.py} (82%)
create mode 100644 bob/ip/binseg/configs/datasets/iostarodtest.py
create mode 100644 bob/ip/binseg/configs/datasets/iostarvessel.py
create mode 100644 bob/ip/binseg/configs/datasets/iostarvessel544test.py
create mode 100644 bob/ip/binseg/configs/datasets/iostarvesseltest.py
create mode 100644 bob/ip/binseg/configs/datasets/refugecup.py
create mode 100644 bob/ip/binseg/configs/datasets/refugecuptest.py
create mode 100644 bob/ip/binseg/configs/datasets/refugeod.py
create mode 100644 bob/ip/binseg/configs/datasets/refugeodtest.py
create mode 100644 bob/ip/binseg/configs/datasets/rimoner3cup.py
create mode 100644 bob/ip/binseg/configs/datasets/rimoner3cuptest.py
create mode 100644 bob/ip/binseg/configs/datasets/rimoner3od.py
create mode 100644 bob/ip/binseg/configs/datasets/rimoner3odtest.py
create mode 100644 bob/ip/binseg/configs/datasets/stare.py
create mode 100644 bob/ip/binseg/configs/datasets/stare544test.py
create mode 100644 bob/ip/binseg/configs/datasets/staretest.py
delete mode 100644 bob/ip/binseg/configs/models/driuadam.py
rename bob/ip/binseg/configs/models/{unetj01.py => driuod.py} (84%)
create mode 100644 bob/ip/binseg/modeling/driupix.py
diff --git a/.gitignore b/.gitignore
index 69dac1eb..fcc2be3d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,6 +22,7 @@ record.txt
core
output_temp
output
+*.DS_Store
### JupyterNotebook ###
diff --git a/README.rst b/README.rst
index 2121792a..a413a5c2 100644
--- a/README.rst
+++ b/README.rst
@@ -3,7 +3,7 @@
.. image:: https://img.shields.io/badge/docs-stable-yellow.svg
:target: https://www.idiap.ch/software/bob/docs/bob/bob.ip.binseg/stable/index.html
.. image:: https://img.shields.io/badge/docs-latest-orange.svg
- :target: https://www.idiap.ch/software/bob/docs/bob/bob.ip.binseg/master/index.html
+ :target: http://beatubulatest.lab.idiap.ch/private/docs/bob/bob.ip.binseg/master/index.html
.. image:: https://gitlab.idiap.ch/bob/bob.ip.binseg/badges/master/build.svg
:target: https://gitlab.idiap.ch/bob/bob.ip.binseg/commits/master
.. image:: https://gitlab.idiap.ch/bob/bob.ip.binseg/badges/master/coverage.svg
diff --git a/bob/ip/binseg/configs/datasets/allvessel544.py b/bob/ip/binseg/configs/datasets/allvessel544.py
new file mode 100644
index 00000000..9044cebc
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/allvessel544.py
@@ -0,0 +1,90 @@
+#!/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
new file mode 100644
index 00000000..55994e9e
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/allvessel544test.py
@@ -0,0 +1,86 @@
+#!/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/chasedb1.py b/bob/ip/binseg/configs/datasets/chasedb1.py
new file mode 100644
index 00000000..7fa0dc09
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb1.py
@@ -0,0 +1,23 @@
+#!/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([
+ Crop(0,18,960,960)
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,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/chasedb1544test.py b/bob/ip/binseg/configs/datasets/chasedb1544test.py
new file mode 100644
index 00000000..aa5d00a5
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb1544test.py
@@ -0,0 +1,20 @@
+#!/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([
+ Resize(544)
+ ,Crop(0,12,544,544)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = CHASEDB1(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/chasedb1test.py b/bob/ip/binseg/configs/datasets/chasedb1test.py
new file mode 100644
index 00000000..4b267b0f
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb1test.py
@@ -0,0 +1,19 @@
+#!/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([
+ Crop(0,18,960,960)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = CHASEDB1(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/drionsdb.py b/bob/ip/binseg/configs/datasets/drionsdb.py
new file mode 100644
index 00000000..cd33c1d2
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drionsdb.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.drionsdb import Database as DRIONS
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ Pad((4,8,4,8))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = DRIONS(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/drivecroptest.py b/bob/ip/binseg/configs/datasets/drionsdbtest.py
similarity index 74%
rename from bob/ip/binseg/configs/datasets/drivecroptest.py
rename to bob/ip/binseg/configs/datasets/drionsdbtest.py
index 230598dc..b65100a6 100644
--- a/bob/ip/binseg/configs/datasets/drivecroptest.py
+++ b/bob/ip/binseg/configs/datasets/drionsdbtest.py
@@ -1,19 +1,19 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-from bob.db.drive import Database as DRIVE
+from bob.db.drionsdb import Database as DRIONS
from bob.ip.binseg.data.transforms import *
from bob.ip.binseg.data.binsegdataset import BinSegDataset
#### Config ####
transforms = Compose([
- CenterCrop((544,544))
+ Pad((4,8,4,8))
,ToTensor()
])
# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
+bobdb = DRIONS(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/dristhigs1cup.py b/bob/ip/binseg/configs/datasets/dristhigs1cup.py
new file mode 100644
index 00000000..f7a69dad
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/dristhigs1cup.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.drishtigs1 import Database as DRISHTI
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ 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)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1cuptest.py b/bob/ip/binseg/configs/datasets/dristhigs1cuptest.py
new file mode 100644
index 00000000..5c2b634e
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/dristhigs1cuptest.py
@@ -0,0 +1,18 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+from bob.db.drishtigs1 import Database as DRISHTI
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ CenterCrop((1760,2048))
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = DRISHTI(protocol = 'default_cup')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1od.py b/bob/ip/binseg/configs/datasets/dristhigs1od.py
new file mode 100644
index 00000000..0bd483c1
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/dristhigs1od.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.drishtigs1 import Database as DRISHTI
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ 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)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/dristhigs1odtest.py b/bob/ip/binseg/configs/datasets/dristhigs1odtest.py
new file mode 100644
index 00000000..ab1edd65
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/dristhigs1odtest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.db.drishtigs1 import Database as DRISHTI
+from bob.ip.binseg.data.transforms import *
+from bob.ip.binseg.data.binsegdataset import BinSegDataset
+
+#### Config ####
+
+transforms = Compose([
+ CenterCrop((1760,2048))
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = DRISHTI(protocol = 'default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/drivecroptrain.py b/bob/ip/binseg/configs/datasets/drive.py
similarity index 100%
rename from bob/ip/binseg/configs/datasets/drivecroptrain.py
rename to bob/ip/binseg/configs/datasets/drive.py
diff --git a/bob/ip/binseg/configs/datasets/hrf.py b/bob/ip/binseg/configs/datasets/hrf.py
new file mode 100644
index 00000000..cb008f7d
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf.py
@@ -0,0 +1,23 @@
+#!/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)
+ ,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/hrf544test.py b/bob/ip/binseg/configs/datasets/hrf544test.py
new file mode 100644
index 00000000..86da428b
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf544test.py
@@ -0,0 +1,20 @@
+#!/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))
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+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/hrftest.py b/bob/ip/binseg/configs/datasets/hrftest.py
new file mode 100644
index 00000000..45f95272
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrftest.py
@@ -0,0 +1,19 @@
+#!/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)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+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/drivetrain.py b/bob/ip/binseg/configs/datasets/iostarod.py
similarity index 82%
rename from bob/ip/binseg/configs/datasets/drivetrain.py
rename to bob/ip/binseg/configs/datasets/iostarod.py
index 6662e1fc..334df2a4 100644
--- a/bob/ip/binseg/configs/datasets/drivetrain.py
+++ b/bob/ip/binseg/configs/datasets/iostarod.py
@@ -1,13 +1,13 @@
#!/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([
+transforms = Compose([
RandomHFlip()
,RandomVFlip()
,RandomRotation()
@@ -16,7 +16,7 @@ transforms = Compose([
])
# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
+bobdb = IOSTAR(protocol='default_od')
# PyTorch dataset
dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/iostarodtest.py b/bob/ip/binseg/configs/datasets/iostarodtest.py
new file mode 100644
index 00000000..ba064507
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarodtest.py
@@ -0,0 +1,18 @@
+#!/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([
+ ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = IOSTAR(protocol='default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/iostarvessel.py b/bob/ip/binseg/configs/datasets/iostarvessel.py
new file mode 100644
index 00000000..ded01bb4
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvessel.py
@@ -0,0 +1,22 @@
+#!/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([
+ 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/iostarvessel544test.py b/bob/ip/binseg/configs/datasets/iostarvessel544test.py
new file mode 100644
index 00000000..e3ccd854
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvessel544test.py
@@ -0,0 +1,19 @@
+#!/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(544)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = IOSTAR(protocol='default_vessel')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/iostarvesseltest.py b/bob/ip/binseg/configs/datasets/iostarvesseltest.py
new file mode 100644
index 00000000..d8fe1371
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostarvesseltest.py
@@ -0,0 +1,18 @@
+#!/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([
+ ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = IOSTAR(protocol='default_vessel')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/refugecup.py b/bob/ip/binseg/configs/datasets/refugecup.py
new file mode 100644
index 00000000..9efac529
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refugecup.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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([
+ Resize((1539))
+ ,Pad((21,46,22,47))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = REFUGE(protocol = 'default_cup')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/refugecuptest.py b/bob/ip/binseg/configs/datasets/refugecuptest.py
new file mode 100644
index 00000000..8ff916e3
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refugecuptest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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([
+ CenterCrop(1632)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = REFUGE(protocol = 'default_cup')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/refugeod.py b/bob/ip/binseg/configs/datasets/refugeod.py
new file mode 100644
index 00000000..5faaf05a
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refugeod.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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([
+ Resize((1539))
+ ,Pad((21,46,22,47))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = REFUGE(protocol = 'default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/refugeodtest.py b/bob/ip/binseg/configs/datasets/refugeodtest.py
new file mode 100644
index 00000000..30085a2f
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refugeodtest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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([
+ CenterCrop(1632)
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = REFUGE(protocol = 'default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/rimoner3cup.py b/bob/ip/binseg/configs/datasets/rimoner3cup.py
new file mode 100644
index 00000000..47b62ba0
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/rimoner3cup.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = RIMONER3(protocol = 'default_cup')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/rimoner3cuptest.py b/bob/ip/binseg/configs/datasets/rimoner3cuptest.py
new file mode 100644
index 00000000..9f227be8
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/rimoner3cuptest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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()
+ ])
+
+# bob.db.dataset init
+bobdb = RIMONER3(protocol = 'default_cup')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/rimoner3od.py b/bob/ip/binseg/configs/datasets/rimoner3od.py
new file mode 100644
index 00000000..4905bec3
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/rimoner3od.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,ColorJitter()
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = RIMONER3(protocol = 'default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='train', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/rimoner3odtest.py b/bob/ip/binseg/configs/datasets/rimoner3odtest.py
new file mode 100644
index 00000000..390f20d7
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/rimoner3odtest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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()
+ ])
+
+# bob.db.dataset init
+bobdb = RIMONER3(protocol = 'default_od')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/datasets/stare.py b/bob/ip/binseg/configs/datasets/stare.py
new file mode 100644
index 00000000..f2c784a9
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare.py
@@ -0,0 +1,23 @@
+#!/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([
+ Pad((2,1,2,2))
+ ,RandomHFlip()
+ ,RandomVFlip()
+ ,RandomRotation()
+ ,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/stare544test.py b/bob/ip/binseg/configs/datasets/stare544test.py
new file mode 100644
index 00000000..09b26873
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare544test.py
@@ -0,0 +1,20 @@
+#!/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([
+ Resize(471)
+ ,Pad((0,37,0,36))
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = STARE(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/staretest.py b/bob/ip/binseg/configs/datasets/staretest.py
new file mode 100644
index 00000000..aab80b9b
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/staretest.py
@@ -0,0 +1,19 @@
+#!/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([
+ Pad((2,1,2,2))
+ ,ToTensor()
+ ])
+
+# bob.db.dataset init
+bobdb = STARE(protocol = 'default')
+
+# PyTorch dataset
+dataset = BinSegDataset(bobdb, split='test', transform=transforms)
\ No newline at end of file
diff --git a/bob/ip/binseg/configs/models/driu.py b/bob/ip/binseg/configs/models/driu.py
index deb789d0..1bc10ef0 100644
--- a/bob/ip/binseg/configs/models/driu.py
+++ b/bob/ip/binseg/configs/models/driu.py
@@ -6,7 +6,7 @@ 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
-from bob.ip.binseg.modeling.losses import WeightedBCELogitsLoss
+from bob.ip.binseg.modeling.losses import SoftJaccardBCELogitsLoss
from bob.ip.binseg.engine.adabound import AdaBound
##### Config #####
@@ -19,7 +19,7 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
# model
@@ -31,9 +31,8 @@ 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 = WeightedBCELogitsLoss(reduction='mean')
+criterion = SoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/driuadam.py b/bob/ip/binseg/configs/models/driuadam.py
deleted file mode 100644
index c801206b..00000000
--- a/bob/ip/binseg/configs/models/driuadam.py
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from torch.optim.lr_scheduler import MultiStepLR
-from bob.ip.binseg.modeling.driu import build_driu
-import torch.optim as optim
-from bob.ip.binseg.modeling.losses import WeightedBCELogitsLoss
-from bob.ip.binseg.utils.model_zoo import modelurls
-
-##### Config #####
-lr = 0.001
-betas = (0.9, 0.999)
-eps = 1e-08
-weight_decay = 0
-amsgrad = False
-
-scheduler_milestones = [150]
-scheduler_gamma = 0.1
-
-# model
-model = build_driu()
-
-# pretrained backbone
-pretrained_backbone = modelurls['vgg16']
-
-# optimizer
-optimizer = optim.Adam(model.parameters(), lr=lr, betas=betas, eps=eps, weight_decay=weight_decay, amsgrad=amsgrad)
-
-# criterion
-criterion = WeightedBCELogitsLoss(reduction='mean')
-
-# scheduler
-scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/unetj01.py b/bob/ip/binseg/configs/models/driuod.py
similarity index 84%
rename from bob/ip/binseg/configs/models/unetj01.py
rename to bob/ip/binseg/configs/models/driuod.py
index da1096cd..199a249a 100644
--- a/bob/ip/binseg/configs/models/unetj01.py
+++ b/bob/ip/binseg/configs/models/driuod.py
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
from torch.optim.lr_scheduler import MultiStepLR
-from bob.ip.binseg.modeling.unet import build_unet
+from bob.ip.binseg.modeling.driuod import build_driuod
import torch.optim as optim
from torch.nn import BCEWithLogitsLoss
from bob.ip.binseg.utils.model_zoo import modelurls
@@ -19,11 +19,11 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
# model
-model = build_unet()
+model = build_driuod()
# pretrained backbone
pretrained_backbone = modelurls['vgg16']
@@ -31,9 +31,8 @@ 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 = SoftJaccardBCELogitsLoss(alpha=0.1)
+criterion = SoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/hed.py b/bob/ip/binseg/configs/models/hed.py
index a586e86e..306ecb80 100644
--- a/bob/ip/binseg/configs/models/hed.py
+++ b/bob/ip/binseg/configs/models/hed.py
@@ -4,7 +4,7 @@
from torch.optim.lr_scheduler import MultiStepLR
from bob.ip.binseg.modeling.hed import build_hed
import torch.optim as optim
-from bob.ip.binseg.modeling.losses import HEDWeightedBCELogitsLoss
+from bob.ip.binseg.modeling.losses import HEDSoftJaccardBCELogitsLoss
from bob.ip.binseg.utils.model_zoo import modelurls
from bob.ip.binseg.engine.adabound import AdaBound
@@ -19,7 +19,7 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
@@ -33,7 +33,7 @@ pretrained_backbone = modelurls['vgg16']
optimizer = AdaBound(model.parameters(), lr=lr, betas=betas, final_lr=final_lr, gamma=gamma,
eps=eps, weight_decay=weight_decay, amsbound=amsbound)
# criterion
-criterion = HEDWeightedBCELogitsLoss(reduction='mean')
+criterion = HEDSoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/m2unet.py b/bob/ip/binseg/configs/models/m2unet.py
index e97ae62d..cb422dca 100644
--- a/bob/ip/binseg/configs/models/m2unet.py
+++ b/bob/ip/binseg/configs/models/m2unet.py
@@ -6,7 +6,7 @@ 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 WeightedBCELogitsLoss
+from bob.ip.binseg.modeling.losses import SoftJaccardBCELogitsLoss
from bob.ip.binseg.engine.adabound import AdaBound
##### Config #####
@@ -19,7 +19,7 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
# model
@@ -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 = WeightedBCELogitsLoss(reduction='mean')
+criterion = SoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/resunet.py b/bob/ip/binseg/configs/models/resunet.py
index 17184497..1a049f14 100644
--- a/bob/ip/binseg/configs/models/resunet.py
+++ b/bob/ip/binseg/configs/models/resunet.py
@@ -6,7 +6,7 @@ from bob.ip.binseg.modeling.resunet import build_res50unet
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 WeightedBCELogitsLoss
+from bob.ip.binseg.modeling.losses import SoftJaccardBCELogitsLoss
from bob.ip.binseg.engine.adabound import AdaBound
##### Config #####
@@ -19,7 +19,7 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
# model
@@ -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 = WeightedBCELogitsLoss(reduction='mean')
+criterion = SoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/configs/models/unet.py b/bob/ip/binseg/configs/models/unet.py
index f034d94d..7c21b042 100644
--- a/bob/ip/binseg/configs/models/unet.py
+++ b/bob/ip/binseg/configs/models/unet.py
@@ -6,7 +6,7 @@ from bob.ip.binseg.modeling.unet import build_unet
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 WeightedBCELogitsLoss
+from bob.ip.binseg.modeling.losses import SoftJaccardBCELogitsLoss
from bob.ip.binseg.engine.adabound import AdaBound
##### Config #####
@@ -19,7 +19,7 @@ gamma = 1e-3
eps = 1e-8
amsbound = False
-scheduler_milestones = [200]
+scheduler_milestones = [800]
scheduler_gamma = 0.1
# model
@@ -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 = WeightedBCELogitsLoss(reduction='mean')
+criterion = SoftJaccardBCELogitsLoss(alpha=0.7)
# scheduler
scheduler = MultiStepLR(optimizer, milestones=scheduler_milestones, gamma=scheduler_gamma)
diff --git a/bob/ip/binseg/data/binsegdataset.py b/bob/ip/binseg/data/binsegdataset.py
index f212c4fe..86fc97df 100644
--- a/bob/ip/binseg/data/binsegdataset.py
+++ b/bob/ip/binseg/data/binsegdataset.py
@@ -7,7 +7,7 @@ class BinSegDataset(Dataset):
A transform object can be passed that will be applied to the image, ground truth and mask (if present).
It supports indexing such that dataset[i] can be used to get ith sample.
- Attributes
+ Parameters
----------
bobdb : :py:mod:`bob.db.base`
Binary segmentation bob database (e.g. bob.db.drive)
@@ -15,6 +15,8 @@ class BinSegDataset(Dataset):
``'train'`` or ``'test'``. Defaults to ``'train'``
transform : :py:mod:`bob.ip.binseg.data.transforms`, optional
A transform or composition of transfroms. Defaults to ``None``.
+ mask : bool
+ whether dataset contains masks or not
"""
def __init__(self, bobdb, split = 'train', transform = None):
self.database = bobdb.samples(split)
diff --git a/bob/ip/binseg/engine/inferencer.py b/bob/ip/binseg/engine/inferencer.py
index 00f60d7c..a1017ed5 100644
--- a/bob/ip/binseg/engine/inferencer.py
+++ b/bob/ip/binseg/engine/inferencer.py
@@ -134,9 +134,9 @@ def do_inference(
"""
logger = logging.getLogger("bob.ip.binseg.engine.inference")
logger.info("Start evaluation")
- logger.info("Split: {}, Output folder: {}, Device: {}".format(data_loader.dataset.split, output_folder, device))
+ logger.info("Output folder: {}, Device: {}".format(output_folder, device))
results_subfolder = os.path.join(output_folder,'results')
- if not os.path.exists(results_subfolder): os.makedirs(results_subfolder)
+ os.makedirs(results_subfolder,exist_ok=True)
model.eval().to(device)
# Sigmoid for probabilities
@@ -206,7 +206,7 @@ def do_inference(
np_avg_metrics = avg_metrics.to_numpy().T
fig_name = "precision_recall.pdf"
logger.info("saving {}".format(fig_name))
- fig = precision_recall_f1iso([np_avg_metrics[0]],[np_avg_metrics[1]], [model.name,None], title=output_folder)
+ fig = precision_recall_f1iso([np_avg_metrics[0]],[np_avg_metrics[1]], [model.name,None], title=output_folder.split('/')[-2:])
fig_filename = os.path.join(results_subfolder, fig_name)
fig.savefig(fig_filename)
diff --git a/bob/ip/binseg/modeling/driupix.py b/bob/ip/binseg/modeling/driupix.py
new file mode 100644
index 00000000..00e40932
--- /dev/null
+++ b/bob/ip/binseg/modeling/driupix.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import torch
+from torch import nn
+from collections import OrderedDict
+from bob.ip.binseg.modeling.backbones.vgg import vgg16
+from bob.ip.binseg.modeling.make_layers import conv_with_kaiming_uniform,convtrans_with_kaiming_uniform, UpsampleCropBlock
+
+class ConcatFuseBlock(nn.Module):
+ """
+ Takes in four feature maps with 16 channels each, concatenates them
+ and applies a 1x1 convolution with 1 output channel.
+ """
+ def __init__(self):
+ super().__init__()
+ self.conv = conv_with_kaiming_uniform(4*16,1,1,1,0)
+
+ def forward(self,x1,x2,x3,x4):
+ x_cat = torch.cat([x1,x2,x3,x4],dim=1)
+ x = self.conv(x_cat)
+ return x
+
+class DRIUPIX(nn.Module):
+ """
+ DRIUPIX head module. DRIU with pixelshuffle instead of ConvTrans2D
+
+ Parameters
+ ----------
+ in_channels_list : list
+ number of channels for each feature map that is returned from backbone
+ """
+ def __init__(self, in_channels_list=None):
+ super(DRIUPIX, self).__init__()
+ in_conv_1_2_16, in_upsample2, in_upsample_4, in_upsample_8 = in_channels_list
+
+ self.conv1_2_16 = nn.Conv2d(in_conv_1_2_16, 16, 3, 1, 1)
+ # Upsample layers
+ self.upsample2 = UpsampleCropBlock(in_upsample2, 16, 4, 2, 0, pixelshuffle=True)
+ self.upsample4 = UpsampleCropBlock(in_upsample_4, 16, 8, 4, 0, pixelshuffle=True)
+ self.upsample8 = UpsampleCropBlock(in_upsample_8, 16, 16, 8, 0, pixelshuffle=True)
+
+ # Concat and Fuse
+ self.concatfuse = ConcatFuseBlock()
+
+ def forward(self,x):
+ """
+ Parameters
+ ----------
+ x : list
+ list of tensors as returned from the backbone network.
+ First element: height and width of input image.
+ Remaining elements: feature maps for each feature level.
+
+ Returns
+ -------
+ :py:class:`torch.Tensor`
+ """
+ hw = x[0]
+ conv1_2_16 = self.conv1_2_16(x[1]) # conv1_2_16
+ upsample2 = self.upsample2(x[2], hw) # side-multi2-up
+ upsample4 = self.upsample4(x[3], hw) # side-multi3-up
+ upsample8 = self.upsample8(x[4], hw) # side-multi4-up
+ out = self.concatfuse(conv1_2_16, upsample2, upsample4, upsample8)
+ return out
+
+def build_driupix():
+ """
+ Adds backbone and head together
+
+ Returns
+ -------
+ :py:class:torch.nn.Module
+ """
+ backbone = vgg16(pretrained=False, return_features = [3, 8, 14, 22])
+ driu_head = DRIUPIX([64, 128, 256, 512])
+
+ model = nn.Sequential(OrderedDict([("backbone", backbone), ("head", driu_head)]))
+ model.name = "DRIUPIX"
+ return model
\ No newline at end of file
diff --git a/bob/ip/binseg/script/binseg.py b/bob/ip/binseg/script/binseg.py
index e56aa2fe..2a90d5ed 100644
--- a/bob/ip/binseg/script/binseg.py
+++ b/bob/ip/binseg/script/binseg.py
@@ -197,12 +197,21 @@ def train(model
required=True,
default='cpu',
cls=ResourceOption)
+@click.option(
+ '--weight',
+ '-w',
+ help='Path or URL to pretrained model',
+ required=False,
+ default=None,
+ cls=ResourceOption
+ )
@verbosity_option(cls=ResourceOption)
def test(model
,output_path
,device
,batch_size
,dataset
+ ,weight
, **kwargs):
""" Run inference and evalaute the model performance """
@@ -216,7 +225,7 @@ def test(model
# checkpointer, load last model in dir
checkpointer = DetectronCheckpointer(model, save_dir = output_path, save_to_disk=False)
- checkpointer.load()
+ checkpointer.load(weight)
do_inference(model, data_loader, device, output_path)
diff --git a/setup.py b/setup.py
index 2b70354f..8b82e9b2 100644
--- a/setup.py
+++ b/setup.py
@@ -58,25 +58,17 @@ setup(
#bob hed train configurations
'bob.ip.binseg.config': [
'DRIU = bob.ip.binseg.configs.models.driu',
- 'DRIUJ = bob.ip.binseg.configs.models.driuj',
- 'DRIUJ7 = bob.ip.binseg.configs.models.driuj7',
- 'DRIUODJ = bob.ip.binseg.configs.models.driuodj',
+ 'DRIUOD = bob.ip.binseg.configs.models.driuod',
'HED = bob.ip.binseg.configs.models.hed',
- 'HEDJ = bob.ip.binseg.configs.models.hedj',
- 'HEDJ7 = bob.ip.binseg.configs.models.hedj7',
- 'HEDODJ = bob.ip.binseg.configs.models.hedodj',
'M2UNet = bob.ip.binseg.configs.models.m2unet',
- 'M2UNetJ = bob.ip.binseg.configs.models.m2unetj',
- 'M2UNetJ7 = bob.ip.binseg.configs.models.m2unetj7',
'UNet = bob.ip.binseg.configs.models.unet',
- 'UNetJ = bob.ip.binseg.configs.models.unetj',
- 'UNetJ7 = bob.ip.binseg.configs.models.unetj7',
- 'UNetODJ = bob.ip.binseg.configs.models.unetodj',
'ResUNet = bob.ip.binseg.configs.models.resunet',
- 'ResUNetJ = bob.ip.binseg.configs.models.resunetj',
'ShapeResUNet = bob.ip.binseg.configs.models.shaperesunet',
+ 'ALLVESSEL544 = bob.ip.binseg.configs.datasets.allvessel544',
+ 'ALLVESSEL544TEST = bob.ip.binseg.configs.datasets.allvessel544test',
'CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1',
'CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test',
+ 'CHASEDB1544TEST = bob.ip.binseg.configs.datasets.chasedb1544test',
'DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb',
'DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest',
'DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od',
@@ -87,10 +79,12 @@ setup(
'DRIVETEST = bob.ip.binseg.configs.datasets.drivetest',
'HRF = bob.ip.binseg.configs.datasets.hrf',
'HRFTEST = bob.ip.binseg.configs.datasets.hrftest',
+ 'HRF544TEST = bob.ip.binseg.configs.datasets.hrf544test',
'IOSTAROD = bob.ip.binseg.configs.datasets.iostarod',
'IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest',
'IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel',
'IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest',
+ 'IOSTARVESSEL544TEST = bob.ip.binseg.configs.datasets.iostarvessel544test',
'REFUGECUP = bob.ip.binseg.configs.datasets.refugecup',
'REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest',
'REFUGEOD = bob.ip.binseg.configs.datasets.refugeod',
@@ -101,6 +95,7 @@ setup(
'RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest',
'STARE = bob.ip.binseg.configs.datasets.stare',
'STARETEST = bob.ip.binseg.configs.datasets.staretest',
+ 'STARE544TEST = bob.ip.binseg.configs.datasets.stare544test',
]
},
--
GitLab