Add configs

.gitignore

@@ -22,6 +22,7 @@ record.txt
 core
 output_temp
 output
+*.DS_Store
 
 
 ### JupyterNotebook ###

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

bob/ip/binseg/configs/datasets/allvessel544.py

+#!/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

bob/ip/binseg/configs/datasets/allvessel544test.py

+#!/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

bob/ip/binseg/configs/datasets/chasedb1.py

+#!/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

bob/ip/binseg/configs/datasets/chasedb1544test.py

+#!/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

bob/ip/binseg/configs/datasets/chasedb1test.py

+#!/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

bob/ip/binseg/configs/datasets/drionsdb.py

+#!/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

bob/ip/binseg/configs/datasets/drivecroptest.py → bob/ip/binseg/configs/datasets/drionsdbtest.py

 #!/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

bob/ip/binseg/configs/datasets/dristhigs1cup.py

+#!/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

bob/ip/binseg/configs/datasets/dristhigs1cuptest.py

+#!/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

bob/ip/binseg/configs/datasets/dristhigs1od.py

+#!/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

bob/ip/binseg/configs/datasets/dristhigs1odtest.py

+#!/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

bob/ip/binseg/configs/datasets/hrf.py

+#!/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

bob/ip/binseg/configs/datasets/hrf544test.py

+#!/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

bob/ip/binseg/configs/datasets/hrftest.py

+#!/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

bob/ip/binseg/configs/datasets/drivetrain.py → bob/ip/binseg/configs/datasets/iostarod.py

 #!/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

bob/ip/binseg/configs/datasets/iostarodtest.py

+#!/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

bob/ip/binseg/configs/datasets/iostarvessel.py

+#!/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