From fa26d033a184a1001855bafdd1be4008af2645eb Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Fri, 10 Apr 2020 12:26:22 +0200
Subject: [PATCH] Remove use of bob.db.hrf
---
.../drivechasedb1iostarhrf608sslstare.py | 2 +-
.../datasets/drivestarechasedb11168.py | 9 -
.../datasets/drivestarechasedb1iostar1168.py | 19 +-
.../drivestarechasedb1iostar1168sslhrf.py | 53 ++--
.../drivestareiostarhrf960sslchase.py | 11 +-
bob/ip/binseg/configs/datasets/hrf.py | 27 +-
bob/ip/binseg/configs/datasets/hrf1024.py | 27 +-
bob/ip/binseg/configs/datasets/hrf1168.py | 20 +-
bob/ip/binseg/configs/datasets/hrf1168test.py | 25 +-
bob/ip/binseg/configs/datasets/hrf544.py | 27 +-
bob/ip/binseg/configs/datasets/hrf544test.py | 31 ++-
bob/ip/binseg/configs/datasets/hrf608.py | 27 +-
bob/ip/binseg/configs/datasets/hrf960.py | 27 +-
bob/ip/binseg/configs/datasets/hrftest.py | 20 +-
bob/ip/binseg/data/hrf/__init__.py | 44 ++++
bob/ip/binseg/data/hrf/default.json | 231 ++++++++++++++++++
bob/ip/binseg/data/hrf/test.py | 77 ++++++
bob/ip/binseg/data/jsondataset.py | 2 +
bob/ip/binseg/script/dataset.py | 7 +-
conda/meta.yaml | 1 -
develop.cfg | 14 +-
doc/api.rst | 1 -
22 files changed, 525 insertions(+), 177 deletions(-)
delete mode 100644 bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
create mode 100644 bob/ip/binseg/data/hrf/__init__.py
create mode 100644 bob/ip/binseg/data/hrf/default.json
create mode 100644 bob/ip/binseg/data/hrf/test.py
diff --git a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
index c2d041a9..e09f9b03 100644
--- a/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
+++ b/bob/ip/binseg/configs/datasets/drivechasedb1iostarhrf608sslstare.py
@@ -26,7 +26,7 @@ from bob.ip.binseg.configs.datasets.hrf608 import dataset as _hrf
_labelled = torch.utils.data.ConcatDataset([_drive, _chase, _iostar, _hrf])
# Use STARE without labels in this setup
-from .stare import dataset as _unlabelled
+from bob.ip.binseg.configs.datasets.stare import dataset as _unlabelled
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb11168.py b/bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
deleted file mode 100644
index 1a7274ee..00000000
--- a/bob/ip/binseg/configs/datasets/drivestarechasedb11168.py
+++ /dev/null
@@ -1,9 +0,0 @@
-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])
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
index 3bb4f28e..b6258f3f 100644
--- a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168.py
@@ -1,10 +1,13 @@
-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
+#!/usr/bin/env python
+# coding=utf-8
-#### Config ####
+"""COVD-HRF (training set) for Vessel Segmentation
+"""
-# PyTorch dataset
-dataset = torch.utils.data.ConcatDataset([drive, stare, chase, iostar])
+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.utils.data
+dataset = torch.utils.data.ConcatDataset([_drive, _stare, _chase, _iostar])
diff --git a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
index 3b3d2f2e..9cf7b838 100644
--- a/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
+++ b/bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168sslhrf.py
@@ -1,43 +1,20 @@
-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 chasedb
-from bob.ip.binseg.configs.datasets.iostarvessel1168 import dataset as iostar
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-import torch
-from bob.ip.binseg.data.binsegdataset import (
- BinSegDataset,
- SSLBinSegDataset,
- UnLabeledBinSegDataset,
-)
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""HRF (SSL training set) for Vessel Segmentation
-#### Config ####
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3504
+x 2336. One set of ground-truth vessel annotations is available.
-# PyTorch dataset
-labeled_dataset = torch.utils.data.ConcatDataset([drive, stare, iostar, chasedb])
+* Reference: [HRF-2013]_
+* Configuration resolution: 1168 x 1648
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose(
- [
- RandomRotation(),
- Crop(0, 108, 2336, 3296),
- Resize((1168)),
- RandomHFlip(),
- RandomVFlip(),
- ColorJitter(),
- ToTensor(),
- ]
-)
+The dataset available in this file is composed of STARE, CHASE-DB1, IOSTAR
+vessel and CHASE-DB1 (with annotated samples) and HRF without labels.
+"""
-# bob.db.dataset init
-hrfbobdb = HRF(protocol="default")
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(
- hrfbobdb, split="train", transform=unlabeled_transforms
-)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
+from bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168 import dataset as _labelled
+from bob.ip.binseg.configs.datasets.hrf1168 import dataset as _unlabelled
+from bob.ip.binseg.data.utils import SSLDataset
+dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py
index e01d70e8..1306a2f4 100644
--- a/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py
+++ b/bob/ip/binseg/configs/datasets/drivestareiostarhrf960sslchase.py
@@ -23,16 +23,7 @@ The dataset available in this file is composed of STARE, CHASE-DB1, IOSTAR
vessel and HRF (with annotated samples) and CHASE-DB1 without labels.
"""
-# Labelled bits
-import torch.utils.data
-from bob.ip.binseg.configs.datasets.drive960 import dataset as _drive
-from bob.ip.binseg.configs.datasets.stare960 import dataset as _stare
-from bob.ip.binseg.configs.datasets.hrf960 import dataset as _hrf
-from bob.ip.binseg.configs.datasets.iostarvessel960 import dataset as _iostar
-_labelled = torch.utils.data.ConcatDataset([_drive, _stare, _hrf, _iostar])
-
-# Use CHASE-DB1 without labels in this setup
+from bob.ip.binseg.configs.datasets.drivestareiostarhrf960 import dataset as _labelled
from bob.ip.binseg.configs.datasets.chasedb1 import dataset as _unlabelled
-
from bob.ip.binseg.data.utils import SSLDataset
dataset = SSLDataset(_labelled, _unlabelled)
diff --git a/bob/ip/binseg/configs/datasets/hrf.py b/bob/ip/binseg/configs/datasets/hrf.py
index b1330209..95df5b00 100644
--- a/bob/ip/binseg/configs/datasets/hrf.py
+++ b/bob/ip/binseg/configs/datasets/hrf.py
@@ -1,13 +1,21 @@
#!/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
+"""HRF (training set) for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3504
+x 2336. One set of ground-truth vessel annotations is available.
-#### Config ####
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 2336 x 3296 (after specific cropping and rescaling)
+* Training samples: 15
+* Split reference: [ORLANDO-2017]_
+"""
-transforms = Compose(
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
[
Crop(0, 108, 2336, 3296),
RandomHFlip(),
@@ -18,8 +26,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1024.py b/bob/ip/binseg/configs/datasets/hrf1024.py
index e07bd883..a1d7cb36 100644
--- a/bob/ip/binseg/configs/datasets/hrf1024.py
+++ b/bob/ip/binseg/configs/datasets/hrf1024.py
@@ -1,13 +1,21 @@
#!/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
+"""HRF (training set) for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3504
+x 2336. One set of ground-truth vessel annotations is available.
-#### Config ####
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 1024 x ? (after specific padding and rescaling)
+* Training samples: 15
+* Split reference: [ORLANDO-2017]_
+"""
-transforms = Compose(
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
[
Pad((0, 584, 0, 584)),
Resize((1024)),
@@ -19,8 +27,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1168.py b/bob/ip/binseg/configs/datasets/hrf1168.py
index 64ebef45..67ece23f 100644
--- a/bob/ip/binseg/configs/datasets/hrf1168.py
+++ b/bob/ip/binseg/configs/datasets/hrf1168.py
@@ -4,23 +4,18 @@
"""HRF (training set) for Vessel Segmentation
The database includes 15 images of each healthy, diabetic retinopathy (DR), and
-glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3504
x 2336. One set of ground-truth vessel annotations is available.
* Reference: [HRF-2013]_
* Original resolution (height x width): 2336 x 3504
-* Configuration resolution: 1168 x 1648 (after specific cropping and rescaling)
+* Configuration resolution: 1168 x 1648 (after specific padding and rescaling)
* Training samples: 15
* Split reference: [ORLANDO-2017]_
"""
-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(
+_transforms = Compose(
[
Crop(0, 108, 2336, 3296), #(upper, left, height, width)
Resize((1168)), # applies to the smaller edge
@@ -32,8 +27,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf1168test.py b/bob/ip/binseg/configs/datasets/hrf1168test.py
index 86d968f4..d73da151 100644
--- a/bob/ip/binseg/configs/datasets/hrf1168test.py
+++ b/bob/ip/binseg/configs/datasets/hrf1168test.py
@@ -1,16 +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
+"""HRF (test set) for Vessel Segmentation
-#### Config ####
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+x 2336. One set of ground-truth vessel annotations is available.
-transforms = Compose([Crop(0, 108, 2336, 3296), Resize((1168)), ToTensor()])
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 1168 x 1648 (after specific cropping and rescaling)
+* Test samples: 30
+* Split reference: [ORLANDO-2017]_
+"""
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose([Crop(0, 108, 2336, 3296), Resize((1168)), ToTensor()])
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf544.py b/bob/ip/binseg/configs/datasets/hrf544.py
index 6cd9ccf0..d45b4247 100644
--- a/bob/ip/binseg/configs/datasets/hrf544.py
+++ b/bob/ip/binseg/configs/datasets/hrf544.py
@@ -1,13 +1,21 @@
#!/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
+"""HRF (training set) for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+x 2336. One set of ground-truth vessel annotations is available.
-#### Config ####
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 544 x 544 (after specific padding and rescaling)
+* Test samples: 30
+* Split reference: [ORLANDO-2017]_
+"""
-transforms = Compose(
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
[
Resize((363)),
Pad((0, 90, 0, 91)),
@@ -19,8 +27,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf544test.py b/bob/ip/binseg/configs/datasets/hrf544test.py
index 45a3e61d..16102bf8 100644
--- a/bob/ip/binseg/configs/datasets/hrf544test.py
+++ b/bob/ip/binseg/configs/datasets/hrf544test.py
@@ -1,16 +1,29 @@
#!/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
+"""HRF (test set) for Vessel Segmentation
-#### Config ####
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+x 2336. One set of ground-truth vessel annotations is available.
-transforms = Compose([Resize((363)), Pad((0, 90, 0, 91)), ToTensor()])
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 544 x 544 (after specific padding and rescaling)
+* Test samples: 30
+* Split reference: [ORLANDO-2017]_
+"""
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
+ [
+ Resize((363)),
+ Pad((0, 90, 0, 91)),
+ ToTensor(),
+ ]
+)
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="test", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf608.py b/bob/ip/binseg/configs/datasets/hrf608.py
index 7b232ea7..a1d4fbf9 100644
--- a/bob/ip/binseg/configs/datasets/hrf608.py
+++ b/bob/ip/binseg/configs/datasets/hrf608.py
@@ -1,13 +1,21 @@
#!/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
+"""HRF (training set) for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+x 2336. One set of ground-truth vessel annotations is available.
-#### Config ####
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 608 x 608 (after specific padding and rescaling)
+* Training samples: 15
+* Split reference: [ORLANDO-2017]_
+"""
-transforms = Compose(
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
[
Pad((0, 345, 0, 345)),
Resize(608),
@@ -19,8 +27,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrf960.py b/bob/ip/binseg/configs/datasets/hrf960.py
index 059a831c..2dd12ef6 100644
--- a/bob/ip/binseg/configs/datasets/hrf960.py
+++ b/bob/ip/binseg/configs/datasets/hrf960.py
@@ -1,13 +1,21 @@
#!/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
+"""HRF (training set) for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+x 2336. One set of ground-truth vessel annotations is available.
-#### Config ####
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 960 x 960 (after specific padding and rescaling)
+* Training samples: 15
+* Split reference: [ORLANDO-2017]_
+"""
-transforms = Compose(
+from bob.ip.binseg.data.transforms import *
+_transforms = Compose(
[
Pad((0, 584, 0, 584)),
Resize((960)),
@@ -19,8 +27,7 @@ transforms = Compose(
]
)
-# bob.db.dataset init
-bobdb = HRF(protocol="default")
-
-# PyTorch dataset
-dataset = BinSegDataset(bobdb, split="train", transform=transforms)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["train"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/hrftest.py b/bob/ip/binseg/configs/datasets/hrftest.py
index d106365a..0ae5d763 100644
--- a/bob/ip/binseg/configs/datasets/hrftest.py
+++ b/bob/ip/binseg/configs/datasets/hrftest.py
@@ -4,26 +4,20 @@
"""HRF (test set) for Vessel Segmentation
The database includes 15 images of each healthy, diabetic retinopathy (DR), and
-glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3304
+glaucomatous eyes. It contains 45 eye fundus images with a resolution of 3504
x 2336. One set of ground-truth vessel annotations is available.
* Reference: [HRF-2013]_
* Original resolution (height x width): 2336 x 3504
-* Configuration resolution: 1168 x 1648 (after specific cropping and rescaling)
+* Configuration resolution: 2336 x 3296 (after specific cropping and rescaling)
* Test samples: 30
* Split reference: [ORLANDO-2017]_
"""
-from bob.db.hrf import Database as HRF
from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
+_transforms = Compose([Crop(0, 108, 2336, 3296), ToTensor()])
-#### 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)
+from bob.ip.binseg.data.utils import DelayedSample2TorchDataset
+from bob.ip.binseg.data.hrf import dataset as hrf
+dataset = DelayedSample2TorchDataset(hrf.subsets("default")["test"],
+ transform=_transforms)
diff --git a/bob/ip/binseg/data/hrf/__init__.py b/bob/ip/binseg/data/hrf/__init__.py
new file mode 100644
index 00000000..e3b3fa80
--- /dev/null
+++ b/bob/ip/binseg/data/hrf/__init__.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""HRF dataset for Vessel Segmentation
+
+The database includes 15 images of each healthy, diabetic retinopathy (DR), and
+glaucomatous eyes. It contains a total of 45 eye fundus images with a
+resolution of 3304 x 2336. One set of ground-truth vessel annotations is
+available.
+
+* Reference: [HRF-2013]_
+* Original resolution (height x width): 2336 x 3504
+* Configuration resolution: 1168 x 1648 (after specific cropping and rescaling)
+* Split reference: [ORLANDO-2017]_
+* Protocol ``default``:
+
+ * Training samples: 15 (including labels)
+ * Test samples: 30 (including labels)
+
+"""
+
+import os
+import pkg_resources
+
+import bob.extension
+
+from ..jsondataset import JSONDataset
+from ..loader import load_pil_rgb, load_pil_1
+
+_protocols = [
+ pkg_resources.resource_filename(__name__, "default.json"),
+ ]
+
+_root_path = bob.extension.rc.get('bob.ip.binseg.hrf.datadir',
+ os.path.realpath(os.curdir))
+
+def _loader(s):
+ return dict(
+ data=load_pil_rgb(s["data"]),
+ label=load_pil_1(s["label"]),
+ )
+
+dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
+"""HRF dataset object"""
diff --git a/bob/ip/binseg/data/hrf/default.json b/bob/ip/binseg/data/hrf/default.json
new file mode 100644
index 00000000..87f29ad5
--- /dev/null
+++ b/bob/ip/binseg/data/hrf/default.json
@@ -0,0 +1,231 @@
+{
+ "train": [
+ [
+ "images/01_dr.JPG",
+ "manual1/01_dr.tif",
+ "mask/01_dr_mask.tif"
+ ],
+ [
+ "images/02_dr.JPG",
+ "manual1/02_dr.tif",
+ "mask/02_dr_mask.tif"
+ ],
+ [
+ "images/03_dr.JPG",
+ "manual1/03_dr.tif",
+ "mask/03_dr_mask.tif"
+ ],
+ [
+ "images/04_dr.JPG",
+ "manual1/04_dr.tif",
+ "mask/04_dr_mask.tif"
+ ],
+ [
+ "images/05_dr.JPG",
+ "manual1/05_dr.tif",
+ "mask/05_dr_mask.tif"
+ ],
+ [
+ "images/01_g.jpg",
+ "manual1/01_g.tif",
+ "mask/01_g_mask.tif"
+ ],
+ [
+ "images/02_g.jpg",
+ "manual1/02_g.tif",
+ "mask/02_g_mask.tif"
+ ],
+ [
+ "images/03_g.jpg",
+ "manual1/03_g.tif",
+ "mask/03_g_mask.tif"
+ ],
+ [
+ "images/04_g.jpg",
+ "manual1/04_g.tif",
+ "mask/04_g_mask.tif"
+ ],
+ [
+ "images/05_g.jpg",
+ "manual1/05_g.tif",
+ "mask/05_g_mask.tif"
+ ],
+ [
+ "images/01_h.jpg",
+ "manual1/01_h.tif",
+ "mask/01_h_mask.tif"
+ ],
+ [
+ "images/02_h.jpg",
+ "manual1/02_h.tif",
+ "mask/02_h_mask.tif"
+ ],
+ [
+ "images/03_h.jpg",
+ "manual1/03_h.tif",
+ "mask/03_h_mask.tif"
+ ],
+ [
+ "images/04_h.jpg",
+ "manual1/04_h.tif",
+ "mask/04_h_mask.tif"
+ ],
+ [
+ "images/05_h.jpg",
+ "manual1/05_h.tif",
+ "mask/05_h_mask.tif"
+ ]
+ ],
+ "test": [
+ [
+ "images/06_dr.JPG",
+ "manual1/06_dr.tif",
+ "mask/06_dr_mask.tif"
+ ],
+ [
+ "images/07_dr.JPG",
+ "manual1/07_dr.tif",
+ "mask/07_dr_mask.tif"
+ ],
+ [
+ "images/08_dr.JPG",
+ "manual1/08_dr.tif",
+ "mask/08_dr_mask.tif"
+ ],
+ [
+ "images/09_dr.JPG",
+ "manual1/09_dr.tif",
+ "mask/09_dr_mask.tif"
+ ],
+ [
+ "images/10_dr.JPG",
+ "manual1/10_dr.tif",
+ "mask/10_dr_mask.tif"
+ ],
+ [
+ "images/11_dr.JPG",
+ "manual1/11_dr.tif",
+ "mask/11_dr_mask.tif"
+ ],
+ [
+ "images/12_dr.JPG",
+ "manual1/12_dr.tif",
+ "mask/12_dr_mask.tif"
+ ],
+ [
+ "images/13_dr.JPG",
+ "manual1/13_dr.tif",
+ "mask/13_dr_mask.tif"
+ ],
+ [
+ "images/14_dr.JPG",
+ "manual1/14_dr.tif",
+ "mask/14_dr_mask.tif"
+ ],
+ [
+ "images/15_dr.JPG",
+ "manual1/15_dr.tif",
+ "mask/15_dr_mask.tif"
+ ],
+ [
+ "images/06_g.jpg",
+ "manual1/06_g.tif",
+ "mask/06_g_mask.tif"
+ ],
+ [
+ "images/07_g.jpg",
+ "manual1/07_g.tif",
+ "mask/07_g_mask.tif"
+ ],
+ [
+ "images/08_g.jpg",
+ "manual1/08_g.tif",
+ "mask/08_g_mask.tif"
+ ],
+ [
+ "images/09_g.jpg",
+ "manual1/09_g.tif",
+ "mask/09_g_mask.tif"
+ ],
+ [
+ "images/10_g.jpg",
+ "manual1/10_g.tif",
+ "mask/10_g_mask.tif"
+ ],
+ [
+ "images/11_g.jpg",
+ "manual1/11_g.tif",
+ "mask/11_g_mask.tif"
+ ],
+ [
+ "images/12_g.jpg",
+ "manual1/12_g.tif",
+ "mask/12_g_mask.tif"
+ ],
+ [
+ "images/13_g.jpg",
+ "manual1/13_g.tif",
+ "mask/13_g_mask.tif"
+ ],
+ [
+ "images/14_g.jpg",
+ "manual1/14_g.tif",
+ "mask/14_g_mask.tif"
+ ],
+ [
+ "images/15_g.jpg",
+ "manual1/15_g.tif",
+ "mask/15_g_mask.tif"
+ ],
+ [
+ "images/06_h.jpg",
+ "manual1/06_h.tif",
+ "mask/06_h_mask.tif"
+ ],
+ [
+ "images/07_h.jpg",
+ "manual1/07_h.tif",
+ "mask/07_h_mask.tif"
+ ],
+ [
+ "images/08_h.jpg",
+ "manual1/08_h.tif",
+ "mask/08_h_mask.tif"
+ ],
+ [
+ "images/09_h.jpg",
+ "manual1/09_h.tif",
+ "mask/09_h_mask.tif"
+ ],
+ [
+ "images/10_h.jpg",
+ "manual1/10_h.tif",
+ "mask/10_h_mask.tif"
+ ],
+ [
+ "images/11_h.jpg",
+ "manual1/11_h.tif",
+ "mask/11_h_mask.tif"
+ ],
+ [
+ "images/12_h.jpg",
+ "manual1/12_h.tif",
+ "mask/12_h_mask.tif"
+ ],
+ [
+ "images/13_h.jpg",
+ "manual1/13_h.tif",
+ "mask/13_h_mask.tif"
+ ],
+ [
+ "images/14_h.jpg",
+ "manual1/14_h.tif",
+ "mask/14_h_mask.tif"
+ ],
+ [
+ "images/15_h.jpg",
+ "manual1/15_h.tif",
+ "mask/15_h_mask.tif"
+ ]
+ ]
+}
\ No newline at end of file
diff --git a/bob/ip/binseg/data/hrf/test.py b/bob/ip/binseg/data/hrf/test.py
new file mode 100644
index 00000000..1cb21407
--- /dev/null
+++ b/bob/ip/binseg/data/hrf/test.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+
+"""Tests for STARE"""
+
+import os
+import nose.tools
+
+from ..utils import rc_variable_set, DelayedSample2TorchDataset
+from ..transforms import Compose, Crop, Resize
+from . import dataset
+
+
+def test_protocol_consitency():
+
+ subset = dataset.subsets("default")
+ nose.tools.eq_(len(subset), 2)
+
+ assert "train" in subset
+ nose.tools.eq_(len(subset["train"]), 15)
+ for s in subset["train"]:
+ assert s.key.startswith(os.path.join("images", "0"))
+
+ assert "test" in subset
+ nose.tools.eq_(len(subset["test"]), 30)
+ for s in subset["test"]:
+ assert s.key.startswith("images")
+
+
+@rc_variable_set('bob.ip.binseg.hrf.datadir')
+def test_loading():
+
+ def _check_sample(s):
+ data = s.data
+ assert isinstance(data, dict)
+ nose.tools.eq_(len(data), 2)
+ assert "data" in data
+ nose.tools.eq_(data["data"].size, (3504, 2336))
+ nose.tools.eq_(data["data"].mode, "RGB")
+ assert "label" in data
+ nose.tools.eq_(data["label"].size, (3504, 2336))
+ nose.tools.eq_(data["label"].mode, "1")
+
+ subset = dataset.subsets("default")
+ for s in subset["train"]: _check_sample(s)
+ for s in subset["test"]: _check_sample(s)
+
+
+@rc_variable_set('bob.ip.binseg.stare.datadir')
+def test_check():
+ nose.tools.eq_(dataset.check(), 0)
+
+
+@rc_variable_set('bob.ip.binseg.stare.datadir')
+def test_torch_dataset():
+
+ def _check_sample(s):
+ nose.tools.eq_(len(s), 3)
+ assert isinstance(s[0], str)
+ nose.tools.eq_(s[1].size, (1648, 1168))
+ nose.tools.eq_(s[1].mode, "RGB")
+ nose.tools.eq_(s[2].size, (1648, 1168))
+ nose.tools.eq_(s[2].mode, "1")
+
+
+ transforms = Compose([Crop(0, 108, 2336, 3296), Resize((1168))])
+
+ subset = dataset.subsets("default")
+
+ torch_dataset = DelayedSample2TorchDataset(subset["train"], transforms)
+ nose.tools.eq_(len(torch_dataset), 15)
+ for s in torch_dataset: _check_sample(s)
+
+ torch_dataset = DelayedSample2TorchDataset(subset["test"], transforms)
+ nose.tools.eq_(len(torch_dataset), 30)
+ for s in torch_dataset: _check_sample(s)
diff --git a/bob/ip/binseg/data/jsondataset.py b/bob/ip/binseg/data/jsondataset.py
index 99c554bf..6ce86a20 100644
--- a/bob/ip/binseg/data/jsondataset.py
+++ b/bob/ip/binseg/data/jsondataset.py
@@ -122,6 +122,8 @@ class JSONDataset:
"""
+ logger.info(f"Checking dataset at '{self.root_path}'...")
+
errors = 0
for proto in self.protocols:
logger.info(f"Checking protocol '{proto}'...")
diff --git a/bob/ip/binseg/script/dataset.py b/bob/ip/binseg/script/dataset.py
index b00d225e..940f9ef0 100644
--- a/bob/ip/binseg/script/dataset.py
+++ b/bob/ip/binseg/script/dataset.py
@@ -113,13 +113,16 @@ def check(dataset, **kwargs):
if dataset: #check only some
to_check = [k for k in to_check if k.group("name") in dataset]
- if not dataset:
+ if not to_check:
click.echo("No configured datasets matching specifications")
click.echo("Try bob binseg dataset list --help to get help in "
"configuring a dataset")
else:
+ errors = 0
for k in to_check:
click.echo(f"Checking \"{k.group('name')}\" dataset...")
module = importlib.import_module(f"...data.{k.group('name')}",
__name__)
- module.dataset.check()
+ errors += module.dataset.check()
+ if not errors:
+ click.echo(f"No errors reported")
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 1b1a7615..dd4d7894 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -79,7 +79,6 @@ test:
- sphinx
- sphinx_rtd_theme
- sphinxcontrib-programoutput
- - bob.db.hrf
- bob.db.drionsdb
- bob.db.rimoner3
- bob.db.drishtigs1
diff --git a/develop.cfg b/develop.cfg
index 9229bdf9..0bc61a9e 100644
--- a/develop.cfg
+++ b/develop.cfg
@@ -4,10 +4,6 @@
[buildout]
parts = scripts
eggs = bob.ip.binseg
- bob.db.drive
- bob.db.stare
- bob.db.chasedb1
- bob.db.hrf
bob.db.drionsdb
bob.db.rimoner3
bob.db.drishtigs1
@@ -16,11 +12,7 @@ eggs = bob.ip.binseg
extensions = bob.buildout
mr.developer
auto-checkout = *
-develop = src/bob.db.drive
- src/bob.db.stare
- src/bob.db.chasedb1
- src/bob.db.hrf
- src/bob.db.drionsdb
+develop = src/bob.db.drionsdb
src/bob.db.rimoner3
src/bob.db.drishtigs1
src/bob.db.refuge
@@ -33,10 +25,6 @@ verbose = true
newest = false
[sources]
-bob.db.drive = git git@gitlab.idiap.ch:bob/bob.db.drive
-bob.db.stare = git git@gitlab.idiap.ch:bob/bob.db.stare
-bob.db.chasedb1 = git git@gitlab.idiap.ch:bob/bob.db.chasedb1
-bob.db.hrf = git git@gitlab.idiap.ch:bob/bob.db.hrf
bob.db.drionsdb = git git@gitlab.idiap.ch:bob/bob.db.drionsdb
bob.db.rimoner3 = git git@gitlab.idiap.ch:bob/bob.db.rimoner3
bob.db.drishtigs1 = git git@gitlab.idiap.ch:bob/bob.db.drishtigs1
diff --git a/doc/api.rst b/doc/api.rst
index 19afcc1e..b16d4422 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -148,7 +148,6 @@ Datasets
bob.ip.binseg.configs.datasets.drive960
bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608
bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare
- bob.ip.binseg.configs.datasets.drivestarechasedb11168
bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024
bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar
bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168
--
GitLab