diff --git a/bob/ip/binseg/configs/datasets/refuge_cup.py b/bob/ip/binseg/configs/datasets/refuge_cup.py
index 029e7898a82f1f62febd232f5056c34dd6b6aed0..13af1da700902c31757027a824cea2a05db7e75b 100644
--- a/bob/ip/binseg/configs/datasets/refuge_cup.py
+++ b/bob/ip/binseg/configs/datasets/refuge_cup.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-"""REFUGE (training set) for Cup Segmentation
+"""REFUGE (training set) for Optic Cup Segmentation
The dataset consists of 1200 color fundus photographs, created for a MICCAI
challenge. The goal of the challenge is to evaluate and compare automated
@@ -10,23 +10,16 @@ dataset of retinal fundus images.
* Reference: [REFUGE-2018]_
* Original resolution (height x width): 2056 x 2124
-* Configuration resolution: 1632 x 1632 (after center cropping)
+* Configuration resolution: 1632 x 1632 (after resizing and padding)
* Training samples: 400
* Split reference: [REFUGE-2018]_
-
-.. warning:
-
- Notice that the data cropping/resizing algorithm applied on training and
- "validation" data are slightly different and need to be cross-checked.
-
"""
from bob.ip.binseg.data.transforms import Resize, Pad
from bob.ip.binseg.configs.datasets.utils import DATA_AUGMENTATION as _DA
_transforms = [Resize(1539), Pad((21, 46, 22, 47))] + _DA
-from bob.db.refuge import Database as REFUGE
-bobdb = REFUGE(protocol="default_cup")
-
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-cup")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refuge_cup_dev.py b/bob/ip/binseg/configs/datasets/refuge_cup_dev.py
new file mode 100644
index 0000000000000000000000000000000000000000..9136756bc96ee1b3bac9d9a25cd4612c7e276382
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refuge_cup_dev.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""REFUGE (validation set) for Optic Cup Segmentation
+
+The dataset consists of 1200 color fundus photographs, created for a MICCAI
+challenge. The goal of the challenge is to evaluate and compare automated
+algorithms for glaucoma detection and optic disc/cup segmentation on a common
+dataset of retinal fundus images.
+
+* Reference: [REFUGE-2018]_
+* Original resolution (height x width): 1634 x 1634
+* Configuration resolution: 1632 x 1632 (after center cropping)
+* Validation samples: 400
+* Split reference: [REFUGE-2018]_
+"""
+
+from bob.ip.binseg.data.transforms import CenterCrop
+_transforms = [CenterCrop(1632)]
+
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-cup")["validation"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refuge_cup_test.py b/bob/ip/binseg/configs/datasets/refuge_cup_test.py
index b1d839fb4586bfa3705adc126b3a0ec6480e8d3e..a42c6a54f6ab4f994dca857906c9cb1345e1edc0 100644
--- a/bob/ip/binseg/configs/datasets/refuge_cup_test.py
+++ b/bob/ip/binseg/configs/datasets/refuge_cup_test.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-"""REFUGE (validation set) for Cup Segmentation
+"""REFUGE (validation set) for Optic Cup Segmentation
The dataset consists of 1200 color fundus photographs, created for a MICCAI
challenge. The goal of the challenge is to evaluate and compare automated
@@ -9,28 +9,16 @@ algorithms for glaucoma detection and optic disc/cup segmentation on a common
dataset of retinal fundus images.
* Reference: [REFUGE-2018]_
-* Original resolution (height x width): 2056 x 2124
+* Original resolution (height x width): 1634 x 1634
* Configuration resolution: 1632 x 1632 (after center cropping)
-* Validation samples: 400
+* Test samples: 400
* Split reference: [REFUGE-2018]_
-
-.. warning:
-
- Notice 2 aspects before using these configurations:
-
- 1. The data cropping/resizing algorithm applied on training and "validation"
- data are slightly different and need to be cross-checked.
- 2. This is the **validation** set! The real **test** set is still not
- integrated to the originating bob.db.refuge package: See
- https://gitlab.idiap.ch/bob/bob.db.refuge/issues/1
-
"""
from bob.ip.binseg.data.transforms import CenterCrop
_transforms = [CenterCrop(1632)]
-from bob.db.refuge import Database as REFUGE
-bobdb = REFUGE(protocol="default_cup")
-
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-cup")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refuge_od.py b/bob/ip/binseg/configs/datasets/refuge_od.py
index 8959b1eb6c4added59637b68c9649356a9ff7d85..352d161dbeaa236379f0f98e7595cc6ce371fc89 100644
--- a/bob/ip/binseg/configs/datasets/refuge_od.py
+++ b/bob/ip/binseg/configs/datasets/refuge_od.py
@@ -10,23 +10,16 @@ dataset of retinal fundus images.
* Reference: [REFUGE-2018]_
* Original resolution (height x width): 2056 x 2124
-* Configuration resolution: 1632 x 1632 (after center cropping)
+* Configuration resolution: 1632 x 1632 (after resizing and padding)
* Training samples: 400
* Split reference: [REFUGE-2018]_
-
-.. warning:
-
- Notice that the data cropping/resizing algorithm applied on training and
- "validation" data are slightly different and need to be cross-checked.
-
"""
from bob.ip.binseg.data.transforms import Resize, Pad
from bob.ip.binseg.configs.datasets.utils import DATA_AUGMENTATION as _DA
-_transforms = [Resize((1539)), Pad((21, 46, 22, 47))] + _DA
-
-from bob.db.refuge import Database as REFUGE
-bobdb = REFUGE(protocol="default_od")
+_transforms = [Resize(1539), Pad((21, 46, 22, 47))] + _DA
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-dataset = BinSegDataset(bobdb, split="train", transforms=_transforms)
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-disc")["train"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refuge_od_dev.py b/bob/ip/binseg/configs/datasets/refuge_od_dev.py
new file mode 100644
index 0000000000000000000000000000000000000000..e404f9cd1ac5c7ee17e5945f44534ef0ffade4f5
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/refuge_od_dev.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""REFUGE (validation set) for Optic Disc Segmentation
+
+The dataset consists of 1200 color fundus photographs, created for a MICCAI
+challenge. The goal of the challenge is to evaluate and compare automated
+algorithms for glaucoma detection and optic disc/cup segmentation on a common
+dataset of retinal fundus images.
+
+* Reference: [REFUGE-2018]_
+* Original resolution (height x width): 1634 x 1634
+* Configuration resolution: 1632 x 1632 (after center cropping)
+* Validation samples: 400
+* Split reference: [REFUGE-2018]_
+"""
+
+from bob.ip.binseg.data.transforms import CenterCrop
+_transforms = [CenterCrop(1632)]
+
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-disc")["validation"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/configs/datasets/refuge_od_test.py b/bob/ip/binseg/configs/datasets/refuge_od_test.py
index 8fb2ea541a9033ab28390f099843cec0553f4cae..8da7a8bb39c35870a7030eab98a4d68b1dda45b2 100644
--- a/bob/ip/binseg/configs/datasets/refuge_od_test.py
+++ b/bob/ip/binseg/configs/datasets/refuge_od_test.py
@@ -9,28 +9,16 @@ algorithms for glaucoma detection and optic disc/cup segmentation on a common
dataset of retinal fundus images.
* Reference: [REFUGE-2018]_
-* Original resolution (height x width): 2056 x 2124
+* Original resolution (height x width): 1634 x 1634
* Configuration resolution: 1632 x 1632 (after center cropping)
-* Validation samples: 400
+* Test samples: 400
* Split reference: [REFUGE-2018]_
-
-.. warning:
-
- Notice 2 aspects before using these configurations:
-
- 1. The data cropping/resizing algorithm applied on training and "validation"
- data are slightly different and need to be cross-checked.
- 2. This is the **validation** set! The real **test** set is still not
- integrated to the originating bob.db.refuge package: See
- https://gitlab.idiap.ch/bob/bob.db.refuge/issues/1
-
"""
from bob.ip.binseg.data.transforms import CenterCrop
_transforms = [CenterCrop(1632)]
-from bob.db.refuge import Database as REFUGE
-bobdb = REFUGE(protocol="default_od")
-
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-dataset = BinSegDataset(bobdb, split="test", transforms=_transforms)
+from bob.ip.binseg.data.utils import SampleList2TorchDataset
+from bob.ip.binseg.data.refuge import dataset as refuge
+dataset = SampleList2TorchDataset(refuge.subsets("optic-disc")["test"],
+ transforms=_transforms)
diff --git a/bob/ip/binseg/data/chasedb1/test.py b/bob/ip/binseg/data/chasedb1/test.py
index a1a4af73f533e948becd2c54cfe930927e6ec392..eab83e67843830f8b2c3adf0b45792dfc5c2bcb9 100644
--- a/bob/ip/binseg/data/chasedb1/test.py
+++ b/bob/ip/binseg/data/chasedb1/test.py
@@ -13,7 +13,7 @@ from . import dataset
from ...test.utils import rc_variable_set
-def test_protocol_consitency():
+def test_protocol_consistency():
subset = dataset.subsets("default")
nose.tools.eq_(len(subset), 2)
diff --git a/bob/ip/binseg/data/drive/test.py b/bob/ip/binseg/data/drive/test.py
index f66027ef13294b236895a0a8068518dd2d4b9bc6..3fac542af22c5f43287e8c5ad82d9bd409bea907 100644
--- a/bob/ip/binseg/data/drive/test.py
+++ b/bob/ip/binseg/data/drive/test.py
@@ -13,7 +13,7 @@ from . import dataset
from ...test.utils import rc_variable_set
-def test_protocol_consitency():
+def test_protocol_consistency():
subset = dataset.subsets("default")
nose.tools.eq_(len(subset), 2)
diff --git a/bob/ip/binseg/data/hrf/test.py b/bob/ip/binseg/data/hrf/test.py
index c6e44ccde07d2d2719dcaf6c6b91a83d8c1f8db5..52207abc16c6336b03089302cbec3e0b8caff591 100644
--- a/bob/ip/binseg/data/hrf/test.py
+++ b/bob/ip/binseg/data/hrf/test.py
@@ -13,7 +13,7 @@ from . import dataset
from ...test.utils import rc_variable_set
-def test_protocol_consitency():
+def test_protocol_consistency():
subset = dataset.subsets("default")
nose.tools.eq_(len(subset), 2)
diff --git a/bob/ip/binseg/data/iostar/test.py b/bob/ip/binseg/data/iostar/test.py
index 865d2eb77fd26c0e3dee76e293457dbc2b4f0d15..128b9b4cfeb49c17a2509d8f3d195d65e3d0597e 100644
--- a/bob/ip/binseg/data/iostar/test.py
+++ b/bob/ip/binseg/data/iostar/test.py
@@ -13,7 +13,7 @@ from . import dataset
from ...test.utils import rc_variable_set
-def test_protocol_consitency():
+def test_protocol_consistency():
subset = dataset.subsets("vessel")
nose.tools.eq_(len(subset), 2)
@@ -43,13 +43,12 @@ def test_protocol_consitency():
@rc_variable_set('bob.ip.binseg.iostar.datadir')
-def test_loading_vessel():
+def test_loading():
from ..utils import count_bw
image_size = (1024, 1024)
- bw_threshold_label = 0.11 #(vessels to background proportion limit)
- def _check_sample(s):
+ def _check_sample(s, bw_threshold_label):
data = s.data
assert isinstance(data, dict)
@@ -95,66 +94,14 @@ def test_loading_vessel():
#pass
subset = dataset.subsets("vessel")
- for s in subset["train"]: _check_sample(s)
- for s in subset["test"]: _check_sample(s)
-
-
-@rc_variable_set('bob.ip.binseg.iostar.datadir')
-def test_loading_optic_disc():
-
- from ..utils import count_bw
- image_size = (1024, 1024)
- bw_threshold_label = 0.04 #(optic-disc to background proportion limit)
-
- def _check_sample(s):
-
- data = s.data
- assert isinstance(data, dict)
- nose.tools.eq_(len(data), 3)
-
- assert "data" in data
- nose.tools.eq_(data["data"].size, image_size)
- nose.tools.eq_(data["data"].mode, "RGB")
-
- assert "label" in data
- nose.tools.eq_(data["label"].size, image_size)
- nose.tools.eq_(data["label"].mode, "1")
- b, w = count_bw(data["label"])
- assert (b+w) == numpy.prod(image_size), \
- f"Counts of black + white ({b}+{w}) do not add up to total " \
- f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
- assert (w/b) < bw_threshold_label, \
- f"The proportion between black and white pixels " \
- f"({w}/{b}={w/b:.2f}) is larger than the allowed threshold " \
- f"of {bw_threshold_label} at '{s.key}':label - this could " \
- f"indicate a loading problem!"
-
- assert "mask" in data
- nose.tools.eq_(data["mask"].size, image_size)
- nose.tools.eq_(data["mask"].mode, "1")
- b, w = count_bw(data["mask"])
- assert (b+w) == numpy.prod(image_size), \
- f"Counts of black + white ({b}+{w}) do not add up to total " \
- f"image size ({numpy.prod(image_size)}) at '{s.key}':mask"
- assert w > b, \
- f"The proportion between white and black pixels " \
- f"({w} > {b}?) is not respected at '{s.key}':mask - " \
- f"this could indicate a loading problem!"
-
- # to visualize images, uncomment the folowing code
- # it should display an image with a faded background representing the
- # original data, blended with green labels and blue area indicating the
- # parts to be masked out.
- #from ..utils import overlayed_image
- #display = overlayed_image(data["data"], data["label"], data["mask"])
- #display.show()
- #import ipdb; ipdb.set_trace()
- #pass
+ bw_threshold_label = 0.11 #(vessels to background proportion limit)
+ for s in subset["train"]: _check_sample(s, bw_threshold_label)
+ for s in subset["test"]: _check_sample(s, bw_threshold_label)
subset = dataset.subsets("optic-disc")
- for s in subset["train"]: _check_sample(s)
- for s in subset["test"]: _check_sample(s)
-
+ bw_threshold_label = 0.04 #(optic-disc to background proportion limit)
+ for s in subset["train"]: _check_sample(s, bw_threshold_label)
+ for s in subset["test"]: _check_sample(s, bw_threshold_label)
@rc_variable_set('bob.ip.binseg.iostar.datadir')
def test_check():
diff --git a/bob/ip/binseg/data/refuge/__init__.py b/bob/ip/binseg/data/refuge/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..717d6cdd4345abc0f4a471cf5e5aba82c5bff2dc
--- /dev/null
+++ b/bob/ip/binseg/data/refuge/__init__.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""REFUGE (training set) for Optic Disc Segmentation
+
+The dataset consists of 1200 color fundus photographs, created for a MICCAI
+challenge. The goal of the challenge is to evaluate and compare automated
+algorithms for glaucoma detection and optic disc/cup segmentation on a common
+dataset of retinal fundus images.
+
+* Reference: [REFUGE-2018]_
+* Protocols ``optic-disc`` and ``cup``:
+ * Training samples:
+ * 400
+ * includes optic-disc and cup labels
+ * includes label: glaucomatous and non-glaucomatous
+ * original resolution: 2056 x 2124
+ * Validation samples: 400:
+ * 400
+ * includes optic-disc and cup labels
+ * original resolution: 1634 x 1634
+ * Test samples:
+ * 400
+ * includes optic-disc and cup labels
+ * includes label: glaucomatous and non-glaucomatous
+ * original resolution:
+* Split reference: [REFUGE-2018]_
+
+.. warning:
+
+ Notice that the data cropping/resizing algorithm applied on training and
+ "validation" data are slightly different and need to be cross-checked.
+
+"""
+
+import os
+import pkg_resources
+
+import bob.extension
+
+from ..jsondataset import JSONDataset
+from ..loader import load_pil_rgb
+
+_protocols = [
+ pkg_resources.resource_filename(__name__, "optic-disc.json"),
+ pkg_resources.resource_filename(__name__, "optic-cup.json"),
+ ]
+
+_root_path = bob.extension.rc.get('bob.ip.binseg.refuge.datadir',
+ os.path.realpath(os.curdir))
+
+def _loader(context, sample):
+ retval = dict(
+ data=load_pil_rgb(sample["data"]),
+ label=load_pil_rgb(sample["label"]),
+ )
+
+ if context["subset"] == "train":
+ # adds binary metadata for glaucoma/non-glaucoma patients
+ retval["glaucoma"] = os.path.basename(sample["label"]).startswith("g")
+ elif context["subset"] == "test":
+ retval["glaucoma"] = sample["label"].split(os.sep)[-2] == "G"
+ elif context["subset"] == "validation":
+ pass
+ else:
+ raise RuntimeError(f"Unknown subset {context['subset']}")
+
+ # optic disc is drawn with gray == 128 and includes the cup, drawn with
+ # black == 0. The rest is white == 255.
+ if context["protocol"] == "optic-disc":
+ retval["label"] = retval["label"].convert("L")
+ retval["label"] = retval["label"].point(lambda p: p<=150, mode="1")
+ elif context["protocol"] == "optic-cup":
+ retval["label"] = retval["label"].convert("L")
+ retval["label"] = retval["label"].point(lambda p: p<=100, mode="1")
+ else:
+ raise RuntimeError(f"Unknown protocol {context['protocol']}")
+
+ return retval
+
+dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader)
+"""REFUGE dataset object"""
diff --git a/bob/ip/binseg/data/refuge/optic-cup.json b/bob/ip/binseg/data/refuge/optic-cup.json
new file mode 120000
index 0000000000000000000000000000000000000000..1691db379cbb117c5bbee85635f3fd864acca98e
--- /dev/null
+++ b/bob/ip/binseg/data/refuge/optic-cup.json
@@ -0,0 +1 @@
+optic-disc.json
\ No newline at end of file
diff --git a/bob/ip/binseg/data/refuge/optic-disc.json b/bob/ip/binseg/data/refuge/optic-disc.json
new file mode 100644
index 0000000000000000000000000000000000000000..cde130a04f5c7240698cdf3382142f0ccacb527e
--- /dev/null
+++ b/bob/ip/binseg/data/refuge/optic-disc.json
@@ -0,0 +1,4808 @@
+{
+ "train": [
+ [
+ "Training400/Glaucoma/g0001.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0001.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0002.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0002.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0003.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0003.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0004.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0004.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0005.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0005.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0006.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0006.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0007.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0007.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0008.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0008.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0009.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0009.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0010.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0010.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0011.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0011.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0012.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0012.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0013.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0013.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0014.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0014.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0015.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0015.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0016.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0016.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0017.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0017.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0018.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0018.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0019.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0019.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0020.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0020.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0021.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0021.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0022.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0022.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0023.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0023.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0024.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0024.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0025.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0025.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0026.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0026.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0027.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0027.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0028.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0028.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0029.jpg",
+ "Annotation-Training400/Disc_Cup_Masks/Glaucoma/g0029.bmp"
+ ],
+ [
+ "Training400/Glaucoma/g0030.jpg",
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+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0319.bmp"
+ ],
+ [
+ "Test400/T0320.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0320.bmp"
+ ],
+ [
+ "Test400/T0321.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0321.bmp"
+ ],
+ [
+ "Test400/T0322.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0322.bmp"
+ ],
+ [
+ "Test400/T0323.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0323.bmp"
+ ],
+ [
+ "Test400/T0324.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0324.bmp"
+ ],
+ [
+ "Test400/T0325.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0325.bmp"
+ ],
+ [
+ "Test400/T0326.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0326.bmp"
+ ],
+ [
+ "Test400/T0327.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0327.bmp"
+ ],
+ [
+ "Test400/T0328.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0328.bmp"
+ ],
+ [
+ "Test400/T0329.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0329.bmp"
+ ],
+ [
+ "Test400/T0330.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0330.bmp"
+ ],
+ [
+ "Test400/T0331.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0331.bmp"
+ ],
+ [
+ "Test400/T0332.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0332.bmp"
+ ],
+ [
+ "Test400/T0333.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0333.bmp"
+ ],
+ [
+ "Test400/T0334.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0334.bmp"
+ ],
+ [
+ "Test400/T0335.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0335.bmp"
+ ],
+ [
+ "Test400/T0336.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0336.bmp"
+ ],
+ [
+ "Test400/T0337.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0337.bmp"
+ ],
+ [
+ "Test400/T0338.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0338.bmp"
+ ],
+ [
+ "Test400/T0339.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0339.bmp"
+ ],
+ [
+ "Test400/T0340.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0340.bmp"
+ ],
+ [
+ "Test400/T0341.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0341.bmp"
+ ],
+ [
+ "Test400/T0342.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0342.bmp"
+ ],
+ [
+ "Test400/T0343.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0343.bmp"
+ ],
+ [
+ "Test400/T0344.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0344.bmp"
+ ],
+ [
+ "Test400/T0345.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0345.bmp"
+ ],
+ [
+ "Test400/T0346.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0346.bmp"
+ ],
+ [
+ "Test400/T0347.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0347.bmp"
+ ],
+ [
+ "Test400/T0348.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0348.bmp"
+ ],
+ [
+ "Test400/T0349.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0349.bmp"
+ ],
+ [
+ "Test400/T0350.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0350.bmp"
+ ],
+ [
+ "Test400/T0351.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0351.bmp"
+ ],
+ [
+ "Test400/T0352.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0352.bmp"
+ ],
+ [
+ "Test400/T0353.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0353.bmp"
+ ],
+ [
+ "Test400/T0354.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0354.bmp"
+ ],
+ [
+ "Test400/T0355.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0355.bmp"
+ ],
+ [
+ "Test400/T0356.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0356.bmp"
+ ],
+ [
+ "Test400/T0357.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0357.bmp"
+ ],
+ [
+ "Test400/T0358.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0358.bmp"
+ ],
+ [
+ "Test400/T0359.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0359.bmp"
+ ],
+ [
+ "Test400/T0360.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0360.bmp"
+ ],
+ [
+ "Test400/T0361.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0361.bmp"
+ ],
+ [
+ "Test400/T0362.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0362.bmp"
+ ],
+ [
+ "Test400/T0363.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0363.bmp"
+ ],
+ [
+ "Test400/T0364.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0364.bmp"
+ ],
+ [
+ "Test400/T0365.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0365.bmp"
+ ],
+ [
+ "Test400/T0366.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0366.bmp"
+ ],
+ [
+ "Test400/T0367.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0367.bmp"
+ ],
+ [
+ "Test400/T0368.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0368.bmp"
+ ],
+ [
+ "Test400/T0369.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0369.bmp"
+ ],
+ [
+ "Test400/T0370.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0370.bmp"
+ ],
+ [
+ "Test400/T0371.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0371.bmp"
+ ],
+ [
+ "Test400/T0372.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0372.bmp"
+ ],
+ [
+ "Test400/T0373.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0373.bmp"
+ ],
+ [
+ "Test400/T0374.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0374.bmp"
+ ],
+ [
+ "Test400/T0375.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0375.bmp"
+ ],
+ [
+ "Test400/T0376.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0376.bmp"
+ ],
+ [
+ "Test400/T0377.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0377.bmp"
+ ],
+ [
+ "Test400/T0378.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0378.bmp"
+ ],
+ [
+ "Test400/T0379.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0379.bmp"
+ ],
+ [
+ "Test400/T0380.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0380.bmp"
+ ],
+ [
+ "Test400/T0381.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0381.bmp"
+ ],
+ [
+ "Test400/T0382.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0382.bmp"
+ ],
+ [
+ "Test400/T0383.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0383.bmp"
+ ],
+ [
+ "Test400/T0384.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0384.bmp"
+ ],
+ [
+ "Test400/T0385.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0385.bmp"
+ ],
+ [
+ "Test400/T0386.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0386.bmp"
+ ],
+ [
+ "Test400/T0387.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0387.bmp"
+ ],
+ [
+ "Test400/T0388.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0388.bmp"
+ ],
+ [
+ "Test400/T0389.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0389.bmp"
+ ],
+ [
+ "Test400/T0390.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0390.bmp"
+ ],
+ [
+ "Test400/T0391.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0391.bmp"
+ ],
+ [
+ "Test400/T0392.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0392.bmp"
+ ],
+ [
+ "Test400/T0393.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0393.bmp"
+ ],
+ [
+ "Test400/T0394.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0394.bmp"
+ ],
+ [
+ "Test400/T0395.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0395.bmp"
+ ],
+ [
+ "Test400/T0396.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0396.bmp"
+ ],
+ [
+ "Test400/T0397.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/G/T0397.bmp"
+ ],
+ [
+ "Test400/T0398.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0398.bmp"
+ ],
+ [
+ "Test400/T0399.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0399.bmp"
+ ],
+ [
+ "Test400/T0400.jpg",
+ "REFUGE-Test-GT/Disc_Cup_Masks/N/T0400.bmp"
+ ]
+ ]
+}
diff --git a/bob/ip/binseg/data/refuge/test.py b/bob/ip/binseg/data/refuge/test.py
new file mode 100644
index 0000000000000000000000000000000000000000..9c6a31e6df792722ed7a33864e41e60288f6475c
--- /dev/null
+++ b/bob/ip/binseg/data/refuge/test.py
@@ -0,0 +1,106 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+
+"""Tests for REFUGE"""
+
+import os
+
+import numpy
+import nose.tools
+from nose.plugins.attrib import attr
+
+from . import dataset
+from ...test.utils import rc_variable_set
+
+
+def test_protocol_consistency():
+
+ for protocol in ("optic-disc", "optic-cup"):
+
+ subset = dataset.subsets(protocol)
+ nose.tools.eq_(len(subset), 3)
+
+ assert "train" in subset
+ nose.tools.eq_(len(subset["train"]), 400)
+ for s in subset["train"]:
+ assert s.key.startswith("Training400")
+
+ assert "validation" in subset
+ nose.tools.eq_(len(subset["validation"]), 400)
+ for s in subset["validation"]:
+ assert s.key.startswith("REFUGE-Validation400")
+
+ assert "test" in subset
+ nose.tools.eq_(len(subset["test"]), 400)
+ for s in subset["test"]:
+ assert s.key.startswith("Test400")
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_loading():
+
+ from ..utils import count_bw
+
+ def _check_sample(
+ s, image_size, glaucoma_label, entries, bw_threshold_label
+ ):
+
+ data = s.data
+ assert isinstance(data, dict)
+ nose.tools.eq_(len(data), entries)
+
+ assert "data" in data
+ nose.tools.eq_(data["data"].size, image_size)
+ nose.tools.eq_(data["data"].mode, "RGB")
+
+ assert "label" in data
+ nose.tools.eq_(data["label"].size, image_size)
+ nose.tools.eq_(data["label"].mode, "1")
+ b, w = count_bw(data["label"])
+ assert (b + w) == numpy.prod(image_size), (
+ f"Counts of black + white ({b}+{w}) do not add up to total "
+ f"image size ({numpy.prod(image_size)}) at '{s.key}':label"
+ )
+ assert (w / b) < bw_threshold_label, (
+ f"The proportion between black and white pixels "
+ f"({w}/{b}={w/b:.3f}) is larger than the allowed threshold "
+ f"of {bw_threshold_label} at '{s.key}':label - this could "
+ f"indicate a loading problem!"
+ )
+
+ if glaucoma_label:
+ assert "glaucoma" in data
+
+ # to visualize images, uncomment the folowing code
+ # it should display an image with a faded background representing the
+ # original data, blended with green labels.
+ # print(f"{s.key}: {data.get('glaucoma')}, w/b = {w/b:.3f}")
+ # from ..utils import overlayed_image
+ # display = overlayed_image(data["data"], data["label"])
+ # display.show()
+ # import ipdb; ipdb.set_trace()
+ # pass
+
+ subset = dataset.subsets("optic-disc")
+ for s in subset["train"]:
+ _check_sample(s, (2124, 2056), True, 3, 0.03)
+ for s in subset["validation"]:
+ _check_sample(s, (1634, 1634), False, 2, 0.045)
+ for s in subset["test"]:
+ _check_sample(s, (1634, 1634), True, 3, 0.03)
+
+ subset = dataset.subsets("optic-cup")
+ for s in subset["train"]:
+ _check_sample(s, (2124, 2056), True, 3, 0.018)
+ for s in subset["validation"]:
+ _check_sample(s, (1634, 1634), False, 2, 0.035)
+ for s in subset["test"]:
+ _check_sample(s, (1634, 1634), True, 3, 0.018)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_check():
+ nose.tools.eq_(dataset.check(), 0)
diff --git a/bob/ip/binseg/data/stare/test.py b/bob/ip/binseg/data/stare/test.py
index 4db5d97f1e96f7046575fb87827c7be508562613..29d71b9627ea2061f826d3557d5bb8e010fe4044 100644
--- a/bob/ip/binseg/data/stare/test.py
+++ b/bob/ip/binseg/data/stare/test.py
@@ -13,7 +13,7 @@ from . import dataset
from ...test.utils import rc_variable_set
-def test_protocol_consitency():
+def test_protocol_consistency():
subset = dataset.subsets("default")
nose.tools.eq_(len(subset), 2)
diff --git a/bob/ip/binseg/test/test_cli.py b/bob/ip/binseg/test/test_cli.py
index 5fab2a89b12dc4a6fbfbed9f78acb9d6639e8cd7..33e3ddaee80df1ab4b5f82e35f26ac76e386dc65 100644
--- a/bob/ip/binseg/test/test_cli.py
+++ b/bob/ip/binseg/test/test_cli.py
@@ -5,6 +5,8 @@
from click.testing import CliRunner
+from nose.plugins.attrib import attr
+
def _check_help(entry_point):
@@ -136,6 +138,7 @@ def test_dataset_check_help():
_check_help(check)
+@attr('slow')
def test_dataset_check():
from ..script.dataset import check
diff --git a/bob/ip/binseg/test/test_config.py b/bob/ip/binseg/test/test_config.py
index c60bafb59ea206d006d502be63ce1c3d497e8fd8..24f5f2c6f283e9b1a6f6062b9371b907a39b36a7 100644
--- a/bob/ip/binseg/test/test_config.py
+++ b/bob/ip/binseg/test/test_config.py
@@ -2,6 +2,7 @@
# coding=utf-8
import nose.tools
+from nose.plugins.attrib import attr
import torch
@@ -12,6 +13,7 @@ from .utils import rc_variable_set
def test_drive_default_train():
from ..configs.datasets.drive import dataset
+ nose.tools.eq_(len(dataset), 20)
for sample in dataset:
nose.tools.eq_(len(sample), 4)
assert isinstance(sample[0], str)
@@ -27,6 +29,7 @@ def test_drive_default_train():
def test_drive_default_test():
from ..configs.datasets.drive_test import dataset
+ nose.tools.eq_(len(dataset), 20)
for sample in dataset:
nose.tools.eq_(len(sample), 4)
assert isinstance(sample[0], str)
@@ -42,6 +45,7 @@ def test_drive_default_test():
def test_stare_default_train():
from ..configs.datasets.stare import dataset
+ nose.tools.eq_(len(dataset), 10)
for sample in dataset:
nose.tools.eq_(len(sample), 3)
assert isinstance(sample[0], str)
@@ -55,6 +59,7 @@ def test_stare_default_train():
def test_stare_default_test():
from ..configs.datasets.stare_test import dataset
+ nose.tools.eq_(len(dataset), 10)
for sample in dataset:
nose.tools.eq_(len(sample), 3)
assert isinstance(sample[0], str)
@@ -68,6 +73,7 @@ def test_stare_default_test():
def test_chasedb1_default_train():
from ..configs.datasets.chasedb1 import dataset
+ nose.tools.eq_(len(dataset), 8)
for sample in dataset:
nose.tools.eq_(len(sample), 3)
assert isinstance(sample[0], str)
@@ -81,6 +87,7 @@ def test_chasedb1_default_train():
def test_chasedb1_default_test():
from ..configs.datasets.chasedb1_test import dataset
+ nose.tools.eq_(len(dataset), 20)
for sample in dataset:
nose.tools.eq_(len(sample), 3)
assert isinstance(sample[0], str)
@@ -94,6 +101,7 @@ def test_chasedb1_default_test():
def test_hrf_default_train():
from ..configs.datasets.hrf_1168 import dataset
+ nose.tools.eq_(len(dataset), 15)
for sample in dataset:
nose.tools.eq_(len(sample), 4)
assert isinstance(sample[0], str)
@@ -109,6 +117,7 @@ def test_hrf_default_train():
def test_hrf_default_test():
from ..configs.datasets.hrf_1168_test import dataset
+ nose.tools.eq_(len(dataset), 30)
for sample in dataset:
nose.tools.eq_(len(sample), 4)
assert isinstance(sample[0], str)
@@ -118,3 +127,93 @@ def test_hrf_default_test():
nose.tools.eq_(sample[2].dtype, torch.float32)
nose.tools.eq_(sample[3].shape, (1, 1168, 1648)) #planes, height, width
nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_disc_train():
+
+ from ..configs.datasets.refuge_od import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_disc_dev():
+
+ from ..configs.datasets.refuge_od_dev import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_disc_test():
+
+ from ..configs.datasets.refuge_od_test import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_cup_train():
+
+ from ..configs.datasets.refuge_cup import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_cup_dev():
+
+ from ..configs.datasets.refuge_cup_dev import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.refuge.datadir")
+@attr("slow")
+def test_refuge_optic_cup_test():
+
+ from ..configs.datasets.refuge_cup_test import dataset
+ nose.tools.eq_(len(dataset), 400)
+ for sample in dataset:
+ nose.tools.eq_(len(sample), 3)
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1632, 1632)) #planes, height, width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
diff --git a/bob/ip/binseg/test/test_summary.py b/bob/ip/binseg/test/test_summary.py
index a218141f2c5f7e9b8064fd376bc859ef53f4d496..a6d9948aed57612f238ec3a1333e7148b5401cb7 100644
--- a/bob/ip/binseg/test/test_summary.py
+++ b/bob/ip/binseg/test/test_summary.py
@@ -22,7 +22,7 @@ class Tester(unittest.TestCase):
self.assertIsInstance(s, str)
self.assertIsInstance(param, int)
- def test__summary_driuod(self):
+ def test_summary_driuod(self):
model = build_driuod()
s, param = summary(model)
self.assertIsInstance(s, str)
diff --git a/conda/meta.yaml b/conda/meta.yaml
index f014c0015526f69a1f9b285c6f76ed6fc334c552..4c9dbfa39356a3d9a6d10b29410493eddaeb03bc 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -62,7 +62,6 @@ test:
- bob.db.drionsdb
- bob.db.rimoner3
- bob.db.drishtigs1
- - bob.db.refuge
about:
summary: Binary Segmentation Benchmark Package for Bob
diff --git a/setup.py b/setup.py
index b8af972471fc99ce9160f2cb7aded9dd9e6fd99a..269925af9ff99faecbeeb48a0bc96f0eea00d3d8 100644
--- a/setup.py
+++ b/setup.py
@@ -102,8 +102,10 @@ setup(
"drishtigs1-cup-test = bob.ip.binseg.configs.datasets.dristhigs1_cup_test",
# refuge
"refuge-cup = bob.ip.binseg.configs.datasets.refuge_cup",
+ "refuge-cup-dev = bob.ip.binseg.configs.datasets.refuge_cup_dev",
"refuge-cup-test = bob.ip.binseg.configs.datasets.refuge_cup_test",
"refuge-od = bob.ip.binseg.configs.datasets.refuge_od",
+ "refuge-od-dev = bob.ip.binseg.configs.datasets.refuge_od_dev",
"refuge-od-test = bob.ip.binseg.configs.datasets.refuge_od_test",
# rim one r3