diff --git a/.gitignore b/.gitignore index c2ad8d26ed5f48739875ede45d8330810c5e1dd0..777eb99ff50db820cb3e6f4b9d21a4093112cc15 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,4 @@ output submitted.sql3 logs/ results/ +.coverage diff --git a/bob/ip/binseg/configs/datasets/rimoner3_cup.py b/bob/ip/binseg/configs/datasets/rimoner3_cup.py index e5bb214d03ad9fd5baa5c8b115f288ca678fb58e..e7dea012233fb1bc067d2466cc72f383688f2fe5 100644 --- a/bob/ip/binseg/configs/datasets/rimoner3_cup.py +++ b/bob/ip/binseg/configs/datasets/rimoner3_cup.py @@ -20,8 +20,7 @@ from bob.ip.binseg.data.transforms import Pad from bob.ip.binseg.configs.datasets.utils import DATA_AUGMENTATION as _DA _transforms = [Pad((8, 8, 8, 8))] + _DA -from bob.db.rimoner3 import Database as RIMONER3 -bobdb = RIMONER3(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.rimoner3 import dataset as rimoner3 +dataset = SampleList2TorchDataset(rimoner3.subsets("optic-cup-exp1")["train"], + transforms=_transforms) diff --git a/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py b/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py index 6ed91adc8e7df3cd8f447bc450bcd73648e997f1..c7f17fca7e9e5c0cb9b66de86c1a50b14ba29746 100644 --- a/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py +++ b/bob/ip/binseg/configs/datasets/rimoner3_cup_test.py @@ -19,8 +19,7 @@ baseline. from bob.ip.binseg.data.transforms import Pad _transforms = [Pad((8, 8, 8, 8))] -from bob.db.rimoner3 import Database as RIMONER3 -bobdb = RIMONER3(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.rimoner3 import dataset as rimoner3 +dataset = SampleList2TorchDataset(rimoner3.subsets("optic-cup-exp1")["test"], + transforms=_transforms) diff --git a/bob/ip/binseg/configs/datasets/rimoner3_od.py b/bob/ip/binseg/configs/datasets/rimoner3_od.py index 3757e2f04bd3db850306a5e75851a9bd0e1d8d2c..b7da94d1e0bf9d09bf0f003067c862cef002d7a4 100644 --- a/bob/ip/binseg/configs/datasets/rimoner3_od.py +++ b/bob/ip/binseg/configs/datasets/rimoner3_od.py @@ -20,8 +20,7 @@ from bob.ip.binseg.data.transforms import Pad from bob.ip.binseg.configs.datasets.utils import DATA_AUGMENTATION as _DA _transforms = [Pad((8, 8, 8, 8))] + _DA -from bob.db.rimoner3 import Database as RIMONER3 -bobdb = RIMONER3(protocol="default_od") - -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.rimoner3 import dataset as rimoner3 +dataset = SampleList2TorchDataset(rimoner3.subsets("optic-disc-exp1")["train"], + transforms=_transforms) diff --git a/bob/ip/binseg/configs/datasets/rimoner3_od_test.py b/bob/ip/binseg/configs/datasets/rimoner3_od_test.py index 9fdb9a1b2c518fdd0d7475a85a48a5f117164abb..4012858ffc5bd07c1506a82f42d8f35aac408dc0 100644 --- a/bob/ip/binseg/configs/datasets/rimoner3_od_test.py +++ b/bob/ip/binseg/configs/datasets/rimoner3_od_test.py @@ -19,8 +19,7 @@ baseline. from bob.ip.binseg.data.transforms import Pad _transforms = [Pad((8, 8, 8, 8))] -from bob.db.rimoner3 import Database as RIMONER3 -bobdb = RIMONER3(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.rimoner3 import dataset as rimoner3 +dataset = SampleList2TorchDataset(rimoner3.subsets("optic-disc-exp1")["test"], + transforms=_transforms) diff --git a/bob/ip/binseg/data/rimoner3/__init__.py b/bob/ip/binseg/data/rimoner3/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..d251bc4f0d27a66eebfc452017fbac3da79865aa --- /dev/null +++ b/bob/ip/binseg/data/rimoner3/__init__.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python +# coding=utf-8 + +"""RIM-ONE r3 (training set) for Cup Segmentation + +The dataset contains 159 stereo eye fundus images with a resolution of 2144 x +1424. The right part of the stereo image is disregarded. Two sets of +ground-truths for optic disc and optic cup are available. The first set is +commonly used for training and testing. The second set acts as a “human” +baseline. A third set, composed of annotation averages may also be used for +training and evaluation purposes. + +* Reference: [RIMONER3-2015]_ +* Original resolution (height x width): 1424 x 1072 +* Split reference: [MANINIS-2016]_ +* Protocols ``optic-disc-exp1``, ``optic-cup-exp1``, ``optic-disc-exp2``, + ``optic-cup-exp2``, ``optic-disc-avg`` and ``optic-cup-avg``: + + * Training: 99 + * Test: 60 +""" + +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__, "optic-disc-exp1.json"), + pkg_resources.resource_filename(__name__, "optic-cup-exp1.json"), + pkg_resources.resource_filename(__name__, "optic-disc-exp2.json"), + pkg_resources.resource_filename(__name__, "optic-cup-exp2.json"), + pkg_resources.resource_filename(__name__, "optic-disc-avg.json"), + pkg_resources.resource_filename(__name__, "optic-cup-avg.json"), + ] + +_root_path = bob.extension.rc.get('bob.ip.binseg.rimoner3.datadir', + os.path.realpath(os.curdir)) + +def _loader(context, sample): + # RIM-ONE r3 provides stereo images - we clip them here to get only the + # left part of the image, which is also annotated + return dict( + data=load_pil_rgb(sample["data"]).crop((0, 0, 1072, 1424)), + label=load_pil_1(sample["label"]).crop((0, 0, 1072, 1424)), + ) + +dataset = JSONDataset(protocols=_protocols, root_path=_root_path, loader=_loader) +"""RIM-ONE r3 dataset object""" diff --git a/bob/ip/binseg/data/rimoner3/optic-cup-avg.json b/bob/ip/binseg/data/rimoner3/optic-cup-avg.json new file mode 100644 index 0000000000000000000000000000000000000000..d464222e32e8f1da24898a0c8a7308564c9d0a7f --- /dev/null +++ b/bob/ip/binseg/data/rimoner3/optic-cup-avg.json @@ -0,0 +1,642 @@ +{ + "train": [ + [ + "Healthy/Stereo Images/N-10-R.jpg", + "Healthy/Average_masks/N-10-R-Cup-Avg.png" + ], + [ + "Healthy/Stereo Images/N-11-L.jpg", + 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+ "Glaucoma and suspects/Stereo Images/S-31-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-31-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-32-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-32-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-33-R.jpg", + "Glaucoma and suspects/Expert2_masks/S-33-R-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-34-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-34-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-35-R.jpg", + "Glaucoma and suspects/Expert2_masks/S-35-R-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-3-R.jpg", + "Glaucoma and suspects/Expert2_masks/S-3-R-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-4-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-4-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-5-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-5-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-6-R.jpg", + "Glaucoma and suspects/Expert2_masks/S-6-R-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-7-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-7-L-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-8-R.jpg", + "Glaucoma and suspects/Expert2_masks/S-8-R-1-Disc-exp2.png" + ], + [ + "Glaucoma and suspects/Stereo Images/S-9-L.jpg", + "Glaucoma and suspects/Expert2_masks/S-9-L-1-Disc-exp2.png" + ] + ] +} diff --git a/bob/ip/binseg/data/rimoner3/test.py b/bob/ip/binseg/data/rimoner3/test.py new file mode 100644 index 0000000000000000000000000000000000000000..6a28b668170b58e648b41adba8db05cb1d4c61ba --- /dev/null +++ b/bob/ip/binseg/data/rimoner3/test.py @@ -0,0 +1,117 @@ +#!/usr/bin/env python +# coding=utf-8 + + +"""Tests for RIM-ONE r3""" + +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-exp1", "optic-cup-exp1", "optic-disc-exp2", + "optic-cup-exp2", "optic-disc-avg", "optic-cup-avg"): + + subset = dataset.subsets(protocol) + nose.tools.eq_(len(subset), 2) + + assert "train" in subset + nose.tools.eq_(len(subset["train"]), 99) + for s in subset["train"]: + assert "Stereo Images" in s.key + + assert "test" in subset + nose.tools.eq_(len(subset["test"]), 60) + for s in subset["test"]: + assert "Stereo Images" in s.key + + +@rc_variable_set("bob.ip.binseg.rimoner3.datadir") +@attr("slow") +def test_loading(): + + from ..utils import count_bw + image_size = (1072, 1424) + + def _check_sample(s, bw_threshold_label): + + data = s.data + assert isinstance(data, dict) + nose.tools.eq_(len(data), 2) + + 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!" + + # to visualize images, uncomment the folowing code + # it should display an image with a faded background representing the + # original data, blended with green labels. + from ..utils import overlayed_image + display = overlayed_image(data["data"], data["label"]) + display.show() + import ipdb; ipdb.set_trace() + + return w/b + + subset = dataset.subsets("optic-cup-exp1") + limit = None + proportions = [_check_sample(s, 0.048) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.042) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + subset = dataset.subsets("optic-disc-exp1") + proportions = [_check_sample(s, 0.088) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.061) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + subset = dataset.subsets("optic-cup-exp2") + proportions = [_check_sample(s, 0.039) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.038) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + subset = dataset.subsets("optic-disc-exp2") + proportions = [_check_sample(s, 0.090) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.065) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + subset = dataset.subsets("optic-cup-avg") + proportions = [_check_sample(s, 0.042) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.040) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + subset = dataset.subsets("optic-disc-avg") + proportions = [_check_sample(s, 0.089) for s in subset["train"][:limit]] + #print(f"max label proportions = {max(proportions)}") + proportions = [_check_sample(s, 0.063) for s in subset["test"][:limit]] + #print(f"max label proportions = {max(proportions)}") + + +@rc_variable_set("bob.ip.binseg.rimoner3.datadir") +@attr("slow") +def test_check(): + nose.tools.eq_(dataset.check(), 0) diff --git a/conda/meta.yaml b/conda/meta.yaml index f8e8db1c68f34b9a4ef37d13b51537b5944c9c75..a4082688604c7423c1ad502438d275b8a6fd6491 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -60,7 +60,6 @@ test: - sphinx_rtd_theme - sphinxcontrib-programoutput - bob.db.drionsdb - - bob.db.rimoner3 about: summary: Binary Segmentation Benchmark Package for Bob diff --git a/doc/api.rst b/doc/api.rst index fae023f1c8b70ca6b3118f18f9574671d2bddf2b..6b6a682e39829650de79ba0e46465940888d0d53 100644 --- a/doc/api.rst +++ b/doc/api.rst @@ -38,6 +38,7 @@ Datasets bob.ip.binseg.data.iostar bob.ip.binseg.data.refuge bob.ip.binseg.data.drishtigs1 + bob.ip.binseg.data.rimoner3 Engines