From 35dcc231bd6f0a6a93ae399907c9b455bce5c4db Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.anjos@idiap.ch>
Date: Thu, 30 Apr 2020 12:48:24 +0200
Subject: [PATCH] [configs.datasets] Add resources for matched test (mtest)
---
.../binseg/configs/datasets/chasedb1/mtest.py | 21 +++
bob/ip/binseg/configs/datasets/drive/mtest.py | 19 +++
bob/ip/binseg/configs/datasets/hrf/mtest.py | 25 +++
.../configs/datasets/iostar/vessel_mtest.py | 21 +++
bob/ip/binseg/configs/datasets/stare/mtest.py | 21 +++
bob/ip/binseg/data/utils.py | 36 ++++-
bob/ip/binseg/test/test_config.py | 150 +++++++++++++++++-
doc/api.rst | 5 +
setup.py | 5 +
9 files changed, 296 insertions(+), 7 deletions(-)
create mode 100644 bob/ip/binseg/configs/datasets/chasedb1/mtest.py
create mode 100644 bob/ip/binseg/configs/datasets/drive/mtest.py
create mode 100644 bob/ip/binseg/configs/datasets/hrf/mtest.py
create mode 100644 bob/ip/binseg/configs/datasets/iostar/vessel_mtest.py
create mode 100644 bob/ip/binseg/configs/datasets/stare/mtest.py
diff --git a/bob/ip/binseg/configs/datasets/chasedb1/mtest.py b/bob/ip/binseg/configs/datasets/chasedb1/mtest.py
new file mode 100644
index 00000000..0860d972
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/chasedb1/mtest.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""CHASE-DB1 cross-evaluation dataset with matched resolution
+
+* Configuration resolution (height x width): 960 x 960
+"""
+
+from bob.ip.binseg.data.transforms import CenterCrop, Pad, Resize
+from bob.ip.binseg.configs.datasets.chasedb1.xtest import dataset as _xt
+
+dataset = {
+ "train": _xt["train"],
+ "test": _xt["test"],
+ "drive": _xt["drive"].copy([CenterCrop((544, 544)), Resize(960)]),
+ "stare": _xt["stare"].copy(
+ [Pad((0, 32, 0, 32)), Resize(960), CenterCrop(960)]
+ ),
+ "hrf": _xt["hrf"].copy([Pad((0, 584, 0, 584)), Resize(960)]),
+ "iostar": _xt["iostar"].copy([Resize(960)]),
+}
diff --git a/bob/ip/binseg/configs/datasets/drive/mtest.py b/bob/ip/binseg/configs/datasets/drive/mtest.py
new file mode 100644
index 00000000..201e7b89
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/drive/mtest.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""DRIVE cross-evaluation dataset with matched resolution
+
+* Configuration resolution: 544 x 544
+"""
+
+from bob.ip.binseg.data.transforms import Resize, Pad, Crop
+from bob.ip.binseg.configs.datasets.drive.xtest import dataset as _xt
+
+dataset = {
+ "train": _xt["train"],
+ "test": _xt["test"],
+ "stare": _xt["stare"].copy([Resize(471), Pad((0, 37, 0, 36))]),
+ "chasedb1": _xt["chasedb1"].copy([Resize(544), Crop(0, 12, 544, 544)]),
+ "hrf": _xt["hrf"].copy([Resize((363)), Pad((0, 90, 0, 91))]),
+ "iostar": _xt["iostar"].copy([Resize(544)]),
+ }
diff --git a/bob/ip/binseg/configs/datasets/hrf/mtest.py b/bob/ip/binseg/configs/datasets/hrf/mtest.py
new file mode 100644
index 00000000..b5f8f646
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/hrf/mtest.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""HRF cross-evaluation dataset with matched resolution
+
+* Configuration resolution: 1168 x 1648
+"""
+
+from bob.ip.binseg.data.transforms import Crop, Pad, Resize
+from bob.ip.binseg.configs.datasets.hrf.xtest import dataset as _xt
+
+dataset = {
+ "train": _xt["train"],
+ "test": _xt["test"],
+ "drive": _xt["drive"].copy(
+ [Crop(75, 10, 416, 544), Pad((21, 0, 22, 0)), Resize(1168)]
+ ),
+ "stare": _xt["stare"].copy(
+ [Crop(50, 0, 500, 705), Resize(1168), Pad((1, 0, 1, 0))]
+ ),
+ "chasedb1": _xt["chasedb1"].copy([Crop(140, 18, 680, 960), Resize(1168)]),
+ "iostar": _xt["iostar"].copy(
+ [Crop(144, 0, 768, 1024), Pad((30, 0, 30, 0)), Resize(1168)]
+ ),
+}
diff --git a/bob/ip/binseg/configs/datasets/iostar/vessel_mtest.py b/bob/ip/binseg/configs/datasets/iostar/vessel_mtest.py
new file mode 100644
index 00000000..c89cf204
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/iostar/vessel_mtest.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""IOSTAR vessel cross-evaluation dataset with matched resolution
+
+* Configuration resolution: 1024 x 1024
+"""
+
+from bob.ip.binseg.data.transforms import CenterCrop, Crop, Pad, Resize
+from bob.ip.binseg.configs.datasets.iostar.vessel_xtest import dataset as _xt
+
+dataset = {
+ "train": _xt["train"],
+ "test": _xt["test"],
+ "drive": _xt["drive"].copy([CenterCrop((540, 540)), Resize(1024)]),
+ "stare": _xt["stare"].copy(
+ [Pad((0, 32, 0, 32)), Resize(1024), CenterCrop(1024)]
+ ),
+ "chasedb1": _xt["chasedb1"].copy([Crop(0, 18, 960, 960), Resize(1024)]),
+ "hrf": _xt["hrf"].copy([Pad((0, 584, 0, 584)), Resize(1024)]),
+}
diff --git a/bob/ip/binseg/configs/datasets/stare/mtest.py b/bob/ip/binseg/configs/datasets/stare/mtest.py
new file mode 100644
index 00000000..4485ff81
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/stare/mtest.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# coding=utf-8
+
+"""STARE cross-evaluation dataset with matched resolution
+
+* Configuration resolution: 704 x 608
+"""
+
+from bob.ip.binseg.data.transforms import CenterCrop, Pad, Resize
+from bob.ip.binseg.configs.datasets.stare.xtest import dataset as _xt
+
+dataset = {
+ "train": _xt["train"],
+ "test": _xt["test"],
+ "drive": _xt["drive"].copy(
+ [CenterCrop((470, 544)), Pad((10, 9, 10, 8)), Resize(608)]
+ ),
+ "chasedb1": _xt["chasedb1"].copy([CenterCrop((829, 960)), Resize(608)]),
+ "hrf": _xt["hrf"].copy([Pad((0, 345, 0, 345)), Resize(608)]),
+ "iostar": _xt["iostar"].copy([Pad((81, 0, 81, 0)), Resize(608)]),
+}
diff --git a/bob/ip/binseg/data/utils.py b/bob/ip/binseg/data/utils.py
index 3d77e9c3..2d1439a6 100644
--- a/bob/ip/binseg/data/utils.py
+++ b/bob/ip/binseg/data/utils.py
@@ -125,6 +125,16 @@ class SampleListDataset(torch.utils.data.Dataset):
It supports indexing such that dataset[i] can be used to get ith sample.
+ Attributes
+ ----------
+
+ transforms : list
+ An accessor to the list of transforms to be applied (excluding the last
+ transform, which is fixed). Notice that, after setting, a last transform
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied
+ - you do not need to add that.
+
+
Parameters
----------
@@ -134,14 +144,36 @@ class SampleListDataset(torch.utils.data.Dataset):
transforms : :py:class:`list`, Optional
a list of transformations to be applied to **both** image and
ground-truth data. Notice a last transform
- (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied.
+ (:py:class:`bob.ip.binseg.data.transforms.ToTensor`) is always applied
+ - you do not need to add that.
"""
def __init__(self, samples, transforms=[]):
self._samples = samples
- self._transforms = Compose(transforms + [ToTensor()])
+ self.transforms = transforms
+
+ @property
+ def transforms(self):
+ return self._transforms.transforms[:-1]
+
+ @transforms.setter
+ def transforms(self, l):
+ self._transforms = Compose(l + [ToTensor()])
+
+ def copy(self, transforms=None):
+ """Returns a deep copy of itself, optionally resetting transforms
+
+ Parameters
+ ----------
+
+ transforms : :py:class:`list`, Optional
+ An optional list of transforms to set in the copy. If not
+ specified, use ``self.transforms``.
+ """
+
+ return SampleListDataset(self._samples, transforms or self.transforms)
def __len__(self):
"""
diff --git a/bob/ip/binseg/test/test_config.py b/bob/ip/binseg/test/test_config.py
index 10d08e49..52e3a2b3 100644
--- a/bob/ip/binseg/test/test_config.py
+++ b/bob/ip/binseg/test/test_config.py
@@ -45,7 +45,35 @@ def test_drive():
_check_subset(dataset["test"], 20)
-@rc_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
+def test_drive_mtest():
+
+ from ..configs.datasets.drive.mtest import dataset
+ nose.tools.eq_(len(dataset), 6)
+
+ from ..configs.datasets.drive.default import dataset as baseline
+ nose.tools.eq_(dataset["train"], baseline["train"])
+ nose.tools.eq_(dataset["test"], baseline["test"])
+
+ for subset in dataset:
+ for sample in dataset[subset]:
+ assert 3 <= len(sample) <= 4
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 544, 544)) #planes, height, width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 544, 544))
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ if len(sample) == 4:
+ nose.tools.eq_(sample[3].shape, (1, 544, 544))
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
@rc_variable_set("bob.ip.binseg.hrf.datadir")
@rc_variable_set("bob.ip.binseg.iostar.datadir")
@@ -74,7 +102,7 @@ def test_drive_covd():
@rc_variable_set("bob.ip.binseg.drive.datadir")
-@rc_variable_set("bob.ip.binseg.stare.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
@rc_variable_set("bob.ip.binseg.hrf.datadir")
@rc_variable_set("bob.ip.binseg.iostar.datadir")
@@ -150,6 +178,34 @@ def test_stare():
_check_subset(dataset["test"], 10)
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
+def test_stare_mtest():
+
+ from ..configs.datasets.stare.mtest import dataset
+ nose.tools.eq_(len(dataset), 6)
+
+ from ..configs.datasets.stare.ah import dataset as baseline
+ nose.tools.eq_(dataset["train"], baseline["train"])
+ nose.tools.eq_(dataset["test"], baseline["test"])
+
+ for subset in dataset:
+ for sample in dataset[subset]:
+ assert 3 <= len(sample) <= 4
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 608, 704)) #planes,height,width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 608, 704)) #planes,height,width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ if len(sample) == 4:
+ nose.tools.eq_(sample[3].shape, (1, 608, 704))
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@stare_variable_set("bob.ip.binseg.stare.datadir")
@rc_variable_set("bob.ip.binseg.drive.datadir")
@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
@rc_variable_set("bob.ip.binseg.hrf.datadir")
@@ -200,7 +256,35 @@ def test_chasedb1():
@rc_variable_set("bob.ip.binseg.drive.datadir")
-@rc_variable_set("bob.ip.binseg.stare.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
+def test_chasedb1_mtest():
+
+ from ..configs.datasets.chasedb1.mtest import dataset
+ nose.tools.eq_(len(dataset), 6)
+
+ from ..configs.datasets.chasedb1.first_annotator import dataset as baseline
+ nose.tools.eq_(dataset["train"], baseline["train"])
+ nose.tools.eq_(dataset["test"], baseline["test"])
+
+ for subset in dataset:
+ for sample in dataset[subset]:
+ assert 3 <= len(sample) <= 4
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 960, 960)) #planes,height,width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 960, 960)) #planes,height,width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ if len(sample) == 4:
+ nose.tools.eq_(sample[3].shape, (1, 960, 960))
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
@rc_variable_set("bob.ip.binseg.hrf.datadir")
@rc_variable_set("bob.ip.binseg.iostar.datadir")
def test_chasedb1_covd():
@@ -249,8 +333,36 @@ def test_hrf():
@rc_variable_set("bob.ip.binseg.drive.datadir")
-@rc_variable_set("bob.ip.binseg.stare.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
+def test_hrf_mtest():
+
+ from ..configs.datasets.hrf.mtest import dataset
+ nose.tools.eq_(len(dataset), 6)
+
+ from ..configs.datasets.hrf.default import dataset as baseline
+ nose.tools.eq_(dataset["train"], baseline["train"])
+ nose.tools.eq_(dataset["test"], baseline["test"])
+
+ for subset in dataset:
+ for sample in dataset[subset]:
+ assert 3 <= len(sample) <= 4
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1168, 1648)) #planes,height,width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1168, 1648)) #planes,height,width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ if len(sample) == 4:
+ nose.tools.eq_(sample[3].shape, (1, 1168, 1648))
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
@rc_variable_set("bob.ip.binseg.iostar.datadir")
def test_hrf_covd():
@@ -300,9 +412,37 @@ def test_iostar():
@rc_variable_set("bob.ip.binseg.drive.datadir")
-@rc_variable_set("bob.ip.binseg.stare.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
+@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
+@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
+def test_iostar_mtest():
+
+ from ..configs.datasets.iostar.vessel_mtest import dataset
+ nose.tools.eq_(len(dataset), 6)
+
+ from ..configs.datasets.iostar.vessel import dataset as baseline
+ nose.tools.eq_(dataset["train"], baseline["train"])
+ nose.tools.eq_(dataset["test"], baseline["test"])
+
+ for subset in dataset:
+ for sample in dataset[subset]:
+ assert 3 <= len(sample) <= 4
+ assert isinstance(sample[0], str)
+ nose.tools.eq_(sample[1].shape, (3, 1024, 1024)) #planes,height,width
+ nose.tools.eq_(sample[1].dtype, torch.float32)
+ nose.tools.eq_(sample[2].shape, (1, 1024, 1024)) #planes,height,width
+ nose.tools.eq_(sample[2].dtype, torch.float32)
+ if len(sample) == 4:
+ nose.tools.eq_(sample[3].shape, (1, 1024, 1024))
+ nose.tools.eq_(sample[3].dtype, torch.float32)
+
+
+@rc_variable_set("bob.ip.binseg.drive.datadir")
+@stare_variable_set("bob.ip.binseg.stare.datadir")
@rc_variable_set("bob.ip.binseg.chasedb1.datadir")
@rc_variable_set("bob.ip.binseg.hrf.datadir")
+@rc_variable_set("bob.ip.binseg.iostar.datadir")
def test_iostar_covd():
from ..configs.datasets.iostar.covd import dataset
diff --git a/doc/api.rst b/doc/api.rst
index c73aedd2..8d145ad5 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -138,23 +138,27 @@ Datasets
bob.ip.binseg.configs.datasets.chasedb1.first_annotator
bob.ip.binseg.configs.datasets.chasedb1.second_annotator
bob.ip.binseg.configs.datasets.chasedb1.xtest
+ bob.ip.binseg.configs.datasets.chasedb1.mtest
bob.ip.binseg.configs.datasets.chasedb1.covd
bob.ip.binseg.configs.datasets.chasedb1.ssl
bob.ip.binseg.configs.datasets.drive.default
bob.ip.binseg.configs.datasets.drive.second_annotator
bob.ip.binseg.configs.datasets.drive.xtest
+ bob.ip.binseg.configs.datasets.drive.mtest
bob.ip.binseg.configs.datasets.drive.covd
bob.ip.binseg.configs.datasets.drive.ssl
bob.ip.binseg.configs.datasets.hrf.default
bob.ip.binseg.configs.datasets.hrf.xtest
+ bob.ip.binseg.configs.datasets.hrf.mtest
bob.ip.binseg.configs.datasets.hrf.default_fullres
bob.ip.binseg.configs.datasets.hrf.covd
bob.ip.binseg.configs.datasets.hrf.ssl
bob.ip.binseg.configs.datasets.iostar.vessel
bob.ip.binseg.configs.datasets.iostar.vessel_xtest
+ bob.ip.binseg.configs.datasets.iostar.vessel_mtest
bob.ip.binseg.configs.datasets.iostar.optic_disc
bob.ip.binseg.configs.datasets.iostar.covd
bob.ip.binseg.configs.datasets.iostar.ssl
@@ -162,6 +166,7 @@ Datasets
bob.ip.binseg.configs.datasets.stare.ah
bob.ip.binseg.configs.datasets.stare.vk
bob.ip.binseg.configs.datasets.stare.xtest
+ bob.ip.binseg.configs.datasets.stare.mtest
bob.ip.binseg.configs.datasets.stare.covd
bob.ip.binseg.configs.datasets.stare.ssl
diff --git a/setup.py b/setup.py
index 11b08d12..bff45cf3 100644
--- a/setup.py
+++ b/setup.py
@@ -62,6 +62,7 @@ setup(
"drive = bob.ip.binseg.configs.datasets.drive.default",
"drive-2nd = bob.ip.binseg.configs.datasets.drive.second_annotator",
"drive-xtest = bob.ip.binseg.configs.datasets.drive.xtest",
+ "drive-mtest = bob.ip.binseg.configs.datasets.drive.mtest",
"drive-covd = bob.ip.binseg.configs.datasets.drive.covd",
"drive-ssl = bob.ip.binseg.configs.datasets.drive.ssl",
@@ -69,12 +70,14 @@ setup(
"stare = bob.ip.binseg.configs.datasets.stare.ah",
"stare-2nd = bob.ip.binseg.configs.datasets.stare.vk",
"stare-xtest = bob.ip.binseg.configs.datasets.stare.xtest",
+ "stare-mtest = bob.ip.binseg.configs.datasets.stare.mtest",
"stare-covd = bob.ip.binseg.configs.datasets.stare.covd",
"stare-ssl = bob.ip.binseg.configs.datasets.stare.ssl",
# iostar
"iostar-vessel = bob.ip.binseg.configs.datasets.iostar.vessel",
"iostar-vessel-xtest = bob.ip.binseg.configs.datasets.iostar.vessel_xtest",
+ "iostar-vessel-mtest = bob.ip.binseg.configs.datasets.iostar.vessel_mtest",
"iostar-disc = bob.ip.binseg.configs.datasets.iostar.optic_disc",
"iostar-vessel-covd = bob.ip.binseg.configs.datasets.iostar.covd",
"iostar-vessel-ssl = bob.ip.binseg.configs.datasets.iostar.ssl",
@@ -82,6 +85,7 @@ setup(
# hrf
"hrf = bob.ip.binseg.configs.datasets.hrf.default",
"hrf-xtest = bob.ip.binseg.configs.datasets.hrf.xtest",
+ "hrf-mtest = bob.ip.binseg.configs.datasets.hrf.mtest",
"hrf-highres = bob.ip.binseg.configs.datasets.hrf.default_fullres",
"hrf-covd = bob.ip.binseg.configs.datasets.hrf.covd",
"hrf-ssl = bob.ip.binseg.configs.datasets.hrf.ssl",
@@ -90,6 +94,7 @@ setup(
"chasedb1 = bob.ip.binseg.configs.datasets.chasedb1.first_annotator",
"chasedb1-2nd = bob.ip.binseg.configs.datasets.chasedb1.second_annotator",
"chasedb1-xtest = bob.ip.binseg.configs.datasets.chasedb1.xtest",
+ "chasedb1-mtest = bob.ip.binseg.configs.datasets.chasedb1.mtest",
"chasedb1-covd = bob.ip.binseg.configs.datasets.chasedb1.covd",
"chasedb1-ssl = bob.ip.binseg.configs.datasets.chasedb1.ssl",
--
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