[configs.datasets] Add resources for matched test (mtest)

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

+#!/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)]),
+}

bob/ip/binseg/configs/datasets/drive/mtest.py

+#!/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)]),
+        }

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

+#!/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)]
+    ),
+}

bob/ip/binseg/configs/datasets/iostar/vessel_mtest.py

+#!/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)]),
+}

bob/ip/binseg/configs/datasets/stare/mtest.py

+#!/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)]),
+}

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):
         """

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

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
 

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",