[bob] Lowercase all new datasets (CXR)

bob/ip/binseg/configs/datasets/JSRT/__init__.py

@@ -4,7 +4,7 @@
 
 def _maker(protocol):
 
-    from ....data.JSRT import dataset as raw
+    from ....data.jsrt import dataset as raw
     from ....data.transforms import Resize
     from .. import make_dataset as mk
 

bob/ip/binseg/configs/datasets/JSRT/default.py

@@ -3,11 +3,11 @@
 
 """Japanese Society of Radiological Technology dataset for Lung Segmentation (default protocol)
 
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Configuration resolution: 512 x 512
-* See :py:mod:`bob.ip.binseg.data.JSRT` for dataset details
+* See :py:mod:`bob.ip.binseg.data.jsrt` for dataset details
 """
 
-from bob.ip.binseg.configs.datasets.JSRT import _maker
+from bob.ip.binseg.configs.datasets.jsrt import _maker
 
 dataset = _maker("default")

bob/ip/binseg/configs/datasets/JSRT/xtest.py

 #!/usr/bin/env python
 # coding=utf-8
 
-"""JSRT cross-evaluation dataset
+"""JSRT CXR cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.JSRT.default import dataset as _jsrt
-from bob.ip.binseg.configs.datasets.MC.default import dataset as _mc
-from bob.ip.binseg.configs.datasets.Shenzhen.default import dataset as _shenzhen
+from bob.ip.binseg.configs.datasets.jsrt.default import dataset as _jsrt
+from bob.ip.binseg.configs.datasets.montgomery.default import dataset as _mc
+from bob.ip.binseg.configs.datasets.shenzhen.default import dataset as _shenzhen
 
 dataset = {
     "train": _jsrt["train"],
     "validation": _jsrt["validation"],
     "test": _jsrt["test"],
-    "MC (train)": _mc["train"],
-    "MC (validation)": _mc["validation"],
-    "MC (test)": _mc["test"],
-    "Shenzhen (train)": _shenzhen["train"],
-    "Shenzhen (validation)": _shenzhen["validation"],
-    "Shenzhen (test)": _shenzhen["test"],
+    "montgomery (train)": _mc["train"],
+    "montgomery (validation)": _mc["validation"],
+    "montgomery (test)": _mc["test"],
+    "shenzhen (train)": _shenzhen["train"],
+    "shenzhen (validation)": _shenzhen["validation"],
+    "shenzhen (test)": _shenzhen["test"],
 }

bob/ip/binseg/configs/datasets/MC/xtest.py

-#!/usr/bin/env python
-# coding=utf-8
-
-"""MC cross-evaluation dataset
-"""
-
-from bob.ip.binseg.configs.datasets.JSRT.default import dataset as _jsrt
-from bob.ip.binseg.configs.datasets.MC.default import dataset as _mc
-from bob.ip.binseg.configs.datasets.Shenzhen.default import dataset as _shenzhen
-
-dataset = {
-    "train": _mc["train"],
-    "validation": _mc["validation"],
-    "test": _mc["test"],
-    "JSRT (train)": _jsrt["train"],
-    "JSRT (validation)": _jsrt["validation"],
-    "JSRT (test)": _jsrt["test"],
-    "Shenzhen (train)": _shenzhen["train"],
-    "Shenzhen (validation)": _shenzhen["validation"],
-    "Shenzhen (test)": _shenzhen["test"],
-}

bob/ip/binseg/configs/datasets/Shenzhen/__init__.py

@@ -2,19 +2,10 @@
 # coding=utf-8
 
 
-def _maker(protocol):
+def _maker(protocol, n):
 
-    from ....data.Shenzhen import dataset as raw
+    from ....data.shenzhen import dataset as raw
     from ....data.transforms import Resize
     from .. import make_dataset as mk
 
-    return mk(raw.subsets(protocol), [Resize((512, 512))])
-
-
-def _maker_256(protocol):
-
-    from ....data.Shenzhen import dataset as raw
-    from ....data.transforms import Resize
-    from .. import make_dataset as mk
-
-    return mk(raw.subsets(protocol), [Resize((256, 256))])
+    return mk(raw.subsets(protocol), [Resize((n, n))])

bob/ip/binseg/configs/datasets/Shenzhen/default.py

@@ -3,11 +3,11 @@
 
 """Shenzhen dataset for Lung Segmentation (default protocol)
 
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Configuration resolution: 512 x 512
-* See :py:mod:`bob.ip.binseg.data.Shenzhen` for dataset details
+* See :py:mod:`bob.ip.binseg.data.shenzhen` for dataset details
 """
 
-from bob.ip.binseg.configs.datasets.Shenzhen import _maker
+from bob.ip.binseg.configs.datasets.shenzhen import _maker
 
-dataset = _maker("default")
+dataset = _maker("default", 512)

bob/ip/binseg/configs/datasets/Shenzhen/default_256.py

@@ -3,11 +3,11 @@
 
 """Shenzhen dataset for Lung Segmentation (default protocol)
 
-* Split reference: [GAÁL-2020]_
-* Configuration resolution: 512 x 512
-* See :py:mod:`bob.ip.binseg.data.Shenzhen` for dataset details
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256 pixels
+* See :py:mod:`bob.ip.binseg.data.shenzhen` for dataset details
 """
 
-from bob.ip.binseg.configs.datasets.Shenzhen import _maker_256
+from bob.ip.binseg.configs.datasets.shenzhen import _maker
 
-dataset = _maker_256("default")
+dataset = _maker("default", 256)

bob/ip/binseg/configs/datasets/Shenzhen/xtest.py

@@ -4,18 +4,18 @@
 """Shenzhen cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.JSRT.default import dataset as _jsrt
-from bob.ip.binseg.configs.datasets.MC.default import dataset as _mc
-from bob.ip.binseg.configs.datasets.Shenzhen.default import dataset as _shenzhen
+from bob.ip.binseg.configs.datasets.jsrt.default import dataset as _jsrt
+from bob.ip.binseg.configs.datasets.montgomery.default import dataset as _mc
+from bob.ip.binseg.configs.datasets.shenzhen.default import dataset as _shenzhen
 
 dataset = {
     "train": _shenzhen["train"],
     "validation": _shenzhen["validation"],
     "test": _shenzhen["test"],
-    "MC (train)": _mc["train"],
-    "MC (validation)": _mc["validation"],
-    "MC (test)": _mc["test"],
-    "JSRT (train)": _jsrt["train"],
-    "JSRT (validation)": _jsrt["validation"],
-    "JSRT (test)": _jsrt["test"],
+    "montgomery (train)": _mc["train"],
+    "montgomery (validation)": _mc["validation"],
+    "montgomery (test)": _mc["test"],
+    "jsrt (train)": _jsrt["train"],
+    "jsrt (validation)": _jsrt["validation"],
+    "jsrt (test)": _jsrt["test"],
 }

bob/ip/binseg/configs/datasets/MC/__init__.py → bob/ip/binseg/configs/datasets/montgomery/__init__.py

@@ -4,7 +4,7 @@
 
 def _maker(protocol):
 
-    from ....data.MC import dataset as raw
+    from ....data.montgomery import dataset as raw
     from ....data.transforms import Resize
     from .. import make_dataset as mk
 

bob/ip/binseg/configs/datasets/MC/default.py → bob/ip/binseg/configs/datasets/montgomery/default.py

@@ -3,11 +3,11 @@
 
 """Montgomery County dataset for Lung Segmentation (default protocol)
 
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Configuration resolution: 512 x 512
-* See :py:mod:`bob.ip.binseg.data.MC` for dataset details
+* See :py:mod:`bob.ip.binseg.data.montgomery` for dataset details
 """
 
-from bob.ip.binseg.configs.datasets.MC import _maker
+from bob.ip.binseg.configs.datasets.montgomery import _maker
 
 dataset = _maker("default")

bob/ip/binseg/configs/datasets/montgomery/xtest.py

+#!/usr/bin/env python
+# coding=utf-8
+
+"""Montgomery County cross-evaluation dataset
+"""
+
+from bob.ip.binseg.configs.datasets.jsrt.default import dataset as _jsrt
+from bob.ip.binseg.configs.datasets.montgomery.default import dataset as _mc
+from bob.ip.binseg.configs.datasets.shenzhen.default import dataset as _shenzhen
+
+dataset = {
+    "train": _mc["train"],
+    "validation": _mc["validation"],
+    "test": _mc["test"],
+    "jsrt (train)": _jsrt["train"],
+    "jsrt (validation)": _jsrt["validation"],
+    "jsrt (test)": _jsrt["test"],
+    "shenzhen (train)": _shenzhen["train"],
+    "shenzhen (validation)": _shenzhen["validation"],
+    "shenzhen (test)": _shenzhen["test"],
+}

bob/ip/binseg/data/JSRT/__init__.py

@@ -10,7 +10,7 @@ available.
 * Reference: [JSRT-2000]_
 * Original resolution (height x width): 2048 x 2048
 * Configuration resolution: 512 x 512 (after rescaling)
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Protocol ``default``:
 
   * Training samples: 172 (including labels)
@@ -36,7 +36,7 @@ _protocols = [
 ]
 
 _root_path = bob.extension.rc.get(
-    "bob.ip.binseg.JSRT.datadir", os.path.realpath(os.curdir)
+    "bob.ip.binseg.jsrt.datadir", os.path.realpath(os.curdir)
 )
 
 

bob/ip/binseg/data/Shenzhen/__init__.py

@@ -11,7 +11,7 @@ available for 566 of the 662 images.
 * Reference: [SHENZHEN-2014]_
 * Original resolution (height x width): Approximately 3K x 3K (varies)
 * Configuration resolution: 512 x 512 (after rescaling)
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Protocol ``default``:
 
   * Training samples: 396 (including labels)
@@ -34,7 +34,7 @@ _protocols = [
 ]
 
 _root_path = bob.extension.rc.get(
-    "bob.ip.binseg.Shenzhen.datadir", os.path.realpath(os.curdir)
+    "bob.ip.binseg.shenzhen.datadir", os.path.realpath(os.curdir)
 )
 
 
@@ -55,4 +55,4 @@ dataset = JSONDataset(
     protocols=_protocols, fieldnames=("data", "label"), loader=_loader
 )
 
-"""Shenzhen dataset object"""
+"""Shenzhen CXR dataset object"""

bob/ip/binseg/data/MC/__init__.py → bob/ip/binseg/data/montgomery/__init__.py

@@ -10,7 +10,7 @@ normal cases.  It contains a total  of 138 resolution of 4020 x 4892, or
 * Reference: [MC-2014]_
 * Original resolution (height x width): 4020 x 4892, or 4892 x 4020
 * Configuration resolution: 512 x 512 (after rescaling)
-* Split reference: [GAÁL-2020]_
+* Split reference: [GAAL-2020]_
 * Protocol ``default``:
 
   * Training samples: 96 (including labels)
@@ -36,7 +36,7 @@ _protocols = [
 ]
 
 _root_path = bob.extension.rc.get(
-    "bob.ip.binseg.MC.datadir", os.path.realpath(os.curdir)
+    "bob.ip.binseg.montgomery.datadir", os.path.realpath(os.curdir)
 )
 
 

bob/ip/binseg/test/test_jsrt.py

@@ -7,7 +7,7 @@
 import numpy
 import pytest
 
-from ..data.JSRT import dataset
+from ..data.jsrt import dataset
 from .utils import count_bw
 
 
@@ -32,7 +32,7 @@ def test_protocol_consistency():
         assert s.key.startswith("JSRT")
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.JSRT.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.jsrt.datadir")
 def test_loading():
 
     image_size = (2048, 2048)
@@ -74,6 +74,6 @@ def test_loading():
     del proportions  # only to satisfy flake8
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.JSRT.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.jsrt.datadir")
 def test_check():
     assert dataset.check() == 0

bob/ip/binseg/test/test_mc.py

@@ -2,12 +2,12 @@
 # coding=utf-8
 
 
-"""Tests for Montgomery County"""
+"""Tests for Montgomery County CXR dataset"""
 
 import numpy
 import pytest
 
-from ..data.MC import dataset
+from ..data.montgomery import dataset
 from .utils import count_bw
 
 
@@ -32,7 +32,7 @@ def test_protocol_consistency():
         assert s.key.startswith("MontgomerySet")
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.MC.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.montgomery.datadir")
 def test_loading():
 
     image_size_1 = (4892, 4020)
@@ -80,6 +80,6 @@ def test_loading():
     del proportions  # only to satisfy flake8
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.MC.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.montgomery.datadir")
 def test_check():
     assert dataset.check() == 0

bob/ip/binseg/test/test_shenzhen.py

@@ -2,12 +2,12 @@
 # coding=utf-8
 
 
-"""Tests for Shenzhen"""
+"""Tests for Shenzhen CXR dataset"""
 
 import numpy
 import pytest
 
-from ..data.Shenzhen import dataset
+from ..data.shenzhen import dataset
 from .utils import count_bw
 
 
@@ -32,7 +32,7 @@ def test_protocol_consistency():
         assert s.key.startswith("ChinaSet_AllFiles")
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.Shenzhen.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.shenzhen.datadir")
 def test_loading():
 
     min_image_size = (1130, 948)
@@ -76,6 +76,6 @@ def test_loading():
     del proportions  # only to satisfy flake8
 
 
-@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.Shenzhen.datadir")
+@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.shenzhen.datadir")
 def test_check():
     assert dataset.check() == 0