From 549dcba0c2e77b394892359b3e7761d5aed5d09e Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Wed, 29 Sep 2021 08:36:12 +0200
Subject: [PATCH] [bob] Lowercase all new datasets (CXR)
---
.../binseg/configs/datasets/JSRT/__init__.py | 2 +-
.../binseg/configs/datasets/JSRT/default.py | 6 +++---
bob/ip/binseg/configs/datasets/JSRT/xtest.py | 20 +++++++++---------
bob/ip/binseg/configs/datasets/MC/xtest.py | 21 -------------------
.../configs/datasets/Shenzhen/__init__.py | 15 +++----------
.../configs/datasets/Shenzhen/default.py | 8 +++----
.../configs/datasets/Shenzhen/default_256.py | 10 ++++-----
.../binseg/configs/datasets/Shenzhen/xtest.py | 18 ++++++++--------
.../datasets/{MC => montgomery}/__init__.py | 2 +-
.../datasets/{MC => montgomery}/default.py | 6 +++---
.../configs/datasets/montgomery/xtest.py | 21 +++++++++++++++++++
bob/ip/binseg/data/JSRT/__init__.py | 4 ++--
bob/ip/binseg/data/Shenzhen/__init__.py | 6 +++---
.../data/{MC => montgomery}/__init__.py | 4 ++--
.../data/{MC => montgomery}/default.json | 0
bob/ip/binseg/test/test_jsrt.py | 6 +++---
bob/ip/binseg/test/test_mc.py | 8 +++----
bob/ip/binseg/test/test_shenzhen.py | 8 +++----
18 files changed, 78 insertions(+), 87 deletions(-)
delete mode 100644 bob/ip/binseg/configs/datasets/MC/xtest.py
rename bob/ip/binseg/configs/datasets/{MC => montgomery}/__init__.py (79%)
rename bob/ip/binseg/configs/datasets/{MC => montgomery}/default.py (53%)
create mode 100644 bob/ip/binseg/configs/datasets/montgomery/xtest.py
rename bob/ip/binseg/data/{MC => montgomery}/__init__.py (94%)
rename bob/ip/binseg/data/{MC => montgomery}/default.json (100%)
diff --git a/bob/ip/binseg/configs/datasets/JSRT/__init__.py b/bob/ip/binseg/configs/datasets/JSRT/__init__.py
index 2d5ca848..35453e83 100644
--- a/bob/ip/binseg/configs/datasets/JSRT/__init__.py
+++ b/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
diff --git a/bob/ip/binseg/configs/datasets/JSRT/default.py b/bob/ip/binseg/configs/datasets/JSRT/default.py
index c8c6fabf..0507092b 100644
--- a/bob/ip/binseg/configs/datasets/JSRT/default.py
+++ b/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: [GAÃL-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")
diff --git a/bob/ip/binseg/configs/datasets/JSRT/xtest.py b/bob/ip/binseg/configs/datasets/JSRT/xtest.py
index 81d2fe2a..b14919ec 100644
--- a/bob/ip/binseg/configs/datasets/JSRT/xtest.py
+++ b/bob/ip/binseg/configs/datasets/JSRT/xtest.py
@@ -1,21 +1,21 @@
#!/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"],
}
diff --git a/bob/ip/binseg/configs/datasets/MC/xtest.py b/bob/ip/binseg/configs/datasets/MC/xtest.py
deleted file mode 100644
index 0a308cd3..00000000
--- a/bob/ip/binseg/configs/datasets/MC/xtest.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/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"],
-}
diff --git a/bob/ip/binseg/configs/datasets/Shenzhen/__init__.py b/bob/ip/binseg/configs/datasets/Shenzhen/__init__.py
index 481afa61..d0887bb5 100644
--- a/bob/ip/binseg/configs/datasets/Shenzhen/__init__.py
+++ b/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))])
diff --git a/bob/ip/binseg/configs/datasets/Shenzhen/default.py b/bob/ip/binseg/configs/datasets/Shenzhen/default.py
index 0a82ef34..b74107a0 100644
--- a/bob/ip/binseg/configs/datasets/Shenzhen/default.py
+++ b/bob/ip/binseg/configs/datasets/Shenzhen/default.py
@@ -3,11 +3,11 @@
"""Shenzhen dataset for Lung Segmentation (default protocol)
-* Split reference: [GAÃL-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)
diff --git a/bob/ip/binseg/configs/datasets/Shenzhen/default_256.py b/bob/ip/binseg/configs/datasets/Shenzhen/default_256.py
index 468a00e6..2152e178 100644
--- a/bob/ip/binseg/configs/datasets/Shenzhen/default_256.py
+++ b/bob/ip/binseg/configs/datasets/Shenzhen/default_256.py
@@ -3,11 +3,11 @@
"""Shenzhen dataset for Lung Segmentation (default protocol)
-* Split reference: [GAÃL-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)
diff --git a/bob/ip/binseg/configs/datasets/Shenzhen/xtest.py b/bob/ip/binseg/configs/datasets/Shenzhen/xtest.py
index 6a42c67d..52da00da 100644
--- a/bob/ip/binseg/configs/datasets/Shenzhen/xtest.py
+++ b/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"],
}
diff --git a/bob/ip/binseg/configs/datasets/MC/__init__.py b/bob/ip/binseg/configs/datasets/montgomery/__init__.py
similarity index 79%
rename from bob/ip/binseg/configs/datasets/MC/__init__.py
rename to bob/ip/binseg/configs/datasets/montgomery/__init__.py
index b4aacadf..54ae569a 100644
--- a/bob/ip/binseg/configs/datasets/MC/__init__.py
+++ b/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
diff --git a/bob/ip/binseg/configs/datasets/MC/default.py b/bob/ip/binseg/configs/datasets/montgomery/default.py
similarity index 53%
rename from bob/ip/binseg/configs/datasets/MC/default.py
rename to bob/ip/binseg/configs/datasets/montgomery/default.py
index 0d06272c..96f94141 100644
--- a/bob/ip/binseg/configs/datasets/MC/default.py
+++ b/bob/ip/binseg/configs/datasets/montgomery/default.py
@@ -3,11 +3,11 @@
"""Montgomery County dataset for Lung Segmentation (default protocol)
-* Split reference: [GAÃL-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")
diff --git a/bob/ip/binseg/configs/datasets/montgomery/xtest.py b/bob/ip/binseg/configs/datasets/montgomery/xtest.py
new file mode 100644
index 00000000..c350b603
--- /dev/null
+++ b/bob/ip/binseg/configs/datasets/montgomery/xtest.py
@@ -0,0 +1,21 @@
+#!/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"],
+}
diff --git a/bob/ip/binseg/data/JSRT/__init__.py b/bob/ip/binseg/data/JSRT/__init__.py
index 42a26cc4..bd913a51 100644
--- a/bob/ip/binseg/data/JSRT/__init__.py
+++ b/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: [GAÃL-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)
)
diff --git a/bob/ip/binseg/data/Shenzhen/__init__.py b/bob/ip/binseg/data/Shenzhen/__init__.py
index 89f9e723..689b72ba 100644
--- a/bob/ip/binseg/data/Shenzhen/__init__.py
+++ b/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: [GAÃL-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"""
diff --git a/bob/ip/binseg/data/MC/__init__.py b/bob/ip/binseg/data/montgomery/__init__.py
similarity index 94%
rename from bob/ip/binseg/data/MC/__init__.py
rename to bob/ip/binseg/data/montgomery/__init__.py
index d479eb61..b1d7844b 100644
--- a/bob/ip/binseg/data/MC/__init__.py
+++ b/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: [GAÃL-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)
)
diff --git a/bob/ip/binseg/data/MC/default.json b/bob/ip/binseg/data/montgomery/default.json
similarity index 100%
rename from bob/ip/binseg/data/MC/default.json
rename to bob/ip/binseg/data/montgomery/default.json
diff --git a/bob/ip/binseg/test/test_jsrt.py b/bob/ip/binseg/test/test_jsrt.py
index e275d81f..37f33614 100644
--- a/bob/ip/binseg/test/test_jsrt.py
+++ b/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
diff --git a/bob/ip/binseg/test/test_mc.py b/bob/ip/binseg/test/test_mc.py
index cfe82bd6..7df4bd01 100644
--- a/bob/ip/binseg/test/test_mc.py
+++ b/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
diff --git a/bob/ip/binseg/test/test_shenzhen.py b/bob/ip/binseg/test/test_shenzhen.py
index d710afda..95a1e2c8 100644
--- a/bob/ip/binseg/test/test_shenzhen.py
+++ b/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
--
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