[pre-commit] make isort compatible with black; use 80 lines

.isort.cfg

 [settings]
-line_length=88
+line_length=80
 order_by_type=true
 lines_between_types=1

.pre-commit-config.yaml

@@ -6,8 +6,9 @@ repos:
     hooks:
       - id: isort
         args: [
+          --profile, "black",
           --force-single-line-imports,
-          --line-length, "88",
+          --line-length, "80",
           --order-by-type,
           --lines-between-types, "1"
         ]
@@ -15,6 +16,9 @@ repos:
     rev: 21.7b0
     hooks:
       - id: black
+        args: [
+          --line-length, "80",
+        ]
   - repo: https://gitlab.com/pycqa/flake8
     rev: 3.9.2
     hooks:

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

@@ -173,7 +173,11 @@ def make_dataset(subsets, transforms):
             # also use it for validation during training
             retval["__valid__"] = retval[key]
 
-    if ("__train__" in retval) and ("train" in retval) and ("__valid__" not in retval):
+    if (
+        ("__train__" in retval)
+        and ("train" in retval)
+        and ("__valid__" not in retval)
+    ):
         # if the dataset does not have a validation set, we use the unaugmented
         # training set as validation set
         retval["__valid__"] = retval["train"]

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

@@ -19,8 +19,12 @@ For details on those datasets, consult:
 from torch.utils.data import ConcatDataset
 
 from bob.ip.binseg.configs.datasets import augment_subset as _augment
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _baseline
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import second_annotator
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _baseline,
+)
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    second_annotator,
+)
 from bob.ip.binseg.configs.datasets.chasedb1.mtest import dataset as _mtest
 
 dataset = dict(**_baseline)

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

@@ -15,15 +15,21 @@ from bob.ip.binseg.data.transforms import Resize
 dataset = {
     "train": _xt["train"],
     "test": _xt["test"],
-    "drive (train)": _xt["drive (train)"].copy([CenterCrop((544, 544)), Resize(960)]),
-    "drive (test)": _xt["drive (test)"].copy([CenterCrop((544, 544)), Resize(960)]),
+    "drive (train)": _xt["drive (train)"].copy(
+        [CenterCrop((544, 544)), Resize(960)]
+    ),
+    "drive (test)": _xt["drive (test)"].copy(
+        [CenterCrop((544, 544)), Resize(960)]
+    ),
     "stare (train)": _xt["stare (train)"].copy(
         [Pad((0, 32, 0, 32)), Resize(960), CenterCrop(960)]
     ),
     "stare (test)": _xt["stare (test)"].copy(
         [Pad((0, 32, 0, 32)), Resize(960), CenterCrop(960)]
     ),
-    "hrf (train)": _xt["hrf (train)"].copy([Pad((0, 584, 0, 584)), Resize(960)]),
+    "hrf (train)": _xt["hrf (train)"].copy(
+        [Pad((0, 584, 0, 584)), Resize(960)]
+    ),
     "hrf (test)": _xt["hrf (test)"].copy([Pad((0, 584, 0, 584)), Resize(960)]),
     "iostar (train)": _xt["iostar (train)"].copy([Resize(960)]),
     "iostar (test)": _xt["iostar (test)"].copy([Resize(960)]),

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

@@ -20,7 +20,9 @@ For details on datasets, consult:
 """
 
 from bob.ip.binseg.configs.datasets.chasedb1.covd import dataset as _covd
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _baseline
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _baseline,
+)
 from bob.ip.binseg.data.utils import SSLDataset
 
 # copy dictionary and replace only the augmented train dataset

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

@@ -4,8 +4,12 @@
 """CHASE-DB1 cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _chase
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import second_annotator
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _chase,
+)
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    second_annotator,
+)
 from bob.ip.binseg.configs.datasets.drive.default import dataset as _drive
 from bob.ip.binseg.configs.datasets.hrf.default import dataset as _hrf
 from bob.ip.binseg.configs.datasets.iostar.vessel import dataset as _iostar

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

@@ -15,15 +15,21 @@ from bob.ip.binseg.data.transforms import Resize
 dataset = {
     "train": _xt["train"],
     "test": _xt["test"],
-    "stare (train)": _xt["stare (train)"].copy([Resize(471), Pad((0, 37, 0, 36))]),
-    "stare (test)": _xt["stare (test)"].copy([Resize(471), Pad((0, 37, 0, 36))]),
+    "stare (train)": _xt["stare (train)"].copy(
+        [Resize(471), Pad((0, 37, 0, 36))]
+    ),
+    "stare (test)": _xt["stare (test)"].copy(
+        [Resize(471), Pad((0, 37, 0, 36))]
+    ),
     "chasedb1 (train)": _xt["chasedb1 (train)"].copy(
         [Resize(544), Crop(0, 12, 544, 544)]
     ),
     "chasedb1 (test)": _xt["chasedb1 (test)"].copy(
         [Resize(544), Crop(0, 12, 544, 544)]
     ),
-    "hrf (train)": _xt["hrf (train)"].copy([Resize((363)), Pad((0, 90, 0, 91))]),
+    "hrf (train)": _xt["hrf (train)"].copy(
+        [Resize((363)), Pad((0, 90, 0, 91))]
+    ),
     "hrf (test)": _xt["hrf (test)"].copy([Resize((363)), Pad((0, 90, 0, 91))]),
     "iostar (train)": _xt["iostar (train)"].copy([Resize(544)]),
     "iostar (test)": _xt["iostar (test)"].copy([Resize(544)]),

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

@@ -4,7 +4,9 @@
 """DRIVE cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _chase
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _chase,
+)
 from bob.ip.binseg.configs.datasets.drive.default import dataset as _drive
 from bob.ip.binseg.configs.datasets.drive.default import second_annotator
 from bob.ip.binseg.configs.datasets.hrf.default import dataset as _hrf

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

@@ -4,7 +4,9 @@
 """HRF cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _chase
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _chase,
+)
 from bob.ip.binseg.configs.datasets.drive.default import dataset as _drive
 from bob.ip.binseg.configs.datasets.hrf.default import dataset as _hrf
 from bob.ip.binseg.configs.datasets.iostar.vessel import dataset as _iostar

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

@@ -15,8 +15,12 @@ from bob.ip.binseg.data.transforms import Resize
 dataset = {
     "train": _xt["train"],
     "test": _xt["test"],
-    "drive (train)": _xt["drive (train)"].copy([CenterCrop((540, 540)), Resize(1024)]),
-    "drive (test)": _xt["drive (test)"].copy([CenterCrop((540, 540)), Resize(1024)]),
+    "drive (train)": _xt["drive (train)"].copy(
+        [CenterCrop((540, 540)), Resize(1024)]
+    ),
+    "drive (test)": _xt["drive (test)"].copy(
+        [CenterCrop((540, 540)), Resize(1024)]
+    ),
     "stare (train)": _xt["stare (train)"].copy(
         [Pad((0, 32, 0, 32)), Resize(1024), CenterCrop(1024)]
     ),
@@ -29,6 +33,8 @@ dataset = {
     "chasedb1 (test)": _xt["chasedb1 (test)"].copy(
         [Crop(0, 18, 960, 960), Resize(1024)]
     ),
-    "hrf (train)": _xt["hrf (train)"].copy([Pad((0, 584, 0, 584)), Resize(1024)]),
+    "hrf (train)": _xt["hrf (train)"].copy(
+        [Pad((0, 584, 0, 584)), Resize(1024)]
+    ),
     "hrf (test)": _xt["hrf (test)"].copy([Pad((0, 584, 0, 584)), Resize(1024)]),
 }

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

@@ -4,7 +4,9 @@
 """IOSTAR vessel cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _chase
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _chase,
+)
 from bob.ip.binseg.configs.datasets.drive.default import dataset as _drive
 from bob.ip.binseg.configs.datasets.hrf.default import dataset as _hrf
 from bob.ip.binseg.configs.datasets.iostar.vessel import dataset as _iostar

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

@@ -27,8 +27,14 @@ dataset = {
     "chasedb1 (test)": _xt["chasedb1 (test)"].copy(
         [CenterCrop((829, 960)), Resize(608)]
     ),
-    "hrf (train)": _xt["hrf (train)"].copy([Pad((0, 345, 0, 345)), Resize(608)]),
+    "hrf (train)": _xt["hrf (train)"].copy(
+        [Pad((0, 345, 0, 345)), Resize(608)]
+    ),
     "hrf (test)": _xt["hrf (test)"].copy([Pad((0, 345, 0, 345)), Resize(608)]),
-    "iostar (train)": _xt["iostar (train)"].copy([Pad((81, 0, 81, 0)), Resize(608)]),
-    "iostar (test)": _xt["iostar (test)"].copy([Pad((81, 0, 81, 0)), Resize(608)]),
+    "iostar (train)": _xt["iostar (train)"].copy(
+        [Pad((81, 0, 81, 0)), Resize(608)]
+    ),
+    "iostar (test)": _xt["iostar (test)"].copy(
+        [Pad((81, 0, 81, 0)), Resize(608)]
+    ),
 }

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

@@ -4,7 +4,9 @@
 """STARE cross-evaluation dataset
 """
 
-from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import dataset as _chase
+from bob.ip.binseg.configs.datasets.chasedb1.first_annotator import (
+    dataset as _chase,
+)
 from bob.ip.binseg.configs.datasets.drive.default import dataset as _drive
 from bob.ip.binseg.configs.datasets.hrf.default import dataset as _hrf
 from bob.ip.binseg.configs.datasets.iostar.vessel import dataset as _iostar

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

@@ -47,8 +47,12 @@ def _raw_data_loader(sample):
         data=load_pil_rgb(os.path.join(_root_path, sample["data"])),
         label=Image.fromarray(
             np.ma.mask_or(
-                np.asarray(load_pil_1(os.path.join(_root_path, sample["label_l"]))),
-                np.asarray(load_pil_1(os.path.join(_root_path, sample["label_r"]))),
+                np.asarray(
+                    load_pil_1(os.path.join(_root_path, sample["label_l"]))
+                ),
+                np.asarray(
+                    load_pil_1(os.path.join(_root_path, sample["label_r"]))
+                ),
             )
         ),
     )
@@ -61,7 +65,9 @@ def _loader(context, sample):
 
 
 dataset = JSONDataset(
-    protocols=_protocols, fieldnames=("data", "label_l", "label_r"), loader=_loader
+    protocols=_protocols,
+    fieldnames=("data", "label_l", "label_r"),
+    loader=_loader,
 )
 
 """Japanese Society of Radiological Technology dataset object"""

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

@@ -47,8 +47,12 @@ def _raw_data_loader(sample):
         data=load_pil_rgb(os.path.join(_root_path, sample["data"])),
         label=Image.fromarray(
             np.ma.mask_or(
-                np.asarray(load_pil_1(os.path.join(_root_path, sample["label_l"]))),
-                np.asarray(load_pil_1(os.path.join(_root_path, sample["label_r"]))),
+                np.asarray(
+                    load_pil_1(os.path.join(_root_path, sample["label_l"]))
+                ),
+                np.asarray(
+                    load_pil_1(os.path.join(_root_path, sample["label_r"]))
+                ),
             )
         ),
     )
@@ -61,7 +65,9 @@ def _loader(context, sample):
 
 
 dataset = JSONDataset(
-    protocols=_protocols, fieldnames=("data", "label_l", "label_r"), loader=_loader
+    protocols=_protocols,
+    fieldnames=("data", "label_l", "label_r"),
+    loader=_loader,
 )
 
 """Montgomery County dataset object"""

bob/ip/binseg/data/dataset.py

@@ -314,6 +314,8 @@ class CSVDataset:
             fileobj.seek(0)
 
         return [
-            self._loader(dict(subset=subset, order=n), dict(zip(self.fieldnames, k)))
+            self._loader(
+                dict(subset=subset, order=n), dict(zip(self.fieldnames, k))
+            )
             for n, k in enumerate(samples)
         ]

bob/ip/binseg/data/drishtigs1/__init__.py

@@ -33,10 +33,18 @@ from ..loader import load_pil_rgb
 from ..loader import make_delayed
 
 _protocols = {
-    "optic-disc-all": pkg_resources.resource_filename(__name__, "optic-disc.json"),
-    "optic-cup-all": pkg_resources.resource_filename(__name__, "optic-cup.json"),
-    "optic-disc-any": pkg_resources.resource_filename(__name__, "optic-disc.json"),
-    "optic-cup-any": pkg_resources.resource_filename(__name__, "optic-cup.json"),
+    "optic-disc-all": pkg_resources.resource_filename(
+        __name__, "optic-disc.json"
+    ),
+    "optic-cup-all": pkg_resources.resource_filename(
+        __name__, "optic-cup.json"
+    ),
+    "optic-disc-any": pkg_resources.resource_filename(
+        __name__, "optic-disc.json"
+    ),
+    "optic-cup-any": pkg_resources.resource_filename(
+        __name__, "optic-cup.json"
+    ),
 }
 
 _root_path = bob.extension.rc.get(
@@ -47,7 +55,9 @@ _root_path = bob.extension.rc.get(
 def _raw_data_loader_all(sample):
     retval = dict(
         data=load_pil_rgb(os.path.join(_root_path, sample["data"])),
-        label=load_pil_rgb(os.path.join(_root_path, sample["label"])).convert("L"),
+        label=load_pil_rgb(os.path.join(_root_path, sample["label"])).convert(
+            "L"
+        ),
     )
     retval["label"] = retval["label"].point(lambda p: p > 254, mode="1")
     return retval
@@ -56,7 +66,9 @@ def _raw_data_loader_all(sample):
 def _raw_data_loader_any(sample):
     retval = dict(
         data=load_pil_rgb(os.path.join(_root_path, sample["data"])),
-        label=load_pil_rgb(os.path.join(_root_path, sample["label"])).convert("L"),
+        label=load_pil_rgb(os.path.join(_root_path, sample["label"])).convert(
+            "L"
+        ),
     )
     retval["label"] = retval["label"].point(lambda p: p > 0, mode="1")
     return retval

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

@@ -60,7 +60,9 @@ def _disc_loader(sample):
     data = load_pil_rgb(os.path.join(_root_path, sample["data"]))
     label = load_pil_1(os.path.join(_root_path, sample["label"]))
     mask = load_pil_1(os.path.join(_root_path, sample["mask"]))
-    label = subtract_mode1_images(invert_mode1_image(label), invert_mode1_image(mask))
+    label = subtract_mode1_images(
+        invert_mode1_image(label), invert_mode1_image(mask)
+    )
     return dict(data=data, label=label, mask=mask)
 
 

bob/ip/binseg/data/sample.py

@@ -13,7 +13,9 @@ from collections.abc import MutableSequence
 def _copy_attributes(s, d):
     """Copies attributes from a dictionary to self"""
     s.__dict__.update(
-        dict([k, v] for k, v in d.items() if k not in ("data", "load", "samples"))
+        dict(
+            [k, v] for k, v in d.items() if k not in ("data", "load", "samples")
+        )
     )