ruff: remove unused imports and fix small typos.

gunpowder/array.py

@@ -1,7 +1,5 @@
 from .freezable import Freezable
 from copy import deepcopy
-from gunpowder.coordinate import Coordinate
-from gunpowder.roi import Roi
 import logging
 import numpy as np
 import copy

gunpowder/batch.py

@@ -1,7 +1,6 @@
 from copy import copy as shallow_copy
 import logging
 import multiprocessing
-import warnings
 
 from .freezable import Freezable
 from .profiling import ProfilingStats
@@ -75,7 +74,7 @@ def __setitem__(self, key, value):
         elif isinstance(value, Graph):
             assert isinstance(
                 key, GraphKey
-            ), f"Only a GraphKey is allowed as key for Graph value."
+            ), "Only a GraphKey is allowed as key for Graph value."
             self.graphs[key] = value
 
         else:

gunpowder/contrib/nodes/add_blobs_from_points.py

@@ -143,7 +143,7 @@ def process(self, batch, request):
                 synapse_ids = []
                 for point_id, point in points.data.items():
                     # pdb.set_trace()
-                    if not point.partner_ids[0] in partner_points.data.keys():
+                    if point.partner_ids[0] not in partner_points.data.keys():
                         logger.warning(
                             "Point %s has no partner. Deleting..." % point_id
                         )

gunpowder/contrib/nodes/add_boundary_distance_gradients.py

@@ -4,7 +4,6 @@
 from gunpowder.array import Array
 from gunpowder.batch_request import BatchRequest
 from gunpowder.nodes.batch_filter import BatchFilter
-from numpy.lib.stride_tricks import as_strided
 from scipy.ndimage.morphology import distance_transform_edt
 
 logger = logging.getLogger(__name__)
@@ -83,7 +82,7 @@ def prepare(self, request):
         return deps
 
     def process(self, batch, request):
-        if not self.gradient_array_key in request:
+        if self.gradient_array_key not in request:
             return
 
         labels = batch.arrays[self.label_array_key].data

gunpowder/contrib/nodes/add_gt_mask_exclusive_zone.py

@@ -1,10 +1,9 @@
 import copy
 import logging
 import numpy as np
-from scipy import ndimage
 
 from gunpowder.nodes.batch_filter import BatchFilter
-from gunpowder.array import Array, ArrayKeys
+from gunpowder.array import Array
 from gunpowder.nodes.rasterize_graph import RasterizationSettings
 from gunpowder.morphology import enlarge_binary_map
 

gunpowder/contrib/nodes/add_nonsymmetric_affinities.py

@@ -1,7 +1,5 @@
-import copy
 import logging
 import numpy as np
-import pdb
 
 from gunpowder.array import Array
 from gunpowder.nodes.batch_filter import BatchFilter

gunpowder/contrib/nodes/hdf5_points_source.py

@@ -5,10 +5,7 @@
 from gunpowder.batch import Batch
 from gunpowder.coordinate import Coordinate
 from gunpowder.ext import h5py
-from gunpowder.graph import GraphKey, Graph
-from gunpowder.graph_spec import GraphSpec
 from gunpowder.profiling import Timing
-from gunpowder.roi import Roi
 from gunpowder.nodes.batch_provider import BatchProvider
 
 logger = logging.getLogger(__name__)

gunpowder/ext/__init__.py

@@ -21,73 +21,73 @@ def __getattr__(self, item):
 
 try:
     import dvision
-except ImportError as e:
+except ImportError:
     dvision = NoSuchModule("dvision")
 
 try:
     import h5py
-except ImportError as e:
+except ImportError:
     h5py = NoSuchModule("h5py")
 
 try:
     import pyklb
-except ImportError as e:
+except ImportError:
     pyklb = NoSuchModule("pyklb")
 
 try:
     import tensorflow
-except ImportError as e:
+except ImportError:
     tensorflow = NoSuchModule("tensorflow")
 
 try:
     import torch
-except ImportError as e:
+except ImportError:
     torch = NoSuchModule("torch")
 
 try:
     import tensorboardX
-except ImportError as e:
+except ImportError:
     tensorboardX = NoSuchModule("tensorboardX")
 
 try:
     import malis
-except ImportError as e:
+except ImportError:
     malis = NoSuchModule("malis")
 
 try:
     import augment
-except ImportError as e:
+except ImportError:
     augment = NoSuchModule("augment")
 
 ZarrFile: Optional[Any] = None
 try:
     import zarr
     from .zarr_file import ZarrFile
-except ImportError as e:
+except ImportError:
     zarr = NoSuchModule("zarr")
     ZarrFile = None
 
 try:
     import daisy
-except ImportError as e:
+except ImportError:
     daisy = NoSuchModule("daisy")
 
 try:
     import jax
-except ImportError as e:
+except ImportError:
     jax = NoSuchModule("jax")
 
 try:
     import jax.numpy as jnp
-except ImportError as e:
+except ImportError:
     jnp = NoSuchModule("jnp")
 
 try:
     import haiku
-except ImportError as e:
+except ImportError:
     haiku = NoSuchModule("haiku")
 
 try:
     import optax
-except ImportError as e:
+except ImportError:
     optax = NoSuchModule("optax")

gunpowder/graph.py

@@ -9,7 +9,6 @@
 from typing import Dict, Optional, Set, Iterator, Any
 import logging
 import itertools
-import warnings
 
 
 logger = logging.getLogger(__name__)
@@ -485,7 +484,7 @@ def _roi_intercept(
 
         offset = outside - inside
         distance = np.linalg.norm(offset)
-        assert not np.isclose(distance, 0), f"Inside and Outside are the same location"
+        assert not np.isclose(distance, 0), "Inside and Outside are the same location"
         direction = offset / distance
 
         # `offset` can be 0 on some but not all axes leaving a 0 in the denominator.

gunpowder/nodes/crop.py

@@ -1,4 +1,3 @@
-import copy
 import logging
 
 from .batch_filter import BatchFilter

gunpowder/nodes/elastic_augment.py

@@ -9,7 +9,6 @@
 from gunpowder.coordinate import Coordinate
 from gunpowder.ext import augment
 from gunpowder.roi import Roi
-from gunpowder.array import ArrayKey
 
 import warnings
 

gunpowder/nodes/exclude_labels.py

@@ -71,7 +71,7 @@ def process(self, batch, request):
                 include_mask[gt.data == label] = 0
 
         # if no ignore mask is provided or requested, we are done
-        if not self.ignore_mask or not self.ignore_mask in request:
+        if not self.ignore_mask or self.ignore_mask not in request:
             return
 
         voxel_size = self.spec[self.labels].voxel_size

gunpowder/nodes/grow_boundary.py

@@ -2,7 +2,6 @@
 from scipy import ndimage
 
 from .batch_filter import BatchFilter
-from gunpowder.array import Array
 
 
 class GrowBoundary(BatchFilter):

gunpowder/nodes/klb_source.py

@@ -1,4 +1,3 @@
-import copy
 import logging
 import numpy as np
 import glob

gunpowder/nodes/merge_provider.py

@@ -1,4 +1,3 @@
-from gunpowder.provider_spec import ProviderSpec
 from gunpowder.batch import Batch
 from gunpowder.batch_request import BatchRequest
 

gunpowder/nodes/pad.py

@@ -7,7 +7,6 @@
 from gunpowder.coordinate import Coordinate
 from gunpowder.batch_request import BatchRequest
 
-from itertools import product
 
 logger = logging.getLogger(__name__)
 

gunpowder/nodes/precache.py

@@ -1,7 +1,4 @@
 import logging
-import multiprocessing
-import time
-import random
 
 from .batch_filter import BatchFilter
 from gunpowder.profiling import Timing

gunpowder/nodes/rasterize_graph.py

@@ -1,4 +1,3 @@
-import copy
 import logging
 import numpy as np
 from scipy.ndimage.filters import gaussian_filter
@@ -12,7 +11,6 @@
 from gunpowder.freezable import Freezable
 from gunpowder.morphology import enlarge_binary_map, create_ball_kernel
 from gunpowder.ndarray import replace
-from gunpowder.graph import GraphKey
 from gunpowder.graph_spec import GraphSpec
 from gunpowder.roi import Roi
 

gunpowder/nodes/shift_augment.py

@@ -4,7 +4,6 @@
 import random
 from gunpowder.roi import Roi
 from gunpowder.coordinate import Coordinate
-from gunpowder.batch_request import BatchRequest
 
 from .batch_filter import BatchFilter
 

gunpowder/nodes/specified_location.py

@@ -1,10 +1,8 @@
 from random import randrange
-from random import choice, seed
 import logging
 import numpy as np
 
 from gunpowder.coordinate import Coordinate
-from gunpowder.batch_request import BatchRequest
 
 from .batch_filter import BatchFilter
 

gunpowder/nodes/squeeze.py

@@ -1,4 +1,3 @@
-import copy
 from typing import List
 import logging
 

gunpowder/nodes/unsqueeze.py

@@ -1,4 +1,3 @@
-import copy
 from typing import List
 import logging
 

gunpowder/producer_pool.py

@@ -6,8 +6,6 @@
 import multiprocessing
 import os
 import sys
-import time
-import traceback
 
 import numpy as np
 

gunpowder/provider_spec.py

@@ -6,15 +6,13 @@
 from gunpowder.graph_spec import GraphSpec
 from gunpowder.roi import Roi
 from .freezable import Freezable
-import time
 import logging
 import copy
 
 logger = logging.getLogger(__name__)
 
 
 import logging
-import warnings
 
 logger = logging.getLogger(__file__)
 

tests/cases/add_affinities.py

@@ -1,10 +1,6 @@
-from .provider_test import ProviderTest
 from gunpowder import *
 from itertools import product
-from unittest import skipIf
-import itertools
 import numpy as np
-import logging
 
 
 class ExampleSource(BatchProvider):

tests/cases/dvid_source.py

@@ -2,7 +2,6 @@
 from unittest import skipIf
 from gunpowder import *
 from gunpowder.ext import dvision, NoSuchModule
-import numpy as np
 import socket
 import logging
 

tests/cases/elastic_augment_points.py

@@ -1,4 +1,3 @@
-import unittest
 from gunpowder import (
     BatchProvider,
     Batch,
@@ -25,7 +24,6 @@
 import numpy as np
 import math
 import time
-import unittest
 
 
 class PointTestSource3D(BatchProvider):

tests/cases/expected_failures.py

@@ -2,7 +2,7 @@
 from gunpowder.nodes.batch_provider import BatchRequestError
 from .helper_sources import ArraySource
 
-from funlib.geometry import Roi, Coordinate
+from funlib.geometry import Coordinate
 
 import numpy as np
 import pytest

tests/cases/intensity_scale_shift.py

@@ -3,7 +3,6 @@
     IntensityScaleShift,
     ArrayKey,
     build,
-    Normalize,
     Array,
     ArraySpec,
     Roi,

tests/cases/jax_train.py

@@ -4,18 +4,15 @@
     BatchRequest,
     ArraySpec,
     Roi,
-    Coordinate,
     ArrayKeys,
     ArrayKey,
     Array,
     Batch,
-    Scan,
-    PreCache,
     build,
 )
 from gunpowder.ext import jax, haiku, optax, NoSuchModule
 from gunpowder.jax import Train, Predict, GenericJaxModel
-from unittest import skipIf, expectedFailure
+from unittest import skipIf
 import numpy as np
 
 import logging

tests/cases/noise_augment.py

@@ -1,7 +1,6 @@
 from .provider_test import ProviderTest
 from gunpowder import IntensityAugment, ArrayKeys, build, Normalize, NoiseAugment
 
-import numpy as np
 
 
 class TestIntensityAugment(ProviderTest):

tests/cases/random_location.py

@@ -3,7 +3,6 @@
     BatchProvider,
     Roi,
     Coordinate,
-    ArrayKeys,
     ArrayKey,
     ArraySpec,
     Array,