From f3f5ffa1e7c560312151f6262a2f5c204bcf9362 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Mon, 2 May 2022 18:51:30 +0200
Subject: [PATCH] Flake8 F errors and several bug fixes
---
bob/bio/vein/algorithm/MiuraMatch.py | 4 +++-
bob/bio/vein/config/maximum_curvature.py | 2 +-
bob/bio/vein/config/principal_curvature.py | 2 +-
bob/bio/vein/config/repeated_line_tracking.py | 2 +-
bob/bio/vein/config/wide_line_detector.py | 2 +-
bob/bio/vein/database/fv3d.py | 1 -
bob/bio/vein/database/verafinger.py | 1 -
bob/bio/vein/extractor/MaximumCurvature.py | 2 --
.../vein/extractor/NormalisedCrossCorrelation.py | 2 --
bob/bio/vein/extractor/PrincipalCurvature.py | 2 --
bob/bio/vein/extractor/__init__.py | 10 +++++-----
bob/bio/vein/preprocessor/crop.py | 2 --
bob/bio/vein/preprocessor/filters.py | 2 --
bob/bio/vein/preprocessor/mask.py | 2 --
bob/bio/vein/preprocessor/preprocessor.py | 3 +--
bob/bio/vein/script/blame.py | 2 +-
bob/bio/vein/script/compare_rois.py | 1 +
bob/bio/vein/script/validate.py | 2 --
bob/bio/vein/script/view_sample.py | 9 +++------
bob/bio/vein/tests/test_tools.py | 16 ++++++++--------
doc/conf.py | 2 --
matlab/compare.py | 2 --
22 files changed, 26 insertions(+), 47 deletions(-)
diff --git a/bob/bio/vein/algorithm/MiuraMatch.py b/bob/bio/vein/algorithm/MiuraMatch.py
index 4633425..774c8f2 100644
--- a/bob/bio/vein/algorithm/MiuraMatch.py
+++ b/bob/bio/vein/algorithm/MiuraMatch.py
@@ -103,7 +103,9 @@ class MiuraMatch(BioAlgorithm):
# yields best results. Otherwise, you may try the other options bellow
# -> check our test_correlation() method on the test units for more
# details and benchmarks.
- Nm = scipy.signal.fftconvolve(image_, numpy.rot90(crop_R, k=2), "valid")
+ Nm = scipy.signal.fftconvolve(
+ image_, numpy.rot90(crop_R, k=2), "valid"
+ )
# 2nd best: use convolve2d or correlate2d directly;
# Nm = scipy.signal.convolve2d(I, numpy.rot90(crop_R, k=2), 'valid')
# 3rd best: use correlate2d
diff --git a/bob/bio/vein/config/maximum_curvature.py b/bob/bio/vein/config/maximum_curvature.py
index 32f816d..3935bec 100644
--- a/bob/bio/vein/config/maximum_curvature.py
+++ b/bob/bio/vein/config/maximum_curvature.py
@@ -17,7 +17,7 @@ import tempfile
from sklearn.pipeline import make_pipeline
-from bob.bio.base.pipelines import BioAlgorithmLegacy, PipelineSimple
+from bob.bio.base.pipelines import PipelineSimple
from bob.bio.base.transformers import (
ExtractorTransformer,
PreprocessorTransformer,
diff --git a/bob/bio/vein/config/principal_curvature.py b/bob/bio/vein/config/principal_curvature.py
index 47cbe72..e761cd6 100644
--- a/bob/bio/vein/config/principal_curvature.py
+++ b/bob/bio/vein/config/principal_curvature.py
@@ -76,7 +76,7 @@ else:
legacy_temp_dir = tempfile.TemporaryDirectory().name
-from bob.bio.base.pipelines import BioAlgorithmLegacy, PipelineSimple
+from bob.bio.base.pipelines import PipelineSimple
biometric_algorithm = MiuraMatch(ch=18, cw=28)
diff --git a/bob/bio/vein/config/repeated_line_tracking.py b/bob/bio/vein/config/repeated_line_tracking.py
index 7407bd4..b5853ea 100644
--- a/bob/bio/vein/config/repeated_line_tracking.py
+++ b/bob/bio/vein/config/repeated_line_tracking.py
@@ -16,7 +16,7 @@ import tempfile
from sklearn.pipeline import make_pipeline
-from bob.bio.base.pipelines import BioAlgorithmLegacy, PipelineSimple
+from bob.bio.base.pipelines import PipelineSimple
from bob.bio.base.transformers import (
ExtractorTransformer,
PreprocessorTransformer,
diff --git a/bob/bio/vein/config/wide_line_detector.py b/bob/bio/vein/config/wide_line_detector.py
index d88d505..5c3be3a 100644
--- a/bob/bio/vein/config/wide_line_detector.py
+++ b/bob/bio/vein/config/wide_line_detector.py
@@ -16,7 +16,7 @@ import tempfile
from sklearn.pipeline import make_pipeline
-from bob.bio.base.pipelines import BioAlgorithmLegacy, PipelineSimple
+from bob.bio.base.pipelines import PipelineSimple
from bob.bio.base.transformers import (
ExtractorTransformer,
PreprocessorTransformer,
diff --git a/bob/bio/vein/database/fv3d.py b/bob/bio/vein/database/fv3d.py
index b51d477..7c60331 100644
--- a/bob/bio/vein/database/fv3d.py
+++ b/bob/bio/vein/database/fv3d.py
@@ -7,7 +7,6 @@ import numpy
from bob.bio.base.database import BioDatabase, BioFile
-from ..preprocessor.utils import poly_to_mask
from . import AnnotatedArray
diff --git a/bob/bio/vein/database/verafinger.py b/bob/bio/vein/database/verafinger.py
index ea3db17..397bb4a 100644
--- a/bob/bio/vein/database/verafinger.py
+++ b/bob/bio/vein/database/verafinger.py
@@ -6,7 +6,6 @@ import os
from bob.bio.base.database import BioDatabase, BioFile
-from ..preprocessor.utils import poly_to_mask
from . import AnnotatedArray
diff --git a/bob/bio/vein/extractor/MaximumCurvature.py b/bob/bio/vein/extractor/MaximumCurvature.py
index 5248d97..518d562 100644
--- a/bob/bio/vein/extractor/MaximumCurvature.py
+++ b/bob/bio/vein/extractor/MaximumCurvature.py
@@ -6,8 +6,6 @@ import math
import numpy
import scipy.ndimage
-import bob.io.base
-
from bob.bio.base.extractor import Extractor
diff --git a/bob/bio/vein/extractor/NormalisedCrossCorrelation.py b/bob/bio/vein/extractor/NormalisedCrossCorrelation.py
index df44560..b1a73e4 100644
--- a/bob/bio/vein/extractor/NormalisedCrossCorrelation.py
+++ b/bob/bio/vein/extractor/NormalisedCrossCorrelation.py
@@ -3,8 +3,6 @@
import numpy
-import bob.io.base
-
from bob.bio.base.extractor import Extractor
diff --git a/bob/bio/vein/extractor/PrincipalCurvature.py b/bob/bio/vein/extractor/PrincipalCurvature.py
index 84c1bbe..45297ec 100644
--- a/bob/bio/vein/extractor/PrincipalCurvature.py
+++ b/bob/bio/vein/extractor/PrincipalCurvature.py
@@ -5,8 +5,6 @@ import numpy
from scipy.ndimage import gaussian_filter
-import bob.io.base
-
from bob.bio.base.extractor import Extractor
diff --git a/bob/bio/vein/extractor/__init__.py b/bob/bio/vein/extractor/__init__.py
index 4f5cbfb..e50ec98 100644
--- a/bob/bio/vein/extractor/__init__.py
+++ b/bob/bio/vein/extractor/__init__.py
@@ -1,9 +1,9 @@
# isort: skip_file
-from .NormalisedCrossCorrelation import NormalisedCrossCorrelation
-from .PrincipalCurvature import PrincipalCurvature
-from .RepeatedLineTracking import RepeatedLineTracking
-from .WideLineDetector import WideLineDetector
-from .MaximumCurvature import MaximumCurvature
+from .NormalisedCrossCorrelation import NormalisedCrossCorrelation # noqa: F401
+from .PrincipalCurvature import PrincipalCurvature # noqa: F401
+from .RepeatedLineTracking import RepeatedLineTracking # noqa: F401
+from .WideLineDetector import WideLineDetector # noqa: F401
+from .MaximumCurvature import MaximumCurvature # noqa: F401
# gets sphinx autodoc done right - don't remove it
__all__ = [_ for _ in dir() if not _.startswith("_")]
diff --git a/bob/bio/vein/preprocessor/crop.py b/bob/bio/vein/preprocessor/crop.py
index 4ca5b2d..d8bffde 100644
--- a/bob/bio/vein/preprocessor/crop.py
+++ b/bob/bio/vein/preprocessor/crop.py
@@ -4,8 +4,6 @@
"""Base utilities for pre-cropping images"""
-import numpy
-
class Cropper(object):
"""This is the base class for all croppers
diff --git a/bob/bio/vein/preprocessor/filters.py b/bob/bio/vein/preprocessor/filters.py
index 9ef0a9c..6714c4c 100644
--- a/bob/bio/vein/preprocessor/filters.py
+++ b/bob/bio/vein/preprocessor/filters.py
@@ -3,8 +3,6 @@
"""Base utilities for post-filtering vein images"""
-import numpy
-
class Filter(object):
"""Objects of this class filter the input image"""
diff --git a/bob/bio/vein/preprocessor/mask.py b/bob/bio/vein/preprocessor/mask.py
index 01dd15d..3e146fb 100644
--- a/bob/bio/vein/preprocessor/mask.py
+++ b/bob/bio/vein/preprocessor/mask.py
@@ -7,8 +7,6 @@ import math
import numpy
import scipy.ndimage
-import skimage.filters
-import skimage.morphology
from .utils import poly_to_mask
diff --git a/bob/bio/vein/preprocessor/preprocessor.py b/bob/bio/vein/preprocessor/preprocessor.py
index c172f13..5d7fb5f 100644
--- a/bob/bio/vein/preprocessor/preprocessor.py
+++ b/bob/bio/vein/preprocessor/preprocessor.py
@@ -1,7 +1,6 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-
-import bob.io.base
+import h5py
from bob.bio.base.preprocessor import Preprocessor as BasePreprocessor
diff --git a/bob/bio/vein/script/blame.py b/bob/bio/vein/script/blame.py
index 2423684..eb2cfde 100644
--- a/bob/bio/vein/script/blame.py
+++ b/bob/bio/vein/script/blame.py
@@ -73,7 +73,7 @@ def main(user_input=None):
cases = int(args["--cases"])
# generates a huge
- from bob.bio.base.score.load import get_negatives_positives, load_score
+ from bob.bio.base.score.load import load_score
scores = []
names = {}
diff --git a/bob/bio/vein/script/compare_rois.py b/bob/bio/vein/script/compare_rois.py
index 9f94384..7eb7981 100644
--- a/bob/bio/vein/script/compare_rois.py
+++ b/bob/bio/vein/script/compare_rois.py
@@ -48,6 +48,7 @@ import operator
import os
import sys
+import h5py
import numpy
import bob.extension.log
diff --git a/bob/bio/vein/script/validate.py b/bob/bio/vein/script/validate.py
index aa46ac7..b338959 100644
--- a/bob/bio/vein/script/validate.py
+++ b/bob/bio/vein/script/validate.py
@@ -172,8 +172,6 @@ def open_multipage_pdf_file(s):
schema.SchemaError: if the path exists
"""
- import matplotlib.pyplot as mpl
-
from matplotlib.backends.backend_pdf import PdfPages
return PdfPages(s)
diff --git a/bob/bio/vein/script/view_sample.py b/bob/bio/vein/script/view_sample.py
index 4c7dd42..16a2daf 100644
--- a/bob/bio/vein/script/view_sample.py
+++ b/bob/bio/vein/script/view_sample.py
@@ -47,6 +47,7 @@ import os
import sys
import docopt
+import h5py
import numpy
import schema
@@ -88,8 +89,6 @@ def save_figures(title, image, mask, image_pp, binary):
bob.io.base.save(image, os.path.join(title, "original.png"))
# add preprocessed image
- from ..preprocessor import utils
-
img = utils.draw_mask_over_image(image_pp, mask)
img = numpy.array(img).transpose(2, 0, 1)
bob.io.base.save(img[:3], os.path.join(title, "preprocessed.png"))
@@ -140,8 +139,6 @@ def proof_figure(title, image, mask, image_pp, binary=None):
mpl.imshow(image, cmap="gray")
# add preprocessed image
- from ..preprocessor import utils
-
img = utils.draw_mask_over_image(image_pp, mask)
mpl.subplot(images, 1, 2)
mpl.title("Preprocessed")
@@ -223,7 +220,7 @@ def main(user_input=None):
try:
from .validate import setup_logger
- logger = setup_logger("bob.bio.vein", args["--verbose"])
+ setup_logger("bob.bio.vein", args["--verbose"])
args = validate(args)
except schema.SchemaError as e:
sys.exit(e)
@@ -258,7 +255,7 @@ def main(user_input=None):
binary = numpy.rot90(binary, k=1)
except Exception:
binary = None
- fig = proof_figure(stem, image, mask, image_pp, binary)
+ proof_figure(stem, image, mask, image_pp, binary)
if args["--save"]:
save_figures(args["--save"], image, mask, image_pp, binary)
else:
diff --git a/bob/bio/vein/tests/test_tools.py b/bob/bio/vein/tests/test_tools.py
index 01abd10..0f0570c 100644
--- a/bob/bio/vein/tests/test_tools.py
+++ b/bob/bio/vein/tests/test_tools.py
@@ -248,7 +248,7 @@ def test_max_curvature_HE():
from ..extractor.MaximumCurvature import MaximumCurvature
MC = MaximumCurvature(sigma=5)
- extr_data = MC(preproc_data)
+ MC(preproc_data)
# preprocessor_utils.show_image((255.*extr_data).astype('uint8'))
@@ -317,7 +317,7 @@ def test_repeated_line_tracking_HE():
profile_w=PROFILE_WIDTH,
seed=0,
)
- extr_data = RLT(preproc_data)
+ RLT(preproc_data)
def test_wide_line_detector():
@@ -384,7 +384,7 @@ def test_wide_line_detector_HE():
g=SUM_NEIGHBOURHOOD,
rescale=RESCALE,
)
- extr_data = WLD(preproc_data)
+ WLD(preproc_data)
def test_miura_match():
@@ -416,16 +416,16 @@ def test_correlate():
template_filename = F(("algorithms", "0001_2_1_120509-135338.mat.hdf5"))
probe_gen_filename = F(("algorithms", "0001_2_2_120509-135558.mat.hdf5"))
- probe_imp_filename = F(("algorithms", "0003_2_1_120509-141255.mat.hdf5"))
+ # probe_imp_filename = F(("algorithms", "0003_2_1_120509-141255.mat.hdf5"))
template_vein = bob.io.base.load(template_filename)
probe_gen_vein = bob.io.base.load(probe_gen_filename)
- probe_imp_vein = bob.io.base.load(probe_imp_filename)
+ # probe_imp_vein = bob.io.base.load(probe_imp_filename)
from ..algorithm.Correlate import Correlate
C = Correlate()
- score_gen = C.score(template_vein, probe_gen_vein)
+ C.score(template_vein, probe_gen_vein)
# we don't check here - no templates
@@ -545,14 +545,14 @@ def test_mask_to_image():
def _check_float(n):
conv = preprocessor_utils.mask_to_image(sample, "float%d" % n)
nose.tools.eq_(conv.dtype, getattr(numpy, "float%d" % n))
- assert numpy.array_equal(conv, [0, 1.0]), "%r != %r" % (conv, target)
+ assert numpy.array_equal(conv, [0, 1.0]), "%r != %r" % (conv, [0, 1.0])
_check_float(32)
_check_float(64)
# This should be unsupported
try:
- conv = preprocessor_utils.mask_to_image(sample, "int16")
+ preprocessor_utils.mask_to_image(sample, "int16")
except TypeError as e:
assert "int16" in str(e)
else:
diff --git a/doc/conf.py b/doc/conf.py
index 8673212..755aff1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,9 +1,7 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-import glob
import os
-import sys
import pkg_resources
diff --git a/matlab/compare.py b/matlab/compare.py
index 3abc531..ee378c9 100644
--- a/matlab/compare.py
+++ b/matlab/compare.py
@@ -29,8 +29,6 @@ G_matlab = bob.io.base.load("mc_g_matlab.hdf5")
G_matlab = G_matlab.T
# Apply Python implementation
-from bob.bio.vein.extractor.MaximumCurvature import MaximumCurvature
-
MC = MaximumCurvature(3)
kappa = MC.detect_valleys(image, region) # OK
--
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