isort: define & apply

.github/workflows/code-format.yml

@@ -38,19 +38,19 @@ jobs:
       - name: yapf
         run: yapf --diff --parallel --recursive .
 
-#  imports-check-isort:
-#    runs-on: ubuntu-20.04
-#    steps:
-#      - uses: actions/checkout@master
-#      - uses: actions/setup-python@v2
-#        with:
-#          python-version: 3.8
-#      - name: Install isort
-#        run: |
-#          pip install isort
-#          pip list
-#      - name: isort
-#        run: isort --check-only .
+  imports-check-isort:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@master
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install isort
+        run: |
+          pip install isort
+          pip list
+      - name: isort
+        run: isort --check-only .
 
   #typing-check-mypy:
   #  runs-on: ubuntu-20.04

birl/benchmark.py

@@ -27,15 +27,23 @@
 
 # this is used while calling this file as a script
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import update_path, create_folder, image_sizes, load_landmarks, load_image, save_image
-from birl.utilities.dataset import image_histogram_matching, common_landmarks
+from birl.utilities.data_io import create_folder, image_sizes, load_image, load_landmarks, save_image, update_path
+from birl.utilities.dataset import common_landmarks, image_histogram_matching
+from birl.utilities.drawing import draw_image_points, draw_images_warped_landmarks, export_figure, overlap_two_images
 from birl.utilities.evaluate import (
-    compute_target_regist_error_statistic, compute_affine_transf_diff, compute_tre_robustness
+    compute_affine_transf_diff,
+    compute_target_regist_error_statistic,
+    compute_tre_robustness,
 )
 from birl.utilities.experiments import (
-    nb_workers, exec_commands, string_dict, iterate_mproc_map, create_basic_parser, parse_arg_params, Experiment
+    create_basic_parser,
+    exec_commands,
+    Experiment,
+    iterate_mproc_map,
+    nb_workers,
+    parse_arg_params,
+    string_dict,
 )
-from birl.utilities.drawing import (export_figure, draw_image_points, draw_images_warped_landmarks, overlap_two_images)
 from birl.utilities.registration import estimate_affine_transform
 
 #: In case provided dataset and complete (true) dataset differ

birl/bm_template.py

@@ -26,8 +26,8 @@
 
 # this is used while calling this file as a script
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import create_basic_parser
 from birl.benchmark import ImRegBenchmark
+from birl.utilities.experiments import create_basic_parser
 
 
 class BmTemplate(ImRegBenchmark):

birl/utilities/data_io.py

@@ -9,14 +9,14 @@
 import warnings
 from functools import wraps
 
-import SimpleITK as sitk
 import cv2 as cv
 import nibabel
 import numpy as np
 import pandas as pd
+import SimpleITK as sitk
 import yaml
 from PIL import Image
-from skimage.color import rgb2gray, gray2rgb
+from skimage.color import gray2rgb, rgb2gray
 
 #: landmarks coordinates, loading from CSV file
 LANDMARK_COORDS = ['X', 'Y']

birl/utilities/dataset.py

@@ -11,21 +11,21 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from PIL import Image
 from cv2 import (
-    IMWRITE_JPEG_QUALITY,
-    IMWRITE_PNG_COMPRESSION,
-    COLOR_RGBA2RGB,
     COLOR_RGB2BGR,
-    INTER_LINEAR,
-    GaussianBlur,
+    COLOR_RGBA2RGB,
     cvtColor,
+    GaussianBlur,
     imwrite,
+    IMWRITE_JPEG_QUALITY,
+    IMWRITE_PNG_COMPRESSION,
+    INTER_LINEAR,
     resize,
 )
 from matplotlib.path import Path
-from scipy import spatial, optimize
-from skimage.color import rgb2hsv, hsv2rgb, rgb2lab, lab2rgb, lch2lab, lab2lch, rgb2hed, hed2rgb, rgb2luv, luv2rgb
+from PIL import Image
+from scipy import optimize, spatial
+from skimage.color import hed2rgb, hsv2rgb, lab2lch, lab2rgb, lch2lab, luv2rgb, rgb2hed, rgb2hsv, rgb2lab, rgb2luv
 from skimage.exposure import rescale_intensity
 from skimage.filters import threshold_otsu
 

birl/utilities/drawing.py

@@ -10,8 +10,9 @@
 
 import matplotlib.pylab as plt
 import numpy as np
+from matplotlib import colors as plt_colors
+from matplotlib import ticker as plt_ticker
 from PIL import ImageDraw
-from matplotlib import colors as plt_colors, ticker as plt_ticker
 
 from birl.utilities.data_io import convert_ndarray2image
 from birl.utilities.dataset import scale_large_images_landmarks

bm_ANHIR/evaluate_submission.py

@@ -73,10 +73,10 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
+from birl.benchmark import _df_drop_unnamed, COL_PAIRED_LANDMARKS, filter_paired_landmarks, ImRegBenchmark
 from birl.utilities.data_io import create_folder, load_landmarks, save_landmarks, update_path
 from birl.utilities.dataset import parse_path_scale
-from birl.utilities.experiments import iterate_mproc_map, parse_arg_params, FORMAT_DATE_TIME, nb_workers
-from birl.benchmark import COL_PAIRED_LANDMARKS, ImRegBenchmark, filter_paired_landmarks, _df_drop_unnamed
+from birl.utilities.experiments import FORMAT_DATE_TIME, iterate_mproc_map, nb_workers, parse_arg_params
 
 NB_WORKERS = nb_workers(0.9)
 NAME_CSV_RESULTS = 'registration-results.csv'

bm_ANHIR/generate_regist_pairs.py

@@ -15,9 +15,9 @@
 import tqdm
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import image_sizes, update_path
-from birl.utilities.dataset import IMAGE_EXTENSIONS, generate_pairing
 from birl.benchmark import ImRegBenchmark
+from birl.utilities.data_io import image_sizes, update_path
+from birl.utilities.dataset import generate_pairing, IMAGE_EXTENSIONS
 
 DATASET_IMAGES = '/datagrid/Medical/dataset_ANHIR/images_private'
 DATASET_LANDMARKS = '/datagrid/Medical/dataset_ANHIR/landmarks_all'

bm_dataset/convert_tiff2png.py

@@ -40,8 +40,8 @@
     )
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import iterate_mproc_map, nb_workers
 from birl.utilities.dataset import args_expand_parse_images
+from birl.utilities.experiments import iterate_mproc_map, nb_workers
 
 DEFAULT_LEVEL = 1
 MAX_LOAD_IMAGE_SIZE = 16000

bm_dataset/create_real_synth_dataset.py

@@ -27,16 +27,16 @@
     print('No display found. Using non-interactive Agg backend')
     matplotlib.use('Agg')
 
-import tqdm
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import tqdm
 from PIL import Image
-from scipy import ndimage, stats, interpolate
-import matplotlib.pyplot as plt
+from scipy import interpolate, ndimage, stats
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import parse_arg_params, nb_workers
 from birl.utilities.data_io import LANDMARK_COORDS
+from birl.utilities.experiments import nb_workers, parse_arg_params
 
 COLUMNS_COORD = LANDMARK_COORDS
 NB_WORKERS = nb_workers(0.8)

bm_dataset/crop_tissue_images.py

@@ -26,9 +26,13 @@
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
 from birl.utilities.dataset import (
-    find_largest_object, project_object_edge, load_large_image, save_large_image, args_expand_parse_images
+    args_expand_parse_images,
+    find_largest_object,
+    load_large_image,
+    project_object_edge,
+    save_large_image,
 )
-from birl.utilities.experiments import iterate_mproc_map, try_decorator, nb_workers
+from birl.utilities.experiments import iterate_mproc_map, nb_workers, try_decorator
 
 NB_WORKERS = nb_workers(0.5)
 SCALE_SIZE = 512

bm_dataset/generate_regist_pairs.py

@@ -25,9 +25,9 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
+from birl.benchmark import ImRegBenchmark
 from birl.utilities.data_io import image_sizes
 from birl.utilities.experiments import parse_arg_params
-from birl.benchmark import ImRegBenchmark
 
 # list of combination options
 OPTIONS_COMBINE = ('first2all', 'each2all')

bm_dataset/rescale_tissue_images.py

@@ -26,9 +26,9 @@
 import cv2 as cv
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import iterate_mproc_map, is_iterable, nb_workers
-from birl.utilities.dataset import (load_large_image, save_large_image, parse_path_scale, args_expand_parse_images)
 from birl.utilities.data_io import create_folder
+from birl.utilities.dataset import args_expand_parse_images, load_large_image, parse_path_scale, save_large_image
+from birl.utilities.experiments import is_iterable, iterate_mproc_map, nb_workers
 
 NB_WORKERS = nb_workers(0.5)
 DEFAULT_SCALES = (5, 10, 15, 20, 25, 50)

bm_dataset/rescale_tissue_landmarks.py

@@ -39,11 +39,11 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import iterate_mproc_map, parse_arg_params, is_iterable
 from birl.utilities.data_io import create_folder, load_landmarks_csv, save_landmarks_csv
-from birl.utilities.dataset import (list_sub_folders, parse_path_scale, compute_bounding_polygon, inside_polygon)
+from birl.utilities.dataset import compute_bounding_polygon, inside_polygon, list_sub_folders, parse_path_scale
+from birl.utilities.experiments import is_iterable, iterate_mproc_map, parse_arg_params
 from birl.utilities.registration import estimate_affine_transform, transform_points
-from bm_dataset.rescale_tissue_images import NB_WORKERS, DEFAULT_SCALES, FOLDER_TEMPLATE
+from bm_dataset.rescale_tissue_images import DEFAULT_SCALES, FOLDER_TEMPLATE, NB_WORKERS
 
 
 def arg_parse_params():

bm_dataset/split_images_two_tissues.py

@@ -25,7 +25,11 @@
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
 from birl.utilities.dataset import (
-    find_split_objects, project_object_edge, load_large_image, save_large_image, args_expand_parse_images
+    args_expand_parse_images,
+    find_split_objects,
+    load_large_image,
+    project_object_edge,
+    save_large_image,
 )
 from birl.utilities.experiments import iterate_mproc_map, nb_workers
 

bm_experiments/bm_ANTs.py

@@ -82,11 +82,15 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
+from birl.benchmark import ImRegBenchmark
 from birl.utilities.data_io import (
-    load_landmarks, save_landmarks, load_config_args, convert_image_to_nifti_gray, convert_image_from_nifti
+    convert_image_from_nifti,
+    convert_image_to_nifti_gray,
+    load_config_args,
+    load_landmarks,
+    save_landmarks,
 )
 from birl.utilities.experiments import exec_commands
-from birl.benchmark import ImRegBenchmark
 from bm_experiments import bm_comp_perform
 
 

bm_experiments/bm_DROP.py

@@ -64,14 +64,18 @@
 import sys
 import time
 
-import SimpleITK as sitk
 import numpy as np
+import SimpleITK as sitk
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
+from birl.benchmark import ImRegBenchmark
 from birl.utilities.data_io import (
-    convert_image_to_mhd, convert_image_from_mhd, save_landmarks, load_landmarks, image_sizes
+    convert_image_from_mhd,
+    convert_image_to_mhd,
+    image_sizes,
+    load_landmarks,
+    save_landmarks,
 )
-from birl.benchmark import ImRegBenchmark
 from bm_experiments import bm_comp_perform
 
 

bm_experiments/bm_DROP2.py

@@ -52,11 +52,11 @@
 import shutil
 import sys
 
-import SimpleITK as sitk
 import numpy as np
+import SimpleITK as sitk
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import save_landmarks, load_landmarks, load_config_args
+from birl.utilities.data_io import load_config_args, load_landmarks, save_landmarks
 from bm_experiments import bm_comp_perform
 from bm_experiments.bm_DROP import BmDROP
 

bm_experiments/bm_RVSS.py

@@ -44,9 +44,9 @@
 import sys
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import load_landmarks, save_landmarks, load_config_yaml
-from birl.utilities.experiments import exec_commands, dict_deep_update
 from birl.benchmark import ImRegBenchmark
+from birl.utilities.data_io import load_config_yaml, load_landmarks, save_landmarks
+from birl.utilities.experiments import dict_deep_update, exec_commands
 from bm_experiments import bm_comp_perform
 from bm_experiments.bm_bUnwarpJ import BmUnwarpJ
 

bm_experiments/bm_bUnwarpJ.py

@@ -55,9 +55,9 @@
 import sys
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import update_path, load_landmarks, save_landmarks, load_config_yaml
-from birl.utilities.experiments import exec_commands, dict_deep_update
 from birl.benchmark import ImRegBenchmark
+from birl.utilities.data_io import load_config_yaml, load_landmarks, save_landmarks, update_path
+from birl.utilities.experiments import dict_deep_update, exec_commands
 from bm_experiments import bm_comp_perform
 
 

bm_experiments/bm_comp_perform.py

@@ -39,13 +39,14 @@
 
 matplotlib.use('Agg')
 import numpy as np
-from skimage import data, io, __version__ as skimage__version
-from skimage.transform import resize, warp, AffineTransform
+from skimage import __version__ as skimage__version
+from skimage import data, io
 from skimage.color import rgb2gray
+from skimage.feature import match_descriptors, ORB
 from skimage.measure import ransac
-from skimage.util import random_noise
 from skimage.restoration import denoise_bilateral, denoise_wavelet
-from skimage.feature import ORB, match_descriptors
+from skimage.transform import AffineTransform, resize, warp
+from skimage.util import random_noise
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
 from birl.utilities.experiments import computer_info

bm_experiments/bm_elastix.py

@@ -75,9 +75,9 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
+from birl.benchmark import ImRegBenchmark
 from birl.utilities.data_io import load_landmarks, save_landmarks, save_landmarks_pts
 from birl.utilities.experiments import exec_commands
-from birl.benchmark import ImRegBenchmark
 from bm_experiments import bm_comp_perform
 
 

bm_experiments/bm_rNiftyReg.py

@@ -46,8 +46,8 @@
 import sys
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.data_io import load_landmarks, save_landmarks
 from birl.benchmark import ImRegBenchmark
+from birl.utilities.data_io import load_landmarks, save_landmarks
 from bm_experiments import bm_comp_perform
 
 

bm_experiments/evaluate_experiment.py

@@ -28,8 +28,8 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from birl.utilities.experiments import iterate_mproc_map, parse_arg_params, nb_workers
-from birl.benchmark import ImRegBenchmark, export_summary_results
+from birl.benchmark import export_summary_results, ImRegBenchmark
+from birl.utilities.experiments import iterate_mproc_map, nb_workers, parse_arg_params
 
 #: default number of used threads
 NB_WORKERS = nb_workers(0.75)

scripts/Python/run_SimpleElastix.py

@@ -35,8 +35,8 @@
 import os
 import sys
 
-import SimpleITK as sitk
 import numpy as np
+import SimpleITK as sitk
 from PIL import Image