Merge 392eef1 into da41621

ark/analysis/dimensionality_reduction.py

@@ -1,10 +1,9 @@
-from sklearn.preprocessing import StandardScaler
-from sklearn.decomposition import PCA
-from sklearn.manifold import TSNE
 import matplotlib.pyplot as plt
 import seaborn as sns
 import umap
-import os
+from sklearn.decomposition import PCA
+from sklearn.manifold import TSNE
+from sklearn.preprocessing import StandardScaler
 
 from ark.utils import misc_utils
 

ark/analysis/dimensionality_reduction_test.py

@@ -1,10 +1,11 @@
-import tempfile
 import os
+import tempfile
+
 import pytest
 
+import ark.settings as settings
 from ark.analysis import dimensionality_reduction
 from ark.utils import test_utils
-import ark.settings as settings
 
 
 def test_plot_dim_reduced_data():

ark/analysis/spatial_analysis.py

@@ -1,11 +1,12 @@
+from itertools import combinations_with_replacement
+
+import numpy as np
 import pandas as pd
 import xarray as xr
-import numpy as np
 from tqdm.auto import tqdm
-from itertools import combinations_with_replacement
-from ark.utils import spatial_analysis_utils, misc_utils, load_utils, io_utils
 
 import ark.settings as settings
+from ark.utils import io_utils, load_utils, misc_utils, spatial_analysis_utils
 
 
 def batch_channel_spatial_enrichment(label_dir, marker_thresholds, all_data, batch_size=5,

ark/analysis/spatial_analysis_test.py

@@ -1,12 +1,12 @@
 import tempfile
-import pytest
+
 import numpy as np
 import pandas as pd
-
-from ark.analysis import spatial_analysis
+import pytest
 
 import ark.settings as settings
-from ark.utils import spatial_analysis_utils, load_utils, test_utils
+from ark.analysis import spatial_analysis
+from ark.utils import load_utils, spatial_analysis_utils, test_utils
 
 EXCLUDE_CHANNELS = [
     "Background",

ark/phenotyping/cell_cluster_utils.py

@@ -1,27 +1,14 @@
-from functools import partial
-import multiprocessing
 import os
-import json
 import subprocess
-import warnings
 
 import feather
 import matplotlib.patches as patches
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-from pyarrow.lib import ArrowInvalid
-import re
-import scipy.ndimage as ndimage
 import scipy.stats as stats
-from shutil import rmtree
-from skimage.io import imread, imsave
-import xarray as xr
 
 from ark.analysis import visualize
-import ark.settings as settings
-from ark.utils import io_utils
-from ark.utils import load_utils
 from ark.utils import misc_utils
 
 

ark/phenotyping/cell_cluster_utils_test.py

@@ -1,27 +1,14 @@
-import json
 import os
-import pytest
-from pytest_cases import parametrize_with_cases
-from shutil import rmtree
 import tempfile
-import textwrap
-import warnings
 
 import feather
-from matplotlib.colors import ListedColormap
 import numpy as np
 import pandas as pd
-from skimage.draw import disk
-import skimage.io as io
-import scipy.ndimage as ndimage
+import pytest
 from sklearn.utils import shuffle
-import xarray as xr
 
 import ark.phenotyping.cell_cluster_utils as cell_cluster_utils
-import ark.utils.io_utils as io_utils
-import ark.utils.load_utils as load_utils
 import ark.utils.misc_utils as misc_utils
-import ark.utils.test_utils as test_utils
 
 parametrize = pytest.mark.parametrize
 

ark/phenotyping/pixel_cluster_utils.py

@@ -1,28 +1,18 @@
-from functools import partial
 import multiprocessing
 import os
-import json
 import subprocess
 import warnings
+from functools import partial
+from shutil import rmtree
 
 import feather
-import matplotlib.patches as patches
-import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-from pyarrow.lib import ArrowInvalid
-import re
 import scipy.ndimage as ndimage
-import scipy.stats as stats
-from shutil import rmtree
+from pyarrow.lib import ArrowInvalid
 from skimage.io import imread, imsave
-import xarray as xr
 
-from ark.analysis import visualize
-import ark.settings as settings
-from ark.utils import io_utils
-from ark.utils import load_utils
-from ark.utils import misc_utils
+from ark.utils import io_utils, load_utils, misc_utils
 
 multiprocessing.set_start_method('spawn', force=True)
 

ark/phenotyping/pixel_cluster_utils_test.py

@@ -1,24 +1,18 @@
-import json
 import os
-import pytest
-from pytest_cases import parametrize_with_cases
-from shutil import rmtree
 import tempfile
-import textwrap
 import warnings
+from shutil import rmtree
 
 import feather
-from matplotlib.colors import ListedColormap
 import numpy as np
 import pandas as pd
-from skimage.draw import disk
-import skimage.io as io
+import pytest
 import scipy.ndimage as ndimage
-from sklearn.utils import shuffle
-import xarray as xr
+import skimage.io as io
+from pytest_cases import parametrize_with_cases
+from skimage.draw import disk
 
 import ark.phenotyping.pixel_cluster_utils as pixel_cluster_utils
-from ark.phenotyping.pixel_cluster_utils import create_fov_pixel_data
 import ark.utils.io_utils as io_utils
 import ark.utils.load_utils as load_utils
 import ark.utils.misc_utils as misc_utils

ark/phenotyping/post_cluster_utils.py

@@ -1,6 +1,7 @@
-import numpy as np
-import matplotlib.pyplot as plt
 import os
+
+import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
 
 from ark.utils import data_utils, load_utils, plot_utils

ark/phenotyping/post_cluster_utils_test.py

@@ -1,8 +1,8 @@
 import os
-import pytest
 
 import numpy as np
 import pandas as pd
+import pytest
 import skimage.io as io
 
 from ark.phenotyping import post_cluster_utils

ark/segmentation/marker_quantification.py

@@ -3,16 +3,13 @@
 
 import numpy as np
 import pandas as pd
-
 import xarray as xr
-
 from skimage.measure import regionprops, regionprops_table
 
-from ark.utils import io_utils, load_utils, misc_utils, segmentation_utils
-from ark.segmentation.signal_extraction import EXTRACTION_FUNCTION
-from ark.segmentation.regionprops_extraction import REGIONPROPS_FUNCTION
-
 import ark.settings as settings
+from ark.segmentation.regionprops_extraction import REGIONPROPS_FUNCTION
+from ark.segmentation.signal_extraction import EXTRACTION_FUNCTION
+from ark.utils import io_utils, load_utils, misc_utils, segmentation_utils
 
 
 def get_single_compartment_props(segmentation_labels, regionprops_base,

ark/segmentation/marker_quantification_test.py

@@ -1,20 +1,17 @@
 import copy
-import numpy as np
 import os
-import pytest
-import skimage.io as io
 import tempfile
-import xarray as xr
 
+import numpy as np
+import pytest
+import skimage.io as io
 import skimage.morphology as morph
+import xarray as xr
 from skimage.morphology import erosion
-from skimage.measure import regionprops
-
-from ark.segmentation import marker_quantification
-from ark.utils import misc_utils
-from ark.utils import test_utils
 
 import ark.settings as settings
+from ark.segmentation import marker_quantification
+from ark.utils import misc_utils, test_utils
 
 
 def test_get_single_compartment_props():

ark/segmentation/regionprops_extraction.py

@@ -1,8 +1,6 @@
-import copy
 
 import numpy as np
 import pandas as pd
-
 from skimage.measure import label, moments, regionprops_table
 
 

ark/segmentation/regionprops_extraction_test.py

@@ -1,13 +1,10 @@
 import copy
 
 import numpy as np
-import pandas as pd
 import xarray as xr
-
 from skimage.draw import ellipse
-from skimage.measure import moments, regionprops, regionprops_table
+from skimage.measure import regionprops
 
-import ark.settings as settings
 import ark.segmentation.regionprops_extraction as regionprops_extraction
 
 

ark/segmentation/signal_extraction_test.py

@@ -1,11 +1,10 @@
 import numpy as np
 import xarray as xr
+from skimage.measure import regionprops
 
 from ark.segmentation import signal_extraction
 from ark.utils import synthetic_spatial_datagen
 
-from skimage.measure import regionprops
-
 
 def test_positive_pixels_extraction():
     # sample params

ark/spLDA/processing_test.py

@@ -5,8 +5,9 @@
 import ark.settings as settings
 import ark.spLDA.processing as pros
 from ark.utils.misc_utils import verify_in_list
-from ark.utils.test_utils import make_cell_table
 from ark.utils.spatial_lda_utils import within_cluster_sums
+from ark.utils.test_utils import make_cell_table
+
 # Generate a test cell table
 N_CELLS = 1000
 TEST_CELL_TABLE = make_cell_table(N_CELLS)

ark/utils/_bootstrapping.pyx

@@ -1,9 +1,9 @@
-from cython cimport cdivision, boundscheck, wraparound
-from cpython.mem cimport PyMem_Malloc, PyMem_Free
+from cpython.mem cimport PyMem_Free, PyMem_Malloc
+from cython cimport boundscheck, cdivision, wraparound
 
 import numpy as np
-cimport numpy as np
 
+cimport numpy as np
 from libc.stdlib cimport rand
 from libc.string cimport memset
 

ark/utils/data_utils.py

@@ -1,15 +1,16 @@
-from optparse import Option
+import math
 import os
 import pathlib
-from typing import List, Optional, Union
-import math
+import shutil
+from typing import List, Union
+
+import datasets
 import feather
-import skimage.io as io
 import numpy as np
+import skimage.io as io
 import xarray as xr
 from tqdm.notebook import tqdm_notebook as tqdm
-import datasets
-import shutil
+
 from ark import settings
 from ark.utils import load_utils
 from ark.utils.misc_utils import verify_in_list

ark/utils/data_utils_test.py

@@ -1,22 +1,21 @@
-import numpy as np
 import os
+import pathlib
 import tempfile
 from shutil import rmtree
-import pytest
+
 import feather
+import numpy as np
 import pandas as pd
-import xarray as xr
+import pytest
 import skimage.io as io
-import pathlib
-from ark.utils import data_utils, test_utils
-from ark.utils.data_utils import (
-    download_example_data,
-    generate_and_save_cell_cluster_masks,
-    generate_and_save_pixel_cluster_masks,
-    relabel_segmentation,
-    label_cells_by_cluster
-)
+import xarray as xr
+
 from ark import settings
+from ark.utils import data_utils, test_utils
+from ark.utils.data_utils import (download_example_data,
+                                  generate_and_save_cell_cluster_masks,
+                                  generate_and_save_pixel_cluster_masks,
+                                  label_cells_by_cluster, relabel_segmentation)
 
 
 def test_save_fov_images():

ark/utils/deepcell_service_utils.py

@@ -1,23 +1,22 @@
+import os
+import time
+import warnings
 from concurrent.futures import ThreadPoolExecutor
+from io import BytesIO
 from json import JSONDecodeError
-import os
 from pathlib import Path
+from urllib.parse import unquote_plus
+from zipfile import ZIP_DEFLATED, ZipFile
+
+import numpy as np
 import requests
 from requests.adapters import HTTPAdapter
 from requests.exceptions import RetryError
 from requests.packages.urllib3.util import Retry
-import time
-from tqdm.notebook import tqdm
-from urllib.parse import unquote_plus
-import warnings
-from concurrent.futures import ThreadPoolExecutor
-import numpy as np
-from scipy import stats
 from skimage import io
 from tifffile import imread
-from io import BytesIO
-from ark.utils import misc_utils
-from zipfile import ZipFile, ZIP_DEFLATED
+from tqdm.notebook import tqdm
+
 from ark.utils import io_utils, misc_utils