imports: format import order

em_stitch/lens_correction/lens_correction_solver.py

@@ -1,19 +1,23 @@
+import glob
+import json
+import logging
+import os
+import warnings
+
+import cv2
+import numpy as np
+
 from argschema import ArgSchemaParser
+from bigfeta import jsongz
+import renderapi
+
 from .schemas import LensCorrectionSchema
-from ..utils.generate_EM_tilespecs_from_metafile import \
-        GenerateEMTileSpecsModule
+from ..utils.generate_EM_tilespecs_from_metafile import (
+    GenerateEMTileSpecsModule)
 from ..utils import utils as common_utils
 from .mesh_and_solve_transform import MeshAndSolveTransform
 from . import utils
-from bigfeta import jsongz
-import logging
-import os
-import glob
-import json
-import numpy as np
-import renderapi
-import cv2
-import warnings
+
 warnings.simplefilter(action='ignore', category=FutureWarning)
 
 logger = logging.getLogger(__name__)

em_stitch/lens_correction/mesh_and_solve_transform.py

@@ -1,21 +1,25 @@
+import copy
+import datetime
+import logging
+import os
+
+from six.moves import urllib
+
+import cv2
 import numpy as np
-import triangle
 import scipy.optimize
-from scipy.spatial import Delaunay
 import scipy.sparse as sparse
 from scipy.sparse import csr_matrix
 from scipy.sparse.linalg import factorized
-import renderapi
-import copy
-import os
-import datetime
-import cv2
-from six.moves import urllib
+from scipy.spatial import Delaunay
+import triangle
+
 from argschema import ArgSchemaParser
+from bigfeta import jsongz
+import renderapi
+
 from .schemas import MeshLensCorrectionSchema
 from .utils import remove_weighted_matches
-from bigfeta import jsongz
-import logging
 
 try:
     # pandas unique is faster than numpy, use where appropriate

em_stitch/lens_correction/schemas.py

@@ -1,11 +1,14 @@
 import warnings
+
 from marshmallow.warnings import ChangedInMarshmallow3Warning
 import marshmallow as mm
+
 from argschema import ArgSchema
 from argschema.schemas import DefaultSchema
 from argschema.fields import (
-        Boolean, InputDir, InputFile, Float, List,
-        Int, OutputDir, Nested, Str, Dict)
+    Boolean, InputDir, InputFile, Float, List,
+    Int, OutputDir, Nested, Str, Dict)
+
 warnings.simplefilter(
         action='ignore',
         category=ChangedInMarshmallow3Warning)

em_stitch/lens_correction/utils.py

@@ -1,11 +1,13 @@
-import numpy as np
-import cv2
-import renderapi
 import time
-from scipy import ndimage
 import logging
-from ..utils import utils as common_utils
 
+import cv2
+import numpy as np
+from scipy import ndimage
+
+import renderapi
+
+from ..utils import utils as common_utils
 
 logger = logging.getLogger(__name__)
 

em_stitch/montage/meta_to_collection.py

@@ -5,11 +5,11 @@
 '''
 
 import argparse
+from enum import IntEnum
 import glob
 import json
 import os
 import sys
-from enum import IntEnum
 
 
 # Position codes in metafile

em_stitch/montage/montage_solver.py

@@ -1,15 +1,17 @@
+import glob
+import json
+import os
+
 from argschema import ArgSchemaParser
+from bigfeta import jsongz
+import bigfeta.bigfeta as bfa
 import renderapi
+
 from em_stitch.montage import meta_to_collection
 from em_stitch.montage.schemas import MontageSolverSchema
-from em_stitch.utils.generate_EM_tilespecs_from_metafile import \
-        GenerateEMTileSpecsModule
+from em_stitch.utils.generate_EM_tilespecs_from_metafile import (
+    GenerateEMTileSpecsModule)
 from em_stitch.utils.utils import pointmatch_filter, get_z_from_metafile
-from bigfeta import jsongz
-import bigfeta.bigfeta as bfa
-import json
-import os
-import glob
 
 dname = os.path.join(
             os.path.dirname(os.path.abspath(__file__)),

em_stitch/montage/schemas.py

@@ -1,10 +1,14 @@
+import os
 import warnings
+
 from marshmallow.warnings import ChangedInMarshmallow3Warning
 import marshmallow as mm
+
 from argschema import ArgSchema
 from argschema.fields import (
-        Boolean, InputDir, InputFile, Float, OutputDir, List, Str, Dict)
-import os
+    Boolean, InputDir, InputFile, Float,
+    OutputDir, List, Str, Dict)
+
 warnings.simplefilter(
         action='ignore',
         category=ChangedInMarshmallow3Warning)

em_stitch/plots/lens_quiver_plots.py

@@ -1,17 +1,21 @@
-import renderapi
-from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.pyplot as plt
-import json
-import numpy as np
+import datetime
 import glob
+import json
 import os
 import re
 import warnings
-import datetime
-from em_stitch.utils.utils import src_from_xy
-from em_stitch.plots.schemas import LensQuiverSchema
+
+from matplotlib.backends.backend_pdf import PdfPages
+import matplotlib.pyplot as plt
+import numpy as np
+
 from argschema import ArgSchemaParser
 from bigfeta import jsongz
+import renderapi
+
+from em_stitch.utils.utils import src_from_xy
+from em_stitch.plots.schemas import LensQuiverSchema
+
 warnings.simplefilter(action='ignore', category=FutureWarning)
 
 example = {

em_stitch/plots/montage_plots.py

@@ -1,13 +1,16 @@
+import json
+import os
+
 from matplotlib.backends.backend_pdf import PdfPages
-from argschema import ArgSchemaParser
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
-import renderapi
 import numpy as np
-import json
+
+from argschema import ArgSchemaParser
 from bigfeta import jsongz
+import renderapi
+
 from em_stitch.plots.schemas import MontagePlotsSchema
-import os
 
 example = {
         "collection_path": "/data/em-131fs3/lctest/T4.2019.04.29b/001738/0/collection.json.gz",

em_stitch/plots/schemas.py

@@ -1,7 +1,7 @@
 from argschema import ArgSchema
 from argschema.fields import (
-        InputDir, InputFile, Str, List, Boolean, Int,
-        OutputFile, Float)
+    InputDir, InputFile, Str, List, Boolean, Int,
+    OutputFile, Float)
 
 
 class LensQuiverSchema(ArgSchema):

em_stitch/plots/view_matches.py

@@ -1,14 +1,17 @@
-from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.pyplot as plt
+import logging
 import os
+
+import cv2
 import numpy as np
-import logging
-from em_stitch.lens_correction.utils import maps_from_tform
+from matplotlib.backends.backend_pdf import PdfPages
+import matplotlib.pyplot as plt
+
+from argschema import ArgSchemaParser
 from bigfeta import jsongz
 import renderapi
-import cv2
+
 from em_stitch.plots.schemas import ViewMatchesSchema
-from argschema import ArgSchemaParser
+from em_stitch.lens_correction.utils import maps_from_tform
 
 logger = logging.getLogger()
 

em_stitch/utils/generate_EM_tilespecs_from_metafile.py

@@ -1,10 +1,13 @@
-import renderapi
-import os
 import json
-import numpy
+import os
 import pathlib
-from bigfeta import jsongz
+
+import numpy
+
 from argschema import ArgSchemaParser
+from bigfeta import jsongz
+import renderapi
+
 from .schemas import GenerateEMTileSpecsParameters
 
 # this is a modification of https://github.com/AllenInstitute/

em_stitch/utils/schemas.py

@@ -1,9 +1,12 @@
 import warnings
+
 from marshmallow.warnings import ChangedInMarshmallow3Warning
+
 from argschema import ArgSchema
 from argschema.fields import (
-        InputDir, InputFile, Float,
-        Int, OutputFile, Str, Boolean)
+    InputDir, InputFile, Float,
+    Int, OutputFile, Str, Boolean)
+
 warnings.simplefilter(
         action='ignore',
         category=ChangedInMarshmallow3Warning)

em_stitch/utils/utils.py

@@ -1,6 +1,8 @@
-import numpy as np
-import cv2
 import json
+
+import cv2
+import numpy as np
+
 import renderapi
 
 

em_stitch/viz/schemas.py

@@ -1,9 +1,12 @@
 import warnings
+
 from marshmallow.warnings import ChangedInMarshmallow3Warning
+
 from argschema import ArgSchema
 from argschema.schemas import DefaultSchema
 from argschema.fields import (
-        Nested, Int, Str, Boolean, List)
+    Nested, Int, Str, Boolean, List)
+
 warnings.simplefilter(
         action='ignore',
         category=ChangedInMarshmallow3Warning)

em_stitch/viz/set_permissions.py

@@ -1,9 +1,12 @@
-from argschema import ArgSchemaParser
-from .schemas import SetPermissionsSchema
+import logging
+import os
+
 import subprocess
 import sys
-import os
-import logging
+
+from argschema import ArgSchemaParser
+
+from .schemas import SetPermissionsSchema
 
 logger = logging.getLogger(__name__)
 

em_stitch/viz/set_update_upload.py

@@ -1,10 +1,12 @@
+import logging
+import os
+
 from argschema import ArgSchemaParser
+
 from em_stitch.viz.schemas import SetUpdateUploadSchema
 from em_stitch.viz.set_permissions import SetPermissions
 from em_stitch.viz.update_urls import UpdateUrls
 from em_stitch.viz.upload_to_render import UploadToRender
-import os
-import logging
 
 logger = logging.getLogger(__name__)
 

em_stitch/viz/update_urls.py

@@ -1,12 +1,15 @@
+import logging
 import os
+import pathlib
 import shutil
+
 from six.moves import urllib
-import pathlib
-from bigfeta import jsongz
+
 from argschema import ArgSchemaParser
-from .schemas import UpdateUrlSchema
+from bigfeta import jsongz
 import renderapi
-import logging
+
+from .schemas import UpdateUrlSchema
 
 logger = logging.getLogger(__name__)
 

em_stitch/viz/upload_to_render.py

@@ -1,9 +1,11 @@
+import logging
+import os
+
 from argschema import ArgSchemaParser
+from bigfeta import jsongz
 import renderapi
+
 from .schemas import UploadToRenderSchema
-from bigfeta import jsongz
-import os
-import logging
 
 logger = logging.getLogger(__name__)