reshape imports and exclude plot folder from pytest config

bigfish/stack/__init__.py

@@ -5,78 +5,135 @@
 build stack of images.
 """
 
-from .utils import (check_array, check_df, check_recipe, check_datamap,
-                    check_parameter, check_range_value,
-                    get_margin_value, get_eps_float32)
-from .io import (read_image, read_dv, read_array, save_image, save_array)
-from .preprocess import (build_stacks, build_stack,
-                         build_stack_no_recipe, rescale,
-                         cast_img_uint8, cast_img_uint16, cast_img_float32,
-                         cast_img_float64)
-from .filter import (log_filter, mean_filter, median_filter, maximum_filter,
-                     minimum_filter, gaussian_filter, remove_background_mean,
-                     remove_background_gaussian, dilation_filter,
-                     erosion_filter)
-from .projection import (maximum_projection, mean_projection,
-                         median_projection, in_focus_selection,
-                         focus_measurement, get_in_focus_indices,
-                         focus_projection, focus_projection_fast)
-from .illumination import (compute_illumination_surface,
-                           correct_illumination_surface)
-from .postprocess import (remove_transcription_site,
-                          extract_spots_from_frame, extract_coordinates_image,
-                          center_mask_coord, from_boundaries_to_surface,
-                          from_surface_to_boundaries, from_binary_to_coord,
-                          complete_coord_boundaries, from_coord_to_frame,
-                          from_coord_to_surface)
-from .preparation import (split_from_background, build_image, get_coordinates,
-                          get_distance_layers, get_surface_layers, build_batch,
-                          get_label, Generator, encode_labels, get_map_label,
-                          format_experimental_data, get_label_encoder,
-                          remove_transcription_site_bis, filter_data,
-                          balance_data, get_gene_encoder)
+from .utils import check_array
+from .utils import check_df
+from .utils import check_parameter
+from .utils import check_range_value
+from .utils import check_recipe
+from .utils import check_datamap
+from .utils import get_margin_value
+from .utils import get_eps_float32
+
+from .io import read_image
+from .io import read_dv
+from .io import read_array
+from .io import save_image
+from .io import save_array
+
+from .preprocess import build_stacks
+from .preprocess import build_stack
+from .preprocess import build_stack_no_recipe
+from .preprocess import rescale
+from .preprocess import cast_img_uint8
+from .preprocess import cast_img_uint16
+from .preprocess import cast_img_float32
+from .preprocess import cast_img_float64
+
+from .filter import mean_filter
+from .filter import median_filter
+from .filter import maximum_filter
+from .filter import minimum_filter
+from .filter import log_filter
+from .filter import gaussian_filter
+from .filter import remove_background_mean
+from .filter import remove_background_gaussian
+from .filter import dilation_filter
+from .filter import erosion_filter
+
+from .projection import maximum_projection
+from .projection import mean_projection
+from .projection import median_projection
+from .projection import focus_projection
+from .projection import focus_projection_fast
+from .projection import focus_measurement
+from .projection import in_focus_selection
+from .projection import get_in_focus_indices
+
+from .illumination import compute_illumination_surface
+from .illumination import correct_illumination_surface
+
+from .postprocess import remove_transcription_site
+from .postprocess import extract_spots_from_frame
+from .postprocess import extract_coordinates_image
+from .postprocess import center_mask_coord
+from .postprocess import from_boundaries_to_surface
+from .postprocess import from_surface_to_boundaries
+from .postprocess import from_binary_to_coord
+from .postprocess import complete_coord_boundaries
+from .postprocess import from_coord_to_frame
+from .postprocess import from_coord_to_surface
+
 from .augmentation import augment_2d
 
 
-_utils = ["check_array", "check_df", "check_recipe", "check_datamap",
-          "check_parameter", "check_range_value",
-          "get_margin_value", "get_eps_float32"]
+_utils = [
+    "check_array",
+    "check_df",
+    "check_recipe",
+    "check_datamap",
+    "check_parameter",
+    "check_range_value",
+    "get_margin_value",
+    "get_eps_float32"]
 
-_io = ["read_image", "read_dv", "read_array", "save_image", "save_array"]
+_io = [
+    "read_image",
+    "read_dv",
+    "read_array",
+    "save_image",
+    "save_array"]
 
-_preprocess = ["build_stacks", "build_stack",
-               "build_stack_no_recipe", "rescale",
-               "cast_img_uint8", "cast_img_uint16", "cast_img_float32",
-               "cast_img_float64"]
+_preprocess = [
+    "build_stacks",
+    "build_stack",
+    "build_stack_no_recipe",
+    "rescale",
+    "cast_img_uint8",
+    "cast_img_uint16",
+    "cast_img_float32",
+    "cast_img_float64"]
 
-_filter = ["log_filter", "mean_filter", "median_filter", "maximum_filter",
-           "minimum_filter", "gaussian_filter", "remove_background_mean",
-           "remove_background_gaussian", "dilation_filter", "erosion_filter"]
+_filter = [
+    "log_filter",
+    "mean_filter",
+    "median_filter",
+    "maximum_filter",
+    "minimum_filter",
+    "gaussian_filter",
+    "remove_background_mean",
+    "remove_background_gaussian",
+    "dilation_filter",
+    "erosion_filter"]
 
-_projection = ["maximum_projection", "mean_projection", "median_projection",
-               "in_focus_selection", "focus_measurement",
-               "get_in_focus_indices", "focus_projection",
-               "focus_projection_fast"]
+_projection = [
+    "maximum_projection",
+    "mean_projection",
+    "median_projection",
+    "in_focus_selection",
+    "focus_measurement",
+    "get_in_focus_indices",
+    "focus_projection",
+    "focus_projection_fast"]
 
-_illumination = ["compute_illumination_surface",
-                 "correct_illumination_surface"]
+_illumination = [
+    "compute_illumination_surface",
+    "correct_illumination_surface"]
 
-_postprocess = ["remove_transcription_site",
-                "extract_spots_from_frame", "extract_coordinates_image",
-                "center_mask_coord", "from_boundaries_to_surface",
-                "from_surface_to_boundaries", "from_binary_to_coord",
-                "complete_coord_boundaries", "from_coord_to_frame",
-                "from_coord_to_surface"]
+_postprocess = [
+    "remove_transcription_site",
+    "extract_spots_from_frame",
+    "extract_coordinates_image",
+    "center_mask_coord",
+    "from_boundaries_to_surface",
+    "from_surface_to_boundaries",
+    "from_binary_to_coord",
+    "complete_coord_boundaries",
+    "from_coord_to_frame",
+    "from_coord_to_surface"]
 
-_augmentation = ["augment_2d"]
+_augmentation = [
+    "augment_2d"]
 
-_preparation = ["split_from_background", "build_image", "get_coordinates",
-                "get_distance_layers", "get_surface_layers", "build_batch",
-                "get_label", "Generator", "encode_labels", "get_map_label",
-                "format_experimental_data", "get_label_encoder",
-                "remove_transcription_site_bis", "filter_data", "balance_data",
-                "get_gene_encoder"]
 
-__all__ = (_utils + _io + _preprocess + _postprocess +
-           _filter + _projection + _illumination +
-           _augmentation + _preparation)
+__all__ = (_utils + _io + _preprocess + _postprocess + _filter + _projection +
+           _illumination + _augmentation)

bigfish/stack/augmentation.py

@@ -5,7 +5,8 @@
 """
 
 import numpy as np
-from .preprocess import check_parameter, check_array
+from .preprocess import check_parameter
+from .preprocess import check_array
 
 
 def augment_2d(image):

bigfish/stack/io.py

@@ -13,7 +13,8 @@
 import numpy as np
 
 from skimage import io
-from .utils import check_array, check_parameter
+from .utils import check_array
+from .utils import check_parameter
 
 
 # ### Read ###

bigfish/stack/preprocess.py

@@ -11,12 +11,20 @@
 import numpy as np
 
 from .io import read_image
-from .utils import (check_array, check_parameter, check_recipe, check_datamap,
-                    check_range_value, fit_recipe,
-                    get_path_from_recipe, get_nb_element_per_dimension,
-                    count_nb_fov)
-
-from skimage import img_as_ubyte, img_as_float32, img_as_float64, img_as_uint
+from .utils import check_array
+from .utils import check_parameter
+from .utils import check_recipe
+from .utils import check_datamap
+from .utils import check_range_value
+from .utils import fit_recipe
+from .utils import get_path_from_recipe
+from .utils import get_nb_element_per_dimension
+from .utils import count_nb_fov
+
+from skimage import img_as_ubyte
+from skimage import img_as_float32
+from skimage import img_as_float64
+from skimage import img_as_uint
 from skimage.exposure import rescale_intensity
 
 

bigfish/stack/tests/test_augmentation.py

@@ -11,9 +11,14 @@
 import numpy as np
 import bigfish.stack as stack
 
-from bigfish.stack.augmentation import (
-    _identity, _flip_h, _flip_v, _transpose, _transpose_inverse, _rotation_90,
-    _rotation_180, _rotation_270)
+from bigfish.stack.augmentation import _identity
+from bigfish.stack.augmentation import _flip_h
+from bigfish.stack.augmentation import _flip_v
+from bigfish.stack.augmentation import _transpose
+from bigfish.stack.augmentation import _transpose_inverse
+from bigfish.stack.augmentation import _rotation_90
+from bigfish.stack.augmentation import _rotation_180
+from bigfish.stack.augmentation import _rotation_270
 
 from numpy.testing import assert_array_equal
 

bigfish/stack/tests/test_utils.py

@@ -11,12 +11,15 @@
 import tempfile
 
 import bigfish.stack as stack
-from bigfish.stack.utils import (fit_recipe, get_path_from_recipe,
-                                 get_nb_element_per_dimension, count_nb_fov)
 
 import numpy as np
 import pandas as pd
 
+from bigfish.stack.utils import fit_recipe
+from bigfish.stack.utils import get_path_from_recipe
+from bigfish.stack.utils import get_nb_element_per_dimension
+from bigfish.stack.utils import count_nb_fov
+
 
 # ### Test sanity check functions ###
 

pytest.ini

@@ -2,3 +2,4 @@
 filterwarnings =
     ignore::DeprecationWarning
     ignore::UserWarning
+norecursedirs = plot