Update for lint rule D413 (#1096)

DigitalSlideArchive · Jan 30, 2024 · 4842be8 · 4842be8
1 parent 1cfae70
commit 4842be8
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diff --git a/histomicstk/cli/NucleiClassification/NucleiClassification.py b/histomicstk/cli/NucleiClassification/NucleiClassification.py
@@ -38,6 +38,7 @@ def set_reference_values(args):
  Returns:
  -------
  dict: Updated configuration parameters with reference values set.
+
  """
  args.reference_mu_lab = [8.63234435, -0.11501964, 0.03868433]
  args.reference_std_lab = [0.57506023, 0.10403329, 0.01364062]
@@ -118,6 +119,7 @@ def process_feature_and_annotation(args):
  Returns:
  -------
  tuple: A tuple containing nuclei annotations (list) and feature data (Dask DataFrame).
+
  """
  print('>> Generating features and annotation')
 
@@ -197,6 +199,7 @@ def read_feature_file(args):
  Returns:
  -------
  dask.dataframe.DataFrame: A Dask DataFrame containing the nuclei feature data.
+
  """
  fname, feature_file_format = os.path.splitext(args.inputNucleiFeatureFile)
 

diff --git a/histomicstk/cli/utils.py b/histomicstk/cli/utils.py
@@ -285,6 +285,7 @@ def get_region_polygons(region):
  -------
  polygons: list
  A list of lists of x, y tuples.
+
  """
  if len(region) % 2 or len(region) < 4:
  msg = 'region must be 4, 6, or a list of 2n values.'
@@ -338,6 +339,7 @@ def polygons_to_binary_mask(polygons, x=0, y=0, width=None, height=None):
  mask: numpy.array
  A 1-bit numpy array where 1 is inside an odd number of polygons. This
  can return None if polygons was None.
+
  """
  import PIL.Image
  import PIL.ImageChops

diff --git a/histomicstk/segmentation/label/remove_overlap_nuclei.py b/histomicstk/segmentation/label/remove_overlap_nuclei.py
@@ -12,6 +12,7 @@ def create_polygon(coordinates):
  Returns:
  -------
  shapely.geometry.Polygon: The polygon created from the points.
+
  """
  return shapely.geometry.Polygon(coordinates).buffer(0)
 
@@ -28,6 +29,7 @@ def convert_polygons_tobbox(nuclei_list):
  -------
  list: The modified 'nuclei_list', where each nuclei object has been transformed
  to a bounding box representation.
+
  """
  for nuclei in nuclei_list:
  # Set 'type' property of the nuclei to 'rectangle'
@@ -68,6 +70,7 @@ def remove_overlap_nuclei(nuclei_list, nuclei_format, return_selected_nuclei=Fal
  -------
  output_list (list): New list with overlapping nuclei removed.
  selected_nuclei (list, optional): Indices of selected nuclei.
+
  """
  polygons = [create_polygon(nuclei['points']) for nuclei in nuclei_list]
 

diff --git a/histomicstk/segmentation/nuclear/detect_tile_nuclei.py b/histomicstk/segmentation/nuclear/detect_tile_nuclei.py
@@ -28,6 +28,7 @@ def detect_tile_nuclei(tile_info, args, src_mu_lab=None,
  -------
  nuclei_annot_list (list): List of nuclei annotations.
  fdata: Computed nuclei features.
+
  """
  # Flags
  single_channel = False