Merge pull request #336 from clEsperanto/reduce-bia-bob-suggestions

Reduce bia bob suggestions

pyclesperanto_prototype/__init__.py

@@ -10,5 +10,5 @@
 from ._tier10 import *
 from ._tier11 import *
 
-__version__ = "0.24.2"
+__version__ = "0.24.3"
 __common_alias__ = "cle"

pyclesperanto_prototype/_tier1/_absolute.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'in assistant'])
 def absolute(source : Image, destination : Image = None) -> Image:
  """Computes the absolute value of every individual pixel x in a given image.
  

pyclesperanto_prototype/_tier1/_binary_and.py

@@ -3,7 +3,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing', 'bia-bob-suggestion'], priority=1, output_creator=create_binary_like)
+@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing'], priority=1, output_creator=create_binary_like)
 def binary_and(operand1 : Image, operand2 : Image, destination : Image = None) -> Image:
  """Computes a binary image (containing pixel values 0 and 1) from two 
  images X and Y by connecting pairs of

pyclesperanto_prototype/_tier1/_binary_or.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing', 'bia-bob-suggestion'], output_creator=create_binary_like)
+@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing'], output_creator=create_binary_like)
 def binary_or(operand1 : Image, operand2 : Image, destination : Image = None) -> Image:
  """Computes a binary image (containing pixel values 0 and 1) from two 
  images X and Y by connecting pairs of

pyclesperanto_prototype/_tier1/_binary_subtract.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing', 'bia-bob-suggestion'], output_creator=create_binary_like)
+@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing'], output_creator=create_binary_like)
 def binary_subtract(minuend : Image, subtrahend : Image, destination : Image = None) -> Image:
  """Subtracts one binary image from another.
  

pyclesperanto_prototype/_tier1/_binary_xor.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing', 'bia-bob-suggestion'], output_creator=create_binary_like)
+@plugin_function(categories=['combine', 'binary processing', 'in assistant', 'combine labels', 'label processing'], output_creator=create_binary_like)
 def binary_xor(operand1 : Image, operand2 : Image, destination : Image = None) -> Image:
  """Computes a binary image (containing pixel values 0 and 1) from two 
  images X and Y by connecting pairs of

pyclesperanto_prototype/_tier1/_count_touching_neighbors.py

@@ -3,7 +3,7 @@
 from .._tier0 import Image
 from .._tier0 import create_vector_from_square_matrix
 
-@plugin_function(output_creator=create_vector_from_square_matrix, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_vector_from_square_matrix, categories=[])
 def count_touching_neighbors(touch_matrix: Image, touching_neighbors_count_destination: Image = None, ignore_background:bool = True) -> Image:
  """Takes a touch matrix as input and delivers a vector with number of 
  touching neighbors per label as a vector.

pyclesperanto_prototype/_tier1/_dilate_sphere.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['binary processing', 'bia-bob-suggestion'], output_creator=create_binary_like)
+@plugin_function(categories=['binary processing'], output_creator=create_binary_like)
 def dilate_sphere(source : Image, destination : Image = None) -> Image:
  """Computes a binary image with pixel values 0 and 1 containing the binary 
  dilation of a given input image.

pyclesperanto_prototype/_tier1/_draw_box.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['bia-bob-suggestion'])
+@plugin_function(categories=[])
 def draw_box(destination: Image, x: int = 0, y: int = 0, z: int = 0, width: int = 1, height: int = 1, depth: int = 1, value : float = 1) -> Image:
  """Draws a box at a given start point with given size. 
  All pixels other than in the box are untouched. Consider using `set(buffer, 

pyclesperanto_prototype/_tier1/_draw_line.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['bia-bob-suggestion'])
+@plugin_function(categories=[])
 def draw_line(destination : Image, x1 : float = 0, y1 : float = 0, z1 : float = 0, x2 : float = 1, y2 : float = 1, z2 : float = 1, thickness : float = 1, value : float = 1) -> Image:
  """Draws a line between two points with a given thickness. 
  

pyclesperanto_prototype/_tier1/_draw_sphere.py

@@ -4,7 +4,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['bia-bob-suggestion'])
+@plugin_function(categories=[])
 def draw_sphere(destination : Image, x : float = 0, y : float = 0, z : float = 0, radius_x : float = 1, radius_y : float = 1, radius_z : float = 1, value : float = 1) -> Image:
  """Draws a sphere around a given point with given radii in x, y and z (if 
  3D). 

pyclesperanto_prototype/_tier1/_erode_sphere.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['binary processing', 'bia-bob-suggestion'], output_creator=create_binary_like)
+@plugin_function(categories=['binary processing'], output_creator=create_binary_like)
 def erode_sphere(source : Image, destination : Image = None) -> Image:
  """Computes a binary image with pixel values 0 and 1 containing the binary 
  erosion of a given input image. 

pyclesperanto_prototype/_tier1/_generate_distance_matrix.py

@@ -3,7 +3,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(output_creator=create_matrix_from_pointlists, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_matrix_from_pointlists, categories=[])
 def generate_distance_matrix(coordinate_list1 :Image, coordinate_list2 :Image, distance_matrix_destination :Image = None) -> Image:
  """Computes the distance between all point coordinates given in two point lists.
  

pyclesperanto_prototype/_tier1/_generate_touch_matrix.py

@@ -3,7 +3,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(output_creator=create_square_matrix_from_labelmap, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_square_matrix_from_labelmap, categories=[])
 def generate_touch_matrix(label_map :Image, touch_matrix_destination :Image = None) -> Image:
  """Takes a labelmap with n labels and generates a (n+1)*(n+1) matrix where 
  all pixels are set to 0 exept those where labels are touching. 

pyclesperanto_prototype/_tier1/_laplace_box.py

@@ -3,7 +3,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'edge detection', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'edge detection', 'in assistant'])
 def laplace_box(source : Image, destination : Image = None) -> Image:
  """Applies the Laplace operator (Box neighborhood) to an image. 
  

pyclesperanto_prototype/_tier1/_laplace_diamond.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'edge detection', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'edge detection'])
 def laplace_diamond(source : Image, destination : Image = None) -> Image:
  """Applies the Laplace operator (Diamond neighborhood) to an image. 
  

pyclesperanto_prototype/_tier1/_mask.py

@@ -2,7 +2,7 @@
 from .._tier0 import Image
 from .._tier0 import plugin_function
 
-@plugin_function(categories=['bia-bob-suggestion'])
+@plugin_function(categories=[])
 def mask(source : Image, mask : Image, destination : Image = None) -> Image:
  """Computes a masked image by applying a binary mask to an image. 
  

pyclesperanto_prototype/_tier1/_mask_label.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['bia-bob-suggestion'])
+@plugin_function(categories=[])
 def mask_label(source : Image, label_map : Image, destination : Image = None, label_index : int = 1) -> Image:
  """Computes a masked image by applying a label mask to an image. 
  

pyclesperanto_prototype/_tier1/_maximum_image_and_scalar.py

@@ -3,7 +3,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'in assistant'])
 def maximum_image_and_scalar(source : Image, destination : Image = None, scalar : float = 0) -> Image:
  """Computes the maximum of a constant scalar s and each pixel value x in a 
  given image X. 

pyclesperanto_prototype/_tier1/_maximum_images.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['combine', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['combine', 'in assistant'])
 def maximum_images(source1 : Image, source2 : Image, destination : Image = None) -> Image:
  """Computes the maximum of a pair of pixel values x, y from two given 
  images X and Y. 

pyclesperanto_prototype/_tier1/_modulo_images.py

@@ -3,7 +3,7 @@
 from .._tier0 import Image
 from .._tier0 import plugin_function
 
-@plugin_function(categories=['combine', 'bia-bob-suggestion'])
+@plugin_function(categories=['combine'])
 def modulo_images(image1 : Image, image2 : Image, destination : Image = None) -> Image:
  """Computes the remainder of a division of pairwise pixel values in two images
 

pyclesperanto_prototype/_tier1/_read_intensities_from_positions.py

@@ -3,7 +3,7 @@
 from pyclesperanto_prototype._tier0 import create_none
 from .._tier0 import plugin_function
 
-@plugin_function(output_creator=create_none, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=[])
 def read_intensities_from_positions(pointlist : Image, intensity_image : Image, values_destination : Image = None) -> Image:
  """Go to positions in a given image specified by a pointlist and read intensities of those pixels. The intensities
  are stored in a new vector.

pyclesperanto_prototype/_tier1/_standard_deviation_z_projection.py

@@ -3,7 +3,7 @@
 from .._tier0 import Image
 from .._tier0 import create_2d_yx
 
-@plugin_function(output_creator=create_2d_yx, categories=['projection', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_2d_yx, categories=['projection', 'in assistant'])
 def standard_deviation_z_projection(source : Image, destination : Image = None) -> Image:
  """Determines the standard deviation intensity projection of an image 
  stack along Z. 

pyclesperanto_prototype/_tier1/_variance_sphere.py

@@ -4,7 +4,7 @@
 from pyclesperanto_prototype._tier0 import radius_to_kernel_size
 
 
-@plugin_function(categories=['filter', 'edge detection', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'edge detection', 'in assistant'])
 def variance_sphere(source: Image, destination: Image = None, radius_x : int = 1, radius_y : int = 1, radius_z : int = 1) -> Image:
  """Computes the local variance of a pixels sphere neighborhood. The sphere size is specified by
  its half-width, half-height and half-depth (radius). If 2D images are given, radius_z will be ignored.

pyclesperanto_prototype/_tier2/_bottom_hat_sphere.py

@@ -5,7 +5,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'background removal', 'in assistant', 'bia-bob-suggestion'], priority=-1)
+@plugin_function(categories=['filter', 'background removal', 'in assistant'], priority=-1)
 def bottom_hat_sphere(source : Image, destination : Image = None, radius_x : float = 1, radius_y : float = 1, radius_z : float = 1) -> Image:
  """Applies a bottom-hat filter for background subtraction to the input image.
  

pyclesperanto_prototype/_tier2/_combine_horizontally.py

@@ -4,7 +4,7 @@
 from .._tier0 import Image
 from .._tier1 import paste
 
-@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant'])
 def combine_horizontally(stack1 : Image, stack2 : Image, destination : Image = None) -> Image:
  """Combines two images or stacks in X. 
  

pyclesperanto_prototype/_tier2/_combine_vertically.py

@@ -4,7 +4,7 @@
 from .._tier0 import Image
 from .._tier1 import paste
 
-@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant'])
 def combine_vertically(stack1 : Image, stack2 : Image, destination : Image = None) -> Image:
  """Combines two images or stacks in Y. 
  

pyclesperanto_prototype/_tier2/_concatenate_stacks.py

@@ -4,7 +4,7 @@
 from .._tier0 import Image
 from .._tier1 import paste
 
-@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant'])
 def concatenate_stacks(stack1 : Image, stack2 : Image, destination : Image = None) -> Image:
  """Concatenates two stacks in Z. 
  

pyclesperanto_prototype/_tier2/_label_spots.py

@@ -6,7 +6,7 @@
 from .._tier1 import sum_x_projection
 from .._tier1 import sum_y_projection
 
-@plugin_function(categories=['label', 'in assistant', 'bia-bob-suggestion'], output_creator=create_labels_like)
+@plugin_function(categories=['label', 'in assistant'], output_creator=create_labels_like)
 def label_spots(input_spots : Image, labelled_spots_destination : Image = None) -> Image:
  """Transforms a binary image with single pixles set to 1 to a labelled 
  spots image. 

pyclesperanto_prototype/_tier2/_opening_sphere.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(categories=['filter', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'in assistant'])
 def opening_sphere(input_image: Image, destination: Image = None, radius_x: int = 1, radius_y: int = 1, radius_z: int = 0) -> Image:
  """Opening operator, sphere-shaped
 

pyclesperanto_prototype/_tier2/_pointlist_to_labelled_spots.py

@@ -8,7 +8,7 @@
 from .._tier1 import set_ramp_x
 from .._tier1 import add_image_and_scalar
 
-@plugin_function(output_creator=create_from_pointlist, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_from_pointlist, categories=[])
 def pointlist_to_labelled_spots(pointlist : Image, spots_destination : Image = None) -> Image:
  """Takes a pointlist with dimensions n times d with n point coordinates in 
  d dimensions and labels corresponding pixels. 

pyclesperanto_prototype/_tier2/_reduce_stack.py

@@ -6,7 +6,7 @@
 from .._tier0 import create
 from .._tier1 import copy_slice
 
-@plugin_function(output_creator=create_none, categories=['transform', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['transform', 'in assistant'])
 def reduce_stack(source : Image, destination : Image = None, reduction_factor : int = 2, offset : int = 0) -> Image:
  """Reduces the number of slices in a stack by a given factor.
  With the offset you have control which slices stay: 

pyclesperanto_prototype/_tier2/_standard_deviation_sphere.py

@@ -1,7 +1,7 @@
 from pyclesperanto_prototype._tier0 import plugin_function
 from pyclesperanto_prototype._tier0 import Image
 
-@plugin_function(categories=['filter', 'edge detection', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'edge detection', 'in assistant'])
 def standard_deviation_sphere(source: Image, destination: Image = None, radius_x : int = 1, radius_y : int = 1, radius_z : int = 1) -> Image:
  """Computes the local standard deviation of a pixels sphere neighborhood. The box size is specified by
  its half-width, half-height and half-depth (radius). If 2D images are given, radius_z will be ignored.

pyclesperanto_prototype/_tier2/_sub_stack.py

@@ -6,7 +6,7 @@
 from .._tier0 import create
 from .._tier1 import copy_slice
 
-@plugin_function(output_creator=create_none, categories=['transform', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['transform', 'in assistant'])
 def sub_stack(source : Image, destination : Image = None, start_z : int = 0, end_z : int = 0) -> Image:
  """Crops multiple Z-slices of a 3D stack into a new 3D stack.
  

pyclesperanto_prototype/_tier3/_absolute_difference.py

@@ -4,7 +4,7 @@
 from pyclesperanto_prototype._tier2 import subtract_images
 from pyclesperanto_prototype._tier1 import absolute
 
-@plugin_function(categories=['combine', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['combine', 'in assistant'])
 def absolute_difference(source1 : Image, source2 : Image, destination : Image = None) -> Image:
  """Determines the absolute difference pixel by pixel between two images.
  

pyclesperanto_prototype/_tier3/_divide_by_gaussian_background.py

@@ -4,7 +4,7 @@
 from pyclesperanto_prototype._tier0 import plugin_function
 from pyclesperanto_prototype._tier1 import divide_images
 
-@plugin_function(categories=['filter', 'background removal', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['filter', 'background removal', 'in assistant'])
 def divide_by_gaussian_background(source : Image, destination : Image = None, sigma_x : float = 2, sigma_y : float = 2, sigma_z : float = 2) -> Image:
  """Applies Gaussian blur to the input image and divides the original by 
  the result. 

pyclesperanto_prototype/_tier3/_exclude_labels_outside_size_range.py

@@ -4,7 +4,7 @@
 from .._tier0 import create_none
 from .._tier0 import create_like
 
-@plugin_function(output_creator=create_none, categories=['label processing', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['label processing', 'in assistant'])
 def exclude_labels_outside_size_range(source : Image, destination : Image = None, minimum_size : float = 0, maximum_size : float = 100) -> Image:
  """Removes labels from a label map which are not within a certain size range.
  

pyclesperanto_prototype/_tier3/_exclude_labels_with_values_out_of_range.py

@@ -4,7 +4,7 @@
 from .._tier0 import create_none
 from .._tier0 import create_like
 
-@plugin_function(output_creator=create_none, categories=['label processing', 'combine', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['label processing', 'combine'])
 def exclude_labels_with_values_out_of_range(values_vector : Image, label_map_input : Image, label_map_destination : Image = None, minimum_value_range : float = 0, maximum_value_range : float = 100) -> Image:
  """This operation removes labels from a labelmap and renumbers the 
  remaining labels. 

pyclesperanto_prototype/_tier3/_exclude_labels_with_values_within_range.py

@@ -4,7 +4,7 @@
 from .._tier0 import create_none
 from .._tier0 import create_like
 
-@plugin_function(output_creator=create_none, categories=['label processing', 'combine', 'bia-bob-suggestion'])
+@plugin_function(output_creator=create_none, categories=['label processing', 'combine'])
 def exclude_labels_with_values_within_range(values_vector : Image, label_map_input : Image, label_map_destination : Image = None, minimum_value_range : float = 0, maximum_value_range : float = 100) -> Image:
  """This operation removes labels from a labelmap and renumbers the 
  remaining labels. 

pyclesperanto_prototype/_tier3/_labelled_spots_to_pointlist.py

@@ -4,7 +4,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(output_creator=create_pointlist_from_labelmap, categories=['bia-bob-suggestion'])
+@plugin_function(output_creator=create_pointlist_from_labelmap, categories=[])
 def labelled_spots_to_pointlist(input_labelled_spots:Image, destination_pointlist :Image = None) -> Image:
  """Generates a coordinate list of points in a labelled spot image. 
  

pyclesperanto_prototype/_tier3/_squared_difference.py

@@ -4,7 +4,7 @@
 from pyclesperanto_prototype._tier2 import subtract_images
 from pyclesperanto_prototype._tier1 import power
 
-@plugin_function(categories=['combine', 'in assistant', 'bia-bob-suggestion'])
+@plugin_function(categories=['combine', 'in assistant'])
 def squared_difference(source1 : Image, source2 : Image, destination : Image = None) -> Image:
  """Determines the squared difference pixel by pixel between two images. 
  

pyclesperanto_prototype/_tier4/_erode_connected_labels.py

@@ -2,7 +2,7 @@
 from .._tier0 import plugin_function
 from .._tier0 import create_labels_like
 
-@plugin_function(categories=['label processing', 'in assistant', 'bia-bob-suggestion'], output_creator=create_labels_like)
+@plugin_function(categories=['label processing', 'in assistant'], output_creator=create_labels_like)
 def erode_connected_labels(labels_input : Image, labels_destination : Image = None, radius: int = 1) -> Image:
  """Erodes labels to a smaller size. Note: Depending on the label image and the radius,
  labels may disappear and labels may split into multiple islands. Thus, overlapping labels of input and output may