napari_cellseg3d.utils

Utilities functions, classes, and variables.

Functions

align_array_sizes(array_shape, target_shape)	Aligns the sizes of two arrays by adding zeros to the smaller one.
channels_fraction_above_threshold(volume[, ...])	Computes the fraction of pixels above a certain value in a 4D volume for each channel.
correct_rotation(image)	Rotates the axes 0 and 2 in [DHW] section of image array.
denormalize_y(image)	De-normalizes the values of an image array to be between [0;255] rather than [0;1].
dice_coeff(y_true, y_pred[, smooth])	Compute Dice-Sorensen coefficient between two numpy arrays.
fill_list_in_between(lst, n, fill_value)	Fills a list with n * elem between each member of list.
fraction_above_threshold(volume[, threshold])	Computes the fraction of pixels above a certain value in a volume.
get_all_matching_files(path[, pattern])	Returns a list of all files in a directory matching the pattern.
get_date_time()	Get date and time in the following format : year_month_day_hour_minute_second.
get_padding_dim(image_shape[, anisotropy_factor])	Finds the nearest and superior power of two for each image dimension to zero-pad it for CNN processing.
get_time()	Get time in the following format : hour:minute:second.
get_time_filepath()	Get time in the following format : hour_minute_second.
load_images(dir_or_path[, filetype, as_folder])	Loads the images in directory, with different behaviour depending on filetype and as_folder.
mkdir_from_str(path[, exist_ok, parents])	Creates a directory from a string path.
normalize_max(image)	Normalizes an image using the max and min value.
normalize_x(image)	Normalizes the values of an image array to be between [-1;1] rather than [0;255].
normalize_y(image)	Normalizes the values of an image array to be between [0;1] rather than [0;255].
parse_default_path(possible_paths[, ...])	Returns a default path based on a vector of paths, some of which might be empty.
quantile_normalization(image[, ...])	Normalizes an image using the quantiles.
remap_image(image[, new_max, new_min, ...])	Normalizes a numpy array or Tensor using the max and min value.
resize(image, zoom_factors)	Resizes an image using the zoom_factors.
save_folder(results_path, folder_name, ...)	Saves a list of images in a folder.
save_layer(results_path, image_name, image)	Saves an image layer at the specified path.
seek_best_dice_coeff_channel(y_pred, y_true)	Compute Dice-Sorensen coefficient between unsupervised model output and ground truth labels; returns the channel with the highest dice coefficient.
show_result(viewer, layer, image, name[, ...])	Adds layers to a viewer to show result to user.
sphericity_axis(semi_major, semi_minor)	Computes the sphericity from volume semi major (a) and semi minor (b) axes.
sphericity_volume_area(volume, surface_area)	Computes the sphericity from volume and area.
time_difference(time_start, time_finish[, ...])	Computes the time difference between two datetime objects.

Classes

Singleton

Singleton class that can only be instantiated once at a time, with said unique instance always being accessed on call.