metadata#

exception MetadataError[source]#: Bases: Exception

exception NotAnOmeFile[source]#: Bases: Exception

class Pattern(pattern_str)[source]#

Bases: object

get_chars_after_cluster_idx(cluster_idx)[source]#

get_chars_before_cluster_idx(cluster_idx)[source]#

get_formatted_pattern()[source]#

highlight_digits(cluster_idx)[source]#

hightlighted_q_marks(n)[source]#

parse_pattern(pattern_str)[source]#

property c_order#

property c_rng#

property clearmap_pattern#

property x_order#

property x_rng#

property y_order#

property y_rng#

property z_order#

property z_rng#

class PatternFinder(folder, tiff_list=None, df=None, axes_order=None)[source]#

Bases: object

classmethod from_mixed_tiff_lists(folder, tiff_list, axes_order=None)[source]#

static get_df_from_file_list(file_names)[source]#

get_sub_tiff_list(x=None, y=None, z=None, c=None)[source]#

get_sub_tiff_paths(x=None, y=None, z=None, c=None)[source]#

classmethod get_tiff_list(df)[source]#

static pattern_from_df(df)[source]#

classmethod split_axis(folder, df, pattern, axis_letter, axes_order=None)[source]#

classmethod split_channel(folder, df, pattern, axes_order=None)[source]#

sub_pattern_str(x=None, y=None, z=None, c=None)[source]#

property c_values#

property tiff_list#

property tiff_paths#

property x_values#

property y_values#

property z_values#

define_auto_resolution(img_path, cfg_res)[source]#

define_auto_stitching_params(img_path, stitching_cfg)[source]#

get_base_dir(cfg)[source]#

get_file_path(cfg, path_name)[source]#

get_ome_dict(img_path)[source]#

get_tiles_by_ext(folder, extension='.ome.tif')[source]#

get_tiles_list_from_sample_folder(src_dir, min_file_number=10, tile_extension='.ome.tif')[source]#

parse_img_res(img_path)[source]#

parse_img_shape(img_path)[source]#

parse_overlaps(img_path)[source]#

pattern_finders_from_base_dir(src_dir, axes_order=None, min_file_number=10, tile_extension='.ome.tif')[source]#

stack_tiles_to_columns(sample_folder, axes_order, remove_tiles=False)[source]#

Parameters:

str (sample_folder) – The folder where the data is located
dict (axes_order) – A dictionary of the type {‘x’: 1, ‘y’: 0, ‘z’: 3, ‘c’: 2} indicating the order of each axis
bool (remove_tiles) – Whether to remove the individual tiles at the end

Returns