use natural sort for ordering input data (#115)

requirements.txt

@@ -7,3 +7,4 @@ wkw==0.0.6
 requests
 black
 cluster_tools==1.36
+natsort

setup.py

@@ -5,7 +5,7 @@
     packages=find_packages(exclude=("tests",)),
     use_scm_version=True,
     setup_requires=['setuptools_scm'],
-    install_requires=["scipy", "numpy", "pillow", "pyyaml", "wkw", "cluster_tools==1.36"],
+    install_requires=["scipy", "numpy", "pillow", "pyyaml", "wkw", "cluster_tools==1.36", "natsort"],
     description="A cubing tool for webKnossos",
     author="Norman Rzepka",
     author_email="norman.rzepka@scalableminds.com",

wkcuber/cubing.py

@@ -3,6 +3,7 @@
 import numpy as np
 from argparse import ArgumentParser
 from os import path
+from natsort import natsorted
 
 from .utils import (
     get_chunks,
@@ -74,8 +75,7 @@ def find_source_filenames(source_path):
         + str(image_reader.readers.keys())
         + "."
     )
-    source_files.sort()
-    return source_files
+    return natsorted(source_files)
 
 
 def read_image_file(file_name, dtype):

wkcuber/tile_cubing.py

@@ -6,6 +6,7 @@
 from argparse import ArgumentParser
 from os import path, listdir
 from PIL import Image
+from natsort import natsorted
 
 from .utils import (
     get_chunks,
@@ -31,8 +32,7 @@ def find_source_sections(source_path):
         f for f in listdir(source_path) if path.isdir(path.join(source_path, f))
     ]
     section_folders = [path.join(source_path, s) for s in section_folders]
-    section_folders.sort()
-    return section_folders
+    return natsorted(section_folders)
 
 
 def parse_tile_file_name(filename):
@@ -49,9 +49,7 @@ def find_source_files(source_section_path):
             path.join(source_section_path, "**", "*"), image_reader.readers.keys()
         )
     ]
-
-    all_source_files.sort()
-    return all_source_files
+    return natsorted(all_source_files)
 
 
 def tile_cubing_job(target_wkw_info, z_batches, source_path, batch_size, tile_size):