Added utils draft, added tests

.gitignore

 **/__pycache__
+*.egg
+*.egg-info*
 .vscode
 .venv

setup.py

@@ -2,12 +2,18 @@
 
 from setuptools import setup, find_packages
 
+entry_points = {
+    "console_scripts": [
+        "robofish-io-validate=robofish.io.app:validate",
+    ]
+}
+
 setup(
     name="robofish-io",
     version="0.1",
     author="",
     author_email="",
-    install_requires=[],
+    install_requires=['h5py'],
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
@@ -21,4 +27,5 @@ setup(
     packages=find_packages("src"),
     package_dir={"": "src"},
     zip_safe=True,
+    entry_points=entry_points,
 )

src/robofish/io/app.py

+# -*- coding: utf-8 -*-
+
+import argparse
+import robofish.io.util as util
+
+def validate():
+    parser = argparse.ArgumentParser(description='TODO')
+    parser.add_argument('path', type=str, nargs='+',
+                        help='TODO')
+    args = parser.parse_args()
+
+    hdf5_dict = util.load_hdf5(args.path)
+    util.validate_dict(hdf5_dict)

src/robofish/io/util.py

+# -*- coding: utf-8 -*-
+
+import os
+import h5py
+import traceback
+
+
+def load_hdf5(paths):
+    """ Load hdf5 files from a given path.
+
+    The function can be given the path to a single single hdf5 file, to a folder, containing hdf5 files, or an array of multiple files or folders.
+
+    Args:
+        path (str): The path to a hdf5 file or folder.
+    Returns:
+        dict: A dictionary where the keys are filenames and the values are the content of the hdf5 files
+    """
+    if not type(paths) is list:
+        paths = [paths]
+
+    hdf5_dict = {}
+
+    for path in paths:
+        if os.path.isdir(path):
+            # Find all hdf5 files in folder
+            files = [path + '/' + file for file in os.listdir(
+                path) if not os.path.isdir(file) and file.endswith('.hdf5')]
+        else:
+            files = [path]
+
+        hdf5_dict.update({os.path.basename(file): h5py.File(file, 'r')
+                          for file in files})
+    return hdf5_dict
+
+def create_from_dict(path, dict):
+    """ Todo """
+
+    f = h5py.File(path, 'w')
+    return f
+
+def validate_dict(hdf5_dict):
+    """ Todo """
+    for path, file in hdf5_dict.items():
+        print(validate(file))
+
+def validate(file):
+    """ Todo """
+
+    # print(list(file.keys()))
+    # print(dict(file['root']))
+
+    # Example dict
+    # {
+    #     'root': {
+    #         'version' : None,
+    #         'world_size': None,
+    #         'entities' : {
+    #             'entity':{
+    #                 'type': None,
+    #                 'poses': [],
+    #                 'outlines': [],
+    #                 'time': {
+    #                         'monotonic points': [],
+    #                         'calendar points': []
+    #                 }
+    #             }
+    # }
+
+    try:
+        version = file['version']
+        world = file['world size']
+        root = file['root']
+
+        entities = root['entities']
+        #for key, value in file.attrs.items():
+        #    print(key, value)
+        return (True, "Valid")
+    except Exception as e:
+        return (False, "Invalid: " + e.args[0])

tests/robofish/io/test_util.py

+import pytest
+import robofish.io
+import robofish.io.util as util
+import os
+import h5py
+
+
+def test_loadhdf5():
+    """ Test the robofish.io.util.load_hdf5 function """
+
+    files = ['../../resources/example1.hdf5', '../../resources/example2.hdf5',
+             '../../resources/', '../not_existent.hdf5']
+
+    files = [os.path.abspath(os.path.dirname(
+        __file__) + '/' + file) for file in files]
+
+    # One file test
+    tracksets = util.load_hdf5(files[0])
+    assert len(tracksets) == 1
+
+    # Two file test
+    tracksets = util.load_hdf5(files[:2])
+    assert len(tracksets) == 2
+
+    # Folder test
+    tracksets = util.load_hdf5(files[2])
+    assert len(tracksets) == 3
+
+    # Folder and file test
+    tracksets = util.load_hdf5(files[:3])
+    assert len(tracksets) == 3
+
+    # Broken file test
+    with pytest.raises(OSError):
+        tracksets = util.load_hdf5(files[3])
+
+
+def test_create_from_dict():
+    test_dict = {
+        'root': {
+            'version': None,
+            'world_size': None,
+            'entities': {
+                'entity': {
+                    'type': None,
+                    'poses': [],
+                    'outlines': [],
+                    'time': {
+                        'monotonic points': [],
+                        'calendar points': []
+                    }
+                }
+            }
+        }
+    }
+
+    testfile_path = os.path.abspath(os.path.dirname(
+        __file__) + '/../../resources/test_dataset.hdf5')
+    h5file = util.create_from_dict(testfile_path, test_dict)
+
+    assert type(h5file) == h5py._hl.files.File
+
+
+if __name__ == '__main__':
+    test_loadhdf5()
+    test_create_from_dict()