import json
import os
import numpy as np
from networkx import node_link_graph, node_link_data
[docs]def parse_file_path(file_path, key=None):
"""Parse input path in order to extract all files
Parameters
----------
file_path: str
Path to either a file or directory
key: str, optional
Section of file name to filter
Returns
-------
input_files: list of str
Parsed file names
"""
input_files = []
if os.path.isfile(file_path):
input_files.append(file_path)
elif os.path.isdir(file_path):
for file_name in os.listdir(file_path):
input_files.append(
os.path.join(file_path, file_name))
if key is not None:
input_files = [
input_file for input_file in input_files
if key in input_file
]
return input_files
[docs]def remove_under(dictionary):
"""Remove any keys from dictionary beginning
with an underscore"""
keys = [key for key in dictionary.keys()]
for key in keys:
if key.startswith('_'):
dictionary.pop(key)
[docs]def remove_dunder(dictionary):
"""Remove any keys from dictionary beginning
with an double underscore"""
keys = [key for key in dictionary.keys()]
for key in keys:
if key.startswith('__') and key.endswith('__'):
dictionary.pop(key)
[docs]def remove_contraction(dictionary):
"""Remove any keys from nested dictionary beginning
with the word `contraction`"""
keys = [key for key in dictionary.keys()]
for key in keys:
if isinstance(key, str) and key.startswith('contraction'):
dictionary.pop(key)
[docs]def pop_recursive(dictionary, pop_func):
"""Recursively remove a named key from dictionary
and any contained dictionaries."""
pop_func(dictionary)
for key, value in dictionary.items():
# If remove_key is in the dict, remove it
if isinstance(value, dict):
pop_recursive(value, pop_func)
# If we have a non-dict iterable which contains a dict,
# call pop.(remove_key) from that as well
elif isinstance(value, (tuple, list)):
for element in value:
if isinstance(element, dict):
pop_recursive(element, pop_func)
return dictionary
[docs]def pop_under_recursive(dictionary):
"""Recursively removes all under keys from a nested dictionary. """
pop_recursive(dictionary, remove_under)
return dictionary
[docs]def pop_dunder_recursive(dictionary):
""" Recursively removes all dunder keys from a nested dictionary. """
pop_recursive(dictionary, remove_dunder)
return dictionary
[docs]def deserialize_networkx_graph(data):
"""Transform JSON serialised data into a
networkx Graph object"""
data = python_to_numpy_recursive(data)
graph = node_link_graph(data)
return graph
[docs]def serialize_networkx_graph(graph):
"""Transform a networkx Graph object into
a JSON serialised dictionary"""
data = node_link_data(graph)
data = numpy_to_python_recursive(data)
return data
[docs]def numpy_to_python_recursive(dictionary):
"""Convert all numpy values in nested dictionary
to pure python values"""
for key, value in dictionary.items():
if isinstance(value, dict):
numpy_to_python_recursive(value)
elif isinstance(value, np.ndarray):
dictionary[key] = value.tolist()
elif isinstance(value, np.int64):
dictionary[key] = int(value)
elif isinstance(value, np.float):
dictionary[key] = float(value)
elif isinstance(value, (list, tuple)):
for element in value:
if isinstance(element, dict):
numpy_to_python_recursive(element)
return dictionary
[docs]def python_to_numpy_recursive(dictionary):
"""Convert all numpy values in nested dictionary
to pure python values"""
for key, value in dictionary.items():
if isinstance(value, dict):
python_to_numpy_recursive(value)
elif isinstance(value, list):
if key in ['xy', 'direction']:
dictionary[key] = np.array(value)
else:
for element in value:
if isinstance(element, dict):
python_to_numpy_recursive(element)
return dictionary
[docs]def check_string(string, pos, sep, word):
"""Checks index 'pos' of 'string' seperated by 'sep' for substring 'word'
If present, removes 'word' and returns amended string
"""
if sep in string:
temp_string = string.split(sep)
if temp_string[pos] == word:
temp_string.pop(pos)
string = sep.join(temp_string)
return string
[docs]def check_file_name(file_name, file_type="", extension=""):
"""
check_file_name(file_name, file_type="", extension="")
Checks file_name for file_type or extension. If present, returns
amended file_name without extension or file_type
"""
file_name = check_string(file_name, -1, '.', extension)
file_name = check_string(file_name, -1, '_', file_type)
return file_name
[docs]def replace_ext(file_name, extension):
"""If an extension exists on file_name,
replace it with new extension. Otherwise
add new extension"""
path, ext = os.path.splitext(file_name)
if ext != f'.{extension}':
file_name = path + f'.{extension}'
return file_name
[docs]def get_file_names(prefix):
"""Return set of paths determined from file prefix"""
image_name = os.path.basename(prefix)
working_dir = os.path.dirname(prefix)
return image_name, working_dir
[docs]def save_json(data, file_name):
"""Saves data as JSON file"""
file_name = replace_ext(file_name, 'json')
try:
with open(f"{file_name}", 'w') as outfile:
json.dump(data, outfile, indent=4)
except IOError as e:
raise IOError(
f"Cannot save to file {file_name}"
) from e
[docs]def load_json(file_name):
"""Loads JSON file as data"""
file_name = replace_ext(file_name, 'json')
try:
with open(file_name, 'r') as infile:
data = json.load(infile)
except IOError as e:
raise IOError(
f"Cannot read file {file_name}"
) from e
return data
[docs]def save_numpy(file_name, array):
"""Saves array as numpy binary"""
file_name = replace_ext(file_name, 'npy')
try:
np.save(file_name, array)
except IOError as e:
raise IOError(
f"Cannot save to file {file_name}"
) from e
[docs]def load_numpy(file_name):
"""Loads numpy binary file as array"""
file_name = replace_ext(file_name, 'npy')
try:
array = np.load(file_name)
except IOError as e:
raise IOError(
f"Cannot read file {file_name}"
) from e
return array