Module bvmpc.bv_utils
This holds utility functions.
Expand source code
"""This holds utility functions."""
from statistics import mean
import os
import re
import sys
import argparse
from datetime import timedelta
from collections.abc import Iterable
import shutil
import numpy as np
import logging
import configparser
from pprint import pprint
import seaborn as sns
import matplotlib.pyplot as plt
def check_fn(item):
if isinstance(item, list) or isinstance(item, np.ndarray):
if len(item) == 0:
return np.nan
return item
def boolean_indexing(v, fillval=np.nan):
"""Index a numpy array using a boolean mask."""
lens = np.array([len(item) for item in v])
mask = lens[:, None] > np.arange(lens.max())
out = np.full(mask.shape, fillval)
out[mask] = np.concatenate(v)
return out
def daterange(start_date, end_date):
"""Yield a generator of dates between start and end date."""
for n in range(int((end_date - start_date).days)):
yield start_date + timedelta(n)
def make_dir_if_not_exists(location):
"""Make directory structure for given location."""
os.makedirs(location, exist_ok=True)
def mycolors(subject, colors_dict=None):
"""Colour options for subject based on number."""
try:
i = int(subject)
if i > 10:
i = i % 4
mycolors = ['tab:red', 'tab:blue', 'tab:green', 'tab:orange',
'tab:brown', 'deeppink', 'tab:olive', 'tab:pink',
'steelblue', 'firebrick', 'mediumseagreen']
color = mycolors[i]
except ValueError:
if colors_dict == None:
print('Color input for required')
exit(-1)
color = colors_dict[subject]
return color
def split_list(list, chunk_limit):
"""Split a list into small chunks based on chunk_limit."""
new_list = [list[i:i + chunk_limit]
for i in range(0, len(list), chunk_limit)]
return new_list
def walk_dict(d, depth=0):
"""Walk a Dictionary."""
for k, v in sorted(d.items(), key=lambda x: x[0]):
spaces = (" ") * depth
if hasattr(v, "items"):
print(spaces + ("%s" % k))
walk_dict(v, depth + 1)
else:
print(spaces + "%s %s" % (k, v))
def get_attrs(d, depth=0):
"""Walk through attributes."""
for k, v in sorted(d.items(), key=lambda x: x[0]):
spaces = (" ") * depth
if len(v.attrs) != 0:
print("{}{} has attrs {}".format(
spaces, k, list(v.attrs.items())
))
if hasattr(v, "items"):
get_attrs(v, depth=depth + 1)
def print_h5(file_location):
"""Print a summary of a h5 file."""
import h5py
with h5py.File(file_location, 'r', libver='latest') as f:
for key, val in f.attrs.items():
print(key, val)
print()
walk_dict(f)
print()
def has_ext(filename, ext):
"""
Check if the filename ends in the extension.
Parameters
----------
filename : str
The name of the file
ext : str
The extension, may have leading dot (e.g txt == .txt)
Returns
-------
bool indicating if the filename has the extension
"""
if ext is None:
return True
if ext[0] != ".":
ext = "." + ext
return filename[-len(ext):].lower() == ext.lower()
def get_all_files_in_dir(
in_dir, ext=None, return_absolute=True,
recursive=False, verbose=False, re_filter=None):
"""
Get all files in the directory with the given extension.
Parameters
----------
in_dir : str
The absolute path to the directory
ext : str, optional. Defaults to None.
The extension of files to get.
return_absolute : bool, optional. Defaults to True.
Whether to return the absolute filename or not.
recursive: bool, optional. Defaults to False.
Whether to recurse through directories.
verbose: bool, optional. Defaults to False.
Whether to print the files found.
Returns
-------
List : A list of filenames
"""
if not os.path.isdir(in_dir):
print("Non existant directory " + str(in_dir))
return []
def match_filter(f):
if re_filter is None:
return True
if not isinstance(re_filter, list):
search_res = re.search(re_filter, f)
return search_res is not None
else:
for re_filt in re_filter:
search_res = re.search(re_filt, f)
if search_res is None:
return False
return True
def ok_file(root_dir, f):
return (
has_ext(f, ext) and match_filter(f) and
os.path.isfile(os.path.join(root_dir, f)))
def convert_to_path(root_dir, f):
return os.path.join(root_dir, f) if return_absolute else f
if verbose:
print("Adding following files from {}".format(in_dir))
if recursive:
onlyfiles = []
for root, _, filenames in os.walk(in_dir):
start_root = root[:len(in_dir)]
if len(root) == len(start_root):
end_root = ""
else:
end_root = root[len(in_dir + os.sep):]
for filename in filenames:
filename = os.path.join(end_root, filename)
if ok_file(start_root, filename):
to_add = convert_to_path(start_root, filename)
if verbose:
print(to_add)
onlyfiles.append(to_add)
else:
onlyfiles = [
convert_to_path(in_dir, f) for f in sorted(os.listdir(in_dir))
if ok_file(in_dir, f)
]
if verbose:
for f in onlyfiles:
print(f)
if verbose:
print()
return onlyfiles
def log_exception(ex, more_info=""):
"""
Log an expection and additional info.
Parameters
----------
ex : Exception
The python exception that occured
more_info :
Additional string to log
Returns
-------
None
"""
template = "{0} because exception of type {1} occurred. Arguments:\n{2!r}"
message = template.format(more_info, type(ex).__name__, ex.args)
print(message)
def chunks(l, n):
"""Yield successive n-sized chunks from l."""
for i in range(0, len(l), n):
yield l[i:i + n]
def save_dict_to_csv(filename, d):
"""Save d to a file."""
with open(filename, "w") as f:
for k, v in d.items():
out_str = k.replace(" ", "_")
if isinstance(v, Iterable):
if isinstance(v, np.ndarray):
v = v.flatten()
else:
v = np.array(v).flatten()
str_arr = [str(x) for x in v]
out_str = out_str + "," + ",".join(str_arr)
else:
out_str += "," + str(v)
f.write(out_str + "\n")
def make_path_if_not_exists(fname):
"""Makes directory structure for given fname"""
os.makedirs(os.path.dirname(fname), exist_ok=True)
def setup_logging(in_dir):
fname = os.path.join(in_dir, 'nc_output.log')
if os.path.isfile(fname):
open(fname, 'w').close()
logging.basicConfig(
filename=fname, level=logging.DEBUG)
mpl_logger = logging.getLogger("matplotlib")
mpl_logger.setLevel(level=logging.WARNING)
def print_config(config, msg=""):
"""Prints the contents of a config file"""
if msg != "":
print(msg)
config_dict = [{x: tuple(config.items(x))} for x in config.sections()]
pprint(config_dict, width=120)
print()
def read_cfg(location, verbose=True):
config = configparser.ConfigParser()
config.read(location)
if verbose:
print_config(config, "Program started with configuration")
return config
def parse_args(parser, verbose=True):
args, unparsed = parser.parse_known_args()
if len(unparsed) != 0:
print("Unrecognised command line argument passed")
print(unparsed)
exit(-1)
if verbose:
if len(sys.argv) > 1:
print("Command line arguments", args)
return args
def get_dirs_matching_regex(start_dir, re_filters=None, return_absolute=True):
"""
Recursively get all directories from start_dir that match regex.
Parameters
----------
start_dir : str
The path to the directory to start at.
re_filter : str, optional. Defaults to None.
The regular expression to match.
Returns all directories is passed as None.
Returns
-------
list
A list of directories matching the regex.
"""
if not os.path.isdir(start_dir):
raise ValueError("Non existant directory " + str(start_dir))
def match_filter(f):
if re_filters is None:
return True
for re_filter in re_filters:
search_res = re.search(re_filter, f)
if search_res is None:
return False
return True
dirs = []
for root, _, _ in os.walk(start_dir):
start_root = root[:len(start_dir)]
if len(root) == len(start_root):
end_root = ""
else:
end_root = root[len(start_dir + os.sep):]
if match_filter(end_root):
to_add = root if return_absolute else end_root
dirs.append(to_add)
return dirs
def interactive_refilt(start_dir, ext=None, write=False, write_loc=None):
re_filt = ""
# Do the interactive setup
files = get_all_files_in_dir(
start_dir, re_filter=None, return_absolute=False,
ext=ext, recursive=True)
print("Without any regex, the result from {} is:".format(start_dir))
for f in files:
print(f)
while True:
this_re_filt = input(
"Please enter the regexes seperated by SIM_SEP to test or quit / qt to move on:\n")
done = (
(this_re_filt.lower() == "quit") or
(this_re_filt.lower() == "qt"))
if done:
break
if this_re_filt == "":
re_filt = None
else:
re_filt = this_re_filt.split(" SIM_SEP ")
files = get_all_files_in_dir(
start_dir, re_filter=re_filt, return_absolute=False,
ext=ext, recursive=True)
print("With {} the result is:".format(re_filt))
for f in files:
print(f)
if re_filt == "":
re_filt = None
print("The final regex was: {}".format(re_filt))
# Save the result
if write:
if write_loc is None:
raise ValueError("Pass a location to write to when writing.")
regex_filts = re_filt
neuro_file = open(write_loc, "r")
temp_file = open("temp.txt", "w")
for line in neuro_file:
if line.startswith(" regex_filter ="):
line = " regex_filter = " + str(regex_filts) + "\n"
print("Set the regex filter to: " + line)
temp_file.write(line)
elif line.startswith("interactive ="):
line = "interactive = False\n"
temp_file.write(line)
else:
temp_file.write(line)
neuro_file.close()
temp_file.close()
os.remove(write_loc)
shutil.move("temp.txt", write_loc)
return re_filt
def find_ranges(iterable):
"""Yield range of consecutive numbers."""
import more_itertools as mit
for group in mit.consecutive_groups(iterable):
group = list(group)
if len(group) == 1:
yield group[0], group[0]
else:
yield group[0], group[-1]
def find_in(a, b):
"""Returns a boolean array of len(b) with True if any elements in a is found in b"""
def t_val(x): return x in a
truth = [t_val(x) for x in b]
return truth
def ordered_set(arr):
"""Returns set in order it was first seen"""
set_a = []
for x in arr:
if x not in set_a:
set_a.append(x)
return set_a
def get_dist(x, plot=False):
"""
x: list
Prints Min, Max, Mean and Values in x
plot: boolean, False
Shows plot of distribution
"""
if type(x) is np.ndarray:
print("Min: ", np.min(x), "\nMax: ", np.max(x),
"\nMean: ", np.mean(x), "\nValues: ", x)
elif type(x) is list:
print("Min: ", min(x), "\nMax: ", max(x),
"\nMean: ", mean(x), "\nValues: ", x)
if plot:
sns.distplot(x)
plt.show()
exit(-1)
def test_all_hier_clustering(data, verbose=False):
""" For testing all perumatations for hierarchical clustering linkage """
import pandas as pd
import scipy.cluster.hierarchy as shc
from scipy.cluster.hierarchy import cophenet
from scipy.spatial.distance import pdist
link_methods = ['single', 'complete',
'average', 'weighted', 'centroid', 'median', 'ward']
link_metric = ['braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon',
'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule']
coph = np.zeros((len(link_methods), len(link_metric)))
for i, link in enumerate(link_methods):
for j, metric in enumerate(link_metric):
try:
Z = shc.linkage(data, method=link, metric=metric)
c, coph_dists = cophenet(Z, pdist(data))
coph[i, j] = c
except:
coph[i, j] = np.nan
max_coph = np.nanmax(coph)
a, b = np.where(coph == max_coph)
coph_df = pd.DataFrame(coph, index=link_methods,
columns=link_metric)
if verbose:
print(coph_df)
print('\nMax Cophentic Correlation Coefficient: ',
coph_df.index.values[a], coph_df.columns.values[b], max_coph)
return coph_df
if __name__ == "__main__":
"""Main entry point."""
PARSER = argparse.ArgumentParser(
description='Process modifiable parameters from command line')
PARSER.add_argument("--loc", type=str, help="h5 location")
ARGS, UNPARSED = PARSER.parse_known_args()
if ARGS.loc is None:
print("Please enter a location through cmd, see -h for help")
exit(-1)
print_h5(ARGS.loc)Functions
def boolean_indexing(v, fillval=nan)-
Index a numpy array using a boolean mask.
Expand source code
def boolean_indexing(v, fillval=np.nan): """Index a numpy array using a boolean mask.""" lens = np.array([len(item) for item in v]) mask = lens[:, None] > np.arange(lens.max()) out = np.full(mask.shape, fillval) out[mask] = np.concatenate(v) return out def check_fn(item)-
Expand source code
def check_fn(item): if isinstance(item, list) or isinstance(item, np.ndarray): if len(item) == 0: return np.nan return item def chunks(l, n)-
Yield successive n-sized chunks from l.
Expand source code
def chunks(l, n): """Yield successive n-sized chunks from l.""" for i in range(0, len(l), n): yield l[i:i + n] def daterange(start_date, end_date)-
Yield a generator of dates between start and end date.
Expand source code
def daterange(start_date, end_date): """Yield a generator of dates between start and end date.""" for n in range(int((end_date - start_date).days)): yield start_date + timedelta(n) def find_in(a, b)-
Returns a boolean array of len(b) with True if any elements in a is found in b
Expand source code
def find_in(a, b): """Returns a boolean array of len(b) with True if any elements in a is found in b""" def t_val(x): return x in a truth = [t_val(x) for x in b] return truth def find_ranges(iterable)-
Yield range of consecutive numbers.
Expand source code
def find_ranges(iterable): """Yield range of consecutive numbers.""" import more_itertools as mit for group in mit.consecutive_groups(iterable): group = list(group) if len(group) == 1: yield group[0], group[0] else: yield group[0], group[-1] def get_all_files_in_dir(in_dir, ext=None, return_absolute=True, recursive=False, verbose=False, re_filter=None)-
Get all files in the directory with the given extension.
Parameters
in_dir:str- The absolute path to the directory
ext : str, optional. Defaults to None. The extension of files to get. return_absolute : bool, optional. Defaults to True. Whether to return the absolute filename or not. recursive: bool, optional. Defaults to False. Whether to recurse through directories. verbose: bool, optional. Defaults to False. Whether to print the files found.
Returns
List:A listoffilenames
Expand source code
def get_all_files_in_dir( in_dir, ext=None, return_absolute=True, recursive=False, verbose=False, re_filter=None): """ Get all files in the directory with the given extension. Parameters ---------- in_dir : str The absolute path to the directory ext : str, optional. Defaults to None. The extension of files to get. return_absolute : bool, optional. Defaults to True. Whether to return the absolute filename or not. recursive: bool, optional. Defaults to False. Whether to recurse through directories. verbose: bool, optional. Defaults to False. Whether to print the files found. Returns ------- List : A list of filenames """ if not os.path.isdir(in_dir): print("Non existant directory " + str(in_dir)) return [] def match_filter(f): if re_filter is None: return True if not isinstance(re_filter, list): search_res = re.search(re_filter, f) return search_res is not None else: for re_filt in re_filter: search_res = re.search(re_filt, f) if search_res is None: return False return True def ok_file(root_dir, f): return ( has_ext(f, ext) and match_filter(f) and os.path.isfile(os.path.join(root_dir, f))) def convert_to_path(root_dir, f): return os.path.join(root_dir, f) if return_absolute else f if verbose: print("Adding following files from {}".format(in_dir)) if recursive: onlyfiles = [] for root, _, filenames in os.walk(in_dir): start_root = root[:len(in_dir)] if len(root) == len(start_root): end_root = "" else: end_root = root[len(in_dir + os.sep):] for filename in filenames: filename = os.path.join(end_root, filename) if ok_file(start_root, filename): to_add = convert_to_path(start_root, filename) if verbose: print(to_add) onlyfiles.append(to_add) else: onlyfiles = [ convert_to_path(in_dir, f) for f in sorted(os.listdir(in_dir)) if ok_file(in_dir, f) ] if verbose: for f in onlyfiles: print(f) if verbose: print() return onlyfiles def get_attrs(d, depth=0)-
Walk through attributes.
Expand source code
def get_attrs(d, depth=0): """Walk through attributes.""" for k, v in sorted(d.items(), key=lambda x: x[0]): spaces = (" ") * depth if len(v.attrs) != 0: print("{}{} has attrs {}".format( spaces, k, list(v.attrs.items()) )) if hasattr(v, "items"): get_attrs(v, depth=depth + 1) def get_dirs_matching_regex(start_dir, re_filters=None, return_absolute=True)-
Recursively get all directories from start_dir that match regex. Parameters
start_dir:str- The path to the directory to start at.
re_filter : str, optional. Defaults to None. The regular expression to match. Returns all directories is passed as None. Returns
list- A list of directories matching the regex.
Expand source code
def get_dirs_matching_regex(start_dir, re_filters=None, return_absolute=True): """ Recursively get all directories from start_dir that match regex. Parameters ---------- start_dir : str The path to the directory to start at. re_filter : str, optional. Defaults to None. The regular expression to match. Returns all directories is passed as None. Returns ------- list A list of directories matching the regex. """ if not os.path.isdir(start_dir): raise ValueError("Non existant directory " + str(start_dir)) def match_filter(f): if re_filters is None: return True for re_filter in re_filters: search_res = re.search(re_filter, f) if search_res is None: return False return True dirs = [] for root, _, _ in os.walk(start_dir): start_root = root[:len(start_dir)] if len(root) == len(start_root): end_root = "" else: end_root = root[len(start_dir + os.sep):] if match_filter(end_root): to_add = root if return_absolute else end_root dirs.append(to_add) return dirs def get_dist(x, plot=False)-
x: list Prints Min, Max, Mean and Values in x plot: boolean, False Shows plot of distribution
Expand source code
def get_dist(x, plot=False): """ x: list Prints Min, Max, Mean and Values in x plot: boolean, False Shows plot of distribution """ if type(x) is np.ndarray: print("Min: ", np.min(x), "\nMax: ", np.max(x), "\nMean: ", np.mean(x), "\nValues: ", x) elif type(x) is list: print("Min: ", min(x), "\nMax: ", max(x), "\nMean: ", mean(x), "\nValues: ", x) if plot: sns.distplot(x) plt.show() exit(-1) def has_ext(filename, ext)-
Check if the filename ends in the extension.
Parameters
filename:str- The name of the file
ext:str- The extension, may have leading dot (e.g txt == .txt)
Returns
bool indicating if the filename has the extension
Expand source code
def has_ext(filename, ext): """ Check if the filename ends in the extension. Parameters ---------- filename : str The name of the file ext : str The extension, may have leading dot (e.g txt == .txt) Returns ------- bool indicating if the filename has the extension """ if ext is None: return True if ext[0] != ".": ext = "." + ext return filename[-len(ext):].lower() == ext.lower() def interactive_refilt(start_dir, ext=None, write=False, write_loc=None)-
Expand source code
def interactive_refilt(start_dir, ext=None, write=False, write_loc=None): re_filt = "" # Do the interactive setup files = get_all_files_in_dir( start_dir, re_filter=None, return_absolute=False, ext=ext, recursive=True) print("Without any regex, the result from {} is:".format(start_dir)) for f in files: print(f) while True: this_re_filt = input( "Please enter the regexes seperated by SIM_SEP to test or quit / qt to move on:\n") done = ( (this_re_filt.lower() == "quit") or (this_re_filt.lower() == "qt")) if done: break if this_re_filt == "": re_filt = None else: re_filt = this_re_filt.split(" SIM_SEP ") files = get_all_files_in_dir( start_dir, re_filter=re_filt, return_absolute=False, ext=ext, recursive=True) print("With {} the result is:".format(re_filt)) for f in files: print(f) if re_filt == "": re_filt = None print("The final regex was: {}".format(re_filt)) # Save the result if write: if write_loc is None: raise ValueError("Pass a location to write to when writing.") regex_filts = re_filt neuro_file = open(write_loc, "r") temp_file = open("temp.txt", "w") for line in neuro_file: if line.startswith(" regex_filter ="): line = " regex_filter = " + str(regex_filts) + "\n" print("Set the regex filter to: " + line) temp_file.write(line) elif line.startswith("interactive ="): line = "interactive = False\n" temp_file.write(line) else: temp_file.write(line) neuro_file.close() temp_file.close() os.remove(write_loc) shutil.move("temp.txt", write_loc) return re_filt def log_exception(ex, more_info='')-
Log an expection and additional info.
Parameters
ex:Exception- The python exception that occured
more_info : Additional string to log
Returns
None
Expand source code
def log_exception(ex, more_info=""): """ Log an expection and additional info. Parameters ---------- ex : Exception The python exception that occured more_info : Additional string to log Returns ------- None """ template = "{0} because exception of type {1} occurred. Arguments:\n{2!r}" message = template.format(more_info, type(ex).__name__, ex.args) print(message) def make_dir_if_not_exists(location)-
Make directory structure for given location.
Expand source code
def make_dir_if_not_exists(location): """Make directory structure for given location.""" os.makedirs(location, exist_ok=True) def make_path_if_not_exists(fname)-
Makes directory structure for given fname
Expand source code
def make_path_if_not_exists(fname): """Makes directory structure for given fname""" os.makedirs(os.path.dirname(fname), exist_ok=True) def mycolors(subject, colors_dict=None)-
Colour options for subject based on number.
Expand source code
def mycolors(subject, colors_dict=None): """Colour options for subject based on number.""" try: i = int(subject) if i > 10: i = i % 4 mycolors = ['tab:red', 'tab:blue', 'tab:green', 'tab:orange', 'tab:brown', 'deeppink', 'tab:olive', 'tab:pink', 'steelblue', 'firebrick', 'mediumseagreen'] color = mycolors[i] except ValueError: if colors_dict == None: print('Color input for required') exit(-1) color = colors_dict[subject] return color def ordered_set(arr)-
Returns set in order it was first seen
Expand source code
def ordered_set(arr): """Returns set in order it was first seen""" set_a = [] for x in arr: if x not in set_a: set_a.append(x) return set_a def parse_args(parser, verbose=True)-
Expand source code
def parse_args(parser, verbose=True): args, unparsed = parser.parse_known_args() if len(unparsed) != 0: print("Unrecognised command line argument passed") print(unparsed) exit(-1) if verbose: if len(sys.argv) > 1: print("Command line arguments", args) return args def print_config(config, msg='')-
Prints the contents of a config file
Expand source code
def print_config(config, msg=""): """Prints the contents of a config file""" if msg != "": print(msg) config_dict = [{x: tuple(config.items(x))} for x in config.sections()] pprint(config_dict, width=120) print() def print_h5(file_location)-
Print a summary of a h5 file.
Expand source code
def print_h5(file_location): """Print a summary of a h5 file.""" import h5py with h5py.File(file_location, 'r', libver='latest') as f: for key, val in f.attrs.items(): print(key, val) print() walk_dict(f) print() def read_cfg(location, verbose=True)-
Expand source code
def read_cfg(location, verbose=True): config = configparser.ConfigParser() config.read(location) if verbose: print_config(config, "Program started with configuration") return config def save_dict_to_csv(filename, d)-
Save d to a file.
Expand source code
def save_dict_to_csv(filename, d): """Save d to a file.""" with open(filename, "w") as f: for k, v in d.items(): out_str = k.replace(" ", "_") if isinstance(v, Iterable): if isinstance(v, np.ndarray): v = v.flatten() else: v = np.array(v).flatten() str_arr = [str(x) for x in v] out_str = out_str + "," + ",".join(str_arr) else: out_str += "," + str(v) f.write(out_str + "\n") def setup_logging(in_dir)-
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def setup_logging(in_dir): fname = os.path.join(in_dir, 'nc_output.log') if os.path.isfile(fname): open(fname, 'w').close() logging.basicConfig( filename=fname, level=logging.DEBUG) mpl_logger = logging.getLogger("matplotlib") mpl_logger.setLevel(level=logging.WARNING) def split_list(list, chunk_limit)-
Split a list into small chunks based on chunk_limit.
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def split_list(list, chunk_limit): """Split a list into small chunks based on chunk_limit.""" new_list = [list[i:i + chunk_limit] for i in range(0, len(list), chunk_limit)] return new_list def test_all_hier_clustering(data, verbose=False)-
For testing all perumatations for hierarchical clustering linkage
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def test_all_hier_clustering(data, verbose=False): """ For testing all perumatations for hierarchical clustering linkage """ import pandas as pd import scipy.cluster.hierarchy as shc from scipy.cluster.hierarchy import cophenet from scipy.spatial.distance import pdist link_methods = ['single', 'complete', 'average', 'weighted', 'centroid', 'median', 'ward'] link_metric = ['braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'] coph = np.zeros((len(link_methods), len(link_metric))) for i, link in enumerate(link_methods): for j, metric in enumerate(link_metric): try: Z = shc.linkage(data, method=link, metric=metric) c, coph_dists = cophenet(Z, pdist(data)) coph[i, j] = c except: coph[i, j] = np.nan max_coph = np.nanmax(coph) a, b = np.where(coph == max_coph) coph_df = pd.DataFrame(coph, index=link_methods, columns=link_metric) if verbose: print(coph_df) print('\nMax Cophentic Correlation Coefficient: ', coph_df.index.values[a], coph_df.columns.values[b], max_coph) return coph_df def walk_dict(d, depth=0)-
Walk a Dictionary.
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def walk_dict(d, depth=0): """Walk a Dictionary.""" for k, v in sorted(d.items(), key=lambda x: x[0]): spaces = (" ") * depth if hasattr(v, "items"): print(spaces + ("%s" % k)) walk_dict(v, depth + 1) else: print(spaces + "%s %s" % (k, v))