# Copyright (C) 2012-2022 C-PAC Developers
# This file is part of C-PAC.
# C-PAC is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
# C-PAC is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.
# You should have received a copy of the GNU Lesser General Public
# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
from CPAC.pipeline.schema import valid_options
from CPAC.utils.docs import docstring_parameter
[docs]def convert_pvalue_to_r(datafile, p_value, two_tailed=False):
'''
Method to calculate correlation threshold from p_value
Parameters
----------
datafile : string
filepath to dataset to extract number of time pts from
p_value : float
significance threshold p-value
two_tailed : boolean (optional); default=False
flag to indicate whether to calculate the two-tailed t-test
threshold for the returned correlation value
Returns
-------
r_value : float
correlation threshold value
'''
import nibabel as nb
import numpy as np
import scipy.stats
# Get two-tailed distribution
if two_tailed:
p_value = p_value / 2
# Load in data and number of time pts
img = nb.load(datafile).get_data()
t_pts = img.shape[-1]
# N-2 degrees of freedom with Pearson correlation (two sample means)
deg_freedom = t_pts-2
# Inverse Survival Function (Inverse of SF)
# Note: survival function (SF) is also known as the complementary
# cumulative distribution function (CCDF): F_(x) = p = P(X > x) = 1 - F(x)
# The inverse will yield: x = F_^-1(p) = F_^-1(P(X > x))
# where x is a value under the distribution of the random variable X
# such that the probability of getting greater than x, is p
t_value = scipy.stats.t.isf(p_value, deg_freedom)
r_value = np.sqrt(t_value ** 2 / (deg_freedom + t_value ** 2))
# Return correlation coefficient
return r_value
# Function to actually do the list merging
def merge_lists(deg_list=[], eig_list=[], lfcd_list=[]):
merged_list = []
merged_list.extend(deg_list)
merged_list.extend(eig_list)
merged_list.extend(lfcd_list)
# and we're hijacking this function to parse out the files instead!
degree_weighted = None
degree_binarized = None
eigen_weighted = None
eigen_binarized = None
lfcd_weighted = None
lfcd_binarized = None
for path in merged_list:
if 'degree' in path and 'Weighted' in path:
degree_weighted = path
elif 'degree' in path and 'Binarize' in path:
degree_binarized = path
elif 'eigen' in path and 'Weighted' in path:
eigen_weighted = path
elif 'eigen' in path and 'Binarize' in path:
eigen_binarized = path
elif 'local_functional' in path and 'Weighted' in path:
lfcd_weighted = path
elif 'local_functional' in path and 'Binarize' in path:
lfcd_binarized = path
return (degree_weighted, degree_binarized, eigen_weighted,
eigen_binarized, lfcd_weighted, lfcd_binarized)
@docstring_parameter(
weight_options=tuple(valid_options['centrality']['weight_options']))
def sep_nifti_subbriks(nifti_file, out_names):
'''Separate sub-briks of niftis and save specified out
Parameters
----------
nifti_file : str
path to NIfTI output of an AFNI centrality tool
out_names : iterable of str
an iterable of strings, each ending with one of {weight_options}
Returns
-------
list
each of the specified outputs as its own file
'''
# pylint: disable=redefined-outer-name,reimported,unused-import
import os
import nibabel as nib
from CPAC.pipeline.schema import valid_options
from CPAC.utils.docs import docstring_parameter # noqa: F401
output_niftis = []
weight_options = valid_options['centrality']['weight_options']
selected_options = {_[::-1].split('_', 1)[0][::-1]: _ for _ in out_names}
nii_img = nib.load(nifti_file)
nii_arr = nii_img.get_data()
nii_affine = nii_img.get_affine()
nii_dims = nii_arr.shape
if nii_dims[-1] != len(weight_options):
if len(nii_dims) == 3 and len(out_names) == 1:
pass
else:
err_msg = 'out_names must have same number of elements as '\
'nifti sub-briks'
raise Exception(err_msg)
for brik, option in enumerate(weight_options):
if option in selected_options:
if len(nii_dims) == 3:
brik_arr = nii_arr
elif len(nii_dims) > 3:
brik_arr = nii_arr[:, :, :, 0, brik]
out_file = os.path.join(os.getcwd(),
selected_options[option] + '.nii.gz')
out_img = nib.Nifti1Image(brik_arr, nii_affine)
out_img.to_filename(out_file)
output_niftis.append(out_file)
return output_niftis
@docstring_parameter(m_options=valid_options['centrality']['method_options'],
t_options=valid_options['centrality'][
'threshold_options'])
def check_centrality_params(method_option, threshold_option, threshold):
'''
Function to check the centrality parameters.
Parameters
----------
method_option : str or int
one of {m_options} or index of option
threshold_option : str
one of {t_options} or index of option
threshold: float
Returns
-------
method_option : str
one of {m_options}
threshold_option : str
one of {t_options}
'''
# Check method option
if isinstance(method_option, int):
if method_option < len(valid_options['centrality']['method_options']):
method_option = valid_options[
'centrality']['method_options'][method_option]
else:
raise MethodOptionError(method_option)
elif not isinstance(method_option, str):
raise TypeError('Method option must be a string, but type \'%s\' '
'provided' % type(method_option).__name__)
# Check threshold option
if type(threshold_option) is list:
threshold_option = threshold_option[0]
if type(threshold_option) is int:
if threshold_option < len(
valid_options['centrality']['threshold_options']
):
threshold_option = valid_options[
'centrality']['threshold_options'][threshold_option]
else:
raise ThresholdOptionError(threshold_option, method_option)
elif type(threshold_option) is not str:
raise TypeError('Threshold option must be a string, but type \'%s\' '
'provided' % type(threshold_option).__name__)
# Format input strings
method_option = method_option.lower().rstrip(' ')
method_options_v1 = ['degree', 'eigenvector', 'lfcd']
if method_option in method_options_v1:
method_option = valid_options['centrality']['method_options'][
method_options_v1.index(method_option)
]
if ' ' not in threshold_option:
threshold_option = ' '.join([threshold_option, 'threshold'])
threshold_option = threshold_option.capitalize().rstrip(' ')
# Check for strings properly formatted
if method_option not in valid_options['centrality']['method_options']:
raise MethodOptionError(method_option)
# Check for strings properly formatted
if threshold_option not in valid_options['centrality'][
'threshold_options'
]:
raise ThresholdOptionError(threshold_option, method_option)
# Check for invalid combinations of method_option + threshold_option
if (
method_option == 'local_functional_connectivity_density' and
threshold_option == 'Sparsity threshold'
):
raise ThresholdOptionError(threshold_option, method_option)
# If it's significance/sparsity thresholding, check for (0,1]
if (
threshold_option == 'Significance threshold' or
threshold_option == 'Sparsity threshold'
):
if threshold <= 0 or threshold > 1:
raise ThresholdError(threshold_option, threshold)
# If it's correlation, check for [-1,1]
elif threshold_option == 'Correlation threshold':
if threshold < -1 or threshold > 1:
raise ThresholdError(threshold_option, threshold)
else:
raise ThresholdOptionError(threshold_option, method_option)
# Return valid method and threshold options
return method_option, threshold_option
class MethodOptionError(ValueError):
"""Raised when a selected centrality method option is not supported.
"""
def __init__(self, method_option):
self.method_option = method_option
self.message = 'Method option \'%s\' not supported' % method_option
super().__init__(self.message)
class ThresholdError(ValueError):
"""Raised when a selected threshold value is not supported for a
selected threshold option.
"""
def __init__(self, threshold_option, threshold):
self.threshold_option = threshold_option
self.threshold = threshold
print(type(threshold))
self.message = f'For \'{threshold_option}\', threshold value must be '
if (
threshold_option == 'Significance threshold' or
threshold_option == 'Sparsity threshold'
):
self.message += 'a positive number greater than 0 '
elif threshold_option == 'Correlation threshold':
self.message += 'greater than or equal to -1 '
else:
raise ThresholdOptionError(threshold_option)
self.message += 'and less than or equal to 1.\n Currently it is set ' \
f'at {threshold}'
super().__init__(self.message)
class ThresholdOptionError(ValueError):
"""Raised when a selected threshold option is not supported for a
selected centrality measure.
"""
def __init__(self, threshold_option, method_option=None):
self.method_option = method_option
self.threshold_option = threshold_option
self.message = f'Threshold option \'{threshold_option}\' not supported'
if self.method_option:
self.message += ' for network centrality measure ' \
f'\'{method_option}\''
self.message += '; fix this in the pipeline config'
if (
method_option == 'local_functional_connectivity_density' and
threshold_option == 'Sparsity threshold'
):
valid_options = ' or '.join([
f"'{t}'" for t in valid_options[
'centrality'
]['threshold_options'] if t != threshold_option
])
self.message += f'. \'{method_option}\' must use {valid_options}.'
super().__init__(self.message)