Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
@due.dcite(Doi('10.1002/mrm.20900'),
description='STE method of combining data across echoes using just '
'SNR/signal and TE.')
def _combine_ste(data, tes):
"""
Combine data across echoes using SNR/signal and TE.
Parameters
----------
data : (M x E x T) array_like
Masked data.
tes : (1 x E) array_like
Echo times in milliseconds.
Returns
-------
combined : (M x T) :obj:`numpy.ndarray`
@due.dcite(BibTeX("""
@inproceedings{minka2001automatic,
title={Automatic choice of dimensionality for PCA},
author={Minka, Thomas P},
booktitle={Advances in neural information processing systems},
pages={598--604},
year={2001}
}
"""),
description='Introduces method for choosing PCA dimensionality '
'automatically')
def run_mlepca(data):
"""
Run Singular Value Decomposition (SVD) on input data,
automatically select components on MLE variance cut-off.
Parameters
@due.dcite(BibTeX(
"""
@inproceedings{minka2001automatic,
title={Automatic choice of dimensionality for PCA},
author={Minka, Thomas P},
booktitle={Advances in neural information processing systems},
pages={598--604},
year={2001}
}
"""),
description='Introduces method for choosing PCA dimensionality '
'automatically')
def run_mlepca(data):
"""
Run Singular Value Decomposition (SVD) on input data.
Parameters
@due.dcite(BibTeX('@article{sorensen1948method,'
'author={S{\\o}rensen, Thorvald},'
'title={A method of establishing groups of equal amplitude '
'in plant sociology based on similarity of species and its '
'application to analyses of the vegetation on Danish commons},'
'year = {1948},'
'publisher = {Wiley Online Library},'
'journal = {Biol. Skr.},'
'volume={5},'
'pages={1--34}}'),
description='Introduction of Sorenson-Dice index by Sorenson in 1948.')
def dice(arr1, arr2):
"""
Compute Dice's similarity index between two numpy arrays. Arrays will be
binarized before comparison.
Parameters
@due.dcite(Doi('10.1002/(SICI)1522-2594(199907)42:1<87::AID-MRM13>3.0.CO;2-O'),
description='T2* method of combining data across echoes using '
'monoexponential equation.')
def _combine_t2s(data, tes, ft2s):
"""
Combine data across echoes using weighted averaging according to voxel-
(and sometimes volume-) wise estimates of T2*.
Parameters
----------
data : (M x E x T) array_like
Masked data.
tes : (1 x E) array_like
Echo times in milliseconds.
ft2s : (M [x T] X 1) array_like
Either voxel-wise or voxel- and volume-wise estimates of T2*.
@due.dcite(BibTeX(
"""
@inproceedings{minka2001automatic,
title={Automatic choice of dimensionality for PCA},
author={Minka, Thomas P},
booktitle={Advances in neural information processing systems},
pages={598--604},
year={2001}
}
"""),
description='Introduces method for choosing PCA dimensionality '
'automatically')
def run_mlepca(data):
"""
Run Singular Value Decomposition (SVD) on input data.
Parameters
__maintainer__,
__email__,
__status__,
__url__,
__packagename__,
__description__,
__longdesc__
)
import warnings
# cmp is not used, so ignore nipype-generated warnings
warnings.filterwarnings('ignore', r'cmp not installed')
# Citation for the algorithm.
due.cite(Doi('10.1016/j.neuroimage.2011.12.028'),
description='Introduces MEICA and tedana.',
version=__version__, path='tedana', cite_module=True)
due.cite(Doi('10.1073/pnas.1301725110'),
description='Improves MEICA and tedana.',
version=__version__, path='tedana', cite_module=True)
# Citation for package version.
due.cite(Doi('10.5281/zenodo.1250562'),
description='The tedana package version 0.0.1',
version='0.0.1', path='tedana', cite_module=True)
import warnings
# cmp is not used, so ignore nipype-generated warnings
warnings.filterwarnings('ignore', r'cmp not installed')
# Citation for the algorithm.
due.cite(Doi('10.1016/j.neuroimage.2011.12.028'),
description='Introduces MEICA and tedana.',
version=__version__, path='tedana', cite_module=True)
due.cite(Doi('10.1073/pnas.1301725110'),
description='Improves MEICA and tedana.',
version=__version__, path='tedana', cite_module=True)
# Citation for package version.
due.cite(Doi('10.5281/zenodo.1250562'),
description='The tedana package version 0.0.1',
version='0.0.1', path='tedana', cite_module=True)
@due.dcite(BibTeX('@article{dice1945measures,'
'author={Dice, Lee R},'
'title={Measures of the amount of ecologic association between species},'
'year = {1945},'
'publisher = {Wiley Online Library},'
'journal = {Ecology},'
'volume={26},'
'number={3},'
'pages={297--302}}'),
description='Introduction of Sorenson-Dice index by Dice in 1945.')
@due.dcite(BibTeX('@article{sorensen1948method,'
'author={S{\\o}rensen, Thorvald},'
'title={A method of establishing groups of equal amplitude '
'in plant sociology based on similarity of species and its '
'application to analyses of the vegetation on Danish commons},'
'year = {1948},'
'publisher = {Wiley Online Library},'