from tedana import model, utils, io
from tedana.decomposition._utils import eimask, dwtmat, idwtmat
from tedana.selection._utils import (getelbow_cons, getelbow)
from tedana.due import due, BibTeX
LGR = logging.getLogger(__name__)
F_MAX = 500
Z_MAX = 8
@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_svd(data):
"""
Run Singular Value Decomposition (SVD) on input data.
Parameters
----------
data : (S [*E] x T) array_like
Optimally combined (S x T) or full multi-echo (S*E x T) data.
Returns
-------
out : (S [x E [x T]]) :obj:`numpy.ndarray`
Unmasked `data` array
"""
out = np.zeros(mask.shape + data.shape[1:], dtype=data.dtype)
out[mask] = data
return out
@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},'
'journal = {Biol. Skr.},'
'volume={5},'
'pages={1--34}}'),
if add_const: # drop beta for intercept, if specified
betas = betas[:, :-1]
if mask is not None:
betas = utils.unmask(betas, mask)
return betas
@due.dcite(BibTeX("""
@article{hughett2007accurate,
title={Accurate Computation of the F-to-z and t-to-z Transforms
for Large Arguments},
author={Hughett, Paul},
journal={Journal of Statistical Software},
volume={23},
number={1},
pages={1--5},
year={2007},
publisher={Foundation for Open Access Statistics}
}
"""),
description='Introduces T-to-Z transform.')
@due.dcite(Doi('10.5281/zenodo.32508'),
description='Python implementation of T-to-Z transform.')
def t_to_z(t_values, dof):
"""
Convert t-values to z-values.
Parameters
----------