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Revert "[REF] Modularize metric calculation" #474

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Nov 22, 2019
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Revert "[REF] Modularize metric calculation" #474

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3 changes: 0 additions & 3 deletions docs/api.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -98,9 +98,6 @@ API
tedana.metrics.dependence_metrics
tedana.metrics.kundu_metrics

:template: module.rst
tedana.metrics.collect
tedana.metrics.dependence

.. _api_selection_ref:

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11 changes: 1 addition & 10 deletions tedana/decay.py
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Expand Up @@ -2,10 +2,8 @@
Functions to estimate S0 and T2* from multi-echo data.
"""
import logging
import numpy as np
import scipy
from scipy import stats

import numpy as np
from tedana import utils

LGR = logging.getLogger(__name__)
Expand Down Expand Up @@ -270,13 +268,6 @@ def fit_decay(data, tes, mask, adaptive_mask, fittype):
t2s_full = utils.unmask(t2s_full, mask)
s0_full = utils.unmask(s0_full, mask)

# set a hard cap for the T2* map
# anything that is 10x higher than the 99.5 %ile will be reset to 99.5 %ile
cap_t2s = stats.scoreatpercentile(t2s_limited.flatten(), 99.5,
interpolation_method='lower')
LGR.debug('Setting cap on T2* map at {:.5f}'.format(cap_t2s * 10))
t2s_limited[t2s_limited > cap_t2s * 10] = cap_t2s

return t2s_limited, s0_limited, t2s_full, s0_full


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7 changes: 2 additions & 5 deletions tedana/metrics/__init__.py
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Expand Up @@ -2,11 +2,8 @@
# ex: set sts=4 ts=4 sw=4 et:

from .kundu_fit import (
kundu_metrics, dependence_metrics
)
from .collect import (
generate_metrics
dependence_metrics, kundu_metrics, get_coeffs, computefeats2
)

__all__ = [
'dependence_metrics', 'kundu_metrics', 'generate_metrics']
'dependence_metrics', 'kundu_metrics', 'get_coeffs', 'computefeats2']
139 changes: 0 additions & 139 deletions tedana/metrics/_utils.py
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