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[DOC] Update docstring for fixed_seed to ref None option #104

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Aug 4, 2018
Merged

[DOC] Update docstring for fixed_seed to ref None option #104

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31ee3c7
Update docstring for fixed_seed to ref None option
emdupre Aug 1, 2018
e53f94a
Write out seed value for ICA
emdupre Aug 2, 2018
aec1915
Docstring for n_vols in writeresults
emdupre Aug 3, 2018
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8 changes: 6 additions & 2 deletions tedana/decomposition/eigendecomp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,9 @@ def tedica(n_components, dd, conv, fixed_seed, cost, final_cost,
conv : :obj:`float`
Convergence limit for ICA
fixed_seed : :obj:`int`
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:obj:int or :obj:None

Seed for ensuring reproducibility of ICA results
Value passed to ``mdp.numx_rand.seed()``.
Set to an integer value for reproducible ICA results;
otherwise, set to -1 for varying results across calls.
cost : {'tanh', 'pow3', 'gaus', 'skew'}
Initial cost function for ICA.
final_cost : {'tanh', 'pow3', 'gaus', 'skew'}
Expand All @@ -281,6 +283,8 @@ def tedica(n_components, dd, conv, fixed_seed, cost, final_cost,

import mdp
climit = float(conv)
if fixed_seed == -1:
fixed_seed = np.random.randint(low=1, high=1000)
mdp.numx_rand.seed(fixed_seed)
icanode = mdp.nodes.FastICANode(white_comp=n_components, approach='symm',
g=cost, fine_g=final_cost,
Expand All @@ -290,4 +294,4 @@ def tedica(n_components, dd, conv, fixed_seed, cost, final_cost,
smaps = icanode.execute(dd) # noqa
mmix = icanode.get_recmatrix().T
mmix = stats.zscore(mmix, axis=0)
return mmix
return mmix, fixed_seed
16 changes: 12 additions & 4 deletions tedana/utils/io.py
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Expand Up @@ -264,7 +264,7 @@ def writefeats(data, mmix, mask, ref_img, suffix=''):
return fname


def writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',
def writect(comptable, n_vols, fixed_seed, acc, rej, midk, empty, ctname='comp_table.txt',
varexpl='-1'):
"""
Saves component table to disk
Expand All @@ -277,6 +277,8 @@ def writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',
component, and (5) normalized variance explained by component
n_vols : :obj:`int`
Number of volumes in original time series
fixed_seed : :obj:`int`
Integer value used in seeding ICA
acc : :obj:`list`
Indices of accepted (BOLD) components in `mmix`
rej : :obj:`list`
Expand Down Expand Up @@ -321,6 +323,7 @@ def writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',

_computed_vars = dict(file=op.abspath(op.curdir),
vex=varexpl,
seed=fixed_seed,
n_components=n_components,
dfe=len(acc),
rjn=len(midk) + len(rej),
Expand All @@ -332,6 +335,7 @@ def writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',
heading = textwrap.dedent("""\
# ME-ICA Component statistics table for: {file} #
# Dataset variance explained by ICA (VEx): {vex:.2f}
# Integer value used in seeding ICA: {seed}
# Total components generated by decomposition (TCo): {n_components}
# No. accepted BOLD-like components, i.e. effective degrees
of freedom for correlation (lower bound; DFe): {dfe}
Expand All @@ -355,8 +359,8 @@ def writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',
sortab[i, 4]))


def writeresults(ts, mask, comptable, mmix, n_vols, acc, rej, midk, empty,
ref_img):
def writeresults(ts, mask, comptable, mmix, n_vols, fixed_seed,
acc, rej, midk, empty, ref_img):
"""
Denoises `ts` and saves all resulting files to disk

Expand All @@ -373,6 +377,10 @@ def writeresults(ts, mask, comptable, mmix, n_vols, acc, rej, midk, empty,
mmix : (C x T) array_like
Mixing matrix for converting input data to component space, where `C`
is components and `T` is the same as in `data`
n_vols : :obj:`int`
Number of volumes in original time series
fixed_seed: :obj:`int`
Integer value used in seeding ICA
acc : :obj:`list`
Indices of accepted (BOLD) components in `mmix`
rej : :obj:`list`
Expand Down Expand Up @@ -425,7 +433,7 @@ def writeresults(ts, mask, comptable, mmix, n_vols, acc, rej, midk, empty,
mmix[:, acc], mask, ref_img, suffix='OC2')
LGR.info('Writing Z-normalized spatial component maps: {}'.format(op.abspath(fout)))

writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt',
writect(comptable, n_vols, fixed_seed, acc, rej, midk, empty, ctname='comp_table.txt',
varexpl=varexpl)
LGR.info('Writing component table: {}'.format(op.abspath('comp_table.txt')))

Expand Down
18 changes: 11 additions & 7 deletions tedana/workflows/tedana.py
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Expand Up @@ -149,7 +149,9 @@ def _get_parser():
parser.add_argument('--seed',
dest='fixed_seed',
type=int,
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This will break with None. Also (and this might not matter to anyone), but typing --fixed_seed None is a little awkward. I think I've seen something like --fixed_seed -1 which would then be coerced to None later.

help='Seeded value for ICA, for reproducibility.',
help=('Value passed to repr(mdp.numx_rand.seed()) '
'Set to an integer value for reproducible ICA results; '
'otherwise, set to -1 for varying results across calls.'),
default=42)
parser.add_argument('--debug',
dest='debug',
Expand Down Expand Up @@ -228,7 +230,9 @@ def tedana_workflow(data, tes, mixm=None, ctab=None, manacc=None, strict=False,
Other Parameters
----------------
fixed_seed : :obj:`int`, optional
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:obj:int or :obj:None, I think.

Seeded value for ICA, for reproducibility.
Value passed to ``mdp.numx_rand.seed()``.
Set to a positive integer value for reproducible ICA results;
otherwise, set to -1 for varying results across calls.
debug : :obj:`bool`, optional
Whether to run in debugging mode or not. Default is False.
quiet : :obj:`bool`, optional
Expand Down Expand Up @@ -388,9 +392,9 @@ def tedana_workflow(data, tes, mixm=None, ctab=None, manacc=None, strict=False,
t2s, t2sG, stabilize, ref_img,
tes=tes, kdaw=kdaw, rdaw=rdaw,
ste=ste, wvpca=wvpca)
mmix_orig = decomposition.tedica(n_components, dd, conv, fixed_seed,
cost=initcost, final_cost=finalcost,
verbose=debug)
mmix_orig, fixed_seed = decomposition.tedica(n_components, dd, conv, fixed_seed,
cost=initcost, final_cost=finalcost,
verbose=debug)
np.savetxt(op.join(out_dir, '__meica_mix.1D'), mmix_orig)
LGR.info('Making second component selection guess from ICA results')
seldict, comptable, betas, mmix = model.fitmodels_direct(catd, mmix_orig,
Expand Down Expand Up @@ -425,8 +429,8 @@ def tedana_workflow(data, tes, mixm=None, ctab=None, manacc=None, strict=False,
LGR.warning('No BOLD components detected! Please check data and '
'results!')

utils.writeresults(OCcatd, mask, comptable, mmix, n_vols, acc, rej, midk,
empty, ref_img)
utils.writeresults(OCcatd, mask, comptable, mmix, fixed_seed, n_vols,
acc, rej, midk, empty, ref_img)
utils.gscontrol_mmix(OCcatd, mmix, mask, acc, ref_img)
if dne:
utils.writeresults_echoes(catd, mmix, mask, acc, rej, midk, ref_img)
Expand Down