From 998f3d776e67cc19084dd66c85270228e2c831c2 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 2 Jul 2018 12:15:55 +0100
Subject: [PATCH] RF: Drop bad component indices
---
fsl/scripts/extract_noise.py | 38 ++++++++++++++++++++++++++++++------
1 file changed, 32 insertions(+), 6 deletions(-)
diff --git a/fsl/scripts/extract_noise.py b/fsl/scripts/extract_noise.py
index de479d0ce..cf271bdf4 100644
--- a/fsl/scripts/extract_noise.py
+++ b/fsl/scripts/extract_noise.py
@@ -5,7 +5,8 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""
+"""This module defines the ``extract_noise`` script, for extracting component
+time series from a MELODIC ``.ica`` directory.
"""
@@ -129,11 +130,21 @@ def parseArgs(args):
return args
-def genComponentIndexList(comps):
- """
+def genComponentIndexList(comps, ncomps):
+ """Turns the given sequence of integers and file paths into a list
+ of 0-based component indices.
+
+ :arg comps: Sequence containing 1-based component indices, and/or paths
+ to FIX/AROMA label text files.
+
+ :arg ncomps: Number of components in the input data - indices larger than
+ this will be ignored.
+
+ :returns: List of 0-based component indices.
"""
allcomps = []
+ badcomps = []
for c in comps:
if isinstance(c, int):
@@ -141,13 +152,27 @@ def genComponentIndexList(comps):
else:
ccomps = fixlabels.loadLabelFile(c, returnIndices=True)[2]
- allcomps.extend([cc - 1 for cc in ccomps])
+ badcomps.extend([cc for cc in ccomps if cc >= ncomps])
+ allcomps.extend([cc - 1 for cc in ccomps if cc < ncomps])
+
+ if len(badcomps) > 0:
+ print('Warning: Ignoring components: {}'.format(badcomps),
+ file=sys.stderr)
return list(sorted(set(allcomps)))
def loadConfoundFiles(conffiles, npts):
- """
+ """Loads the given confound files, and copies them all into a single 2D
+ ``(npoints, nconfounds)`` matrix.
+
+ :arg conffiles: Sequence of paths to files containing confound time series
+ (where each row corresponds to a time point, and each
+ column corresponds to a single confound).
+
+ :arg npts: Expected number of time points
+
+ :returns: A ``(npoints, nconfounds)`` ``numpy`` matrix.
"""
matrices = []
@@ -162,7 +187,8 @@ def loadConfoundFiles(conffiles, npts):
if mat.shape[0] != npts:
print('Warning: confound file {} does not have correct number of '
'points (expected {}, has {}). Output will be truncated or '
- 'padded with NaNs.'.format(cfile, npts, mat.shape[1]))
+ 'padded with NaNs.'.format(cfile, npts, mat.shape[1]),
+ file=sys.stderr)
matrices.append(mat)
totalcols = sum([m.shape[0] for m in matrices])
--
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