From 8b19e44950b481d897a56b787b498e833be9d129 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 18 Apr 2017 14:23:38 +0100
Subject: [PATCH] Fixes and adjustments to fixlabels.load/saveLabelFile -
ability to specify labels which correspond to 'signal'.
---
fsl/data/fixlabels.py | 70 ++++++++++++++++++++++++++--------------
fsl/data/melodicimage.py | 1 -
2 files changed, 46 insertions(+), 25 deletions(-)
diff --git a/fsl/data/fixlabels.py b/fsl/data/fixlabels.py
index f948a307c..8cc0a99c9 100644
--- a/fsl/data/fixlabels.py
+++ b/fsl/data/fixlabels.py
@@ -62,8 +62,9 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
- One or more labels for the component (multiple labels must be
comma-separated).
- ``'True'`` if the component has been classified as *bad*,
- ``'False'`` otherwise.
-
+ ``'False'`` otherwise. This field is optional - if the last
+ comma-separated token on a line is not equal (case-insensitive)
+ to ``True`` or ``False``, it is interpreted as a component label.
The last line of the file contains the index (starting from 1) of all
*bad* components, i.e. those components which are not classified as
@@ -74,7 +75,7 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
:arg includeLabel: If the file contains a single line containing a list
component indices, this label will be used for the
components in the list. Defaults to 'Unclassified
- noise' for FIX-like files, and 'Motion' for
+ noise' for FIX-like files, and 'Movement' for
ICA-AROMA-like files.
:arg excludeLabel: If the file contains a single line containing component
@@ -88,7 +89,8 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
the corresponding component.
"""
- filename = op.abspath(filename)
+ signalLabels = None
+ filename = op.abspath(filename)
with open(filename, 'rt') as f:
lines = f.readlines()
@@ -128,6 +130,8 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
if excludeLabel is None:
if line[0] == '[': excludeLabel = 'Signal'
else: excludeLabel = 'Unknown'
+ else:
+ signalLabels = [excludeLabel]
# Remove any leading/trailing
# whitespace or brackets.
@@ -176,8 +180,11 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
raise InvalidLabelFileError(
'Invalid FIX classification file - '
'line {}: {}'.format(i + 1, compLine))
-
- compLabels = tokens[1:-1]
+
+ if tokens[-1].lower() in ('true', 'false'):
+ compLabels = tokens[1:-1]
+ else:
+ compLabels = tokens[1:]
if compIdx != i + 1:
raise InvalidLabelFileError(
@@ -193,9 +200,10 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
for i, labels in enumerate(allLabels):
comp = i + 1
- noise = isNoisyComponent(labels)
+ noise = isNoisyComponent(labels, signalLabels)
if noise and (comp not in noisyComps):
+ print(signalLabels)
raise InvalidLabelFileError('Noisy component {} has invalid '
'labels: {}'.format(comp, labels))
@@ -203,7 +211,7 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
i = comp - 1
labels = allLabels[i]
- noise = isNoisyComponent(labels)
+ noise = isNoisyComponent(labels, signalLabels)
if not noise:
raise InvalidLabelFileError('Noisy component {} is missing '
@@ -212,24 +220,31 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
return melDir, allLabels
-def saveLabelFile(allLabels, filename, dirname=None, listBad=True):
+def saveLabelFile(allLabels,
+ filename,
+ dirname=None,
+ listBad=True,
+ signalLabels=None):
"""Saves the given classification labels to the specified file. The
classifications are saved in the format described in the
:func:`loadLabelFile` method.
- :arg allLabels: A list of lists, one list for each component, where
- each list contains the labels for the corresponding
- component.
+ :arg allLabels: A list of lists, one list for each component, where
+ each list contains the labels for the corresponding
+ component.
+
+ :arg filename: Name of the file to which the labels should be saved.
- :arg filename: Name of the file to which the labels should be saved.
+ :arg dirname: If provided, is output as the first line of the file.
+ Intended to be a relative path to the MELODIC analysis
+ directory with which this label file is associated.
- :arg dirname: If provided, is output as the first line of the file.
- Intended to be a relative path to the MELODIC analysis
- directory with which this label file is associated.
+ :arg listBad: If ``True`` (the default), the last line of the file
+ will contain a comma separated list of components which
+ are deemed 'noisy' (see :func:`isNoisyComponent`).
- :arg listBad: If ``True`` (the default), the last line of the file
- will contain a comma separated list of components which
- are deemed 'noisy' (see :func:`isNoisyComponent`).
+ :arg signalLabels: Labels which should be deemed 'signal' - see the
+ :func:`isNoisyComponent` function.
"""
lines = []
@@ -243,7 +258,7 @@ def saveLabelFile(allLabels, filename, dirname=None, listBad=True):
for i, labels in enumerate(allLabels):
comp = i + 1
- noise = isNoisyComponent(labels)
+ noise = isNoisyComponent(labels, signalLabels)
# Make sure there are no
# commas in any label names
@@ -263,13 +278,20 @@ def saveLabelFile(allLabels, filename, dirname=None, listBad=True):
f.write('\n'.join(lines) + '\n')
-def isNoisyComponent(labels):
+def isNoisyComponent(labels, signalLabels=None):
"""Given a set of component labels, returns ``True`` if the component
is ultimately classified as noise, ``False`` otherwise.
- """
- labels = [l.lower() for l in labels]
- noise = ('signal' not in labels) and ('unknown' not in labels)
+ :arg signalLabels: Labels which are deemed signal. If a component has
+ no labels in this list, it is deemed noise. Defaults
+ to ``['Signal', 'Unknown']`.
+ """
+ if signalLabels is None:
+ signalLabels = ['signal', 'unknown']
+
+ signalLabels = [l.lower() for l in signalLabels]
+ labels = [l.lower() for l in labels]
+ noise = not any([sl in labels for sl in signalLabels])
return noise
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 948248ccc..61931a3e4 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -14,7 +14,6 @@ import os.path as op
from . import image as fslimage
from . import melodicanalysis as melanalysis
-from . import melodiclabels as mellabels
class MelodicImage(fslimage.Image):
--
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