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#!/usr/bin/env python
#
# fixlabels.py - Functions for loading/saving FIX/ICA-AROMA label files.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module contains functions for loading/saving FIX/ICA-AROMA label files.
.. autosummary::
:nosignatures:
loadLabelFile
saveLabelFile
isNoisyComponent
InvalidLabelFileError
"""
import os.path as op
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def loadLabelFile(filename,
includeLabel=None,
excludeLabel=None,
returnIndices=False):
"""Loads component labels from the specified file. The file is assuemd
to be of the format generated by FIX, Melview or ICA-AROMA; such a file
should have a structure resembling the following::
filtered_func_data.ica
1, Signal, False
2, Unclassified Noise, True
3, Unknown, False
4, Signal, False
5, Unclassified Noise, True
6, Unclassified Noise, True
7, Unclassified Noise, True
8, Signal, False
[2, 5, 6, 7]
.. note:: This function will also parse files which only contain a
component list, e.g.::
[2, 5, 6, 7]
The square brackets may or may not be present, i.e. the
following format is also accepted (this format is generated
by ICA-AROMA)::
2, 5, 6, 7
In this case, the returned melodic directory path will be
``None``. The ``includeLabel`` and ``excludeLabel`` arguments
allow you to control the labels assigned to included/excluded
components.
The first line of the file contains the name of the melodic directory.
Then, one line is present for each component, containing the following,
separated by commas:
- The component index (starting from 1).
- One or more labels for the component (multiple labels must be
comma-separated).
- ``'True'`` if the component has been classified as *bad*,
``'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
signal or unknown.
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:arg filename: Name of the label file to load.
: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 'Movement' for
ICA-AROMA-like files.
:arg excludeLabel: If the file contains a single line containing component
indices, this label will be used for the components
that are not in the list. Defaults to 'Signal' for
FIX-like files, and 'Unknown' for ICA-AROMA-like files.
:arg returnIndices: Defaults to ``False``. If ``True``, a list containing
the noisy component numbers that were listed in the
file is returned.
:returns: A tuple containing:
- The path to the melodic directory as specified in the label
file
- A list of lists, one list per component, with each list
containing the labels for the corresponding component.
- If ``returnIndices is True``, a list of the noisy component
indices (starting from 1) that were specified in the file.
"""
signalLabels = None
filename = op.abspath(filename)
with open(filename, 'rt') as f:
lines = f.readlines()
if len(lines) < 1:
raise InvalidLabelFileError('Invalid FIX classification '
'file - not enough lines')
lines = [l.strip() for l in lines]
lines = [l for l in lines if l != '']
# If the file contains a single
# line, we assume that it is just
# a comma-separated list of noise
# components.
if len(lines) == 1:
line = lines[0]
# if the list is contained in
# square brackets, we assume
# that it is a FIX output file,
# where included components have
# been classified as noise, and
# excluded components as signal.
#
# Otherwise we assume that it
# is an AROMA file, where
# included components have
# been classified as being due
# to motion, and excluded
# components unclassified.
if includeLabel is None:
if line[0] == '[': includeLabel = 'Unclassified noise'
else: includeLabel = 'Movement'
if excludeLabel is None:
if line[0] == '[': excludeLabel = 'Signal'
else: excludeLabel = 'Unknown'
else:
signalLabels = [excludeLabel]
# Remove any leading/trailing
# whitespace or brackets.
line = lines[0].strip(' []')
melDir = None
noisyComps = [int(i) for i in line.split(',')]
allLabels = []
for i in range(max(noisyComps)):
if (i + 1) in noisyComps: allLabels.append([includeLabel])
else: allLabels.append([excludeLabel])
# Otherwise, we assume that
# it is a full label file.
else:
melDir = lines[0]
noisyComps = lines[-1].strip(' []').split(',')
noisyComps = [c for c in noisyComps if c != '']
noisyComps = [int(c) for c in noisyComps]
# The melodic directory path should
# either be an absolute path, or
# be specified relative to the location
# of the label file.
if not op.isabs(melDir):
melDir = op.join(op.dirname(filename), melDir)
# Parse the labels for every component
allLabels = []
for i, compLine in enumerate(lines[1:-1]):
tokens = compLine.split(',')
tokens = [t.strip() for t in tokens]
if len(tokens) < 3:
raise InvalidLabelFileError(
'Invalid FIX classification file - '
'line {}: {}'.format(i + 1, compLine))
try:
compIdx = int(tokens[0])
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except ValueError:
raise InvalidLabelFileError(
'Invalid FIX classification file - '
'line {}: {}'.format(i + 1, compLine))
if tokens[-1].lower() in ('true', 'false'):
compLabels = tokens[1:-1]
else:
compLabels = tokens[1:]
if compIdx != i + 1:
raise InvalidLabelFileError(
'Invalid FIX classification file - wrong component '
'number at line {}: {}'.format(i + 1, compLine))
allLabels.append(compLabels)
# Validate the labels against
# the noisy list - all components
# in the noisy list should not
# have 'signal' or 'unknown' labels
for i, labels in enumerate(allLabels):
comp = i + 1
noise = isNoisyComponent(labels, signalLabels)
if noise and (comp not in noisyComps):
raise InvalidLabelFileError('Noisy component {} has invalid '
'labels: {}'.format(comp, labels))
for comp in noisyComps:
i = comp - 1
labels = allLabels[i]
noise = isNoisyComponent(labels, signalLabels)
if not noise:
raise InvalidLabelFileError('Noisy component {} is missing '
'a noise label'.format(comp))
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if returnIndices: return melDir, allLabels, noisyComps
else: return melDir, allLabels
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 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. If
not provided, a ``'.'`` is output as the first line.
: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 = []
noisyComps = []
# The first line - the melodic directory name
if dirname is None:
dirname = '.'
lines.append(dirname)
# A line for each component
for i, labels in enumerate(allLabels):
comp = i + 1
noise = isNoisyComponent(labels, signalLabels)
# Make sure there are no
# commas in any label names
labels = [l.replace(',', '_') for l in labels]
tokens = [str(comp)] + labels + [str(noise)]
lines.append(', '.join(tokens))
if noise:
noisyComps.append(comp)
# A line listing the bad components
if listBad:
lines.append('[' + ', '.join([str(c) for c in noisyComps]) + ']')
with open(filename, 'wt') as f:
f.write('\n'.join(lines) + '\n')
def isNoisyComponent(labels, signalLabels=None):
"""Given a set of component labels, returns ``True`` if the component
is ultimately classified as noise, ``False`` otherwise.
:arg signalLabels: Labels which are deemed signal. If a component has
no labels in this list, it is deemed noise. Defaults
"""
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
class InvalidLabelFileError(Exception):
"""Exception raised by the :func:`loadLabelFile` function when an attempt
is made to load an invalid label file.
"""
pass