From 8be19316b5be2b1f742a1bc827f7382ceeae95b5 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 27 Sep 2024 17:26:23 +0100
Subject: [PATCH] MNT: Modify saveLabelFile to support saving classification
probabilities
---
fsl/data/fixlabels.py | 39 ++++++++++++++++++++++++---------------
1 file changed, 24 insertions(+), 15 deletions(-)
diff --git a/fsl/data/fixlabels.py b/fsl/data/fixlabels.py
index 8388daac..8ce2f2dd 100644
--- a/fsl/data/fixlabels.py
+++ b/fsl/data/fixlabels.py
@@ -343,33 +343,40 @@ def saveLabelFile(allLabels,
filename,
dirname=None,
listBad=True,
- signalLabels=None):
+ signalLabels=None,
+ probabilities=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. If
- not provided, a ``'.'`` is output as the first line.
+ :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 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.
+ :arg signalLabels: Labels which should be deemed 'signal' - see the
+ :func:`isNoisyComponent` function.
+
+ :arg probabilities: Classification probabilities. If provided, the
+ probability for each component is saved to the file.
"""
lines = []
noisyComps = []
+ if probabilities is not None and len(probabilities) != len(allLabels):
+ raise ValueError('len(probabilities) != len(allLabels)')
+
# The first line - the melodic directory name
if dirname is None:
dirname = '.'
@@ -387,6 +394,9 @@ def saveLabelFile(allLabels,
labels = [l.replace(',', '_') for l in labels]
tokens = [str(comp)] + labels + [str(noise)]
+ if probabilities is not None:
+ tokens.append(f'{probabilities[i]:0.6f}')
+
lines.append(', '.join(tokens))
if noise:
@@ -422,4 +432,3 @@ class InvalidLabelFileError(Exception):
"""Exception raised by the :func:`loadLabelFile` function when an attempt
is made to load an invalid label file.
"""
- pass
--
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