From dbafefba6b43a32843655f553c91e6ae19d93b4b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 16 Feb 2017 11:12:35 +0000
Subject: [PATCH] New path function which determines the unique prefix of a
file name. Used by new gifti function relatedFiles
---
fsl/data/gifti.py | 65 ++++++++++++++++++++++++++++++++++++++++++-----
fsl/utils/path.py | 35 +++++++++++++++++++++++++
2 files changed, 93 insertions(+), 7 deletions(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 41d38e3ba..8472b6005 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -17,10 +17,12 @@ are available:
:nosignatures:
GiftiSurface
- extractGiftiSurface
+ loadGiftiSurface
+ relatedFiles
"""
+import glob
import os.path as op
import nibabel as nib
@@ -49,12 +51,11 @@ class GiftiSurface(mesh.TriangleMesh):
"""Load the given GIFTI file using ``nibabel``, and extracts surface
data using the :func:`extractGiftiSurface` function.
- :arg infile: A GIFTI surface file
+ :arg infile: A GIFTI surface file (``*.surf.gii``).
"""
-
surfimg = nib.load(infile)
- vertices, indices = extractGiftiSurface(surfimg)
+ vertices, indices = loadGiftiSurface(surfimg)
mesh.TriangleMesh.__init__(self, vertices, indices)
@@ -67,10 +68,19 @@ class GiftiSurface(mesh.TriangleMesh):
def loadVertexData(self, dataSource):
- """Attempts to load scalar data associated with each vertex of this
- ``GiftiSurface`` from the given ``dataSource``.
+ """Attempts to load data associated with each vertex of this
+ ``GiftiSurface`` from the given ``dataSource``.
+
+ Currently, only the first ``DataArray`` contained in the
+ file is returned.
+
+ - ``*.func.gii``
+ - ``*.shape.gii``
+ - ``*.label.gii``
+ - ``*.time.gii``
"""
+ # TODO support 4D
# TODO make this more robust
norms = nib.load(dataSource)
return norms.darrays[0].data
@@ -87,7 +97,7 @@ EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI surface file']
"""
-def extractGiftiSurface(surfimg):
+def loadGiftiSurface(surfimg):
"""Extracts surface data from the given ``nibabel.gifti.GiftiImage``.
The image is expected to contain the following``<DataArray>`` elements:
@@ -140,3 +150,44 @@ def extractGiftiSurface(surfimg):
raise ValueError('no array witbh intent "triangle"found')
return vertices, indices
+
+
+def relatedFiles(fname):
+ """Given a GIFTI file, returns a list of other GIFTI files in the same
+ directory which appear to be related with the given one. Files which
+ share the same prefix are assumed to be related to the given file.
+
+ """
+
+ try:
+ # We want to return all files in the same
+ # directory which have the following name:
+
+ #
+ # [prefix].*.[type].gii
+ #
+ # where
+ # - prefix is the file prefix, and which
+ # may include periods.
+ #
+ # - we don't care about the middle
+ #
+ # - type is func, shape, label, or time
+
+ # We determine the unique prefix of the
+ # given file, and back-up to the most
+ # recent period. Then search for other
+ # files which have that same (non-unique)
+ # prefix.
+ prefix = fslpath.uniquePrefix(fname)
+ prefix = prefix[:prefix.rfind('.')]
+
+ funcs = glob.glob('{}*.func.gii' .format(prefix))
+ shapes = glob.glob('{}*.shape.gii'.format(prefix))
+ labels = glob.glob('{}*.label.gii'.format(prefix))
+ times = glob.glob('{}*.time.gii' .format(prefix))
+
+ return funcs + shapes + labels + times
+
+ except:
+ return []
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 7ee72abf3..86fd939c1 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -19,9 +19,11 @@ paths.
splitExt
getFileGroup
removeDuplicates
+ uniquePrefix
"""
+import glob
import os.path as op
@@ -404,3 +406,36 @@ def removeDuplicates(paths, allowedExts=None, fileGroups=None):
unique.append(groupFiles[0])
return unique
+
+
+def uniquePrefix(path):
+ """Return the longest prefix for the given file name which unambiguously
+ identifies it, relative to the other files in the same directory.
+
+ Raises a :exc:`ValueError` if a unique prefix could not be found (which
+ will never happen if the path is valid).
+ """
+
+ dirname, filename = op.split(path)
+
+ idx = 0
+ prefix = op.join(dirname, filename[0])
+ hits = glob.glob('{}*'.format(prefix))
+
+ while True:
+
+ # Found a unique prefix
+ if len(hits) == 1:
+ break
+
+ # Should never happen if path is valid
+ elif len(hits) == 0 or idx >= len(filename) - 1:
+ raise ValueError('No unique prefix for {}'.format(filename))
+
+ # Not unique - continue looping
+ else:
+ idx += 1
+ prefix = prefix + filename[idx]
+ hits = [h for h in hits if h.startswith(prefix)]
+
+ return prefix
--
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