Skip to content
Snippets Groups Projects
Commit 3f736041 authored by Paul McCarthy's avatar Paul McCarthy
Browse files

FEATFSFDesign is used by featanalysis functions, and FEATImage class.

parent 87a5537f
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
fsl/data/featanalysis.py
+ 17
− 82
View file @ 3f736041
......@@ -22,7 +22,6 @@ following functions are provided:
loadDesign
loadContrasts
loadSettings
getEVNames
getThresholds
loadClusterResults
......@@ -47,10 +46,12 @@ import logging
import os.path as op
import numpy as np
import fsl.data.image as fslimage
import fsl.utils.path as fslpath
import fsl.utils.transform as transform
from . import image as fslimage
from . import featdesign
log = logging.getLogger(__name__)
......@@ -138,36 +139,6 @@ def getTopLevelAnalysisDir(path):
return fslpath.shallowest(path, ['.ica', '.gica', '.feat', '.gfeat'])
def loadDesign(featdir):
"""Loads the design matrix from a FEAT directory.
Returns a ``numpy`` array containing the design matrix data, where the
first dimension corresponds to the data points, and the second to the EVs.
:arg featdir: A FEAT directory.
"""
matrix = None
designmat = op.join(featdir, 'design.mat')
log.debug('Loading FEAT design matrix from {}'.format(designmat))
with open(designmat, 'rt') as f:
while True:
line = f.readline()
if line.strip() == '/Matrix':
break
matrix = np.loadtxt(f, ndmin=2)
if matrix is None or matrix.size == 0:
raise RuntimeError('{} does not appear to be a '
'valid design.mat file'.format(designmat))
return matrix
def loadContrasts(featdir):
"""Loads the contrasts from a FEAT directory. Returns a tuple containing:
......@@ -265,6 +236,20 @@ def loadSettings(featdir):
return settings
def loadDesign(featdir, settings):
"""Loads the design matrix from a FEAT directory.
:arg featdir: A FEAT directory.
:arg settings: Dictionary containing FEAT settings (see
:func:`loadSettings`).
:returns: a :class:`.FEATFSFDesign` instance which represents the
design matrix.
"""
return featdesign.FEATFSFDesign(featdir, settings)
def getThresholds(settings):
"""Given a FEAT settings dictionary, returns a dictionary of
``{stat : threshold}`` mappings, containing the thresholds used
......@@ -543,53 +528,3 @@ def getClusterMaskFile(featdir, contrast):
"""
mfile = op.join(featdir, 'cluster_mask_zstat{}'.format(contrast + 1))
return fslimage.addExt(mfile, mustExist=True)
def getEVNames(settings):
"""Returns the names of every EV in the FEAT analysis which has the given
``settings`` (see the :func:`loadSettings` function).
An error of some sort will be raised if the EV names cannot be determined
from the FEAT settings.
:arg settings: A FEAT settings dictionary (see :func:`loadSettings`).
"""
numEVs = int(settings['evs_real'])
titleKeys = [s for s in settings.keys() if s.startswith('evtitle')]
derivKeys = [s for s in settings.keys() if s.startswith('deriv_yn')]
def key(k):
return int(''.join([c for c in k if c.isdigit()]))
titleKeys = sorted(titleKeys, key=key)
derivKeys = sorted(derivKeys, key=key)
evnames = []
for titleKey, derivKey in zip(titleKeys, derivKeys):
# Figure out the ev number from
# the design.fsf key - skip over
# 'evtitle' (an offset of 7)
evnum = int(titleKey[7:])
# Sanity check - the evnum
# for the deriv_yn key matches
# that for the evtitle key
if evnum != int(derivKey[8:]):
raise RuntimeError('design.fsf seem to be corrupt')
title = settings[titleKey]
deriv = settings[derivKey]
if deriv == '0':
evnames.append(title)
else:
evnames.append(title)
evnames.append('{} - {}'.format(title, 'temporal derivative'))
if len(evnames) != numEVs:
raise RuntimeError('The number of EVs in design.fsf does not '
'match the number of EVs in design.mat')
return evnames
fsl/data/featdesign.py
+ 68
− 9
View file @ 3f736041
......@@ -64,6 +64,18 @@ following types of *confound* EVs:
- *Confound* EVs. These are any other EVs added by the user.
Module contents
---------------
In addition to the :class:`FEATFSFDesign` class, this module contains a few
other functions and classes that may be useful to advanced users.
The :func:`loadDesignMat` function loads the ``design.mat`` file from a
FEAT directory, and returns it as a numpy array.
The following functions, defined in this module, will analyse a FEAT analysis
to determine the contents of its design matrix (these functions are called by
the :meth:`FEATFSFDesign.__init__` method, but may be called directly):
......@@ -115,7 +127,7 @@ class FEATFSFDesign(object):
with FSL 5.0.9 and older.
"""
def __init__(self, featDir, settings, designMatrix):
def __init__(self, featDir, settings):
"""Create a ``FEATFSFDesign``.
:arg featDir: Path to the FEAT directory.
......@@ -123,14 +135,13 @@ class FEATFSFDesign(object):
:arg settings: A dictionary containing the FEAT analysis
settings from its ``design.fsf`` file (see
:func:`.featanalysis.loadSettings`).
:arg designMatrix: The FEAT design matrix (a numpy array - see
:func:`.featanalysis.loadDesign`).
"""
# Get some information about the analysis
version = float(settings['version'])
level = int( settings['level'])
# Get the design matrix, and some
# information about the analysis
designMatrix = loadDesignMat(featDir)
version = float(settings['version'])
level = int( settings['level'])
# Print a warning if we're
# using an old version of FEAT
......@@ -165,13 +176,31 @@ class FEATFSFDesign(object):
# see the VoxelwisEV class.
if ev.filename is not None: ev.image = fslimage.Image(ev.filename)
else: ev.image = None
def getEVs(self):
"""Returns a list containing the :class:`EV` instances that represent
each column of this ``FEATFSFDesign``.
"""
return list(self.__evs)
def getDesign(self, x, y, z):
"""Returns the design matrix for the specified voxel. """
def getDesign(self, voxel=None):
"""Returns the design matrix for the specified voxel.
:arg voxel: A tuple containing the ``(x, y, z)`` voxel coordinates
of interest. If ``None`` (the default), the design
matrix is returned, with any voxelwise EV columns
containing the mean voxelwise EV data.
"""
design = np.array(self.__design)
if voxel is None:
return design
x, y, z = voxel
for ev in self.__evs:
if not isinstance(ev, (VoxelwiseEV, VoxelwiseConfoundEV)):
......@@ -581,3 +610,33 @@ def getHigherLevelEVs(featDir, settings, designMat):
evs.append(VoxelwiseEV(len(evs), origIdx, title, filename))
return evs
def loadDesignMat(featdir):
"""Loads the design matrix from a FEAT directory.
Returns a ``numpy`` array containing the design matrix data, where the
first dimension corresponds to the data points, and the second to the EVs.
:arg featdir: A FEAT directory.
"""
matrix = None
designmat = op.join(featdir, 'design.mat')
log.debug('Loading FEAT design matrix from {}'.format(designmat))
with open(designmat, 'rt') as f:
while True:
line = f.readline()
if line.strip() == '/Matrix':
break
matrix = np.loadtxt(f, ndmin=2)
if matrix is None or matrix.size == 0:
raise FSFError('{} does not appear to be a '
'valid design.mat file'.format(designmat))
return matrix
fsl/data/featimage.py
+ 29
− 12
View file @ 3f736041
......@@ -29,8 +29,8 @@ class FEATImage(fslimage.Image):
import fsl.data.featimage as featimage
# You can pass in the name of the
# .feat/.gfeat directory, or any
# file contained within that directory.
# .feat directory, or any file
# contained within that directory.
img = featimage.FEATImage('myanalysis.feat/filtered_func_data.nii.gz')
# Query information about the FEAT analysis
......@@ -74,10 +74,10 @@ class FEATImage(fslimage.Image):
settings = featanalysis.loadSettings( featDir)
if featanalysis.hasStats(featDir):
design = featanalysis.loadDesign( featDir)
design = featanalysis.loadDesign( featDir, settings)
names, cons = featanalysis.loadContrasts(featDir)
else:
design = np.zeros((0, 0))
design = None
names, cons = [], []
fslimage.Image.__init__(self, path, **kwargs)
......@@ -88,7 +88,6 @@ class FEATImage(fslimage.Image):
self.__contrastNames = names
self.__contrasts = cons
self.__settings = settings
self.__evNames = featanalysis.getEVNames(settings)
self.__residuals = None
self.__pes = [None] * self.numEVs()
......@@ -124,32 +123,47 @@ class FEATImage(fslimage.Image):
"""Returns ``True`` if the analysis for this ``FEATImage`` contains
a statistical analysis.
"""
return self.__design.size > 0
return self.__design is not None
def getDesign(self):
def getDesign(self, voxel=None):
"""Returns the analysis design matrix as a :mod:`numpy` array
with shape :math:`numPoints\\times numEVs`.
See :meth:`.FEATFSFDesign.getDesign`.
"""
return np.array(self.__design)
if self.__design is None:
return None
return self.__design.getDesign(voxel)
def numPoints(self):
"""Returns the number of points (e.g. time points, number of
subjects, etc) in the analysis.
"""
return self.__design.shape[0]
if self.__design is None:
return None
return self.__design.getDesign().shape[0]
def numEVs(self):
"""Returns the number of explanatory variables (EVs) in the analysis.
"""
return self.__design.shape[1]
if self.__design is None:
return None
return len(self.__design.getEVs())
def evNames(self):
"""Returns a list containing the name of each EV in the analysis."""
return list(self.__evNames)
if self.__design is None:
return None
return [ev.title for ev in self.__design.getEVs()]
def numContrasts(self):
......@@ -285,6 +299,9 @@ class FEATImage(fslimage.Image):
otherwise.
"""
if self.__design is None:
raise RuntimeError('No design')
if not fullmodel:
contrast = np.array(contrast)
contrast = contrast / np.sqrt((contrast ** 2).sum())
......@@ -295,7 +312,7 @@ class FEATImage(fslimage.Image):
if len(contrast) != numEVs:
raise ValueError('Contrast is wrong length')
X = self.__design
X = self.__design.getDesign(xyz)
data = self.data[x, y, z, :]
modelfit = np.zeros(len(data))
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment