From b0271a872a9a65332a5f4bc20b4ed181d8a32398 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 1 Sep 2015 15:49:42 +0100
Subject: [PATCH] Documentation for all modules in the fsl.data package.
---
doc/fsl.data.rst | 16 --
fsl/data/__init__.py | 16 +-
fsl/data/atlases.py | 246 ++++++++++++++++++++-------
fsl/data/constants.py | 76 +++++++--
fsl/data/featimage.py | 103 +++++++++--
fsl/data/featresults.py | 143 +++++++++++++---
fsl/data/image.py | 190 ++++++++++++---------
fsl/data/model.py | 136 ++++++++++-----
fsl/data/strings.py | 23 ++-
fsl/fsleyes/views/timeseriespanel.py | 2 +-
fsl/utils/colourbarbitmap.py | 2 +-
11 files changed, 710 insertions(+), 243 deletions(-)
diff --git a/doc/fsl.data.rst b/doc/fsl.data.rst
index f768559d5..31516eabd 100644
--- a/doc/fsl.data.rst
+++ b/doc/fsl.data.rst
@@ -1,22 +1,6 @@
fsl.data package
================
-Submodules
-----------
-
-.. toctree::
-
- fsl.data.atlases
- fsl.data.constants
- fsl.data.featimage
- fsl.data.featresults
- fsl.data.image
- fsl.data.model
- fsl.data.strings
-
-Module contents
----------------
-
.. automodule:: fsl.data
:members:
:undoc-members:
diff --git a/fsl/data/__init__.py b/fsl/data/__init__.py
index 27a9696ea..7372461c5 100644
--- a/fsl/data/__init__.py
+++ b/fsl/data/__init__.py
@@ -4,4 +4,18 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""Data structures and models."""
+"""This module contains various data types and associated I/O routines,
+models, constants, and other data-like things used throughout ``fslpy``.
+
+
+ .. autosummary::
+ :nosignatures:
+
+ ~fsl.data.image.Image
+ ~fsl.data.featimage.FEATImage
+ ~fsl.data.model.Model
+ ~fsl.data.featresults
+ ~fsl.data.atlases
+ ~fsl.data.strings
+ ~fsl.data.constants
+"""
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index dd5165a7b..b747ae867 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -6,45 +6,82 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides access to the atlas images which are contained in
-``$FSLDIR/data/atlases/``.
-
-Instances of the :class:`Atlas` class is a
-
-MNI152
-
-
-<atlas>
- <header>
- <name></name> # Atlas name
- <type></type> # 'Probabilistic' or 'Label'
- <images>
- <imagefile>
- </imagefile> # If type is Probabilistic, path
- # to 4D image file, one volume per
- # label, Otherwise, if type is
- # Label, path to 3D label file
- # (identical to the summaryimagefile
- # below)
-
- <summaryimagefile> # Path to 3D summary file, with each
- </summaryimagefile> # region having value (index + 1)
-
- </images>
- ... # More images - generally both
- # 1mm and 2mm versions (in
- # MNI152 space) are available
- </header>
- <data>
- # index - index of corresponding volume in 4D image file
- # x |
- # y |- XYZ *voxel* coordinates into the first image of the <images> list
- # z |
- <label index="0" x="0" y="0" z="0">Name</label>
- ...
- </data>
-</atlas>
+``$FSLDIR/data/atlases/``. This directory contains XML files which describe
+all of the available atlases. An XML atlas description file is assumed to
+have a structure that looks like the following:
+
+.. code-block:: xml
+
+ <atlas>
+ <header>
+ <name></name> # Atlas name
+ <type></type> # 'Probabilistic' or 'Label'
+ <images>
+ <imagefile>
+ </imagefile> # If type is Probabilistic, path
+ # to 4D image file, one volume per
+ # label, Otherwise, if type is
+ # Label, path to 3D label file
+ # (identical to the summaryimagefile
+ # below)
+
+ <summaryimagefile> # Path to 3D summary file, with each
+ </summaryimagefile> # region having value (index + 1)
+
+ </images>
+ ... # More images - generally both
+ # 1mm and 2mm versions (in
+ # MNI152 space) are available
+ </header>
+ <data>
+
+ # index - For probabilistic atlases, index of corresponding volume in
+ # 4D image file. For label images, the value of voxels which
+ # are in the corresponding region.
+ #
+ # x |
+ # y |- XYZ *voxel* coordinates into the first image of the <images>
+ # | list
+ # z |
+ <label index="0" x="0" y="0" z="0">Name</label>
+ ...
+ </data>
+ </atlas>
+
+
+This module reads in all of these XML files, and builds a list of
+:class:`AtlasDescription` instances, each of which contains information about
+one atlas. Each atlas is assigned an identifier, which is simply the XML file
+name describing the atlas, sans-suffix. For exmaple, the atlas described by:
+
+ ``$FSLDIR/data/atlases/HarvardOxford-Cortical.xml``
+
+is given the identifier
+
+ ``HarvardOxford-Cortical``
+
+
+The following functions provide access to the available
+:class:`AtlasDescription` instances:
+
+.. autosummary::
+ :nosignatures:
+
+ listAtlases
+ getAtlasDescription
+
+
+The :func:`loadAtlas` function allows you to load an atlas image, which will
+be one of the following atlas-specific :class:`.Image` sub-classes:
+
+.. autosummary::
+ :nosignatures:
+
+ LabelAtlas
+ ProbabilisticAtlas
"""
+
import os
import xml.etree.ElementTree as et
import os.path as op
@@ -61,30 +98,14 @@ import fsl.utils.transform as transform
log = logging.getLogger(__name__)
-ATLAS_DIR = None
-
-def _setAtlasDir():
- global ATLAS_DIR
-
- if ATLAS_DIR is not None:
- return
-
- if os.environ.get('FSLDIR', None) is None:
- log.warn('$FSLDIR is not set - atlases are not available')
- else:
- ATLAS_DIR = op.join(os.environ['FSLDIR'], 'data', 'atlases')
-
-ATLAS_DESCRIPTIONS = collections.OrderedDict()
-
-
def listAtlases(refresh=False):
"""Returns a dictionary containing :class:`AtlasDescription` objects for
all available atlases.
:arg refresh: If ``True``, or if the atlas desriptions have not
previously been loaded, atlas descriptions are
- loaded from the atlas files. Otherwise, prefviously
+ loaded from the atlas files. Otherwise, previously
loaded descriptions are returned (see
:attr:`ATLAS_DESCRIPTIONS`).
"""
@@ -109,7 +130,6 @@ def listAtlases(refresh=False):
for i, desc in enumerate(atlasDescs):
desc.index = i
ATLAS_DESCRIPTIONS[desc.atlasID] = desc
-
return atlasDescs
@@ -161,12 +181,50 @@ def loadAtlas(atlasID, loadSummary=False):
class AtlasDescription(object):
- """Loads the data stored in an Atlas XML description, and makes said
- information accessible via instance attributes.
+ """An ``AtlasDescription`` instance parses and stores the information
+ stored in the XML file that describes one atlas.
+
+ The following attributes are available on an ``AtlasDescription`` instance:
+
+ ================= ======================================================
+ ``atlasID`` The atlas ID, as described above.
+ ``name`` Name of the atlas.
+ ``atlasType`` Atlas type - either *probabilistic* or *label*.
+ ``images`` A list of images available for this atlas - usually
+ :math:`1mm^3` and :math:`2mm^3` images are present.
+ ``summaryImages`` For probabilistic atlases, a list of *summary* images,
+ which are just 3D labelled variants of the atlas.
+ ``labels`` A list of ``AtlasLabel`` objects, describing each
+ region / label in the atlas.
+ ================= ======================================================
+
+ Each ``AtlasLabel`` instance in the ``labels`` list contains the
+ following attributes:
+
+ ========= ==============================================================
+ ``name`` Region name
+ ``index`` For probabilistic atlases, the volume index into the 4D atlas
+ image that corresponds to this region. For label atlases, the
+ value of voxels that are in this region. For summary images of
+ probabilistic atlases, add 1 to this value to get the
+ corresponding voxel values.
+ ``x`` X coordinate of the region in world space
+ ``y`` Y coordinate of the region in world space
+ ``z`` Z coordinate of the region in world space
+ ========= ==============================================================
+
+ .. note:: The ``x``, ``y`` and ``z`` label coordinates are pre-calculated
+ centre-of-gravity coordinates, as listed in the atlas xml file.
+ They are in the coordinate system defined by the atlas image
+ transformation matrix (typically MNI152 space).
"""
def __init__(self, filename):
+ """Create an ``AtlasDescription`` instance.
+
+ :arg filename: Name of the XML file describing the atlas.
+ """
log.debug('Loading atlas description from {}'.format(filename))
@@ -237,8 +295,21 @@ class AtlasDescription(object):
class Atlas(fslimage.Image):
+ """This is the base class for the :class:`LabelAtlas` and
+ :class:`ProbabilisticAtlas` classes. It contains some initialisation
+ logic common to both.
+ """
+
def __init__(self, atlasDesc, isLabel=False):
+ """Initialise an ``Atlas``.
+
+ :arg atlasDesc: The :class:`AtlasDescription` instance which describes
+ the atlas.
+
+ :arg isLabel: Pass in ``True`` for label atlases, ``False`` for
+ probabilistic atlases.
+ """
# Choose the atlas image
# with the highest resolution
@@ -262,17 +333,30 @@ class Atlas(fslimage.Image):
# their sform_codes are correctly set
self.nibImage.get_header().set_sform(
None, code=constants.NIFTI_XFORM_MNI_152)
-
self.desc = atlasDesc
class LabelAtlas(Atlas):
+ """A 3D atlas which contains integer labels for each region.
+
+ The ``LabelAtlas`` class provides the :meth:`label` method, which
+ makes looking up the label at a location easy.
+ """
def __init__(self, atlasDesc):
+ """Create a ``LabelAtlas`` instance.
+
+ :arg atlasDesc: The :class:`AtlasDescription` instance describing
+ the atlas.
+ """
Atlas.__init__(self, atlasDesc, isLabel=True)
+
def label(self, worldLoc):
+ """Looks up and returns the label of the region at the given world
+ location, or ``np.nan`` if the location is out of bounds.
+ """
voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
@@ -294,12 +378,27 @@ class LabelAtlas(Atlas):
class ProbabilisticAtlas(Atlas):
+ """A 4D atlas which contains one volume for each region.
+
+ The ``ProbabilisticAtlas`` provides the :meth`proportions` method,
+ which makes looking up region probabilities easy.
+ """
def __init__(self, atlasDesc):
+ """Create a ``ProbabilisticAtlas`` instance.
+
+ :arg atlasDesc: The :class:`AtlasDescription` instance describing
+ the atlas.
+ """
Atlas.__init__(self, atlasDesc, isLabel=False)
def proportions(self, worldLoc):
+ """:returns: a list of values, one per region, which represent
+ the probability of each region for the given world
+ location. Returns an empty list if the given
+ location is out of bounds.
+ """
voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
if voxelLoc[0] < 0 or \
@@ -311,3 +410,34 @@ class ProbabilisticAtlas(Atlas):
return []
return self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
+
+
+
+ATLAS_DIR = None
+"""This attribute stores the absolute path to ``$FSLDIR/data/atlases/``. It is
+``None`` if ``$FSLDIR`` is not set. See :func:`_setAtlasDir`.
+"""
+
+
+ATLAS_DESCRIPTIONS = collections.OrderedDict()
+"""This dictionary contains an ``{atlasID : AtlasDescription}`` mapping for
+all atlases contained in ``$FSLDIR/data/atlases/``.
+"""
+
+
+def _setAtlasDir():
+ """Called by the :func:`listAtlases`, :func:`getAtlasDescription` and
+ :func:`loadAtlas` functions.
+
+ Sets the :data:`ATLAS_DIR` attribute if it has not already been set, and
+ if the ``$FSLDIR`` environment variable is set.
+ """
+ global ATLAS_DIR
+
+ if ATLAS_DIR is not None:
+ return
+
+ if os.environ.get('FSLDIR', None) is None:
+ log.warn('$FSLDIR is not set - atlases are not available')
+ else:
+ ATLAS_DIR = op.join(os.environ['FSLDIR'], 'data', 'atlases')
diff --git a/fsl/data/constants.py b/fsl/data/constants.py
index d2fa0bfde..52a2f8200 100644
--- a/fsl/data/constants.py
+++ b/fsl/data/constants.py
@@ -4,22 +4,78 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module defines some constant values used throughout ``fsleyes``.
+
+
+The following constants relate to the orientation of an axis, in either
+voxel or world space:
+
+.. autosummary::
+ ORIENT_L2R
+ ORIENT_R2L
+ ORIENT_P2A
+ ORIENT_A2P
+ ORIENT_I2S
+ ORIENT_S2I
+ ORIENT_UNKNOWN
+
+
+These constants relate to the *space* in which a NIFTI1 image is assumed to be
+(i.e. the transformed coordinate space); they are defined in the NIFTI1
+specification:
+
+.. autosummary::
+ NIFTI_XFORM_UNKNOWN
+ NIFTI_XFORM_SCANNER_ANAT
+ NIFTI_XFORM_ALIGNED_ANAT
+ NIFTI_XFORM_TALAIRACH
+ NIFTI_XFORM_MNI_152
+"""
+
+
+ORIENT_L2R = 0
+"""The axis goes from left to right."""
+
+
+ORIENT_R2L = 1
+"""The axis goes from right to left."""
+
+
+ORIENT_P2A = 2
+"""The axis goes from posterior to anterior."""
+
+
+ORIENT_A2P = 3
+"""The axis goes from anterior to posterior."""
+
+
+ORIENT_I2S = 4
+"""The axis goes from inferior to superior."""
+
+
+ORIENT_S2I = 5
+"""The axis goes from superior to inferior."""
+
-# Constants which represent the orientation
-# of an axis, in either voxel or world space.
ORIENT_UNKNOWN = -1
-ORIENT_L2R = 0
-ORIENT_R2L = 1
-ORIENT_P2A = 2
-ORIENT_A2P = 3
-ORIENT_I2S = 4
-ORIENT_S2I = 5
+"""The axis has an unknown orientation."""
-# Constants from the NIFTI1 specification that define
-# the 'space' in which an image is assumed to be.
NIFTI_XFORM_UNKNOWN = 0
+"""Arbitrary coordinates."""
+
+
NIFTI_XFORM_SCANNER_ANAT = 1
+"""Scanner-based anatomical coordinates."""
+
+
NIFTI_XFORM_ALIGNED_ANAT = 2
+"""Coordinates aligned to another file's, or to anatomical "truth"."""
+
+
NIFTI_XFORM_TALAIRACH = 3
+"""Coordinates aligned to Talairach-Tournoux Atlas; (0,0,0)=AC, etc."""
+
+
NIFTI_XFORM_MNI_152 = 4
+"""MNI 152 normalized coordinates."""
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index c87121f21..59d409158 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -5,10 +5,10 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`FEATImage` class, a subclass of
-:class:`.Image` designed for the ``filtered_func_data`` file of a FEAT
-analysis.
+:class:`.Image` designed to encapsulate data from a FEAT analysis.
"""
+
import os.path as op
import numpy as np
@@ -18,11 +18,49 @@ import featresults
class FEATImage(fslimage.Image):
+ """An ``Image`` from a FEAT analysis.
+
+ The :class:`FEATImage` class makes use of the functions defined in the
+ :mod:`.featresults` module.
+
+
+ An example of using the ``FEATImage`` class::
+
+ import fsl.data.featimage as featimage
+
+ # You can pass in the name of the
+ # .feat/.gfeat directory, or any
+ # file contained within that directory.
+ img = featimage.FEATImage('myanalysis.feat/filtered_func_data.nii.gz')
+
+ # Query information about the FEAT analysis
+ print img.numEVs()
+ print img.contrastNames()
+ print img.numPoints()
+
+ # Get the model fit residuals
+ res4d = img.getResiduals()
+
+ # Get the full model fit for voxel
+ # [23, 30, 42] (in this example, we
+ # have 4 EVs - the first argument
+ # is a contrast vector).
+ img.fit([1, 1, 1, 1], [23, 30, 42], fullmodel=True)
+ """
+
def __init__(self, path, **kwargs):
- """
- The specified ``path`` may be a FEAT analysis directory, or the model
- data input file (e.g. ``analysis.feat/filtered_func_data.nii.gz``).
+ """Create a ``FEATImage`` instance.
+
+ :arg path: A FEAT analysis directory, or an image file contained
+ within such a directory.
+
+ :arg kwargs: Passed to the :meth:`.Image.__init__` constructor.
+
+ .. note:: If a FEAT directory is passed in for the ``path``
+ argument, this ``FEATImage`` instance will encapsulate
+ the model input data, typically called
+ ``<directory>.feat/filtered_func_data.nii.gz``.
"""
featDir = featresults.getFEATDir(path)
@@ -59,53 +97,82 @@ class FEATImage(fslimage.Image):
def getFEATDir(self):
+ """Returns the FEAT directory this image is contained in."""
return self.__featDir
def getAnalysisName(self):
+ """Returns the FEAT analysis name, which is the FEAT directory
+ name, minus the ``.feat`` / ``.gfeat`` suffix.
+ """
return self.__analysisName
def getDesign(self):
+ """Returns the analysis design matrix as a :mod:`numpy` array
+ with shape :math:`numPoints\\times numEVs`.
+ """
return np.array(self.__design)
def numPoints(self):
+ """Returns the number of points (e.g. time points, number of
+ subjects, etc) in the analysis.
+ """
return self.__design.shape[0]
def numEVs(self):
+ """Returns the number of explanatory variables (EVs) in the analysis.
+ """
return self.__design.shape[1]
def evNames(self):
+ """Returns a list containing the name of each EV in the analysis."""
return list(self.__evNames)
def numContrasts(self):
+ """Returns the number of contrasts in the analysis."""
return len(self.__contrasts)
def contrastNames(self):
+ """Returns a list containing the name of each contrast in the analysis.
+ """
return list(self.__contrastNames)
def contrasts(self):
+ """Returns a list containing the analysis contrast vectors.
+
+ See :func:`.featresults.loadContrasts`
+
+ """
return [list(c) for c in self.__contrasts]
def thresholds(self):
+ """Returns the statistical thresholds used in the analysis.
+
+ See :func:`.featresults.getThresholds`
+ """
return featresults.getThresholds(self.__settings)
def clusterResults(self, contrast):
+ """Returns the clusters found in the analysis.
+ See :func:.featresults.loadClusterResults`
+ """
return featresults.loadClusterResults(self.__featDir,
self.__settings,
contrast)
def getPE(self, ev):
+ """Returns the PE image for the given EV (0-indexed). """
if self.__pes[ev] is None:
pefile = featresults.getPEFile(self.__featDir, ev)
@@ -120,6 +187,7 @@ class FEATImage(fslimage.Image):
def getResiduals(self):
+ """Returns the residuals of the full model fit. """
if self.__residuals is None:
resfile = featresults.getResidualFile(self.__featDir)
@@ -131,6 +199,7 @@ class FEATImage(fslimage.Image):
def getCOPE(self, con):
+ """Returns the COPE image for the given contrast (0-indexed). """
if self.__copes[con] is None:
copefile = featresults.getPEFile(self.__featDir, con)
@@ -145,6 +214,8 @@ class FEATImage(fslimage.Image):
def getZStats(self, con):
+ """Returns the Z statistic image for the given contrast (0-indexed).
+ """
if self.__zstats[con] is None:
zfile = featresults.getZStatFile(self.__featDir, con)
@@ -160,6 +231,8 @@ class FEATImage(fslimage.Image):
def getClusterMask(self, con):
+ """Returns the cluster mask image for the given contrast (0-indexed).
+ """
if self.__clustMasks[con] is None:
mfile = featresults.getClusterMaskFile(self.__featDir, con)
@@ -175,12 +248,22 @@ class FEATImage(fslimage.Image):
def fit(self, contrast, xyz, fullmodel=False):
- """
+ """Calculates the model fit for the given contrast vector
+ at the given voxel.
Passing in a contrast of all 1s, and ``fullmodel=True`` will
get you the full model fit. Pass in ``fullmodel=False`` for
all other contrasts, otherwise the model fit values will not
be scaled correctly.
+
+ :arg contrast: The contrast vector (pass all 1s for a full model
+ fit).
+
+ :arg xyz: Coordinates of the voxel to calculate the model fit
+ for.
+
+ :arg fullmodel: Set to ``True`` for a full model fit, ``False``
+ otherwise.
"""
if not fullmodel:
@@ -205,11 +288,11 @@ class FEATImage(fslimage.Image):
return modelfit + data.mean()
- def reducedData(self, xyz, contrast, fullmodel=False):
- """
+ def partialFit(self, contrast, xyz, fullmodel=False):
+ """Calculates and returns the partial model fit for the specified
+ contrast vector at the specified voxel.
- Passing in a contrast of all 1s, and ``fullmodel=True`` will
- get you the model fit residuals.
+ See :meth:`fit` for details on the arguments.
"""
x, y, z = xyz
diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index 4d3ae675f..1a65c2ce9 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -6,7 +6,34 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides a few utility functions for loading/querying the
-contents of a FEAT analysis directory.
+contents of a FEAT analysis directory. They are primarily for use by the
+:class:`.FEATImage` class, but are available for other uses if needed. The
+following functions are provided:
+
+.. autosummary::
+ :nosignatures:
+
+ isFEATDir
+ getFEATDir
+ loadDesign
+ loadContrasts
+ loadSettings
+ getEVNames
+ getThresholds
+ loadClusterResults
+
+
+The following functions return the names of various files of interest:
+
+.. autosummary::
+ :nosignatures:
+
+ getDataFile
+ getResidualFile
+ getPEFile
+ getCOPEFile
+ getZStatFile
+ getClusterMaskFile
"""
@@ -25,8 +52,9 @@ log = logging.getLogger(__name__)
def isFEATDir(path):
"""Returns ``True`` if the given path looks like a FEAT directory, or
looks like the input data for a FEAT analysis, ``False`` otherwise.
- """
+ :arg path: A file / directory path.
+ """
dirname, filename = op.split(path)
@@ -50,6 +78,15 @@ def isFEATDir(path):
def getFEATDir(path):
+ """Given the path of any file/directory which is within a ``.feat`` or
+ ``.gfeat`` directory, strips all trailing components of the path name,
+ and returns the root FEAT directory.
+
+ Returns ``None`` if the given path is not contained within a ``.feat``
+ or ``.gfeat`` directory.
+
+ :arg path: A file / directory path.
+ """
sufs = ['.feat', '.gfeat']
idxs = [(path.rfind(s), s) for s in sufs]
@@ -68,10 +105,12 @@ def getFEATDir(path):
def loadDesign(featdir):
- """Loads the design matrix from a FEAT folder.
+ """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
@@ -96,11 +135,14 @@ def loadDesign(featdir):
def loadContrasts(featdir):
- """Loads the contrasts from a FEAT folder. Returns a tuple containing:
+ """Loads the contrasts from a FEAT directory. Returns a tuple containing:
- - A dictionary of ``{contrastnum : name}`` mappings
+ - A dictionary of ``{contrastnum : name}`` mappings (the ``contrastnum``
+ values are 1-indexed).
- A list of contrast vectors (each of which is a list itself).
+
+ :arg featdir: A FEAT directory.
"""
matrix = None
@@ -151,9 +193,12 @@ def loadContrasts(featdir):
def loadSettings(featdir):
- """Loads the analysis settings from a a FEAT folder.
+ """Loads the analysis settings from a FEAT directory.
+
+ Returns a dict containing the settings specified in the ``design.fsf``
+ file within the directory
- Returns a dict containing the settings specified in the given file.
+ :arg featdir: A FEAT directory.
"""
settings = {}
@@ -183,6 +228,18 @@ def loadSettings(featdir):
def getThresholds(settings):
+ """Given a FEAT settings dictionary, returns a dictionary of
+ ``{stat : threshold}`` mappings, containing the thresholds used
+ in the FEAT statistical analysis.
+
+ The following keys will be present. Threshold values will be ``None``
+ if the respective statistical thresholding was not carried out:
+
+ - ``p``: P-value thresholding
+ - ``z``: Z-statistic thresholding
+
+ :arg settings: A FEAT settings dictionary (see :func:`loadSettings`).
+ """
return {
'p' : settings.get('prob_thresh', None),
'z' : settings.get('z_thresh', None)
@@ -191,13 +248,43 @@ def getThresholds(settings):
def loadClusterResults(featdir, settings, contrast):
"""If cluster thresholding was used in the FEAT analysis, this function
- will load and return the cluster results for the specified contrast
- (which is assumed to be 0-indexed).
+ will load and return the cluster results for the specified (0-indexed)
+ contrast number.
- If there are no cluster results for the given contrast,
- ``None`` is returned.
+ If there are no cluster results for the given contrast, ``None`` is
+ returned.
An error will be raised if the cluster file cannot be parsed.
+
+ :arg featdir: A FEAT directory.
+ :arg settings: A FEAT settings dictionary.
+ :arg contrast: 0-indexed contrast number.
+
+ :returns: A list of ``Cluster`` instances, each of which contains
+ information about one cluster. A ``Cluster`` object has the
+ following attributes:
+
+ ============ =========================================
+ ``index`` Cluster index.
+ ``nvoxels`` Number of voxels in cluster.
+ ``p`` Cluster p value.
+ ``logp`` :math:`-log_{10}` of the cluster P value.
+ ``zmax`` Maximum Z value in cluster.
+ ``zmaxx`` X voxel coordinate of maximum Z value.
+ ``zmaxy`` Y voxel coordinate of maximum Z value.
+ ``zmaxz`` Z voxel coordinate of maximum Z value.
+ ``zcogx`` X voxel coordinate of cluster centre of
+ gravity.
+ ``zcogy`` Y voxel coordinate of cluster centre of
+ gravity.
+ ``zcogz`` Z voxel coordinate of cluster centre of
+ gravity.
+ ``copemax`` Maximum COPE value in cluster.
+ ``copemaxx`` X voxel coordinate of maximum COPE value.
+ ``copemaxy`` Y voxel coordinate of maximum COPE value.
+ ``copemaxz`` Z voxel coordinate of maximum COPE value.
+ ``copemean`` Mean COPE of all voxels in the cluster.
+ ============ =========================================
"""
# Cluster files are named like
@@ -209,7 +296,6 @@ def loadClusterResults(featdir, settings, contrast):
clusterFile = op.join(
featdir, 'cluster_zstat{}.txt'.format(contrast + 1))
-
if not op.exists(clusterFile):
# If the analysis was performed in standard
@@ -334,8 +420,10 @@ def loadClusterResults(featdir, settings, contrast):
def getDataFile(featdir):
- """Returns the name of the file in the FEAT results which contains
+ """Returns the name of the file in the FEAT directory which contains
the model input data (typically called ``filtered_func_data.nii.gz``).
+
+ :arg featdir: A FEAT directory.
"""
# Assuming here that there is only
@@ -346,6 +434,8 @@ def getDataFile(featdir):
def getResidualFile(featdir):
"""Returns the name of the file in the FEAT results which contains
the model fit residuals (typically called ``res4d.nii.gz``).
+
+ :arg featdir: A FEAT directory.
"""
# Assuming here that there is only
@@ -354,33 +444,40 @@ def getResidualFile(featdir):
def getPEFile(featdir, ev):
- """Returns the path of the PE file for the specified ``ev``, which is
- assumed to be 0-indexed.
- """
+ """Returns the path of the PE file for the specified EV.
+ :arg featdir: A FEAT directory.
+ :arg ev: The EV number (0-indexed).
+ """
pefile = op.join(featdir, 'stats', 'pe{}.*'.format(ev + 1))
return glob.glob(pefile)[0]
def getCOPEFile(featdir, contrast):
- """Returns the path of the COPE file for the specified ``contrast``, which
- is assumed to be 0-indexed.
+ """Returns the path of the COPE file for the specified contrast.
+
+ :arg featdir: A FEAT directory.
+ :arg contrast: The contrast number (0-indexed).
"""
copefile = op.join(featdir, 'stats', 'cope{}.*'.format(contrast + 1))
return glob.glob(copefile)[0]
def getZStatFile(featdir, contrast):
- """Returns the path of the Z-statistic file for the specified
- ``contrast``, which is assumed to be 0-indexed.
+ """Returns the path of the Z-statistic file for the specified contrast.
+
+ :arg featdir: A FEAT directory.
+ :arg contrast: The contrast number (0-indexed).
"""
zfile = op.join(featdir, 'stats', 'zstat{}.*'.format(contrast + 1))
return glob.glob(zfile)[0]
def getClusterMaskFile(featdir, contrast):
- """Returns the path of the cluster mask file for the specified
- ``contrast``, which is assumed to be 0-indexed.
+ """Returns the path of the cluster mask file for the specified contrast.
+
+ :arg featdir: A FEAT directory.
+ :arg contrast: The contrast number (0-indexed).
"""
mfile = op.join(featdir, 'cluster_mask_zstat{}.*'.format(contrast + 1))
return glob.glob(mfile)[0]
@@ -392,6 +489,8 @@ def getEVNames(settings):
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'])
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 87ae8d265..2547614fd 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -5,9 +5,32 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""Provides the :class:`Image` class, for representing 3D/4D NIFTI images.
+"""This module provides the :class:`Image` class, for representing 3D/4D NIFTI1
+images. The ``nibabel`` package is used for file I/O.
+
+.. note:: Currently, only NIFTI1 images are supported.
+
+
+It is very easy to load a NIFTI image::
+
+ from fsl.data.image import Image
+ myimg = Image('MNI152_T1_2mm.nii.gz')
+
+
+A number of other functions are also provided for working with image files and
+file names:
+
+.. autosummary::
+ :nosignatures:
+
+ isSupported
+ removeExt
+ addExt
+ loadImage
+ saveImage
"""
+
import logging
import tempfile
import os
@@ -28,30 +51,28 @@ class Image(props.HasProperties):
"""Class which represents a 3D/4D image. Internally, the image is
loaded/stored using :mod:`nibabel`.
- In addition to the class-level properties defined below, the following
- attributes are present on an :class:`Image` object:
-
- :ivar nibImage: The :mod:`nibabel` image object.
-
- :ivar shape: A list/tuple containing the number of voxels
- along each image dimension.
-
- :ivar pixdim: A list/tuple containing the size of one voxel
- along each image dimension.
-
- :ivar voxToWorldMat: A 4*4 array specifying the affine transformation
- for transforming voxel coordinates into real world
- coordinates.
-
- :ivar worldToVoxMat: A 4*4 array specifying the affine transformation
- for transforming real world coordinates into voxel
- coordinates.
-
- :ivar dataSource: The name of the file that the image was loaded from.
-
- :ivar tempFile: The name of the temporary file which was created (in
- the event that the image was large and was gzipped -
- see :func:`_loadImageFile`).
+
+ In addition to the :attr:`name`, :attr:`data`, and :attr:`saved`
+ properties, the following attributes are present on an ``Image`` instance:
+
+
+ ================= ====================================================
+ ``nibImage`` The :mod:`nibabel` image object.
+ ``dataSource`` The name of the file that the image was loaded from.
+ ``tempFile`` The name of the temporary file which was created (in
+ the event that the image was large and was gzipped -
+ see :func:`loadImage`).
+ ``shape`` A list/tuple containing the number of voxels along
+ each image dimension.
+ ``pixdim`` A list/tuple containing the size of one voxel along
+ each image dimension.
+ ``voxToWorldMat`` A 4*4 array specifying the affine transformation
+ for transforming voxel coordinates into real world
+ coordinates.
+ ``worldToVoxMat`` A 4*4 array specifying the affine transformation
+ for transforming real world coordinates into voxel
+ coordinates.
+ ================= ====================================================
"""
@@ -77,14 +98,15 @@ class Image(props.HasProperties):
name=None,
header=None,
loadData=True):
- """Initialise an Image object with the given image data or file name.
+ """Create an ``Image`` object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image
object.
- :arg xform: A ``4*4`` affine transformation matrix which transforms
- voxel coordinates into real world coordinates.
+ :arg xform: A :math:`4\\times 4` affine transformation matrix
+ which transforms voxel coordinates into real world
+ coordinates.
:arg name: A name for the image.
@@ -100,9 +122,13 @@ class Image(props.HasProperties):
via the :meth:`loadData` method.
"""
- self.nibImage = None
- self.dataSource = None
- self.tempFile = None
+ self.nibImage = None
+ self.dataSource = None
+ self.tempFile = None
+ self.shape = None
+ self.pixdim = None
+ self.voxToWorldMat = None
+ self.worldToVoxMat = None
if header is not None:
header = header.copy()
@@ -173,8 +199,28 @@ class Image(props.HasProperties):
def __del__(self):
+ """Prints a log message. """
log.memory('{}.del ({})'.format(type(self).__name__, id(self)))
+
+
+ def __hash__(self):
+ """Returns a number which uniquely idenfities this ``Image`` instance
+ (the result of ``id(self)``).
+ """
+ return id(self)
+
+
+ def __str__(self):
+ """Return a string representation of this ``Image`` instance."""
+ return '{}({}, {})'.format(self.__class__.__name__,
+ self.name,
+ self.dataSource)
+
+ def __repr__(self):
+ """See the :meth:`__str__` method."""
+ return self.__str__()
+
def loadData(self):
"""Loads the image data from the file. This method only needs to
@@ -253,28 +299,8 @@ class Image(props.HasProperties):
return saveImage(self)
- def __hash__(self):
- """Returns a number which uniquely idenfities this :class:`Image`
- object (the result of ``id(self)``).
- """
- return id(self)
-
-
- def __str__(self):
- """Return a string representation of this :class:`Image`."""
- return '{}({}, {})'.format(self.__class__.__name__,
- self.name,
- self.dataSource)
-
-
- def __repr__(self):
- """See the :meth:`__str__` method."""
- return self.__str__()
-
-
def is4DImage(self):
- """Returns ``True`` if this image is 4D, ``False`` otherwise.
- """
+ """Returns ``True`` if this image is 4D, ``False`` otherwise. """
return len(self.shape) > 3 and self.shape[3] > 1
@@ -283,7 +309,14 @@ class Image(props.HasProperties):
indicating the space to which the (transformed) image is oriented.
The ``code`` parameter may be either ``sform`` (the default) or
- ``qform`` in which case the corresponding matrix is used.
+ ``qform`` in which case the corresponding matrix is used.
+
+ :returns: one of the following codes:
+ - :data:`~.constants.NIFTI_XFORM_UNKNOWN`
+ - :data:`~.constants.NIFTI_XFORM_SCANNER_ANAT`
+ - :data:`~.constants.NIFTI_XFORM_ALIGNED_ANAT`
+ - :data:`~.constants.NIFTI_XFORM_TALAIRACH`
+ - :data:`~.constants.NIFTI_XFORM_MNI_152`
"""
if code is None: code = 'sform_code'
@@ -306,21 +339,22 @@ class Image(props.HasProperties):
This method returns one of the following values, indicating the
direction in which coordinates along the specified axis increase:
- - :attr:`~fsl.data.constants.ORIENT_L2R`: Left to right
- - :attr:`~fsl.data.constants.ORIENT_R2L`: Right to left
- - :attr:`~fsl.data.constants.ORIENT_A2P`: Anterior to posterior
- - :attr:`~fsl.data.constants.ORIENT_P2A`: Posterior to anterior
- - :attr:`~fsl.data.constants.ORIENT_I2S`: Inferior to superior
- - :attr:`~fsl.data.constants.ORIENT_S2I`: Superior to inferior
- - :attr:`~fsl.data.constants.ORIENT_UNKNOWN`: Orientation is unknown
+
+ - :attr:`~.constants.ORIENT_L2R`: Left to right
+ - :attr:`~.constants.ORIENT_R2L`: Right to left
+ - :attr:`~.constants.ORIENT_A2P`: Anterior to posterior
+ - :attr:`~.constants.ORIENT_P2A`: Posterior to anterior
+ - :attr:`~.constants.ORIENT_I2S`: Inferior to superior
+ - :attr:`~.constants.ORIENT_S2I`: Superior to inferior
+ - :attr:`~.constants.ORIENT_UNKNOWN`: Orientation is unknown
The returned value is dictated by the XForm code contained in the
- image file header (see the :meth:`getXFormCode` method). Basically,
- if the XForm code is 'unknown', this method will return -1 for all
- axes. Otherwise, it is assumed that the image is in RAS orientation
- (i.e. the X axis increases from left to right, the Y axis increases
- from posterior to anterior, and the Z axis increases from inferior
- to superior).
+ image file header (see the :meth:`getXFormCode` method). Basically, if
+ the XForm code is *unknown*, this method will return
+ ``ORIENT_UNKNOWN`` for all axes. Otherwise, it is assumed that the
+ image is in RAS orientation (i.e. the X axis increases from left to
+ right, the Y axis increases from posterior to anterior, and the Z axis
+ increases from inferior to superior).
"""
if self.getXFormCode(code) == constants.NIFTI_XFORM_UNKNOWN:
@@ -335,7 +369,10 @@ class Image(props.HasProperties):
def getVoxelOrientation(self, axis, code=None):
"""Returns a code representing the (estimated) orientation of the
- specified voxelwise axis.
+ specified data axis.
+
+ :arg code: May be either ``qform`` or ``sform``, specifying which
+ transformation to use.
See the :meth:`getWorldOrientation` method for a description
of the return value.
@@ -368,10 +405,11 @@ class Image(props.HasProperties):
# so i'm just providing '*.gz'for now
ALLOWED_EXTENSIONS = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.gz']
"""The file extensions which we understand. This list is used as the default
-if if the ``allowedExts`` parameter is not passed to any of the functions
+if the ``allowedExts`` parameter is not passed to any of the functions
below.
"""
+
EXTENSION_DESCRIPTIONS = ['Compressed NIFTI1 images',
'NIFTI1 images',
'ANALYZE75 images',
@@ -386,8 +424,7 @@ DEFAULT_EXTENSION = '.nii.gz'
def isSupported(filename, allowedExts=None):
- """
- Returns ``True`` if the given file has a supported extension, ``False``
+ """Returns ``True`` if the given file has a supported extension, ``False``
otherwise.
:arg filename: The file name to test.
@@ -402,8 +439,7 @@ def isSupported(filename, allowedExts=None):
def removeExt(filename, allowedExts=None):
- """
- Removes the extension from the given file name. Returns the filename
+ """Removes the extension from the given file name. Returns the filename
unmodified if it does not have a supported extension.
:arg filename: The file name to strip.
@@ -429,11 +465,7 @@ def removeExt(filename, allowedExts=None):
return filename[:-extLen]
-def addExt(
- prefix,
- mustExist=True,
- allowedExts=None,
- defaultExt=None):
+def addExt(prefix, mustExist=True, allowedExts=None, defaultExt=None):
"""Adds a file extension to the given file ``prefix``.
If ``mustExist`` is False, and the file does not already have a
@@ -571,9 +603,9 @@ def saveImage(image, fromDir=None):
the image.
- :param image: The :class:`.Image` instance to be saved.
+ :arg image: The :class:`.Image` instance to be saved.
- :param str fromDir: Directory in which the file dialog should start.
+ :arg fromDir: Directory in which the file dialog should start.
If ``None``, the most recently visited directory
(via this method) is used, or the directory from
the given image, or the current working directory.
diff --git a/fsl/data/model.py b/fsl/data/model.py
index 1598f73db..a336304ba 100644
--- a/fsl/data/model.py
+++ b/fsl/data/model.py
@@ -1,9 +1,20 @@
#!/usr/bin/env python
#
-# model.py -
+# model.py - The Model class, for VTK polygon data.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module providse the :class:`Model` class, which represents a 3D model.
+
+.. note:: I/O support is very limited - currently, the only supported file
+ type is the VTK legacy file format, containing the ``POLYDATA``
+ dataset. the :class:`Model` class assumes that every polygon defined
+ in an input file is a triangle (i.e. refers to three vertices).
+
+ See http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf
+ for an overview of the VTK legacy file format.
+"""
+
import logging
@@ -14,53 +25,22 @@ import numpy as np
log = logging.getLogger(__name__)
-ALLOWED_EXTENSIONS = ['.vtk']
-EXTENSION_DESCRIPTIONS = ['VTK polygon model file']
-
-
-def loadVTKPolydataFile(infile):
-
- lines = None
-
- with open(infile, 'rt') as f:
- lines = f.readlines()
-
- lines = [l.strip() for l in lines]
-
- if lines[3] != 'DATASET POLYDATA':
- raise ValueError('')
-
- nVertices = int(lines[4].split()[1])
- nPolygons = int(lines[5 + nVertices].split()[1])
- nIndices = int(lines[5 + nVertices].split()[2]) - nPolygons
-
- vertices = np.zeros((nVertices, 3), dtype=np.float32)
- polygonLengths = np.zeros( nPolygons, dtype=np.uint32)
- indices = np.zeros( nIndices, dtype=np.uint32)
-
- for i in range(nVertices):
- vertLine = lines[i + 5]
- vertices[i, :] = map(float, vertLine.split())
-
- indexOffset = 0
- for i in range(nPolygons):
-
- polyLine = lines[6 + nVertices + i].split()
- polygonLengths[i] = int(polyLine[0])
-
- start = indexOffset
- end = indexOffset + polygonLengths[i]
- indices[start:end] = map(int, polyLine[1:])
-
- indexOffset += polygonLengths[i]
+class Model(object):
+ """The ``Model`` class represents a 3D model. A model is defined by a
+ collection of vertices and indices. The indices index into the list of
+ vertices, and define a set of triangles which make the model.
+ """
- return vertices, polygonLengths, indices
+ def __init__(self, data, indices=None):
+ """Create a ``Model`` instance.
-class Model(object):
+ :arg data: Can either be a file name, or a :math:`N\\times 3`
+ ``numpy`` array containing vertex data. If ``data`` is
+ a file name, it is passed to the
+ :func:`loadVTKPolydataFile` function.
- def __init__(self, data, indices=None):
- """
+ :arg indices: A list of indices into the vertex data.
"""
if isinstance(data, basestring):
@@ -90,17 +70,85 @@ class Model(object):
def __del__(self):
+ """Prints a log message."""
log.memory('{}.del ({})'.format(type(self).__name__, id(self)))
def __repr__(self):
+ """Rewturns a string representation of this ``Model`` instance. """
return '{}({}, {})'.format(type(self).__name__,
self.name,
self.dataSource)
def __str__(self):
+ """Rewturns a string representation of this ``Model`` instance. """
return self.__repr__()
def getBounds(self):
+ """Returns a tuple of values which define a minimal bounding box that
+ will contain all vertices in this ``Model`` instance. The bounding
+ box is arranged like so:
+
+ ``((xlow, ylow, zlow), (xhigh, yhigh, zhigh))``
+ """
return (self.__loBounds, self.__hiBounds)
+
+
+ALLOWED_EXTENSIONS = ['.vtk']
+"""A list of file extensions which could contain :class:`Model` data. """
+
+
+EXTENSION_DESCRIPTIONS = ['VTK polygon model file']
+"""A description for each of the extensions in :data:`ALLOWED_EXTENSIONS`."""
+
+
+def loadVTKPolydataFile(infile):
+ """Loads a vtk legacy file containing a ``POLYDATA`` data set.
+
+ :arg infile: Name of a file to load from.
+
+ :returns: a tuple containing three values:
+
+ - A :math:`N\\times 3` ``numpy`` array containing :math:`N`
+ vertices.
+ - A 1D ``numpy`` array containing the lengths of each polygon.
+ - A 1D ``numpy`` array containing the vertex indices for all
+ polygons.
+ """
+
+ lines = None
+
+ with open(infile, 'rt') as f:
+ lines = f.readlines()
+
+ lines = [l.strip() for l in lines]
+
+ if lines[3] != 'DATASET POLYDATA':
+ raise ValueError('Only the POLYDATA data type is supported')
+
+ nVertices = int(lines[4].split()[1])
+ nPolygons = int(lines[5 + nVertices].split()[1])
+ nIndices = int(lines[5 + nVertices].split()[2]) - nPolygons
+
+ vertices = np.zeros((nVertices, 3), dtype=np.float32)
+ polygonLengths = np.zeros( nPolygons, dtype=np.uint32)
+ indices = np.zeros( nIndices, dtype=np.uint32)
+
+ for i in range(nVertices):
+ vertLine = lines[i + 5]
+ vertices[i, :] = map(float, vertLine.split())
+
+ indexOffset = 0
+ for i in range(nPolygons):
+
+ polyLine = lines[6 + nVertices + i].split()
+ polygonLengths[i] = int(polyLine[0])
+
+ start = indexOffset
+ end = indexOffset + polygonLengths[i]
+ indices[start:end] = map(int, polyLine[1:])
+
+ indexOffset += polygonLengths[i]
+
+ return vertices, polygonLengths, indices
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 127a89b4d..df9fd6a79 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -4,10 +4,31 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module contains a collection of strings used throughout ``fslpy`` for
+display purposes. Most of the strings are used by FSLeyes.
+
+
+The strings are stored in :class:`.TypeDict` dictionaries, roughly organised
+into the following categories:
+
+
+ - :data:`messages`: Messages to be displayed to the user.
+ - :data:`titles`: Titles of windows, panels, and dialogs.
+ - :data:`actions`: Names of actions tied to menu options, buttons, etc.
+ - :data:`labels`: Labels for miscellaneous things.
+ - :data:`properties`: Display names for ``props.HasProperties`` properties.
+ - :data:`choices`: Display names for ``props.HasProperties`` choice
+ properties.
+ - :data:`anatomy`: Anatomical and orientation labels.
+ - :data:`nifti`: Labels for NIFTI header fields.
+ - :data:`feat`: FEAT specific names and labels.
+"""
+
from fsl.utils.typedict import TypeDict
import fsl.data.constants as constants
+
messages = TypeDict({
'FSLDirDialog.FSLDirNotSet' : 'The $FSLDIR environment variable '
@@ -101,7 +122,6 @@ messages = TypeDict({
})
-
titles = TypeDict({
'FSLDirDialog' : '$FSLDIR is not set',
@@ -202,6 +222,7 @@ actions = TypeDict({
'OrthoEditProfile.createROIFromSelection' : 'ROI',
})
+
labels = TypeDict({
'FSLDirDialog.locate' : 'Locate $FSLDIR',
diff --git a/fsl/fsleyes/views/timeseriespanel.py b/fsl/fsleyes/views/timeseriespanel.py
index f8e3d9072..63f058e52 100644
--- a/fsl/fsleyes/views/timeseriespanel.py
+++ b/fsl/fsleyes/views/timeseriespanel.py
@@ -343,7 +343,7 @@ class FEATReducedTimeSeries(TimeSeries):
def getData(self):
- data = self.overlay.reducedData(self.coords, self.contrast, False)
+ data = self.overlay.partialFit(self.contrast, self.coords, False)
return TimeSeries.getData(self, ydata=data)
diff --git a/fsl/utils/colourbarbitmap.py b/fsl/utils/colourbarbitmap.py
index 25aeed4c3..3199b4eef 100644
--- a/fsl/utils/colourbarbitmap.py
+++ b/fsl/utils/colourbarbitmap.py
@@ -50,7 +50,7 @@ def colourBarBitmap(cmap,
:arg label: Text label to show next to the colour bar.
- :arg orientation: Either ``vertical`` or `horizontal``.
+ :arg orientation: Either ``vertical`` or ``horizontal``.
:arg labelside: If ``orientation`` is ``vertical`` ``labelSide`` may
be either ``left`` or ``right``. Otherwise, if
--
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