diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index c62f427e6158146253b46b27b62cc43abc1c24d1..3f0e300616938ffaae9841817eefa77099201322 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -89,12 +89,6 @@ class FEATImage(fslimage.Image):
def clusterResults(self, contrast):
- # If thresholdType is not 3, stats
- # has not been run, or cluster
- # thresholding has not been performed
- if featresults.getThresholdType(self.__settings) != 3:
- return None
-
return featresults.loadClusterResults(self.__featDir,
self.__settings,
contrast)
diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index 0c47992f0d8daddee58c5b1b70bfc058130634ff..b26ec7be2a4ff9eec0954ac84f1d9e383139a1af 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -10,11 +10,15 @@ contents of a FEAT analysis directory.
"""
+import logging
import glob
import os.path as op
import numpy as np
+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.
@@ -57,6 +61,8 @@ def loadDesign(featdir):
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:
@@ -85,6 +91,8 @@ def loadContrasts(featdir):
numContrasts = 0
names = {}
designcon = op.join(featdir, 'design.con')
+
+ log.debug('Loading FEAT contrasts from {}'.format(designcon))
with open(designcon, 'rt') as f:
@@ -135,6 +143,8 @@ def loadSettings(featdir):
settings = {}
designfsf = op.join(featdir, 'design.fsf')
+ log.debug('Loading FEAT settings from {}'.format(designfsf))
+
with open(designfsf, 'rt') as f:
for line in f.readlines():
@@ -150,53 +160,23 @@ def loadSettings(featdir):
if key.startswith('fmri(') and key.endswith(')'):
key = key[5:-1]
-
+
settings[key] = val
return settings
-def getThresholdType(settings):
- """Returns the type of statistical thresholding used in the FEAT
- analysis described in the given settings dict (see the
- :func:`loadSettings` function).
-
- Returns a number describing the thresholding approach:
-
- -1 : Statistical analysis has not been performed
- 0 : No thresholding has been performed
- 1 : Uncorrected P-value thresholding
- 2 : Voxel-corrected thresholding
- 3 : Cluster-corrected thresholding
- """
-
- poststats = int(settings['poststats_yn'])
- threstype = int(settings['thresh'])
-
- if poststats != 1:
- return -1
-
- return threstype
-
-
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).
- If thresholding has not been performed, or cluster threhsolding was not
- used, ``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.
"""
- # poststats_yn != 1 means that
- # stats has not been performed
- #
- # thres=3 corresponds to
- # cluster thresholding
- if int(settings['poststats_yn']) != 1 or \
- int(settings['thresh']) != 3:
- return None
-
# This dict provides a mapping between
# Cluster object (see below) attribute
# names, and the corresponding column
@@ -212,9 +192,10 @@ def loadClusterResults(featdir, settings, contrast):
'Z-MAX X (vox)' : ('zmaxx', int),
'Z-MAX Y (vox)' : ('zmaxy', int),
'Z-MAX Z (vox)' : ('zmaxz', int),
- 'Z-COG X (vox)' : ('zcogx', int),
- 'Z-COG Y (vox)' : ('zcogy', int),
- 'Z-COG Z (vox)' : ('zcogz', int),
+ 'Z-COG X (vox)' : ('zcogx', float),
+ 'Z-COG Y (vox)' : ('zcogy', float),
+ 'Z-COG Z (vox)' : ('zcogz', float),
+ 'COPE-MAX' : ('copemax', float),
'COPE-MAX X (vox)' : ('copemaxx', int),
'COPE-MAX Y (vox)' : ('copemaxy', int),
'COPE-MAX Z (vox)' : ('copemaxz', int),
@@ -226,7 +207,7 @@ def loadClusterResults(featdir, settings, contrast):
# information about one cluster.
class Cluster(object):
def __init__(self, **kwargs):
- for name, val in kwargs:
+ for name, val in kwargs.items():
attrName, atype = colmap[name]
if val is not None:
@@ -236,6 +217,12 @@ def loadClusterResults(featdir, settings, contrast):
clusterFile = op.join(featdir, 'cluster_zstat{}.txt'.format(contrast + 1))
+ if not op.exists(clusterFile):
+ return None
+
+ log.debug('Loading cluster results for contrast {} from {}'.format(
+ contrast, clusterFile))
+
# An error will be raised if the
# cluster file does not exist (e.g.
# if the specified contrast index
@@ -260,6 +247,10 @@ def loadClusterResults(featdir, settings, contrast):
colNames = colNames.split('\t')
clusterLines = [cl .split('\t') for cl in clusterLines]
+ # No clusters
+ if len(clusterLines) == 0:
+ return None
+
# Turn each cluster line into a
# Cluster instance. An error will
# be raised if the columm names
@@ -309,6 +300,9 @@ def getCOPEFile(featdir, contrast):
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.
"""
numEVs = int(settings['evs_real'])
diff --git a/fsl/fslview/displaycontext/displaycontext.py b/fsl/fslview/displaycontext/displaycontext.py
index cf527f4735e66b2fa37225aa3d27dd7d41da0993..125c65802b0465ce52e97754fb0b3a55c537a67c 100644
--- a/fsl/fslview/displaycontext/displaycontext.py
+++ b/fsl/fslview/displaycontext/displaycontext.py
@@ -107,6 +107,9 @@ class DisplayContext(props.SyncableHasProperties):
if overlay is None:
raise ValueError('No overlay specified')
+ if overlay not in self.__overlayList:
+ raise ValueError('Overlay is not in list')
+
if isinstance(overlay, int):
overlay = self.__overlayList[overlay]
@@ -141,7 +144,10 @@ class DisplayContext(props.SyncableHasProperties):
"""
if overlay is None:
- raise ValueError('No overlay specified')
+ raise ValueError('No overlay specified')
+
+ if overlay not in self.__overlayList:
+ raise ValueError('Overlay is not in list')
try:
return self.getDisplay(overlay, overlayType).getDisplayOpts()