diff --git a/doc/fsl.data.featanalysis.rst b/doc/fsl.data.featanalysis.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9ff9fb16fc954a5c86d266cffcc3ed79f28591d3
--- /dev/null
+++ b/doc/fsl.data.featanalysis.rst
@@ -0,0 +1,9 @@
+:orphan:
+
+fsl.data.featanalysis module
+============================
+
+.. automodule:: fsl.data.featanalysis
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.data.featresults.rst b/doc/fsl.data.featresults.rst
deleted file mode 100644
index 2459ec5232ad423741a8757c825b3c323b5f1c88..0000000000000000000000000000000000000000
--- a/doc/fsl.data.featresults.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-:orphan:
-
-fsl.data.featresults module
-===========================
-
-.. automodule:: fsl.data.featresults
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/fsl/data/featresults.py b/fsl/data/featanalysis.py
similarity index 98%
rename from fsl/data/featresults.py
rename to fsl/data/featanalysis.py
index df2acbe5039799920f76829d1570359bcb665c8e..448164cd467268d3e11eb18f51f8c51c68456a89 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featanalysis.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
#
-# featresults.py - Utility functions for loading/querying the contents of
+# featanalysis.py - Utility functions for loading/querying the contents of
# a FEAT analysis directory.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
@@ -42,6 +42,7 @@ The following functions return the names of various files of interest:
"""
+import collections
import logging
import os.path as op
import numpy as np
@@ -238,7 +239,7 @@ def loadSettings(featdir):
:arg featdir: A FEAT directory.
"""
- settings = {}
+ settings = collections.OrderedDict()
designfsf = op.join(featdir, 'design.fsf')
log.debug('Loading FEAT settings from {}'.format(designfsf))
@@ -254,7 +255,7 @@ def loadSettings(featdir):
tkns = line.split(None, 2)
key = tkns[1].strip()
- val = tkns[2].strip().strip("'").strip('"')
+ val = tkns[2].strip(' \'"')
if key.startswith('fmri(') and key.endswith(')'):
key = key[5:-1]
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 7befd0d0636c19ba60f82b559e750845eef2e434..1f4218abca4669aafb5704692847aea623c786c4 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -14,14 +14,14 @@ import os.path as op
import numpy as np
from . import image as fslimage
-from . import featresults
+from . import featanalysis
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.
+ :mod:`.featanalysis` module.
An example of using the ``FEATImage`` class::
@@ -66,16 +66,16 @@ class FEATImage(fslimage.Image):
if op.isdir(path):
path = op.join(path, 'filtered_func_data')
- if not featresults.isFEATImage(path):
+ if not featanalysis.isFEATImage(path):
raise ValueError('{} does not appear to be data '
'from a FEAT analysis'.format(path))
featDir = op.dirname(path)
- settings = featresults.loadSettings( featDir)
+ settings = featanalysis.loadSettings( featDir)
- if featresults.hasStats(featDir):
- design = featresults.loadDesign( featDir)
- names, cons = featresults.loadContrasts(featDir)
+ if featanalysis.hasStats(featDir):
+ design = featanalysis.loadDesign( featDir)
+ names, cons = featanalysis.loadContrasts(featDir)
else:
design = np.zeros((0, 0))
names, cons = [], []
@@ -88,7 +88,7 @@ class FEATImage(fslimage.Image):
self.__contrastNames = names
self.__contrasts = cons
self.__settings = settings
- self.__evNames = featresults.getEVNames(settings)
+ self.__evNames = featanalysis.getEVNames(settings)
self.__residuals = None
self.__pes = [None] * self.numEVs()
@@ -117,7 +117,7 @@ class FEATImage(fslimage.Image):
which this FEAT analysis is a part, or ``None`` if this analysis
is not part of another analysis.
"""
- return featresults.getTopLevelAnalysisDir(self.__featDir)
+ return featanalysis.getTopLevelAnalysisDir(self.__featDir)
def hasStats(self):
@@ -166,7 +166,7 @@ class FEATImage(fslimage.Image):
def contrasts(self):
"""Returns a list containing the analysis contrast vectors.
- See :func:`.featresults.loadContrasts`
+ See :func:`.featanalysis.loadContrasts`
"""
return [list(c) for c in self.__contrasts]
@@ -175,26 +175,26 @@ class FEATImage(fslimage.Image):
def thresholds(self):
"""Returns the statistical thresholds used in the analysis.
- See :func:`.featresults.getThresholds`
+ See :func:`.featanalysis.getThresholds`
"""
- return featresults.getThresholds(self.__settings)
+ return featanalysis.getThresholds(self.__settings)
def clusterResults(self, contrast):
"""Returns the clusters found in the analysis.
- See :func:.featresults.loadClusterResults`
+ See :func:.featanalysis.loadClusterResults`
"""
- return featresults.loadClusterResults(self.__featDir,
- self.__settings,
- contrast)
+ return featanalysis.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)
+ pefile = featanalysis.getPEFile(self.__featDir, ev)
self.__pes[ev] = fslimage.Image(
pefile,
name='{}: PE{} ({})'.format(
@@ -209,7 +209,7 @@ class FEATImage(fslimage.Image):
"""Returns the residuals of the full model fit. """
if self.__residuals is None:
- resfile = featresults.getResidualFile(self.__featDir)
+ resfile = featanalysis.getResidualFile(self.__featDir)
self.__residuals = fslimage.Image(
resfile,
name='{}: residuals'.format(self.__analysisName))
@@ -221,7 +221,7 @@ class FEATImage(fslimage.Image):
"""Returns the COPE image for the given contrast (0-indexed). """
if self.__copes[con] is None:
- copefile = featresults.getPEFile(self.__featDir, con)
+ copefile = featanalysis.getPEFile(self.__featDir, con)
self.__copes[con] = fslimage.Image(
copefile,
name='{}: COPE{} ({})'.format(
@@ -237,7 +237,7 @@ class FEATImage(fslimage.Image):
"""
if self.__zstats[con] is None:
- zfile = featresults.getZStatFile(self.__featDir, con)
+ zfile = featanalysis.getZStatFile(self.__featDir, con)
self.__zstats[con] = fslimage.Image(
zfile,
@@ -254,7 +254,7 @@ class FEATImage(fslimage.Image):
"""
if self.__clustMasks[con] is None:
- mfile = featresults.getClusterMaskFile(self.__featDir, con)
+ mfile = featanalysis.getClusterMaskFile(self.__featDir, con)
self.__clustMasks[con] = fslimage.Image(
mfile,
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index cd819a0791d8371701a24862cfcc5a46486188ad..3338b063536265bd41c8965489dad8b4d6bf0956 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -39,9 +39,9 @@ import numpy as np
import props
-import fsl.utils.path as fslpath
-import fsl.data.image as fslimage
-import fsl.data.featresults as featresults
+import fsl.utils.path as fslpath
+import fsl.data.image as fslimage
+import fsl.data.featanalysis as featanalysis
log = logging.getLogger(__name__)
@@ -112,9 +112,9 @@ def getTopLevelAnalysisDir(path):
directories, the path to the highest-level (i.e. the shallowest in the
file system) directory is returned. Otherwise, ``None`` is returned.
- See :func:`.featresults.getTopLevelAnalysisDir`.
+ See :func:`.featanalysis.getTopLevelAnalysisDir`.
"""
- return featresults.getTopLevelAnalysisDir(path)
+ return featanalysis.getTopLevelAnalysisDir(path)
def getDataFile(meldir):