From 218ad4c5df4108df1c56a60abade7d19af52f60b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Sat, 4 Jun 2016 17:10:54 +0100
Subject: [PATCH] Other fsl.data modules updated to new Image API where needed.
---
fsl/data/atlases.py | 6 +++---
fsl/data/featimage.py | 6 +++---
fsl/data/image.py | 7 ++++---
fsl/data/imagewrapper.py | 4 ++--
fsl/data/melodicanalysis.py | 4 +---
fsl/data/melodicimage.py | 4 +++-
fsl/data/tensorimage.py | 4 +++-
7 files changed, 19 insertions(+), 16 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index b4148551c..ecb5f0af5 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -296,7 +296,7 @@ class AtlasDescription(object):
imagefile = op.join(ATLAS_DIR, '.' + imagefile)
summaryimagefile = op.join(ATLAS_DIR, '.' + summaryimagefile)
- i = fslimage.Image(imagefile, loadData=False)
+ i = fslimage.Image(imagefile, loadData=False, calcRange=False)
self.images .append(imagefile)
self.summaryImages.append(summaryimagefile)
@@ -425,7 +425,7 @@ class LabelAtlas(Atlas):
voxelLoc[2] >= self.shape[2]:
return np.nan
- val = self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2]]
+ val = self[voxelLoc[0], voxelLoc[1], voxelLoc[2]]
if self.desc.atlasType == 'label':
return val
@@ -473,7 +473,7 @@ class ProbabilisticAtlas(Atlas):
voxelLoc[2] >= self.shape[2]:
return []
- return self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
+ return self[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 40cffe7e0..2f650c8b6 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -313,12 +313,12 @@ class FEATImage(fslimage.Image):
raise ValueError('Contrast is wrong length')
X = self.__design.getDesign(xyz)
- data = self.data[x, y, z, :]
+ data = self[x, y, z, :]
modelfit = np.zeros(len(data))
for i in range(numEVs):
- pe = self.getPE(i).data[x, y, z]
+ pe = self.getPE(i)[x, y, z]
modelfit += X[:, i] * pe * contrast[i]
return modelfit + data.mean()
@@ -332,7 +332,7 @@ class FEATImage(fslimage.Image):
"""
x, y, z = xyz
- residuals = self.getResiduals().data[x, y, z, :]
+ residuals = self.getResiduals()[x, y, z, :]
modelfit = self.fit(contrast, xyz, fullmodel)
return residuals + modelfit
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 8bdde463f..8847799e1 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -374,9 +374,10 @@ class Image(Nifti1, notifier.Notifier):
:meth:`loadData` method.
:arg calcRange: If ``True`` (the default), the image range is
- calculated immediately (vi a call to :meth:`calcRange`).
- Otherwise, the image range is incrementally updated as
- more data is read from memory or disk.
+ calculated immediately (vi a call to
+ :meth:`calcRange`). Otherwise, the image range is
+ incrementally updated as more data is read from memory
+ or disk.
"""
import nibabel as nib
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index a666b51cc..962a50898 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -194,8 +194,8 @@ class ImageWrapper(notifier.Notifier):
self.__range[1],
self.__sliceCoverage))
- dmin = np.nanmin(data)
- dmax = np.nanmax(data)
+ dmin = float(np.nanmin(data))
+ dmax = float(np.nanmax(data))
if oldmin is None: oldmin = dmin
if oldmax is None: oldmax = dmax
diff --git a/fsl/data/melodicanalysis.py b/fsl/data/melodicanalysis.py
index 29a75aeb1..9de847d43 100644
--- a/fsl/data/melodicanalysis.py
+++ b/fsl/data/melodicanalysis.py
@@ -33,8 +33,6 @@ import logging
import os.path as op
import numpy as np
-import props
-
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
import fsl.data.featanalysis as featanalysis
@@ -159,7 +157,7 @@ def getNumComponents(meldir):
contained in the given directrory.
"""
- icImg = fslimage.Image(getICFile(meldir), loadData=False)
+ icImg = fslimage.Image(getICFile(meldir), loadData=False, calcRange=False)
return icImg.shape[3]
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 9f5729a71..85f7f4611 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -79,7 +79,9 @@ class MelodicImage(fslimage.Image):
dataFile = self.getDataFile()
if dataFile is not None:
- dataImage = fslimage.Image(dataFile, loadData=False)
+ dataImage = fslimage.Image(dataFile,
+ loadData=False,
+ calcRange=False)
if dataImage.is4DImage():
self.tr = dataImage.pixdim[3]
diff --git a/fsl/data/tensorimage.py b/fsl/data/tensorimage.py
index 86ae221cb..2587cc189 100644
--- a/fsl/data/tensorimage.py
+++ b/fsl/data/tensorimage.py
@@ -125,7 +125,9 @@ class TensorImage(fslimage.Nifti1):
else:
paths = path
- fslimage.Nifti1.__init__(self, paths['l1'], loadData=False)
+ fslimage.Nifti1.__init__(self, paths['l1'],
+ loadData=False,
+ calcRange=False)
self.__v1 = fslimage.Image(paths['v1'])
self.__v2 = fslimage.Image(paths['v2'])
--
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