diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py index b4148551cc69893c1fb58359ab6e7a29ef1ec337..ecb5f0af560888b6773c204a0110f5add78538b2 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 40cffe7e05d2f3126c69ae0e19df830ba0953c57..2f650c8b6206f09a258a1cd35a4ea6dbff434bdb 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 8bdde463f2e789e17f44b09ccbb719c57dcc9a9b..8847799e1dfaf8503e0efe057d2255a99a05e97e 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 a666b51ccd517591ca29e30cb6b97ef2dbd20a27..962a50898329c739418c247934f886b38216cc54 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 29a75aeb1aac14790ada6887e2bf9256491ddab4..9de847d439741b64a980bf34355dcca1693bdbfe 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 9f5729a71d497fb80a676331eb4c210818e6dafb..85f7f46116fcdb223be59136ce9ee6753f58cdfd 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 86ae221cb496c91a0fb8ec36c14f97a76578e321..2587cc18929e49aff413721166a37f28b5845e77 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'])