diff --git a/fsl/data/image.py b/fsl/data/image.py
index 5a7b68a083530c7c2185f2871efef85bbe97ece5..e1a839dc0b2039af959322074a02f464acea7739 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -90,7 +90,12 @@ class Image(props.HasProperties):
"""
- def __init__(self, image, xform=None, name=None, loadData=True):
+ def __init__(self,
+ image,
+ xform=None,
+ name=None,
+ header=None,
+ loadData=True):
"""Initialise an Image object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
@@ -102,6 +107,11 @@ class Image(props.HasProperties):
:arg name: A name for the image.
+ :arg header: If not ``None``, assumed to be a
+ :class:`nibabel.nifti1.Nifti1Header` to be used as the
+ image header. Not applied to images loaded from file,
+ or existing :mod:`nibabel` images.
+
:arg loadData: Defaults to ``True``. If ``False``, the image data is
not loaded - this is useful if you're only interested
in the header data, as the file will be loaded much
@@ -113,6 +123,9 @@ class Image(props.HasProperties):
self.imageFile = None
self.tempFile = None
+ if header is not None:
+ header = header.copy()
+
# The image parameter may be the name of an image file
if isinstance(image, basestring):
@@ -136,10 +149,14 @@ class Image(props.HasProperties):
# to 1mm^3 in real world space)
elif isinstance(image, np.ndarray):
- if xform is None: xform = np.identity(4)
+ if xform is None:
+ if header is None: xform = np.identity(4)
+ else: xform = header.get_best_affine()
if name is None: name = 'Numpy array'
- self.nibImage = nib.nifti1.Nifti1Image(image, xform)
+ self.nibImage = nib.nifti1.Nifti1Image(image,
+ xform,
+ header=header)
self.name = name
# otherwise, we assume that it is a nibabel image
diff --git a/fsl/fslview/actions/copyimage.py b/fsl/fslview/actions/copyimage.py
index d3e5345608736709b37c9225006cd74f48d13b72..89fd7c6e3385f93a4355187eb4f098f647073604 100644
--- a/fsl/fslview/actions/copyimage.py
+++ b/fsl/fslview/actions/copyimage.py
@@ -40,10 +40,10 @@ class CopyImageAction(actions.Action):
if image is None:
return
- data = np.copy(image.data)
- xform = image.voxToWorldMat
- name = '{}_copy'.format(image.name)
- copy = fslimage.Image(data, xform, name)
+ data = np.copy(image.data)
+ header = image.nibImage.get_header()
+ name = '{}_copy'.format(image.name)
+ copy = fslimage.Image(data, name=name, header=header)
# TODO copy display properties
diff --git a/fsl/fslview/controls/atlaspanel.py b/fsl/fslview/controls/atlaspanel.py
index 0dcaf6e72a6be2c6cd4d6c580e06bea72ac4e744..ae6c30fc62c6629ab403f628c104c499958f2010 100644
--- a/fsl/fslview/controls/atlaspanel.py
+++ b/fsl/fslview/controls/atlaspanel.py
@@ -119,10 +119,10 @@ class AtlasPanel(fslpanel.FSLViewPanel):
log.debug('{}/{} clicked'.format(atlasID, label.name))
if isinstance(atlas, atlases.ProbabilisticAtlas):
- pass
+ self.toggleOverlay(atlasID, labelIndex, False)
elif isinstance(atlas, atlases.LabelAtlas):
- self.toggleLabelOverlay(atlasID, labelIndex)
+ self.toggleOverlay(atlasID, labelIndex, True)
@@ -146,11 +146,10 @@ class AtlasPanel(fslpanel.FSLViewPanel):
pass
- def toggleProbabilisticOverlay(self, atlasID, labelIndex):
- pass
-
- def toggleLabelOverlay(self, atlasID, labelIndex):
+ def toggleOverlay(self, atlasID, labelIndex, label):
+ """
+ """
desc = self.atlasDescs[atlasID]
overlayName = '{}/{}'.format(atlasID, desc.labels[labelIndex].name)
@@ -166,26 +165,35 @@ class AtlasPanel(fslpanel.FSLViewPanel):
if atlas is None:
atlas = atlases.loadAtlas(self.atlasDescs[atlasID], True)
- if desc.atlasType == 'probabilistic': labelVal = labelIndex + 1
- elif desc.atlasType == 'label': labelVal = labelIndex
+ if label:
+ if desc.atlasType == 'probabilistic':
+ labelVal = labelIndex + 1
+ elif desc.atlasType == 'label':
+ labelVal = labelIndex
- mask = np.zeros(atlas.shape, dtype=np.uint8)
- mask[atlas.data == labelIndex] = labelVal
+ mask = np.zeros(atlas.shape, dtype=np.uint8)
+ mask[atlas.data == labelIndex] = labelVal
+ else:
+ mask = atlas.data[..., labelIndex]
overlay = fslimage.Image(
mask,
- atlas.voxToWorldMat,
+ header=atlas.nibImage.get_header(),
name=overlayName)
- overlay.imageType = 'mask'
+
+ if label:
+ overlay.imageType = 'mask'
log.debug('Adding overlay {}'.format(overlayName))
self._imageList.append(overlay)
display = self._displayCtx.getDisplayProperties(overlay)
- display.getDisplayOpts().colour = np.random.random(3)
-
+ if label:
+ display.getDisplayOpts().colour = np.random.random(3)
+ else:
+ display.getDisplayOpts().cmap = 'hot'
diff --git a/fsl/fslview/displaycontext/volumeopts.py b/fsl/fslview/displaycontext/volumeopts.py
index 4485112421449978edbe10dea0bf78a2d5e0b1cc..00125ed33eb249b9d00f086503e18b8d09a585d3 100644
--- a/fsl/fslview/displaycontext/volumeopts.py
+++ b/fsl/fslview/displaycontext/volumeopts.py
@@ -52,7 +52,7 @@ class VolumeOpts(fsldisplay.DisplayOpts):
"""Image values which map to the minimum and maximum colour map colours."""
- clipLow = props.Boolean(default=False)
+ clipLow = props.Boolean(default=True)
"""If ``True``, don't display voxel values which are lower than
the :attr:`displayRange`.
"""
diff --git a/fsl/fslview/editor/editor.py b/fsl/fslview/editor/editor.py
index 04d94daf85c9b64e732d9f8559c7b5ecf7bce885..356221338282c828d43980358a16b2967b787d80 100644
--- a/fsl/fslview/editor/editor.py
+++ b/fsl/fslview/editor/editor.py
@@ -260,10 +260,10 @@ class Editor(props.HasProperties):
image = self._imageList[imageIdx]
mask = np.array(self._selection.selection, dtype=np.uint8)
- xform = image.voxToWorldMat
- name = '{}_mask'.format(image.name)
+ header = image.nibImage.get_header()
+ name = '{}_mask'.format(image.name)
- roiImage = fslimage.Image(mask, xform, name)
+ roiImage = fslimage.Image(mask, name=name, header=header)
self._imageList.insert(imageIdx + 1, roiImage)
@@ -276,8 +276,8 @@ class Editor(props.HasProperties):
roi[self._selection.selection] = image.data[self._selection.selection]
- xform = image.voxToWorldMat
- name = '{}_roi'.format(image.name)
+ header = image.nibImage.get_header()
+ name = '{}_roi'.format(image.name)
- roiImage = fslimage.Image(roi, xform, name)
+ roiImage = fslimage.Image(roi, name=name, header=header)
self._imageList.insert(imageIdx + 1, roiImage)