diff --git a/fsl/data/image.py b/fsl/data/image.py
index 81bbf2e84e27c1194682cfa007f01930a7cfbb0d..15326071ddd2c68ebcb6b7780b376a66a6ed8910 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -9,7 +9,6 @@
See the :mod:`fsl.data.imageio` module for image loading/saving
functionality.
-
"""
import logging
@@ -52,7 +51,7 @@ class Image(props.HasProperties):
for transforming real world coordinates into voxel
coordinates.
- :ivar imageFile: The name of the file that the image was loaded from.
+ :ivar dataSource: The name of the file that the image was loaded from.
:ivar tempFile: The name of the temporary file which was created (in
the event that the image was large and was gzipped -
@@ -105,9 +104,9 @@ class Image(props.HasProperties):
via the :meth:`loadData` method.
"""
- self.nibImage = None
- self.imageFile = None
- self.tempFile = None
+ self.nibImage = None
+ self.dataSource = None
+ self.tempFile = None
if header is not None:
header = header.copy()
@@ -117,16 +116,16 @@ class Image(props.HasProperties):
nibImage, filename = iio.loadImage(iio.addExt(image))
self.nibImage = nibImage
- self.imageFile = image
+ self.dataSource = image
# if the returned file name is not the same as
# the provided file name, that means that the
# image was opened from a temporary file
if filename != image:
- self.name = iio.removeExt(op.basename(self.imageFile))
+ self.name = iio.removeExt(op.basename(self.dataSource))
self.tempFile = nibImage.get_filename()
else:
- self.name = iio.removeExt(op.basename(self.imageFile))
+ self.name = iio.removeExt(op.basename(self.dataSource))
self.saved = True
@@ -255,7 +254,7 @@ class Image(props.HasProperties):
"""Return a string representation of this :class:`Image`."""
return '{}({}, {})'.format(self.__class__.__name__,
self.name,
- self.imageFile)
+ self.dataSource)
def __repr__(self):
diff --git a/fsl/data/imageio.py b/fsl/data/imageio.py
index 58d23169c7ae9032840a8cab9f7593842ed70e55..662272c469b84e1acd38fef6c80fafafec35d983 100644
--- a/fsl/data/imageio.py
+++ b/fsl/data/imageio.py
@@ -281,13 +281,13 @@ def saveImage(image, imageList=None, fromDir=None):
lastDir = getattr(saveImage, 'lastDir', None)
if lastDir is None:
- if image.imageFile is None: lastDir = os.getcwd()
- else: lastDir = op.dirname(image.imageFile)
+ if image.dataSource is None: lastDir = os.getcwd()
+ else: lastDir = op.dirname(image.dataSource)
# TODO make image.name safe (spaces to
# underscores, filter non-alphanumeric)
- if image.imageFile is None: filename = image.name
- else: filename = op.basename(image.imageFile)
+ if image.dataSource is None: filename = image.name
+ else: filename = op.basename(image.dataSource)
filename = removeExt(filename)
@@ -338,7 +338,7 @@ def saveImage(image, imageList=None, fromDir=None):
log.debug('Saving image ({}) to {}'.format(image, path))
nib.save(nibImage, path)
- image.imageFile = path
+ image.dataSource = path
except Exception as e:
diff --git a/fsl/data/model.py b/fsl/data/model.py
index 31327fa2445d961a6e3272c898aa1598a5e45580..86370c79afc0caebaac3adc189c597f5a7e5ed8c 100644
--- a/fsl/data/model.py
+++ b/fsl/data/model.py
@@ -5,8 +5,8 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-
-import numpy as np
+import os.path as op
+import numpy as np
def loadVTKPolydataFile(infile):
@@ -62,6 +62,12 @@ class PolygonModel(object):
if np.any(lengths != 3):
raise RuntimeError('All polygons in VTK file must be '
'triangles ({})'.format(infile))
+
+ self.name = op.basename(infile)
+ self.dataSource = infile
+ else:
+ self.name = 'Model'
+ self.dataSource = 'Model'
if indices is None:
indices = np.arange(data.shape[0], dtype=np.uint32)
diff --git a/fsl/fslview/controls/overlaylistpanel.py b/fsl/fslview/controls/overlaylistpanel.py
index 17e453a4b57c3709a458064513f4d36d4085b99b..c8e8c399fc5a63a53a50a4d6ab85237dc8948f35 100644
--- a/fsl/fslview/controls/overlaylistpanel.py
+++ b/fsl/fslview/controls/overlaylistpanel.py
@@ -54,7 +54,7 @@ class ListItemWidget(wx.Panel):
self.name,
self._saveStateChanged)
else:
- log.warn('No support for non-volumetric overlays yet')
+ log.warn('No save button support for non-volumetric overlays')
self.saveButton.Enable(False)
self.saveButton.Bind(wx.EVT_BUTTON, self._onSaveButton)
@@ -81,8 +81,12 @@ class ListItemWidget(wx.Panel):
def _saveStateChanged(self, *a):
- idx = self.listBox.IndexOf(self.overlay)
+ if not isinstance(self.overlay, fslimage.Image):
+ return
+
+ idx = self.listBox.IndexOf(self.overlay)
+
self.saveButton.Enable(not self.overlay.saved)
if self.overlay.saved:
@@ -192,8 +196,8 @@ class OverlayListPanel(fslpanel.FSLViewPanel):
def _overlayNameChanged(self, value, valid, overlay, propName):
- idx = self._displayCtx.getOverlayOrder( overlay)
- display = self._displayCtx.getDisplay(overlay)
+ idx = self._displayCtx.getOverlayOrder(overlay)
+ display = self._displayCtx.getDisplay( overlay)
name = display.name
if name is None:
@@ -218,12 +222,7 @@ class OverlayListPanel(fslpanel.FSLViewPanel):
name = display.name
if name is None: name = ''
- if isinstance(overlay, fslimage.Image):
- tooltip = overlay.imageFile
-
- else:
- log.warn('No support for non-volumetric overlays yet')
- tooltip = 'Non-volumetric overlay - I don\'t know what to do'
+ tooltip = overlay.dataSource
self._listBox.Append(name, overlay, tooltip)
diff --git a/fsl/fslview/overlay.py b/fsl/fslview/overlay.py
index 9f8d665a91ea241e1f506aa98c1d320c399625e0..407f058f24f88a028ffb3e80c59e8ce11be54578 100644
--- a/fsl/fslview/overlay.py
+++ b/fsl/fslview/overlay.py
@@ -4,7 +4,12 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module defines the :class:`OverlayList` class, which is a simple but
+fundamental class in FSLView - it is a container for all displayed overlays.
+Only one ``OverlayList`` ever exists, and it is shared throughout the entire
+application.
+"""
import logging
@@ -27,12 +32,23 @@ class OverlayList(props.HasProperties):
:attr:`overlays` property, allowing the :class:`OverlayList` to be used
as if it were a list itself.
+ There are no restrictions on the type of objects which may be contained
+ in the ``OverlayList``, but all objects must have a few attributes:
- An overlay object must have an attribute called ``name``.
+ - ``name`` ...
+
+ - ``dataSoruce`` ..
"""
- overlays = props.List()
+ def __validateOverlay(self, atts, overlay):
+ return (hasattr(overlay, 'name') and
+ hasattr(overlay, 'dataSource'))
+
+
+ overlays = props.List(
+ listType=props.Object(allowInvalid=False,
+ validateFunc=__validateOverlay))
"""A list of overlay objects to be displayed"""
diff --git a/fsl/fslview/views/canvaspanel.py b/fsl/fslview/views/canvaspanel.py
index 5f213a9fe00ee8b3c0c2383de237adf2362cc1a6..a42cbe481fd084cc2d3c7cb5da16766cc2fcd0eb 100644
--- a/fsl/fslview/views/canvaspanel.py
+++ b/fsl/fslview/views/canvaspanel.py
@@ -135,7 +135,7 @@ def _takeScreenShot(overlayList, displayCtx, canvas):
continue
display = displayCtx.getDisplay(overlay)
- fname = overlay.imageFile
+ fname = overlay.dataSource
# Skip invisible/unsaved/in-memory images
if not (display.enabled and overlay.saved):
diff --git a/fsl/tools/fslview_parseargs.py b/fsl/tools/fslview_parseargs.py
index 7be92e8231ff804a46b26c0051ea135dab495b70..fbcf7fbcf0e5b9884ef5cec14e2c19c8b52c741b 100644
--- a/fsl/tools/fslview_parseargs.py
+++ b/fsl/tools/fslview_parseargs.py
@@ -884,7 +884,9 @@ def applyOverlayArgs(args, overlayList, displayCtx, **kwargs):
# per-overlay display arguments
for i, overlay in enumerate(overlayList):
- display = displayCtx.getDisplay(overlay)
+ display = displayCtx.getDisplay(overlay)
+ display.name = overlay.name
+
_applyArgs(args.overlays[i], display)
# Retrieve the DisplayOpts instance