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Commit c4728e1d authored by Paul McCarthy's avatar Paul McCarthy
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Updated fslview_parseargs to align with DisplayOpts class hierarchy 

changes, and a couple of other bugfixes.
parent 32f4bab9
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fsl/fslview/displaycontext/display.py
+ 7
− 8
View file @ c4728e1d
......@@ -18,9 +18,8 @@ import logging
import props
import fsl.data.image as fslimage
import fsl.data.model as fslmodel
import fsl.data.strings as strings
import fsl.data.strings as strings
import fsl.utils.typedict as td
log = logging.getLogger(__name__)
......@@ -222,11 +221,11 @@ import maskopts
import modelopts
OVERLAY_TYPES = {
OVERLAY_TYPES = td.TypeDict({
fslimage.Image : ['volume', 'mask', 'rgbvector', 'linevector'],
fslmodel.PolygonModel : ['model']
}
'Image' : ['volume', 'mask', 'rgbvector', 'linevector'],
'PolygonModel' : ['model']
})
"""This dictionary provides a mapping between the overlay classes, and
the way in which they may be represented.
......@@ -244,5 +243,5 @@ DISPLAY_OPTS_MAP = {
}
"""This dictionary provides a mapping between each overlay type, and
the :class:`DisplayOpts` subclass which contains overlay type-specific
display options.
\display options.
"""
fsl/fslview/displaycontext/volumeopts.py
+ 3
− 14
View file @ c4728e1d
......@@ -14,7 +14,6 @@ import numpy as np
import props
import fsl.data.image as fslimage
import fsl.data.strings as strings
import fsl.utils.transform as transform
import fsl.fslview.colourmaps as fslcm
......@@ -76,7 +75,7 @@ class ImageOpts(fsldisplay.DisplayOpts):
self.__setupTransforms()
# is this a 4D volume?
if self.is4D():
if self.overlay.is4DImage():
self.setConstraint('volume', 'maxval', overlay.shape[3] - 1)
self.addListener('transform', self.name, self.__transformChanged)
......@@ -108,7 +107,7 @@ class ImageOpts(fsldisplay.DisplayOpts):
"""
return transform.axisBounds(
self.__overlay.shape[:3], self.getTransform('voxel', 'display'))
self.overlay.shape[:3], self.getTransform('voxel', 'display'))
def __setupTransforms(self):
......@@ -118,13 +117,7 @@ class ImageOpts(fsldisplay.DisplayOpts):
These matrices are accessible via the :meth:`getTransform` method.
"""
# TODO This is obviously volumetric specific
if not isinstance(self.__overlay, fslimage.Image):
log.warn('Non-volumetric types not supported yet')
return
image = self.__overlay
image = self.overlay
voxToIdMat = np.eye(4)
voxToPixdimMat = np.diag(list(image.pixdim[:3]) + [1.0])
......@@ -178,10 +171,6 @@ class ImageOpts(fsldisplay.DisplayOpts):
value of :attr:`transform`.
"""
# TODO non-volumetric types
if not isinstance(self.__overlay, fslimage.Image):
raise RuntimeError('Non-volumetric types not supported yet')
if xform is None:
xform = self.transform
......
fsl/tools/fslview_parseargs.py
+ 24
− 27
View file @ c4728e1d
......@@ -60,14 +60,7 @@ import fsl.utils.transform as transform
import fsl.fslview.colourmaps as colourmaps
colourmaps.initColourMaps()
import fsl.fslview.displaycontext.display as fsldisplay
import fsl.fslview.displaycontext.volumeopts as volumeopts
import fsl.fslview.displaycontext.vectoropts as vectoropts
import fsl.fslview.displaycontext.maskopts as maskopts
import fsl.fslview.displaycontext.sceneopts as sceneopts
import fsl.fslview.displaycontext.orthoopts as orthoopts
import fsl.fslview.displaycontext.lightboxopts as lightboxopts
import fsl.fslview.displaycontext as fsldisplay
log = logging.getLogger(__name__)
......@@ -113,14 +106,14 @@ OPTIONS = td.TypeDict({
# - so make sure transform is listed before
# interpolation!
'Display' : ['name',
'transform',
'overlayType',
'interpolation',
'resolution',
'volume',
'alpha',
'brightness',
'contrast'],
'ImageOpts' : ['transform',
'resolution',
'volume'],
'VolumeOpts' : ['displayRange',
'clippingRange',
'invert',
......@@ -147,6 +140,7 @@ GROUPNAMES = td.TypeDict({
'LightBoxOpts' : 'LightBox display options',
'Display' : 'Overlay display options',
'ImageOpts' : 'Image options',
'VolumeOpts' : 'Volume options',
'VectorOpts' : 'Vector options',
'MaskOpts' : 'Mask options',
......@@ -197,14 +191,15 @@ ARGUMENTS = td.TypeDict({
'Display.name' : ('n', 'name'),
'Display.interpolation' : ('in', 'interp'),
'Display.resolution' : ('r', 'resolution'),
'Display.transform' : ('tf', 'transform'),
'Display.overlayType' : ('ot', 'overlayType'),
'Display.volume' : ('vl', 'volume'),
'Display.alpha' : ('a', 'alpha'),
'Display.brightness' : ('b', 'brightness'),
'Display.contrast' : ('c', 'contrast'),
'ImageOpts.resolution' : ('r', 'resolution'),
'ImageOpts.transform' : ('tf', 'transform'),
'ImageOpts.volume' : ('vl', 'volume'),
'VolumeOpts.displayRange' : ('dr', 'displayRange'),
'VolumeOpts.clippingRange' : ('cr', 'clippingRange'),
'VolumeOpts.cmap' : ('cm', 'cmap'),
......@@ -271,14 +266,16 @@ HELP = td.TypeDict({
'Display.name' : 'Overlay name',
'Display.interpolation' : 'Interpolation',
'Display.resolution' : 'Resolution',
'Display.transform' : 'Transformation',
'Display.overlayType' : 'Overlay type',
'Display.volume' : 'Volume',
'Display.alpha' : 'Opacity',
'Display.brightness' : 'Brightness',
'Display.contrast' : 'Contrast',
'ImageOpts.resolution' : 'Resolution',
'ImageOpts.transform' : 'Transformation',
'ImageOpts.volume' : 'Volume',
'VolumeOpts.displayRange' : 'Display range',
'VolumeOpts.clippingRange' : 'Clipping range',
'VolumeOpts.cmap' : 'Colour map',
......@@ -411,7 +408,7 @@ def _configSceneParser(sceneParser):
"""Adds options to the given argument parser which allow
the user to specify colour bar properties.
"""
_configParser(sceneopts.SceneOpts, sceneParser)
_configParser(fsldisplay.SceneOpts, sceneParser)
def _configOrthoParser(orthoParser):
......@@ -419,7 +416,7 @@ def _configOrthoParser(orthoParser):
configure an orthographic display.
"""
OrthoOpts = orthoopts.OrthoOpts
OrthoOpts = fsldisplay.OrthoOpts
_configParser(OrthoOpts, orthoParser)
# Extra configuration options that are
......@@ -446,7 +443,7 @@ def _configLightBoxParser(lbParser):
"""Adds options to the given parser allowing the user to
configure a lightbox display.
"""
_configParser(lightboxopts.LightBoxOpts, lbParser)
_configParser(fsldisplay.LightBoxOpts, lbParser)
def _configOverlayParser(ovlParser):
......@@ -455,9 +452,9 @@ def _configOverlayParser(ovlParser):
"""
Display = fsldisplay.Display
VolumeOpts = volumeopts.VolumeOpts
VectorOpts = vectoropts.VectorOpts
MaskOpts = maskopts .MaskOpts
VolumeOpts = fsldisplay.VolumeOpts
VectorOpts = fsldisplay.VectorOpts
MaskOpts = fsldisplay.MaskOpts
dispDesc = 'Each display option will be applied to the '\
'overlay which is listed before that option.'
......@@ -617,7 +614,7 @@ def parseArgs(mainParser, argv, name, desc, toolOptsDesc='[options]'):
# the user to specify another image file
# by which the vector image colours are
# to be modulated
fileOpts.append(ARGUMENTS[vectoropts.VectorOpts, 'modulate'])
fileOpts.append(ARGUMENTS[fsldisplay.VectorOpts, 'modulate'])
# There is a possibility that the user
# may specify an overlay name which is the
......@@ -807,8 +804,8 @@ def generateSceneArgs(overlayList, displayCtx, sceneOpts):
args += ['--{}'.format(ARGUMENTS['Main.scene'][1])]
if isinstance(sceneOpts, orthoopts .OrthoOpts): args += ['ortho']
elif isinstance(sceneOpts, lightboxopts.LightBoxOpts): args += ['lightbox']
if isinstance(sceneOpts, fsldisplay.OrthoOpts): args += ['ortho']
elif isinstance(sceneOpts, fsldisplay.LightBoxOpts): args += ['lightbox']
else: raise ValueError('Unrecognised SceneOpts '
'type: {}'.format(type(sceneOpts).__name__))
......@@ -898,7 +895,7 @@ def applyOverlayArgs(args, overlayList, displayCtx, **kwargs):
# value. If the modulate file is not valid,
# I print a warning, and clear the modulate
# option.
if isinstance(opts, vectoropts.VectorOpts) and \
if isinstance(opts, fsldisplay.VectorOpts) and \
isinstance(overlay, fslimage.Image) and \
args.overlays[i].modulate is not None:
......
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