diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index ca35e5fdca3afa37523b061af09cf599d712292e..f89b9d827090790ca51a4e11e2b9f89ed78c4703 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python
#
-# fslimage.py - Object representing a 3D image.
+# fslimage.py - Classes representing a 3D image, and the display
+# properties of a 3D image.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -13,9 +14,17 @@ import matplotlib.colors as mplcolors
import fsl.props as props
import fsl.data.imagefile as imagefile
+
class Image(object):
+ """
+ Class which represents a 3D image. Interally, the image is loaded/stored
+ using nibabel.
+ """
def __init__(self, image):
+ """
+ Initialise an Image object with the given image data or file name.
+ """
# The image parameter may be the name of an image file
if isinstance(image, str):
@@ -43,15 +52,30 @@ class Image(object):
self.zlen = zlen
-
class ImageDisplay(props.HasProperties):
"""
+ A class which describes how an image should be displayed.
"""
+
+ def updateColourMap(self, newVal):
+ """
+ When a colour property changes, this method is called -
+ it reconfigures the colour map accordingly.
+ """
+
+ if self.rangeClip:
+ self.cmap.set_under(self.cmap(0.0), alpha=0.0)
+ self.cmap.set_over( self.cmap(1.0), alpha=0.0)
+ else:
+ self.cmap.set_under(self.cmap(0.0), alpha=1.0)
+ self.cmap.set_over( self.cmap(1.0), alpha=1.0)
+
alpha = props.Double(minval=0.0, maxval=1.0, default=1.0)
displayMin = props.Double()
displayMax = props.Double()
- rangeClip = props.Boolean(default=False)
+ rangeClip = props.Boolean(default=False,
+ preNotifyFunc=updateColourMap)
_view = props.VGroup(('displayMin', 'displayMax', 'alpha', 'rangeClip'))
_labels = {
@@ -63,6 +87,10 @@ class ImageDisplay(props.HasProperties):
def __init__(self, image):
+ """
+ Create an ImageDisplay for the specified image. The image
+ parameter should be an Image object (defined above).
+ """
self.image = image
@@ -73,18 +101,3 @@ class ImageDisplay(props.HasProperties):
self.dataMax = self.image.data.max()
self.displayMin = self.dataMin # use cal_min/cal_max instead?
self.displayMax = self.dataMax
-
- self.addListener(
- 'rangeClip',
- 'ImageRangeClip_{}'.format(id(self)),
- self.updateColourMap)
-
- def updateColourMap(self, *a):
-
- if self.rangeClip:
- self.cmap.set_under(self.cmap(0.0), alpha=0.0)
- self.cmap.set_over( self.cmap(1.0), alpha=0.0)
- else:
- self.cmap.set_under(self.cmap(0.0), alpha=1.0)
- self.cmap.set_over( self.cmap(1.0), alpha=1.0)
-
diff --git a/fsl/props/properties.py b/fsl/props/properties.py
index 2e94c20b2f5d8c3c1ea56f2ed17574da0a179bbf..b1296fc8cf51f70e96691f7cd808b022180965c4 100644
--- a/fsl/props/properties.py
+++ b/fsl/props/properties.py
@@ -128,6 +128,8 @@
import types
import logging
+from collections import OrderedDict
+
log = logging.getLogger(__name__)
@@ -149,7 +151,6 @@ class PropertyValue(object):
- value: Initial value.
- name: Variable name - if not provided, a default,
unique name is created.
-
"""
if name is None: name = '{}_{}'.format(prop.label, id(self))
@@ -157,7 +158,7 @@ class PropertyValue(object):
self.prop = prop
self.owner = owner
self.name = name
- self.changeListeners = {}
+ self.changeListeners = OrderedDict()
self._value = value
self._lastValue = value
self._lastValid = self.isValid()
@@ -219,6 +220,11 @@ class PropertyValue(object):
log.debug('Variable {} changed: {}'.format(self.name, newValue))
+ # Call the PropertyBase prenotify function first, if there is one
+ if self.prop.preNotifyFunc is not None:
+ log.debug('Calling preNotify function for {}'.format(self.name))
+ self.prop.preNotifyFunc(self.owner, newValue)
+
# Validate the new value and notify any registered listeners
self.validateAndNotify()
@@ -302,30 +308,40 @@ class PropertyBase(object):
"""
- def __init__(self, default=None, required=False, validateFunc=None):
+ def __init__(self,
+ default=None,
+ required=False,
+ validateFunc=None,
+ preNotifyFunc=None):
"""
Parameters:
- - default: Default/initial value.
+ - default: Default/initial value.
- - required: Boolean determining whether or not this
- property must have a value. May alternately
- be a function which accepts one parameter,
- the owning HasProperties instance, and
- returns True or False.
+ - required: Boolean determining whether or not this
+ property must have a value. May alternately
+ be a function which accepts one parameter,
+ the owning HasProperties instance, and
+ returns True or False.
- - validateFunc: Custom validation function. Must accept
- two parameters: a reference to the
- HasProperties instance, the owner of
- this property; and the new property
- value. Should return True if the property
- value is valid, False otherwise.
+ - validateFunc: Custom validation function. Must accept
+ two parameters: a reference to the
+ HasProperties instance, the owner of
+ this property; and the new property
+ value. Should return True if the property
+ value is valid, False otherwise.
+
+ - preNotifyFunc: Function to be called whenever the property
+ value(s) changes. This function is called
+ by the PropertyValue object(s) before any
+ listeners are notified.
"""
self.label = None
self.default = default
self.required = required
self.validateFunc = validateFunc
- self.changeListeners = {}
+ self.preNotifyFunc = preNotifyFunc
+ self.changeListeners = OrderedDict()
def addListener(self, instance, name, callback):
diff --git a/fsl/utils/slicecanvas.py b/fsl/utils/slicecanvas.py
index 952576df16f85169a82902871883464772d74863..b037baf30cff3a728888bace2b2c8876dd9d0a6e 100644
--- a/fsl/utils/slicecanvas.py
+++ b/fsl/utils/slicecanvas.py
@@ -197,7 +197,9 @@ class SliceCanvas(wxgl.GLCanvas):
parent - WX parent object
- image - A fsl.data.image.Image object, or a 3D numpy array.
+ image - A fsl.data.fslimage.Image object, or a
+ fsl.data.fslimage.ImageDisplay object, or a 3D numpy
+ array.
zax - Axis perpendicular to the plane to be displayed
(the 'depth' axis), default 0.
@@ -272,34 +274,34 @@ class SliceCanvas(wxgl.GLCanvas):
self.Bind(wx.EVT_PAINT, self.draw)
+ # Add a bunch of listeners to the image display
+ # object, so we can update the view when image
+ # display properties are changed.
def refreshNeeded(*a):
self.Refresh()
def colourUpdateNeeded(*a):
self.updateColourBuffer()
- self.Refresh()
+ self.Refresh()
+
+ lnrName = 'SliceCanvas_{{}}_{}'.format(id(self))
self.imageDisplay.addListener(
- 'alpha',
- 'SliceCanvasAlpha_{}'.format(id(self)),
- refreshNeeded)
+ 'alpha', lnrName.format('alpha'), refreshNeeded)
+
self.imageDisplay.addListener(
- 'displayMin',
- 'SliceCanvasDisplayMin_{}'.format(id(self)),
- colourUpdateNeeded)
+ 'displayMin', lnrName.format('displayMin'), colourUpdateNeeded)
+
self.imageDisplay.addListener(
- 'displayMax',
- 'SliceCanvasDisplayMax_{}'.format(id(self)),
- colourUpdateNeeded)
+ 'displayMax', lnrName.format('displayMax'), colourUpdateNeeded)
+
self.imageDisplay.addListener(
- 'rangeClip',
- 'SliceCanvasRangeClip_{}'.format(id(self)),
- colourUpdateNeeded)
+ 'rangeClip', lnrName.format('rangeClip'), colourUpdateNeeded)
def _initGLData(self):
"""
- Initialises the GL buffers which are copied to the GPU,
+ Initialises the GL buffers which are copied to the GPU,
and used to render the voxel data.
"""
@@ -319,7 +321,7 @@ class SliceCanvas(wxgl.GLCanvas):
shaders.compileShader(vertex_shader, gl.GL_VERTEX_SHADER),
shaders.compileShader(fragment_shader, gl.GL_FRAGMENT_SHADER))
- # Indexes of all vertex/fragment shader parameters
+ # Indices of all vertex/fragment shader parameters
self.inVertexPos = gl.glGetAttribLocation( self.shaders, 'inVertex')
self.voxelValuePos = gl.glGetAttribLocation( self.shaders, 'voxelValue')
self.inPositionPos = gl.glGetAttribLocation( self.shaders, 'inPosition')
@@ -391,16 +393,25 @@ class SliceCanvas(wxgl.GLCanvas):
iDisplay = self.imageDisplay
+ # Here we are creating a range of values to be passed
+ # to the matplotlib.colors.Colormap instance of the
+ # image display. We scale this range such that data
+ # values which lie outside the configured display range
+ # will map to values below 0.0 or above 1.0. It is
+ # assumed that the Colormap instance is configured to
+ # generate appropriate colours for these out-of-range
+ # values.
+
+ normalRange = np.linspace(0.0, 1.0, self.colourResolution)
+ normalStep = 1.0 / (self.colourResolution - 1)
+
normMin = (iDisplay.displayMin - iDisplay.dataMin) / \
(iDisplay.dataMax - iDisplay.dataMin)
normMax = (iDisplay.displayMax - iDisplay.dataMin) / \
(iDisplay.dataMax - iDisplay.dataMin)
- normalStep = 1.0 / (self.colourResolution - 1)
- newStep = normalStep / (normMax - normMin)
-
- normalRange = np.linspace(0.0, 1.0, self.colourResolution)
- newRange = (normalRange - normMin) * (newStep / normalStep)
+ newStep = normalStep / (normMax - normMin)
+ newRange = (normalRange - normMin) * (newStep / normalStep)
# Create [self.colourResolution] rgb values,
# spanning the entire range of the image