diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index 217903edac89ae7df300aa8b1757c48005ea1f8e..9c24bc971330a52a7bf80b86cb5520b7f4e4dee7 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -6,6 +6,8 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+import os.path as op
+
import numpy as np
import nibabel as nib
import matplotlib.cm as mplcm
@@ -39,7 +41,7 @@ class Image(object):
# otherwise, we assume that it is a nibabel image
self.nibImage = image
self.data = image.get_data()
- self.name = image.get_filename()
+ self.name = op.basename(image.get_filename())
xdim,ydim,zdim = self.nibImage.get_shape()
xlen,ylen,zlen = self.nibImage.get_header().get_zooms()
@@ -52,6 +54,10 @@ class Image(object):
self.ylen = ylen
self.zlen = zlen
+ # ImageDisplay instance used to describe
+ # how this image is to be displayed
+ self.display = ImageDisplay(self)
+
# This attribute may be used to point to an OpenGL
# buffer which is to be shared between multiple users
# (e.g. two SliceCanvas instances which are displaying
@@ -61,7 +67,9 @@ class Image(object):
class ImageDisplay(props.HasProperties):
"""
- A class which describes how an image should be displayed.
+ A class which describes how an image should be displayed. There should
+ be no need to manually instantiate ImageDisplay objects - one is created
+ for each Image object, and is accessed via the Image.display attribute.
"""
def updateColourMap(self, newVal):
@@ -81,7 +89,7 @@ class ImageDisplay(props.HasProperties):
cmap.set_over( cmap(1.0), alpha=1.0)
# The display properties of an image
- enabled = props.Boolean()
+ enabled = props.Boolean(default=True)
alpha = props.Double(minval=0.0, maxval=1.0, default=1.0)
displayMin = props.Double()
displayMax = props.Double()
@@ -125,13 +133,51 @@ class ImageDisplay(props.HasProperties):
class ImageList(object):
"""
Class representing a collection of images to be displayed together.
+ Provides basic list-like functionality, and a listener interface
+ allowing callback functions to be notified when the image collection
+ changes (e.g. an image is added or removed).
"""
- def __init__(self, images=None, displays=None):
- if images is None: images = []
- if displays is None: displays = []
+ def __init__(self, images=None):
+ """
+ """
+
+ if images is None: images = []
+
+ self._images = images
+ self._listeners = []
+
+
+ def __len__ (self): return self._images.__len__()
+ def __getitem__ (self, key): return self._images.__getitem__(key)
+ def __iter__ (self): return self._images.__iter__()
+ def __contains__(self, image): return self._images.__contains__(image)
+
+
+ def append(self, image):
+ self._images.append(image)
+ self.notify()
+
+
+ def pop(self, index=-1):
+ self._images.pop(index)
+ self.notify()
+
+
+ def insert(self, index, image):
+ self._images.insert(index, image)
+ self.notify()
+
+
+ def extend(self, images):
+ self._images.extend(images)
+ self.notify()
+
- self.images = images
- self.displays = displays
+ def addListener (self, listener): self._listeners.append(listener)
+ def removeListener(self, listener): self._listeners.remove(listener)
+ def notify (self):
+ for listener in self._listeners:
+ listener(self)
diff --git a/fsl/props/widgets.py b/fsl/props/widgets.py
index 349bd768489a4b14fec8f584ccce7a8e5cb76b9b..a37ccd7f09288e7aea68627ccbdf00890878ceb0 100644
--- a/fsl/props/widgets.py
+++ b/fsl/props/widgets.py
@@ -315,6 +315,7 @@ def _Number(parent, hasProps, propObj, propVal):
params['min'] = minval
params['max'] = maxval
params['initial'] = value
+ params['value'] = '{}'.format(value)
# The minval and maxval attributes have not both
# been set, so we create a spinbox instead of a slider.
diff --git a/fsl/utils/imageview.py b/fsl/utils/imageview.py
index 5e75097c264dfc8bad2661d138ecdabb44912e9c..4e5ccd459461bee6e5aacdcaa3c58a74262a2bef 100644
--- a/fsl/utils/imageview.py
+++ b/fsl/utils/imageview.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
#
# imgshow.py - A wx/OpenGL widget for displaying and interacting with a
-# collection of 3D image. Displays three canvases, each of which shows
+# collection of 3D images. Displays three canvases, each of which shows
# a slice of the images along each dimension.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
@@ -9,14 +9,15 @@
import sys
-# import logging
-# logging.basicConfig(
-# format='%(levelname)8s '\
-# '%(filename)20s '\
-# '%(lineno)4d: '\
-# '%(funcName)s - '\
-# '%(message)s',
-# level=logging.DEBUG)
+if False:
+ import logging
+ logging.basicConfig(
+ format='%(levelname)8s '\
+ '%(filename)20s '\
+ '%(lineno)4d: '\
+ '%(funcName)s - '\
+ '%(message)s',
+ level=logging.DEBUG)
import wx
import wx.lib.newevent as wxevent
@@ -32,15 +33,22 @@ class ImageView(wx.Panel):
def __init__(self, parent, imageList, *args, **kwargs):
"""
Creates three SliceCanvas objects, each displaying a
- different axis of the given 3D numpy image.
+ different axis of the given image list.
"""
+
+ if isinstance(imageList, fslimage.Image):
+ imageList = fslimage.ImageList(imageList)
+
+ if not isinstance(imageList, fslimage.ImageList):
+ raise TypeError(
+ 'imageList must be a fsl.data.fslimage.ImageList instance')
self.imageList = imageList
wx.Panel.__init__(self, parent, *args, **kwargs)
self.SetMinSize((300,100))
- self.shape = imageList.images[0].data.shape
+ self.shape = imageList[0].data.shape
self.canvasPanel = wx.Panel(self)
@@ -51,12 +59,12 @@ class ImageView(wx.Panel):
self.zcanvas = slicecanvas.SliceCanvas(
self.canvasPanel, imageList, zax=2, context=self.xcanvas.context)
-
self.controlPanel = wx.Notebook(self)
- for i in range(len(imageList.images)):
+
+ for image in imageList:
- controlPanel = props.buildGUI(self.controlPanel, self.imageList.displays[i])
- self.controlPanel.AddPage(controlPanel, '{}'.format(i))
+ displayProps = props.buildGUI(self.controlPanel, image.display)
+ self.controlPanel.AddPage(displayProps, image.name)
self.mainSizer = wx.BoxSizer(wx.VERTICAL)
self.canvasSizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -178,8 +186,7 @@ class ImageFrame(wx.Frame):
def __init__(self, parent, imageList, title=None):
wx.Frame.__init__(self, parent, title=title)
- self.imageList = imageList
- self.panel = ImageView(self, imageList)
+ self.panel = ImageView(self, imageList)
self.Layout()
@@ -191,8 +198,7 @@ if __name__ == '__main__':
app = wx.App()
images = map(fslimage.Image, sys.argv[1:])
- displays = map(fslimage.ImageDisplay, images)
- imageList = fslimage.ImageList(images, displays)
+ imageList = fslimage.ImageList(images)
frame = ImageFrame(
None,
diff --git a/fsl/utils/slicecanvas.py b/fsl/utils/slicecanvas.py
index 30de77b4ccd625c3b51272b4ea2699e7e5a99c71..5216b48f032910a2fea92c3a2f43e65c5eef6f80 100644
--- a/fsl/utils/slicecanvas.py
+++ b/fsl/utils/slicecanvas.py
@@ -211,9 +211,20 @@ class SliceCanvas(wxgl.GLCanvas):
wxgl.GLCanvas.__init__(self, parent, **kwargs)
+ # Use the provided shared GL
+ # context, or create a new one
if context is None: self.context = wxgl.GLContext(self)
else: self.context = context
+ # If a single image has been provided,
+ # make it into a list of length 1
+ if isinstance(imageList, fslimage.Image):
+ imageList = fslimage.ImageList(imageList)
+
+ if not isinstance(imageList, fslimage.ImageList):
+ raise TypeError(
+ 'imageList must be a fsl.data.fslimage.ImageList instance')
+
# TODO Currently, the displayed x/horizontal and
# y/vertical axes are defined by their order in
# the image. Allow the caller to specify which
@@ -227,7 +238,7 @@ class SliceCanvas(wxgl.GLCanvas):
self.zax = zax
# Currently all images must be of the same dimensions
- ref = self.imageList.images[0]
+ ref = self.imageList[0]
self.xdim = ref.data.shape[self.xax]
self.ydim = ref.data.shape[self.yax]
@@ -248,55 +259,19 @@ class SliceCanvas(wxgl.GLCanvas):
self._colourResolution = 256
- # This flag is set by the _initGLData method when it
+ # These fields are set by the _initGLData method when it
# has finished initialising the OpenGL data buffers
- self.glReady = False
+ self.glReady = False
+ self.glImageData = None
self.Bind(wx.EVT_PAINT, self.draw)
- for i in range(len(self.imageList.images)):
- self._configDisplayListeners(i)
-
-
- def _configDisplayListeners(self, idx):
- """
- """
-
- image = self.imageList.images [idx]
- display = self.imageList.displays[idx]
-
- # Add a bunch of listeners to the image display
- # object for each image, so we can update the
- # view when image display properties are changed.
- def refreshNeeded(*a):
- self.Refresh()
-
- def colourUpdateNeeded(*a):
- self.updateColourBuffer(idx)
- self.Refresh()
-
- lnrName = 'SliceCanvas_{{}}_{}'.format(id(self))
-
- display.addListener(
- 'alpha', lnrName.format('alpha'), refreshNeeded)
-
- display.addListener(
- 'displayMin', lnrName.format('displayMin'), colourUpdateNeeded)
-
- display.addListener(
- 'displayMax', lnrName.format('displayMax'), colourUpdateNeeded)
-
- display.addListener(
- 'rangeClip', lnrName.format('rangeClip'), colourUpdateNeeded)
-
- display.addListener(
- 'cmap', lnrName.format('cmap'), colourUpdateNeeded)
-
def _initGLData(self):
"""
Initialises the GL buffers which are copied to the GPU,
- and used to render the voxel data.
+ and used to render the voxel data. This method is only
+ called once, on the first draw.
"""
# A bit hacky. We can only set the GL context (and create
@@ -322,54 +297,65 @@ class SliceCanvas(wxgl.GLCanvas):
self.alphaPos = gl.glGetUniformLocation(self.shaders, 'alpha')
self.colourMapPos = gl.glGetUniformLocation(self.shaders, 'colourMap')
- self.imageData = []
+ self.glImageData = []
- for idx,image in enumerate(self.imageList.images):
+ for idx in range(len(self.imageList)):
+ self.glImageData.append(self._initGLImageData(idx))
+ self._configDisplayListeners(idx)
+ self.updateColourBuffer(idx)
- # Data stored in the geometry buffer. Defines
- # the geometry of a single voxel, rendered as
- # a triangle strip.
- geomData = np.array([0, 0,
- 1, 0,
- 0, 1,
- 1, 1], dtype=np.uint8)
+ self.glReady = True
- # Data stored in the position buffer. Defines
- # the location of every voxel in a single slice.
- positionData = np.zeros((self.xdim*self.ydim, 2), dtype=np.uint16)
- yidxs,xidxs = np.meshgrid(np.arange(self.ydim),
- np.arange(self.xdim),
- indexing='ij')
- positionData[:,0] = xidxs.ravel()
- positionData[:,1] = yidxs.ravel()
- geomBuffer = vbo.VBO(geomData, gl.GL_STATIC_DRAW)
- positionBuffer = vbo.VBO(positionData, gl.GL_STATIC_DRAW)
+ def _initGLImageData(self, idx):
+ """
+ """
- # The image buffer, containing the image data itself
- imageBuffer = self._initImageBuffer(image)
+ image = self.imageList[idx]
+
+ # Data stored in the geometry buffer. Defines
+ # the geometry of a single voxel, rendered as
+ # a triangle strip.
+ geomData = np.array([0, 0,
+ 1, 0,
+ 0, 1,
+ 1, 1], dtype=np.uint8)
- # The colour buffer, containing a map of
- # colours (stored on the GPU as a 1D texture)
- colourBuffer = gl.glGenTextures(1)
+ # Data stored in the position buffer. Defines
+ # the location of every voxel in a single slice.
+ positionData = np.zeros((self.xdim*self.ydim, 2), dtype=np.uint16)
+ yidxs,xidxs = np.meshgrid(np.arange(self.ydim),
+ np.arange(self.xdim),
+ indexing='ij')
+ positionData[:,0] = xidxs.ravel()
+ positionData[:,1] = yidxs.ravel()
- imageData = GLImageData(
- image, imageBuffer, colourBuffer, positionBuffer, geomBuffer)
+ geomBuffer = vbo.VBO(geomData, gl.GL_STATIC_DRAW)
+ positionBuffer = vbo.VBO(positionData, gl.GL_STATIC_DRAW)
- self.imageData.append(imageData)
+ # The image buffer, containing the image data itself
+ imageBuffer = self._initImageBuffer(idx)
- self.updateColourBuffer(idx)
+ # The colour buffer, containing a map of
+ # colours (stored on the GPU as a 1D texture)
+ colourBuffer = gl.glGenTextures(1)
+
+ glImageData = GLImageData(
+ image, imageBuffer, colourBuffer, positionBuffer, geomBuffer)
- self.glReady = True
+
+ return glImageData
- def _initImageBuffer(self, image):
+ def _initImageBuffer(self, idx):
"""
Initialises the buffer used to store the image data. If a 'master'
canvas was set when this SliceCanvas object was constructed, its
image buffer is used instead.
"""
+ image = self.imageList[idx]
+
# If a master canvas was passed to the
# constructor, let's share its image data.
if image.glBuffer is not None:
@@ -394,15 +380,52 @@ class SliceCanvas(wxgl.GLCanvas):
return imageBuffer
+ def _configDisplayListeners(self, idx):
+ """
+ """
+
+ image = self.imageList[idx]
+ display = image.display
+
+ # Add a bunch of listeners to the image display
+ # object for each image, so we can update the
+ # view when image display properties are changed.
+ def refreshNeeded(*a):
+ self.Refresh()
+
+ def colourUpdateNeeded(*a):
+ self.updateColourBuffer(idx)
+ self.Refresh()
+
+ lnrName = 'SliceCanvas_{{}}_{}'.format(id(self))
+
+ display.addListener(
+ 'alpha', lnrName.format('alpha'), refreshNeeded)
+ display.addListener(
+ 'enabled', lnrName.format('enabled'), refreshNeeded)
+
+ display.addListener(
+ 'displayMin', lnrName.format('displayMin'), colourUpdateNeeded)
+
+ display.addListener(
+ 'displayMax', lnrName.format('displayMax'), colourUpdateNeeded)
+
+ display.addListener(
+ 'rangeClip', lnrName.format('rangeClip'), colourUpdateNeeded)
+
+ display.addListener(
+ 'cmap', lnrName.format('cmap'), colourUpdateNeeded)
+
+
def updateColourBuffer(self, idx):
"""
- Regenerates the colour buffer used to colour a slice. After
- calling this method, you will need to call Refresh() for the
- change to take effect.
+ Regenerates the colour buffer used to colour a slice of the
+ specified image. After calling this method, you will need to
+ call Refresh() for the change to take effect.
"""
- iDisplay = self.imageList.displays[idx]
- colourBuffer = self.imageData[idx].colourBuffer
+ iDisplay = self.imageList [idx].display
+ colourBuffer = self.glImageData[idx].colourBuffer
# Here we are creating a range of values to be passed
# to the matplotlib.colors.Colormap instance of the
@@ -496,18 +519,21 @@ class SliceCanvas(wxgl.GLCanvas):
gl.glEnable(gl.GL_BLEND)
gl.glBlendFunc(gl.GL_SRC_ALPHA, gl.GL_ONE_MINUS_SRC_ALPHA)
- for i in range(len(self.imageData)):
+ for i in range(len(self.glImageData)):
+
+ image = self.imageList[i]
+ imageDisplay = image.display
+ geomBuffer = self.glImageData[i].geomBuffer
+ imageBuffer = self.glImageData[i].imageBuffer
+ positionBuffer = self.glImageData[i].positionBuffer
+ colourBuffer = self.glImageData[i].colourBuffer
- image = self.imageList.images[i]
- imageDisplay = self.imageList.displays[i]
- geomBuffer = self.imageData[i].geomBuffer
- imageBuffer = self.imageData[i].imageBuffer
- positionBuffer = self.imageData[i].positionBuffer
- colourBuffer = self.imageData[i].colourBuffer
+ if not imageDisplay.enabled:
+ continue
# Set up the colour buffer
gl.glEnable(gl.GL_TEXTURE_1D)
- gl.glActiveTexture(gl.GL_TEXTURE0)
+ gl.glActiveTexture(gl.GL_TEXTURE0)
gl.glBindTexture(gl.GL_TEXTURE_1D, colourBuffer)
gl.glUniform1i(self.colourMapPos, 0)