From 1a54c6c216512313a0aaad705884538cce2508db Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 22 Apr 2014 13:42:51 +0100
Subject: [PATCH] ImageView supports multiple images. Pretty hacky at this
stage, needs cleaning up. Have gone back to storing image data as uint8s.
---
fsl/data/fslimage.py | 25 ++++++++++++++++----
fsl/utils/imageview.py | 51 ++++++++++++++++++++++------------------
fsl/utils/slicecanvas.py | 20 +++++++++-------
3 files changed, 59 insertions(+), 37 deletions(-)
diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index 3717e76a9..217903eda 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
#
-# fslimage.py - Classes representing a 3D image, the display
-# properties of a 3D image, and a collection of 3D images.
+# fslimage.py - Classes for representing 3D images, display
+# properties of 3D images, and collections of 3D images.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -39,6 +39,7 @@ 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()
xdim,ydim,zdim = self.nibImage.get_shape()
xlen,ylen,zlen = self.nibImage.get_header().get_zooms()
@@ -51,6 +52,10 @@ class Image(object):
self.ylen = ylen
self.zlen = zlen
+ # 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
+ # a different view of the same image)
self.glBuffer = None
@@ -59,7 +64,6 @@ 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 -
@@ -76,6 +80,8 @@ class ImageDisplay(props.HasProperties):
cmap.set_under(cmap(0.0), alpha=1.0)
cmap.set_over( cmap(1.0), alpha=1.0)
+ # The display properties of an image
+ enabled = props.Boolean()
alpha = props.Double(minval=0.0, maxval=1.0, default=1.0)
displayMin = props.Double()
displayMax = props.Double()
@@ -85,9 +91,14 @@ class ImageDisplay(props.HasProperties):
cmap = props.ColourMap(default=mplcm.Greys_r,
preNotifyFunc=updateColourMap)
-
- _view = props.VGroup(('displayMin', 'displayMax', 'alpha', 'rangeClip', 'cmap'))
+ _view = props.VGroup(('enabled',
+ 'displayMin',
+ 'displayMax',
+ 'alpha',
+ 'rangeClip',
+ 'cmap'))
_labels = {
+ 'enabled' : 'Enabled',
'displayMin' : 'Min.',
'displayMax' : 'Max.',
'alpha' : 'Opacity',
@@ -112,6 +123,9 @@ class ImageDisplay(props.HasProperties):
class ImageList(object):
+ """
+ Class representing a collection of images to be displayed together.
+ """
def __init__(self, images=None, displays=None):
@@ -120,3 +134,4 @@ class ImageList(object):
self.images = images
self.displays = displays
+
diff --git a/fsl/utils/imageview.py b/fsl/utils/imageview.py
index d651bb597..5e75097c2 100644
--- a/fsl/utils/imageview.py
+++ b/fsl/utils/imageview.py
@@ -1,8 +1,8 @@
#!/usr/bin/env python
#
-# imgshow.py - A wx/OpenGL widget for displaying and interacting with a 3D
-# image. Displays three canvases, each of which shows a slice of the image
-# along each dimension.
+# imgshow.py - A wx/OpenGL widget for displaying and interacting with a
+# collection of 3D image. Displays three canvases, each of which shows
+# a slice of the images along each dimension.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -29,27 +29,21 @@ LocationEvent, EVT_LOCATION_EVENT = wxevent.NewEvent()
class ImageView(wx.Panel):
- def __init__(self, parent, image, *args, **kwargs):
+ def __init__(self, parent, imageList, *args, **kwargs):
"""
Creates three SliceCanvas objects, each displaying a
different axis of the given 3D numpy image.
"""
- if not isinstance(image, fslimage.Image):
- image = fslimage.Image(image)
-
- self.imageDisplay = fslimage.ImageDisplay(image)
-
- imageList = fslimage.ImageList([image], [self.imageDisplay])
+ self.imageList = imageList
wx.Panel.__init__(self, parent, *args, **kwargs)
self.SetMinSize((300,100))
- self.shape = image.data.shape
+ self.shape = imageList.images[0].data.shape
+
+ self.canvasPanel = wx.Panel(self)
- self.canvasPanel = wx.Panel(self)
- self.controlPanel = props.buildGUI(self, self.imageDisplay)
-
self.xcanvas = slicecanvas.SliceCanvas(
self.canvasPanel, imageList, zax=0)
self.ycanvas = slicecanvas.SliceCanvas(
@@ -57,6 +51,13 @@ 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)):
+
+ controlPanel = props.buildGUI(self.controlPanel, self.imageList.displays[i])
+ self.controlPanel.AddPage(controlPanel, '{}'.format(i))
+
self.mainSizer = wx.BoxSizer(wx.VERTICAL)
self.canvasSizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -170,28 +171,32 @@ class ImageView(wx.Panel):
class ImageFrame(wx.Frame):
"""
- Convenience class for displaying an image in a standalone window.
+ Convenience class for displaying a collection of images in a standalone
+ window.
"""
- def __init__(self, parent, image, title=None):
+ def __init__(self, parent, imageList, title=None):
wx.Frame.__init__(self, parent, title=title)
- self.image = image
- self.panel = ImageView(self, image)
+ self.imageList = imageList
+ self.panel = ImageView(self, imageList)
self.Layout()
if __name__ == '__main__':
- if len(sys.argv) != 2:
- print 'usage: imageview.py filename'
+ if len(sys.argv) < 2:
+ print 'usage: imageview.py filename [filename]'
sys.exit(1)
- app = wx.App()
- image = fslimage.Image(sys.argv[1])
+ app = wx.App()
+ images = map(fslimage.Image, sys.argv[1:])
+ displays = map(fslimage.ImageDisplay, images)
+ imageList = fslimage.ImageList(images, displays)
+
frame = ImageFrame(
None,
- image,
+ imageList,
title=sys.argv[1])
frame.Show()
diff --git a/fsl/utils/slicecanvas.py b/fsl/utils/slicecanvas.py
index 4f052fba6..30de77b4c 100644
--- a/fsl/utils/slicecanvas.py
+++ b/fsl/utils/slicecanvas.py
@@ -44,7 +44,7 @@ class GLImageData(object):
slice).
The third buffer, the 'image buffer' contains the image data itself,
- scaled to lie between 0.0 and 1.0. It is used to calculate voxel colours.
+ scaled to lie between 0 and 255. It is used to calculate voxel colours.
Finally, the texture, the 'colour buffer', is used to store a lookup table
containing colours.
@@ -375,11 +375,13 @@ class SliceCanvas(wxgl.GLCanvas):
if image.glBuffer is not None:
return image.glBuffer
- # The image data is cast to single precision floating
- # point, and normalised to lie between 0.0 and 1.0
+ # The image data is normalised to lie
+ # between 0 and 256, and cast to uint8
imageData = np.array(image.data, dtype=np.float32)
- imageData = (imageData - imageData.min()) / \
- (imageData.max() - imageData.min())
+ imageData = 255.0*(imageData - imageData.min()) / \
+ (imageData.max() - imageData.min())
+ imageData = np.array(imageData, dtype=np.uint8)
+
# Then flattened, with fortran dimension ordering,
# so the data, as stored on the GPU, has its first
@@ -558,10 +560,10 @@ class SliceCanvas(wxgl.GLCanvas):
gl.glVertexAttribPointer(
self.voxelValuePos,
1,
- gl.GL_FLOAT,
- gl.GL_FALSE,
- imageStride*4,
- imageBuffer + imageOffset*4)
+ gl.GL_UNSIGNED_BYTE,
+ gl.GL_TRUE,
+ imageStride,
+ imageBuffer + imageOffset)
gl.glEnableVertexAttribArray(self.voxelValuePos)
arbia.glVertexAttribDivisorARB(self.voxelValuePos, 1)
--
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