From fafbf849303a1980b81b5ec22779ca5d651a8501 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 22 Oct 2014 15:08:21 +0100
Subject: [PATCH] Bugfixes to transform.py ('x' variable overwriting
transformation matrix), LightBoxPanel (not passing displayCtx to
LightBoxCanvas), fslview_parseargs (using imageList.bounds instead of
displayCtx.bounds), ImageList (didn't remove bounds-related code),
ImageDisplay (attempting to offset transformation matrices for affine, when
only supposed to do it for id/pixdim)
---
fsl/data/image.py | 62 +-----------------------------
fsl/fslview/displaycontext.py | 9 +++--
fsl/fslview/views/lightboxpanel.py | 3 +-
fsl/tools/fslview_parseargs.py | 6 +--
fsl/utils/transform.py | 16 ++++----
5 files changed, 19 insertions(+), 77 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 42fa6944f..3e3e5595a 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -8,7 +8,6 @@
"""Classes for representing 3D/4D images and collections of said images."""
import os
-import sys
import logging
import tempfile
import collections
@@ -322,9 +321,7 @@ class ImageList(props.HasProperties):
"""Class representing a collection of images to be displayed together.
Contains a :class:`props.properties_types.List` property containing
- :class:`Image` objects, and some other properties on which listeners may
- register themselves to be notified when the properties of the image
- collection changes (e.g. image bounds).
+ :class:`Image` objects.
An :class:`ImageList` object has a few wrapper methods around the
:attr:`images` property, allowing the :class:`ImageList` to be used
@@ -350,14 +347,6 @@ class ImageList(props.HasProperties):
self.images = images
- self.addListener(
- 'images',
- self.__class__.__name__,
- self._imageListChanged)
-
- # initialise image bounds
- self._imageListChanged()
-
# set the _lastDir attribute,
# used by the addImages method
if len(images) == 0: self._lastDir = os.getcwd()
@@ -423,55 +412,6 @@ class ImageList(props.HasProperties):
return True
- def _imageListChanged(self, *a):
- """Called whenever an item is added or removed from the :attr:`images`
- list. Registers listeners with the properties of each image, and
- calls the :meth:`_updateImageBounds` method.
- """
-
- for img in self.images:
-
- # This may be called multiple times on each image,
- # but it doesn't matter, as any listener which has
- # previously been registered with an image will
- # just be replaced by the new one here.
- img.addListener(
- 'transform',
- self.__class__.__name__,
- self._updateImageBounds,
- overwrite=True)
-
- self._updateImageBounds()
-
-
- def _updateImageBounds(self, *a):
- """Called whenever an item is added or removed from the
- :attr:`images` list, or an image property changes. Updates
- the :attr:`bounds` property.
- """
-
- if len(self.images) == 0:
- minBounds = [0.0, 0.0, 0.0]
- maxBounds = [0.0, 0.0, 0.0]
-
- else:
- minBounds = 3 * [ sys.float_info.max]
- maxBounds = 3 * [-sys.float_info.max]
-
- for img in self.images:
-
- for ax in range(3):
-
- lo, hi = img.imageBounds(ax)
-
- if lo < minBounds[ax]: minBounds[ax] = lo
- if hi > maxBounds[ax]: maxBounds[ax] = hi
-
- self.bounds[:] = [minBounds[0], maxBounds[0],
- minBounds[1], maxBounds[1],
- minBounds[2], maxBounds[2]]
-
-
# Wrappers around the images list property, allowing this
# ImageList object to be used as if it is actually a list.
def __len__( self): return self.images.__len__()
diff --git a/fsl/fslview/displaycontext.py b/fsl/fslview/displaycontext.py
index 118a9ddb4..401907b8f 100644
--- a/fsl/fslview/displaycontext.py
+++ b/fsl/fslview/displaycontext.py
@@ -325,9 +325,10 @@ class ImageDisplay(props.HasProperties):
# for pixdim/identity transformations, we want the world
# location (0, 0, 0) to map to voxel location (0, 0, 0)
- for i in range(3):
- self.voxToDisplayMat[3, i] = pixdim[i] * 0.5
- self.displayToVoxMat[3, i] = -0.5
+ if self.transform in ('id', 'pixdim'):
+ for i in range(3):
+ self.voxToDisplayMat[3, i] = pixdim[i] * 0.5
+ self.displayToVoxMat[3, i] = -0.5
# When transform is changed to 'affine', enable interpolation
# and, when changed to 'pixdim' or 'id', disable interpolation
@@ -483,7 +484,7 @@ class DisplayContext(props.HasProperties):
minBounds = 3 * [ sys.float_info.max]
maxBounds = 3 * [-sys.float_info.max]
- for img in self.images:
+ for img in self._imageList.images:
display = img.getAttribute('display')
xform = display.voxToDisplayMat
diff --git a/fsl/fslview/views/lightboxpanel.py b/fsl/fslview/views/lightboxpanel.py
index bf01aafff..bcd3d2c7a 100644
--- a/fsl/fslview/views/lightboxpanel.py
+++ b/fsl/fslview/views/lightboxpanel.py
@@ -90,7 +90,8 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
self._scrollbar = wx.ScrollBar(self, style=wx.SB_VERTICAL)
self._lbCanvas = lightboxcanvas.LightBoxCanvas(self.getCanvasPanel(),
- imageList)
+ imageList,
+ displayCtx)
# My properties are the canvas properties
self.bindProps('sliceSpacing', self._lbCanvas)
diff --git a/fsl/tools/fslview_parseargs.py b/fsl/tools/fslview_parseargs.py
index c07bc0e7e..74fa76398 100644
--- a/fsl/tools/fslview_parseargs.py
+++ b/fsl/tools/fslview_parseargs.py
@@ -255,9 +255,9 @@ def handleImageArgs(args):
loc = imageList[0].voxToWorld([args.voxelloc])[0]
else:
- loc = [imageList.bounds.xlo + 0.5 * imageList.bounds.xlen,
- imageList.bounds.ylo + 0.5 * imageList.bounds.ylen,
- imageList.bounds.zlo + 0.5 * imageList.bounds.zlen]
+ loc = [displayCtx.bounds.xlo + 0.5 * displayCtx.bounds.xlen,
+ displayCtx.bounds.ylo + 0.5 * displayCtx.bounds.ylen,
+ displayCtx.bounds.zlo + 0.5 * displayCtx.bounds.zlen]
displayCtx.location.xyz = loc
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index 9cf3b688e..8c08894ba 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -19,7 +19,7 @@ def invert(x):
return linalg.inv(x)
-def axisBounds(shape, x, axis):
+def axisBounds(shape, xform, axis):
"""Returns the (lo, hi) bounds of the specified axis."""
x, y, z = shape
@@ -38,7 +38,7 @@ def axisBounds(shape, x, axis):
points[6, :] = [x, y, -0.5]
points[7, :] = [x, y, z]
- tx = transform(points, x)
+ tx = transform(points, xform)
lo = tx[:, axis].min()
hi = tx[:, axis].max()
@@ -46,7 +46,7 @@ def axisBounds(shape, x, axis):
return (lo, hi)
-def axisLength(shape, x, axis):
+def axisLength(shape, xform, axis):
"""Return the length, in real world units, of the specified axis.
"""
@@ -54,13 +54,13 @@ def axisLength(shape, x, axis):
points[:] = [-0.5, -0.5, -0.5]
points[1, axis] = shape[axis] - 0.5
- tx = transform(points, x)
+ tx = transform(points, xform)
# euclidean distance between each boundary point
return sum((tx[0, :] - tx[1, :]) ** 2) ** 0.5
-def transform(p, x, axes=None):
+def transform(p, xform, axes=None):
"""Transforms the given set of points ``p`` according to the given affine
transformation ``x``. The transformed points are returned as a
:class:``numpy.float64`` array.
@@ -73,9 +73,9 @@ def transform(p, x, axes=None):
y = p[:, 1]
z = p[:, 2]
- t[:, 0] = x * x[0, 0] + y * x[1, 0] + z * x[2, 0] + x[3, 0]
- t[:, 1] = x * x[0, 1] + y * x[1, 1] + z * x[2, 1] + x[3, 1]
- t[:, 2] = x * x[0, 2] + y * x[1, 2] + z * x[2, 2] + x[3, 2]
+ t[:, 0] = x * xform[0, 0] + y * xform[1, 0] + z * xform[2, 0] + xform[3, 0]
+ t[:, 1] = x * xform[0, 1] + y * xform[1, 1] + z * xform[2, 1] + xform[3, 1]
+ t[:, 2] = x * xform[0, 2] + y * xform[1, 2] + z * xform[2, 2] + xform[3, 2]
if axes is None: axes = [0, 1, 2]
--
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