From ef5ea65e9889520b3dc31451073e9fbc53fd4a7a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 23 Oct 2014 10:52:34 +0100
Subject: [PATCH] ImageDisplay object calculates/stores transformation matrices
for moving between each of the three spaces (voxel, display, and world)
---
fsl/data/image.py | 17 ++++++++++-------
fsl/fslview/displaycontext.py | 12 ++++++++++++
fsl/fslview/strings.py | 1 -
fsl/utils/transform.py | 8 ++++++--
4 files changed, 28 insertions(+), 10 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 3e3e5595a..398fa221e 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -18,13 +18,14 @@ import numpy as np
import nibabel as nib
import props
-import fsl.data.imagefile as imagefile
+import fsl.data.imagefile as imagefile
+import fsl.utils.transform as transform
log = logging.getLogger(__name__)
-# Constants which represent the orientation of an axis,
-# in either voxel or world space.
+# Constants which represent the orientation
+# of an axis, in either voxel or world space.
ORIENT_UNKNOWN = -1
ORIENT_L2R = 0
ORIENT_R2L = 1
@@ -41,10 +42,6 @@ NIFTI_XFORM_ALIGNED_ANAT = 2
NIFTI_XFORM_TALAIRACH = 3
NIFTI_XFORM_MNI_152 = 4
-# My own code, used to indicate that the
-# image is being displayed in voxel space
-NIFTI_XFORM_VOXEL = 5
-
def _loadImageFile(filename):
"""Given the name of an image file, loads it using nibabel.
@@ -133,6 +130,10 @@ class Image(props.HasProperties):
for transforming voxel coordinates into real world
coordinates.
+ :ivar worldToVoxMat: A 4*4 array specifying the affine transformation
+ for transforming real world coordinates into voxel
+ coordinates.
+
:ivar imageFile: The name of the file that the image was loaded from.
:ivar tempFile: The name of the temporary file which was created (in
@@ -198,6 +199,7 @@ class Image(props.HasProperties):
self.shape = self.nibImage.get_shape()
self.pixdim = self.nibImage.get_header().get_zooms()
self.voxToWorldMat = np.array(self.nibImage.get_affine())
+ self.worldToVoxMat = transform.invert(self.voxToWorldMat)
if len(self.shape) < 3 or len(self.shape) > 4:
raise RuntimeError('Only 3D or 4D images are supported')
@@ -301,6 +303,7 @@ class Image(props.HasProperties):
"""
return self._attributes[name]
+
def delAttribute(self, name):
"""Delete and return the value of the attribute with the given name.
diff --git a/fsl/fslview/displaycontext.py b/fsl/fslview/displaycontext.py
index 401907b8f..c1ca8b63d 100644
--- a/fsl/fslview/displaycontext.py
+++ b/fsl/fslview/displaycontext.py
@@ -286,6 +286,9 @@ class ImageDisplay(props.HasProperties):
self.setConstraint('worldResolution', 'minval', min(image.pixdim[:3]))
self.worldResolution = min(image.pixdim[:3])
+ self.voxToWorldMat = image.voxToWorldMat.transpose()
+ self.worldToVoxMat = image.worldToVoxMat.transpose()
+
# is this a 4D volume?
if image.is4DImage():
self.setConstraint('volume', 'maxval', image.shape[3] - 1)
@@ -320,9 +323,18 @@ class ImageDisplay(props.HasProperties):
voxToDisplayMat = np.array(voxToDisplayMat, dtype=np.float32)
displayToVoxMat = transform.invert(voxToDisplayMat)
+ # Transformation matrices for moving between the voxel
+ # coordinate system and the display coordinate system
self.voxToDisplayMat = voxToDisplayMat.transpose()
self.displayToVoxMat = displayToVoxMat.transpose()
+ # Matrices for moving between the display coordinate
+ # system, and the image world coordinate system
+ self.displayToWorldMat = transform.concat(self.displayToVoxMat,
+ self.voxToWorldMat)
+ self.worldToDisplayMat = transform.invert(self.displayToWorldMat)
+
+
# for pixdim/identity transformations, we want the world
# location (0, 0, 0) to map to voxel location (0, 0, 0)
if self.transform in ('id', 'pixdim'):
diff --git a/fsl/fslview/strings.py b/fsl/fslview/strings.py
index 903e922c7..dc395e16d 100644
--- a/fsl/fslview/strings.py
+++ b/fsl/fslview/strings.py
@@ -94,7 +94,6 @@ imageAxisHighShortLabels = {
fslimage.ORIENT_UNKNOWN : '?'}
imageSpaceLabels = {
- fslimage.NIFTI_XFORM_VOXEL : 'Voxel',
fslimage.NIFTI_XFORM_UNKNOWN : 'Unknown',
fslimage.NIFTI_XFORM_SCANNER_ANAT : 'Scanner anatomical',
fslimage.NIFTI_XFORM_ALIGNED_ANAT : 'Aligned anatomical',
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index 8c08894ba..0c66d4020 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -1,7 +1,6 @@
#!/usr/bin/env python
#
-# transform.py - Functions for applying affine transformations to
-# coordinates.
+# transform.py - Functions for working with affine transformation matrices.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -19,6 +18,11 @@ def invert(x):
return linalg.inv(x)
+def concat(x1, x2):
+ """Combines the two matrices (returns the dot product)."""
+ return linalg.dot(x1, x2)
+
+
def axisBounds(shape, xform, axis):
"""Returns the (lo, hi) bounds of the specified axis."""
x, y, z = shape
--
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