From 30a248dcf4e6ded9f127f667b95c5c97be184cdf Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 9 Apr 2019 22:42:08 +0100
Subject: [PATCH] RF: Include identity transforms in image affines. Basic flirt
matrix read/write routines
---
fsl/data/image.py | 3 +++
fsl/utils/transform/flirt.py | 12 ++++++++++++
2 files changed, 15 insertions(+)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 5570be15f..189117fe3 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -376,6 +376,9 @@ class Nifti(notifier.Notifier, meta.Meta):
[ x, 0, 0])
voxToScaledVoxMat = transform.concat(flip, voxToScaledVoxMat)
+ affines['fsl', 'fsl'] = np.eye(4)
+ affines['voxel', 'voxel'] = np.eye(4)
+ affines['world', 'world'] = np.eye(4)
affines['voxel', 'world'] = voxToWorldMat
affines['world', 'voxel'] = transform.invert(voxToWorldMat)
affines['voxel', 'fsl'] = voxToScaledVoxMat
diff --git a/fsl/utils/transform/flirt.py b/fsl/utils/transform/flirt.py
index c669eb9c4..56b193e07 100644
--- a/fsl/utils/transform/flirt.py
+++ b/fsl/utils/transform/flirt.py
@@ -17,9 +17,21 @@ matrices. The following functions are available:
"""
+import numpy as np
+
from .affine import concat
+def readFlirt(fname):
+ """Reads a FLIRT matrix from a file. """
+ return np.loadtxt(fname)
+
+
+def writeFlirt(xform, fname):
+ """Writes the given FLIRT matrix to a file. """
+ np.savetxt(fname, xform, fmt='%1.15g')
+
+
def fromFlirt(xform, src, ref, from_='voxel', to='world'):
"""Convert a FLIRT affine matrix into another affine.
--
GitLab