From 98a8d42ca3a94f97d3bb5e39ed8fab418ea43a9d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 22 Sep 2020 12:58:43 +0100
Subject: [PATCH] RF: readFnirt function allows field type to be specified in
case file has no intent code set
---
fsl/transform/fnirt.py | 44 ++++++++++++++++++++++++++----------------
1 file changed, 27 insertions(+), 17 deletions(-)
diff --git a/fsl/transform/fnirt.py b/fsl/transform/fnirt.py
index 6357fb9ec..36dbda8c6 100644
--- a/fsl/transform/fnirt.py
+++ b/fsl/transform/fnirt.py
@@ -257,7 +257,7 @@ def _readFnirtCoefficientField(fname, img, src, ref):
fieldToRefMat=fieldToRefMat)
-def readFnirt(fname, src, ref, defType=None):
+def readFnirt(fname, src, ref, defType=None, intent=None):
"""Reads a non-linear FNIRT transformation image, returning
a :class:`.DeformationField` or :class:`.CoefficientField` depending
on the file type.
@@ -268,28 +268,38 @@ def readFnirt(fname, src, ref, defType=None):
:arg defType: Deformation type - either ``'absolute'`` or ``'relative'``.
Only used if the file is a deformation field. If not
provided, is automatically inferred from the data.
+ :arg intent: NIFTI intent code of ``fname``. e.g.
+ :attr:`.constants.FSL_FNIRT_DISPLACEMENT_FIELD`. If not
+ provided, the intent is read from the image header.
"""
- # Figure out whether the file
- # is a deformation field or
- # a coefficient field
-
- img = fslimage.Image(fname, loadData=False)
- disps = (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
- constants.FSL_TOPUP_FIELD)
- coefs = (constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
- constants.FSL_DCT_COEFFICIENTS,
- constants.FSL_QUADRATIC_SPLINE_COEFFICIENTS,
- constants.FSL_TOPUP_CUBIC_SPLINE_COEFFICIENTS,
- constants.FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS)
+ if defType not in (None, 'absolute', 'relative'):
+ raise ValueError('defType must be None, "absolute" or "relative" '
+ '(passed in as {})'.format(defType))
+
+ # Figure out whether the file is a
+ # deformation field or a coefficient
+ # field by checking the intent code.
+ # If the intent is provided, assume
+ # that the caller knows the type of
+ # the field.
+ img = fslimage.Image(fname, loadData=False)
+ intent = intent or img.intent
+ disps = (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
+ constants.FSL_TOPUP_FIELD)
+ coefs = (constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
+ constants.FSL_DCT_COEFFICIENTS,
+ constants.FSL_QUADRATIC_SPLINE_COEFFICIENTS,
+ constants.FSL_TOPUP_CUBIC_SPLINE_COEFFICIENTS,
+ constants.FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS)
- if img.intent in disps:
+ if intent in disps:
return _readFnirtDeformationField(fname, img, src, ref, defType)
- elif img.intent in coefs:
+ elif intent in coefs:
return _readFnirtCoefficientField(fname, img, src, ref)
else:
- raise ValueError('Cannot determine type of nonlinear '
- 'file {}'.format(fname))
+ raise ValueError('Cannot determine type of nonlinear warp field '
+ '{} (intent code: {})'.format(fname, intent))
def toFnirt(field):
--
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