From 9fd9e62d640855db4856a8bfd4785b1fa8cd8037 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 10 Apr 2017 13:45:02 +0100
Subject: [PATCH] Fixes for nifti units, and to image initialisation
---
fsl/data/constants.py | 13 +++++++++++++
fsl/data/image.py | 27 +++++++++++++++++++++++----
2 files changed, 36 insertions(+), 4 deletions(-)
diff --git a/fsl/data/constants.py b/fsl/data/constants.py
index d257945ec..5a870ccf0 100644
--- a/fsl/data/constants.py
+++ b/fsl/data/constants.py
@@ -85,6 +85,19 @@ NIFTI_XFORM_ANALYZE = 5
"""Code which indicates that this is an ANALYZE image, not a NIFTI image. """
+# NIFTI unit codes
+NIFTI_UNITS_UNKNOWN = 0
+NIFTI_UNITS_METER = 1
+NIFTI_UNITS_MM = 2
+NIFTI_UNITS_MICRON = 3
+NIFTI_UNITS_SEC = 8
+NIFTI_UNITS_MSEC = 16
+NIFTI_UNITS_USEC = 24
+NIFTI_UNITS_HZ = 32
+NIFTI_UNITS_PPM = 40
+NIFTI_UNITS_RADS = 48
+
+
# NIFTI file intent codes
NIFTI_INTENT_NONE = 0
NIFTI_INTENT_CORREL = 2
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 4efea8e02..0952f5855 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -332,6 +332,10 @@ class Nifti(notifier.Notifier):
def xyzUnits(self):
"""Returns the NIFTI XYZ dimension unit code. """
+ # analyze images have no unit field
+ if self.niftiVersion == 0:
+ return constants.NIFTI_UNITS_MM
+
# The nibabel get_xyzt_units returns labels,
# but we want the NIFTI codes. So we use
# the (undocumented) nifti1.unit_codes field
@@ -345,6 +349,10 @@ class Nifti(notifier.Notifier):
def timeUnits(self):
"""Returns the NIFTI time dimension unit code. """
+ # analyze images have no unit field
+ if self.niftiVersion == 0:
+ return constants.NIFTI_UNITS_SEC
+
# See xyzUnits
units = self.header.get_xyzt_units()[1]
units = nib.nifti1.unit_codes[units]
@@ -742,10 +750,20 @@ class Image(Nifti):
# We default to NIFTI1 and not
# NIFTI2, because the rest of
- # FSL is not yet NIFTI2 compatible.
- nibImage = nib.nifti1.Nifti1Image(image,
- xform,
- header=header)
+ # FSL is not yet NIFTI2 compatible.
+ if header is None:
+ ctr = nib.nifti1.Nifti1Image
+
+ # But if a nibabel header has been provided,
+ # we use the corresponding image type
+ if isinstance(header, nib.nifti2.Nifti2Header):
+ ctr = nib.nifti2.Nifti2Image
+ elif isinstance(header, nib.nifti1.Nifti1Header):
+ ctr = nib.nifti1.Nifti1Image
+ elif isinstance(header, nib.analyze.AnalyzeHeader):
+ ctr = nib.analyze.AnalyzeImage
+
+ nibImage = ctr(image, xform, header=header)
# otherwise, we assume that it is a nibabel image
else:
@@ -1026,6 +1044,7 @@ class Image(Nifti):
.. note:: Modifying image data will force the entire image to be
loaded into memory if it has not already been loaded.
"""
+ values = np.array(values)
log.debug('{}: __setitem__ [{} = {}]'.format(self.name,
sliceobj,
--
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