From f2ce0ed9fd600fba0d88a3c9664a8157263b52e5 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 18 May 2020 16:20:41 +0100
Subject: [PATCH] RF: Better support for nifti1/2 + FSLOUTPUTTYPE
---
fsl/data/image.py | 21 +++++++++++++--------
tests/test_image.py | 22 ++++++++++++++--------
2 files changed, 27 insertions(+), 16 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index f02023ff9..a12f39b12 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -39,7 +39,6 @@ import json
import string
import logging
import tempfile
-import warnings
import six
import numpy as np
@@ -1099,11 +1098,12 @@ class Image(Nifti):
if header is not None: xform = header.get_best_affine()
else: xform = np.identity(4)
- # We default to NIFTI1 and not
- # NIFTI2, because the rest of
- # FSL is not yet NIFTI2 compatible.
+ # default to NIFTI1 if FSLOUTPUTTYPE
+ # is not set, just to be safe.
if header is None:
- ctr = nib.nifti1.Nifti1Image
+ outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')
+ if 'NIFTI2' in outputType: ctr = nib.Nifti2Image
+ else: ctr = nib.Nifti1Image
# make sure that the data type is correct,
# in case this header was passed in from
@@ -1648,9 +1648,14 @@ def defaultExt():
# TODO: Add analyze support.
options = {
- 'NIFTI' : '.nii',
- 'NIFTI_PAIR' : '.img',
- 'NIFTI_GZ' : '.nii.gz',
+ 'NIFTI' : '.nii',
+ 'NIFTI2' : '.nii',
+ 'NIFTI_GZ' : '.nii.gz',
+ 'NIFTI2_GZ' : '.nii.gz',
+ 'NIFTI_PAIR' : '.img',
+ 'NIFTI2_PAIR' : '.img',
+ 'NIFTI_PAIR_GZ' : '.img.gz',
+ 'NIFTI2_PAIR_GZ' : '.img.gz',
}
outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')
diff --git a/tests/test_image.py b/tests/test_image.py
index 75ec686a9..d5fbd94c0 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -246,6 +246,11 @@ def _test_Image_atts(imgtype):
allowedExts = fslimage.ALLOWED_EXTENSIONS
fileGroups = fslimage.FILE_GROUPS
+ typeMap = {np.uint8 : constants.NIFTI_DT_UINT8,
+ np.int16 : constants.NIFTI_DT_INT16,
+ np.int32 : constants.NIFTI_DT_INT32,
+ np.float32 : constants.NIFTI_DT_FLOAT32,
+ np.float64 : constants.NIFTI_DT_FLOAT64}
# (file, dims, pixdims, dtype)
dtypes = [np.uint8, np.int16, np.int32, np.float32, np.double]
@@ -307,14 +312,15 @@ def _test_Image_atts(imgtype):
assert tuple(i.nibImage.shape) == tuple(dims)
assert tuple(i.nibImage.header.get_zooms()) == tuple(pixdims)
- assert i.nvals == 1
- assert i.ndim == expndims
- assert i.dtype == dtype
- assert i.name == op.basename(path)
- assert i.dataSource == fslpath.addExt(path,
- allowedExts=allowedExts,
- mustExist=True,
- fileGroups=fileGroups)
+ assert i.nvals == 1
+ assert i.ndim == expndims
+ assert i.dtype == dtype
+ assert i.niftiDataType == typeMap[dtype]
+ assert i.name == op.basename(path)
+ assert i.dataSource == fslpath.addExt(path,
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
i = None
--
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