diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index ddf56a5b72b4449b4079c1c63c8ebbb5f00f9d38..bdc60a5bc84f7cc3bc6e612de03c8727441c77ef 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,12 +10,26 @@ Added
^^^^^
+* New :func:`.cifti` module, providing classes and functions for working with
+ `CIFTI <https://www.nitrc.org/projects/cifti/>`_ data.
* New :func:`.winpath` and :func:`wslpath` functions for working with paths
when using FSL in a Windows Subsystem for Linux (WSL) environment.
* New :func:`.wslcmd` function for generating a path to a FSL command installed
in a WSL environment.
* New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed
in a WSL environment.
+* New :meth:`.Image.niftiDataType` property.
+* The :class:`.FileTree` class has been updated to allow creation of
+ deep copies via the new :meth:`.FileTree.copy` method.
+
+
+Changed
+^^^^^^^
+
+
+* :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or
+ NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment
+ variable.
Fixed
diff --git a/fsl/data/constants.py b/fsl/data/constants.py
index 5a870ccf03f5dd457fd39bd70137b9448891282f..00b60acb22f0e9fb71d4608f0a7d791d7d893dbd 100644
--- a/fsl/data/constants.py
+++ b/fsl/data/constants.py
@@ -98,6 +98,36 @@ NIFTI_UNITS_PPM = 40
NIFTI_UNITS_RADS = 48
+# NIFTI datatype codes
+NIFTI_DT_NONE = 0
+NIFTI_DT_UNKNOWN = 0
+NIFTI_DT_BINARY = 1
+NIFTI_DT_UNSIGNED_CHAR = 2
+NIFTI_DT_SIGNED_SHORT = 4
+NIFTI_DT_SIGNED_INT = 8
+NIFTI_DT_FLOAT = 16
+NIFTI_DT_COMPLEX = 32
+NIFTI_DT_DOUBLE = 64
+NIFTI_DT_RGB = 128
+NIFTI_DT_ALL = 255
+NIFTI_DT_UINT8 = 2
+NIFTI_DT_INT16 = 4
+NIFTI_DT_INT32 = 8
+NIFTI_DT_FLOAT32 = 16
+NIFTI_DT_COMPLEX64 = 32
+NIFTI_DT_FLOAT64 = 64
+NIFTI_DT_RGB24 = 128
+NIFTI_DT_INT8 = 256
+NIFTI_DT_UINT16 = 512
+NIFTI_DT_UINT32 = 768
+NIFTI_DT_INT64 = 1024
+NIFTI_DT_UINT64 = 1280
+NIFTI_DT_FLOAT128 = 1536
+NIFTI_DT_COMPLEX128 = 1792
+NIFTI_DT_COMPLEX256 = 2048
+NIFTI_DT_RGBA32 = 2304
+
+
# 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 eb9c468cc50a9831833b50bbe3cd758576297e18..a12f39b12eec26064096a23dcc9365726588e3d2 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
@@ -560,6 +559,11 @@ class Nifti(notifier.Notifier, meta.Meta):
"""Returns the NIFTI intent code of this image. """
return self.header.get('intent_code', constants.NIFTI_INTENT_NONE)
+ @property
+ def niftiDataType(self):
+ """Returns the NIFTI data type code of this image. """
+ return self.header.get('datatype', constants.NIFTI_DT_UNKNOWN)
+
@intent.setter
def intent(self, val):
@@ -1094,11 +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
@@ -1643,9 +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 75ec686a9cdfba1d682d7b992fdd9820e1573512..b7de2def252e4f8bf4edcf672ebb773eafc38ee5 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
@@ -493,8 +499,9 @@ def test_splitExt():
def test_defaultExt():
- fslOutputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ']
- exts = ['.nii', '.img', '.nii.gz']
+ fslOutputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', 'NIFTI_PAIR_GZ',
+ 'NIFTI2', 'NIFTI2_PAIR', 'NIFTI2_GZ', 'NIFTI2_PAIR_GZ']
+ exts = ['.nii', '.img', '.nii.gz', '.img.gz'] * 2
os.environ.pop('FSLOUTPUTTYPE', None)
assert fslimage.defaultExt() == '.nii.gz'
@@ -506,6 +513,35 @@ def test_defaultExt():
assert fslimage.defaultExt() == e
+def test_defaultImageType():
+
+ fslOutputTypes = [None,
+ 'NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', 'NIFTI_PAIR_GZ',
+ 'NIFTI2', 'NIFTI2_PAIR', 'NIFTI2_GZ', 'NIFTI2_PAIR_GZ']
+ exts = ['.nii.gz'] + \
+ ['.nii', '.img', '.nii.gz', '.img.gz'] * 2
+
+ with tempdir():
+ for o, e in zip(fslOutputTypes, exts):
+
+ if o is None:
+ os.environ.pop('FSLOUTPUTTYPE', None)
+ else:
+ os.environ['FSLOUTPUTTYPE'] = o
+
+ if o is None or 'NIFTI2' not in o:
+ exptype = nib.Nifti1Image
+ else:
+ exptype = nib.Nifti2Image
+
+ img = fslimage.Image(np.random.randint(1, 10, (30, 30, 30)))
+
+ assert type(img.nibImage) == exptype
+
+ img.save('image')
+ assert op.exists('image' + e)
+
+
def test_fixExt():
with tempdir():