From ca9022b936c347cd38c08b29cfbdd954db75f32e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 16 Apr 2021 18:06:37 +0100
Subject: [PATCH] RF: Make sure name/dataSource are set the same, regardless of
whether image is created from a str or Path obj
---
fsl/data/image.py | 62 ++++++++++++++++++++++-------------------------
1 file changed, 29 insertions(+), 33 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 3dfe8a81..b5d0cad7 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -32,22 +32,21 @@ and file names:
"""
-import os
-import os.path as op
-import itertools as it
-import json
-import string
-import logging
-import tempfile
-
-import six
-import numpy as np
+import os
+import os.path as op
+import itertools as it
+import json
+import string
+import logging
+import tempfile
+
+from pathlib import Path
+from typing import Union
+import numpy as np
import nibabel as nib
import nibabel.fileslice as fileslice
-from pathlib import Path
-
import fsl.utils.meta as meta
import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
@@ -58,6 +57,10 @@ import fsl.data.constants as constants
import fsl.data.imagewrapper as imagewrapper
+PathLike = Union[str, Path]
+ImageSource = Union[PathLike, nib.Nifti1Image, np.ndarray, 'Image']
+
+
log = logging.getLogger(__name__)
@@ -993,21 +996,21 @@ class Image(Nifti):
def __init__(self,
- image,
- name=None,
- header=None,
- xform=None,
- loadData=True,
- calcRange=True,
- threaded=False,
- dataSource=None,
- loadMeta=False,
+ image : ImageSource,
+ name : str = None,
+ header : nib.Nifti1Header = None,
+ xform : np.ndarray = None,
+ loadData : bool = True,
+ calcRange : bool = True,
+ threaded : bool = False,
+ dataSource : PathLike = None,
+ loadMeta : bool = False,
**kwargs):
"""Create an ``Image`` object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
- or a Path object pointing to an image file, or a
- :mod:`numpy` array, or a :mod:`nibabel` image object,
+ or a Path object pointing to an image file, or a
+ :mod:`numpy` array, or a :mod:`nibabel` image object,
or an ``Image`` object.
:arg name: A name for the image.
@@ -1086,16 +1089,11 @@ class Image(Nifti):
header.set_qform(xform, code=qform)
# The image parameter may be the name of an image file
- if isinstance(image, six.string_types):
+ if isinstance(image, (str, Path)):
image = op.abspath(addExt(image))
nibImage = nib.load(image, **kwargs)
dataSource = image
saved = True
- # The image parameter may be a Path object pointing to an image file
- elif isinstance(image, Path):
- nibImage = nib.load(image, **kwargs)
- dataSource = str(image)
- saved = True
# Or a numpy array - we wrap it in a nibabel image,
# with an identity transformation (each voxel maps
@@ -1141,15 +1139,13 @@ class Image(Nifti):
nibImage = image
# Figure out the name of this image, if
- # it has not beenbeen explicitly passed in
+ # it has not been explicitly passed in
if name is None:
# If this image was loaded
# from disk, use the file name.
- if isinstance(image, six.string_types):
+ if isinstance(image, (str, Path)):
name = removeExt(op.basename(image))
- elif isinstance(image, Path):
- name = image.name
# Or the image was created from a numpy array
elif isinstance(image, np.ndarray):
--
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