From 66b8a3a9645939e8adc2e559984897b55cf21ccc Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 16 Jun 2016 14:12:20 +0100
Subject: [PATCH] Image.save method implemented, and working with/without
IndexedGzipFile.
---
fsl/data/image.py | 96 +++++++++++++++++++++++++++++++++++------------
1 file changed, 71 insertions(+), 25 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index cb672750c..8387dce2c 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -18,8 +18,8 @@ It is very easy to load a NIFTI image::
myimg = Image('MNI152_T1_2mm.nii.gz')
-A number of other functions are also provided for working with image files and
-file names:
+A handful of other functions are also provided for working with image files
+and file names:
.. autosummary::
:nosignatures:
@@ -27,8 +27,7 @@ file names:
looksLikeImage
removeExt
addExt
- loadImage
- saveImage
+ loadIndexedImageFile
"""
@@ -400,21 +399,7 @@ class Image(Nifti1, notifier.Notifier):
# ref to the file object - we'll close
# it when we are destroyed.
if indexed and image.endswith('.gz'):
-
- import indexed_gzip as igzip
-
- log.debug('Loading {} using indexed gzip'.format(image))
-
- fobj = igzip.IndexedGzipFile(
- filename=image,
- spacing=4194304,
- readbuf_size=131072)
-
- fmap = nib.Nifti1Image.make_file_map()
- fmap['image'].fileobj = fobj
- nibImage = nib.Nifti1Image.from_file_map(fmap)
-
- fileobj = fobj
+ nibImage, fileobj = loadIndexedImageFile(image)
# Otherwise we let nibabel
# manage the file reference(s)
@@ -614,17 +599,52 @@ class Image(Nifti1, notifier.Notifier):
if ``filename`` is ``None``.
"""
+ import nibabel as nib
+
if self.__dataSource is None and filename is None:
raise ValueError('A file name must be specified')
if filename is None:
filename = self.__dataSource
+ filename = op.abspath(filename)
+
log.debug('Saving {} to {}'.format(self.name, filename))
-
- raise NotImplementedError()
- # TODO Update self.__dataSource if necessary
+ # If this Image is not managing its
+ # own file object, nibabel does all
+ # of the hard work.
+ if self.__fileobj is None:
+ nib.save(self.__nibImage, filename)
+
+ # Otherwise we've got our own file
+ # handle to an IndexedGzipFile
+ else:
+ # Currently indexed_gzip does not support
+ # writing. So we're going to use nibabel
+ # to save the image, then close and re-open
+ # the file.
+ #
+ # Unfortunately this means that we'll
+ # lose the file index (and fast random
+ # access) - I'll fix this when I get a
+ # chance to work on indexed_gzip a bit
+ # more.
+ #
+ # Hopefully I should be able to add write
+ # support to indexed_gzip, such that it
+ # re-builds the index while writing the
+ # compressed data. And then be able to
+ # transfer the index generated from the
+ # write to a new read-only file handle.
+ nib.save(self.__nibImage, filename)
+ self.__fileobj.close()
+ self.__nibImage, self.__fileobj = loadIndexedImageFile(filename)
+
+ self.__dataSource = filename
+ self.__saveState = True
+
+ self.notify(notifier_topic='saveState')
def __getitem__(self, sliceobj):
@@ -669,10 +689,12 @@ class Image(Nifti1, notifier.Notifier):
self.__suppressDataRange = False
if values.size > 0:
-
- self.__saveState = False
+
self.notify(notifier_topic='data')
- self.notify(notifier_topic='saveState')
+
+ if self.__saveState:
+ self.__saveState = False
+ self.notify(notifier_topic='saveState')
if not np.all(np.isclose(oldRange, newRange)):
self.notify(notifier_topic='dataRange')
@@ -740,3 +762,27 @@ def addExt(prefix, mustExist=True):
ALLOWED_EXTENSIONS,
mustExist,
DEFAULT_EXTENSION)
+
+
+def loadIndexedImageFile(filename):
+ """Loads the given image file using ``nibabel`` and ``indexed_gzip``.
+
+ Returns a tuple containing the ``Nifti1Image``, and the open
+ ``IndexedGzipFile`` handle.
+ """
+
+ import nibabel as nib
+ import indexed_gzip as igzip
+
+ log.debug('Loading {} using indexed gzip'.format(filename))
+
+ fobj = igzip.IndexedGzipFile(
+ filename=filename,
+ spacing=4194304,
+ readbuf_size=131072)
+
+ fmap = nib.Nifti1Image.make_file_map()
+ fmap['image'].fileobj = fobj
+ image = nib.Nifti1Image.from_file_map(fmap)
+
+ return image, fobj
--
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