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Commit bad9585c authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF: Image object no longer has special code for opening with indexed_gzip - 

this is all handled by nibabel. Also never keeps its own ref to file object.
Image.save always saves to a temp file, then moves that to the destination -
avoid any problems with mmap/indexed_gzip.
parent 172829d3
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with 52 additions and 145 deletions
fsl/data/image.py
+ 52
− 145
View file @ bad9585c
......@@ -29,7 +29,6 @@ and file names:
getExt
removeExt
defaultExt
loadIndexedImageFile
"""
......@@ -39,6 +38,7 @@ import shutil
import string
import logging
import tempfile
import warnings
import six
import numpy as np
......@@ -52,6 +52,7 @@ import fsl.utils.transform as transform
import fsl.utils.notifier as notifier
import fsl.utils.memoize as memoize
import fsl.utils.path as fslpath
import fsl.utils.deprecated as deprecated
import fsl.data.constants as constants
import fsl.data.imagewrapper as imagewrapper
......@@ -794,10 +795,8 @@ class Image(Nifti):
incrementally updated as more data is read from memory
or disk.
:arg indexed: If ``True``, and the file is gzipped, it is opened
using the :mod:`indexed_gzip` package. Otherwise the
file is opened by ``nibabel``. Ignored if ``loadData``
is ``True``.
:arg indexed: Deprecated. Has no effect, and will be removed in
``fslpy`` 3.0.
:arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
separate thread for data range calculation. Defaults
......@@ -812,10 +811,13 @@ class Image(Nifti):
"""
nibImage = None
fileobj = None
if indexed is not False:
warnings.warn('The indexed argument is deprecated '
'and has no effect',
category=DeprecationWarning)
if loadData:
indexed = False
threaded = False
# Take a copy of the header if one has
......@@ -841,24 +843,8 @@ class Image(Nifti):
# The image parameter may be the name of an image file
if isinstance(image, six.string_types):
image = op.abspath(addExt(image))
# Use indexed_gzip to open gzip files
# if requested - this provides fast
# on-disk access to the compressed
# data.
#
# If using indexed_gzip, we store a
# ref to the file object - we'll close
# it when we are destroyed.
if indexed and image.endswith('.gz'):
nibImage, fileobj = loadIndexedImageFile(image)
# Otherwise we let nibabel
# manage the file reference(s)
else:
nibImage = nib.load(image, **kwargs)
image = op.abspath(addExt(image))
nibImage = nib.load(image, **kwargs)
dataSource = image
# Or a numpy array - we wrap it in a nibabel image,
......@@ -916,17 +902,16 @@ class Image(Nifti):
Nifti.__init__(self, nibImage.header)
self.name = name
self.__lName = '{}_{}'.format(id(self), self.name)
self.__dataSource = dataSource
self.__fileobj = fileobj
self.__threaded = threaded
self.__nibImage = nibImage
self.__saveState = dataSource is not None
self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
self.name,
loadData=loadData,
threaded=threaded)
self.name = name
self.__lName = '{}_{}'.format(id(self), self.name)
self.__dataSource = dataSource
self.__threaded = threaded
self.__nibImage = nibImage
self.__saveState = dataSource is not None
self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
self.name,
loadData=loadData,
threaded=threaded)
# Listen to ourself for changes
# to the voxToWorldMat, so we
......@@ -965,10 +950,6 @@ class Image(Nifti):
self.__nibImage = None
self.__imageWrapper = None
if getattr(self, '__fileobj', None) is not None:
self.__fileobj.close()
self.__fileobj = None
def getImageWrapper(self):
"""Returns the :class:`.ImageWrapper` instance used to manage
......@@ -1139,85 +1120,44 @@ class Image(Nifti):
log.debug('Saving {} to {}'.format(self.name, filename))
# If this Image is not managing its
# own file object, and the image is not
# memory-mapped, nibabel does all of
# the hard work.
newnibimage = False
sample = self[(slice(0, 5),) + (0,) * (len(self.shape) - 1)]
ismmap = isinstance(sample, np.memmap)
if self.__fileobj is None and (not ismmap):
nib.save(self.__nibImage, filename)
# We save the image out to a temp file,
# then close the old image, move the
# temp file to the real destination,
# then re-open the file.
tmphd, tmpfname = tempfile.mkstemp(suffix=op.splitext(filename)[1])
os.close(tmphd)
# If the image is memory-mapped, we need
# to close and re-open the image
elif self.__fileobj is None:
try:
nib.save(self.__nibImage, tmpfname)
# We save the image out to a temp file,
# then close the old image, move the
# temp file to the real destination,
# then re-open the file.
newnibimage = True
tmphd, tmpfname = tempfile.mkstemp(suffix=op.splitext(filename)[1])
os.close(tmphd)
# nibabel should close any old
# file handles when the image/
# header refs are deleted
self.__nibImage = None
self.header = None
try:
nib.save(self.__nibImage, tmpfname)
shutil.copy(tmpfname, filename)
self.__nibImage = None
self.header = None
self.__nibImage = nib.load(filename)
self.header = self.__nibImage.header
shutil.copy(tmpfname, filename)
finally:
os.remove(tmpfname)
raise
self.__nibImage = nib.load(filename)
self.header = self.__nibImage.header
except Exception:
os.remove(tmpfname)
raise
# 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.
newnibimage = True
nib.save(self.__nibImage, filename)
self.__fileobj.close()
self.__nibImage, self.__fileobj = loadIndexedImageFile(filename)
self.header = self.__nibImage.header
# If we've created a new nibabel image,
# Because we've created a new nibabel image,
# we have to create a new ImageWrapper
# instance too, as we have just destroyed
# the nibabel image we gave to the last
# one.
if newnibimage:
self.__imageWrapper.deregister(self.__lName)
self.__imageWrapper = imagewrapper.ImageWrapper(
self.nibImage,
self.name,
loadData=False,
dataRange=self.dataRange,
threaded=self.__threaded)
self.__imageWrapper.register(self.__lName, self.__dataRangeChanged)
self.__imageWrapper.deregister(self.__lName)
self.__imageWrapper = imagewrapper.ImageWrapper(
self.nibImage,
self.name,
loadData=False,
dataRange=self.dataRange,
threaded=self.__threaded)
self.__imageWrapper.register(self.__lName, self.__dataRangeChanged)
self.__dataSource = filename
self.__saveState = True
......@@ -1455,40 +1395,7 @@ def defaultExt():
return options.get(outputType, '.nii.gz')
@deprecated.deprecated('2.0.0', '3.0.0', 'Use nibabel.load instead.')
def loadIndexedImageFile(filename):
"""Loads the given image file using ``nibabel`` and ``indexed_gzip``.
Returns a tuple containing the ``nibabel`` NIFTI image, and the open
``IndexedGzipFile`` handle.
If ``indexed_gzip`` is not present, the image is loaded normally via
``nibabel.load``.
"""
import threading
try:
import indexed_gzip as igzip
except ImportError:
return nib.load(filename), None
log.debug('Loading {} using indexed gzip'.format(filename))
# guessed_image_type returns a
# ref to one of the Nifti1Image
# or Nifti2Image classes.
ftype = nib.loadsave.guessed_image_type(filename)
fobj = igzip.SafeIndexedGzipFile(
filename=filename,
spacing=4194304,
readbuf_size=1048576)
# See the read_segments
# function below
fobj._arrayproxy_lock = threading.Lock()
fmap = ftype.make_file_map()
fmap['image'].fileobj = fobj
image = ftype.from_file_map(fmap)
return image, fobj
"""Deprecated - this call is equivalent to calling ``nibabel.load``. """
return nib.load(filename)
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