From 2adb571163559fa8ba3e14e4ef6a58c3867f9625 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 29 Jun 2016 11:55:28 +0100
Subject: [PATCH] Image uses a SafeIndexedGzipFile for indexed images.
ImageWrapper can optionally be told to calculate data ranges on a separate
thread.
---
fsl/data/image.py | 19 ++++++++++++++----
fsl/data/imagewrapper.py | 43 +++++++++++++++++++++++++++++++++++++---
2 files changed, 55 insertions(+), 7 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index abc1160e5..d2d7e967a 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -370,7 +370,8 @@ class Image(Nifti1, notifier.Notifier):
xform=None,
loadData=True,
calcRange=True,
- indexed=False):
+ indexed=False,
+ threaded=False):
"""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,
@@ -406,6 +407,11 @@ class Image(Nifti1, notifier.Notifier):
: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``.
+
+
+ :arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
+ separate thread for data range calculation. Defaults
+ to ``False``.
"""
import nibabel as nib
@@ -480,7 +486,8 @@ class Image(Nifti1, notifier.Notifier):
self.__suppressDataRange = False
self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
self.name,
- loadData=loadData)
+ loadData=loadData,
+ threaded=threaded)
if calcRange:
self.calcRange()
@@ -510,7 +517,11 @@ class Image(Nifti1, notifier.Notifier):
def __del__(self):
- """Closes any open file handles. """
+ """Closes any open file handles, and clears some references. """
+
+ self.__nibImage = None
+ self.__imageWrapper = None
+
if self.__fileobj is not None:
self.__fileobj.close()
@@ -805,7 +816,7 @@ def loadIndexedImageFile(filename):
log.debug('Loading {} using indexed gzip'.format(filename))
- fobj = igzip.IndexedGzipFile(
+ fobj = igzip.SafeIndexedGzipFile(
filename=filename,
spacing=4194304,
readbuf_size=131072)
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 13f0dbe67..dd13a7aaf 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -41,6 +41,7 @@ import numpy as np
import nibabel as nib
import fsl.utils.notifier as notifier
+import fsl.utils.async as async
log = logging.getLogger(__name__)
@@ -121,7 +122,12 @@ class ImageWrapper(notifier.Notifier):
"""
- def __init__(self, image, name=None, loadData=False, dataRange=None):
+ def __init__(self,
+ image,
+ name=None,
+ loadData=False,
+ dataRange=None,
+ threaded=False):
"""Create an ``ImageWrapper``.
:arg image: A ``nibabel.Nifti1Image``.
@@ -137,6 +143,10 @@ class ImageWrapper(notifier.Notifier):
:arg dataRange: A tuple containing the initial ``(min, max)`` data
range to use. See the :meth:`reset` method for
important information about this parameter.
+
+ :arg threaded: If ``True``, the data range is updated on a
+ :class:`.TaskThread`. Otherwise (the default), the
+ data range is updated directly on reads/writes.
"""
self.__image = image
@@ -167,6 +177,22 @@ class ImageWrapper(notifier.Notifier):
if loadData:
self.loadData()
+ if not threaded:
+ self.__taskThread = None
+ else:
+ self.__taskThread = async.TaskThread()
+ self.__taskThread.start()
+
+
+ def __del__(self):
+ """If this ``ImageWrapper`` was created with ``threaded=True``,
+ the :class:`.TaskThread` is stopped.
+ """
+ self.__image = None
+ if self.__taskThread is not None:
+ self.__taskThread.stop()
+ self.__taskThraed = None
+
def reset(self, dataRange=None):
"""Reset the internal state and known data range of this
@@ -426,7 +452,12 @@ class ImageWrapper(notifier.Notifier):
# the provided data to avoid
# reading it in again.
- self.__expandCoverage(slices)
+ if self.__taskThread is None:
+ self.__expandCoverage(slices)
+ else:
+ name = '{}_read_{}'.format(id(self), slices)
+ if not self.__taskThread.isQueued(name):
+ self.__taskThread.enqueue(name, self.__expandCoverage, slices)
def __updateDataRangeOnWrite(self, slices, data):
@@ -476,7 +507,13 @@ class ImageWrapper(notifier.Notifier):
self.__coverage[:, :, vol] = np.nan
self.__volRanges[ vol, :] = np.nan
- self.__expandCoverage(slices)
+
+ if self.__taskThread is None:
+ self.__expandCoverage(slices)
+ else:
+ name = '{}_write_{}'.format(id(self), slices)
+ if not self.__taskThread.isQueued(name):
+ self.__taskThread.enqueue(name, self.__expandCoverage, slices)
def __getitem__(self, sliceobj):
--
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