From 9c4ce29a4ecd02a920cbd4f3b50ecf70d63bc437 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 6 Jun 2016 18:44:21 +0100
Subject: [PATCH] Image.calcRange thresholding is done on bytes, not voxels.
---
fsl/data/image.py | 33 +++++++++++++++++++++++----------
fsl/data/imagewrapper.py | 2 ++
2 files changed, 25 insertions(+), 10 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 9ba6b6642..d52861277 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -531,31 +531,44 @@ class Image(Nifti1, notifier.Notifier):
"""Forces calculation of the image data range.
:arg sizethres: If not ``None``, specifies an image size threshold
- (threshold on the number of values). If the number
- of values in the image is greater than this threshold,
- the range is calculated on a sample (the first volume
- for a 4D image, or slice for a 3D image).
+ (total number of bytes). If the number of bytes in
+ the image is greater than this threshold, the range
+ is calculated on a sample (the first volume for a
+ 4D image, or slice for a 3D image).
"""
# The ImageWrapper automatically calculates
# the range of the specified slice, whenever
# it gets indexed. All we have to do is
# access a portion of the data to trigger the
- # range calculation.
+ # range calculation.
+ nbytes = np.prod(self.shape) * self.dtype.itemsize
# If an image size threshold has not been specified,
# then we'll calculate the full data range right now.
- if sizethres is None:
+ if sizethres is None or nbytes < sizethres:
+ log.debug('{}: Forcing calculation of full '
+ 'data range'.format(self.name))
self.__imageWrapper[:]
+
+ else:
+ log.debug('{}: Calculating data range '
+ 'from sample'.format(self.name))
- # Otherwise if the number of values in the
- # image is bigger than the size threshold,
- # we'll calculate the range from a sample:
- elif np.prod(self.shape) < sizethres:
+ # Otherwise if the number of values in the
+ # image is bigger than the size threshold,
+ # we'll calculate the range from a sample:
if len(self.shape) == 3: self.__imageWrapper[:, :, 0]
else: self.__imageWrapper[:, :, :, 0]
+ def loadData(self):
+ """Makes sure that the image data is loaded into memory.
+ See :meth:`.ImageWrapper.loadData`.
+ """
+ self.__imageWrapper.loadData()
+
+
def __getitem__(self, sliceobj):
"""Access the image data with the specified ``sliceobj``.
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index e7450ce49..3ea32d1cb 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -224,6 +224,8 @@ class ImageWrapper(notifier.Notifier):
:arg sliceobj: Something which can slice the image data.
"""
+ log.debug('Getting image data: {}'.format(sliceobj))
+
sliceobj = nib.fileslice.canonical_slicers(
sliceobj, self.__image.shape)
--
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