From e5e0cc963130842a3bba9c6929332e8f15c08372 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 15 Jun 2016 10:48:08 +0100
Subject: [PATCH] Bugfix in ImageWrapper.__expandCoverage - variable name
clashes.
Bugfix in ImageWrapper.calcExpansion - could not handle slice outside of
coverage, but overlapping with some dimensions.
Initial support in Image class for data editing.
---
fsl/data/image.py | 58 +++++++++++++++++++++++++++++++++------
fsl/data/imagewrapper.py | 59 +++++++++++++++++++++++++++-------------
2 files changed, 90 insertions(+), 27 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index b624d6b80..802172675 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -458,13 +458,14 @@ class Image(Nifti1, notifier.Notifier):
Nifti1.__init__(self, nibImage.get_header())
- self.name = name
- self.__dataSource = dataSource
- self.__nibImage = nibImage
- self.__saveState = dataSource is not None
- self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
- self.name,
- loadData=loadData)
+ self.name = name
+ self.__dataSource = dataSource
+ self.__nibImage = nibImage
+ self.__saveState = dataSource is not None
+ self.__suppressDataRange = False
+ self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
+ self.name,
+ loadData=loadData)
if calcRange:
self.calcRange()
@@ -561,7 +562,8 @@ class Image(Nifti1, notifier.Notifier):
Notifies any listeners of this ``Image`` (registered through the
:class:`.Notifier` interface) on the ``'dataRange'`` topic.
"""
- self.notify(notifier_topic='dataRange')
+ if not self.__suppressDataRange:
+ self.notify(notifier_topic='dataRange')
def calcRange(self, sizethres=None):
@@ -606,11 +608,19 @@ class Image(Nifti1, notifier.Notifier):
self.__imageWrapper.loadData()
+ def save(self, filename=None):
+ raise NotImplementedError()
+
+
def __getitem__(self, sliceobj):
"""Access the image data with the specified ``sliceobj``.
:arg sliceobj: Something which can slice the image data.
"""
+
+
+ log.debug('{}: __getitem__ [{}]'.format(self.name, sliceobj))
+
data = self.__imageWrapper.__getitem__(sliceobj)
if len(data.shape) > len(self.shape):
@@ -621,6 +631,38 @@ class Image(Nifti1, notifier.Notifier):
return data
+ def __setitem__(self, sliceobj, values):
+ """Set the image data at ``sliceobj`` to ``values``.
+
+ :arg sliceobj: Something which can slice the image data.
+ :arg values: New image data.
+
+ .. note:: Modifying image data will force the entire image to be
+ loaded into memory if it has not already been loaded.
+ """
+
+ log.debug('{}: __setitem__ [{} = {}]'.format(self.name,
+ sliceobj,
+ values.shape))
+
+ self.__suppressDataRange = True
+ oldRange = self.__imageWrapper.dataRange
+
+ self.__imageWrapper.__setitem__(sliceobj, values)
+
+ newRange = self.__imageWrapper.dataRange
+ self.__suppressDataRange = False
+
+ if values.size > 0:
+
+ self.__saveState = False
+ self.notify(notifier_topic='data')
+ self.notify(notifier_topic='saveState')
+
+ if not np.all(np.isclose(oldRange, newRange)):
+ self.notify(notifier_topic='dataRange')
+
+
# TODO The wx.FileDialog does not
# seem to handle wildcards with
# multiple suffixes (e.g. '.nii.gz'),
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 0ae4fb36d..7d0f21ea5 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -336,19 +336,19 @@ class ImageWrapper(notifier.Notifier):
given ``slices``.
"""
- log.debug('Updating image {} data range [slice: {}] (current range: '
- '[{}, {}]; current coverage: {})'.format(
+ volumes, expansions = calcExpansion(slices, self.__coverage)
+
+ log.debug('Updating image {} data range [slice: {}] '
+ '(current range: [{}, {}]; '
+ 'number of expansions: {}; '
+ 'current coverage: {})'.format(
self.__name,
slices,
self.__range[0],
self.__range[1],
+ len(volumes),
self.__coverage))
- volumes, expansions = calcExpansion(slices, self.__coverage)
-
- oldmin, oldmax = self.__range
- newmin, newmax = oldmin, oldmax
-
# The calcExpansion function splits up the
# expansions on volumes - here we calculate
# the min/max per volume/expansion, and
@@ -356,39 +356,41 @@ class ImageWrapper(notifier.Notifier):
# coverage and data range.
for vol, exp in zip(volumes, expansions):
- oldmin, oldmax = self.__volRanges[vol, :]
+ oldvmin, oldvmax = self.__volRanges[vol, :]
- data = self.__getData(exp, isTuple=True)
- newmin = float(np.nanmin(data))
- newmax = float(np.nanmax(data))
+ data = self.__getData(exp, isTuple=True)
+ newvmin = float(np.nanmin(data))
+ newvmax = float(np.nanmax(data))
- if (not np.isnan(oldmin)) and oldmin < newmin: newmin = oldmin
- if (not np.isnan(oldmax)) and oldmax > newmax: newmax = oldmax
+ if (not np.isnan(oldvmin)) and oldvmin < newvmin: newvmin = oldvmin
+ if (not np.isnan(oldvmax)) and oldvmax > newvmax: newvmax = oldvmax
# Update the stored range and
# coverage for each volume
- self.__volRanges[vol, :] = newmin, newmax
+ self.__volRanges[vol, :] = newvmin, newvmax
self.__coverage[..., vol] = adjustCoverage(
self.__coverage[..., vol], exp)
# Calculate the new known data
# range over the entire image
# (i.e. over all volumes).
- newmin = np.nanmin(self.__volRanges[:, 0])
- newmax = np.nanmax(self.__volRanges[:, 1])
+ newmin = float(np.nanmin(self.__volRanges[:, 0]))
+ newmax = float(np.nanmax(self.__volRanges[:, 1]))
+ oldmin, oldmax = self.__range
self.__range = (newmin, newmax)
self.__covered = self.__imageIsCovered()
- if not np.all(np.isclose([oldmin, newmin], [oldmax, newmax])):
+ if any((oldmin is None, oldmax is None)) or \
+ not np.all(np.isclose([oldmin, oldmax], [newmin, newmax])):
log.debug('Image {} range changed: [{}, {}] -> [{}, {}]'.format(
self.__name,
oldmin,
oldmax,
newmin,
newmax))
- self.notify()
-
+ self.notify()
+
def __updateDataRangeOnRead(self, slices, data):
"""Called by :meth:`__getitem__`. Calculates the minimum/maximum
@@ -446,6 +448,13 @@ class ImageWrapper(notifier.Notifier):
# coverage is necessary?
lowVol, highVol = slices[self.__numRealDims - 1]
+ log.debug('Image {} data written - clearing known data '
+ 'range on volumes {} - {} (write slice: {})'.format(
+ self.__name,
+ lowVol,
+ highVol,
+ slices))
+
for vol in range(lowVol, highVol):
self.__coverage[:, :, vol] = np.nan
self.__volRanges[ vol, :] = np.nan
@@ -800,6 +809,18 @@ def calcExpansion(slices, coverage):
expansion[dimy][0] = expLow
expansion[dimy][1] = expHigh
+
+ # If no range exists for any of the
+ # other dimensions, the range for
+ # all expansions will be the current
+ # coverage
+ for dimy in range(numDims):
+ if dimy == dimx:
+ continue
+
+ if np.any(np.isnan(expansion[dimy])):
+ expansion[dimy] = coverage[:, dimy, vol]
+
# Finish off this expansion
expansion = finishExpansion(expansion, vol)
--
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