From a2b84c22268dd01bd5b30f39f34c209863284e29 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 24 Feb 2015 09:53:15 +0000
Subject: [PATCH] Handle NIFTI images which have the wrong number of dimensions
in their header
---
fsl/data/image.py | 24 +++++++++++++++++++--
fsl/fslview/gl/textures.py | 43 ++++++++++++++++++++++++++++++++++++++
2 files changed, 65 insertions(+), 2 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index e1a839dc0..5e8df1193 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -190,8 +190,28 @@ class Image(props.HasProperties):
be called if the ``loadData`` parameter passed to :meth:`__init__`
was ``False``.
"""
- self.data = self.nibImage.get_data()
- self.data.flags.writeable = False
+
+ data = self.nibImage.get_data()
+
+ # Squeeze out empty dimensions, as
+ # 3D image can sometimes be listed
+ # as having 4 or more dimensions
+ shape = data.shape
+
+ for i in reversed(range(len(shape))):
+ if shape[i - 1] == 1:
+ data = data.squeeze(axis=i - 1)
+
+ data.flags.writeable = False
+
+ log.debug('Loaded image data ({}) - original '
+ 'shape {}, squeezed shape {}'.format(
+ self.name,
+ shape,
+ data.shape))
+
+ self.data = data
+
def applyChange(self, offset, newVals, vol=None):
diff --git a/fsl/fslview/gl/textures.py b/fsl/fslview/gl/textures.py
index ee84237ad..9737c2aaf 100644
--- a/fsl/fslview/gl/textures.py
+++ b/fsl/fslview/gl/textures.py
@@ -354,6 +354,49 @@ class ImageTexture(object):
voxValXform = transform.scaleOffsetXform(scale, offset)
+ if log.getEffectiveLevel() == logging.DEBUG:
+
+ if texDtype == gl.GL_UNSIGNED_BYTE:
+ sTexDtype = 'GL_UNSIGNED_BYTE'
+ elif texDtype == gl.GL_UNSIGNED_SHORT:
+ sTexDtype = 'GL_UNSIGNED_SHORT'
+
+ if texFmt == gl.GL_LUMINANCE:
+ sTexFmt = 'GL_LUMINANCE'
+ elif texFmt == gl.GL_LUMINANCE_ALPHA:
+ sTexFmt = 'GL_LUMINANCE_ALPHA'
+ elif texFmt == gl.GL_RGB:
+ sTexFmt = 'GL_RGB'
+ elif texFmt == gl.GL_RGBA:
+ sTexFmt = 'GL_RGBA'
+
+ if intFmt == gl.GL_LUMINANCE8:
+ sIntFmt = 'GL_LUMINANCE8'
+ elif intFmt == gl.GL_LUMINANCE16:
+ sIntFmt = 'GL_LUMINANCE16'
+ elif intFmt == gl.GL_LUMINANCE8_ALPHA8:
+ sIntFmt = 'GL_LUMINANCE8_ALPHA8'
+ elif intFmt == gl.GL_LUMINANCE16_ALPHA16:
+ sIntFmt = 'GL_LUMINANCE16_ALPHA16'
+ elif intFmt == gl.GL_RGB8:
+ sIntFmt = 'GL_RGB8'
+ elif intFmt == gl.GL_RGB16:
+ sIntFmt = 'GL_RGB16'
+ elif intFmt == gl.GL_RGBA8:
+ sIntFmt = 'GL_RGBA8'
+ elif intFmt == gl.GL_RGBA16:
+ sIntFmt = 'GL_RGBA16'
+
+ log.debug('Image texture ({}) is to be stored as {}/{}/{} '
+ '(normalised: {} - scale {}, offset {})'.format(
+ self.image,
+ sTexDtype,
+ sTexFmt,
+ sIntFmt,
+ self.normalise,
+ scale,
+ offset))
+
return texFmt, intFmt, texDtype, voxValXform
--
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