From 8f9bed31244ec7f75b9d0c696fc178ff37744124 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 8 Dec 2017 15:59:04 +1030
Subject: [PATCH] Using nibabel version of axcodes2ornt instead of dcmstack
version, as the latter is buggy. Didn't bother to figure out the bug.
---
fsl/data/dcmstack/dcmstack.py | 42 +----------------------------------
1 file changed, 1 insertion(+), 41 deletions(-)
diff --git a/fsl/data/dcmstack/dcmstack.py b/fsl/data/dcmstack/dcmstack.py
index 549427bad..0e20a6d3a 100644
--- a/fsl/data/dcmstack/dcmstack.py
+++ b/fsl/data/dcmstack/dcmstack.py
@@ -12,6 +12,7 @@ from nibabel.nifti1 import Nifti1Extensions
from nibabel.spatialimages import HeaderDataError
from nibabel.orientations import (io_orientation,
apply_orientation,
+ axcodes2ornt,
inv_ornt_aff)
import numpy as np
from .dcmmeta import DcmMetaExtension, NiftiWrapper
@@ -132,47 +133,6 @@ def ornt_transform(start_ornt, end_ornt):
end_out_idx)
return result
-def axcodes2ornt(axcodes, labels=None):
- """ Convert axis codes `axcodes` to an orientation
-
- Parameters
- ----------
- axcodes : (N,) tuple
- axis codes - see ornt2axcodes docstring
- labels : optional, None or sequence of (2,) sequences
- (2,) sequences are labels for (beginning, end) of output axis. That
- is, if the first element in `axcodes` is ``front``, and the second
- (2,) sequence in `labels` is ('back', 'front') then the first
- row of `ornt` will be ``[1, 1]``. If None, equivalent to
- ``(('L','R'),('P','A'),('I','S'))`` - that is - RAS axes.
-
- Returns
- -------
- ornt : (N,2) array-like
- oritation array - see io_orientation docstring
-
- Examples
- --------
- >>> axcodes2ornt(('F', 'L', 'U'), (('L','R'),('B','F'),('D','U')))
- [[1, 1],[0,-1],[2,1]]
- """
-
- if labels is None:
- labels = zip('LPI', 'RAS')
-
- n_axes = len(axcodes)
- ornt = np.ones((n_axes, 2), dtype=np.int8) * np.nan
- for code_idx, code in enumerate(axcodes):
- for label_idx, codes in enumerate(labels):
- if code is None:
- continue
- if code in codes:
- if code == codes[0]:
- ornt[code_idx, :] = [label_idx, -1]
- else:
- ornt[code_idx, :] = [label_idx, 1]
- break
- return ornt
def reorder_voxels(vox_array, affine, voxel_order):
'''Reorder the given voxel array and corresponding affine.
--
GitLab