From 599a5de45b36d02d7a4b2ad84c1677ecefa2263c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 9 Apr 2019 22:45:32 +0100
Subject: [PATCH] ENH: Prototype X5 io module and x5<->flirt converter program.
---
fsl/scripts/fsl_convert_x5.py | 82 ++++++++++++++++++++++++++++++
fsl/utils/transform/__init__.py | 8 +++
fsl/utils/transform/x5.py | 89 +++++++++++++++++++++++++++++++++
3 files changed, 179 insertions(+)
create mode 100644 fsl/scripts/fsl_convert_x5.py
create mode 100644 fsl/utils/transform/x5.py
diff --git a/fsl/scripts/fsl_convert_x5.py b/fsl/scripts/fsl_convert_x5.py
new file mode 100644
index 000000000..248f6e260
--- /dev/null
+++ b/fsl/scripts/fsl_convert_x5.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+#
+# fsl_convert_x5.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import os.path as op
+import sys
+import shutil
+import logging
+import argparse
+
+import fsl.data.image as fslimage
+import fsl.utils.transform as transform
+
+
+log = logging.getLogger(__name__)
+
+
+def parseArgs(args):
+
+ parser = argparse.ArgumentParser('fsl_convert_x5')
+ subparsers = parser.add_subparsers(dest='ctype')
+ flirt = subparsers.add_parser('flirt')
+
+ flirt.add_argument('input')
+ flirt.add_argument('output')
+ flirt.add_argument('-s', '--source')
+ flirt.add_argument('-r', '--reference')
+ flirt.add_argument('-if', '--input_format', choices=('x5', 'mat'))
+ flirt.add_argument('-of', '--output_format', choices=('x5', 'mat'))
+
+ args = parser.parse_args(args)
+
+ def getfmt(fname):
+ ext = op.splitext(fname)[1]
+ if ext not in ('.x5', '.mat'):
+ raise argparse.ArgumentError('Could not infer format from '
+ 'filename: {}'.format(args.input))
+ return ext[1:]
+
+ if args.ctype == 'flirt':
+ if args.input_format is None: args.input_format = getfmt(args.input)
+ if args.output_format is None: args.output_format = getfmt(args.output)
+
+ return args
+
+
+def flirtToX5(args):
+ src = fslimage.Image(args.source)
+ ref = fslimage.Image(args.reference)
+ xform = transform.readFlirt(args.input)
+ transform.writeFlirtX5(args.output, xform, src, ref)
+
+
+def X5ToFlirt(args):
+ xform, src, ref = transform.readFlirtX5(args.input)
+ xform = transform.toFlirt(xform, src, ref, 'world', 'world')
+ transform.writeFlirt(xform, args.output)
+
+
+def main(args=None):
+
+ if args is None:
+ args = sys.argv[1:]
+
+ args = parseArgs(args)
+ ctype = args.ctype
+
+ if ctype == 'flirt':
+ infmt = args.input_format
+ outfmt = args.output_format
+
+ if (infmt, outfmt) == ('x5', 'mat'): X5ToFlirt(args)
+ elif (infmt, outfmt) == ('mat', 'x5'): flirtToX5(args)
+ else: shutil.copy(args.input, args.output)
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/utils/transform/__init__.py b/fsl/utils/transform/__init__.py
index b0ebfbb8e..52fae19d6 100644
--- a/fsl/utils/transform/__init__.py
+++ b/fsl/utils/transform/__init__.py
@@ -25,8 +25,16 @@ from .affine import ( # noqa
transform,
transformNormal,
rmsdev)
+
from .flirt import ( # noqa
+ readFlirt,
+ writeFlirt,
fromFlirt,
toFlirt,
flirtMatrixToSform,
sformToFlirtMatrix)
+
+from .x5 import ( # noqa
+ readFlirtX5,
+ writeFlirtX5
+)
diff --git a/fsl/utils/transform/x5.py b/fsl/utils/transform/x5.py
new file mode 100644
index 000000000..7f6f8c404
--- /dev/null
+++ b/fsl/utils/transform/x5.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+#
+# x5.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""
+
+Functions for reading/writing linear/non-linear FSL transformations from/to
+BIDS X5 files.
+"""
+
+import json
+
+import numpy as np
+import numpy.linalg as npla
+import nibabel as nib
+import h5py
+
+from . import flirt
+
+
+def _writeLinearTransform(group, xform):
+ group.attrs['Type'] = 'linear'
+ group.create_dataset('Transform', data=xform)
+ group.create_dataset('Inverse', data=npla.inv(xform))
+
+
+def _readLinearTransform(group):
+ if group.attrs['Type'] != 'linear':
+ raise ValueError('Not a linear transform')
+ return np.array(group['Transform'])
+
+
+def _writeLinearMapping(group, img):
+ group.attrs['Type'] = 'image'
+ group.attrs['Size'] = img.shape[ :3]
+ group.attrs['Scales'] = img.pixdim[:3]
+
+ mapping = group.create_group('Mapping')
+ _writeLinearTransform(mapping, img.getAffine('voxel', 'world'))
+
+def _readLinearMapping(group):
+
+ import fsl.data.image as fslimage
+
+ if group.attrs['Type'] != 'image':
+ raise ValueError('Not an image mapping')
+
+ shape = group.attrs['Size']
+ pixdim = group.attrs['Scales']
+ xform = _readLinearTransform(group['Mapping'])
+
+ hdr = nib.Nifti2Header()
+ hdr.set_data_shape(shape)
+ hdr.set_zooms( pixdim)
+ hdr.set_sform( xform, 'aligned')
+ return fslimage.Nifti(hdr)
+
+
+def writeFlirtX5(fname, xform, src, ref):
+ """
+ """
+
+ xform = flirt.fromFlirt(xform, src, ref, 'world', 'world')
+
+ with h5py.File(fname, 'w') as f:
+ f.attrs['Format'] = 'X5'
+ f.attrs['Version'] = '0.0.1'
+ f.attrs['Metadata'] = json.dumps({'software' : 'flirt'})
+
+ _writeLinearTransform(f, xform)
+
+ from_ = f.create_group('/From')
+ to = f.create_group('/To')
+
+ _writeLinearMapping(from_, src)
+ _writeLinearMapping(to, ref)
+
+
+def readFlirtX5(fname):
+ """
+ """
+ with h5py.File(fname, 'r') as f:
+ xform = _readLinearTransform(f['/'])
+ src = _readLinearMapping( f['/From'])
+ ref = _readLinearMapping( f['/To'])
+
+ return xform, src, ref
--
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