From 65a51503713685764497e7d5f47c139d49c50314 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jul 2019 14:32:36 +0100
Subject: [PATCH] ENH: parse_data.Image allows additional Image.__init__
arguments to be passed. Used by fsl_convert_x5
---
fsl/scripts/fsl_convert_x5.py | 42 ++++++++++++++++++++---------------
fsl/transform/x5.py | 20 ++++++++++++++++-
fsl/utils/parse_data.py | 12 ++++++----
3 files changed, 51 insertions(+), 23 deletions(-)
diff --git a/fsl/scripts/fsl_convert_x5.py b/fsl/scripts/fsl_convert_x5.py
index 33f063c15..f7bf84981 100644
--- a/fsl/scripts/fsl_convert_x5.py
+++ b/fsl/scripts/fsl_convert_x5.py
@@ -9,17 +9,18 @@ transformation file formats.
"""
-import os.path as op
-import sys
-import shutil
-import logging
-import argparse
-from collections import OrderedDict
+import os.path as op
+import functools as ft
+import sys
+import shutil
+import logging
+import argparse
-import fsl.data.image as fslimage
-import fsl.transform.flirt as flirt
-import fsl.transform.fnirt as fnirt
-import fsl.transform.x5 as x5
+import fsl.data.image as fslimage
+import fsl.utils.parse_data as parse_data
+import fsl.transform.flirt as flirt
+import fsl.transform.fnirt as fnirt
+import fsl.transform.x5 as x5
log = logging.getLogger(__name__)
@@ -49,11 +50,14 @@ def parseArgs(args):
subparsers = parser.add_subparsers(dest='ctype')
flirt = subparsers.add_parser('flirt')
fnirt = subparsers.add_parser('fnirt')
+ imgtype = ft.partial(parse_data.Image, loadData=False)
flirt.add_argument('input', help=helps['input'])
flirt.add_argument('output', help=helps['output'])
- flirt.add_argument('-s', '--source', help=helps['source'])
- flirt.add_argument('-r', '--reference', help=helps['reference'])
+ flirt.add_argument('-s', '--source', help=helps['source'],
+ type=imgtype)
+ flirt.add_argument('-r', '--reference', help=helps['reference'],
+ type=imgtype)
flirt.add_argument('-if', '--input_format', help=helps['input_format'],
choices=('x5', 'mat'))
flirt.add_argument('-of', '--output_format', help=helps['output_format'],
@@ -61,8 +65,10 @@ def parseArgs(args):
fnirt .add_argument('input', help=helps['input'])
fnirt .add_argument('output', help=helps['output'])
- fnirt .add_argument('-s', '--source', help=helps['source'])
- fnirt .add_argument('-r', '--reference', help=helps['reference'])
+ fnirt .add_argument('-s', '--source', help=helps['source'],
+ type=imgtype)
+ fnirt .add_argument('-r', '--reference', help=helps['reference'],
+ type=imgtype)
fnirt .add_argument('-if', '--input_format', help=helps['input_format'],
choices=('x5', 'nii'))
fnirt .add_argument('-of', '--output_format', help=helps['output_format'],
@@ -109,8 +115,8 @@ def flirtToX5(args):
"""Convert a linear FLIRT transformation matrix to an X5 transformation
file.
"""
- src = fslimage.Image(args.source, loadData=False)
- ref = fslimage.Image(args.reference, loadData=False)
+ src = args.source
+ ref = args.reference
xform = flirt.readFlirt(args.input)
xform = flirt.fromFlirt(xform, src, ref, 'world', 'world')
x5.writeLinearX5(args.output, xform, src, ref)
@@ -127,8 +133,8 @@ def fnirtToX5(args):
"""Convert a non-linear FNIRT transformation into an X5 transformation
file.
"""
- src = fslimage.Image(args.source, loadData=False)
- ref = fslimage.Image(args.reference, loadData=False)
+ src = args.source
+ ref = args.reference
field = fnirt.readFnirt(args.input, src=src, ref=ref)
field = fnirt.fromFnirt(field, 'world', 'world')
x5.writeNonLinearX5(args.output, field)
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index 5d25dced4..f14a165a0 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -10,6 +10,7 @@ transformations from/to BIDS X5 files. The following functions are available:
.. autosummary::
:nosignatures:
+ inferType
readLinearX5
writeLinearX5
readNonLinearX5
@@ -339,6 +340,23 @@ class X5Error(Exception):
pass
+def inferType(fname):
+ """Return the type of the given X5 file - either ``'linear'``or
+ ``'nonlinear'``.
+
+ :arg fname: Name of a X5 file
+ :returns: ``'linear'``or ``'nonlinear'``
+ """
+ with h5py.File(fname, 'r') as f:
+
+ ftype = f.attrs.get('Type')
+
+ if ftype not in ('linear', 'nonlinear'):
+ raise X5Error('Unknown type: {}'.format(ftype))
+
+ return ftype
+
+
def readLinearX5(fname):
"""Read a linear X5 transformation file from ``fname``.
@@ -565,7 +583,7 @@ def _readDeformation(group):
def _writeDeformation(group, field):
- """Write a deformation fieldto the given group.
+ """Write a deformation field to the given group.
:arg group: A ``h5py.Group`` object
:arg field: A :class:`.DeformationField` object
diff --git a/fsl/utils/parse_data.py b/fsl/utils/parse_data.py
index 20e51d752..1c16e97de 100644
--- a/fsl/utils/parse_data.py
+++ b/fsl/utils/parse_data.py
@@ -8,8 +8,9 @@
Argparse is the built-in python library for resolving command line arguments.
-The functions in this module can be passed on to the ``type`` argument in the ``ArgumentParser.add_command`` method
-to interpret command line arguments as neuroimageing objects (.e.g, NIFTI image files)
+The functions in this module can be passed on to the ``type`` argument in the
+``ArgumentParser.add_command`` method to interpret command line arguments as
+neuroimaging objects (.e.g, NIFTI image files)
.. autosummary::
@@ -27,18 +28,21 @@ from fsl.utils import path
import argparse
-def Image(filename):
+def Image(filename, *args, **kwargs):
"""
Reads in an image from a NIFTI or Analyze file.
:arg filename: filename provided by the user
:return: fsl.data.image.Image object
+
+ All other arguments are passed through to the :class:`.Image` upon
+ creation.
"""
try:
full_filename = image.addExt(filename)
except path.PathError as e:
raise argparse.ArgumentTypeError(*e.args)
- return image.Image(full_filename)
+ return image.Image(full_filename, *args, **kwargs)
def ImageOut(basename):
--
GitLab