From f02bd21f0e000cfe12da30b5d39f3948817ca717 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Thu, 26 Apr 2018 11:08:09 +0100
Subject: [PATCH] ENH: added command line support for output images (in FSL
style)
---
fsl/utils/parse_data.py | 10 ++++++++++
tests/test_parse_data.py | 33 ++++++++++++++++++++++++++++++++-
2 files changed, 42 insertions(+), 1 deletion(-)
diff --git a/fsl/utils/parse_data.py b/fsl/utils/parse_data.py
index 613e33b57..90fa56761 100644
--- a/fsl/utils/parse_data.py
+++ b/fsl/utils/parse_data.py
@@ -40,6 +40,16 @@ def Image(filename):
return image.Image(full_filename)
+def ImageOut(basename):
+ """
+ Uses the FSL convention to create a complete image output filename
+
+ :param basename: filename provided by the user
+ :return: filename with extension
+ """
+ return image.addExt(basename, mustExist=False)
+
+
def Mesh(filename):
"""
Reads in a mesh from either a GIFTI (.surf.gii) or a VTK (.vtk) file
diff --git a/tests/test_parse_data.py b/tests/test_parse_data.py
index eb1bc02d1..77a8dce24 100644
--- a/tests/test_parse_data.py
+++ b/tests/test_parse_data.py
@@ -6,7 +6,7 @@
#
import argparse
-from fsl.utils import parse_data, tempdir
+from fsl.utils import parse_data, tempdir, path
import os.path as op
from fsl.data.vtk import VTKMesh
from fsl.data.gifti import GiftiMesh
@@ -14,6 +14,7 @@ from fsl.data.image import Image
from fsl.data.atlases import Atlas
from pytest import raises
from .test_image import make_image
+import os
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -84,6 +85,36 @@ def test_image():
image_parser.parse_args([double_filename])
+def test_image_out():
+ image_parser = argparse.ArgumentParser("Reads an image")
+ image_parser.add_argument("image_out", type=parse_data.ImageOut)
+ for fsl_output_type, extension in (
+ ('NIFTI', '.nii'),
+ ('NIFTI_PAIR', '.img'),
+ ('NIFTI_GZ', '.nii.gz')
+ ):
+ os.environ['FSLOUTPUTTYPE'] = fsl_output_type
+ args = image_parser.parse_args(['test'])
+ assert path.hasExt(args.image_out, extension)
+ assert args.image_out == 'test' + extension
+
+ args = image_parser.parse_args(['test.nii'])
+ assert path.hasExt(args.image_out, '.nii')
+ assert args.image_out == 'test.nii'
+
+ args = image_parser.parse_args(['test.nii.gz'])
+ assert path.hasExt(args.image_out, '.nii.gz')
+ assert args.image_out == 'test.nii.gz'
+
+ args = image_parser.parse_args(['test.img'])
+ assert path.hasExt(args.image_out, '.img')
+ assert args.image_out == 'test.img'
+
+ args = image_parser.parse_args(['test.surf.gii'])
+ assert path.hasExt(args.image_out, extension)
+ assert args.image_out == 'test.surf.gii' + extension
+
+
def test_atlas():
atlas_parser = argparse.ArgumentParser('reads an atlas')
atlas_parser.add_argument('atlas', type=parse_data.Atlas)
--
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