diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7f46e780467d7fd2a594e3b50ed942c316807919..96f59e61235dd6bc3b8a775e1a3ca01b2c19cd2e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,25 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.3.0 (Under development)
+-------------------------
+
+
+Added
+^^^^^
+
+* New ported versions of various core FSL tools, including ``imrm``, ``imln``,
+ ``imtest``, ``fsl_abspath``, ``remove_ext``, ``Text2Vest``, and
+ ``Vest2Text``.
+
+
+Changed
+^^^^^^^
+
+
+* Adjustments to tests and documentation
+
+
3.2.2 (Thursday 9th July 2020)
------------------------------
diff --git a/fsl/data/image.py b/fsl/data/image.py
index ce01645b4c544f263c0ea05cd2cd38be7fa0f604..7c2bdbcba722e8f0017ce0bba46269283f8e4d8b 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1625,18 +1625,20 @@ def removeExt(filename):
return fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
-def fixExt(filename):
+def fixExt(filename, **kwargs):
"""Fix the extension of ``filename``.
For example, if a file name is passed in as ``file.nii.gz``, but the
file is actually ``file.nii``, this function will fix the file name.
If ``filename`` already exists, it is returned unchanged.
+
+ All other arguments are passed through to :func:`addExt`.
"""
if op.exists(filename):
return filename
else:
- return addExt(removeExt(filename))
+ return addExt(removeExt(filename), **kwargs)
def defaultExt():
diff --git a/fsl/data/vest.py b/fsl/data/vest.py
index b0b33c73fa41ab045c849d079f52d73d40baccf6..9fe10c103ad8dc278d4ec4b163883803ecc6830f 100644
--- a/fsl/data/vest.py
+++ b/fsl/data/vest.py
@@ -11,9 +11,14 @@
looksLikeVestLutFile
loadVestLutFile
+ loadVestFile
+ generateVest
"""
+import textwrap as tw
+import io
+
import numpy as np
@@ -76,3 +81,70 @@ def loadVestLutFile(path, normalise=True):
else:
return colours
+
+
+def loadVestFile(path, ignoreHeader=True):
+ """Loads numeric data from a VEST file, returning it as a ``numpy`` array.
+
+ :arg ignoreHeader: if ``True`` (the default), the matrix shape specified
+ in the VEST header information is ignored, and the shape
+ inferred from the data. Otherwise, if the number of
+ rows/columns specified in the VEST header information
+ does not match the matrix shape, a ``ValueError`` is
+ raised.
+
+ :returns: a ``numpy`` array containing the matrix data in the
+ VEST file.
+ """
+
+ data = np.loadtxt(path, comments=['#', '/'])
+
+ if not ignoreHeader:
+ nrows, ncols = None, None
+ with open(path, 'rt') as f:
+ for line in f:
+ if 'NumWaves' in line: ncols = int(line.split()[1])
+ elif 'NumPoints' in line: nrows = int(line.split()[1])
+ else: continue
+
+ if (ncols is not None) and (nrows is not None):
+ break
+
+ if tuple(data.shape) != (nrows, ncols):
+ raise ValueError(f'Invalid VEST file ({path}) - data shape '
+ f'({data.shape}) does not match header '
+ f'({nrows}, {ncols})')
+
+ return data
+
+
+def generateVest(data):
+ """Generates VEST-formatted text for the given ``numpy`` array.
+
+ :arg data: A 1D or 2D numpy array.
+ :returns: A string containing a VEST header, and the ``data``.
+ """
+
+ data = np.asanyarray(data)
+
+ if len(data.shape) not in (1, 2):
+ raise ValueError(f'unsupported number of dimensions: {data.shape}')
+
+ data = np.atleast_2d(data)
+
+ if np.issubdtype(data.dtype, np.integer): fmt = '%d'
+ else: fmt = '%0.12f'
+
+ sdata = io.StringIO()
+ np.savetxt(sdata, data, fmt=fmt)
+ sdata = sdata.getvalue()
+
+ nrows, ncols = data.shape
+
+ vest = tw.dedent(f"""
+ /NumWaves {ncols}
+ /NumPoints {nrows}
+ /Matrix
+ """).strip() + '\n' + sdata
+
+ return vest.strip()
diff --git a/fsl/scripts/Text2Vest.py b/fsl/scripts/Text2Vest.py
new file mode 100644
index 0000000000000000000000000000000000000000..15989f945f0a39ef73163e9c6840eff893f2e5c7
--- /dev/null
+++ b/fsl/scripts/Text2Vest.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+#
+# Text2Vest.py - Convert an ASCII text matrix file into a VEST file.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""``Text2Vest`` simply takes a plain text ASCII text matrix file, and
+adds a VEST header.
+"""
+
+
+import sys
+
+import numpy as np
+
+import fsl.data.vest as fslvest
+
+
+usage = "Usage: Text2Vest <text_file> <vest_file>"
+
+
+def main(argv=None):
+ """Convert a plain text file to a VEST file. """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) != 2:
+ print(usage)
+ return 0
+
+ infile, outfile = argv
+ data = np.loadtxt(infile)
+ vest = fslvest.generateVest(data)
+
+ with open(outfile, 'wt') as f:
+ f.write(vest)
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/Vest2Text.py b/fsl/scripts/Vest2Text.py
new file mode 100644
index 0000000000000000000000000000000000000000..b12d8166a32a8ffd8eb2de33ada2e886ba9f8b39
--- /dev/null
+++ b/fsl/scripts/Vest2Text.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+#
+# Vest2Text.py - Convert a VEST matrix file into a plain text ASCII file.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""``Vest2Text`` takes a VEST file containing a 2D matrix, and converts it
+into a plain-text ASCII file.
+"""
+
+
+import sys
+
+import numpy as np
+
+import fsl.data.vest as fslvest
+
+
+usage = "Usage: Vest2Text <vest_file> <text_file>"
+
+
+def main(argv=None):
+ """Convert a VEST file to a plain text file. """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) != 2:
+ print(usage)
+ return 0
+
+ infile, outfile = argv
+ data = fslvest.loadVestFile(infile)
+
+ if np.issubdtype(data.dtype, np.integer): fmt = '%d'
+ else: fmt = '%0.12f'
+
+ np.savetxt(outfile, data, fmt=fmt)
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/__init__.py b/fsl/scripts/__init__.py
index 4ef1e04becbabc6280ce9106f84d943d0e8e923b..499b221767c7e66e8ff8bac70c7cc1ff14cf5120 100644
--- a/fsl/scripts/__init__.py
+++ b/fsl/scripts/__init__.py
@@ -5,5 +5,12 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""The ``fsl.scripts`` package contains all of the executable scripts provided
-by ``fslpy``.
+by ``fslpy``, and other python-based FSL packages.
+
+.. note:: The ``fsl.scripts`` namespace is a ``pkgutil``-style *namespace
+ package* - it can be used across different projects - see
+ https://packaging.python.org/guides/packaging-namespace-packages/ for
+ details.
"""
+
+__path__ = __import__('pkgutil').extend_path(__path__, __name__) # noqa
diff --git a/fsl/scripts/fsl_abspath.py b/fsl/scripts/fsl_abspath.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed4775874326abda6c6d3881892d6988a006f2a4
--- /dev/null
+++ b/fsl/scripts/fsl_abspath.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+#
+# fsl_abspath.py - Make a path absolute
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""The fsl_abspath command - makes relative paths absolute.
+"""
+
+
+import os.path as op
+import sys
+
+
+usage = """
+usage: fsl_abspath path
+""".strip()
+
+
+def main(argv=None):
+ """fsl_abspath - make a relative path absolute. """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) != 1:
+ print(usage)
+ return 1
+
+ print(op.realpath(argv[0]))
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/fsl_ents.py b/fsl/scripts/fsl_ents.py
index eb78ed83ebb585787d5864c67aac98b7b3786296..1590c9b4491865c7256a3ccb87a27c047b88b772 100644
--- a/fsl/scripts/fsl_ents.py
+++ b/fsl/scripts/fsl_ents.py
@@ -9,8 +9,6 @@ time series from a MELODIC ``.ica`` directory.
"""
-from __future__ import print_function
-
import os.path as op
import sys
import argparse
diff --git a/fsl/scripts/imcp.py b/fsl/scripts/imcp.py
index 81f53a83d5fdd682c80f41a208641c3273a8985d..d2fcc1eda66a6c01f43bbdb246ce46ade699e82f 100755
--- a/fsl/scripts/imcp.py
+++ b/fsl/scripts/imcp.py
@@ -12,8 +12,6 @@ The :func:`main` function is essentially a wrapper around the
"""
-from __future__ import print_function
-
import os.path as op
import sys
import warnings
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index ed85e4120d2e9024f2848e9be28eab43ce18e068..1e756dee6f79d5e3f4a5f087ba355c5a795771bd 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -9,8 +9,6 @@ NIFTI/ANALYZE image files.
"""
-from __future__ import print_function
-
import sys
import warnings
import fsl.utils.path as fslpath
diff --git a/fsl/scripts/imln.py b/fsl/scripts/imln.py
new file mode 100644
index 0000000000000000000000000000000000000000..88955f3cb36300853f58f276f6e4dedb6ffda18e
--- /dev/null
+++ b/fsl/scripts/imln.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+#
+# imln.py - Create symbolic links to image files.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module defines the ``imln`` application, for creating sym-links
+to NIFTI image files.
+
+.. note:: When creating links to relative paths, ln requires that the path is
+ relative to the link location, rather than the invocation
+ location. This is *not* currently supported by imln, and possibly
+ never will be.
+"""
+
+
+import os.path as op
+import os
+import sys
+import warnings
+
+import fsl.utils.path as fslpath
+
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=FutureWarning)
+ import fsl.data.image as fslimage
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are supported by ``imln``. """
+
+
+usage = """
+Usage: imln <file1> <file2>
+ Makes a link (called file2) to file1
+ NB: filenames can be basenames or include an extension
+""".strip()
+
+
+def main(argv=None):
+ """``imln`` - create sym-links to images. """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) != 2:
+ print(usage)
+ return 1
+
+ target, linkbase = argv
+ target = fslpath.removeExt(target, ALLOWED_EXTENSIONS)
+ linkbase = fslpath.removeExt(linkbase, ALLOWED_EXTENSIONS)
+
+ # Target must exist, so we can
+ # infer the correct extension(s).
+ # Error on incomplete file groups
+ # (e.g. a.img without a.hdr).
+ try:
+ targets = fslpath.getFileGroup(target,
+ allowedExts=ALLOWED_EXTENSIONS,
+ fileGroups=fslimage.FILE_GROUPS,
+ unambiguous=True)
+ except Exception as e:
+ print(f'Error: {e}')
+ return 1
+
+ for target in targets:
+ if not op.exists(target):
+ continue
+
+ ext = fslpath.getExt(target, ALLOWED_EXTENSIONS)
+ link = f'{linkbase}{ext}'
+
+ try:
+
+ # emulate old imln behaviour - if
+ # link already exists, it is removed
+ if op.exists(link):
+ os.remove(link)
+
+ os.symlink(target, link)
+
+ except Exception as e:
+ print(f'Error: {e}')
+ return 1
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/immv.py b/fsl/scripts/immv.py
index c25a99e04c535f3cd26690f5600213e4d3d23ebe..febe422747c27558c98cf6243816980837aaa603 100755
--- a/fsl/scripts/immv.py
+++ b/fsl/scripts/immv.py
@@ -13,8 +13,6 @@ The :func:`main` function is essentially a wrapper around the
"""
-from __future__ import print_function
-
import os.path as op
import sys
import warnings
diff --git a/fsl/scripts/imrm.py b/fsl/scripts/imrm.py
new file mode 100644
index 0000000000000000000000000000000000000000..bd81103325b6d8dea25f0b88f02c3bbb40555f6c
--- /dev/null
+++ b/fsl/scripts/imrm.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+#
+# imrm.py - Remove image files.
+#
+# Author: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
+#
+"""This module defines the ``imrm`` application, for removing NIFTI image
+files.
+"""
+
+
+import itertools as it
+import os.path as op
+import os
+import sys
+import warnings
+
+import fsl.utils.path as fslpath
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=FutureWarning)
+ import fsl.data.image as fslimage
+
+
+usage = """Usage: imrm <list of image names to remove>
+NB: filenames can be basenames or not
+""".strip()
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are removed by ``imrm``. """
+
+
+def main(argv=None):
+ """Removes all images which are specified on the command line. """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) < 1:
+ print(usage)
+ return 1
+
+ prefixes = [fslpath.removeExt(p, ALLOWED_EXTENSIONS) for p in argv]
+
+ for prefix, ext in it.product(prefixes, ALLOWED_EXTENSIONS):
+
+ path = f'{prefix}{ext}'
+
+ if op.exists(path):
+ os.remove(path)
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/imtest.py b/fsl/scripts/imtest.py
new file mode 100644
index 0000000000000000000000000000000000000000..f03c28442b52ed79f535b12aae444e310cf83bc3
--- /dev/null
+++ b/fsl/scripts/imtest.py
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+#
+# imtest.py - Test whether an image file exists or not.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""The ``imtest`` script can be used to test whether an image file exists or
+not, without having to know the file suffix (.nii, .nii.gz, etc).
+"""
+
+
+import os.path as op
+import sys
+import warnings
+
+import fsl.utils.path as fslpath
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=FutureWarning)
+ import fsl.data.image as fslimage
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are supported by ``imln``. """
+
+
+def main(argv=None):
+ """Test if an image path exists, and prints ``'1'`` if it does or ``'0'``
+ if it doesn't.
+ """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ # emulate old fslio/imtest - always return 0
+ if len(argv) != 1:
+ print('0')
+ return 0
+
+ path = fslpath.removeExt(argv[0], ALLOWED_EXTENSIONS)
+ path = op.realpath(path)
+
+ # getFileGroup will raise an error
+ # if the image (including all
+ # components - i.e. header and
+ # image) does not exist
+ try:
+ fslpath.getFileGroup(path,
+ allowedExts=ALLOWED_EXTENSIONS,
+ fileGroups=fslimage.FILE_GROUPS,
+ unambiguous=True)
+ print('1')
+ except fslpath.PathError:
+ print('0')
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/fsl/scripts/remove_ext.py b/fsl/scripts/remove_ext.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc21094ff113576cc808f25fc3dbde1b7f38ff4f
--- /dev/null
+++ b/fsl/scripts/remove_ext.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+#
+# remove_ext.py - Remove file extensions from NIFTI image paths
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import sys
+import warnings
+
+import fsl.utils.path as fslpath
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=FutureWarning)
+ import fsl.data.image as fslimage
+
+
+usage = """Usage: remove_ext <list of image paths to remove extension from>
+""".strip()
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are removed by ``remove_ext``. """
+
+
+def main(argv=None):
+ """Removes file extensions from all paths which are specified on the
+ command line.
+ """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ if len(argv) < 1:
+ print(usage)
+ return 1
+
+ removed = []
+
+ for path in argv:
+ removed.append(fslpath.removeExt(path, ALLOWED_EXTENSIONS))
+
+ print(' '.join(removed))
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/setup.py b/setup.py
index eee141bd0972ba372349a7d1037d076d7b9dd021..1a971bf2a3eb5facc9b5b4ca56168ee8aa9b485d 100644
--- a/setup.py
+++ b/setup.py
@@ -118,9 +118,16 @@ setup(
entry_points={
'console_scripts' : [
- 'immv = fsl.scripts.immv:main',
'imcp = fsl.scripts.imcp:main',
+ 'imln = fsl.scripts.imln:main',
+ 'immv = fsl.scripts.immv:main',
+ 'imrm = fsl.scripts.imrm:main',
'imglob = fsl.scripts.imglob:main',
+ 'imtest = fsl.scripts.imtest:main',
+ 'remove_ext = fsl.scripts.remove_ext:main',
+ 'fsl_abspath = fsl.scripts.fsl_abspath:main',
+ 'Text2Vest = fsl.scripts.Text2Vest:main',
+ 'Vest2Text = fsl.scripts.Vest2Text:main',
'atlasq = fsl.scripts.atlasq:main',
'atlasquery = fsl.scripts.atlasq:atlasquery_emulation',
'fsl_ents = fsl.scripts.fsl_ents:main',
diff --git a/tests/test_imglob.py b/tests/test_imglob.py
deleted file mode 100644
index 9a8e838d1321fd45c91c1d94188700067423097f..0000000000000000000000000000000000000000
--- a/tests/test_imglob.py
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-#
-# test_imglob.py -
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-
-import pytest
-
-import fsl.scripts.imglob as imglob
-
-from . import testdir
-
-
-def test_imglob_shouldPass():
-
- # (files to create, paths, output, expected)
- tests = [
-
- # normal usage, one file
- ('file.hdr file.img', 'file', None, 'file'),
- ('file.hdr file.img', 'file', 'prefix', 'file'),
- ('file.hdr file.img', 'file', 'primary', 'file.hdr'),
- ('file.hdr file.img', 'file', 'all', 'file.hdr file.img'),
-
- # incomplete file pair
- ('file.hdr', 'file', 'prefix', 'file'),
- ('file.hdr', 'file.hdr', 'prefix', 'file'),
- ('file.hdr', 'file.img', 'prefix', 'file'),
- ('file.hdr', 'file', 'primary', 'file.hdr'),
- ('file.hdr', 'file.hdr', 'primary', 'file.hdr'),
- ('file.hdr', 'file.img', 'primary', 'file.hdr'),
- ('file.hdr', 'file', 'all', 'file.hdr'),
- ('file.hdr', 'file.hdr', 'all', 'file.hdr'),
- ('file.hdr', 'file.img', 'all', 'file.hdr'),
-
- # same file specified multiple times
- ('file.hdr file.img', 'file file', 'prefix', 'file'),
- ('file.hdr file.img', 'file file.img', 'prefix', 'file'),
- ('file.hdr file.img', 'file file.img file.hdr', 'prefix', 'file'),
- ('file.hdr file.img', 'file file', 'primary', 'file.hdr'),
- ('file.hdr file.img', 'file file.img', 'primary', 'file.hdr'),
- ('file.hdr file.img', 'file file.img file.hdr', 'primary', 'file.hdr'),
- ('file.hdr file.img', 'file file', 'all', 'file.hdr file.img'),
- ('file.hdr file.img', 'file file.img', 'all', 'file.hdr file.img'),
- ('file.hdr file.img', 'file file.img file.hdr', 'all', 'file.hdr file.img'),
-
- # multiple files same prefix
- ('file.hdr file.img file.nii', 'file', 'prefix', 'file'),
- ('file.hdr file.img file.nii', 'file', 'primary', 'file.hdr file.nii'),
- ('file.hdr file.img file.nii', 'file', 'all', 'file.hdr file.img file.nii'),
-
- # multiple files
- ('file1.hdr file1.img file2.nii', 'file1', 'prefix', 'file1'),
- ('file1.hdr file1.img file2.nii', 'file1', 'primary', 'file1.hdr'),
- ('file1.hdr file1.img file2.nii', 'file1', 'all', 'file1.hdr file1.img'),
-
- ('file1.hdr file1.img file2.nii', 'file1 file2', 'prefix', 'file1 file2'),
- ('file1.hdr file1.img file2.nii', 'file1 file2', 'primary', 'file1.hdr file2.nii'),
- ('file1.hdr file1.img file2.nii', 'file1 file2', 'all', 'file1.hdr file1.img file2.nii'),
-
- # no file
- ('file.nii', 'bag', 'prefix', ''),
- ('file.nii', 'bag', 'primary', ''),
- ('file.nii', 'bag', 'all', ''),
-
- # incomplete prefix
- ('file.nii', 'fi', 'prefix', ''),
- ('file.nii', 'fi', 'primary', ''),
- ('file.nii', 'fi', 'all', ''),
- ]
-
-
- for to_create, paths, output, expected in tests:
- with testdir(to_create.split()) as td:
-
- paths = paths.split()
- expected = expected.split()
- result = imglob.imglob(paths, output)
-
- assert sorted(result) == sorted(expected)
-
-
-def test_imglob_shouldFail():
-
- with pytest.raises(ValueError):
- imglob.imglob([], 'bag')
diff --git a/tests/test_scripts/test_fsl_abspath.py b/tests/test_scripts/test_fsl_abspath.py
new file mode 100644
index 0000000000000000000000000000000000000000..1657128978f003dc551789e00d4f24f161c797ae
--- /dev/null
+++ b/tests/test_scripts/test_fsl_abspath.py
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+#
+# test_fsl_abspath.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import os.path as op
+
+import fsl.scripts.fsl_abspath as fsl_abspath
+
+from tests import tempdir, CaptureStdout
+
+
+def test_usage():
+ assert fsl_abspath.main([]) != 0
+
+
+def test_fsl_abspath():
+
+ # fsl_abspath just calls os.path.realpath
+
+ with tempdir() as td:
+
+ oneup = op.dirname(td)
+
+ # (input, expected)
+ tests = [
+ ('file', f'{td}/file'),
+ ('./file', f'{td}/file'),
+ ('../file', f'{oneup}/file'),
+
+ ('/file', '/file'),
+ ('/one/two/file', '/one/two/file'),
+ ]
+
+ for input, expected in tests:
+ cap = CaptureStdout()
+
+ with cap:
+ ret = fsl_abspath.main([input])
+
+ assert ret == 0
+ assert cap.stdout.strip() == expected
diff --git a/tests/test_scripts/test_imglob.py b/tests/test_scripts/test_imglob.py
index 0f8e934509ce68359d17a8a8794bbaaa47f1a691..5ce2c2bc517dfcc00fa5c4be69886fd360de570e 100644
--- a/tests/test_scripts/test_imglob.py
+++ b/tests/test_scripts/test_imglob.py
@@ -1,6 +1,9 @@
#!/usr/bin/env python
-import mock
+
+from unittest import mock
+
+import pytest
import fsl.scripts.imglob as imglob
@@ -8,7 +11,7 @@ from .. import testdir
from .. import CaptureStdout
-def test_imglob_script_shouldPass():
+def test_imglob_shouldPass1():
# (files to create, args, expected)
tests = [
@@ -50,8 +53,81 @@ def test_imglob_script_shouldPass():
assert capture.stdout.strip().split() == expected.split()
+def test_imglob_shouldPass2():
+
+ # (files to create, paths, output, expected)
+ tests = [
+
+ # normal usage, one file
+ ('file.hdr file.img', 'file', None, 'file'),
+ ('file.hdr file.img', 'file', 'prefix', 'file'),
+ ('file.hdr file.img', 'file', 'primary', 'file.hdr'),
+ ('file.hdr file.img', 'file', 'all', 'file.hdr file.img'),
+
+ # incomplete file pair
+ ('file.hdr', 'file', 'prefix', 'file'),
+ ('file.hdr', 'file.hdr', 'prefix', 'file'),
+ ('file.hdr', 'file.img', 'prefix', 'file'),
+ ('file.hdr', 'file', 'primary', 'file.hdr'),
+ ('file.hdr', 'file.hdr', 'primary', 'file.hdr'),
+ ('file.hdr', 'file.img', 'primary', 'file.hdr'),
+ ('file.hdr', 'file', 'all', 'file.hdr'),
+ ('file.hdr', 'file.hdr', 'all', 'file.hdr'),
+ ('file.hdr', 'file.img', 'all', 'file.hdr'),
+
+ # same file specified multiple times
+ ('file.hdr file.img', 'file file', 'prefix', 'file'),
+ ('file.hdr file.img', 'file file.img', 'prefix', 'file'),
+ ('file.hdr file.img', 'file file.img file.hdr', 'prefix', 'file'),
+ ('file.hdr file.img', 'file file', 'primary', 'file.hdr'),
+ ('file.hdr file.img', 'file file.img', 'primary', 'file.hdr'),
+ ('file.hdr file.img', 'file file.img file.hdr', 'primary', 'file.hdr'),
+ ('file.hdr file.img', 'file file', 'all', 'file.hdr file.img'),
+ ('file.hdr file.img', 'file file.img', 'all', 'file.hdr file.img'),
+ ('file.hdr file.img', 'file file.img file.hdr', 'all', 'file.hdr file.img'),
+
+ # multiple files same prefix
+ ('file.hdr file.img file.nii', 'file', 'prefix', 'file'),
+ ('file.hdr file.img file.nii', 'file', 'primary', 'file.hdr file.nii'),
+ ('file.hdr file.img file.nii', 'file', 'all', 'file.hdr file.img file.nii'),
+
+ # multiple files
+ ('file1.hdr file1.img file2.nii', 'file1', 'prefix', 'file1'),
+ ('file1.hdr file1.img file2.nii', 'file1', 'primary', 'file1.hdr'),
+ ('file1.hdr file1.img file2.nii', 'file1', 'all', 'file1.hdr file1.img'),
+
+ ('file1.hdr file1.img file2.nii', 'file1 file2', 'prefix', 'file1 file2'),
+ ('file1.hdr file1.img file2.nii', 'file1 file2', 'primary', 'file1.hdr file2.nii'),
+ ('file1.hdr file1.img file2.nii', 'file1 file2', 'all', 'file1.hdr file1.img file2.nii'),
+
+ # no file
+ ('file.nii', 'bag', 'prefix', ''),
+ ('file.nii', 'bag', 'primary', ''),
+ ('file.nii', 'bag', 'all', ''),
+
+ # incomplete prefix
+ ('file.nii', 'fi', 'prefix', ''),
+ ('file.nii', 'fi', 'primary', ''),
+ ('file.nii', 'fi', 'all', ''),
+ ]
+
+
+ for to_create, paths, output, expected in tests:
+ with testdir(to_create.split()) as td:
+
+ paths = paths.split()
+ expected = expected.split()
+ result = imglob.imglob(paths, output)
+
+ assert sorted(result) == sorted(expected)
+
+
+
def test_imglob_script_shouldFail():
+ with pytest.raises(ValueError):
+ imglob.imglob([], 'bag')
+
capture = CaptureStdout()
with capture:
diff --git a/tests/test_scripts/test_imln.py b/tests/test_scripts/test_imln.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9fea4e4fc00f9cf9b94370c801f4fb1d9a4606b
--- /dev/null
+++ b/tests/test_scripts/test_imln.py
@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+#
+# test_imln.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+import os.path as op
+from unittest import mock
+
+import pytest
+
+from fsl.utils.tempdir import tempdir
+import fsl.utils.path as fslpath
+import fsl.scripts.imln as imln
+
+from tests import touch
+
+
+def test_usage():
+ assert imln.main([]) != 0
+ with mock.patch('sys.argv', []):
+ assert imln.main() != 0
+
+
+def test_imln():
+
+ # (files, command, expected links)
+ tests = [
+ ('a.nii', 'a.nii link.nii', 'link.nii'),
+ ('a.nii', 'a link', 'link.nii'),
+ ('a.nii', 'a.nii link', 'link.nii'),
+ ('a.nii', 'a link.nii', 'link.nii'),
+ ('a.nii', 'a link.nii.gz', 'link.nii'),
+ ('a.nii.gz', 'a.nii.gz link.nii.gz', 'link.nii.gz'),
+ ('a.nii.gz', 'a link', 'link.nii.gz'),
+ ('a.nii.gz', 'a.nii.gz link', 'link.nii.gz'),
+ ('a.nii.gz', 'a link.nii.gz', 'link.nii.gz'),
+ ('a.nii.gz', 'a link.nii', 'link.nii.gz'),
+
+ ('a.img a.hdr', 'a link', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a link.img', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a link.hdr', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.img link', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.hdr link', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.img link.img', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.hdr link.hdr', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.img link.hdr', 'link.img link.hdr'),
+ ('a.img a.hdr', 'a.hdr link.img', 'link.img link.hdr'),
+ ]
+
+
+ for files, command, explinks in tests:
+ with tempdir():
+ files = files.split()
+ command = command.split()
+ explinks = explinks.split()
+
+ for f in files:
+ touch(f)
+
+ assert imln.main(command) == 0
+
+ assert sorted(os.listdir('.')) == sorted(files + explinks)
+
+ for f, l in zip(sorted(files), sorted(explinks)):
+ assert op.islink(l)
+ assert op.isfile(f) and not op.islink(f)
+ assert op.realpath(l) == op.abspath(f)
+
+
+ # subdirs - imln currently only
+ # works with absolute paths (we
+ # make all paths absolute below)
+ tests = [
+ ('dir/a.nii', 'dir/a dir/link', 'dir/link.nii'),
+ ('dir/a.img dir/a.hdr', 'dir/a dir/link', 'dir/link.img dir/link.hdr'),
+ ('dir/a.nii', 'dir/a link', 'link.nii'),
+ ('dir/a.img dir/a.hdr', 'dir/a link', 'link.img link.hdr'),
+ ('a.nii', 'a dir/link', 'dir/link.nii'),
+ ('a.img a.hdr', 'a dir/link', 'dir/link.img dir/link.hdr'),
+ ]
+ for files, command, explinks in tests:
+ with tempdir():
+ files = files.split()
+ command = [op.abspath(c) for c in command.split()]
+ explinks = explinks.split()
+
+ os.mkdir('dir')
+
+ for f in files:
+ touch(f)
+
+ assert imln.main(command) == 0
+
+ for f, l in zip(sorted(files), sorted(explinks)):
+ assert op.islink(l)
+ assert op.isfile(f) and not op.islink(f)
+ assert op.realpath(l) == op.abspath(f)
+
+ # error cases
+ # (files, commnad)
+ tests = [
+ ('a.img', 'a link'),
+ ('a.nii a.img a.hdr', 'a link'),
+ ]
+ for files, command in tests:
+ with tempdir():
+ files = files.split()
+ command = command.split()
+
+ for f in files:
+ touch(f)
+
+ assert imln.main(command) != 0
+ assert sorted(os.listdir('.')) == sorted(files)
diff --git a/tests/test_scripts/test_imrm.py b/tests/test_scripts/test_imrm.py
new file mode 100644
index 0000000000000000000000000000000000000000..d6682400a4d93696b996c5f78884be181ae04016
--- /dev/null
+++ b/tests/test_scripts/test_imrm.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+#
+# test_imrm.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+
+from fsl.utils.tempdir import tempdir
+import fsl.scripts.imrm as imrm
+
+from tests import touch
+
+def test_imrm_usage():
+ assert imrm.main([]) != 0
+
+
+def test_imrm():
+ # (files present, command, expected)
+ tests = [
+ ('a.nii', 'a', ''),
+ ('a.nii.gz', 'a', ''),
+ ('a.img a.hdr', 'a', ''),
+ ('a.img', 'a', ''),
+ ('a.hdr', 'a', ''),
+ ('a.nii b.nii', 'a', 'b.nii'),
+ ('a.nii b.nii', 'a b', ''),
+ ('a.nii b.nii', 'a b.nii', ''),
+
+ # suffix doesn't have to be correct
+ ('a.nii.gz', 'a.nii', ''),
+
+ # files don't exist -> no problem
+ ('a.nii', 'b', 'a.nii'),
+ ]
+
+ for files, command, expected in tests:
+ with tempdir():
+
+ for f in files.split():
+ touch(f)
+
+ print('files', files)
+ print('command', command)
+ print('expected', expected)
+
+ ret = imrm.main(('imrm ' + command).split())
+
+ assert ret == 0
+ assert sorted(os.listdir()) == sorted(expected.split())
diff --git a/tests/test_scripts/test_imtest.py b/tests/test_scripts/test_imtest.py
new file mode 100644
index 0000000000000000000000000000000000000000..819afa959175391d8b6fc44c986fe7b12e2021b3
--- /dev/null
+++ b/tests/test_scripts/test_imtest.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+#
+# test_imtest.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+import os.path as op
+
+import fsl.utils.path as fslpath
+from fsl.utils.tempdir import tempdir
+
+import fsl.scripts.imtest as imtest
+
+from tests import CaptureStdout, touch
+
+
+def test_wrongargs():
+ cap = CaptureStdout()
+ with cap:
+ assert imtest.main([]) == 0
+ assert cap.stdout.strip() == '0'
+
+
+def test_imtest():
+ # (files, input, expected)
+ tests = [
+ ('a.nii', 'a', '1'),
+ ('a.nii', 'a.nii', '1'),
+ ('a.nii', 'a.nii.gz', '1'), # imtest is suffix-agnostic
+
+ ('a.img a.hdr', 'a', '1'),
+ ('a.img a.hdr', 'a.img', '1'),
+ ('a.img a.hdr', 'a.hdr', '1'),
+ ('a.img', 'a', '0'),
+ ('a.img', 'a.img', '0'),
+ ('a.img', 'a.hdr', '0'),
+ ('a.hdr', 'a', '0'),
+ ('a.hdr', 'a.img', '0'),
+ ('a.hdr', 'a.hdr', '0'),
+
+ ('dir/a.nii', 'dir/a', '1'),
+ ('dir/a.img dir/a.hdr', 'dir/a', '1'),
+ ]
+
+ for files, input, expected in tests:
+ with tempdir():
+ for f in files.split():
+ dirname = op.dirname(f)
+ if dirname != '':
+ os.makedirs(dirname, exist_ok=True)
+ touch(f)
+
+ cap = CaptureStdout()
+ with cap:
+ assert imtest.main([input]) == 0
+
+ assert cap.stdout.strip() == expected
+
+ # test that sym-links are
+ # followed correctly
+ with tempdir():
+ touch('image.nii.gz')
+ os.symlink('image.nii.gz', 'link.nii.gz')
+ cap = CaptureStdout()
+ with cap:
+ assert imtest.main(['link']) == 0
+ assert cap.stdout.strip() == '1'
+
+ # sym-links in sub-directories
+ # (old imtest would not work
+ # in this scenario)
+ with tempdir():
+ os.mkdir('subdir')
+ impath = op.join('subdir', 'image.nii.gz')
+ lnpath = op.join('subdir', 'link.nii.gz')
+ touch(impath)
+ os.symlink('image.nii.gz', lnpath)
+ cap = CaptureStdout()
+ with cap:
+ assert imtest.main([lnpath]) == 0
+ assert cap.stdout.strip() == '1'
diff --git a/tests/test_scripts/test_remove_ext.py b/tests/test_scripts/test_remove_ext.py
new file mode 100644
index 0000000000000000000000000000000000000000..bb65a893af9d8dd6f3b6abcb5f60b1f7b4e576d9
--- /dev/null
+++ b/tests/test_scripts/test_remove_ext.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+#
+# test_remove_ext.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import fsl.scripts.remove_ext as remove_ext
+
+from tests import CaptureStdout
+
+def test_usage():
+ assert remove_ext.main([]) != 0
+
+def test_remove_ext():
+ # (input, expected output)
+ tests = [
+ ('a', 'a'),
+ ('a.nii', 'a'),
+ ('a.nii.gz', 'a'),
+ ('a.txt', 'a.txt'),
+ ('a.nii b.img c.hdr', 'a b c'),
+ ('a.nii b.img b.hdr', 'a b b'),
+ ('a b.img c.txt', 'a b c.txt'),
+ ('a.nii.gz b c.mnc', 'a b c'),
+ ]
+
+ for input, expected in tests:
+
+ cap = CaptureStdout()
+ with cap:
+ ret = remove_ext.main(input.split())
+
+ assert ret == 0
+
+ got = cap.stdout.split()
+ assert sorted(got) == sorted(expected.split())
diff --git a/tests/test_scripts/test_vest2text.py b/tests/test_scripts/test_vest2text.py
new file mode 100644
index 0000000000000000000000000000000000000000..15cca4f5a22eb0d96cff4827ff4a3309489b4f05
--- /dev/null
+++ b/tests/test_scripts/test_vest2text.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+#
+# test_vest2text.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import numpy as np
+
+import fsl.data.vest as fslvest
+import fsl.scripts.Text2Vest as Text2Vest
+import fsl.scripts.Vest2Text as Vest2Text
+
+from tests import tempdir
+
+
+def test_usage():
+ assert Vest2Text.main([]) == 0
+ assert Text2Vest.main([]) == 0
+
+
+def test_Vest2Text():
+ with tempdir():
+ data = np.random.random((20, 10))
+ vest = fslvest.generateVest(data)
+
+ with open('data.vest', 'wt') as f:
+ f.write(vest)
+
+ assert Vest2Text.main(['data.vest', 'data.txt']) == 0
+
+ got = np.loadtxt('data.txt')
+
+ assert np.all(np.isclose(data, got))
+
+
+def test_Text2Vest():
+ with tempdir():
+ data = np.random.random((20, 10))
+
+ np.savetxt('data.txt', data)
+
+ assert Text2Vest.main(['data.txt', 'data.vest']) == 0
+
+ got = fslvest.loadVestFile('data.vest', ignoreHeader=False)
+
+ assert np.all(np.isclose(data, got))
diff --git a/tests/test_vest.py b/tests/test_vest.py
index 407c502ef633880cfb072581be1a2a47e7a97581..a49f5fc3afb7c5469438a8facf70aed35a079ca1 100644
--- a/tests/test_vest.py
+++ b/tests/test_vest.py
@@ -6,16 +6,20 @@
#
-import os.path as op
-import shutil
-import tempfile
-import warnings
+import os.path as op
+import textwrap as tw
+import io
+import shutil
+import tempfile
+import warnings
-import numpy as np
-import pytest
+import numpy as np
+import pytest
import fsl.data.vest as vest
+from tests import tempdir
+
testfile1 = """%!VEST-LUT
%%BeginInstance
@@ -214,3 +218,75 @@ def test_loadVestLutFile():
finally:
shutil.rmtree(testdir)
+
+
+def test_generateVest():
+ def readvest(vstr):
+ lines = vstr.split('\n')
+ nrows = [l for l in lines if 'NumPoints' in l][0]
+ ncols = [l for l in lines if 'NumWaves' in l][0]
+ nrows = int(nrows.split()[1])
+ ncols = int(ncols.split()[1])
+ data = '\n'.join(lines[3:])
+ data = np.loadtxt(io.StringIO(data)).reshape((nrows, ncols))
+
+ return ((nrows, ncols), data)
+
+ # shape, expectedshape
+ tests = [
+ ((10, ), ( 1, 10)),
+ ((10, 1), (10, 1)),
+ (( 1, 10), ( 1, 10)),
+ (( 3, 5), ( 3, 5)),
+ (( 5, 3), ( 5, 3))
+ ]
+
+ for shape, expshape in tests:
+ data = np.random.random(shape)
+ vstr = vest.generateVest(data)
+
+ gotshape, gotdata = readvest(vstr)
+
+ data = data.reshape(expshape)
+
+ assert expshape == gotshape
+ assert np.all(np.isclose(data, gotdata))
+
+
+def test_loadVestFile():
+ def genvest(data, path, shapeOverride=None):
+ if shapeOverride is None:
+ nrows, ncols = data.shape
+ else:
+ nrows, ncols = shapeOverride
+
+ with open(path, 'wt') as f:
+ f.write(f'/NumWaves {ncols}\n')
+ f.write(f'/NumPoints {nrows}\n')
+ f.write( '/Matrix\n')
+
+ if np.issubdtype(data.dtype, np.integer): fmt = '%d'
+ else: fmt = '%0.12f'
+
+ np.savetxt(f, data, fmt=fmt)
+
+ with tempdir():
+ data = np.random.randint(1, 100, (10, 20))
+ genvest(data, 'data.vest')
+ assert np.all(data == vest.loadVestFile('data.vest'))
+
+ data = np.random.random((20, 10))
+ genvest(data, 'data.vest')
+ assert np.all(np.isclose(data, vest.loadVestFile('data.vest')))
+
+ # should pass
+ vest.loadVestFile('data.vest', ignoreHeader=False)
+
+ # invalid VEST header
+ genvest(data, 'data.vest', (10, 20))
+
+ # default behaviour - ignore header
+ assert np.all(np.isclose(data, vest.loadVestFile('data.vest')))
+
+ with pytest.raises(ValueError):
+ vest.loadVestFile('data.vest', ignoreHeader=False)