fsl/scripts/__init__.py

-#!/usr/bin/env python
-#
-# __init__.py - The fsl.scripts package.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""The ``fsl.scripts`` package contains all of the executable scripts provided
-by ``fslpy``.
-"""

fsl/scripts/atlasq.py

@@ -19,20 +19,9 @@ import              warnings
 import              logging
 import numpy     as np
 
-# if h5py <= 2.7.1 is installed,
-# it will be imported via nibabel,
-# and will cause a numpy warning
-# to be emitted.
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.data.image as fslimage
-
-# If wx is not present, then fsl.utils.platform
-# will complain that it is not present.
-logging.getLogger('fsl.utils.platform').setLevel(logging.ERROR)
-
-import fsl.data.atlases as fslatlases  # noqa
-import fsl.version      as fslversion  # noqa
+import fsl.data.image   as fslimage
+import fsl.data.atlases as fslatlases
+import fsl.version      as fslversion
 
 
 log = logging.getLogger(__name__)
@@ -381,7 +370,7 @@ def maskQuery(atlas, masks, *args, **kwargs):
 
             labels = []
             props  = []
-            zprops = atlas.maskProportions(mask)
+            zprops = atlas.maskValues(mask)
 
             for i in range(len(zprops)):
                 if zprops[i] > 0:
@@ -405,7 +394,7 @@ def coordQuery(atlas, coords, voxel, *args, **kwargs):
 
         if isinstance(atlas, fslatlases.ProbabilisticAtlas):
 
-            props   = atlas.proportions(coord, voxel=voxel)
+            props   = atlas.values(coord, voxel=voxel)
             labels  = []
             nzprops = []
 
@@ -569,10 +558,10 @@ def parseArgs(args):
     usages = {
         'main'    : 'usage: atlasq [-h] command [options]',
         'ohi'     : textwrap.dedent("""
-                     usage: atlasq ohi -h
-                            atlasq ohi --dumpatlases
-                            atlasq ohi -a atlas -c X,Y,Z
-                            atlasq ohi -a atlas -m mask
+                     usage: atlasquery -h
+                            atlasquery --dumpatlases
+                            atlasquery -a atlas -c X,Y,Z
+                            atlasquery -a atlas -m mask
         """).strip(),
         'list'    : 'usage: atlasq list [-e]',
         'summary' : 'usage: atlasq summary atlas',

fsl/scripts/fsl_abspath.py

+#!/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())

fsl/scripts/fsl_apply_x5.py

+#!/usr/bin/env python
+#
+# fsl_apply_x5.py - Apply an X5 transformation to an image.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""The ``fsl_apply_x5`` script can be used to apply an X5 transformation file
+to resample an image.
+"""
+
+
+import functools as ft
+import              sys
+import              argparse
+
+import fsl.transform.x5         as x5
+import fsl.transform.nonlinear  as nonlinear
+import fsl.utils.parse_data     as parse_data
+import fsl.utils.image.resample as resample
+import fsl.data.image           as fslimage
+
+
+def parseArgs(args):
+    """Parses command-line arguments.
+
+    :arg args: Sequence of command-line arguments. If ``None``, ``sys.argv``
+               is used
+    :returns:  An ``argparse.Namespace`` object containing parsed arguments
+    """
+
+    parser = argparse.ArgumentParser('fsl_apply_x5')
+    flags  = {
+        'input'  : ('input',),
+        'xform'  : ('xform',),
+        'output' : ('output',),
+        'interp' : ('-i', '--interp'),
+        'ref'    : ('-r', '--ref'),
+    }
+
+    helps  = {
+        'input'  : 'Input image',
+        'xform'  : 'X5 transformation file',
+        'output' : 'Output image',
+        'interp' : 'Interpolation (default: linear)',
+        'ref'    : 'Alternate reference image (default: '
+                   'reference specified in X5 file)',
+    }
+    opts = {
+        'input'  : dict(help=helps['input'],
+                        type=parse_data.Image),
+        'xform'  : dict(help=helps['xform']),
+        'output' : dict(help=helps['output'],
+                        type=parse_data.ImageOut),
+        'interp' : dict(help=helps['interp'],
+                        choices=('nearest', 'linear', 'cubic'),
+                        default='linear'),
+        'ref'    : dict(help=helps['ref'],
+                        type=parse_data.Image),
+    }
+
+    parser.add_argument(*flags['input'],  **opts['input'])
+    parser.add_argument(*flags['xform'],  **opts['xform'])
+    parser.add_argument(*flags['output'], **opts['output'])
+    parser.add_argument(*flags['interp'], **opts['interp'])
+    parser.add_argument(*flags['ref'],    **opts['ref'])
+
+    if len(args) == 0:
+        parser.print_help()
+        sys.exit(0)
+
+    args = parser.parse_args(args)
+
+    if   args.interp == 'nearest': args.interp = 0
+    elif args.interp == 'linear':  args.interp = 1
+    elif args.interp == 'cubic':   args.interp = 3
+
+    return args
+
+
+def applyLinear(args):
+    """Applies a linear X5 transformation file to the input.
+
+    :arg args: ``argparse.Namespace`` object
+    :returns:  The transformed input as an :class:`.Image` object
+    """
+
+    input           = args.input
+    xform, src, ref = x5.readLinearX5(args.xform)
+
+    if args.ref is not None:
+        ref = args.ref
+
+    res, xform = resample.resampleToReference(input,
+                                              ref,
+                                              matrix=xform,
+                                              order=args.interp)
+
+    return fslimage.Image(res, xform=xform, header=ref.header)
+
+
+def applyNonlinear(args):
+    """Applies a non-linear X5 transformation file to the input.
+
+    :arg args: ``argparse.Namespace`` object
+    :returns:  The transformed input as an :class:`.Image` object
+    """
+
+    field = x5.readNonLinearX5(args.xform)
+
+    if args.ref is None: ref = field.ref
+    else:                ref = args.ref
+
+    result = nonlinear.applyDeformation(args.input,
+                                        field,
+                                        ref=ref,
+                                        order=args.interp,
+                                        mode='constant')
+
+    return fslimage.Image(result, header=ref.header)
+
+
+def main(args=None):
+    """Entry point. Parse command-line arguments, then calls
+    :func:`applyLinear` or :func:`applyNonlinear` depending on the x5 file
+    type.
+    """
+
+    if args is None:
+        args = sys.argv[1:]
+
+    print()
+    print('Warning: this version of fsl_apply_x5 is a development release.\n'
+          'Interface, behaviour, and input/output formats of future versions\n'
+          'may differ substantially from this version.')
+    print()
+
+    args = parseArgs(args)
+
+    if x5.inferType(args.xform) == 'linear':
+        result = applyLinear(args)
+    else:
+        result = applyNonlinear(args)
+
+    result.save(args.output)
+
+
+if __name__ == '__main__':
+    sys.exit(main())

fsl/scripts/fsl_convert_x5.py

 #!/usr/bin/env python
 #
-# fsl_convert_x5.py -
+# fsl_convert_x5.py - Convert between FSL and X5 transformation files.
 #
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
+"""This script can be used to convert between FSL and X5 linear and non-linear
+transformation file formats.
+"""
 
 
-import os.path as op
-import            sys
-import            shutil
-import            logging
-import            argparse
+import os.path   as op
+import functools as ft
+import textwrap  as tw
+import              sys
+import              shutil
+import              logging
+import              argparse
 
-import fsl.data.image as fslimage
-import fsl.transform  as transform
+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__)
 
 
 def parseArgs(args):
+    """Create an argument parser and parse the given ``args``.
+
+    :arg args: Sequence of commane line arguments.
+    :return:   An ``argparse.Namespace`` object containing parsed arguments.
+    """
+
+    helps = {
+        'input'         : 'Input file',
+        'output'        : 'Output file',
+        'source'        : 'Source image',
+        'reference'     : 'Reference image',
+        'input_format'  : 'Input format - if not provided, the input format '
+                          'is automatically inferred from the input file '
+                          'name.',
+        'output_format' : 'Output format - if not provided, the output format '
+                          'is automatically inferred from the output file '
+                          'name.',
+    }
+
+    epilog = tw.dedent("""
+    If the input and output file formats are the same, the input file
+    is simply copied to the output file.
+    """).strip()
 
     parser     = argparse.ArgumentParser('fsl_convert_x5')
     subparsers = parser.add_subparsers(dest='ctype')
-    flirt      = subparsers.add_parser('flirt')
-    fnirt      = subparsers.add_parser('fnirt')
-
-
-    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'))
-
-    intype  = fnirt.add_mutually_exclusive_group()
-    outtype = fnirt.add_mutually_exclusive_group()
-
-    fnirt  .add_argument('input')
-    fnirt  .add_argument('output')
-    fnirt  .add_argument('-s',  '--source')
-    fnirt  .add_argument('-r',  '--reference')
-    fnirt  .add_argument('-if', '--input_format',  choices=('x5', 'nii'))
-    fnirt  .add_argument('-of', '--output_format', choices=('x5', 'nii'))
-    intype .add_argument('-ai', '--absin',  action='store_const', const='absolute', dest='inDispType')
-    intype .add_argument('-ri', '--relin',  action='store_const', const='relative', dest='inDispType')
-    outtype.add_argument('-ao', '--absout', action='store_const', const='absolute', dest='outDispType')
-    outtype.add_argument('-ro', '--relout', action='store_const', const='relative', dest='outDispType')
-
-    args = parser.parse_args(args)
-
-    if args.ctype is None:
+    flirt      = subparsers.add_parser('flirt', epilog=epilog)
+    fnirt      = subparsers.add_parser('fnirt', epilog=epilog)
+    imgtype    = parse_data.Image
+
+    flirt.add_argument('input',                  help=helps['input'])
+    flirt.add_argument('output',                 help=helps['output'])
+    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'],
+                       choices=('x5', 'mat'))
+
+    fnirt  .add_argument('input',                  help=helps['input'])
+    fnirt  .add_argument('output',                 help=helps['output'])
+    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'],
+                         choices=('x5', 'nii'))
+
+    if len(args) == 0:
         parser.print_help()
         sys.exit(0)
 
-    def getfmt(arg, fname):
+    if len(args) == 1:
+        if   args[0] == 'flirt':
+            flirt.print_help()
+            sys.exit(0)
+        elif args[0] == 'fnirt':
+            fnirt.print_help()
+            sys.exit(0)
+
+    args = parser.parse_args(args)
+
+    # If input/output formats were not
+    # specified, infer them from the
+    # file names
+    def getfmt(arg, fname, exist):
         ext = op.splitext(fname)[1]
         if ext in ('.mat', '.x5'):
             return ext[1:]
-        if fslimage.looksLikeImage(fslimage.fixExt(fname)):
+
+        fname = fslimage.addExt(fname, mustExist=exist)
+
+        if fslimage.looksLikeImage(fname):
             return 'nii'
         parser.error('Could not infer format from '
                      'filename: {}'.format(args.input))
 
-    if args.input_format  is None: args.input_format  = getfmt('input',  args.input)
-    if args.output_format is None: args.output_format = getfmt('output', args.output)
+    if args.input_format  is None:
+        args.input_format  = getfmt('input',  args.input, True)
+    if args.output_format is None:
+        args.output_format = getfmt('output', args.output, False)
+
+    # The source and reference arguments are
+    # required if the input is a FLIRT matrix
+    # or a FNIRT displacement/coefficient field.
+    if args.input_format in ('mat', 'nii') and \
+       (args.source is None or args.reference is None):
+        parser.error('You must specify a source and reference '
+                     'when the input is not an X5 file!')
 
     return args
 
 
 def flirtToX5(args):
-    src   = fslimage.Image(args.source,    loadData=False)
-    ref   = fslimage.Image(args.reference, loadData=False)
-    xform = transform.readFlirt(args.input)
-    xform = transform.fromFlirt(xform, src, ref, 'world', 'world')
-    transform.writeLinearX5(args.output, xform, src, ref)
+    """Convert a linear FLIRT transformation matrix to an X5 transformation
+    file.
+    """
+    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)
 
 
 def X5ToFlirt(args):
-    xform, src, ref = transform.readLinearX5(args.input)
-    xform           = transform.toFlirt(xform, src, ref, 'world', 'world')
-    transform.writeFlirt(xform, args.output)
+    """Convert a linear X5 transformation file to a FLIRT matrix. """
+    xform, src, ref = x5.readLinearX5(args.input)
+    xform           = flirt.toFlirt(xform, src, ref, 'world', 'world')
+    flirt.writeFlirt(xform, args.output)
 
 
 def fnirtToX5(args):
-    src   = fslimage.Image(args.source,    loadData=False)
-    ref   = fslimage.Image(args.reference, loadData=False)
-    field = transform.readFnirt(args.input,
-                                src=src,
-                                ref=ref,
-                                dispType=args.inDispType)
-    field = transform.fromFnirt(field, 'world', 'world')
-    transform.writeNonLinearX5(args.output, field)
+    """Convert a non-linear FNIRT transformation into an X5 transformation
+    file.
+    """
+    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)
 
 
 def X5ToFnirt(args):
-    field = transform.readNonLinearX5(args.input)
-    field = transform.toFnirt(field, 'world', 'world')
-    transform.writeFnirt(field, args.output)
+    """Convert a non-linear X5 transformation file to a FNIRT-style
+    transformation file.
+    """
+    field = x5.readNonLinearX5(args.input)
+    field = fnirt.toFnirt(field)
+    field.save(args.output)
 
 
 def doFlirt(args):
+    """Converts a linear FIRT transformation file to or from the X5 format. """
     infmt  = args.input_format
     outfmt = args.output_format
 
@@ -110,6 +174,9 @@ def doFlirt(args):
 
 
 def doFnirt(args):
+    """Converts a non-linear FNIRT transformation file to or from the X5
+    format.
+    """
     infmt  = args.input_format
     outfmt = args.output_format
 
@@ -119,15 +186,28 @@ def doFnirt(args):
 
 
 def main(args=None):
+    """Entry point. Calls :func:`doFlirt` or :func:`doFnirt` depending on
+    the sub-command specified in the arguments.
+
+    :arg args: Sequence of command-line arguments. If not provided,
+               ``sys.argv`` is used.
+    """
 
     if args is None:
         args = sys.argv[1:]
 
-    args   = parseArgs(args)
-    ctype  = args.ctype
+    print()
+    print('Warning: this version of fsl_convert_x5 is a development release.\n'
+          'Interface, behaviour, and input/output formats of future versions\n'
+          'may differ substantially from this version.')
+    print()
+
+    args = parseArgs(args)
+
+    if   args.ctype == 'flirt': doFlirt(args)
+    elif args.ctype == 'fnirt': doFnirt(args)
 
-    if   ctype == 'flirt': doFlirt(args)
-    elif ctype == 'fnirt': doFnirt(args)
+    return 0
 
 
 if __name__ == '__main__':

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
@@ -18,12 +16,8 @@ import            warnings
 
 import numpy   as np
 
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-
-    import fsl.data.fixlabels       as fixlabels
-    import fsl.data.melodicanalysis as melanalysis
+import fsl.data.fixlabels       as fixlabels
+import fsl.data.melodicanalysis as melanalysis
 
 
 DTYPE = np.float64

fsl/scripts/imcp.py

@@ -12,19 +12,13 @@ The :func:`main` function is essentially a wrapper around the
 """
 
 
-from __future__ import print_function
-
 import os.path        as op
 import                   sys
-import                   warnings
+import                   logging
 
 import fsl.utils.path as fslpath
-
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.utils.imcp as imcp
-    import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
 
 
 usage = """Usage:
@@ -59,6 +53,11 @@ def main(argv=None):
         print(usage)
         return 1
 
+    # When converting to NIFTI2, nibabel
+    # emits an annoying message via log.warning:
+    #   sizeof_hdr should be 540; set sizeof_hdr to 540
+    logging.getLogger('nibabel').setLevel(logging.ERROR)
+
     try:
         srcs = [fslimage.fixExt(s) for s in srcs]
         srcs = fslpath.removeDuplicates(

fsl/scripts/imglob.py

@@ -9,17 +9,11 @@ NIFTI/ANALYZE image files.
 """
 
 
-from __future__ import print_function
-
+import itertools      as it
+import                   glob
 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: imglob [-extension/extensions] <list of names>
@@ -27,8 +21,17 @@ Usage: imglob [-extension/extensions] <list of names>
        -extensions for image list with full extensions
 """.strip()
 
-exts   = fslimage.ALLOWED_EXTENSIONS
-groups = fslimage.FILE_GROUPS
+
+# The lists below are defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts   = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.hdr.gz']
+"""List of supported image file extensions. """
+
+
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
 
 
 def imglob(paths, output=None):
@@ -61,12 +64,38 @@ def imglob(paths, output=None):
 
     imgfiles = []
 
+    # Expand any wildcard paths if provided.
+    # Depending on the way that imglob is
+    # invoked, this may not get done by the
+    # calling shell.
+    #
+    # We also have to handle incomplete
+    # wildcards, e.g. if the user provides
+    # "img_??", we need to add possible
+    # file suffixes before it can be
+    # expanded.
+    expanded = []
+    for path in paths:
+        if any(c in path for c in '*?[]'):
+            if fslpath.hasExt(path, exts):
+                globs = [path]
+            else:
+                globs = [f'{path}{ext}' for ext in exts]
+            globs = [glob.glob(g) for g in globs]
+            expanded.extend(it.chain(*globs))
+        else:
+            expanded.append(path)
+
+    paths = expanded
+
     # Build a list of all image files (both
     # hdr and img and otherwise) that match
     for path in paths:
         try:
-            path = fslimage.removeExt(path)
-            imgfiles.extend(fslimage.addExt(path, unambiguous=False))
+            path = fslpath.removeExt(path, allowedExts=exts)
+            imgfiles.extend(fslpath.addExt(path,
+                                           allowedExts=exts,
+                                           unambiguous=False))
         except fslpath.PathError:
             continue
 

fsl/scripts/imln.py

+#!/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 fsl.utils.path as fslpath
+
+
+# The lists below are defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
+
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
+
+
+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,   exts)
+    linkbase         = fslpath.removeExt(linkbase, exts)
+
+    # 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=exts,
+                                       fileGroups=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, exts)
+        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())

fsl/scripts/immv.py

@@ -13,19 +13,13 @@ The :func:`main` function is essentially a wrapper around the
 """
 
 
-from __future__ import print_function
-
 import os.path        as op
 import                   sys
-import                   warnings
+import                   logging
 
 import fsl.utils.path as fslpath
-
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.utils.imcp as imcp
-    import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
 
 
 usage = """Usage:
@@ -60,6 +54,11 @@ def main(argv=None):
         print(usage)
         return 1
 
+    # When converting to NIFTI2, nibabel
+    # emits an annoying message via log.warning:
+    #   sizeof_hdr should be 540; set sizeof_hdr to 540
+    logging.getLogger('nibabel').setLevel(logging.ERROR)
+
     try:
         srcs = [fslimage.fixExt(s) for s in srcs]
         srcs = fslpath.removeDuplicates(

fsl/scripts/imrm.py

+#!/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 os.path            as op
+import                       os
+import                       sys
+import fsl.scripts.imglob as imglob
+
+
+usage = """Usage: imrm <list of image names to remove>
+NB: filenames can be basenames or not
+""".strip()
+
+
+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
+
+    paths = imglob.imglob(argv, 'all')
+
+    for path in paths:
+        if op.exists(path):
+            os.remove(path)
+
+    return 0
+
+
+if __name__ == '__main__':
+    sys.exit(main())

fsl/scripts/imtest.py

+#!/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 fsl.utils.path as fslpath
+
+
+# The lists below are defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
+
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
+
+
+def imtest(path):
+    """Returns ``True`` if the given image path exists, False otherwise. """
+
+    path = fslpath.removeExt(path, exts)
+    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=exts,
+                             fileGroups=groups,
+                             unambiguous=True)
+        return True
+
+    except fslpath.PathError:
+        return False
+
+
+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
+
+    if imtest(argv[0]):
+        print('1')
+    else:
+        print('0')
+
+    return 0
+
+
+if __name__ == '__main__':
+    sys.exit(main())

fsl/scripts/remove_ext.py

+#!/usr/bin/env python
+#
+# remove_ext.py - Remove file extensions from NIFTI image paths
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import                   sys
+import fsl.utils.path as fslpath
+
+
+usage = """Usage: remove_ext <list of image paths to remove extension from>
+""".strip()
+
+
+# This list is defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.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, exts))
+
+    print(' '.join(removed))
+
+    return 0
+
+
+if __name__ == '__main__':
+    sys.exit(main())

tests/__init__.py → fsl/tests/__init__.py

@@ -10,6 +10,7 @@
 import              os
 import              sys
 import              glob
+import              hashlib
 import              shutil
 import              fnmatch
 import              logging
@@ -20,14 +21,12 @@ import os.path   as op
 import numpy     as np
 import nibabel   as nib
 
-from six import StringIO
+from io import StringIO
 
-
-try: from unittest import mock
-except ImportError: import mock
+from unittest import mock
 
 import fsl.data.image                     as fslimage
-from   fsl.utils.tempdir import              tempdir
+from   fsl.utils.tempdir  import             tempdir
 from   fsl.utils.platform import platform as fslplatform
 
 
@@ -50,7 +49,10 @@ def mockFSLDIR(**kwargs):
                 if not op.isdir(subdir):
                     os.makedirs(subdir)
                 for fname in files:
-                    touch(op.join(subdir, fname))
+                    fname = op.join(subdir, fname)
+                    touch(fname)
+                    if subdir == bindir:
+                        os.chmod(fname, 0o755)
             fslplatform.fsldir = fsldir
             fslplatform.fsldevdir = None
 
@@ -68,7 +70,7 @@ def touch(fname):
         pass
 
 
-class CaptureStdout(object):
+class CaptureStdout:
     """Context manager which captures stdout and stderr. """
 
     def __init__(self):
@@ -87,6 +89,7 @@ class CaptureStdout(object):
 
         sys.stdout = self.__mock_stdout
         sys.stderr = self.__mock_stderr
+        return self
 
 
     def __exit__(self, *args, **kwargs):
@@ -145,6 +148,8 @@ def testdir(contents=None, suffix=""):
             shutil.rmtree(self.testdir)
 
     return ctx(contents)
+testdir.__test__ = False
+
 
 def make_dummy_files(paths):
     """Creates dummy files for all of the given paths. """
@@ -284,7 +289,8 @@ def make_mock_feat_analysis(featdir,
                             copes=True,
                             zstats=True,
                             residuals=True,
-                            clustMasks=True):
+                            clustMasks=True,
+                            zfstats=True):
 
     if xform is None:
         xform = np.eye(4)
@@ -317,6 +323,7 @@ def make_mock_feat_analysis(featdir,
             data = np.ravel_multi_index(data, shape)
             data = data.reshape(list(shape) + [1]).repeat(timepoints, axis=3)
             data[..., :] += range(i, i + timepoints)
+            data = data.astype(np.int32)
 
             img = nib.nifti1.Nifti1Image(data, xform)
 
@@ -341,6 +348,11 @@ def make_mock_feat_analysis(featdir,
         otherFiles .extend(files)
         otherShapes.extend([shape] * len(files))
 
+    if zfstats:
+        files = glob.glob(op.join(featdir, 'stats', 'zfstat*nii.gz'))
+        otherFiles .extend(files)
+        otherShapes.extend([shape] * len(files))
+
     if residuals:
         files = glob.glob(op.join(featdir, 'stats', 'res4d.nii.gz'))
         otherFiles .extend(files)
@@ -428,3 +440,10 @@ def make_random_mask(filename, shape, xform, premask=None, minones=1):
     img.save(filename)
 
     return img
+
+
+def sha256(filename):
+    hashobj = hashlib.sha256()
+    with open(filename, 'rb') as f:
+        hashobj.update(f.read())
+    return hashobj.hexdigest()

tests/test_assertions.py → fsl/tests/test_assertions.py

@@ -14,8 +14,8 @@ import pytest
 import fsl.utils.assertions as assertions
 import fsl.utils.tempdir    as tempdir
 
-from . import make_random_image
-from . import testdir
+from fsl.tests import make_random_image
+from fsl.tests import testdir
 
 
 def test_assertFileExists():
@@ -160,14 +160,14 @@ def test_assertIsMelodicDir():
         ('analysis.ica', [                      'melodic_mix', 'melodic_FTmix'], False),
         ('analysis.ica', ['melodic_IC.nii.gz',                 'melodic_FTmix'], False),
         ('analysis.ica', ['melodic_IC.nii.gz',  'melodic_mix'],                  False),
-        ('analysis',     ['melodic_IC.nii.gz',  'melodic_mix', 'melodic_FTmix'], False),
-        ('analysis',     ['melodic_oIC.nii.gz', 'melodic_mix', 'melodic_FTmix'], False),
+        ('analysis',     ['melodic_IC.nii.gz',  'melodic_mix', 'melodic_FTmix'], True),
+        ('analysis',     [                      'melodic_mix', 'melodic_FTmix'], False),
     ]
 
     for dirname, paths, expected in tests:
         with testdir(paths, dirname):
             if expected:
-                assertions.assertIsMelodicDir(dirname)
+                assertions.assertIsMelodicDir('.')
             else:
                 with pytest.raises(AssertionError):
                     assertions.assertIsMelodicDir(dirname)

tests/test_atlases.py → fsl/tests/test_atlases.py

@@ -13,14 +13,15 @@ import              os
 import os.path   as op
 import numpy     as np
 
-import mock
+
+from unittest import mock
 import pytest
 
-import tests
+import fsl.tests                as tests
 import fsl.utils.image.resample as resample
 import fsl.data.atlases         as atlases
 import fsl.data.image           as fslimage
-import fsl.transform            as transform
+import fsl.transform.affine     as affine
 
 
 datadir = op.join(op.dirname(__file__), 'testdata')
@@ -40,7 +41,8 @@ dummy_atlas_desc = """<?xml version="1.0" encoding="ISO-8859-1"?>
   <header>
     <name>{name}</name>
     <shortname>{shortname}</shortname>
-    <type>Label</type>
+    <type>{atlastype}</type>
+    {extraheader}
     <images>
       <imagefile>/{shortname}/{filename}</imagefile>
        <summaryimagefile>/{shortname}/My{filename}</summaryimagefile>
@@ -52,7 +54,8 @@ dummy_atlas_desc = """<?xml version="1.0" encoding="ISO-8859-1"?>
   </data>
 </atlas>
 """
-def _make_dummy_atlas(savedir, name, shortName, filename):
+def _make_dummy_atlas(
+        savedir, name, shortName, filename, atlastype='Label', extraheader=''):
     mladir     = op.join(savedir, shortName)
     mlaxmlfile = op.join(savedir, '{}.xml'.format(shortName))
     mlaimgfile = op.join(savedir, shortName, '{}.nii.gz'.format(filename))
@@ -70,7 +73,9 @@ def _make_dummy_atlas(savedir, name, shortName, filename):
         desc = dummy_atlas_desc.format(
             name=name,
             shortname=shortName,
-            filename=filename)
+            filename=filename,
+            atlastype=atlastype,
+            extraheader=extraheader)
         f.write(desc)
 
     return mlaxmlfile
@@ -142,6 +147,28 @@ def test_AtlasDescription():
         registry.getAtlasDescription('non-existent-atlas')
 
 
+def test_StatisticHeader():
+    with tests.testdir() as testdir:
+        hdr = '<statistic>T</statistic>' \
+              '<units></units>' \
+              '<precision>3</precision>' \
+              '<upper>75</upper>'
+        xmlfile = _make_dummy_atlas(testdir,
+                                    'statlas',
+                                    'STA',
+                                    'StAtlas',
+                                    atlastype='Statistic',
+                                    extraheader=hdr)
+
+        desc = atlases.AtlasDescription(xmlfile, 'StAtlas')
+        assert desc.atlasType == 'statistic'
+        assert desc.statistic == 'T'
+        assert desc.units     == ''
+        assert desc.precision == 3
+        assert desc.lower     == 0
+        assert desc.upper     == 75
+
+
 def test_add_remove_atlas():
 
     with tests.testdir() as testdir:
@@ -225,8 +252,7 @@ def test_load_atlas():
     reg = atlases.registry
     reg.rescanAtlases()
 
-    probatlas    = reg.loadAtlas('harvardoxford-cortical',
-                                 calcRange=False, loadData=False)
+    probatlas    = reg.loadAtlas('harvardoxford-cortical')
     probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
     lblatlas     = reg.loadAtlas('talairach')
 
@@ -250,6 +276,9 @@ def test_get():
             assert (target == atlas.get(index=label.index).data).all()
             assert (target == atlas.get(value=label.value).data).all()
             assert (target == atlas.get(name=label.name).data).all()
+            if atlas is lblatlas:
+                target = target * label.value
+                assert (target == atlas.get(value=label.value, binary=False).data).all()
 
 
 def test_find():
@@ -257,8 +286,7 @@ def test_find():
     reg = atlases.registry
     reg.rescanAtlases()
 
-    probatlas    = reg.loadAtlas('harvardoxford-cortical',
-                                 calcRange=False, loadData=False)
+    probatlas    = reg.loadAtlas('harvardoxford-cortical')
     probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
     lblatlas     = reg.loadAtlas('talairach')
 
@@ -305,8 +333,7 @@ def test_prepareMask():
     reg = atlases.registry
     reg.rescanAtlases()
 
-    probatlas    = reg.loadAtlas('harvardoxford-cortical',
-                                 loadData=False, calcRange=False)
+    probatlas    = reg.loadAtlas('harvardoxford-cortical')
     probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
     lblatlas     = reg.loadAtlas('talairach')
 
@@ -326,7 +353,7 @@ def test_prepareMask():
             np.random.random(list(ashape) + [2]))
         wrongspace    = fslimage.Image(
             np.random.random((20, 20, 20)),
-            xform=transform.concat(atlas.voxToWorldMat, np.diag([2, 2, 2, 1])))
+            xform=affine.concat(atlas.voxToWorldMat, np.diag([2, 2, 2, 1])))
 
         with pytest.raises(atlases.MaskError):
             atlas.prepareMask(wrongdims)

tests/test_atlases_query.py → fsl/tests/test_atlases_query.py

@@ -13,11 +13,11 @@ import                    pytest
 
 import fsl.data.atlases         as fslatlases
 import fsl.data.image           as fslimage
-import fsl.transform            as transform
+import fsl.transform.affine     as affine
 import fsl.utils.image.resample as resample
 import fsl.utils.cache          as cache
 
-from . import (testdir, make_random_mask)
+from fsl.tests import (testdir, make_random_mask)
 
 
 pytestmark = pytest.mark.fsltest
@@ -41,17 +41,16 @@ _atlases = cache.Cache()
 def _get_atlas(atlasID, res, summary=False):
     atlas = _atlases.get((atlasID, res, summary), default=None)
     if atlas is None:
+        atlas = fslatlases.loadAtlas(atlasID,
+                                     loadSummary=summary,
+                                     resolution=res)
+
+        # We need some atlases to be loaded into memory,
+        # so we can use boolean-mask-based indexing
         if summary or atlasID in ('talairach', 'striatum-structural',
                                   'jhu-labels', 'smatt'):
-            kwargs = {}
-        else:
-            kwargs = {'loadData'  : False,
-                      'calcRange' : False}
+            atlas.data
 
-        atlas = fslatlases.loadAtlas(atlasID,
-                                     loadSummary=summary,
-                                     resolution=res,
-                                     **kwargs)
         _atlases.put((atlasID, res, summary), atlas)
 
     return atlas
@@ -85,7 +84,7 @@ def _get_zero_mask(aimg):
         elif isinstance(aimg, fslatlases.ProbabilisticAtlas):
 
             # Keep memory usage down
-            zmask = np.ones(aimg.shape[:3], dtype=np.bool)
+            zmask = np.ones(aimg.shape[:3], dtype=bool)
             for vol in range(aimg.shape[-1]):
                 zmask = np.logical_and(zmask, aimg[..., vol] == 0)
 
@@ -155,7 +154,7 @@ def _gen_coord_voxel_query(atlas, qtype, qin, **kwargs):
             dlo = (0, 0, 0)
             dhi = atlas.shape
         else:
-            dlo, dhi = transform.axisBounds(atlas.shape, atlas.voxToWorldMat)
+            dlo, dhi = affine.axisBounds(atlas.shape, atlas.voxToWorldMat)
 
         dlen = [hi - lo for lo, hi in zip(dlo, dhi)]
 
@@ -190,7 +189,7 @@ def _gen_coord_voxel_query(atlas, qtype, qin, **kwargs):
         coords = np.array(coords, dtype=dtype)
 
         if not voxel:
-            coords = transform.transform(coords, atlas.voxToWorldMat)
+            coords = affine.transform(coords, atlas.voxToWorldMat)
 
     return tuple([dtype(c) for c in coords])
 
@@ -200,7 +199,7 @@ def _eval_coord_voxel_query(atlas, query, qtype, qin):
     voxel = qtype == 'voxel'
 
     if voxel: vx, vy, vz = query
-    else:     vx, vy, vz = transform.transform(query, atlas.worldToVoxMat)
+    else:     vx, vy, vz = affine.transform(query, atlas.worldToVoxMat)
 
     vx, vy, vz = [int(round(v)) for v in [vx, vy, vz]]
 
@@ -218,8 +217,8 @@ def _eval_coord_voxel_query(atlas, query, qtype, qin):
         elif qin == 'out':
             expval = []
 
-        assert atlas.proportions(     query, voxel=voxel) == expval
-        assert atlas.coordProportions(query, voxel=voxel) == expval
+        assert atlas.values(     query, voxel=voxel) == expval
+        assert atlas.coordValues(query, voxel=voxel) == expval
 
     if   isinstance(atlas, fslatlases.LabelAtlas):         evalLabel()
     elif isinstance(atlas, fslatlases.ProbabilisticAtlas): evalProb()
@@ -284,7 +283,7 @@ def _eval_mask_query(atlas, query, qtype, qin):
         rmask = resample.resample(
             mask, atlas.shape[:3], dtype=np.float32, order=0)[0]
 
-    rmask = np.array(rmask, dtype=np.bool)
+    rmask = np.array(rmask, dtype=bool)
 
     def evalLabel():
 
@@ -343,13 +342,13 @@ def _eval_mask_query(atlas, query, qtype, qin):
 
         if qin == 'out':
             with pytest.raises(fslatlases.MaskError):
-                atlas.maskProportions(mask)
+                atlas.maskValues(mask)
             with pytest.raises(fslatlases.MaskError):
-                atlas.proportions(    mask)
+                atlas.values(    mask)
             return
 
-        props  = atlas.    proportions(mask)
-        props2 = atlas.maskProportions(mask)
+        props  = atlas.    values(mask)
+        props2 = atlas.maskValues(mask)
 
         assert np.all(np.isclose(props, props2))
 

fsl/tests/test_bids.py

+#!/usr/bin/env python
+#
+# test_bids.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import                  json
+import os.path   as     op
+import itertools as     it
+from   pathlib   import Path
+
+import pytest
+
+from fsl.utils.tempdir import tempdir
+import fsl.utils.bids  as     fslbids
+
+
+def test_parseFilename():
+    badtests = ['bad_file.txt']
+
+    for test in badtests:
+        with pytest.raises(ValueError):
+            fslbids.parseFilename(test)
+
+    tests = [
+        ('sub-01_ses-01_t1w.nii.gz',
+         ({'sub' : '01', 'ses' : '01'}, 't1w')),
+        ('a-1_b-2_c-3_d-4_e.json',
+         ({'a' : '1', 'b' : '2', 'c' : '3', 'd' : '4'}, 'e')),
+    ]
+
+    for filename, expect in tests:
+        assert fslbids.parseFilename(filename) == expect
+
+
+def test_isBIDSDir():
+    with tempdir():
+        assert not fslbids.isBIDSDir('.')
+    with tempdir():
+        Path('dataset_description.json').touch()
+        assert fslbids.isBIDSDir('.')
+
+
+def test_inBIDSDir():
+    with tempdir():
+        Path('a/b/c').mkdir(parents=True)
+        Path('dataset_description.json').touch()
+        assert fslbids.inBIDSDir(Path('.'))
+        assert fslbids.inBIDSDir(Path('a'))
+        assert fslbids.inBIDSDir(Path('a/b'))
+        assert fslbids.inBIDSDir(Path('a/b/c'))
+    with tempdir():
+        Path('a/b/c').mkdir(parents=True)
+        assert not fslbids.inBIDSDir(Path('.'))
+        assert not fslbids.inBIDSDir(Path('a'))
+        assert not fslbids.inBIDSDir(Path('a/b'))
+        assert not fslbids.inBIDSDir(Path('a/b/c'))
+
+
+def test_isBIDSFile():
+    goodfiles = [
+        Path('sub-01_ses-01_t1w.nii.gz'),
+        Path('sub-01_ses-01_t1w.nii'),
+        Path('sub-01_ses-01_t1w.json'),
+        Path('a-1_b-2_c-3_d-4_e.nii.gz'),
+        Path('sub-01_ses-01_t1w.txt'),
+    ]
+    badfiles = [
+        Path('sub-01_ses-01.nii.gz'),
+        Path('sub-01_ses-01_t1w'),
+        Path('sub-01_ses-01_t1w.'),
+        Path('sub_ses-01_t1w.nii.gz'),
+        Path('sub-01_ses_t1w.nii.gz'),
+    ]
+    with tempdir():
+        Path('dataset_description.json').touch()
+        for f in goodfiles: assert     fslbids.isBIDSFile(f)
+        for f in badfiles:  assert not fslbids.isBIDSFile(f)
+    with tempdir():
+        for f in it.chain(goodfiles, badfiles):
+            assert not fslbids.isBIDSFile(f)
+
+
+def test_loadMetadata():
+    dd    = Path('dataset_description.json')
+    t1    = Path('sub-01/func/sub-01_task-stim_bold.nii.gz')
+    json1 = Path('sub-01/func/sub-01_task-stim_bold.json')
+    json2 = Path('sub-01/sub-01_bold.json')
+    json3 = Path('sub-01_t1w.json')
+    json4 = Path('sub-01/task-stim_bold.json')
+    meta1 = {'a' : '1',   'b' : '2'}
+    meta2 = {'a' : '10',  'c' : '3'}
+    meta3 = {'a' : '109', 'b' : '99'}
+    meta4 = {'c' : '9',   'd' : '5'}
+
+    with tempdir():
+        dd.touch()
+        Path(op.dirname(t1)).mkdir(parents=True)
+        t1.touch()
+        assert fslbids.loadMetadata(t1) == {}
+        json1.write_text(json.dumps(meta1))
+        assert fslbids.loadMetadata(t1) == meta1
+        json2.write_text(json.dumps(meta2))
+        assert fslbids.loadMetadata(t1) == {**meta2, **meta1}
+        json3.write_text(json.dumps(meta3))
+        assert fslbids.loadMetadata(t1) == {**meta2, **meta1}
+        json4.write_text(json.dumps(meta4))
+        assert fslbids.loadMetadata(t1) == {**meta4, **meta2, **meta1}
+
+
+def test_loadMetadata_control_characters():
+    dd     = Path('dataset_description.json')
+    t1     = Path('sub-01/func/sub-01_task-stim_bold.nii.gz')
+    json1  = Path('sub-01/func/sub-01_task-stim_bold.json')
+    meta1  =  {"a" : "1",  "b" : "2\x19\x20"}
+    smeta1 = '{"a" : "1",  "b" : "2\x19\x20"}'
+
+    with tempdir():
+        dd.touch()
+        Path(op.dirname(t1)).mkdir(parents=True)
+        t1.touch()
+        assert fslbids.loadMetadata(t1) == {}
+        json1.write_text(smeta1)
+        assert fslbids.loadMetadata(t1) == meta1
+
+
+def test_loadMetadata_symlinked():
+    ddreal = Path('a')
+    t1real = Path('b')
+    j1real = Path('c')
+    j2real = Path('d')
+    j3real = Path('e')
+    j4real = Path('f')
+    dd     = Path('data/dataset_description.json')
+    t1     = Path('data/sub-01/func/sub-01_task-stim_bold.nii.gz')
+    json1  = Path('data/sub-01/func/sub-01_task-stim_bold.json')
+    json2  = Path('data/sub-01/sub-01_bold.json')
+    json3  = Path('data/sub-01_t1w.json')
+    json4  = Path('data/sub-01/task-stim_bold.json')
+    meta1  = {'a' : '1',   'b' : '2'}
+    meta2  = {'a' : '10',  'c' : '3'}
+    meta3  = {'a' : '109', 'b' : '99'}
+    meta4  = {'c' : '9',   'd' : '5'}
+
+    with tempdir():
+        ddreal.touch()
+        t1real.touch()
+        j1real.write_text(json.dumps(meta1))
+        j2real.write_text(json.dumps(meta2))
+        j3real.write_text(json.dumps(meta3))
+        j4real.write_text(json.dumps(meta4))
+
+        Path(op.dirname(t1)).mkdir(parents=True)
+        dd   .symlink_to(op.join('..',             ddreal))
+        t1   .symlink_to(op.join('..', '..', '..', t1real))
+        json1.symlink_to(op.join('..', '..', '..', j1real))
+        json2.symlink_to(op.join('..', '..',       j2real))
+        json3.symlink_to(op.join('..',             j3real))
+        json4.symlink_to(op.join('..', '..',       j4real))
+
+        assert fslbids.loadMetadata(t1) == {**meta4, **meta2, **meta1}

tests/test_cache.py → fsl/tests/test_cache.py

@@ -113,7 +113,55 @@ def test_expiry():
     with pytest.raises(cache.Expired):
         c.get(0)
 
+    with pytest.raises(cache.Expired):
+        c.get(1)
+
     assert c.get(1, default='default') == 'default'
 
     # And that the cache is empty
     assert len(c) == 0
+
+
+def test_lru():
+    c = cache.Cache(maxsize=3, lru=True)
+
+    c[0] = '0'
+    c[1] = '1'
+    c[2] = '2'
+    c[3] = '3'
+
+    # normal behaviour - first inserted
+    # is dropped
+    with pytest.raises(KeyError):
+        assert c.get(0)
+
+    # lru behaviour - oldest accessed is
+    # dropped
+    c[1]
+    c[4] = '4'
+    with pytest.raises(KeyError):
+        c[2]
+
+    c[1]
+    c[3]
+    c[4]
+    assert len(c) == 3
+
+
+
+def test_accessors():
+    c = cache.Cache(maxsize=3)
+
+    c[0] = '0'
+    c[1] = '1'
+    c[2] = '2'
+    c[3] = '3'
+
+    assert list(c.keys())   == [ 1,        2,        3]
+    assert list(c.values()) == ['1',      '2',      '3']
+    assert list(c.items())  == [(1, '1'), (2, '2'), (3, '3')]
+
+    assert 0 not in c
+    assert 1     in c
+    assert 2     in c
+    assert 3     in c