Merge branch 'msc' of https://git.fmrib.ox.ac.uk/paulmc/fslpy into msc

fsl/utils/run.py

@@ -166,8 +166,8 @@ def run(*args, **kwargs):
                      - stderr: Optional file-like object to which the command's
                                standard error stream can be forwarded.
 
-                     - cmd:    If ``True``, the command itself is logged to the
-                               standard output stream(s).
+                     - cmd:    Optional file-like object to which the command itself 
+                               is logged.
 
     :returns:      If ``submit`` is provided, the return value of
                    :func:`.fslsub` is returned. Otherwise returns a single
@@ -194,7 +194,7 @@ def run(*args, **kwargs):
     tee            = log   .get('tee',      False)
     logStdout      = log   .get('stdout',   None)
     logStderr      = log   .get('stderr',   None)
-    logCmd         = log   .get('cmd',      False)
+    logCmd         = log   .get('cmd',      None)
     args           = _prepareArgs(args)
 
     if not bool(submit):
@@ -272,8 +272,8 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
     :arg logStderr: Optional file-like object to which the command's standard
                     error stream can be forwarded.
 
-    :arg logCmd:    If ``True``, the command itself is logged to the standard
-                    output stream(s).
+    :arg logCmd:    Optional file-like object to which the command itself is
+                    logged.
 
     :arg args:      Command to run
 
@@ -308,15 +308,13 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
             if logStdout is not None: outstreams.append(logStdout)
             if logStderr is not None: errstreams.append(logStderr)
 
-            # log the command to
-            # stdout if requested
-            if logCmd:
+            # log the command if requested
+            if logCmd is not None:
                 cmd = ' '.join(args) + '\n'
-                for o in outstreams:
-                    if 'b' in getattr(o, 'mode', 'w'):
-                        o.write(cmd.encode('utf-8'))
-                    else:
-                        o.write(cmd)
+                if 'b' in getattr(logCmd, 'mode', 'w'):
+                    logCmd.write(cmd.encode('utf-8'))
+                else:
+                    logCmd.write(cmd)
 
             stdoutt = _forwardStream(proc.stdout, *outstreams)
             stderrt = _forwardStream(proc.stderr, *errstreams)
@@ -340,23 +338,35 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
 
 
 def runfsl(*args, **kwargs):
-    """Call a FSL command and return its output. This function simply prepends
-    ``$FSLDIR/bin/`` to the command before passing it to :func:`run`.
+    """Call a FSL command and return its output. 
+    
+      This function searches for the command in the following
+      locations (ordered by priority):
+      
+      1. ``FSL_PREFIX``
+      2. ``$FSLDEVDIR/bin``
+      3. ``$FSLDIR/bin``
+
+      If found, the full path to the command is then passed to :func:`run`.
     """
-
-    prefix = None
+    prefixes = []
 
     if FSL_PREFIX is not None:
-        prefix = FSL_PREFIX
-    elif fslplatform.fsldevdir is not None:
-        prefix = op.join(fslplatform.fsldevdir, 'bin')
-    elif fslplatform.fsldir is not None:
-        prefix = op.join(fslplatform.fsldir, 'bin')
-    else:
+        prefixes.append(FSL_PREFIX)
+    if fslplatform.fsldevdir is not None:
+        prefixes.append(op.join(fslplatform.fsldevdir, 'bin'))
+    if fslplatform.fsldir is not None:
+        prefixes.append(op.join(fslplatform.fsldir, 'bin'))
+    
+    if not prefixes:
         raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
 
-    args    = _prepareArgs(args)
-    args[0] = op.join(prefix, args[0])
+    args = _prepareArgs(args)
+    for prefix in prefixes:
+        cmdpath = op.join(prefix, args[0])
+        if op.isfile(cmdpath):
+            args[0] = cmdpath
+            break
 
     return run(*args, **kwargs)
 

fsl/wrappers/__init__.py

@@ -80,8 +80,10 @@ from .wrapperutils import (LOAD,)           # noqa
 from .bet          import (bet,             # noqa
                            robustfov)
 from .eddy         import (eddy_cuda,       # noqa
-                           topup)
+                           topup,
+                           applytopup)
 from .fast         import (fast,)           # noqa
+from .fsl_anat     import (fsl_anat,)       # noqa
 from .flirt        import (flirt,           # noqa
                            invxfm,
                            applyxfm,

fsl/wrappers/bet.py

@@ -35,6 +35,7 @@ def bet(input, output, **kwargs):
         'robust'        : 'R',
         'fracintensity' : 'f',
         'seg'           : 'n',
+        'centre'        : 'c',
     }
 
     valmap = {
@@ -55,6 +56,14 @@ def bet(input, output, **kwargs):
     }
 
     cmd  = ['bet', input, output]
+
+    # The 'centre' argument requires three co-ordinates and can't be passed
+    # as a single value, so needs to be handled separately. Assume it is 
+    # passed as a Python sequence
+    centre = kwargs.pop("c", None)
+    if centre is not None:
+        cmd += ['c', ] + list(centre)
+
     cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
 
     return cmd

fsl/wrappers/eddy.py

@@ -61,8 +61,8 @@ def eddy_cuda(imain, mask, index, acqp, bvecs, bvals, out, **kwargs):
     return cmd
 
 
-@wutils.fileOrImage('imain', 'fout', 'iout')
-@wutils.fileOrArray('datain')
+@wutils.fileOrImage('imain', 'fout', 'iout', outprefix='out')
+@wutils.fileOrArray('datain', outprefix='out')
 @wutils.fslwrapper
 def topup(imain, datain, **kwargs):
     """Wrapper for the ``topup`` command."""
@@ -78,3 +78,25 @@ def topup(imain, datain, **kwargs):
     cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
 
     return cmd
+
+@wutils.fileOrImage('imain', 'out')
+@wutils.fileOrArray('datain')
+@wutils.fslwrapper
+def applytopup(imain, datain, index, **kwargs):
+    """Wrapper for the ``applytopup`` command."""
+
+    valmap = {
+        'verbose' : wutils.SHOW_IF_TRUE
+    }
+
+    asrt.assertFileExists(datain)
+    asrt.assertIsNifti(imain)
+
+    cmd  = [
+        'applytopup', '--imain={}'.format(imain), 
+        '--inindex={}'.format(index), 
+        '--datain={}'.format(datain),
+    ]
+    cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+
+    return cmd

fsl/wrappers/fast.py

@@ -33,12 +33,19 @@ def fast(imgs, out='fast', **kwargs):
 
     asrt.assertIsNifti(*imgs)
 
+    valmap = {
+        'nobias' : wutils.SHOW_IF_TRUE,
+        'verbose' : wutils.SHOW_IF_TRUE,
+        'Prior' : wutils.SHOW_IF_TRUE,
+        'segments' : wutils.SHOW_IF_TRUE,
+    }
+
     argmap = {
         'n_classes' : 'class',
     }
 
     cmd  = ['fast', '-v', '--out=%s' % out]
-    cmd += wutils.applyArgStyle('--=', argmap=argmap, **kwargs)
+    cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
     cmd += imgs
 
     return cmd

fsl/wrappers/flirt.py

@@ -59,14 +59,15 @@ def flirt(src, ref, **kwargs):
     return cmd
 
 
-def applyxfm(src, ref, mat, out, interp='spline'):
+def applyxfm(src, ref, mat, out, interp='spline', **kwargs):
     """Convenience function which runs ``flirt -applyxfm ...``."""
     return flirt(src,
                  ref,
                  out=out,
                  applyxfm=True,
                  init=mat,
-                 interp=interp)
+                 interp=interp,
+                 **kwargs)
 
 
 @wutils.fileOrArray()

fsl/wrappers/fnirt.py

@@ -27,12 +27,12 @@ from . import wrapperutils  as wutils
                     'refout', 'refmask', 'inmask')
 @wutils.fileOrArray('aff')
 @wutils.fslwrapper
-def fnirt(src, ref, **kwargs):
+def fnirt(src, **kwargs):
     """Wrapper for the ``fnirt`` command."""
 
-    asrt.assertIsNifti(src, ref)
+    asrt.assertIsNifti(src)
 
-    cmd  = ['fnirt', '--in={}'.format(src), '--ref={}'.format(ref)]
+    cmd  = ['fnirt', '--in={}'.format(src)]
     cmd += wutils.applyArgStyle('--=', **kwargs)
 
     return cmd
@@ -41,7 +41,7 @@ def fnirt(src, ref, **kwargs):
 @wutils.fileOrImage('src', 'ref', 'out', 'warp', 'mask')
 @wutils.fileOrArray('premat', 'postmat')
 @wutils.fslwrapper
-def applywarp(src, ref, out, warp, **kwargs):
+def applywarp(src, ref, out, **kwargs):
     """Wrapper for the ``applywarp`` command. """
 
     valmap = {
@@ -55,8 +55,7 @@ def applywarp(src, ref, out, warp, **kwargs):
     cmd = ['applywarp',
            '--in={}'.format(src),
            '--ref={}'.format(ref),
-           '--out={}'.format(out),
-           '--warp={}'.format(warp)]
+           '--out={}'.format(out)]
 
     cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
 
@@ -76,7 +75,7 @@ def invwarp(warp, ref, out, **kwargs):
         'verbose'      : wutils.SHOW_IF_TRUE,
     }
 
-    asrt.assertIsNifti(warp, ref, out)
+    asrt.assertIsNifti(warp, ref)
 
     cmd  = ['invwarp',
             '--warp={}'.format(warp),
@@ -88,7 +87,7 @@ def invwarp(warp, ref, out, **kwargs):
     return cmd
 
 
-@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap')
+@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap', 'jacobian')
 @wutils.fileOrArray('premat', 'midmat', 'postmat')
 @wutils.fslwrapper
 def convertwarp(out, ref, **kwargs):
@@ -99,7 +98,6 @@ def convertwarp(out, ref, **kwargs):
         'rel'        : wutils.SHOW_IF_TRUE,
         'absout'     : wutils.SHOW_IF_TRUE,
         'relout'     : wutils.SHOW_IF_TRUE,
-        'jacobian'   : wutils.SHOW_IF_TRUE,
         'jstats'     : wutils.SHOW_IF_TRUE,
         'constrainj' : wutils.SHOW_IF_TRUE,
         'verbose'    : wutils.SHOW_IF_TRUE,
@@ -107,5 +105,4 @@ def convertwarp(out, ref, **kwargs):
 
     cmd  = ['convertwarp', '--ref={}'.format(ref), '--out={}'.format(out)]
     cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
-
     return cmd

fsl/wrappers/fsl_anat.py

+#!/usr/bin/env python
+#
+# fsl_anat.py - Wrapper for the FSL_ANAT command.
+#
+# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
+#
+"""This module provides the :func:`fsl_anat` function, a wrapper for the FSL
+`FSL_ANAT <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat>`_ command.
+"""
+
+import six
+
+import fsl.utils.assertions as asrt
+from . import wrapperutils  as wutils
+
+@wutils.fileOrImage('img', outprefix='out')
+@wutils.fslwrapper
+def fsl_anat(img, out='fsl_anat', **kwargs):
+    """Wrapper for the ``fsl_anat`` command.
+
+    :arg img:       Input structural image
+    :arg out:       Output directory name
+    """
+    asrt.assertIsNifti(img)
+
+    valmap = {
+        'strongbias' : wutils.SHOW_IF_TRUE,
+        'weakbias' : wutils.SHOW_IF_TRUE,
+        'noreorient' : wutils.SHOW_IF_TRUE,
+        'nocrop' : wutils.SHOW_IF_TRUE,
+        'nobias' : wutils.SHOW_IF_TRUE,
+        'noreg' : wutils.SHOW_IF_TRUE,
+        'nononlinreg' : wutils.SHOW_IF_TRUE,
+        'noseg' : wutils.SHOW_IF_TRUE,
+        'nosubcortseg' : wutils.SHOW_IF_TRUE,
+        'nosearch' : wutils.SHOW_IF_TRUE,
+        'nocleanup' : wutils.SHOW_IF_TRUE,
+    }
+
+    argmap = {
+    }
+
+    img_type = kwargs.pop("img_type", "T1")
+    cmd  = ['fsl_anat', '-i', img, '-o', out, '-t', img_type]
+    smoothing = kwargs.pop("bias_smoothing", None)
+    if smoothing is not None:
+        cmd += ['-s', str(smoothing)]
+
+    cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
+
+    return cmd

fsl/wrappers/wrapperutils.py

@@ -152,11 +152,13 @@ def cmdwrapper(func):
     :func:`fsl.utils.run.run` function in a standardised manner.
     """
     def wrapper(*args, **kwargs):
+        stdout = kwargs.pop('stdout', True)
+        stderr = kwargs.pop('stderr', False)
+        exitcode = kwargs.pop('exitcode', False)
         submit = kwargs.pop('submit', None)
-        stderr = kwargs.pop('stderr', True)
         log    = kwargs.pop('log',    {'tee' : True})
         cmd    = func(*args, **kwargs)
-        return run.run(cmd, stderr=stderr, log=log, submit=submit)
+        return run.run(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
     return _update_wrapper(wrapper, func)
 
 
@@ -166,11 +168,13 @@ def fslwrapper(func):
     :func:`fsl.utils.run.runfsl` function in a standardised manner.
     """
     def wrapper(*args, **kwargs):
+        stdout = kwargs.pop('stdout', True)
+        stderr = kwargs.pop('stderr', False)
+        exitcode = kwargs.pop('exitcode', False)
         submit = kwargs.pop('submit', None)
-        stderr = kwargs.pop('stderr', True)
         log    = kwargs.pop('log',    {'tee' : True})
         cmd    = func(*args, **kwargs)
-        return run.runfsl(cmd, stderr=stderr, log=log, submit=submit)
+        return run.runfsl(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
     return _update_wrapper(wrapper, func)
 
 
@@ -192,7 +196,7 @@ generated command line arguments.
 """
 
 
-def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
+def applyArgStyle(style, valsep=None, argmap=None, valmap=None, singlechar_args=False, **kwargs):
     """Turns the given ``kwargs`` into command line options. This function
     is intended to be used to automatically generate command line options
     from arguments passed into a Python function.
@@ -251,6 +255,9 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
                  The argument for any options not specified in the ``valmap``
                  will be converted into strings.
 
+    :arg singlechar_args: If True, single character arguments always take a single
+                          hyphen prefix (e.g. -h) regardless of the style
+
     :arg kwargs: Arguments to be converted into command-line options.
 
     :returns:    A list containing the generated command-line options.
@@ -276,7 +283,7 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
     if valmap is None: valmap = {}
 
     def fmtarg(arg):
-        if   style in ('-',  '-='):  arg =  '-{}'.format(arg)
+        if   style in ('-',  '-=') or (singlechar_args and len(arg) == 1):  arg =  '-{}'.format(arg)
         elif style in ('--', '--='): arg = '--{}'.format(arg)
         return arg
 
@@ -303,11 +310,12 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
 
     for k, v in kwargs.items():
 
+        if v is None: continue
+
         k    = argmap.get(k, k)
         mapv = valmap.get(k, fmtval(v))
         k    = fmtarg(k)
 
-
         if mapv in (SHOW_IF_TRUE, HIDE_IF_TRUE):
             if (mapv is SHOW_IF_TRUE and     v) or \
                (mapv is HIDE_IF_TRUE and not v):
@@ -849,7 +857,6 @@ class _FileOrThing(object):
         for prefixed in it.chain(*allPrefixed):
             fullpath = prefixed
             prefixed = op.relpath(prefixed, workdir)
-
             for prefPat, prefName in prefixes.items():
                 if not fnmatch.fnmatch(prefixed, '{}*'.format(prefPat)):
                     continue
@@ -862,10 +869,17 @@ class _FileOrThing(object):
                 # not of the correct type.
                 fval = self.__load(fullpath)
                 if fval is not None:
-                    prefixed = self.__removeExt(prefixed)
+                    noext = self.__removeExt(prefixed)
                     prefPat  = prefPat.replace('\\', '\\\\')
-                    prefixed = re.sub('^' + prefPat, prefName, prefixed)
-                    result[prefixed] = fval
+                    noext = re.sub('^' + prefPat, prefName, noext)
+                    # If there is already an item in result with the
+                    # name (stripped of prefix), then instead store
+                    # the result with the full prefixed name
+                    if noext not in result:
+                        result[noext] = fval
+                    else:
+                        withext = re.sub('^' + prefPat, prefName, prefixed)
+                        result[withext] = fval
                     break
 
         return result
@@ -887,8 +901,11 @@ def fileOrImage(*args, **kwargs):
 
         infile = None
 
-        if isinstance(val, (fslimage.Image, nib.nifti1.Nifti1Image)):
-            intypes.append(type(val))
+        if isinstance(val, fslimage.Image):
+            intypes.append(fslimage.Image)
+
+        elif isinstance(val, nib.nifti1.Nifti1Image):
+            intypes.append(nib.nifti1.Nifti1Image)
 
         if isinstance(val, fslimage.Image):
             val = val.nibImage