fsl/data/mghimage.py

@@ -10,8 +10,8 @@ Freesurfer ``mgh``/``mgz`` image files.
 
 
 import os.path as op
+import            pathlib
 
-import            six
 import numpy   as np
 import nibabel as nib
 
@@ -47,7 +47,7 @@ class MGHImage(fslimage.Image):
         All other arguments are passed through to :meth:`Image.__init__`
         """
 
-        if isinstance(image, six.string_types):
+        if isinstance(image, (str, pathlib.Path)):
             filename = op.abspath(image)
             name     = op.basename(filename)
             image    = nib.load(image)

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()

fsl/scripts/Text2Vest.py

+#!/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, ndmin=2)
+    vest            = fslvest.generateVest(data)
+
+    with open(outfile, 'wt') as f:
+        f.write(vest)
+
+    return 0
+
+
+if __name__ == '__main__':
+    sys.exit(main())

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/fsl_apply_x5.py

@@ -55,7 +55,7 @@ def parseArgs(args):
                         choices=('nearest', 'linear', 'cubic'),
                         default='linear'),
         'ref'    : dict(help=helps['ref'],
-                        type=ft.partial(parse_data.Image, loadData=False)),
+                        type=parse_data.Image),
     }
 
     parser.add_argument(*flags['input'],  **opts['input'])