ENH: New replacement Text2Vest2Text scripts

fsl/data/vest.py

@@ -87,10 +87,12 @@ 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. Otherwise,
-                       if the number of rows/columns specified in the VEST
-                       header information does not match the matrix shape,
-                       a ``ValueError`` is raised.
+                       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.
     """
@@ -108,8 +110,10 @@ def loadVestFile(path, ignoreHeader=True):
                 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
 

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

fsl/scripts/Vest2Text.py

+#!/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())