ENH: convert_x5 updated to handle non-linear. Nothing is tested

fsl/scripts/fsl_convert_x5.py

@@ -24,43 +24,100 @@ def parseArgs(args):
     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('-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)
 
-    def getfmt(fname):
+    if args.ctype is None:
+        parser.print_help()
+        sys.exit(0)
+
+    def getfmt(arg, fname):
         ext = op.splitext(fname)[1]
-        if ext not in ('.x5', '.mat'):
-            raise argparse.ArgumentError('Could not infer format from '
-                                         'filename: {}'.format(args.input))
-        return ext[1:]
+        if ext in ('.mat', '.x5'):
+            return ext[1:]
+        if fslimage.looksLikeImage(fslimage.fixExt(fname)):
+            return 'nii'
+        parser.error('Could not infer format from '
+                     'filename: {}'.format(args.input))
 
-    if args.ctype == 'flirt':
-        if args.input_format  is None: args.input_format  = getfmt(args.input)
-        if args.output_format is None: args.output_format = getfmt(args.output)
+    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)
 
     return args
 
 
 def flirtToX5(args):
-    src   = fslimage.Image(args.source)
-    ref   = fslimage.Image(args.reference)
+    src   = fslimage.Image(args.source,    loadData=False)
+    ref   = fslimage.Image(args.reference, loadData=False)
     xform = transform.readFlirt(args.input)
-    transform.writeFlirtX5(args.output, xform, src, ref)
+    xform = transform.fromFlirt(xform, src, ref, 'world', 'world')
+    transform.writeLinearX5(args.output, xform, src, ref)
 
 
 def X5ToFlirt(args):
-    xform, src, ref = transform.readFlirtX5(args.input)
+    xform, src, ref = transform.readLinearX5(args.input)
     xform           = transform.toFlirt(xform, src, ref, 'world', 'world')
     transform.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)
+
+
+def X5ToFnirt(args):
+    field = transform.readNonLinearX5(args.input)
+    field = transform.toFnirt(field, 'world', 'world')
+    transform.writeFnirt(field, args.output)
+
+
+def doFlirt(args):
+    infmt  = args.input_format
+    outfmt = args.output_format
+
+    if   (infmt, outfmt) == ('x5', 'mat'): X5ToFlirt(args)
+    elif (infmt, outfmt) == ('mat', 'x5'): flirtToX5(args)
+    else: shutil.copy(args.input, args.output)
+
+
+def doFnirt(args):
+    infmt  = args.input_format
+    outfmt = args.output_format
+
+    if   (infmt, outfmt) == ('x5', 'nii'): X5ToFnirt(args)
+    elif (infmt, outfmt) == ('nii', 'x5'): fnirtToX5(args)
+    else: shutil.copy(args.input, args.output)
+
+
 def main(args=None):
 
     if args is None:
@@ -69,13 +126,8 @@ def main(args=None):
     args   = parseArgs(args)
     ctype  = args.ctype
 
-    if ctype == 'flirt':
-        infmt  = args.input_format
-        outfmt = args.output_format
-
-        if   (infmt, outfmt) == ('x5', 'mat'): X5ToFlirt(args)
-        elif (infmt, outfmt) == ('mat', 'x5'): flirtToX5(args)
-        else: shutil.copy(args.input, args.output)
+    if   ctype == 'flirt': doFlirt(args)
+    elif ctype == 'fnirt': doFnirt(args)
 
 
 if __name__ == '__main__':