Fixed output naming issue and added cost options

poldracklab · Dec 9, 2017 · bea538b · bea538b
1 parent 27f3ee7
commit bea538b
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/pydeface/__main__.py b/pydeface/__main__.py
@@ -51,6 +51,10 @@ def main():
         help="Apply the created face mask to other images. Can take multiple "
              "arguments.")
 
+    parser.add_argument(
+        "--cost", metavar='mutualinfo', required=False, default='mutualinfo',
+        help="FSL-FLIRT cost function. Default is 'mutualinfo'.")
+
     parser.add_argument(
         "--template", metavar='path', required=False,
         help=("Optional template image that will be used as the registration "
@@ -92,7 +96,7 @@ def main():
 
     # register template to infile
     flirt = fsl.FLIRT()
-    flirt.inputs.cost_func = 'mutualinfo'
+    flirt.inputs.cost_func = args.cost
     flirt.inputs.in_file = template
     flirt.inputs.out_matrix_file = tmpmat
     flirt.inputs.out_file = tmpfile2
@@ -116,7 +120,7 @@ def main():
     outfile_img = Nifti1Image(outdata, infile_img.get_affine(),
                               infile_img.get_header())
     outfile_img.to_filename(outfile)
-    print('Defaced input saved as:\n  %s' % outfile)
+    print("Defaced image saved as:\n  %s" % outfile)
 
     # apply mask to other given images
     if args.applyto is not None:
@@ -126,7 +130,8 @@ def main():
             outdata = applyfile_img.get_data() * tmpfile_img.get_data()
             applyfile_img = Nifti1Image(outdata, applyfile_img.get_affine(),
                                         applyfile_img.get_header())
-            outfile_img.to_filename(applyfile)
+            outfile = output_checks(applyfile)
+            applyfile_img.to_filename(outfile)
             print('  %s' % applyfile)
 
     if args.nocleanup:

diff --git a/pydeface/utils.py b/pydeface/utils.py
@@ -26,16 +26,18 @@ def initial_checks(template=None, facemask=None):
     return template, facemask
 
 
-def output_checks(outfile, infile, force=False):
+def output_checks(infile, outfile=None, force=False):
     """Determine output file name."""
     if force is None:
         force = False
+    if outfile is None:
+        outfile = infile.replace('.nii', '_defaced.nii')
 
     if os.path.exists(outfile) and force:
         print('Previous output will be overwritten.')
     elif os.path.exists(outfile):
         raise Exception("%s already exists. Remove it first or use '--force' "
                         "flag to overwrite." % outfile)
     else:
-        outfile = infile.replace('.nii', '_defaced.nii')
+        pass
     return outfile