Merge pull request #418 from arnaudbore/fix_todos

Fix todos

scripts/scil_concatenate_dwi.py

@@ -26,16 +26,16 @@ def _build_arg_parser():
     p.add_argument('out_dwi',
                    help='The name of the output DWI file.')
     p.add_argument('out_bval',
-                   help='The name of the output b-values.')
+                   help='The name of the output b-values file (.bval).')
     p.add_argument('out_bvec',
-                   help='The name of the output b-vectors.')
+                   help='The name of the output b-vectors file (.bvec).')
 
     p.add_argument('--in_dwis', nargs='+',
                    help='The DWI file (.nii) to concatenate.')
     p.add_argument('--in_bvals', nargs='+',
-                   help='The b-values in FSL format.')
+                   help='The b-values files in FSL format (.bval).')
     p.add_argument('--in_bvecs', nargs='+',
-                   help='The b-vectors in FSL format.')
+                   help='The b-vectors files in FSL format (.bvec).')
 
     p.add_argument('--data_type',
                    help='Data type of the output image. Use the format: '

scripts/scil_extract_dwi_shell.py

@@ -28,52 +28,49 @@
                              assert_inputs_exist, assert_outputs_exist)
 from scilpy.utils.bvec_bval_tools import extract_dwi_shell
 
-# TODO switch from parser to p
-# TODO switch to in_*
-# TODO switch to out_*
+
 def _build_arg_parser():
-    parser = argparse.ArgumentParser(
+    p = argparse.ArgumentParser(
         description=__doc__,
         formatter_class=argparse.RawTextHelpFormatter)
 
-    parser.add_argument('dwi',
-                        help='The DW image file to split.')
+    p.add_argument('in_dwi',
+                   help='The DW image file to split.')
 
-    parser.add_argument('bvals',
-                        help='The b-values in FSL format.')
+    p.add_argument('in_bval',
+                   help='The b-values file in FSL format (.bval).')
 
-    parser.add_argument('bvecs',
-                        help='The b-vectors in FSL format.')
+    p.add_argument('in_bvec',
+                   help='The b-vectors file in FSL format (.bvec).')
 
-    parser.add_argument('bvals_to_extract', nargs='+',
-                        metavar='bvals-to-extract', type=int,
-                        help='The list of b-values to extract. For example '
-                             '0 2000.')
+    p.add_argument('in_bvals_to_extract', nargs='+',
+                   type=int,
+                   help='The list of b-values to extract. For example 0 2000.')
 
-    parser.add_argument('output_dwi',
-                        help='The name of the output DWI file.')
+    p.add_argument('out_dwi',
+                   help='The name of the output DWI file.')
 
-    parser.add_argument('output_bvals',
-                        help='The name of the output b-values.')
+    p.add_argument('out_bval',
+                   help='The name of the output b-value file (.bval).')
 
-    parser.add_argument('output_bvecs',
-                        help='The name of the output b-vectors')
+    p.add_argument('out_bvec',
+                   help='The name of the output b-vector file (.bvec).')
 
-    parser.add_argument('--block-size', '-s',
-                        metavar='INT', type=int,
-                        help='Loads the data using this block size. '
-                             'Useful\nwhen the data is too large to be '
-                             'loaded in memory.')
+    p.add_argument('--block-size', '-s',
+                   metavar='INT', type=int,
+                   help='Loads the data using this block size. '
+                        'Useful\nwhen the data is too large to be '
+                        'loaded in memory.')
 
-    parser.add_argument('--tolerance', '-t',
-                        metavar='INT', type=int, default=20,
-                        help='The tolerated gap between the b-values to '
-                             'extract\nand the actual b-values.')
+    p.add_argument('--tolerance', '-t',
+                   metavar='INT', type=int, default=20,
+                   help='The tolerated gap between the b-values to '
+                        'extract\nand the actual b-values.')
 
-    add_verbose_arg(parser)
-    add_overwrite_arg(parser)
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
 
-    return parser
+    return p
 
 
 def main():
@@ -83,28 +80,28 @@ def main():
     if args.verbose:
         logging.basicConfig(level=logging.INFO)
 
-    assert_inputs_exist(parser, [args.dwi, args.bvals, args.bvecs])
-    assert_outputs_exist(parser, args, [args.output_dwi, args.output_bvals,
-                                        args.output_bvecs])
+    assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec])
+    assert_outputs_exist(parser, args, [args.out_dwi, args.out_bval,
+                                        args.out_bvec])
 
-    bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
+    bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
 
     # Find the volume indices that correspond to the shells to extract.
     tol = args.tolerance
 
-    img = nib.load(args.dwi)
+    img = nib.load(args.in_dwi)
+
+    outputs = extract_dwi_shell(img, bvals, bvecs, args.in_bvals_to_extract,
+                                tol, args.block_size)
 
-    outputs = extract_dwi_shell(img, bvals, bvecs, args.bvals_to_extract, tol,
-                                args.block_size)
     indices, shell_data, new_bvals, new_bvecs = outputs
 
     logging.info("Selected indices: {}".format(indices))
 
-    np.savetxt(args.output_bvals, new_bvals, '%d')
-    np.savetxt(args.output_bvecs, new_bvecs.T, '%0.15f')
-    # use named argument header=
-    nib.save(nib.Nifti1Image(shell_data, img.affine, img.header),
-             args.output_dwi)
+    np.savetxt(args.out_bval, new_bvals, '%d')
+    np.savetxt(args.out_bvec, new_bvecs.T, '%0.15f')
+    nib.save(nib.Nifti1Image(shell_data, img.affine, header=img.header),
+             args.out_dwi)
 
 
 if __name__ == "__main__":