ENH: Add nib-roi command to crop (maybe flip) axes

Author: effigies

nibabel/cmdline/roi.py

@@ -0,0 +1,64 @@
+import argparse
+import nibabel as nb
+
+
+def lossless_slice(img, slicers):
+    if not nb.imageclasses.spatial_axes_first(img):
+        raise ValueError("Cannot slice an image that is not known to have spatial axes first")
+
+    roi_img = img.__class__(
+        img.dataobj._get_unscaled(slicers),
+        affine=img.slicer.slice_affine(slicers),
+        header=img.header)
+    roi_img.header.set_slope_inter(img.dataobj.slope, img.dataobj.inter)
+    return roi_img
+
+
+def parse_slice(crop, allow_step=True):
+    if crop is None:
+        return slice(None)
+    start, stop, *extra = [int(val) if val else None for val in crop.split(":")]
+    if len(extra) > 1:
+        raise ValueError(f"Cannot parse specification: {crop}")
+    if extra and not allow_step:
+        raise ValueError(f"Step entry not permitted: {crop}")
+
+    step = extra[0] if extra else None
+    if step not in (1, -1, None):
+        raise ValueError(f"Downsampling is not supported: {crop}")
+
+    return slice(start, stop, step)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Crop images to a region of interest",
+                                     epilog="If a start or stop value is omitted, the start or end of the axis is assumed.")
+    parser.add_argument("-i", metavar="I1:I2[:-1]",
+                        help="Start/stop [flip] along first axis (0-indexed)")
+    parser.add_argument("-j", metavar="J1:J2[:-1]",
+                        help="Start/stop [flip] along second axis (0-indexed)")
+    parser.add_argument("-k", metavar="K1:K2[:-1]",
+                        help="Start/stop [flip] along third axis (0-indexed)")
+    parser.add_argument("-t", metavar="T1:T2", help="Start/stop along fourth axis (0-indexed)")
+    parser.add_argument("in_file", help="Image file to crop")
+    parser.add_argument("out_file", help="Output file name")
+
+    opts = parser.parse_args()
+
+    try:
+        islice = parse_slice(opts.i)
+        jslice = parse_slice(opts.j)
+        kslice = parse_slice(opts.k)
+        tslice = parse_slice(opts.t, allow_step=False)
+    except ValueError as err:
+        print(f"Could not parse input arguments. Reason follows.\n{err}")
+        return 1
+
+    img = nb.load(opts.in_file)
+    try:
+        sliced_img = lossless_slice(img, (islice, jslice, kslice, tslice)[:img.ndim])
+    except:
+        print("Could not slice image. Full traceback follows.")
+        raise
+    nb.save(sliced_img, opts.out_file)
+    return 0

setup.cfg

@@ -77,6 +77,7 @@ console_scripts =
     nib-nifti-dx=nibabel.cmdline.nifti_dx:main
     nib-tck2trk=nibabel.cmdline.tck2trk:main
     nib-trk2tck=nibabel.cmdline.trk2tck:main
+    nib-roi=nibabel.cmdline.roi:main
     parrec2nii=nibabel.cmdline.parrec2nii:main
 
 [options.package_data]