From 0bf992071776c9a87c36f1827b8b5700705c1213 Mon Sep 17 00:00:00 2001 From: Bradley Lowekamp Date: Tue, 6 Apr 2021 13:29:37 -0400 Subject: [PATCH] Use URI format for output of precomputed-pyramid On windows the "C:/" full paths are not supported by volume-to-precomputed-pyramid. --- pytools/ng/mrc2ngpc.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pytools/ng/mrc2ngpc.py b/pytools/ng/mrc2ngpc.py index 7397403..09aa982 100644 --- a/pytools/ng/mrc2ngpc.py +++ b/pytools/ng/mrc2ngpc.py @@ -18,6 +18,7 @@ import os.path import sys import logging +from pathlib import Path @click.command() @@ -74,7 +75,8 @@ def main(input_image, output_precompute, flat, gzip): if not gzip: cmd_opts.append("--no-gzip") - cmd = ["volume-to-precomputed-pyramid"] + cmd_opts + [nifti_filename, output_precompute] + cmd = ["volume-to-precomputed-pyramid"] + cmd_opts + [nifti_filename, + Path(output_precompute).as_uri()] logger.info("Executing conversion of NIFTI to Neruoglancer precompute pyramid...") logger.debug(f"Executing: {cmd}")