Revert "fuse: always use zlib compression when creating tiffs"

This reverts commit f9e8136.
lens-biophotonics · Jun 9, 2022 · 408ab78 · 408ab78
1 parent 348c7ba
commit 408ab78
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/zetastitcher/fuse/__main__.py b/zetastitcher/fuse/__main__.py
@@ -57,6 +57,9 @@ def parse_args():
 
     group.add_argument('-c', '--ch', type=int, dest='channel', help='channel')
 
+    group.add_argument('-c', type=str, default=0, dest='compression',
+                       choices=[str(i) for i in range(10)] + ['lzma'],
+                       help='compression')
     group.add_argument('--downsample-xy', metavar='S', type=int, required=False,
                        help='downsample XY plane by factor S')
 
@@ -158,6 +161,11 @@ def preprocess_and_check_args(args):
     elif args.nz is not None:
         args.zmax = args.zmin + args.nz
 
+    try:
+        args.compression = int(args.compression)
+    except ValueError:
+        pass
+
 
 def compute_absolute_positions(args, fm):
     xcorr_fm = XcorrFileMatrix.from_yaml(fm.input_path)
@@ -239,7 +247,8 @@ def main():
     logger.info(f'fused shape, whole volume: {fr.output_shape}, {bytes_human}')
     if args.output_filename is not None:
 
-        keys = ['zmin', 'zmax', 'output_filename', 'debug', 'channel', 'downsample_xy']
+        keys = ['zmin', 'zmax', 'output_filename', 'debug', 'channel',
+                'compression', 'downsample_xy']
 
         for k in keys:
             setattr(fr, k, getattr(args, k))