set-scale utility

iohub/cli/cli.py

@@ -3,6 +3,8 @@
 from iohub._version import __version__
 from iohub.convert import TIFFConverter
 from iohub.reader import print_info
+from iohub.update_scale_metadata import update_scale_metadata as _update_scale_metadata
+from mantis.cli.parsing import input_position_dirpaths
 
 VERSION = __version__
 
@@ -117,3 +119,32 @@ def convert(
         chunks=chunks,
     )
     converter.run(check_image=check_image)
+
+
+@cli.command()
+@click.help_option("-h", "--help")
+@input_position_dirpaths()
+@click.option(
+   "--x-scale",
+   "-x",
+    required=False,
+    type=float,
+    help="New x scale",
+)
+@click.option(
+   "--y-scale",
+   "-y",
+    required=False,
+    type=float,
+    help="New y scale",
+)
+@click.option(
+   "--z-scale",
+   "-z",
+    required=False,
+    type=float,
+    help="New z scale",
+)
+def update_scale_metadata(input_position_dirpaths, z_scale, y_scale, x_scale):
+    """Update scale metadata in OME-Zarr datasets"""
+    _update_scale_metadata(input_position_dirpaths, z_scale=z_scale, y_scale=y_scale, x_scale=x_scale)

iohub/update_scale_metadata.py

@@ -0,0 +1,44 @@
+from typing import List
+
+from iohub import open_ome_zarr
+from iohub.ngff_meta import TransformationMeta
+
+
+def update_scale_metadata(
+    input_position_dirpaths: List[str],
+    z_scale: float = None,
+    y_scale: float = None,
+    x_scale: float = None,
+):
+    with open_ome_zarr(input_position_dirpaths[0]) as input_dataset:
+        print(
+            f"The first dataset in the list you provided has (z, y, x) scale {input_dataset.scale[2:]}"
+        )
+
+    print(
+        "Please enter the new z, y, and x scales that you would like to apply to all of the positions in the list."
+    )
+    print(
+        "The old scale will be saved in a metadata field named 'old_scale', and the new scale will adhere to the NGFF spec."
+    )
+    new_scale = [z_scale, y_scale, x_scale]
+    for i, character in enumerate("zyx"):
+        if new_scale[i] is None:
+            new_scale[i] = (float(input(f"Enter a new {character} scale: ")))
+
+    for input_position_dirpath in input_position_dirpaths:
+        with open_ome_zarr(input_position_dirpath, layout="fov", mode="a") as input_dataset:
+            input_dataset.zattrs['old_scale'] = input_dataset.scale[2:]
+            transform = [
+                TransformationMeta(
+                    type="scale",
+                    scale=(
+                        1,
+                        1,
+                    )
+                    + tuple(new_scale),
+                )
+            ]
+            input_dataset.set_transform("0", transform=transform)
+
+    print(f"The dataset now has (z, y, x) scale {tuple(new_scale)}.")