Pass scale metadata through recorder reconstruct (#399)

* pass scale metadata through reconstruct

* test scale passing

recOrder/cli/apply_inverse_transfer_function.py

@@ -2,6 +2,7 @@
 import numpy as np
 import torch
 from iohub import open_ome_zarr
+from iohub.ngff_meta import TransformationMeta
 from waveorder.models import (
  inplane_oriented_thick_pol3d,
  isotropic_fluorescent_thick_3d,
@@ -122,6 +123,9 @@ def apply_inverse_transfer_function_cli(
  1,
  )
  + input_dataset.data.shape[3:], # chunk by YX
+ transform=[
+ TransformationMeta(type="scale", scale=input_dataset.scale)
+ ],
  )
  else:
  output_array = output_dataset[0]

recOrder/tests/cli_tests/test_reconstruct.py

@@ -1,6 +1,7 @@
 import numpy as np
 from click.testing import CliRunner
 from iohub.ngff import open_ome_zarr
+from iohub.ngff_meta import TransformationMeta
 
 from recOrder.cli import settings
 from recOrder.cli.main import cli
@@ -18,7 +19,13 @@ def test_reconstruct(tmp_path):
  mode="w",
  channel_names=channel_names,
  )
- dataset.create_zeros("0", (5, 4, 4, 5, 6), dtype=np.uint16)
+ input_scale = [1, 2, 3, 4, 5]
+ dataset.create_zeros(
+ "0",
+ (5, 4, 4, 5, 6),
+ dtype=np.uint16,
+ transform=[TransformationMeta(type="scale", scale=input_scale)],
+ )
 
  # Setup options
  birefringence_settings = settings.BirefringenceSettings(
@@ -111,4 +118,6 @@ def test_reconstruct(tmp_path):
  assert result_path.exists()
  assert result_inv.exit_code == 0
  assert "Reconstructing" in result_inv.output
- assert "Reconstructing" in result_inv.output
+
+ # Check scale transformations pass through
+ assert input_scale == result_dataset.scale