From de79ed3bdab3b5472c3b008a281b31522ce2a4a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jord=C3=A3o=20Bragantini?= <jordao.bragantini@czbiohub.org>
Date: Wed, 11 Oct 2023 20:38:21 +0200
Subject: [PATCH] Added option to not check copied data (#192)

---
 iohub/cli/cli.py      | 20 ++++++++++++++++++--
 tests/cli/test_cli.py |  7 ++++---
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 729c73ad..befdeb3d 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -90,7 +90,23 @@ def info(files, verbose):
     help="Zarr chunk size given as 'XY', 'XYZ', or a tuple of chunk "
     "dimensions. If 'XYZ', chunk size will be limited to 500 MB.",
 )
-def convert(input, output, format, scale_voxels, grid_layout, chunks):
+@click.option(
+    "--check-image/--no-check-image",
+    "-chk/-no-chk",
+    required=False,
+    is_flag=True,
+    default=True,
+    help="Checks copied image data with original data.",
+)
+def convert(
+    input,
+    output,
+    format,
+    scale_voxels,
+    grid_layout,
+    chunks,
+    check_image,
+):
     """Converts Micro-Manager TIFF datasets to OME-Zarr"""
     converter = TIFFConverter(
         input_dir=input,
@@ -100,4 +116,4 @@ def convert(input, output, format, scale_voxels, grid_layout, chunks):
         grid_layout=grid_layout,
         chunks=chunks,
     )
-    converter.run()
+    converter.run(check_image=check_image)
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index 9830b898..1d1fa150 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -90,20 +90,21 @@ def test_cli_info_ome_zarr(setup_test_data, setup_hcs_ref, verbose):
     assert "scale (um)" in result_pos.output
 
 
-@given(f=st.booleans(), g=st.booleans(), s=st.booleans())
+@given(f=st.booleans(), g=st.booleans(), s=st.booleans(), chk=st.booleans())
 @settings(
     suppress_health_check=[HealthCheck.function_scoped_fixture], deadline=20000
 )
 def test_cli_convert_ome_tiff(
-    setup_test_data, setup_mm2gamma_ome_tiffs, f, g, s
+    setup_test_data, setup_mm2gamma_ome_tiffs, f, g, s, chk,
 ):
     _, _, input_dir = setup_mm2gamma_ome_tiffs
     runner = CliRunner()
     f = "-f ometiff" if f else ""
     g = "-g" if g else ""
+    chk = "--check-image" if chk else "--no-check-image"
     with TemporaryDirectory() as tmp_dir:
         output_dir = os.path.join(tmp_dir, "converted.zarr")
-        cmd = ["convert", "-i", input_dir, "-o", output_dir, "-s", s]
+        cmd = ["convert", "-i", input_dir, "-o", output_dir, "-s", s, chk]
         if f:
             cmd += ["-f", "ometiff"]
         if g: