From 47a43f19f81f24f5173e526cc79150e513c9ccb4 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Tue, 2 Jul 2024 12:48:21 -0700
Subject: [PATCH] add back `t_idx` param

---
 mantis/cli/utils.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/mantis/cli/utils.py b/mantis/cli/utils.py
index c593d607..11ea3e5c 100644
--- a/mantis/cli/utils.py
+++ b/mantis/cli/utils.py
@@ -218,6 +218,11 @@ def apply_transform_to_zyx_and_save_v2(
         output_channel_indices = [int(x) for x in output_channel_indices if x.isdigit()]
     click.echo(f"input_channel_indices: {input_channel_indices}")
 
+    # Check if t_idx should be added to kwargs to have different transformations for different timepoints
+    all_func_params = inspect.signature(func).parameters.keys()
+    if "t_idx" in all_func_params:
+        kwargs["t_idx"] = t_idx
+
     # Process CZYX vs ZYX
     if input_channel_indices is not None:
         click.echo(f"Processing t={t_idx}")