From 5d11e2454eff28948813c7024efc388850088ea7 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Fri, 19 Jan 2024 12:00:53 -0500
Subject: [PATCH 1/2] ENH: allow setting of fixed_parameters when creating a
 transform

Also point users to create_transform method
---
 ants/core/ants_transform_io.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/ants/core/ants_transform_io.py b/ants/core/ants_transform_io.py
index c33643aa..482410c2 100644
--- a/ants/core/ants_transform_io.py
+++ b/ants/core/ants_transform_io.py
@@ -16,13 +16,16 @@
 
 
 def new_ants_transform(
-    precision="float", dimension=3, transform_type="AffineTransform", parameters=None
+    precision="float", dimension=3, transform_type="AffineTransform", parameters=None, fixed_parameters=None
 ):
     """
     Create a new ANTsTransform
 
     ANTsR function: None
 
+    This is a simplified method for creating an ANTsTransform, mostly used internally.
+    See create_ants_transform for more options.
+
     Example
     -------
     >>> import ants
@@ -42,6 +45,9 @@ def new_ants_transform(
     if parameters is not None:
         ants_tx.set_parameters(parameters)
 
+    if fixed_parameters is not None:
+        ants_tx.set_fixed_parameters(fixed_parameters)
+
     return ants_tx
 
 
@@ -268,7 +274,7 @@ def transform_to_displacement_field(xfrm, ref):
         displacement field ANTsTransform
 
     ref : ANTs Image
-         
+
     Returns
     -------
     ANTsVectorImage
@@ -285,7 +291,7 @@ def transform_to_displacement_field(xfrm, ref):
     >>> atx = ants.transform_from_displacement_field( vec )
     >>> field = ants.transform_to_displacement_field( atx, fi )
     """
-    
+
     if not xfrm.type == 'DisplacementFieldTransform':
         raise ValueError("Transform must be of DisplacementFieldTransform type")
     libfn = utils.get_lib_fn("antsTransformToDisplacementFieldF%i" % xfrm.dimension)

From 76d8a2851e78e3634508121e5fa23e7848f69a7d Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Fri, 19 Jan 2024 12:03:38 -0500
Subject: [PATCH 2/2] STYLE: Indentation

---
 ants/core/ants_transform_io.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ants/core/ants_transform_io.py b/ants/core/ants_transform_io.py
index 482410c2..99232d20 100644
--- a/ants/core/ants_transform_io.py
+++ b/ants/core/ants_transform_io.py
@@ -16,7 +16,8 @@
 
 
 def new_ants_transform(
-    precision="float", dimension=3, transform_type="AffineTransform", parameters=None, fixed_parameters=None
+    precision="float", dimension=3, transform_type="AffineTransform", parameters=None,
+    fixed_parameters=None
 ):
     """
     Create a new ANTsTransform