From 49927f9fb5c5ecd90e92600edf0266428f5f54c6 Mon Sep 17 00:00:00 2001
From: Anthony Lombardi <anthony.lombardi@kitware.com>
Date: Wed, 10 Jul 2024 14:27:39 -0400
Subject: [PATCH] BUG: Fix partial volume flip

Regression introduced in e036c2249dc564c2cca03914837248dae6d06666 where,
on config generation, the partial volumes would be automatically flipped
in the x and y directions. This caused issues with post-processing.
---
 AutoscoperM/AutoscoperM.py              | 7 +++----
 AutoscoperM/Resources/UI/AutoscoperM.ui | 4 ++--
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/AutoscoperM/AutoscoperM.py b/AutoscoperM/AutoscoperM.py
index b23e8c7..f91b289 100644
--- a/AutoscoperM/AutoscoperM.py
+++ b/AutoscoperM/AutoscoperM.py
@@ -1494,11 +1494,10 @@ def createAndAddSlicer2AutoscoperTransformNode(volumeNode: slicer.vtkMRMLVolumeN
 
         slicer2autoscoper = vtk.vtkMatrix4x4()
         slicer2autoscoper.Identity()
-        # Rotation matrix for a 180 x-axis rotation
-        slicer2autoscoper.SetElement(1, 1, -slicer2autoscoper.GetElement(1, 1))
-        slicer2autoscoper.SetElement(1, 2, -slicer2autoscoper.GetElement(1, 2))
+        # Rotation matrix for a 180 y-axis rotation
+        slicer2autoscoper.SetElement(0, 0, -slicer2autoscoper.GetElement(0, 0))
         slicer2autoscoper.SetElement(2, 2, -slicer2autoscoper.GetElement(2, 2))
-        slicer2autoscoper.SetElement(0, 3, -volSize[0])  # Offset -X
+        slicer2autoscoper.SetElement(1, 3, -volSize[1])  # Offset -Y
 
         slicer2autoscoperNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLinearTransformNode")
         slicer2autoscoperNode.SetMatrixTransformToParent(slicer2autoscoper)
diff --git a/AutoscoperM/Resources/UI/AutoscoperM.ui b/AutoscoperM/Resources/UI/AutoscoperM.ui
index ecd300d..fa522ef 100644
--- a/AutoscoperM/Resources/UI/AutoscoperM.ui
+++ b/AutoscoperM/Resources/UI/AutoscoperM.ui
@@ -727,7 +727,7 @@
              <string>Flip Y</string>
             </property>
             <property name="checked">
-             <bool>true</bool>
+             <bool>false</bool>
             </property>
            </widget>
           </item>
@@ -764,7 +764,7 @@
              <string>Flip X</string>
             </property>
             <property name="checked">
-             <bool>true</bool>
+             <bool>false</bool>
             </property>
            </widget>
           </item>