From 8c6f860edc73a3ab0f6b0b4d142c1383fd2adce8 Mon Sep 17 00:00:00 2001
From: Anthony Lombardi <anthony.lombardi@kitware.com>
Date: Mon, 11 Mar 2024 09:49:34 -0400
Subject: [PATCH] BUG: Fix config generation

---
 AutoscoperM/AutoscoperM.py       | 6 +++++-
 AutoscoperM/AutoscoperMLib/IO.py | 9 +++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/AutoscoperM/AutoscoperM.py b/AutoscoperM/AutoscoperM.py
index 2fdb6d2..ec100c8 100644
--- a/AutoscoperM/AutoscoperM.py
+++ b/AutoscoperM/AutoscoperM.py
@@ -631,13 +631,17 @@ def onGenerateConfig(self):
             int(self.ui.flipZ.isChecked()),
         ]
 
+        if self.logic.is_4d:
+            voxel_spacing = self.logic.getItemInSequence(volumeNode, 0).GetSpacing()
+        else:
+            voxel_spacing = volumeNode.GetSpacing()
         # generate the config file
         configFilePath = IO.generateConfigFile(
             mainOutputDir,
             [tiffSubDir, vrgSubDir, calibrationSubDir],
             trialName,
             volumeFlip=volumeFlip,
-            voxelSize=volumeNode.GetSpacing(),
+            voxelSize=voxel_spacing,
             renderResolution=[int(width / 2), int(height / 2)],
             optimizationOffsets=optimizationOffsets,
         )
diff --git a/AutoscoperM/AutoscoperMLib/IO.py b/AutoscoperM/AutoscoperMLib/IO.py
index 5614959..7b1813e 100644
--- a/AutoscoperM/AutoscoperMLib/IO.py
+++ b/AutoscoperM/AutoscoperMLib/IO.py
@@ -158,8 +158,17 @@ def writeVolume(volumeNode: slicer.vtkMRMLVolumeNode, filename: str):
     :param volumeNode: Volume node
     :param filename: Output file name
     """
+    # tfm = vtk.vtkMatrix4x4()
+    # tfm.Identity()
+    # tfm.SetElement(0, 0, -1)
+    # tfm.SetElement(1, 1, -1)
+    # transformNode = slicer.vtkMRMLLinearTransformNode()
+    # transformNode.SetMatrixTransformToParent(tfm)
+    # slicer.mrmlScene.AddNode(transformNode)
     slicer.util.exportNode(volumeNode, filename, {"useCompression": False}, world=True)
 
+    # slicer.mrmlScene.RemoveNode(transformNode)
+
 
 def castVolumeForTIFF(volumeNode: slicer.vtkMRMLVolumeNode):
     """