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): """