Mask the background out of loaded MRIs (#387)

OpenLIFUData/OpenLIFUData.py

@@ -57,6 +57,7 @@
     ensure_list,
     replace_widget,
 )
+from OpenLIFULib.volume_thresholding import load_volume_and_threshold_background
 from OpenLIFULib.virtual_fit_results import (
     add_virtual_fit_results_from_openlifu_session_format,
     clear_virtual_fit_results,
@@ -2301,7 +2302,7 @@ def load_volume_from_openlifu(self, volume_dir: Path, volume_metadata: Dict):
                 slicer.mrmlScene.RemoveNode(loaded_volumes[idx])
 
         volume_filepath = Path(volume_dir,volume_metadata['data_filename'])
-        loadedVolumeNode = slicer.util.loadVolume(volume_filepath)
+        loadedVolumeNode = load_volume_and_threshold_background(volume_filepath)
         # Note: OnNodeAdded/updateLoadedObjectsView is called before openLIFU metadata is assigned to the node so need
         # call updateLoadedObjectsView again to display openlifu name/id.
         assign_openlifu_metadata_to_volume_node(loadedVolumeNode, volume_metadata)
@@ -2313,7 +2314,7 @@ def load_volume_from_file(self, filepath: str) -> None:
         parent_dir = Path(filepath).parent
         # Load volume using use slicer default volume name and id based on filepath
         if slicer.app.coreIOManager().fileType(filepath) == 'VolumeFile':
-            slicer.util.loadVolume(filepath)
+            load_volume_and_threshold_background(filepath)
 
         # If the user selects a json file, infer volume filepath information based on the volume_metadata.
         elif Path(filepath).suffix == '.json':

OpenLIFULib/CMakeLists.txt

@@ -25,6 +25,7 @@ set(MODULE_PYTHON_SCRIPTS
   OpenLIFULib/transducer_tracking_wizard_utils.py
   OpenLIFULib/events.py
   OpenLIFULib/notifications.py
+  OpenLIFULib/volume_thresholding.py
 )
 
 set(MODULE_PYTHON_RESOURCES

OpenLIFULib/OpenLIFULib/session.py

@@ -8,6 +8,7 @@
 )
 from slicer.parameterNodeWrapper import parameterPack
 from OpenLIFULib.util import get_openlifu_data_parameter_node
+from OpenLIFULib.volume_thresholding import load_volume_and_threshold_background
 from OpenLIFULib.lazyimport import openlifu_lz
 from OpenLIFULib.parameter_node_utils import SlicerOpenLIFUSessionWrapper, SlicerOpenLIFUPhotoscanWrapper
 from OpenLIFULib.targets import (
@@ -147,7 +148,7 @@ def initialize_from_openlifu_session(
         """
 
         # Load volume
-        volume_node = slicer.util.loadVolume(volume_info['data_abspath'])
+        volume_node = load_volume_and_threshold_background(volume_info['data_abspath'])
         assign_openlifu_metadata_to_volume_node(volume_node, volume_info)
 
         # Load targets

OpenLIFULib/OpenLIFULib/skinseg.py

@@ -55,4 +55,4 @@ def get_skin_segmentation(volume : Union[vtkMRMLScalarVolumeNode, str]) -> vtkMR
     elif len(skin_mesh_node) > 1:
         raise RuntimeError(f"Found multiple skin segmentation models affiliated with volume {volume_id}")
     else:
-        return skin_mesh_node[0]
+        return skin_mesh_node[0]

OpenLIFULib/OpenLIFULib/volume_thresholding.py

@@ -0,0 +1,48 @@
+"""Volume thresholding tools"""
+
+import logging
+import vtk
+import slicer
+from slicer import vtkMRMLScalarVolumeNode
+from OpenLIFULib.util import BusyCursor
+from OpenLIFULib.lazyimport import openlifu_lz
+
+def cast_volume_to_float(volume_node:vtkMRMLScalarVolumeNode) -> None:
+    """Converts a volume node to float, replacing the underlying vtkImageData."""
+    image_cast = vtk.vtkImageCast()
+    image_cast.SetInputData(volume_node.GetImageData())
+    image_cast.SetOutputScalarTypeToDouble()
+    image_cast.Update()
+    volume_node.SetAndObserveImageData(image_cast.GetOutput())
+
+    # I am not certain that the display node will know to update itself to handle the new image data type,
+    # so I hope poking `CreateDefaultDisplayNodes` here makes it do the right thing. If it's not needed then it's harmless anyway:
+    volume_node.CreateDefaultDisplayNodes()
+
+def threshold_volume_by_foreground_mask(volume_node:vtkMRMLScalarVolumeNode) -> None:
+    """Compute the foreground mask for a loaded volume and threshold the volume to strip out the background.
+    This modifies the values of the background region in the volume and sets them to 1 less than the minimum value in the volume.
+    This way we can simply enable volume thresholding to remove
+    It can take a moment to actually compute the foreground mask.
+    """
+    volume_array = slicer.util.arrayFromVolume(volume_node)
+    volume_array_min = volume_array.min()
+
+    background_value = volume_array_min - 1
+    if background_value < volume_node.GetImageData().GetScalarTypeMin(): # e.g. if volume_array_min is 0 and it's an unsigned int type
+        logging.info("Casting volume to float for the sake of `threshold_volume_by_foreground_mask`.")
+        cast_volume_to_float(volume_node)
+
+    foreground_mask = openlifu_lz().seg.skinseg.compute_foreground_mask(volume_array)
+    slicer.util.arrayFromVolume(volume_node)[~foreground_mask] = background_value
+    volume_node.GetDisplayNode().SetThreshold(volume_array_min,volume_array.max())
+    volume_node.GetDisplayNode().SetApplyThreshold(1)
+    volume_node.GetDisplayNode().SetAutoThreshold(0)
+    volume_node.Modified()
+
+def load_volume_and_threshold_background(volume_filepath) -> vtkMRMLScalarVolumeNode:
+    """Load a volume node from file, and also set the background values to a certain value that can be threshoded out, and threshold it out."""
+    volume_node = slicer.util.loadVolume(volume_filepath)
+    with BusyCursor():
+        threshold_volume_by_foreground_mask(volume_node)
+    return volume_node