Merge pull request #5 from dzenanz/main

Miscellaneous fixes

CMakeLists.txt

@@ -10,7 +10,7 @@ set(EXTENSION_CONTRIBUTORS "MONAI Consortium")
 set(EXTENSION_DESCRIPTION "This extension helps to run chain of MONAI transforms and visualize every stage over an image/label. See more information in <a href=\"https://github.com/Project-MONAI/MONAILabel\">MONAILabel documentation</a>.")
 set(EXTENSION_ICONURL "https://raw.githubusercontent.com/Project-MONAI/SlicerMONAIViz/main/MONAIViz/Resources/Icons/MONAIViz.png")
 set(EXTENSION_SCREENSHOTURLS "https://github.com/Project-MONAI/SlicerMONAIViz/raw/main/Screenshots/1.jpg https://github.com/Project-MONAI/SlicerMONAIViz/raw/main/Screenshots/2.jpg https://github.com/Project-MONAI/SlicerMONAIViz/raw/main/Screenshots/3.jpg https://github.com/Project-MONAI/SlicerMONAIViz/raw/main/Screenshots/4.jpg")
-set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies
+set(EXTENSION_DEPENDS "PyTorch") # Specified as a list or "NA" if no dependencies
 
 #-----------------------------------------------------------------------------
 # Extension dependencies

MONAIViz/MONAIViz.py

@@ -435,7 +435,16 @@ def onAddTransform(self):
 
         t = self.ui.transformsComboBox.currentText
         m = self.ui.modulesComboBox.currentText
-        self.addTransform(-1, None, t, None)
+
+        v = ""
+        if t[-1] == "d":  # this is a dictionary transform
+            # now exclude some transforms whose name happens to end with d
+            if t not in ["AffineGrid", "Decollated", "RandAffineGrid", "RandDeformGrid"]:
+                image_key = slicer.util.settingsValue("SlicerMONAIViz/imageKey", "image")
+                label_key = slicer.util.settingsValue("SlicerMONAIViz/labelKey", "label")
+                v = f"keys=['{image_key}', '{label_key}']"
+
+        self.addTransform(-1, None, t, v)
 
     def addTransform(self, pos, m, t, v):
         table = self.ui.transformTable
@@ -558,6 +567,7 @@ def onRunTransform(self):
             volumeNode.SetOrigin(origin)
             volumeNode.SetSpacing(spacing)
             volumeNode.SetIJKToRASDirections(direction)
+            # logging.info(f"Volume direction: {direction}")
 
             l = self.ctx.get_tensor(key=label_key)
             labelNode = None
@@ -568,6 +578,7 @@ def onRunTransform(self):
                 labelNode.SetOrigin(origin)
                 labelNode.SetSpacing(spacing)
                 labelNode.SetIJKToRASDirections(direction)
+                # logging.info(f"Label direction: {direction}")
             slicer.util.setSliceViewerLayers(volumeNode, label=labelNode, fit=True)
 
             self.ctx.set_next(next_idx, next_exp)
@@ -852,8 +863,8 @@ def get_tensor_osd(self, key, scale=False):
             else key_tensor.affine.numpy()
         )
 
-        convert_aff_mat = np.diag([-1, -1, 1, 1])
-        affine = convert_aff_mat @ affine
+        # convert_aff_mat = np.diag([-1, -1, 1, 1])  # RAS <-> LPS conversion matrix
+        # affine = convert_aff_mat @ affine  # convert from RAS to LPS
 
         dim = affine.shape[0] - 1
         _origin_key = (slice(-1), -1)