using ColonSegNet-07112023-2359.onnx and out720x576.mp4 #34

SciKit-Surgery · Nov 10, 2023 · ba3d76c · ba3d76c
1 parent 7c38160
commit ba3d76c
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/nvidia-clara-agx/colonoscopy_segmentation/colonoscopy_segmentation.py b/nvidia-clara-agx/colonoscopy_segmentation/colonoscopy_segmentation.py
@@ -46,11 +46,15 @@ def compute(self, op_input, op_output, context):
         in_message = op_input.receive("in")
 
         # Transpose
-        tensor = cp.asarray(in_message.get("inference_output_tensor")).get()
+        tensor = cp.asarray(in_message.get("inference_output_tensor"))
+        print(f"tensor.min()={cp.min(tensor)}")
+        print(f"tensor.max()={cp.max(tensor)}")
+        print(f"tensor.mean()={cp.mean(tensor)}")
+        print(f"tensor.shape={tensor.shape}")
 
         # Create output message
         out_message = Entity(context)
-        out_message.add(hs.as_tensor(tensor), "out_tensor")
+        out_message.add(hs.as_tensor(tensor), "inference_output_tensor")
         op_output.emit(out_message, "out")
 
 
@@ -80,7 +84,8 @@ def __init__(self, data, source="replayer"):
         self.sample_data_path = data
 
         self.model_path_map = {
-            "ultrasound_seg": os.path.join(self.sample_data_path, "colon.onnx"),
+            #"ultrasound_seg": os.path.join(self.sample_data_path, "colon.onnx"),
+            "ultrasound_seg": os.path.join(self.sample_data_path, "ColonSegNet-07112023-2359.onnx"),
         }
 
     def compose(self):
@@ -205,6 +210,7 @@ def compose(self):
         self.add_flow(segmentation_preprocessor, segmentation_inference, {("", "receivers")})
         self.add_flow(segmentation_inference, info_op, {("transmitter", "in")})
         self.add_flow(info_op, segmentation_postprocessor, {("out", "")})
+        #self.add_flow(segmentation_inference, segmentation_postprocessor, {("transmitter", "")})
         self.add_flow(
             segmentation_postprocessor,
             segmentation_visualizer,

diff --git a/nvidia-clara-agx/colonoscopy_segmentation/colonoscopy_segmentation.yaml b/nvidia-clara-agx/colonoscopy_segmentation/colonoscopy_segmentation.yaml
@@ -15,8 +15,8 @@
 # limitations under the License.
 ---
 replayer:  # VideoStreamReplayer
-  basename: "colon_exam_720x576"
-  #basename: "out720x576"
+  #basename: "colon_exam_720x576"
+  basename: "out720x576"
   frame_rate: 0 # as specified in timestamps
   repeat: true # default: false
   realtime: true # default: true
@@ -40,11 +40,13 @@ segmentation_preprocessor:  # FormatConverter
     resize_height: 512
 
 segmentation_postprocessor:  # Postprocessor
-  in_tensor_name: out_tensor
+  in_tensor_name: inference_output_tensor
   network_output_type: sigmoid
   data_format: nchw
 
 segmentation_visualizer:  # Holoviz
+  height: 512
+  width: 512
   color_lut: [
     [0.65, 0.81, 0.89, 0.1],
     [0.2, 0.63, 0.17, 0.7],