Error when executing engine_pool.json docker command - Annotation Server

[ephssmk]

Hello Everyone,

I am trying to start the annotation server by running the below command,

/opt/nvidia/medical/aas/start_aas.sh --config /var/tmp/models/engine_pool.json

However, I am getting the below error as shown in the attached file.

Do note that I am only trying for the annotation_spleen model.

Please find my engine_pool.json code

{
"name": "MyAnnotationSpleenModel",
"class": "Dextr3dCroppedEngine",
"module": "medical.aas.dextr3dcropped",
"config_file": "/var/tmp/models/annotation_spleen.json",
"labels": ["spleen"]
}

Request your help

[ephssmk]

Can anyone please help me with this?

[aharouni]

Hi

Looks like your engine_pool.json is missing [ and ] in the beginning and end, so your file should look like

[
{
“name”: “MyAnnotationSpleenModel”,
“class”: “Dextr3dCroppedEngine”,
“module”: “medical.aas.dextr3dcropped”,
“config_file”: “/var/tmp/models/spleen.json”,
“labels”: [“spleen”]
}
]

This should fix the error.
Also please note the blog https://devblogs.nvidia.com/annotation-transfer-learning-clara-train/ was recently updated.

[ephssmk]

Hello,

I was following the blog suggested above and was able to execute example.cpp file after making multiple modifications. Will the blog be upated?

Please find my example.cpp file which I used

#include </home/selva/include/nvidia/aiaa/client.h>
#include <iostream>

using namespace nvidia;
using namespace aiaa;
using namespace Pixel;

int main() {
   try {
      // Create AIAA Client object
      nvidia::aiaa::Client client("http://127.0.0.1:5000/v1");

      // List all models
      nvidia::aiaa::ModelList modelList = client.models();
      std::cout << "Models Supported by AIAA Server: " << modelList.toJson() << std::endl;

      // Get matching model for organ Spleen
      nvidia::aiaa::Model model = modelList.getMatchingModel("spleen");
      std::cout << "Selected AIAA Model for organ 'Spleen' is: " << model.toJson(2) << std::endl;

 // More API calls can follow here...
      std::string inputImageFile = "image.nii.gz";
      std::string outputDextr3dImageFile = "result.nii.gz";
      nvidia::aiaa::PointSet point3Set = nvidia::aiaa::PointSet::fromJson("[[1,2,3]]");
      int PAD = 20; // Padding boundary
      Pixel::Type pt = INT;
      std::string ROI_SIZE = "128x128x128";
      const int SIGMA = 3;

      int ret = client.dextr3D(model, point3Set, inputImageFile,pt, outputDextr3dImageFile);

      int pointRatio = 10;
      nvidia::aiaa::PolygonsList result = client.maskToPolygon(pointRatio, outputDextr3dImageFile);

      int neighborhoodSize = 10;
      nvidia::aiaa::Polygons p1 = nvidia::aiaa::Polygons::fromJson("[[10,20],[20,30]");
      nvidia::aiaa::Polygons p2 = nvidia::aiaa::Polygons::fromJson("[[10,20],[21,31]]");
      int polygonIndex = 0;
      int vertexIndex = 1;
      std::string input2DImageFile = "image_slice_2D.png";
      std::string output2DImageFile = "updated_slice_2D.png";
      // fixPolygon():: Call Fix Polygon with new Polygon Points
      nvidia::aiaa::Polygons results = client.fixPolygon(p1, p2, neighborhoodSize, polygonIndex, vertexIndex, 
  input2DImageFile, output2DImageFile);

   } catch (nvidia::aiaa::exception& e) {
      std::cerr << "nvidia::aiaa::exception => nvidia.aiaa.error." << e.id << "; description: " << e.name()<< std::endl;

 } catch (nvidia::aiaa::exception& e) {
      std::cerr << "nvidia::aiaa::exception => nvidia.aiaa.error." << e.id << "; description: " << e.name() << std::endl;

 }

   return 0;
}

Though I was able to successfully compile and execute after fixing some issues with example.cpp, I also had the below error as shown in the attachment. As I am new to image processing and analysis, trying to learn.

[Alvin]

Can you post your spleen.json?

[ephssmk]

Here is the spleen.json

{
    "model_format": "trtmodel",
    "model_path": "/var/tmp/models/annotation_spleen/model.trt.pb",
    "thresh": 0.5,
    "result_dir": "/var/tmp/experiments/aiaa",

    "input_nodes":
    {
        "image": "cond/Merge"
    },

    "output_nodes":
    {
        "model": "NV_OUTPUT_LABEL"
    },

    "batch_size": 1,

    "pre_transforms":
    [    
        {
            "name": "transforms.VolumeTo4dArray",
            "fields": ["image", "label"]
        },           
        {
            "name": "transforms.ScaleIntensityRange",
            "field": "image",
            "a_min": -1024,
            "a_max": 1024,
            "b_min": -1.0,
            "b_max": 1.0,
            "clip": true
        },        
        {
            "name": "transforms.AddExtremePointsChannel",
            "image_field": "image",
            "label_field": "label",
            "sigma": 3,
            "pert": 0
        }                
    ],

    "post_transforms":
    [ 
        {
            "name": "transforms.SplitAcrossChannels",
            "applied_key": "model", 
            "channel_names": ["background", "prediction"]
        }        
    ],

    "writers":
    [
        {
            "applied_key": "prediction",
            "name": "writers.WriteNiftyResults",
            "dtype": "float32"
        }               
    ]
}

[ephssmk]

Hello Alvin,

Any issue with my spleen.json file?

[Alvin]

It looks correct.

Are building your own custom AIAA client?

[ephssmk]

No. Curently,we aren’t planning to build custom client. We are only using MITK. So, then I think we don’t have to bother about example.cpp file.

Thanks
Selva