336 Add MedNIST Classification example to Triton Demo

deployment/Triton/.gitignore

@@ -2,4 +2,7 @@
 __pycache__
 #  Ignore Pipenv files
 Pipfile
-Pipfile.loc
+Pipfile.lock
+# Image Input Files
+*.jpeg
+*.gz

deployment/Triton/Dockerfile

@@ -41,17 +41,22 @@ FROM nvcr.io/nvidia/tritonserver:21.04-py3
 
 # create model directory in container
 RUN mkdir -p /models/monai_covid/1
-RUN mkdir -p /models/monai_covid/
-
+RUN mkdir -p /models/mednist_class/1
 # install project-specific dependencies
 COPY requirements.txt .
+
 RUN pip install -r requirements.txt
 RUN rm requirements.txt
 
 # copy contents of model project into model repo in container image
 COPY models/monai_covid/config.pbtxt /models/monai_covid
 COPY models/monai_covid/1/model.py /models/monai_covid/1
-#COPY models/monai_covid/1/covid19_model.ts /models/monai_covid/1  #moved to google drive
+
+
+# copy contents of model project into model repo in container image
+COPY models/mednist_class/config.pbtxt /models/mednist_class
+COPY models/mednist_class/1/model.py /models/mednist_class/1
+
 
 ENTRYPOINT [ "tritonserver", "--model-repository=/models"]
-#ENTRYPOINT [ "tritonserver", "--model-repository=/models", "--log-verbose=1"]
+# ENTRYPOINT [ "tritonserver", "--model-repository=/models", "--log-verbose=1"]

deployment/Triton/README.md

@@ -83,7 +83,7 @@ $ ./triton_build.sh
 2. Run Triton Container Image in Background Terminal using provided shell script
 The supplied script will start the demo container with Triton and expose the three ports to localhost needed for the application to send inference requests. 
 ```
-$ ./triton_run_local.sh
+$ ./run_triton_local.sh
 ```
 3. Install environment for client
 The client environment should have Python 3 installed and should have the necessary packages installed. 
@@ -171,7 +171,7 @@ filename = 'client/test_data/volume-covid19-A-0000.nii.gz'
 ```
 - The client calls the Triton Service using the external port configured previously.
 ```python:
-with httpclient.InferenceServerClient("localhost:8000") as client:
+with httpclient.InferenceServerClient("localhost:7555") as client:
 ```
 - The Triton inference response is returned :
 ```python:
@@ -182,6 +182,23 @@ response = client.infer(model_name,
 
 result = response.get_response()
 ```
+-------
+## MedNIST Classification Example
+
+- Added to this demo as alternate demo using the MedNIST dataset in a classification example.
+- To run the MedNIST example use the same steps as shown in the [Quick Start](#quick-start) with the following changes at step 5. 
+5. Run the client program (for the MedNIST example)
+The [client](./client/client_mednist.py) program will take an optional file input and perform classification on body parts using the MedNIST data set.  A small subset of the database is included. 
+```
+$ mkdir -p client/test_data/MedNist
+$ python -u client/client_mednist.py client/test_data/MedNist
+```
+Alternatively, the user can just run the shell script provided the previous steps 1 -4 in the [Quick Start](#quick-start) were followed.
+```
+$ ./mednist_client_run.sh
+```
+The expected result is variety of classification results for body images and local inference times.
+
 -------
 ## Usage
 [See Triton Inference Server/python_backend documentation](https://github.com/triton-inference-server/python_backend#usage)

deployment/Triton/client/client.py

@@ -85,7 +85,7 @@ def open_nifti_files(input_path):
         print("No valid inputs provided")
         sys.exit(1)
 
-    with httpclient.InferenceServerClient("localhost:8000") as client:
+    with httpclient.InferenceServerClient("localhost:7555") as client:
         image_bytes = b''
         for nifti_file in nifti_files:
             with open(nifti_file, 'rb') as f:

deployment/Triton/client/client_mednist.py

@@ -0,0 +1,123 @@
+# Copyright 2020 - 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#  * Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#  * Neither the name of NVIDIA CORPORATION nor the names of its
+#    contributors may be used to endorse or promote products derived
+#    from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+# OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+from tritonclient.utils import *
+import tritonclient.grpc as grpcclient
+import tritonclient.http as httpclient
+
+import argparse
+import numpy as np
+import os
+import sys
+import time
+from uuid import uuid4
+import glob
+
+from monai.apps.utils import download_and_extract
+from monai.transforms.utils import convert_to_numpy
+
+MEDNIST_CLASSES = ["AbdomenCT", "BreastMRI", "CXR", "ChestCT", "Hand", "HeadCT"]
+
+
+
+model_name = "mednist_class"
+gdrive_path = "https://drive.google.com/uc?id=1HQk4i4vXKUX_aAYR4wcZQKd-qk5Lcm_W"
+mednist_filename = "MedNIST_demo.tar.gz"
+md5_check = "3f24a5833bb0455a7815c4e0ecc8a810"
+
+
+def open_jpeg_files(input_path):
+    return sorted(glob.glob(os.path.join(input_path, "*.jpeg")))
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(description='Triton CLI for MedNist classification inference from JPEG data')
+    parser.add_argument(
+        'input',
+        type=str,
+        help="Path to JPEG file or directory containing JPEG files to send for MedNist classification"
+    )
+    args = parser.parse_args()
+
+    jpeg_files = []
+    extract_dir = "./client/test_data/MedNist"
+    tar_save_path = os.path.join(extract_dir, mednist_filename)
+    if os.path.isdir(args.input):  # check for directory existence
+        # Grab files from Google Drive and place in directory
+        download_and_extract(gdrive_path, tar_save_path, output_dir=extract_dir, hash_val=md5_check, hash_type="md5")
+        jpeg_files = open_jpeg_files(args.input)
+
+    elif os.path.isfile(args.input):
+        jpeg_files = [args.input]
+
+    if not jpeg_files:
+        print("No valid inputs provided")
+        sys.exit(1)
+
+    with httpclient.InferenceServerClient("localhost:7555") as client:
+        image_bytes = b''
+        for jpeg_file in jpeg_files:
+            with open(jpeg_file, 'rb') as f:
+                image_bytes = f.read()
+
+            input0_data = np.array([[image_bytes]], dtype=np.bytes_)
+
+            inputs = [
+                httpclient.InferInput("INPUT0", input0_data.shape, np_to_triton_dtype(input0_data.dtype)),
+            ]
+
+            inputs[0].set_data_from_numpy(input0_data)
+
+            outputs = [
+                httpclient.InferRequestedOutput("OUTPUT0"),
+            ]
+
+            inference_start_time = time.time() * 1000
+            response = client.infer(model_name,
+                                    inputs,
+                                    request_id=str(uuid4().hex),
+                                    outputs=outputs,)
+            inference_time = time.time() * 1000 - inference_start_time
+
+            result = response.get_response()
+            print("Classification result for `{}`: {}.  (Inference time: {:6.0f} ms)".format(
+                jpeg_file,
+                response.as_numpy("OUTPUT0").astype(str)[0],
+                inference_time,
+            ))

deployment/Triton/client_run.sh

@@ -36,5 +36,13 @@
 # OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-python -u client/client.py client/test_data
+# if no argument provided use default `client/test_data` name
+if [ $# -eq 0 ]
+then
+    echo "No arguments supplied defaulting 'client/test_data'"
+    input_name="client/test_data"
+else
+# otherwise use the first argument as the operator image
+    input_name=$1
+fi
+python -u client/client.py $input_name

deployment/Triton/mednist_client_run.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+# Copyright 2020 - 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#  * Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#  * Neither the name of NVIDIA CORPORATION nor the names of its
+#    contributors may be used to endorse or promote products derived
+#    from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+# OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# if no argument provided use default `client/test_data` name
+if [ $# -eq 0 ]
+then
+    echo "No arguments supplied defaulting './client/test_data/MedNist/demo'"
+    input_name="./client/test_data/MedNist"
+    # check if the output directory exists
+    if [ -d $input_name ] 
+    then
+        echo "Directory $PWD/client/test_data/MedNist exists." 
+    else
+        echo "Error: Directory $PWD/client/test_data/MedNist does not exist. 
+Please create the directory to save data to disk from the Clara operator."
+        exit 1
+    fi
+else
+# otherwise use the first argument as the operator image
+    input_name=$1
+fi
+python -u client/client_mednist.py $input_name
+