add polyp det

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

applications/polyp_detection/Dockerfile

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+# syntax=docker/dockerfile:1
+
+# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# 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.
+
+
+FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.7.0-dgpu
+
+WORKDIR /colon_workspace
+
+# Install dependencies
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+# TODO: after having the final model weights, upload to some place instead
+COPY rtdetrv2_timm_r50_nvimagenet_pretrained.onnx .

applications/polyp_detection/README.md

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+# Polyp Detection
+
+## Build Docker
+
+```Bash
+docker build -t nvcr.io/nvidia/clara-holoscan/holoscan:v2.7.0-dgpu-polyp-det -f Dockerfile .
+```
+
+## Run Application
+
+### Run Docker
+
+Please mount the directory that contains `holohub/` into `/colon`. For example, my folder is under `/raid/colon_reproduce`.
+
+```Bash
+docker run --rm -it --gpus=all --ipc=host -p 8888:8888 -v /raid/colon_reproduce:/colon nvcr.io/nvidia/clara-holoscan/holoscan:v2.7.0-dgpu-polyp-det
+```
+
+### Generate TensorRT model
+
+```Bash
+trtexec --onnx=rtdetrv2_timm_r50_nvimagenet_pretrained.onnx --saveEngine=rt_detrv2_timm_r50_nvimagenet_pretrained_demo.trt \
+--minShapes=images:1x3x640x640,orig_target_sizes:1x2 \
+--optShapes=images:128x3x640x640,orig_target_sizes:128x2 \
+--maxShapes=images:128x3x640x640,orig_target_sizes:128x2 \
+--allowGPUFallback
+```
+
+### Grab example video
+
+(todo) need to upload after license permisison
+
+### Convert Video into GXF Entities
+
+```Bash
+apt-get update && apt-get install -y ffmpeg
+git clone https://github.com/nvidia-holoscan/holoscan-sdk.git
+ffmpeg -i <prepared video>.mp4 -pix_fmt rgb24 -f rawvideo pipe:1 | python holoscan-sdk/scripts/convert_video_to_gxf_entities.py --width 1164 --height 1034 --channels 3 --framerate 30 --directory /colon/holohub/data/polyp_detection/
+```
+
+### Run application
+
+```Bash
+cd /colon/holohub/applications/polyp_detection
+python polyp_detection.py --data /colon/holohub/data/polyp_detection/
+```

applications/polyp_detection/metadata.json

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+{
+	"application": {
+		"name": "Polyp detection",
+		"authors": [
+			{
+				"name": "Holoscan Team",
+				"affiliation": "NVIDIA"
+			}
+		],
+		"language": "Python",
+		"version": "1.0",
+		"changelog": {
+			"1.0": "Initial Release"
+		},
+		"holoscan_sdk": {
+			"minimum_required_version": "0.5.0",
+			"tested_versions": [
+				"0.5.0"
+			]
+		},
+		"platforms": [
+			"amd64",
+			"arm64"
+		],
+		"tags": [
+			"Colonoscopy",
+			"Detection"
+		],
+		"ranking": 1,
+		"dependencies": {
+			"libraries": []
+		},
+		"run": {
+			"command": "python3 polyp_detection.py --data <holohub_data_dir>/polyp_detection",
+			"workdir": "holohub_app_source"
+		}
+	}
+}