Enable packaging of the applications using Holoscan CLI

Signed-off-by: Victor Chang <vicchang@nvidia.com>

Author: mocsharp

applications/endoscopy_tool_tracking/README.md

@@ -109,3 +109,7 @@ There are a two launch profiles configured for this application:
 
 1. **(debugpy) endoscopy_tool_tracking/python**: This launch profile enables debugging of Python code.
 2. **(pythoncpp) endoscopy_tool_tracking/python**: This launch profile enables debugging of Python and C++ code.
+
+## Containerize the application
+
+To containerize the application, first build the application, run the `package-app.sh` script in the [cpp](./cpp/package-app.sh) or the [python](./python/package-app.sh) directory and then follow the generated output to package and run the application.

applications/endoscopy_tool_tracking/cpp/endoscopy_tool_tracking.yaml

@@ -14,6 +14,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 ---
+application:
+  title: Holohub - Endoscopy Tool Tracking
+  version: 1.0
+  inputFormats: []
+  outputFormats: ["screen"]
+
+resources:
+  cpu: 2
+  gpu: 1
+  memory: 1Gi
+  gpuMemory: 1Gi
+
 extensions:
   - gxf_extensions/lstm_tensor_rt_inference/libgxf_lstm_tensor_rt_inference.so
 # Uncomment the following extension when using deltacast as a source

applications/endoscopy_tool_tracking/cpp/main.cpp

@@ -17,14 +17,14 @@
 
 #include <getopt.h>
 
-#include "holoscan/holoscan.hpp"
 #include <holoscan/operators/aja_source/aja_source.hpp>
 #include <holoscan/operators/format_converter/format_converter.hpp>
 #include <holoscan/operators/holoviz/holoviz.hpp>
 #include <holoscan/operators/video_stream_recorder/video_stream_recorder.hpp>
 #include <holoscan/operators/video_stream_replayer/video_stream_replayer.hpp>
 #include <lstm_tensor_rt_inference.hpp>
 #include <tool_tracking_postprocessor.hpp>
+#include "holoscan/holoscan.hpp"
 #ifdef VTK_RENDERER
 #include <vtk_renderer.hpp>
 #endif
@@ -181,10 +181,8 @@ class App : public holoscan::Application {
     }
 #ifdef VTK_RENDERER
     if (this->visualizer_name == "vtk") {
-      visualizer_operator = make_operator<ops::VtkRendererOp>("vtk",
-                                                      from_config("vtk_op"),
-                                                      Arg("width") = width,
-                                                      Arg("height") = height);
+      visualizer_operator = make_operator<ops::VtkRendererOp>(
+          "vtk", from_config("vtk_op"), Arg("width") = width, Arg("height") = height);
     }
 #endif
 
@@ -279,43 +277,62 @@ class App : public holoscan::Application {
 };
 
 /** Helper function to parse the command line arguments */
-bool parse_arguments(int argc, char** argv, std::string& config_name, std::string& data_path) {
-  static struct option long_options[] = {{"data", required_argument, 0, 'd'}, {0, 0, 0, 0}};
+bool parse_arguments(int argc, char** argv, std::string& data_path, std::string& config_path) {
+  static struct option long_options[] = {
+      {"data", required_argument, 0, 'd'}, {"config", required_argument, 0, 'c'}, {0, 0, 0, 0}};
 
-  while (int c = getopt_long(argc, argv, "d", long_options, NULL)) {
+  while (int c = getopt_long(argc, argv, "d:c:", long_options, NULL)) {
     if (c == -1 || c == '?') break;
 
     switch (c) {
+      case 'c':
+        config_path = optarg;
+        break;
       case 'd':
         data_path = optarg;
         break;
       default:
-        std::cout << "Unknown arguments returned: " << c << std::endl;
+        holoscan::log_error("Unhandled option '{}'", static_cast<char>(c));
         return false;
     }
   }
 
-  if (optind < argc) { config_name = argv[optind++]; }
   return true;
 }
 
 /** Main function */
 int main(int argc, char** argv) {
-  auto app = holoscan::make_application<App>();
-
   // Parse the arguments
-  std::string data_path = "";
-  std::string config_name = "";
-  if (!parse_arguments(argc, argv, config_name, data_path)) { return 1; }
-
-  if (config_name != "") {
-    app->config(config_name);
-  } else {
-    auto config_path = std::filesystem::canonical(argv[0]).parent_path();
-    config_path += "/endoscopy_tool_tracking.yaml";
-    app->config(config_path);
+  std::string config_path = "";
+  std::string data_directory = "";
+  if (!parse_arguments(argc, argv, data_directory, config_path)) { return 1; }
+  if (data_directory.empty()) {
+    // Get the input data environment variable
+    auto input_path = std::getenv("HOLOSCAN_INPUT_PATH");
+    if (input_path == nullptr || input_path[0] == '\0') {
+      HOLOSCAN_LOG_ERROR(
+          "Input data not provided. Use --data or set HOLOSCAN_INPUT_PATH environment variable.");
+      exit(-1);
+    }
+    data_directory = std::string(input_path);
   }
 
+  if (config_path.empty()) {
+    // Get the input data environment variable
+    auto config_file_path = std::getenv("HOLOSCAN_CONFIG_PATH");
+    if (config_file_path == nullptr || config_file_path[0] == '\0') {
+      auto config_file = std::filesystem::canonical(argv[0]).parent_path();
+      config_path = config_file / std::filesystem::path("endoscopy_tool_tracking.yaml");
+    } else {
+      config_path = config_file_path;
+    }
+  }
+
+  auto app = holoscan::make_application<App>();
+
+  HOLOSCAN_LOG_INFO("Using configuration file from {}", data_directory);
+  app->config(config_path);
+
   auto source = app->from_config("source").as<std::string>();
   app->set_source(source);
 
@@ -325,7 +342,8 @@ int main(int argc, char** argv) {
   auto visualizer_name = app->from_config("visualizer").as<std::string>();
   app->set_visualizer_name(visualizer_name);
 
-  if (data_path != "") app->set_datapath(data_path);
+  HOLOSCAN_LOG_INFO("Using input data from {}", data_directory);
+  app->set_datapath(data_directory);
 
   app->run();
 

applications/endoscopy_tool_tracking/cpp/package-app.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+# 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.
+
+GIT_ROOT=$(readlink -f ./$(git rev-parse --show-cdup))
+
+# Utilities
+
+YELLOW="\e[1;33m"
+RED="\e[1;31m"
+NOCOLOR="\e[0m"
+
+print_error() {
+    echo -e "${RED}ERROR${NOCOLOR}:" $*
+}
+
+if [ ! -d $GIT_ROOT/build/endoscopy_tool_tracking ]; then
+    print_error "Please build the Endoscopy Tool Tracking application first with the following command:"
+    print_error "./dev_container build_and_run endoscopy_tool_tracking"
+    exit -1
+fi
+
+APP_PATH="$GIT_ROOT/endoscopy_tool_tracking_cpp"
+echo Creating application directory $APP_PATH...
+mkdir -p $APP_PATH
+echo Copying application files to $APP_PATH...
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/applications/endoscopy_tool_tracking/cpp/endoscopy_tool_tracking $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/applications/endoscopy_tool_tracking/cpp/endoscopy_tool_tracking.yaml $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/gxf_extensions/lstm_tensor_rt_inference/*.so $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/operators/lstm_tensor_rt_inference/liblstm_tensor_rt_inference.so $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/operators/tool_tracking_postprocessor/libtool_tracking_postprocessor.so $APP_PATH
+
+echo Updating application configuration...
+sed -e s!gxf_extensions/lstm_tensor_rt_inference/!!g -i $APP_PATH/endoscopy_tool_tracking.yaml
+
+
+echo -e "done\n"
+echo -e Use the following commands to package and run the Endoscopy Tool Tracking application:\n
+echo -e "Package the application:\n"
+echo -e "${YELLOW}holoscan package -c $APP_PATH/endoscopy_tool_tracking.yaml --platform x64-workstation -t holohub-endoscopy-tool-tracking-cpp $APP_PATH/endoscopy_tool_tracking --include onnx holoviz${NOCOLOR}"
+echo -e "Run the application:\n"
+echo -e "${YELLOW}holoscan run -r \$(docker images | grep "holohub-endoscopy-tool-tracking-cpp" | awk '{print \$1\":\"\$2}') -i $GIT_ROOT/data/endoscopy${NOCOLOR}"

applications/endoscopy_tool_tracking/python/endoscopy_tool_tracking.py

@@ -303,7 +303,7 @@ def compose(self):
     parser.add_argument(
         "-d",
         "--data",
-        default="none",
+        default=os.environ.get("HOLOSCAN_INPUT_PATH", None),
         help=("Set the data path"),
     )
     args = parser.parse_args()

applications/endoscopy_tool_tracking/python/endoscopy_tool_tracking.yaml

@@ -14,6 +14,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 ---
+application:
+  title: Holohub - Endoscopy Tool Tracking
+  version: 1.0
+  inputFormats: []
+  outputFormats: ["screen"]
+
+resources:
+  cpu: 2
+  gpu: 1
+  memory: 1Gi
+  gpuMemory: 1Gi
+
 extensions:
 - gxf_extensions/lstm_tensor_rt_inference/libgxf_lstm_tensor_rt_inference.so
 - gxf_extensions/yuan_qcap/libgxf_qcap_source.so

applications/endoscopy_tool_tracking/python/package-app.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+# 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.
+
+GIT_ROOT=$(readlink -f ./$(git rev-parse --show-cdup))
+
+# Utilities
+
+YELLOW="\e[1;33m"
+RED="\e[1;31m"
+NOCOLOR="\e[0m"
+
+print_error() {
+    echo -e "${RED}ERROR${NOCOLOR}:" $*
+}
+
+if [ ! -d $GIT_ROOT/build/endoscopy_tool_tracking ]; then
+    print_error "Please build the Endoscopy Tool Tracking application first with the following command:"
+    print_error "./dev_container build_and_run endoscopy_tool_tracking"
+    exit -1
+fi
+
+APP_PATH="$GIT_ROOT/endoscopy_tool_tracking_python"
+echo Creating application directory $APP_PATH...
+mkdir -p $APP_PATH
+echo Copying application files to $APP_PATH...
+cp -f $GIT_ROOT/applications/endoscopy_tool_tracking/python/endoscopy_tool_tracking.py $APP_PATH
+cp -f $GIT_ROOT/applications/endoscopy_tool_tracking/python/endoscopy_tool_tracking.yaml $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/gxf_extensions/lstm_tensor_rt_inference/*.so $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/operators/lstm_tensor_rt_inference/liblstm_tensor_rt_inference.so $APP_PATH
+cp -f $GIT_ROOT/build/endoscopy_tool_tracking/operators/tool_tracking_postprocessor/libtool_tracking_postprocessor.so $APP_PATH
+cp -rf $GIT_ROOT/build/endoscopy_tool_tracking/python/lib/holohub $APP_PATH
+echo Updating application configuration...
+sed -e s!gxf_extensions/lstm_tensor_rt_inference/!!g -i $APP_PATH/endoscopy_tool_tracking.yaml
+
+
+echo -e "done\n"
+echo -e Use the following commands to package and run the Endoscopy Tool Tracking application:\n
+echo -e "Package the application:\n"
+echo -e "${YELLOW}holoscan package -c $APP_PATH/endoscopy_tool_tracking.yaml --platform x64-workstation -t holohub-endoscopy-tool-tracking-python $APP_PATH/endoscopy_tool_tracking.py --include onnx holoviz${NOCOLOR}"
+echo -e "Run the application:\n"
+echo -e "${YELLOW}holoscan run -r \$(docker images | grep "holohub-endoscopy-tool-tracking-python" | awk '{print \$1\":\"\$2}') -i $GIT_ROOT/data/endoscopy${NOCOLOR}"

applications/object_detection_torch/README.md

@@ -71,3 +71,7 @@ On aarch64, if application is executed from within the holoscan sdk container an
 ```bash
 export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/hpcx/ompi/lib"
 ```
+
+## Containerize the application
+
+To containerize the application, first build the application and then run the `package-app.sh` script and follow the generated output to package and run the application.

applications/object_detection_torch/main.cpp

@@ -264,6 +264,18 @@ int main(int argc, char **argv) {
     return 1;
   }
 
+  if (data_path.empty()) {
+    // Get the input data environment variable
+    auto input_path = std::getenv("HOLOSCAN_INPUT_PATH");
+    if (input_path == nullptr || input_path[0] == '\0') {
+      HOLOSCAN_LOG_ERROR(
+          "Input data not provided. Use --data or set HOLOSCAN_INPUT_PATH environment variable.");
+      exit(-1);
+    }
+    data_path = std::string(input_path);
+  }
+  HOLOSCAN_LOG_INFO("Using input data from {}", data_path);
+
   if (config_name != "") {
     app->config(config_name);
   } else {
@@ -277,8 +289,7 @@ int main(int argc, char **argv) {
 
   auto source = app->from_config("source").as<std::string>();
   app->set_source(source);
-  if (data_path != "")
-    app->set_datapath(data_path);
+  app->set_datapath(data_path);
   app->run();
 
   return 0;

applications/object_detection_torch/object_detection_torch.yaml

@@ -14,6 +14,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 ---
+application:
+  title: Holohub - Object Detection Torch
+  version: 1.0
+  inputFormats: []
+  outputFormats: ["screen"]
+
+resources:
+  cpu: 2
+  gpu: 1
+  memory: 1Gi
+  gpuMemory: 2Gi
+
 extensions:
 
 source: "replayer" # or "aja"

applications/object_detection_torch/package-app.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+# 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.
+
+GIT_ROOT=$(readlink -f ./$(git rev-parse --show-cdup))
+
+# Utilities
+
+YELLOW="\e[1;33m"
+RED="\e[1;31m"
+NOCOLOR="\e[0m"
+
+print_error() {
+    echo -e "${RED}ERROR${NOCOLOR}:" $*
+}
+
+if [ ! -d $GIT_ROOT/build/object_detection_torch ]; then
+    print_error "Please build the Object Detection Torch application first with the following command:"
+    print_error "./dev_container build_and_run object_detection_torch"
+    exit -1
+fi
+
+APP_PATH="$GIT_ROOT/object_detection_torch"
+echo Creating application directory $APP_PATH...
+mkdir -p $APP_PATH
+echo Copying application files to $APP_PATH...
+cp -f $GIT_ROOT/build/object_detection_torch/applications/object_detection_torch/object_detection_torch $APP_PATH
+cp -f $GIT_ROOT/build/object_detection_torch/applications/object_detection_torch/object_detection_torch.yaml $APP_PATH
+
+echo -e "done\n"
+echo -e Use the following commands to package and run the Object Detection Torch application:\n
+echo -e "Package the application:\n"
+echo -e "${YELLOW}holoscan package -c $APP_PATH/object_detection_torch.yaml --platform x64-workstation -t holohub-object-detection-torch $APP_PATH/object_detection_torch --include onnx holoviz torch${NOCOLOR}"
+echo -e "Run the application:\n"
+echo -e "${YELLOW}holoscan run -r \$(docker images | grep "holohub-object-detection-torch" | awk '{print \$1\":\"\$2}') -i $GIT_ROOT/data/object_detection_torch${NOCOLOR}"