Merge branch 'main' into add-real-colon-polyp-detection

applications/aja_video_capture/cpp/CMakeLists.txt

@@ -13,6 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+find_package(holoscan 3.0 REQUIRED)
+
 # Create example
 add_executable(aja_capture
   aja_capture.cpp
@@ -39,7 +41,7 @@ if(BUILD_TESTING)
 
   set(RECORDING_DIR ${CMAKE_CURRENT_BINARY_DIR}/recording_output)
   set(SOURCE_VIDEO_BASENAME video_replayer_output)
-  set(VALIDATION_FRAMES_DIR ${Holoscan-examples_SOURCE_DIR}/../tests/data/validation_frames/aja_capture/)
+  set(VALIDATION_FRAMES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tests/)
 
   file(MAKE_DIRECTORY ${RECORDING_DIR})
 
@@ -51,7 +53,7 @@ if(BUILD_TESTING)
   # Patch the current example to enable recording the rendering window
   add_custom_command(OUTPUT aja_capture_test.cpp
     COMMAND patch -u -o aja_capture_test.cpp ${CMAKE_CURRENT_SOURCE_DIR}/aja_capture.cpp
-      ${Holoscan-examples_SOURCE_DIR}/../tests/data/validation_frames/aja_capture/cpp_aja_capture.patch
+      ${CMAKE_CURRENT_SOURCE_DIR}/../tests/cpp_aja_capture.patch
   )
 
   # Create the test executable
@@ -78,26 +80,26 @@ if(BUILD_TESTING)
   )
 
   # Add the test and make sure it runs
-  add_test(NAME EXAMPLE_CPP_AJA_CAPTURE_TEST
+  add_test(NAME AJA_CAPTURE_CPP_TEST
     COMMAND ${CMAKE_CURRENT_BINARY_DIR}/aja_capture_test ${CONFIG_FILE}
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
   )
-  set_tests_properties(EXAMPLE_CPP_AJA_CAPTURE_TEST PROPERTIES
+  set_tests_properties(AJA_CAPTURE_CPP_TEST PROPERTIES
     PASS_REGULAR_EXPRESSION "Scheduler stopped: Some entities are waiting for execution"
   )
 
   # Add a test to check the validity of the frames
-  add_test(NAME EXAMPLE_CPP_AJA_CAPTURE_RENDER_TEST
-      COMMAND python3 ${Holoscan-examples_SOURCE_DIR}/../scripts/video_validation.py
+  add_test(NAME AJA_CAPTURE_CPP_RENDER_TEST
+      COMMAND python3 ${CMAKE_SOURCE_DIR}/utilities/video_validation.py
       --source_video_dir ${RECORDING_DIR}
       --source_video_basename ${SOURCE_VIDEO_BASENAME}
       --output_dir ${RECORDING_DIR}
       --validation_frames_dir ${VALIDATION_FRAMES_DIR}
       WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
   )
 
-  set_tests_properties(EXAMPLE_CPP_AJA_CAPTURE_RENDER_TEST PROPERTIES
-  DEPENDS EXAMPLE_CPP_AJA_CAPTURE_TEST
+  set_tests_properties(AJA_CAPTURE_CPP_RENDER_TEST PROPERTIES
+  DEPENDS AJA_CAPTURE_CPP_TEST
   PASS_REGULAR_EXPRESSION "Valid video output!"
   )
 

applications/aja_video_capture/python/CMakeLists.txt

@@ -25,7 +25,7 @@ if(BUILD_TESTING)
 
   set(RECORDING_DIR ${CMAKE_CURRENT_BINARY_DIR}/recording_output)
   set(SOURCE_VIDEO_BASENAME python_aja_capture_output)
-  set(VALIDATION_FRAMES_DIR ${Holoscan-examples_SOURCE_DIR}/../tests/data/validation_frames/aja_capture/)
+  set(VALIDATION_FRAMES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tests/)
 
   file(MAKE_DIRECTORY ${RECORDING_DIR})
 
@@ -38,35 +38,35 @@ if(BUILD_TESTING)
   # Patch the current example to enable recording the rendering window
   add_custom_command(OUTPUT aja_capture_test.py
     COMMAND patch -u -o aja_capture_test.py ${CMAKE_CURRENT_SOURCE_DIR}/aja_capture.py
-      ${Holoscan-examples_SOURCE_DIR}/../tests/data/validation_frames/aja_capture/python_aja_capture.patch
+      ${CMAKE_CURRENT_SOURCE_DIR}/../tests/python_aja_capture.patch
   )
 
   add_custom_target(python_aja_capture_test ALL
     DEPENDS "aja_capture_test.py"
   )
 
-  add_test(NAME EXAMPLE_PYTHON_AJA_CAPTURE_TEST
+  add_test(NAME AJA_CAPTURE_PYTHON_TEST
     COMMAND python3 aja_capture_test.py --config python_aja_capture_config.yaml
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   )
 
-  set_tests_properties(EXAMPLE_PYTHON_AJA_CAPTURE_TEST PROPERTIES
+  set_tests_properties(AJA_CAPTURE_PYTHON_TEST PROPERTIES
     DEPENDS "aja_capture_test.py"
     PASS_REGULAR_EXPRESSION "Scheduler stopped: Some entities are waiting for execution"
   )
 
   # Add a test to check the validity of the frames
-  add_test(NAME EXAMPLE_PYTHON_AJA_CAPTURE_RENDER_TEST
-      COMMAND python3 ${Holoscan-examples_SOURCE_DIR}/../scripts/video_validation.py
+  add_test(NAME AJA_CAPTURE_PYTHON_RENDER_TEST
+      COMMAND python3 ${CMAKE_SOURCE_DIR}/utilities/video_validation.py
       --source_video_dir ${RECORDING_DIR}
       --source_video_basename ${SOURCE_VIDEO_BASENAME}
       --output_dir ${RECORDING_DIR}
       --validation_frames_dir ${VALIDATION_FRAMES_DIR}
       WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
   )
 
-  set_tests_properties(EXAMPLE_PYTHON_AJA_CAPTURE_RENDER_TEST PROPERTIES
-    DEPENDS EXAMPLE_PYTHON_AJA_CAPTURE_TEST
+  set_tests_properties(AJA_CAPTURE_PYTHON_RENDER_TEST PROPERTIES
+    DEPENDS AJA_CAPTURE_PYTHON_TEST
     PASS_REGULAR_EXPRESSION "Valid video output!"
   )
 

applications/aja_video_capture/python/aja_capture.py

@@ -19,7 +19,9 @@
 
 from holoscan.conditions import CountCondition
 from holoscan.core import Application
-from holoscan.operators import AJASourceOp, HolovizOp
+from holoscan.operators import HolovizOp
+
+from holohub.aja_source import AJASourceOp
 
 
 class AJACaptureApp(Application):

applications/aja_video_capture/tests/cpp_aja_capture.patch

@@ -0,0 +1,37 @@
+diff --git a/applications/aja_video_capture/cpp/aja_capture.cpp b/applications/aja_video_capture/cpp/aja_capture.cpp
+index 890ec9ab..8431555c 100644
+--- a/applications/aja_video_capture/cpp/aja_capture.cpp
++++ b/applications/aja_video_capture/cpp/aja_capture.cpp
+@@ -19,6 +19,11 @@
+ #include <holoscan/operators/holoviz/holoviz.hpp>
+
+ #include <aja_source.hpp>
++
++#include <holoscan/operators/video_stream_recorder/video_stream_recorder.hpp>
++#include <holoscan/operators/video_stream_replayer/video_stream_replayer.hpp>
++#include <holoscan/operators/format_converter/format_converter.hpp>
++
+ class App : public holoscan::Application {
+  public:
+   void compose() override {
+@@ -30,6 +35,21 @@ class App : public holoscan::Application {
+
+     // Flow definition
+     add_flow(source, visualizer, {{"video_buffer_output", "receivers"}});
++
++    // Recorder to validate the video output
++    std::shared_ptr<Operator> recorder_format_converter;
++    recorder_format_converter = make_operator<ops::FormatConverterOp>(
++        "recorder_format_converter",
++        Arg("in_dtype", std::string("rgba8888")),
++        Arg("out_dtype", std::string("rgb888")));
++    auto recorder = make_operator<ops::VideoStreamRecorderOp>(
++        "recorder",
++        Arg("directory", std::string(RECORDING_DIR)),
++        Arg("basename", std::string(SOURCE_VIDEO_BASENAME)));
++    add_flow(visualizer, recorder_format_converter, {{"render_buffer_output", "source_video"}});
++    add_flow(recorder_format_converter, recorder);
++    visualizer->add_arg(Arg("enable_render_buffer_output", true));
++    visualizer->add_arg(Arg("allocator", make_resource<UnboundedAllocator>("allocator")));
+   }
+ };

applications/aja_video_capture/tests/python_aja_capture.patch

@@ -0,0 +1,37 @@
+diff --git a/applications/aja_video_capture/python/aja_capture.py b/applications/aja_video_capture/python/aja_capture.py
+index 3d12ebda..7d43943f 100644
+--- a/applications/aja_video_capture/python/aja_capture.py
++++ b/applications/aja_video_capture/python/aja_capture.py
+@@ -20,6 +20,8 @@ import os
+ from holoscan.conditions import CountCondition
+ from holoscan.core import Application
+ from holoscan.operators import HolovizOp
++from holoscan.operators import VideoStreamRecorderOp, FormatConverterOp
++from holoscan.resources import UnboundedAllocator
+
+ from holohub.aja_source import AJASourceOp
+
+@@ -46,6 +48,23 @@ class AJACaptureApp(Application):
+         visualizer = HolovizOp(self, name="holoviz", **self.kwargs("holoviz"))
+
+         self.add_flow(source, visualizer, {("video_buffer_output", "receivers")})
++        recorder_format_converter = FormatConverterOp(
++            self,
++            name="recorder_format_converter",
++            in_dtype="rgba8888",
++            out_dtype="rgb888",
++            pool=UnboundedAllocator(self, name="pool")
++        )
++        recorder = VideoStreamRecorderOp(
++            self,
++            name="recorder",
++            **self.kwargs("recorder")
++        )
++
++        visualizer.add_arg(allocator=UnboundedAllocator(self, name="allocator"))
++
++        self.add_flow(visualizer, recorder_format_converter, {("render_buffer_output", "source_video")})
++        self.add_flow(recorder_format_converter, recorder)
+
+
+ def main(config_file):

applications/endoscopy_out_of_body_detection/python/main.py

@@ -20,14 +20,15 @@
 
 from holoscan.core import Application
 from holoscan.operators import (
-    AJASourceOp,
     FormatConverterOp,
     InferenceOp,
     InferenceProcessorOp,
     VideoStreamReplayerOp,
 )
 from holoscan.resources import UnboundedAllocator
 
+from holohub.aja_source import AJASourceOp
+
 
 class EndoscopyOutOfBodyDetectionApp(Application):
     """Endoscopy Out-of-Body Detection"""

applications/holochat/README.md

@@ -22,13 +22,13 @@ HoloChat is an AI-driven chatbot, built on top of a **locally hosted Code-Llama
 **If running local LLM**:
 - **GPU**: NVIDIA dGPU w/ >= 28 GB VRAM
 - **Memory**: \>= 28 GB of available disk memory
-  - Needed to download [fine-tuned Code Llama 34B](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara-holoscan/models/phind-codellama-34b-v2-q5_k_m) and [BGE-Large](https://huggingface.co/BAAI/bge-large-en) embedding model
+  - Needed to download [fine-tuned Code Llama 34B](https://huggingface.co/TheBloke/Phind-CodeLlama-34B-v2-GGUF) and [BGE-Large](https://huggingface.co/BAAI/bge-large-en) embedding model
 
 *Tested using [NVIDIA IGX Orin](https://www.nvidia.com/en-us/edge-computing/products/igx/) w/ RTX A6000 and [Dell Precision 5820 Workstation](https://www.dell.com/en-us/shop/desktop-computers/precision-5820-tower-workstation/spd/precision-5820-workstation/xctopt5820us) w/ RTX A6000
 
 ## Running HoloChat: 🏃💨
 **When running HoloChat, you have two LLM options:**
-- Local: Uses [Phind-CodeLlama-34B-v2]((https://huggingface.co/Phind/Phind-CodeLlama-34B-v2)) running on your local machine using Llama.cpp
+- Local: Uses [Phind-CodeLlama-34B-v2](https://huggingface.co/Phind/Phind-CodeLlama-34B-v2) running on your local machine using Llama.cpp
 - Remote: Uses [Llama-3-70b-Instruct](https://build.nvidia.com/meta/llama3-70b) using the [NVIDIA NIM API](https://build.nvidia.com/explore/discover)
 
 ### TLDR; 🥱
@@ -46,7 +46,7 @@ echo "NVIDIA_API_KEY=<api_key_here>" > ./applications/holochat/.env
 ### Build Notes: ⚙️
 
 **Build Time:**
-- HoloChat uses a [PyTorch container](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch) from [NGC](https://catalog.ngc.nvidia.com/?filters=&orderBy=weightPopularDESC&query=) and may also download the [~23 GB Phind LLM](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara-holoscan/models/phind-codellama-34b-v2-q5_k_m) from NGC. As such, the first time building this application **will likely take ~45 minutes** depending on your internet speeds. However, this is a one-time set-up and subsequent runs of HoloChat should take seconds to launch.
+- HoloChat uses a [PyTorch container](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch) from [NGC](https://catalog.ngc.nvidia.com/?filters=&orderBy=weightPopularDESC&query=) and may also download the [~23 GB Phind LLM](https://huggingface.co/TheBloke/Phind-CodeLlama-34B-v2-GGUF) from HuggingFace. As such, the first time building this application **will likely take ~45 minutes** depending on your internet speeds. However, this is a one-time set-up and subsequent runs of HoloChat should take seconds to launch.
 
 **Build Location:**
 

applications/holochat/holochat.sh

@@ -54,9 +54,7 @@ function build_db {
 function download_llama {
     mkdir -p "$BASE_DIR/docs"
     if [ ! -f "$BASE_DIR/models/phind-codellama-34b-v2.Q5_K_M.gguf" ]; then
-        wget -nc -P "$BASE_DIR/models" https://api.ngc.nvidia.com/v2/models/nvidia/clara-holoscan/phind-codellama-34b-v2-q5_k_m/versions/2.0/zip
-        unzip -n "$BASE_DIR/models/zip" -d "$BASE_DIR/models/"
-        rm "$BASE_DIR/models/zip"
+        wget -nc -P "$BASE_DIR/models" https://huggingface.co/TheBloke/Phind-CodeLlama-34B-v2-GGUF/resolve/main/phind-codellama-34b-v2.Q5_K_M.gguf
     else
         echo "Model already exists, skipping download."
     fi