use GPU

configure.sh

@@ -54,6 +54,9 @@ ensure_prereqs() {
     echo "Installing tzdata"
     sudo $APT_GET install -y -qq tzdata
 
+    echo "Installing exiftool"
+    sudo $APT_GET install -y -qq libimage-exiftool-perl 
+
     UBUNTU_VERSION=$(lsb_release -r)
     if [[ "$UBUNTU_VERSION" == *"20.04"* ]]; then
         echo "Enabling PPA for Ubuntu GIS"

opendm/staindetection.py

@@ -54,15 +54,25 @@ def create_overlay(self, original_image, segm_mask):
             interpolation=cv2.INTER_NEAREST,
         )
 
+        # # Create a red color mask for stains
+        # stain_mask = np.zeros_like(original_image)
+        # stain_mask[resized_segm_mask > 0] = [0, 0, 255]  # Set red color for stains
+
+        # # Combine the original image with the stain mask using alpha blending
+        # alpha = 0.5  # Transparency level (0.5 for 50% transparency)
+        # overlay_image = cv2.addWeighted(
+        #     original_image, 1 - alpha, stain_mask, alpha, 0
+        # )
+
         # Create a red color mask for stains
         stain_mask = np.zeros_like(original_image)
         stain_mask[resized_segm_mask > 0] = [0, 0, 255]  # Set red color for stains
 
-        # Combine the original image with the stain mask using alpha blending
-        alpha = 0  # Transparency level (0.5 for 50% transparency)
-        overlay_image = cv2.addWeighted(
-            original_image, 1 - alpha, stain_mask, alpha, 0
-        )
+        # Directly modify the original image based on the mask
+        original_image[resized_segm_mask > 0] = stain_mask[resized_segm_mask > 0]
+
+        # cv2.imwrite("output_onnx_overlay.jpg", original_image)
+
 
 
-        return overlay_image
+        return original_image

start-dev-env-stain.sh

@@ -0,0 +1,145 @@
+#!/bin/bash
+set -eo pipefail
+__dirname=$(cd $(dirname "$0"); pwd -P)
+cd "${__dirname}"
+
+if [ "$1" = "--setup" ]; then
+    export HOME=/home/$2
+
+    if [ ! -f .setupdevenv ]; then
+        echo "Recompiling environment... this might take a while."
+        bash configure.sh reinstall
+
+        touch .setupdevenv
+        apt update && apt install -y vim git
+        chown -R $3:$4 /code
+        chown -R $3:$4 /var/www
+    fi
+
+    echo "Adding $2 to /etc/passwd"
+    echo "$2:x:$3:$4::/home/$2:/bin/bash" >> /etc/passwd
+    echo "Adding $2 to /etc/group"
+    echo "$2:x:$4:" >> /etc/group
+    echo "Adding $2 to /etc/shadow"
+    echo "$2:x:14871::::::" >> /etc/shadow
+    echo "$2   ALL=(ALL)   NOPASSWD:ALL" >> /etc/sudoers
+    echo "odm   ALL=(ALL)   NOPASSWD:ALL" >> /etc/sudoers
+    echo "echo '' && echo '' && echo '' && echo '###################################' && echo 'ODM Dev Environment Ready. Hack on!' && echo '###################################' && echo '' && cd /code" > $HOME/.bashrc
+
+    # Install qt creator
+    if hash qtcreator 2>/dev/null; then
+        has_qtcreator="YES"
+    fi
+
+    if [ "$has_qtcreator" != "YES" ] && [ "$5" == "YES" ]; then 
+        apt install -y libxrender1 gdb qtcreator
+    fi
+
+    # Install liquidprompt
+    if [ ! -e "$HOME/liquidprompt" ]; then
+        git clone https://github.com/nojhan/liquidprompt.git --depth 1 $HOME/liquidprompt
+    fi
+
+    if [ -e "$HOME/liquidprompt" ]; then
+        echo "source $HOME/liquidprompt/liquidprompt" >> $HOME/.bashrc
+        echo "export LP_PS1_PREFIX='(odmdev)'" >> $HOME/.bashrc
+    fi
+
+    # Colors
+    echo "alias ls='ls --color=auto'" >> $HOME/.bashrc
+
+    # Python paths
+    echo $(python3 /code/opendm/context.py) >> $HOME/.bashrc
+
+    # Vim 
+    printf "syntax on\nset showmatch\nset ts=4\nset sts=4\nset sw=4\nset autoindent\nset smartindent\nset smarttab\nset expandtab" > $HOME/.vimrc
+
+    # Misc aliases
+    echo "alias pdal=/code/SuperBuild/install/bin/pdal" >> $HOME/.bashrc
+    echo "alias opensfm=/code/SuperBuild/install/bin/opensfm/bin/opensfm" >> $HOME/.bashrc
+
+
+    su -c bash $2
+    exit 0
+fi
+
+platform="Linux" # Assumed
+uname=$(uname)
+case $uname in
+	"Darwin")
+	platform="MacOS"
+	;;
+	MINGW*)
+	platform="Windows"
+	;;
+esac
+
+if [[ $platform != "Linux" && $platform != "MacOS" ]]; then
+	echo "This script only works on Linux and MacOS."
+    exit 1
+fi
+
+if hash docker 2>/dev/null; then
+    has_docker="YES"
+fi
+if hash nvidia-smi 2>/dev/null; then
+    has_nvidia_smi="YES"
+fi
+
+
+if [ "$has_docker" != "YES" ]; then
+    echo "You need to install docker before running this script."
+    exit 1
+fi
+
+IMAGE_SET=NO
+if [[ ! -z $IMAGE ]]; then
+    IMAGE_SET=YES
+fi
+export PORT="${PORT:=3003}"
+export QTC="${QTC:=NO}"
+export IMAGE="${IMAGE:=opendronemap/nodeodm}"
+export GPU="${GPU:=YES}"
+
+if [ -z "$DATA" ]; then
+    echo "Usage: DATA=/path/to/datasets [VARS] $0"
+    echo
+    echo "VARS:"
+    echo "	DATA	Path to directory that contains datasets for testing. The directory will be mounted in /datasets. If you don't have any, simply set it to a folder outside the ODM repository."
+    echo "	PORT	Port to expose for NodeODM (default: $PORT)"
+    echo "	IMAGE	Docker image to use (default: $IMAGE)"
+    echo "	GPU	Enable GPU support (default: $GPU)"
+    echo "	QTC	When set to YES, installs QT Creator for C++ development (default: $QTC)"
+    exit 1
+fi
+
+
+echo "Starting development environment..."
+echo "Datasets path: $DATA"
+echo "Expose port: $PORT"
+echo "QT Creator: $QTC"
+echo "Image: $IMAGE"
+echo "GPU: $GPU"
+
+if [ ! -e "$HOME"/.odm-dev-home ]; then
+    mkdir -p "$HOME"/.odm-dev-home
+fi
+
+USER_ID=$(id -u)
+GROUP_ID=$(id -g)
+USER=$(id -un)
+GPU_FLAGS=""
+if [[ "$GPU" != "NO" ]]; then
+    if [[ "$IMAGE_SET" = "NO" ]]; then
+        IMAGE="$IMAGE:gpu"
+    fi
+
+    GPU_FLAGS="--gpus all"
+    if [[ "$has_nvidia_smi" = "YES" ]]; then
+        GPU_FLAGS="$GPU_FLAGS --device /dev/nvidia0 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidia-modeset --device /dev/nvidiactl"
+    fi
+fi
+
+xhost + || true
+docker run -ti --entrypoint bash --name odmdevstain_gpu --hostname odmdevstain_gpu --user root -v $(pwd):/code -v "$DATA":/datasets -p $PORT:3000 $GPU_FLAGS --privileged -e DISPLAY -e LANG=C.UTF-8 -e LC_ALL=C.UTF-8 -v="/tmp/.X11-unix:/tmp/.X11-unix:rw" -v="$HOME/.odm-dev-home:/home/$USER" $IMAGE -c "/code/start-dev-env.sh --setup $USER $USER_ID $GROUP_ID $QTC"
+exit 0

start-dev-env.sh

@@ -99,7 +99,7 @@ fi
 export PORT="${PORT:=3000}"
 export QTC="${QTC:=NO}"
 export IMAGE="${IMAGE:=opendronemap/nodeodm}"
-export GPU="${GPU:=NO}"
+export GPU="${GPU:=YES}"
 
 if [ -z "$DATA" ]; then
     echo "Usage: DATA=/path/to/datasets [VARS] $0"