install_abba.sh

#!/bin/bash

################################################################################
# Help                                                                         #
################################################################################
function Help()
{
   # Display Help
   echo ------ Aligning Big Brains And Altlases Installer Script -------------
   echo "This batch file downloads and install ABBA components on your computer."
   echo "Aligning Big Brains and Atlases (ABBA for short) needs Fiji, QuPath "
   echo "and elastix, and a set of custom plugins."
   echo
   echo "You can specify the folder where to install these components as an "
   echo "argument of this script. For instance: "
   echo ""
   echo "Windows:"
   echo "./install_abba.sh \"C:/\""
   echo ""
   echo "If no path is specified, you will be asked for one."
   echo
}

while getopts ":h" option; do
   case $option in
      h) # display Help
         Help
         exit;;
   esac
done


# ----------------- FUNCTIONS -------------------

# Wait for user 
function pause(){
   read -p "$*"
}

# Returns
function getuserdir(){
    local  __resultvar=$1
	local  myresult=
		while true ; do
			read -r -p "Path: " myresult
			if [ -d "$myresult" ] ; then
				break
			fi
			echo "$myresult is not a directory... try without slash at the end (unless it's the root drive like C:/)"
		done
    eval $__resultvar="'$myresult'"
}

# ----------------- COMPONENTS VERSION -----------
qupath_version=0.3.1
abba_extension_version=0.1.1
elastix_version=5.0.1

qupath_abba_extension_url="https://github.com/BIOP/qupath-extension-abba/releases/download/${abba_extension_version}/qupath-extension-abba-${abba_extension_version}.zip"

# ----------------- MAIN --------------------------

echo ------ Aligning Big Brains And Altlases Installer Script -------------
echo "This batch file downloads and install ABBA components on your computer"
if [[ "$OSTYPE" == "linux-gnu"* ]]; then
	echo "Your OS: Linux"
elif [[ "$OSTYPE" == "darwin"* ]]; then
    echo "Your OS: Mac OSX"
elif [[ "$OSTYPE" == "msys" ]]; then
    echo "Your OS: Windows"
else
    echo "Unknown OS, the script will exit: $OSTYPE"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
fi
echo "- Latest ImageJ/Fiji"
echo -e " \t - Update Fiji"
echo -e " \t - Enable ABBA Update Site"
echo "- QuPath version: $qupath_version"
echo "- Elastix version: $elastix_version"
echo "- ABBA QuPath Extension: $abba_extension_version"

# ------- INSTALLATION PATH VALIDATION

echo ------- Installation path validation

if [ $# -eq 0 ] 
then
	echo "Please enter the installation path for ABBA's components"
	getuserdir path_install
else 	
	if [ -d "$1" ] ; then
		path_install=$1
	else
		echo $1 is not a valid path
		echo "Please enter the installation path for ABBA's components"
		getuserdir path_install
	fi	
fi

echo "All components will be installed in:"
echo "$path_install"

# MAKE TEMP FOLDER IN CASE DOWNLOADS ARE NECESSARY
temp_dl_dir="$path_install/temp_dl"
mkdir "$temp_dl_dir"

# ------ SETTING UP IMAGEJ/FIJI
echo ------ Setting up ImageJ/Fiji ------

if [[ "$OSTYPE" == "linux-gnu"* ]]; then
	echo "Linux unsupported - please contribute to this installer to support it!"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
elif [[ "$OSTYPE" == "darwin"* ]]; then
	fiji_executable_file="Contents/MacOS/ImageJ-macosx"
	fiji_url="https://downloads.imagej.net/fiji/latest/fiji-macosx.zip"
elif [[ "$OSTYPE" == "msys" ]]; then
	fiji_executable_file="ImageJ-win64.exe"
	fiji_url="https://downloads.imagej.net/fiji/latest/fiji-win64.zip"
fi

fiji_path="$path_install/Fiji.app/$fiji_executable_file"

echo "Looking for Fiji executable: $fiji_path"
if [[ -f "$fiji_path" ]]; then
    echo "Fiji detected, bypassing installation"
else
	echo "Fiji not present, downloading it"
	fiji_zip_path="$temp_dl_dir/fiji.zip"
	curl "$fiji_url" -# -o "$fiji_zip_path"
	echo "Unzipping Fiji in $path_install"
	unzip "$fiji_zip_path" -d "$path_install/"
fi

if [[ -f "$fiji_path" ]]; then
    echo "Fiji successfully installed."
else
	echo "Fiji installation failed, please retry with administrator rights or install in a folder requiring less priviledge"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
fi

# Updating several times because there may be some issues with removing some files after a single update is performed
echo "Updating Fiji"
"$fiji_path" --update update
echo "Fiji updated"

echo "Enabling ABBA update site"
"$fiji_path" --update add-update-site "ABBA" "https://biop.epfl.ch/Fiji-ABBA-Exp/"
echo "ABBA update site enabled"

echo "Updating Fiji"
"$fiji_path" --update update
echo "Fiji updated"

echo "Updating Fiji one last time" 
"$fiji_path" --update update
echo "Fiji is now up-to-date"

echo "Setting up default ABBA atlases folder"

mkdir -p "$path_install/abba_atlases"

echo -n "$path_install/abba_atlases">"$path_install/Fiji.app/plugins/BIOP/ABBA_Atlas_folder.txt"

# ------ SETTING UP ELASTIX ------
echo ------ Setting up Elastix ------

if [[ "$OSTYPE" == "linux-gnu"* ]]; then
	echo "Linux unsupported - please contribute to this installer to support it!"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
elif [[ "$OSTYPE" == "darwin"* ]]; then
	elastix_os_subpath="elastix-$elastix_version-mac"
	elastix_executable_file="bin/elastix"
	transformix_executable_file="bin/transformix"
	elastix_url="https://github.com/SuperElastix/elastix/releases/download/${elastix_version}/elastix-${elastix_version}-mac.zip"
elif [[ "$OSTYPE" == "msys" ]]; then
	elastix_os_subpath="elastix-$elastix_version-win64"
	elastix_executable_file="elastix.exe"
	transformix_executable_file="transformix.exe"
	elastix_url="https://github.com/SuperElastix/elastix/releases/download/${elastix_version}/elastix-${elastix_version}-win64.zip"
	
	echo "-- Windows specific: checking whether Visual Studio redistributable is installed"
	
	# Does the registry key exist?
	MSYS_NO_PATHCONV=1 reg query "HKLM\\SOFTWARE\\Microsoft\\VisualStudio\\14.0\\VC\\Runtimes\\x64" /v Major >dummy
	errorlevel=$?

	if [[ "$errorlevel" == "0" ]]; then
	    echo "VS Redistributable is installed."
	else 
	    echo "VS Redistributable is not installed - downloading it"
	    vc_redist_url="https://aka.ms/vs/16/release/vc_redist.x64.exe"
	    vc_redist_path="$temp_dl_dir/vc_redist_install.exe"
	    curl "$vc_redist_url" -L -# -o "$vc_redist_path"
	    echo "Launching VC redist install - Do not restart your computer at the end of the install"
	    "$vc_redist_path"
	    # Does the registry key exist NOW ?
	    MSYS_NO_PATHCONV=1 reg query "HKLM\\SOFTWARE\\Microsoft\\VisualStudio\\14.0\\VC\\Runtimes\\x64" /v Major >dummy
		errorlevel=$?
		if [[ "$errorlevel" == "0" ]]; then
		  echo "VS Redistributable is now installed."
		else 
		  echo "Something went wrong during VS redistributable installation!"
		  pause "Press [Enter] to end the script"
		  exit 1 # We cannot proceed	  
		fi
	fi
fi

elastix_path="$path_install/$elastix_os_subpath/$elastix_executable_file"
transformix_path="$path_install/$elastix_os_subpath/$transformix_executable_file"

if [[ -f "$elastix_path" ]]; then
    echo "Elastix detected, bypassing installation"
else
	echo "Elastix not present, downloading it from $elastix_url"
	elastix_zip_path="$temp_dl_dir/elastix.zip"
	curl "$elastix_url" -L -# -o "$elastix_zip_path"
	echo "Unzipping Elastix in $path_install"
	unzip "$elastix_zip_path" -d "$path_install"
fi

if [[ -f "$elastix_path" ]]; then
    echo "Elastix successfully installed."
else
	echo "Elastix installation failed, please retry with administrator rights or install in a folder requiring less privilege"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
fi

echo --- Setting Elastix and Transformix path in Fiji
argElastixPath="elastixPath=\"$elastix_path\""
argTransformixPath="transformixPath=\"$transformix_path\""
all_args="$argElastixPath,$argTransformixPath"
"$fiji_path" --ij2 --run SetElastixPath.groovy "$all_args"

# ------ SETTING UP QUPATH ------
echo ------ Setting up QuPath ------

if [[ "$OSTYPE" == "linux-gnu"* ]]; then
	echo "Linux unsupported - please contribute to this installer to support it!"
	pause "Press [Enter] to end the script"
	exit 1 # We cannot proceed
elif [[ "$OSTYPE" == "darwin"* ]]; then
	qupath_executable_file="Contents/MacOS/QuPath"
	qupath_url="https://github.com/qupath/qupath/releases/download/v${qupath_version}/QuPath-${qupath_version}-Mac.pkg"
	qupath_path="/Applications/QuPath.app/$qupath_executable_file"
	echo "$qupath_path"
	if [[ -f "$qupath_path" ]]; then
		echo "QuPath detected, bypassing installation"
	else
		echo "QuPath not present, downloading it from $qupath_url"
		qupath_zip_path="$temp_dl_dir/qupath.pkg"
		curl "$qupath_url" -L -# -o "$qupath_zip_path"
		echo "Installing QuPath, you will need to enter your admin password for the install (or install QuPath before running the script)"
		sudo installer -pkg "$qupath_zip_path" -target /
		if [[ -f "$qupath_path" ]]; then
			echo "QuPath successfully installed"
		else
			echo "QuPath installation failed, please retry with administrator rights or install in a folder requiring less privilege"
			pause "Press [Enter] to end the script"
			exit 1 # We cannot proceed
		fi
	fi
elif [[ "$OSTYPE" == "msys" ]]; then
	qupath_executable_file="QuPath-${qupath_version}.exe"
	qupath_url="https://github.com/qupath/qupath/releases/download/v${qupath_version}/QuPath-${qupath_version}-Windows.zip"
	qupath_path="$path_install/QuPath-${qupath_version}/$qupath_executable_file"
	if [[ -f "$qupath_path" ]]; then
		echo "QuPath detected, bypassing installation"
	else
		echo "QuPath not present, downloading it from $qupath_url"
		qupath_zip_path="$temp_dl_dir/qupath.zip"
		curl "$qupath_url" -L -# -o "$qupath_zip_path"
		echo "Unzipping QuPath"
		unzip "$qupath_zip_path" -d "$path_install"
		if [[ -f "$qupath_path" ]]; then
			echo "QuPath successfully installed"
		else
			echo "QuPath installation failed, please retry with administrator rights or install in a folder requiring less priviledge"
			pause "Press [Enter] to end the script"
			exit 1 # We cannot proceed
		fi
	fi	
fi

echo ------ Setting up QuPath extension ------

# See https://imagej.net/scripting/headless to deal with the mess of single quotes vs double quotes
argQuPathUserPath="defaultQuPathUserPath=\"$path_install/QuPath Common Data_0.3\""
argQuPathPrefNode="quPathPrefsNode=\"io.github.qupath/0.3\""
argQuPathExtensionURL="quPathExtensionURL=\"$qupath_abba_extension_url\""
argQuitAfterInstall="quitAfterInstall=\"true\""
all_args="$argQuPathUserPath,$argQuPathPrefNode,$argQuPathExtensionURL,$argQuitAfterInstall"
"$fiji_path" --ij2 --run InstallQuPathExtension.groovy "$all_args"

echo "Removing temporary download folder $temp_dl_dir"
rm -r "$temp_dl_dir"

echo ------ INSTALLATION DONE ------
echo "You should be able to run either Fiji or QuPath and access ABBA's functionalities"
echo "If this script failed, please post the errors in forum.image.sc with the ABBA tag"