Finish renaming app to SIUE Fat Segmentation Tool

Rename MacDeployScript to MacDeployScript.sh

Ignore MacDeployScript.sh from Git.

Add sample MacDeployScript with indicators like this <INSERT-HERE> to change for custom path.

.gitignore

@@ -43,5 +43,5 @@ CMakeLists.txt.user
 error.log
 
 # Installation Scripts, ignore these since they contain path dependent scripts that will be different from computer to computer
-MacDeployScript
-WindowsInstaller.iss
+MacDeployScript.sh
+WindowsInstaller.iss

MacDeployScript.sh.sample

@@ -0,0 +1,122 @@
+#!/bin/bash
+
+# Location of libraries to import into app bundle
+LIB_DIR=/usr/local/lib
+
+# Application name
+APP_NAME="SIUE Fat Segmentation Tool"
+
+# Version
+VERSION=v1.0.2.0
+
+# Release type (Debug|Release)
+RELEASE=Debug
+
+# Name for DMG
+DMG_NAME=$APP_NAME-$VERSION-$RELEASE-OSX_x64
+
+# Location of the application bundle to include libraries
+APP_DIR=<PATH-TO-APP-REMOVE-DEBUG/RELEASE-PREFIX>-$RELEASE/$APP_NAME.app
+
+# Location of DMG directory that contains contents of what the DMG will have in it
+DMG_DIR=$APP_DIR/../dmg_folder
+
+# Location of the actual application binary inside app bundle
+APP_BIN=Contents/MacOS/$APP_NAME
+
+# Location of macdeployqt file
+MACDEPLOYQT=<PATH-TO-MACDEPLOYQT>/macdeployqt
+
+# List of third-party libraries that will be imported to the App bundle
+# Do NOT include Qt libraries or system libraries because Qt libraries are handled by macdeployqt and system libraries do not need to be imported
+#
+# Run otool -L /path/to/app/Contents/MacOS/app to get a list of dependencies for program. Exclude any Qt file or files beginning with /System/* or /usr/lib/*
+# The remaining libraries beginning with @rpath or /usr/local/lib will likely need to be imported
+#
+# For each library, run otool -L LIB_NAME on that library to get a list of dependencies for THAT library. Note which libraries require which dependencies because that
+# needs to be changed. Include all of the libraries dependencies in the LIBS list too. (Only if it is new and not already included in list).
+# This is recursive. So for each new library, you MUST run otool on it to get dependencies for THAT library then.
+LIBS=(
+	"libnifticdf.2.dylib"
+	"libniftiio.2.dylib"
+	"libopencv_core.3.2.dylib"
+	"libopencv_imgproc.3.2.dylib"
+	"libopencv_highgui.3.2.dylib"
+	"libopencv_video.3.2.dylib"
+	"libznz.2.dylib"
+	"libopencv_videoio.3.2.dylib"
+	"libopencv_imgcodecs.3.2.dylib"
+)
+
+# When replacing the old path name to the new one, use these directory prefixes. Should NOT need to be changed. This changes any directories beginning with @rpath or $LIB_DIR
+OLD_PATH_DIRS=($LIB_DIR "@rpath")
+
+# Contains a multidimensional array of dependencies between libraries. First value indicates the dependency and the second value is the library that contains the dependency.
+# 
+# As specified above in LIBS documentation, run otool -L LIB_NAME for each library and note the dependencies. If any third-party dependencies are present, include them below
+# so they are changed upon running of script.
+DEPS=(
+	"libznz.2.dylib" "libniftiio.2.dylib"
+
+	"libopencv_imgproc.3.2.dylib" "libopencv_imgproc.3.2.dylib"
+
+	"libopencv_videoio.3.2.dylib" "libopencv_highgui.3.2.dylib"
+	"libopencv_imgcodecs.3.2.dylib" "libopencv_highgui.3.2.dylib"
+	"libopencv_imgproc.3.2.dylib" "libopencv_highgui.3.2.dylib"
+	"libopencv_core.3.2.dylib" "libopencv_highgui.3.2.dylib"
+
+	"libopencv_imgproc.3.2.dylib" "libopencv_video.3.2.dylib"
+	"libopencv_core.3.2.dylib" "libopencv_video.3.2.dylib"
+
+	"libopencv_imgcodecs.3.2.dylib" "libopencv_videoio.3.2.dylib"	
+	"libopencv_imgproc.3.2.dylib" "libopencv_videoio.3.2.dylib"
+	"libopencv_core.3.2.dylib" "libopencv_videoio.3.2.dylib"
+
+	"libopencv_imgproc.3.2.dylib" "libopencv_imgcodecs.3.2.dylib"
+	"libopencv_core.3.2.dylib" "libopencv_imgcodecs.3.2.dylib"
+)
+
+# Run macdeployqt to fix Qt library dependencies
+$MACDEPLOYQT "$APP_DIR"
+
+# Loop through each library and copy the library to Frameworks dir in app bundle, add ID using install_name and change the library name in main application to use relative path
+for i in "${LIBS[@]}"
+do
+	cp $LIB_DIR/$i "$APP_DIR/Contents/Frameworks/$i"
+
+	install_name_tool -id @executable_path/../Frameworks/$i "$APP_DIR/Contents/Frameworks/$i"
+
+	for j in "${OLD_PATH_DIRS[@]}"
+	do
+		install_name_tool -change $j/$i @executable_path/../Frameworks/$i "$APP_DIR/$APP_BIN"
+	done
+done
+
+# Loop through each dependency between libraries and change the corresponding name to new relative path in library
+ARR_SIZE=${#DEPS[@]}
+for i in "${OLD_PATH_DIRS[@]}"
+do
+	for ((j=0; j<$ARR_SIZE; j = j + 2))
+	do
+		install_name_tool -change $i/${DEPS[$j]} @executable_path/../Frameworks/${DEPS[$j]} "$APP_DIR/Contents/Frameworks/${DEPS[$j+1]}"
+	done
+done
+
+# Create dmg directory
+mkdir "$DMG_DIR"
+
+# Remove EVERYTHING from dmg directory.
+rm -rf "$DMG_DIR/*"
+
+# Copy app bundle to dmg folder
+cp -R "$APP_DIR" "$DMG_DIR/"
+
+# Create symlink of Applications in folder so user can drag application to folder
+ln -s /Applications "$DMG_DIR/Applications"
+
+# Create DMG file with contents being the contents of $DMG_DIR
+hdiutil create -volname "$APP_NAME" -srcfolder "$DMG_DIR" -ov -format UDZO "$APP_DIR/../$DMG_NAME.dmg"
+
+# Output otool result to see if all dependencies were met
+otool -L "$APP_DIR/$APP_BIN"
+otool -L "$APP_DIR/Contents/Frameworks/lib"*