Update dependencies

Effectively, at this point this is only sent to log file

.gitignore

@@ -2,3 +2,4 @@
 .idea/
 target/
 
+.DS_Store

.scalafmt.conf

@@ -1,4 +1,4 @@
-version = 3.7.4
+version = 3.8.3
 
 runner.dialect = scala3
 

ReadMe.md

@@ -15,6 +15,8 @@ IJP ImageJ Launcher is a clean implementation on the core function of starting [
     * [Installing Fiji on Mac OS X Arm64](#installing-fiji-on-mac-os-x-arm64)
     * [Installing Fiji on Windows x64](#installing-fiji-on-windows-x64)
     * [Troubleshooting](#troubleshooting)
+        * [Start-up log `~/.ijp_imagej_launcher.log`](#start-up-log-ijpimagejlauncherlog)
+        * [Starting from command prompt](#starting-from-command-prompt)
 * [Developer Setup](#developer-setup)
 
 <!-- TOC -->
@@ -33,7 +35,10 @@ the logic flow is too complex to correct without a significant rewrite.
 Features
 --------
 
-* Uses similar options to the original ImageJ Launcher, si IJP Launcher can be drop-in replacement
+Here are the futures that are already implemented (see release notes for futures ofa specific release):
+
+* Uses similar options to the original ImageJ Launcher, so IJP Launcher can be used as a drop-in replacement
+* Intended to be used with Java 11 or newer (the original launcher can be used for Java 8)
 * Provides native executable for various OS/Hardware systems
     - Windows
     - Mac OS X Arm64 (Apple Silicon)
@@ -48,7 +53,7 @@ Features
     - Search ImageJ directory for available Java executables
 * Determines the amount of memory used by JVM based on total system memory use 75% of the max
 * Determines available `imagej-launcher*.jar`
-* Performs updates pending after the last time ImageJ was closed
+* **Performs updates** pending after the last time ImageJ was closed
 
 Full List of Command Line Options
 ---------------------------------
@@ -77,7 +82,7 @@ This example will show how to:
 
 **1. Download FIJI without JRE**
 
-Go to https://fiji.sc/ and select "Download the no-JRE version".
+Go to https://imagej.net/software/fiji/downloads and download the **"No JRE"** version (not specific to any OS).
 That should get file called `fiji-nojre.zip`
 
 **2. Unzip the `fiji-nojre.zip` in a folder of choice**
@@ -95,41 +100,49 @@ Inside the `Fiji.app` folder create a new folder called `java`.
 In browser open https://adoptium.net/temurin/releases/
 Select:
 
-* operating system: `macOS`
+* Operating System: `macOS`
-* architecture: `aarch64` also known as Apple Silicon or Arm64
+* Architecture: `aarch64` also known as Apple Silicon or Arm64
-* package: `JRE` (`JDK` is fine too, is larger and supports Java compilation)
+* Package Type: `JRE` (`JDK` is fine too, is larger and supports Java compilation)
-* version: `11-LTS` (`17-LTS` will work too, but you will not have JavaScript available, if you want to use it)
+* Version: `11-LTS` (`17-LTS` will work too, but you will not have JavaScript available, if you want to use it)
 
 Click on `tar.gz` button to download and save to the `java` folder you created earlier.
-You should have file like `OpenJDK11U-jre_x64_windows_hotspot_11.0.19_7.tar.gz`.
+You should have file like `OpenJDK11U-jre_aarch64_mac_hotspot_11.0.20_8.tar.gz`.
 
-**5. Uncompress into the `java` folder**
+**5. Uncompress into the `Fiji.app/java` folder**
 
-That will create folder like `jdk-11.0.19+7-jre`.
+That will create folder like `jdk-11.0.20+8-jre`.
 This is the Java VM that IJP ImageJ Launcher will use to start Fiji.
 
-**6. Download the IJP ImageJ Launcher to the Fiji.app directory**
+**6. Download the IJP ImageJ Launcher and uncompress**
 
-Go to [Releases], download "IJP-ImageJ-Launcher-0.1.0-macosx-arm64"
+Go to [Releases], download "IJP-ImageJ-Launcher-0.2.0-macosx-arm64.zip"
-and "IJP-ImageJ-Launcher-0.1.0-macosx-arm64.command", save them to the `Fiji.app` folder.
 
-The "*.command" file is a helper that can be used to launch Fiji without using command prompt.
+Uncompress "IJP-ImageJ-Launcher-0.2.0-macosx-arm64.zip".
-Future versions of the IJP Launcher, after v.0.1.0, may eliminate the need for using this file.
+Inside you will get `ImageJ-macosx`.
 
-**7. Start ImageJ**
+**7. Add to Fiji.app**
 
-In the `Fiji.app` folder double-click on `IJP-ImageL-Launcher-0.1.0-macosx-arm64.command` file (note the extension "*
+Inside `Fiji.app` locate folder `Contents/MacOS`.
-.command")
-That should start Fiji.
-You may need to open Settings and allow the IJP ImageJ Launcher to run.
 
-You can also create an alis on the Desktop to avoid navigating to the `Fiji.app` folder each time.
+Copy `ImageJ-macosx` to the `Contents/MacOS` folder, replacing `ImageJ-macosx` that was there.
-Using Finder, press `Option`+`Command` and drag the *.command file to the Desktop.
+
-The original *.command file will stay were it is and a new icon/alias (wth a little arrow at the bottom) will be created
+**8. Move Fiji.app to the Application folder**
-on the Desktop.
+
-Now you can double-click on the new alias on the Desktop to start Fiji.
+At this point you can move the `Fiji.app` folder to the Applications folder and use is as a regular msOS application.
-You can rename the Desktop alias to whatever you like, for instance, `Fiji`, but do not change names of the downloaded
+
-files, otherwise the alias (and *.command) may no longer work, and you will need to use terminal to start the launcher.
+**9. Troubleshooting**
+
+When you attempt to run Fiji with the new Launcher you may get a warning dialog
+![macOS_warning_dialog_01.png](assets%2FmacOS_warning_dialog_01.png)
+
+Possible work-around
+
+1. Delete `Fuji.app` folder
+2. Uncompressed `fiji-nojre.zip` to recreate `Fuji.app` folder, but do not make any changes to it yet. You may need to do it is different folder than before.
+3. Control-clock on `Fuji.app` and select "Open". You will see dialog saying 
+    "macOS cannot verify the developer of “Fiji”. Are you sure you want to open it?"
+4. Click on "Open". You will see Fiji logo, but the application will close since it is not setup yet
+5. Now you can repeat steps "3. Create place for Java (JRE)" to "7. Add to Fiji.app" above
 
 If you have problems installing, please report in [Discussions] or [Image.sc Forum]
 
@@ -143,7 +156,7 @@ This example will show how to:
 
 **1. Download FIJI without JRE**
 
-Go to https://fiji.sc/ and select "Download the no-JRE version".
+Go to https://imagej.net/software/fiji/downloads and download the **"No JRE"** version (not specific to any OS).
 That should get file called `fiji-nojre.zip`
 
 **2. Unzip the `fiji-nojre.zip` in a folder of choice**
@@ -160,31 +173,31 @@ Inside the `Fiji.app` folder create a new folder called `java`.
 In browser open https://adoptium.net/temurin/releases/
 Select:
 
-* operating system: `Windows`
+* Operating System: `Windows`
-* architecture: `x64` also known as Apple Silicon or Arm64
+* Architecture: `x64` also known as Apple Silicon or Arm64
-* package: `JRE` (`JDK` is fine too, is larger and supports Java compilation)
+* Package Type: `JRE` (`JDK` is fine too, is larger and supports Java compilation)
-* version: `11-LTS` (`17-LTS` will work too, but you will not have JavaScript available, if you want to use it)
+* Version: `11-LTS` (`17-LTS` will work too, but you will not have JavaScript available, if you want to use it)
 
 Click on `.zip` button to download and save to the `java` folder you created earlier.
-You should have file like `OpenJDK11U-jre_x64_windows_hotspot_11.0.19_7.zip`.
+You should have file like `OpenJDK11U-jre_x64_windows_hotspot_11.0.20_8.zip`.
 
-**5. Uncompress into the `java` folder**
+**5. Uncompress into the `Fiji.app/java` folder**
 
-That will create folder like `jdk-11.0.19+7-jre`.
+That will create folder like `jdk-11.0.20+8-jre`.
 This is the Java VM that IJP ImageJ Launcher will use to start Fiji.
 
 **6. Download the IJP ImageJ Launcher to the Fiji.app directory**
 
-Go to [Releases], download "IJP-ImageJ-Launcher-0.1.0-windows_x64.exe", save it to the `Fiji.app` folder.
+Go to [Releases], download "IJP-ImageJ-Launcher-0.2.0-windows_x64.exe", save it to the `Fiji.app` folder.
 
 **7. Start ImageJ**
 
-In the `Fiji.app` folder double-click on `IJP-ImageJ-Launcher-0.1.0-windows_x64.exe`.
+In the `Fiji.app` folder double-click on `IJP-ImageJ-Launcher-0.2.0-windows_x64.exe`.
 That should start Fiji.
 
 You can also create a shortcut on the Desktop to avoid navigating to the `Fiji.app` folder each time.
 
-**_Left_**-click on the `IJP-ImageJ-Launcher-0.1.0-windows_x64.exe` and drag it to the Desktop.
+**_Left_**-click on the `IJP-ImageJ-Launcher-0.2.0-windows_x64.exe` and drag it to the Desktop.
 Once you release mouse button, a pop-up manu will open, select "Create shortcut here".
 Now you can double-click on the new shortcut on the Desktop to start Fiji.
 
@@ -194,6 +207,13 @@ If you have problems installing, please report in [Discussions] or [Image.sc For
 
 ### Troubleshooting
 
+#### Start-up log `~/.ijp_imagej_launcher.log`
+
+The IJP-ImageJ-Launcher writes diagnostic info to a file `.ijp_imagej_launcher.log` in the users home directory.
+The information recorded is some as using `--debug` on command line.
+
+#### Starting from command prompt
+
 You can start the IJP Image Launcher from the terminal and see diagnostic printouts that may help troubleshoot potential
 issues.
 

build.sbt

@@ -1,6 +1,6 @@
-scalaVersion         := "3.3.0"
+scalaVersion := "3.3.3"
 //name                 := "IJP-ImageJ-Launcher"
-version              := "0.1.0"
+version              := "0.2.0.1-SNAPSHOT"
 versionScheme        := Some("early-semver")
 organization         := "net.sf.ij-plugins"
 homepage             := Some(new URI("https://github.com/ij-plugins/ijp-imagej-launcher").toURL)
@@ -17,13 +17,25 @@ logLevel := Level.Info
 
 libraryDependencies ++= Seq(
   "com.github.scopt" %%% "scopt"     % "4.1.0",
-  "com.lihaoyi"      %%% "os-lib" % "0.9.1"
+  "com.lihaoyi"      %%% "os-lib"    % "0.9.3",
+  "org.scalatest"    %%% "scalatest" % "3.2.18" % Test
+)
+
+scalacOptions ++= Seq(
+  "-unchecked",
+  "-deprecation",
+  "-explain",
+  "-explain-types",
+  "-rewrite",
+  "-source:3.3-migration",
+//  "-Wvalue-discard",
+  "-Wunused:all"
 )
 
 Compile / run / mainClass := Some("ij_plugins.imagej_launcher.Main")
 
 // import to add Scala Native options
-import scala.scalanative.build._
+import scala.scalanative.build.*
 
 // defaults set with common options shown
 nativeConfig ~= { c =>
@@ -36,3 +48,8 @@ nativeConfig ~= { c =>
 //nativeConfig ~= { c =>
 //  c.withCompileOptions(c.compileOptions ++ Seq("-v"))
 //}
+
+// Version info generation from SBT configuration
+enablePlugins(BuildInfoPlugin)
+buildInfoKeys    := Seq[BuildInfoKey](name, version, scalaVersion, sbtVersion)
+buildInfoPackage := "ij_plugins.imagej_launcher"

extras/IJP-ImageJ-Launcher-0.1.0-macosx-arm64.command

@@ -1,4 +1,4 @@
 #!/bin/bash
 DIR=$(cd "$(dirname "$0")" && pwd -P)
 echo "$DIR"
-"$DIR"/IJP-ImageL-Launcher-0.1.0-macosx-arm64 --debug --ij-dir "$DIR"
+"$DIR"/IJP-ImageJ-Launcher-0.1.0-macosx-arm64 --debug --ij-dir "$DIR"

notes/v.0.2.0.md

@@ -0,0 +1,8 @@
+Feature release: support better system integration on macOS - support installing ImageJ/Fiji in the application
+directory.
+See macOS installation info in the [ReadMe](https://github.com/ij-plugins/ijp-imagej-launcher)
+
+* Use launcher location to infer `ij-dir`. #5
+* Session log is saved to `~/.ijp_imagej_launcher.log` to facilitate troubleshooting when not running from command
+  prompt. The log is reset for each session. #6
+* Better inference of ImageJ directory on macOS - consider launcher being in subdirectory "Contents/MacOS" #7

project/build.properties

@@ -1 +1,6 @@
-sbt.version = 1.8.3
+#
+# Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+# Author's e-mail: jpsacha at gmail.com
+#
+
+sbt.version = 1.10.2

project/buildinfo.sbt

@@ -0,0 +1,2 @@
+// https://github.com/sbt/sbt-buildinfo
+addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.12.0")

project/plugins.sbt

@@ -1 +1,3 @@
-addSbtPlugin("org.scala-native" % "sbt-scala-native" % "0.4.12")
+// https://github.com/scala-native/scala-native
+resolvers ++= Resolver.sonatypeOssRepos("snapshots")
+addSbtPlugin("org.scala-native" % "sbt-scala-native" % "0.4.17")

src/main/resources/scala-native/argv0.c

@@ -0,0 +1,40 @@
+
+#include <stdio.h>
+
+#if defined(__linux__)
+#include <unistd.h>
+#include <limits.h>
+#elif defined(__APPLE__)
+#include <stdint.h>
+#include <sys/syslimits.h>
+#elif defined(_WIN32)
+#include <windows.h>
+#endif
+
+size_t path_max() {
+#ifdef _WIN32
+    return MAX_PATH;
+#else
+    return PATH_MAX + 1;
+#endif
+}
+
+void get_exe_path(char* exe_path, size_t size) {
+
+    exe_path[0] = 0;
+
+#if defined(__linux__)
+//    char arg1[20];
+//    sprintf( arg1, "/proc/%d/exe", getpid() );
+//    printf("arg1 = %d\n", arg1);
+//    readlink( arg1, exepath, PATH_MAX );
+    readlink( "/proc/self/exe", exe_path, size );
+#elif defined(__APPLE__)
+    if (_NSGetExecutablePath(exe_path, &size) != 0)
+        printf("ERROR: buffer too small; need size %lu\n", size);
+#elif defined(_WIN32)
+    unsigned int len = GetModuleFileNameA(GetModuleHandleA(0x0), exe_path, size);
+    if (len == 0) // memory not sufficient or general error occurred
+        printf("ERROR: buffer too small or general error.\n");
+#endif
+}

src/main/scala/ij_plugins/imagej_launcher/IJConfigFile.scala

@@ -0,0 +1,114 @@
+/*
+ * Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+ * Author's e-mail: jpsacha at gmail.com
+ */
+
+package ij_plugins.imagej_launcher
+
+import os.Path
+
+object IJConfigFile:
+
+  private val FileName: String         = "ImageJ.cfg"
+  private val MagicHeader: String      = "# ImageJ startup properties"
+  private val MaxHeapMBKey: String     = "maxheap.mb"
+  private val JvmArgsKey: String       = "jvmargs"
+  private val LegacyModeKey: String    = "legacy.mode"
+  private val AssignmentSymbol: String = "="
+  private val CommentSymbol: String    = "#"
+
+  /**
+   * Read `ImageJ.cfg` from a specified directory.
+   * The configuration file must be in ImageJ2 format (with magic header "# ImageJ startup properties").
+   *
+   * @param dir directory where `ImageJ.cfg` is located
+   * @param logger logger
+   * @return option containing the configuration file (Right).
+   *         The option is empty if file is not present in input `dir`.
+   *         An error message is returned if file is present but cannot be read without errors (Left).
+   */
+  def readFromDir(dir: Path)(using logger: Logger): Either[String, Option[IJCConfig]] =
+    logger.debug(s"Reading ImageJ configuration from directory: $dir")
+    val path = dir / FileName
+    logger.debug(s"  Looking for $FileName in: '$path'")
+    readFromFile(path)
+
+  private[imagej_launcher] def readFromFile(ijConfigFile: Path)(using logger: Logger): Either[String, Option[IJCConfig]] =
+    if os.exists(ijConfigFile) then
+      val lines = os.read.lines(ijConfigFile)
+      val cfgE =
+        lines.headOption match
+          case Some(line) =>
+            if line.trim.startsWith(MagicHeader) then
+              logger.debug(s"  Parsing $FileName")
+              for
+                props      <- parseProps(lines)
+                maxHeapMB  <- parseLong(props, MaxHeapMBKey)
+                jvmArgs    <- parseString(props, JvmArgsKey)
+                legacyMode <- parseBoolean(props, LegacyModeKey)
+              yield Option(IJCConfig(maxHeapMB, jvmArgs, legacyMode))
+            else
+              Left(s"$FileName is invalid, does not contain header: '$MagicHeader'")
+          case None =>
+            Left(s"$FileName is empty.")
+
+      // Add context to the error message, if there is one
+      cfgE.left.map(e => s"Failed to read $FileName. $e")
+    else
+      logger.debug(s"  $FileName not found: $ijConfigFile")
+      Right(None)
+
+  private[imagej_launcher] def parseProps(lines: Seq[String]): Either[String, Map[String, String]] =
+    // Parse each line
+    val lineResults: Seq[Either[String, (String, String)]] =
+      lines
+        .zipWithIndex
+        .filter { case (line, _) => !line.startsWith(CommentSymbol) }
+        .map { case (line, lineNumber) =>
+          val index = line.indexOf(AssignmentSymbol)
+          if index > 0 then
+            val key = line.substring(0, index).trim
+            if !key.isBlank then
+              Right(key -> line.substring(index + 1).trim)
+            else
+              Left(s"Error in line $lineNumber: key cannot be empty: '$line'")
+          else if index == 0 then
+            Left(s"Error in line $lineNumber: line cannot start with an assignment symbol '$AssignmentSymbol': '$line'")
+          else
+            Left(s"Error in line $lineNumber: no assignment symbol '$AssignmentSymbol' present: '$line'")
+        }
+
+    // Separate lines with errors
+    val errors = lineResults.collect { case e: Left[?, ?] => e }
+    if errors.isEmpty then
+      // Convert key->value pairs to a map
+      val r =
+        lineResults
+          .collect { case e: Right[?, ?] => e }
+          .map(_.value)
+          .toMap
+      Right(r)
+    else
+      Left(errors.map(_.value).mkString("\n"))
+
+  private def parseLong(props: Map[String, String], key: String): Either[String, Long] =
+    parseString(props, key).flatMap: s =>
+      s.toLongOption match
+        case Some(v) => Right(v)
+        case None    => Left(s"Failed to parse '$s' as an integer.")
+
+  private def parseString(props: Map[String, String], key: String): Either[String, String] =
+    props.get(key) match
+      case Some(v) => Right(v)
+      case None    => Left(s"No key named '$key'.")
+
+  private def parseBoolean(props: Map[String, String], key: String): Either[String, Boolean] =
+    parseString(props, key).flatMap: s =>
+      s.toBooleanOption match
+        case Some(v) => Right(v)
+        case None    => Left(s"Failed to parse '$s' as a boolean.")
+
+  /** Configuration loaded from `ImageJ.cfg`. */
+  case class IJCConfig(maxHeapMB: Long, jvmArgs: String, legacyMode: Boolean)
+
+end IJConfigFile

src/main/scala/ij_plugins/imagej_launcher/IJDir.scala

@@ -0,0 +1,73 @@
+/*
+ * Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+ * Author's e-mail: jpsacha at gmail.com
+ */
+
+package ij_plugins.imagej_launcher
+
+import ij_plugins.imagej_launcher.Main.Config
+import os.{FilePath, Path}
+
+import scala.util.control.NonFatal
+
+object IJDir:
+
+  /** Name of an ImageJ sub-directory containing jars */
+  val jarsDirName = "jars"
+
+  /** Locate ImageJ directory */
+  def locate(config: Config)(using logger: Logger): Either[String, Path] =
+    logger.debug("Looking for ImageJ directory")
+
+    config.ijDir match
+      case Some(d) =>
+        logger.debug(s"  Considering provided ij-dir: '$d'")
+        asPath(d.getPath).flatMap: p =>
+          logger.debug(s"    '$p'")
+          if isIJDir(p) then Right(p)
+          else Left(s"ij-dir is not an ImageJ directory [$p]")
+      case None =>
+        logger.debug("  Considering application directory")
+        val appPath = Native.applicationPath()
+        logger.debug(s"  Application directory: '$appPath'")
+        inferIJDir(appPath) match
+          case Some(p) =>
+            Right(p)
+          case None =>
+            logger.debug("  Application directory is not an ImageJ directory")
+            logger.debug("  Considering current working directory")
+            val cwd = os.pwd
+            logger.debug(s"  Current working directory: '$cwd'")
+            inferIJDir(cwd) match
+              case Some(p) =>
+                Right(p)
+              case None =>
+                logger.debug("  Current working directory is not an ImageJ directory.")
+                Left("Cannot locate ImageJ directory.")
+
+  private def inferIJDir(path: Path): Option[Path] =
+    if isIJDir(path) then
+      Option(path)
+    else if path.endsWith(os.rel / "Contents" / "MacOS") then
+      Option(path / os.up / os.up)
+    else
+      None
+
+  private def isIJDir(path: Path): Boolean =
+    os.exists(path) &&
+      os.isDir(path) &&
+      os.list(path).exists(f => f.last == jarsDirName && os.isDir(f))
+
+  private def asPath(filePath: String): Either[String, Path] =
+    if filePath.trim.startsWith("~") then
+      try
+        Right(Path.expandUser(filePath))
+      catch
+        case NonFatal(ex) =>
+          Left(s"Not an absolute path: '$filePath' [${ex.getMessage}]")
+    else
+      FilePath(filePath) match
+        case p: Path => Right(p)
+        case _       => Left(s"Not an absolute path: '$filePath'")
+
+end IJDir

src/main/scala/ij_plugins/imagej_launcher/Launcher.scala

@@ -5,6 +5,7 @@
 
 package ij_plugins.imagej_launcher
 
+import ij_plugins.imagej_launcher.IJDir.jarsDirName
 import ij_plugins.imagej_launcher.Launcher.javaExeFileName
 import ij_plugins.imagej_launcher.Main.Config
 import os.Path
@@ -12,9 +13,7 @@ import os.Path
 import java.io.File
 import java.lang.ProcessBuilder.Redirect
 
-class Launcher(logger: Logger):
+class Launcher(using logger: Logger):
-
-  private val jarsDirName = "jars"
 
   def run(config: Config): Unit =
     prepareLaunch(config) match
@@ -29,33 +28,16 @@ class Launcher(logger: Logger):
 
   private def prepareLaunch(config: Config): Either[String, Seq[String]] =
     for
-      ijDir       <- locateIJDir(config)
+      ijDir       <- IJDir.locate(config)
-      _           <- Updater.update(Path(ijDir), config.dryRun, logger)
+      _           <- Updater.update(ijDir, config.dryRun)
-      launcherJar <- findImageJLauncherJar(ijDir)
+      ijConfig    <- IJConfigFile.readFromDir(ijDir)
-      javaExe     <- locateJavaExecutable(config, ijDir)
+      launcherJar <- findImageJLauncherJar(ijDir.toIO)
+      javaExe     <- locateJavaExecutable(config, ijDir.toIO)
       systemType  <- determineSystemType()
     yield
       val maxMemoryMB = determineMaxMemoryMB()
       logger.info(s"Max memory to use: ${maxMemoryMB}MB")
-      buildCommandLine(ijDir, javaExe, launcherJar, systemType, maxMemoryMB)
+      buildCommandLine(ijDir.toIO, javaExe, launcherJar, systemType, maxMemoryMB)
-
-  private def locateIJDir(config: Config): Either[String, File] =
-    logger.debug("Looking for ImageJ directory")
-
-    val dir = config.ijDir match
-      case Some(d) =>
-        logger.debug("  Considering provided ij-dir")
-        d
-      case None =>
-        logger.debug("  Considering current directory")
-        new File(".").getCanonicalFile
-
-    dir.listFiles().find(f => f.getName == jarsDirName && f.isDirectory) match
-      case Some(_) =>
-        logger.info(s"  ImageJ directory set to: '$dir'")
-        Right(dir)
-      case None =>
-        Left(s"Cannot locate ImageJ directory. No subdirectory '$jarsDirName' in '$dir''")
 
   private def findImageJLauncherJar(ijDir: File): Either[String, File] =
     logger.debug("Looking for 'imagej-launcher*.jar'")
@@ -197,6 +179,7 @@ class Launcher(logger: Logger):
       "plugins",
       "net.imagej.Main"
     )
+  end buildCommandLine
 
   private def launch(command: Seq[String]): Unit =
     logger.debug("launchImageJ ...")

src/main/scala/ij_plugins/imagej_launcher/Logger.scala

@@ -5,20 +5,60 @@
 
 package ij_plugins.imagej_launcher
 
-import ij_plugins.imagej_launcher.Logger.Level
+import ij_plugins.imagej_launcher.Logger.{Level, logToFile}
+import os.Path
+
+import java.nio.file.{Files, StandardOpenOption}
+import scala.util.control.NonFatal
 
 class Logger(val level: Level = Level.Info):
+
   def debug(msg: String): Unit = pprint(Level.Debug, msg)
   def info(msg: String): Unit  = pprint(Level.Info, msg)
   def error(msg: String): Unit = pprint(Level.Error, msg)
 
   private def pprint(l: Level, message: String): Unit =
+    val m = f"${l.name}%-5s: $message"
     if l.level <= level.level then println(f"${l.name}%-5s: $message")
+    logToFile(m)
 
 object Logger:
+
+  private val LogFile: Path         = os.home / ".ijp_imagej_launcher.log"
+  private var logFileReset: Boolean = true
+
   enum Level(val level: Int, val name: String):
     case Off   extends Level(0, "OFF")
     case Error extends Level(200, "ERROR")
     case Info  extends Level(400, "INFO")
     case Debug extends Level(500, "DEBUG")
     case All   extends Level(Int.MaxValue, "DEBUG")
+
+  private def logToFile(message: String): Unit =
+    try
+      if logFileReset && os.exists(LogFile) then
+        val _ = os.remove(LogFile)
+        logFileReset = false
+
+      val data  = readableTimeStamp() + ": " + message + "\n"
+      val lines = data.getBytes()
+      val _ = Files.write(
+        LogFile.toNIO,
+        lines,
+        StandardOpenOption.CREATE,
+        StandardOpenOption.APPEND,
+        StandardOpenOption.WRITE
+      )
+    catch
+      case NonFatal(_) =>
+      // Ignore exceptions
+
+  private def readableTimeStamp(): String =
+    // Simple implementation returns GMT time (no date)
+    // Use custom code as DateTimeFormatter is not available in Scala Native 0.4.14
+    val t   = System.currentTimeMillis()
+    val sss = t                               % 1000
+    val ss  = (t / 1000L).toInt               % 60
+    val mm  = (t / (1000L * 60L)).toInt       % 60
+    val hh  = (t / (1000L * 60L * 60L)).toInt % 24
+    f"$hh%02d-$mm%02d-$ss%02d_$sss%03dZ"

src/main/scala/ij_plugins/imagej_launcher/Main.scala

@@ -5,15 +5,14 @@
 
 package ij_plugins.imagej_launcher
 
-import scopt.{DefaultOEffectSetup, OParser}
+import scopt.OParser
 
 import java.io.File
 
 object Main:
   private var logger         = new Logger()
-  private val AppName = "ijp-imagej-launcher"
+  private val AppName        = "IJP-ImageJ-Launcher"
-  //  private val AppVersion = s"${Version.version} [${Version.buildTimeStr}]"
+  private val AppVersion     = BuildInfo.version
-  private val AppVersion     = s"0.1.0"
   private val VersionMessage = s"v.$AppVersion"
   private val AppDescription =
     """Native launcher for ImageJ2
@@ -29,6 +28,7 @@ object Main:
       case None =>
 
   private def parseCommandLine(args: Array[String]): Option[Config] =
+    logger.debug("Command line: " + args.map("'" + _ + "'").mkString(", "))
     val builder = OParser.builder[Config]
     val parser1 =
       import builder.*
@@ -69,7 +69,7 @@ object Main:
 
   private def setupLogger(logLevel: Logger.Level): Unit = logger = new Logger(logLevel)
 
-  private def runLauncher(config: Config): Unit = new Launcher(logger).run(config)
+  private def runLauncher(config: Config): Unit = new Launcher(using logger).run(config)
 
   case class Config(
     logLevel: Logger.Level = Logger.Level.Error,

src/main/scala/ij_plugins/imagej_launcher/Native.scala

@@ -1,9 +1,29 @@
 package ij_plugins.imagej_launcher
 
-import scala.scalanative.unsafe.extern
+import os.{Path, up}
+
+import scala.scalanative.unsafe
+import scala.scalanative.unsafe.*
 
 object Native:
 
+  def applicationPath(): Path =
+    val maxPath: CSize = argv0.path_max()
+    // use Zone to manage native memory
+    val exePath =
+      Zone { implicit z =>
+        val buffer: CString = alloc[CChar](maxPath)
+        argv0.get_exe_path(buffer, maxPath)
+        unsafe.fromCString(buffer)
+      }
+    Path(exePath) / up
+
   @extern
   object mem:
     def determineTotalSystemMemory(): Long = extern
+
+  @extern
+  private object argv0:
+    def path_max(): CSize = extern
+
+    def get_exe_path(exe_path: CString, size: CSize): Unit = extern

src/main/scala/ij_plugins/imagej_launcher/Updater.scala

@@ -1,6 +1,11 @@
+/*
+ * Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+ * Author's e-mail: jpsacha at gmail.com
+ */
+
 package ij_plugins.imagej_launcher
 
-import os.{Path, RelPath}
+import os.Path
 
 import scala.util.control.NonFatal
 
@@ -13,7 +18,7 @@ object Updater:
    * @param logger configured logger
    * @return Number of files processed or an error message.
    */
-  def update(ijDir: Path, dryRun: Boolean, logger: Logger): Either[String, Long] =
+  def update(ijDir: Path, dryRun: Boolean)(using logger: Logger): Either[String, Long] =
     try
       val updateDir = ijDir / "update"
       // Count used only for debug info
@@ -23,8 +28,7 @@ object Updater:
         os.walk(updateDir)
           .filter(os.isFile)
           .foreach: src =>
-//            val relativeDir = src.relativeTo(updateDir)
+            val dst = ijDir / src.relativeTo(updateDir)
-            val dst = ijDir / relativeTo(src, updateDir)
             if os.size(src) == 0 then
               logger.debug(s"remove: $dst")
               if !dryRun then os.remove(dst)
@@ -35,7 +39,7 @@ object Updater:
               if !dryRun then os.move(src, dst, replaceExisting = true, createFolders = true)
             count += 1
         logger.debug(s"Delete update directory: $updateDir")
-        if !dryRun then deleteEmptyDirs(updateDir, logger)
+        if !dryRun then deleteEmptyDirs(updateDir)
         Right(count)
       else
         logger.info("No update found")
@@ -45,30 +49,11 @@ object Updater:
         ex.printStackTrace()
         Left(s"Failed to perform update: ${ex.getMessage} - ${ex.getClass.getSimpleName}")
 
-  private def relativeTo(src: Path, base: Path): RelPath =
+  private def deleteEmptyDirs(dir: Path)(using logger: Logger): Unit =
-    // This does what src.relativeTo(base) should do
-    // Problems is in the native code on Windows,
-    // os.Path#relativeTo creates relative path by adding `../` at the beginning of the absolute path,
-    // co you may get `../C:\a\b` which leads to a exception soon after.
-    // The issue is with Scala Native implementation of java.nio.file.Path#relativize on Windows,
-    // See https://github.com/scala-native/scala-native/issues/3293
-
-    // This implementation is very limited but sufficient for our use.
-    // It assumes specific relation between src and base.
-
-    val srcStr  = src.toString
-    val baseStr = base.toString
-    require(baseStr.nonEmpty)
-    require(srcStr.startsWith(baseStr))
-
-    val relStr = srcStr.drop(baseStr.length + 1)
-    RelPath(relStr)
-
-  private def deleteEmptyDirs(dir: Path, logger: Logger): Unit =
     logger.debug(s"Cleaning directory: $dir")
     os.list(dir)
       .filter(os.isDir)
-      .foreach(p => deleteEmptyDirs(p, logger))
+      .foreach(p => deleteEmptyDirs(p))
 
     if os.list(dir).isEmpty then
       logger.debug(s"Removing empty dir: $dir")

src/test/scala/ij_plugins/imagej_launcher/IJConfigFileTest.scala

@@ -0,0 +1,33 @@
+/*
+ * Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+ * Author's e-mail: jpsacha at gmail.com
+ */
+
+package ij_plugins.imagej_launcher
+
+import org.scalatest.flatspec.AnyFlatSpec
+
+class IJConfigFileTest extends AnyFlatSpec:
+
+  given logger:Logger = new Logger(Logger.Level.All)
+
+  "IJConfigFile" should "read valid config files" in:
+    val path = os.pwd / "test" / "data" / "config_valid" / "ImageJ.cfg"
+
+    IJConfigFile.readFromFile(path) match
+      case Right(cfg) =>
+        logger.debug(cfg.toString)
+        assert(cfg.nonEmpty)
+      case Left(err) =>
+        logger.debug(s"Unexpected error: $err")
+        fail()
+
+  it should "fail reading invalid config files" in:
+    val path = os.pwd / "test" / "data" / "config_invalid" / "ImageJ.cfg"
+
+    IJConfigFile.readFromFile(path) match
+      case Right(cfg) =>
+        logger.debug(cfg.toString)
+        fail(s"Expected to return errors when reading config, but read config as: $cfg")
+      case Left(err) =>
+        logger.debug(s"Expected error\n:$err")

src/test/scala/ij_plugins/imagej_launcher/PathSpec.scala

@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2000-2023 Jarek Sacha. All Rights Reserved.
+ * Author's e-mail: jpsacha at gmail.com
+ */
+
+package ij_plugins.imagej_launcher
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should
+
+import java.nio.file.FileSystems
+import scala.scalanative.runtime.Platform.isWindows
+
+class PathSpec extends AnyFlatSpec with should.Matchers:
+
+  "A Path" should "should `relativize` jars on Windows (Scala Native #3293)" in {
+    if isWindows() then
+      // This to test that fix for Scala Native #3293 implemented, it should be part of Scala Native 0.4.13
+      // See https://github.com/scala-native/scala-native/issues/3293
+
+      //    val src = Path.of("C:\\a\\b\\c.jar")
+      val src = FileSystems.getDefault.getPath("C:\\a\\b\\c.jar")
+      //    val base = Path.of("C:\\a")
+      val base = FileSystems.getDefault.getPath("C:\\a")
+
+      val rel = base.relativize(src)
+      rel.toString should be("b\\c.jar")
+  }

src/test/scala/ij_plugins/imagej_launcher/UpdaterDemo.scala

@@ -4,6 +4,7 @@ import os.Path
 
 @main
 def updaterDemo(ijDir: String): Unit =
-  Updater.update(Path(ijDir), dryRun = false, new Logger(Logger.Level.Debug)) match
+  given logger: Logger = new Logger(Logger.Level.Debug)
+  Updater.update(Path(ijDir), dryRun = false) match
     case Right(count) => println(s"Processed $count files")
     case Left(error)  => println(s"Failed with error: $error")

test/data/config_invalid/ImageJ.cfg

@@ -0,0 +1,4 @@
+# ImageJ startup properties
+maxheap.mb = 1024m
+jvmargs = -XX:+HeapDumpOnOutOfMemoryError -Xincgc
+legacy.mode = false

test/data/config_valid/ImageJ.cfg

@@ -0,0 +1,4 @@
+# ImageJ startup properties
+maxheap.mb = 1024
+jvmargs = -XX:+HeapDumpOnOutOfMemoryError -Xincgc
+legacy.mode = false