diff --git a/.github/workflows/gradle.yml b/.github/workflows/gradle.yml
new file mode 100644
index 0000000..2a01281
--- /dev/null
+++ b/.github/workflows/gradle.yml
@@ -0,0 +1,42 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
+
+name: Java CI with Gradle
+
+on:
+ push:
+ branches: [ "main" ]
+ pull_request:
+ branches: [ "main" ]
+ workflow_dispatch:
+
+permissions:
+ contents: read
+
+jobs:
+ build:
+
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up JDK 17 # TODO: check Java version
+ uses: actions/setup-java@v3
+ with:
+ java-version: '17'
+ distribution: 'temurin'
+ - name: Validate Gradle wrapper
+ uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
+ - name: Build with Gradle
+ uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+ with:
+ arguments: build
+ - uses: actions/upload-artifact@v3
+ with:
+ name: jar
+ path: build/libs
+ retention-days: 7
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..8057f78
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,33 @@
+name: Make draft release
+
+on:
+ push:
+ tags: ["v*"]
+ workflow_dispatch:
+
+jobs:
+ release:
+ permissions:
+ contents: write
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ - name: Define version env variable
+ run: |
+ echo "VERSION=$(echo ${{ github.ref_name }} | sed -r 's/v([0-9]+\.[0-9]+\.?[0-9]?)/\1/'" >> $GITHUB_ENV
+ - name: Set up JDK 17
+ uses: actions/setup-java@v3
+ with:
+ java-version: '17'
+ distribution: 'temurin'
+ - name: Validate Gradle wrapper
+ uses: gradle/wrapper-validation-action@v1.1.0
+ - name: Build with Gradle
+ uses: gradle/gradle-build-action@v2.7.1
+ with:
+ arguments: build -Pversion=$VERSION
+ - name: Release
+ env:
+ GH_TOKEN: ${{ github.token }}
+ run: gh release create --draft ${{ github.ref_name }} --title ${{ github.ref_name }} build/libs/*
diff --git a/.gitignore b/.gitignore
index 524f096..66258b1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,24 +1,41 @@
-# Compiled class file
-*.class
-
-# Log file
-*.log
-
-# BlueJ files
-*.ctxt
-
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
-
-# Package Files #
-*.jar
-*.war
-*.nar
-*.ear
-*.zip
-*.tar.gz
-*.rar
-
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
-replay_pid*
+# Javadocs
+docs/
+
+# Maven
+deploy/
+target/
+log/
+
+# IntelliJ
+.idea/
+*.iml
+out/
+
+# Gradle
+# Use local properties (e.g. to set a specific JDK)
+gradle.properties
+build/
+.gradle/
+gradle.properties
+
+# Eclipse
+.settings/
+.project
+.classpath
+
+# VSCode
+.vscode/
+
+# Mac
+.DS_Store
+
+# Java
+hs_err*.log
+
+# Other
+*.tmp
+*.bak
+*.swp
+*~.nib
+*thumbs.db
+bin/
diff --git a/README.md b/README.md
index 2ec3405..41ee83c 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,115 @@
-# basic-stitching
-Based on QuPath extension template - for basic tiling with no overlap resolution
+# QuPath extension template
+
+This repo contains a template and instructions to help create a new extension for [QuPath](https://qupath.github.io).
+
+It already contains two minimal extensions, so the first task is to make sure that they work.
+Then, it's a matter of customizing the code to make it more useful.
+
+> There are two extensions to show that you can use either Java or Groovy.
+
+## Build the extension
+
+Building the extension with Gradle should be pretty easy - you don't even need to install Gradle separately, because the
+[Gradle Wrapper](https://docs.gradle.org/current/userguide/gradle_wrapper.html) will take care of that.
+
+Open a command prompt, navigate to where the code lives, and use
+```bash
+gradlew build
+```
+
+The built extension should be found inside `build/libs`.
+You can drag this onto QuPath to install it.
+You'll be prompted to create a user directory if you don't already have one.
+
+The minimal extension here doesn't do much, but it should at least install a new command under the 'Extensions' menu in
+QuPath.
+
+> In case your extension contains external dependencies beyond what QuPath already includes, you can create a
+> [single jar file](https://imperceptiblethoughts.com/shadow/introduction/#benefits-of-shadow) that bundles these along
+> with your extension by using
+> ```bash
+> gradlew shadowJar
+> ```
+> If you don't do that, you'll need to drag *all* the extra dependences onto QuPath to install them as well.
+
+
+## Set up in an IDE (optional)
+
+During development, things are likely to be much easier if you work within an IDE.
+
+QuPath itself is developed using IntelliJ, and you can import the extension template there.
+
+However, for development and testing, it can help to import QuPath *and* the extension and have them in your IDE side-by-side.
+
+In IntelliJ, you can do this in a few steps:
+* Get QuPath's source code, as described at https://qupath.readthedocs.io/en/0.4/docs/reference/building.html
+* Store your extension code in a directory *beside* QuPath's code. So it should be located next to the `qupath` code directory.
+* Import QuPath into IntelliJ as a Gradle project (you don't need to import the extension yet!)
+ * See https://www.jetbrains.com/help/idea/work-with-gradle-projects.html
+* Within `qupath/settings.gradle` add the line `includeFlat 'your-extension-code-directory'` (updating the code directory as needed)
+* Refresh the Gradle project in IntelliJ, and your extension code should appear
+* Create a [Run configuration](https://www.jetbrains.com/help/idea/run-debug-configuration.html) in IntelliJ to launch QuPath. An example of how that looks is shown below:
+
+
+
+Now when you run QuPath from IntelliJ, your extension should (hopefully) be found - there's no need to add it by drag & drop.
+
+## Customize the extension
+
+There are a few fixed steps to customizing the extension, and then the main creative part where you add your own code.
+
+### Update `settings.gradle`
+
+Open `settings.gradle` and check the comment lines flagged with `\\TODO`.
+These point you towards parts you may well need to change.
+
+### Update `build.gradle`
+
+Open `build.gradle` and follow a similar process to with `settings.gradle`, to update the bits flagged with `\\TODO`.
+
+### Create the extension Java or Groovy file(s)
+
+For the extension to work, you need to create at least one file that extends `qupath.lib.gui.extensions.QuPathExtension`.
+
+There are two examples in the template, in two languages:
+* **Java:** `qupath.ext.template.DemoExtension.java`.
+* **Groovy:** `qupath.ext.template.DemoGroovyExtension.java`.
+
+You can pick the one that corresponds to the language you want to use, and delete the other.
+
+Then take your chosen file and rename it, edit it, move it to another package... basically, make it your own.
+
+> Please **don't neglect this step!**
+> If you do, there's a chance of multiple extensions being created with the same class names... and causing confusion later.
+
+### Update the `META-INF/services` file
+
+For QuPath to *find* the extension later, the full class name needs to be available in `resources/META-INFO/services/qupath.lib.gui.extensions.QuPathExtensions`.
+
+So remember to edit that file to include the class name that you actually used for your extension.
+
+### Specify your license
+
+Add a license file to your GitHub repo so that others know what they can and can't do with your extension.
+
+This should be compatible with QuPath's license -- see https://github.com/qupath/qupath
+
+### Replace this readme
+
+Don't forget to replace the contents of this readme with your own!
+
+
+## Getting help
+
+For questions about QuPath and/or creating new extensions, please use the forum at https://forum.image.sc/tag/qupath
+
+------
+
+## License
+
+This is just a template, you're free to use it however you like.
+You can treat the contents of *this repository only* as being under [the Unlicense](https://unlicense.org) (except for the Gradle wrapper, which has its own license included).
+
+If you use it to create a new QuPath extension, I'd strongly encourage you to select a suitable open-source license for the extension.
+
+Note that *QuPath itself* is available under the GPL, so you do have to abide by those terms: see https://github.com/qupath/qupath for more.
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..d1edea2
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,172 @@
+plugins {
+ // Main gradle plugin for building a Java library
+ id 'java-library'
+ // Support writing the extension in Groovy (remove this if you don't want to)
+ id 'groovy'
+ // To create a shadow/fat jar that bundle up all dependencies
+ id 'com.github.johnrengelman.shadow' version '8.1.1'
+ // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
+ id 'org.bytedeco.gradle-javacpp-platform'
+ id 'org.openjfx.javafxplugin' version '0.1.0'
+ id 'maven-publish'
+}
+
+
+ext.moduleName = 'qupath.extension.basic-stitching'
+group = 'qupath.ext.basicstitching'
+
+base {
+ archivesName = rootProject.name
+ version = '0.2.0'
+ description = 'Provides basic tiling, no overlap resolution yet.'
+}
+
+
+// The default 'gradle.ext.qupathVersion' reads this from settings.gradle.
+ext.qupathVersion = gradle.ext.qupathVersion
+
+
+// Should be Java 17 for QuPath v0.5.0
+ext.qupathJavaVersion = 17
+
+/**
+ * Define dependencies.
+ * - Using 'shadow' indicates that they are already part of QuPath, so you don't need
+ * to include them in your extension. If creating a single 'shadow jar' containing your
+ * extension and all dependencies, these won't be added.
+ * - Using 'implementation' indicates that you need the dependency for the extension to work,
+ * and it isn't part of QuPath already. If you are creating a single 'shadow jar', the
+ * dependency should be bundled up in the extension.
+ * - Using 'testImplementation' indicates that the dependency is only needed for testing,
+ * but shouldn't be bundled up for use in the extension.
+ */
+dependencies {
+
+ // Main QuPath user interface jar.
+ // Automatically includes other QuPath jars as subdependencies.
+ shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
+
+ // For logging - the version comes from QuPath's version catalog at
+ // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml
+ // See https://docs.gradle.org/current/userguide/platforms.html
+ shadow libs.slf4j
+
+ // If you aren't using Groovy, this can be removed
+ shadow libs.bundles.groovy
+
+ testImplementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
+ testImplementation libs.junit
+ implementation "io.github.qupath:qupath-extension-bioformats:${qupathVersion}"
+}
+
+/*
+ * Manifest info
+ */
+jar {
+ manifest {
+ attributes("Implementation-Title": project.name,
+ "Implementation-Version": archiveVersion,
+ "Automatic-Module-Name": moduleName)
+ }
+}
+
+/**
+ * Copy necessary attributes, see
+ * - https://github.com/qupath/qupath-extension-template/issues/9
+ * - https://github.com/openjfx/javafx-gradle-plugin#variants
+ */
+configurations.shadow {
+ def runtimeAttributes = configurations.runtimeClasspath.attributes
+ runtimeAttributes.keySet().each { key ->
+ if (key in [Usage.USAGE_ATTRIBUTE, OperatingSystemFamily.OPERATING_SYSTEM_ATTRIBUTE, MachineArchitecture.ARCHITECTURE_ATTRIBUTE])
+ attributes.attribute(key, runtimeAttributes.getAttribute(key))
+ }
+}
+
+/*
+ * Copy the LICENSE file into the jar... if we have one (we should!)
+ */
+processResources {
+ from ("${projectDir}/LICENSE") {
+ into 'licenses/'
+ }
+}
+
+/*
+ * Define extra 'copyDependencies' task to copy dependencies into the build directory.
+ */
+tasks.register("copyDependencies", Copy) {
+ description "Copy dependencies into the build directory for use elsewhere"
+ group "QuPath"
+
+ from configurations.default
+ into 'build/libs'
+}
+
+/*
+ * Ensure Java 17 compatibility, and include sources and javadocs when building.
+ */
+java {
+ toolchain {
+ languageVersion = JavaLanguageVersion.of(qupathJavaVersion)
+ }
+ withSourcesJar()
+ withJavadocJar()
+}
+
+/*
+ * Create javadocs for all modules/packages in one place.
+ * Use -PstrictJavadoc=true to fail on error with doclint (which is rather strict).
+ */
+tasks.withType(Javadoc) {
+ options.encoding = 'UTF-8'
+ def strictJavadoc = findProperty('strictJavadoc')
+ if (!strictJavadoc) {
+ options.addStringOption('Xdoclint:none', '-quiet')
+ }
+}
+
+/*
+ * Specify that the encoding should be UTF-8 for source files
+ */
+tasks.named('compileJava') {
+ options.encoding = 'UTF-8'
+}
+
+/*
+ * Avoid 'Entry .gitkeep is a duplicate but no duplicate handling strategy has been set.'
+ * when using withSourcesJar()
+ */
+tasks.withType(org.gradle.jvm.tasks.Jar) {
+ duplicatesStrategy = DuplicatesStrategy.INCLUDE
+}
+
+/*
+ * Support tests with JUnit.
+ */
+tasks.named('test') {
+ useJUnitPlatform()
+}
+
+// Looks redundant to include this here and in settings.gradle,
+// but helps overcome some gradle trouble when including this as a subproject
+// within QuPath itself (which is useful during development).
+repositories {
+ // Add this if you need access to dependencies only installed locally
+ // mavenLocal()
+
+ mavenCentral()
+
+ // Add scijava - which is where QuPath's jars are hosted
+ maven {
+ url "https://maven.scijava.org/content/groups/public"
+ }
+}
+
+publishing {
+ publications {
+ myLibrary(MavenPublication) {
+ from components.java
+ }
+ }
+}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 0000000..249e583
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 0000000..a595206
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
new file mode 100644
index 0000000..a69d9cb
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,240 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+# Gradle start up script for POSIX generated by Gradle.
+#
+# Important for running:
+#
+# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+# noncompliant, but you have some other compliant shell such as ksh or
+# bash, then to run this script, type that shell name before the whole
+# command line, like:
+#
+# ksh Gradle
+#
+# Busybox and similar reduced shells will NOT work, because this script
+# requires all of these POSIX shell features:
+# * functions;
+# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+# * compound commands having a testable exit status, especially «case»;
+# * various built-in commands including «command», «set», and «ulimit».
+#
+# Important for patching:
+#
+# (2) This script targets any POSIX shell, so it avoids extensions provided
+# by Bash, Ksh, etc; in particular arrays are avoided.
+#
+# The "traditional" practice of packing multiple parameters into a
+# space-separated string is a well documented source of bugs and security
+# problems, so this is (mostly) avoided, by progressively accumulating
+# options in "$@", and eventually passing that to Java.
+#
+# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+# see the in-line comments for details.
+#
+# There are tweaks for specific operating systems such as AIX, CygWin,
+# Darwin, MinGW, and NonStop.
+#
+# (3) This script is generated from the Groovy template
+# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# within the Gradle project.
+#
+# You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+ APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
+ [ -h "$app_path" ]
+do
+ ls=$( ls -ld "$app_path" )
+ link=${ls#*' -> '}
+ case $link in #(
+ /*) app_path=$link ;; #(
+ *) app_path=$APP_HOME$link ;;
+ esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+ echo "$*"
+} >&2
+
+die () {
+ echo
+ echo "$*"
+ echo
+ exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD=$JAVA_HOME/jre/sh/java
+ else
+ JAVACMD=$JAVA_HOME/bin/java
+ fi
+ if [ ! -x "$JAVACMD" ] ; then
+ die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+ fi
+else
+ JAVACMD=java
+ which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+# * args from the command line
+# * the main class name
+# * -classpath
+# * -D...appname settings
+# * --module-path (only if needed)
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+ APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+ CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+ JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+ # Now convert the arguments - kludge to limit ourselves to /bin/sh
+ for arg do
+ if
+ case $arg in #(
+ -*) false ;; # don't mess with options #(
+ /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
+ [ -e "$t" ] ;; #(
+ *) false ;;
+ esac
+ then
+ arg=$( cygpath --path --ignore --mixed "$arg" )
+ fi
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
+ done
+fi
+
+# Collect all arguments for the java command;
+# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+# shell script including quotes and variable substitutions, so put them in
+# double quotes to make sure that they get re-expanded; and
+# * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+ "-Dorg.gradle.appname=$APP_BASE_NAME" \
+ -classpath "$CLASSPATH" \
+ org.gradle.wrapper.GradleWrapperMain \
+ "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+ die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+# set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+ printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+ xargs -n1 |
+ sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+ tr '\n' ' '
+ )" '"$@"'
+
+exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
new file mode 100644
index 0000000..f127cfd
--- /dev/null
+++ b/gradlew.bat
@@ -0,0 +1,91 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
+@rem ##########################################################################
+@rem
+@rem Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%"=="" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if %ERRORLEVEL% equ 0 goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if %ERRORLEVEL% equ 0 goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/qupath-intellij.png b/qupath-intellij.png
new file mode 100644
index 0000000..bcbd526
Binary files /dev/null and b/qupath-intellij.png differ
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 0000000..c439a40
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,45 @@
+pluginManagement {
+ plugins {
+ // Gradle is awkward about declaring versions for plugins
+ // Specifying it here, rather than build.gradle, makes it possible
+ // to include the extension as a subproject of QuPath itself
+ // (which is useful during development)
+ id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9'
+ }
+}
+
+
+rootProject.name = 'basic-stitching'
+
+
+// Note that the QuPath API isn't stable; something designed for
+// 0.X.a should work with 0.X.b, but not necessarily with 0.Y.a.
+gradle.ext.qupathVersion = "0.5.0"
+
+dependencyResolutionManagement {
+
+ // Access QuPath's version catalog for dependency versions
+ versionCatalogs {
+ libs {
+ from("io.github.qupath:qupath-catalog:${gradle.ext.qupathVersion}")
+ }
+ }
+
+ repositories {
+
+ mavenCentral()
+
+ // Add scijava - which is where QuPath's jars are
+ maven {
+ url "https://maven.scijava.org/content/groups/public"
+ }
+ maven {
+ url "https://maven.scijava.org/content/repositories/releases"
+ }
+
+ maven {
+ url "https://maven.scijava.org/content/repositories/snapshots"
+ }
+
+ }
+}
diff --git a/src/main/groovy/qupath/ext/basicstitching/BasicStitchingExtension.groovy b/src/main/groovy/qupath/ext/basicstitching/BasicStitchingExtension.groovy
new file mode 100644
index 0000000..113ee55
--- /dev/null
+++ b/src/main/groovy/qupath/ext/basicstitching/BasicStitchingExtension.groovy
@@ -0,0 +1,61 @@
+package qupath.ext.basicstitching
+
+import javafx.scene.control.MenuItem
+import qupath.ext.basicstitching.functions.StitchingGUI
+import qupath.lib.common.Version
+import qupath.lib.gui.QuPathGUI
+import qupath.lib.gui.extensions.QuPathExtension
+
+/**
+ TODO: create public functions so that stitching can be run from command line or a script
+ CHECK: Always build AND publish to maven local for use with qp-scope
+ ./gradlew publishToMavenLocal
+
+ */
+class BasicStitchingExtension implements QuPathExtension {
+
+ // Setting the variables here is enough for them to be available in the extension
+ String name = "Basic stitching"
+ String description = "Basic stitching extension that puts tiles together into pyramidal ome.tif files, no overlap resolution or flat field correction."
+ Version QuPathVersion = Version.parse("v0.5.0")
+
+// @Override
+// void installExtension(QuPathGUI qupath) {
+// qupath.installActions(ActionTools.getAnnotatedActions(new BSCommands(qupath)))
+// addMenuItem(qupath)
+// }
+ @Override
+ void installExtension(QuPathGUI qupath) {
+ addMenuItem(qupath)
+ }
+ /**
+ * Get the description of the extension.
+ *
+ * @return The description of the extension.
+ */
+ @Override
+ public String getDescription() {
+ return "Stitch tiles into a pyramidal ome.tif";
+ }
+
+ /**
+ * Get the name of the extension.
+ *
+ * @return The name of the extension.
+ */
+ @Override
+ public String getName() {
+ return "BasicStitching";
+ }
+
+ private void addMenuItem(QuPathGUI qupath) {
+ def menu = qupath.getMenu("Extensions>${name}", true)
+ def fileNameStitching = new MenuItem("Basic Stitching Extension")
+ fileNameStitching.setOnAction(e -> {
+ StitchingGUI.createGUI()
+
+ })
+ menu.getItems() << fileNameStitching
+ }
+
+}
diff --git a/src/main/groovy/qupath/ext/basicstitching/functions/StitchingGUI.groovy b/src/main/groovy/qupath/ext/basicstitching/functions/StitchingGUI.groovy
new file mode 100644
index 0000000..bd728b0
--- /dev/null
+++ b/src/main/groovy/qupath/ext/basicstitching/functions/StitchingGUI.groovy
@@ -0,0 +1,405 @@
+// TODO Progress bar for stitching
+// TODO Estimate size of stitched image to predict necessary memory
+// Warn user if size exceeds QuPath's allowed limits.
+
+package qupath.ext.basicstitching.functions
+
+import javafx.scene.Node
+import javafx.scene.control.*
+import javafx.scene.layout.GridPane
+import javafx.stage.DirectoryChooser
+import javafx.stage.Modality
+import org.slf4j.Logger
+import org.slf4j.LoggerFactory
+import qupath.ext.basicstitching.stitching.StitchingImplementations
+import qupath.lib.gui.scripting.QPEx
+
+import java.awt.*
+
+import static qupath.ext.basicstitching.utilities.UtilityFunctions.getCompressionTypeList
+
+class StitchingGUI {
+
+ private static final Logger logger = LoggerFactory.getLogger(StitchingGUI.class);
+ static TextField folderField = new TextField();
+ static ComboBox compressionBox = new ComboBox<>();
+ static TextField pixelSizeField = new TextField("0.4988466");
+ static TextField downsampleField = new TextField("1");
+ static TextField matchStringField = new TextField("20x");
+ static ComboBox stitchingGridBox = new ComboBox<>(); // New combo box for stitching grid options
+ static Button folderButton = new Button("Select Folder");
+ // Declare labels as static fields
+ static Label stitchingGridLabel = new Label("Stitching Method:");
+ static Label folderLabel = new Label("Folder location:");
+ static Label compressionLabel = new Label("Compression type:");
+ static Label pixelSizeLabel = new Label("Pixel size, microns:");
+ static Label downsampleLabel = new Label("Downsample:");
+ static Label matchStringLabel = new Label("Stitch sub-folders with text string:");
+ static Hyperlink githubLink = new Hyperlink("GitHub ReadMe");
+
+ // Map to hold the positions of each GUI element
+ private static Map guiElementPositions = new HashMap<>();
+
+
+ static void createGUI() {
+ // Create the dialog
+ def dlg = new Dialog()
+ dlg.initModality(Modality.APPLICATION_MODAL)
+ dlg.setTitle("Input Stitching Method and Options")
+ dlg.setHeaderText("Enter your settings below:")
+
+ // Set the content
+ dlg.getDialogPane().setContent(createContent())
+
+ // Add Okay and Cancel buttons
+ dlg.getDialogPane().getButtonTypes().addAll(ButtonType.OK, ButtonType.CANCEL)
+
+ // Show the dialog and capture the response
+ def result = dlg.showAndWait()
+
+ // Handling the response
+ if (result.isPresent() && result.get() == ButtonType.OK) {
+ String folderPath = folderField.getText() // Assuming folderField is accessible
+ String compressionType = compressionBox.getValue() // Assuming compressionBox is accessible
+
+ // Check if pixelSizeField and downsampleField are not empty
+ double pixelSize = pixelSizeField.getText() ? Double.parseDouble(pixelSizeField.getText()) : 0
+ // Default to 0 if empty
+ double downsample = downsampleField.getText() ? Double.parseDouble(downsampleField.getText()) : 1
+ // Default to 1 if empty
+
+ String matchingString = matchStringField.getText() // Assuming matchStringField is accessible
+ String stitchingType = stitchingGridBox.getValue()
+ // Call the function with collected data
+ String finalImageName = StitchingImplementations.stitchCore(stitchingType, folderPath, folderPath, compressionType, pixelSize, downsample, matchingString)
+ //stitchByFileName(folderPath, compressionType, pixelSize, downsample, matchingString)
+ }
+
+ }
+
+/**
+ * Creates and returns a GridPane containing all the components for the GUI.
+ * This method initializes the positions of each component in the grid,
+ * adds the components to the grid, and sets their initial visibility.
+ *
+ * @return A GridPane containing all the configured components.
+ */
+ private static GridPane createContent() {
+ // Create a new GridPane for layout
+ GridPane pane = new GridPane();
+
+ // Set horizontal and vertical gaps between grid cells
+ pane.setHgap(10);
+ pane.setVgap(10);
+
+ // Initialize the positions of each component in the grid
+ initializePositions();
+
+ // Add various components to the grid pane
+ // Each method call below corresponds to a specific component or a group of components
+ addStitchingGridComponents(pane); // Adds a combo box for selecting the stitching method
+ addFolderSelectionComponents(pane); // Adds components for selecting the folder location
+ addMatchStringComponents(pane); // Adds a text field for entering the matching string
+ addCompressionComponents(pane); // Adds a combo box for selecting the compression type
+ addPixelSizeComponents(pane); // Adds a text field for entering the pixel size
+ addDownsampleComponents(pane); // Adds a text field for entering the downsample value
+
+ // Add a hyperlink to the GitHub repository at the bottom of the pane
+ addGitHubLinkComponent(pane);
+
+ // Update the components' visibility based on the current selection in the stitching method combo box
+ updateComponentsBasedOnSelection(pane);
+
+ // Return the fully configured GridPane
+ return pane;
+ }
+
+
+/**
+ * Adds a label and its associated control to the specified GridPane.
+ * The method uses the guiElementPositions map to determine the correct
+ * row index for the label and control in the grid. If the row index is
+ * not found, an error is logged.
+ *
+ * @param pane The GridPane to which the label and control are added.
+ * @param label The label to be added to the grid.
+ * @param control The control (e.g., TextField, ComboBox) associated with the label.
+ */
+ private static void addToGrid(GridPane pane, Node label, Node control) {
+ // Retrieve the row index for the label from the guiElementPositions map
+ Integer rowIndex = guiElementPositions.get(label);
+
+ // Check if the row index was found
+ if (rowIndex != null) {
+ // Add the label and control to the grid at the specified row index
+ pane.add(label, 0, rowIndex); // Add label to column 0
+ pane.add(control, 1, rowIndex); // Add control to column 1
+ } else {
+ // Log an error if the row index is not found
+ logger.error("Row index not found for component: " + label);
+ }
+ }
+
+/**
+ * Adds a GitHub repository hyperlink to the GridPane. The hyperlink is configured to open
+ * the GitHub page in the default web browser when clicked. The position of the hyperlink in the
+ * GridPane is determined based on its predefined row index in the guiElementPositions map.
+ *
+ * @param pane The GridPane to which the GitHub hyperlink is to be added.
+ */
+ private static void addGitHubLinkComponent(GridPane pane) {
+ // Set up the action on the hyperlink to open the GitHub repository URL
+ // in the user's default web browser when clicked.
+ githubLink.setOnAction(e -> {
+ try {
+ // Open the GitHub repository URL
+ Desktop.getDesktop().browse(new URI("https://github.com/MichaelSNelson/BasicStitching"));
+ } catch (Exception ex) {
+ // Log any error encountered while trying to open the URL
+ logger.error("Error opening link", ex);
+ }
+ });
+
+ // Retrieve the pre-defined row index for the hyperlink from the guiElementPositions map.
+ // This determines where the hyperlink will be placed in the GridPane.
+ Integer rowIndex = guiElementPositions.get(githubLink);
+
+ // Add the hyperlink to the specified row in the GridPane, spanning across 2 columns.
+ pane.add(githubLink, 0, rowIndex, 2, 1);
+ }
+
+
+/**
+ * Initializes the positions of GUI elements in the GridPane. This method assigns a unique
+ * row index to each GUI element by incrementally increasing a position counter. The positions
+ * are stored in the guiElementPositions map, which maps each GUI element (Node) to its row index
+ * in the GridPane.
+ */
+ private static void initializePositions() {
+ // Start with a position counter at 0.
+ int currentPosition = 0;
+
+ // Dynamically assign row positions to each GUI element.
+ // The order of these statements dictates their vertical order in the GridPane.
+
+ guiElementPositions.put(stitchingGridLabel, currentPosition++);
+ // Position for stitching grid label and combo box
+ guiElementPositions.put(folderLabel, currentPosition++); // Position for folder label and text field
+ guiElementPositions.put(compressionLabel, currentPosition++); // Position for compression label and combo box
+ guiElementPositions.put(pixelSizeLabel, currentPosition++); // Position for pixel size label and text field
+ guiElementPositions.put(downsampleLabel, currentPosition++); // Position for downsample label and text field
+ guiElementPositions.put(matchStringLabel, currentPosition++);
+ // Position for matching string label and text field
+ guiElementPositions.put(githubLink, currentPosition++); // Position for the GitHub hyperlink
+
+ // More components can be added here following the same pattern.
+ }
+
+
+/**
+ * Adds stitching grid components to the specified GridPane. This method configures a combo box
+ * for selecting the stitching method and adds it along with its label to the GridPane.
+ * It clears any existing items in the combo box and adds a predefined set of stitching options.
+ * The default stitching method is set, and an action is defined to update component visibility
+ * based on the selected stitching method.
+ *
+ * @param pane The GridPane to which the stitching grid components are to be added.
+ */
+ private static void addStitchingGridComponents(GridPane pane) {
+ // Clear any existing items in the combo box to avoid duplicates
+ stitchingGridBox.getItems().clear();
+
+ // Add a set of predefined stitching options to the combo box
+ stitchingGridBox.getItems().addAll(
+ "Vectra tiles with metadata",
+ "Filename[x,y] with coordinates in microns",
+ "Coordinates in TileConfiguration.txt file"
+ );
+
+ // Set the default value for the combo box
+ stitchingGridBox.setValue("Coordinates in TileConfiguration.txt file");
+
+ // Define an action to be performed when a new item is selected in the combo box
+ // This action updates the visibility of other components based on the selection
+ stitchingGridBox.setOnAction(e -> updateComponentsBasedOnSelection(pane));
+
+ // Add the stitching method label and the combo box to the GridPane
+ // using the addToGrid helper method
+ addToGrid(pane, stitchingGridLabel as Node, stitchingGridBox as Node);
+ }
+
+
+/**
+ * Adds components for folder selection to the specified GridPane. This method configures a text field
+ * for displaying the selected folder path and a button to open a directory chooser dialog.
+ * It attempts to set a default folder path and defines the action for the button to select a folder.
+ * The text field and the button are added to the GridPane in their designated positions.
+ *
+ * @param pane The GridPane to which the folder selection components are to be added.
+ */
+ private static void addFolderSelectionComponents(GridPane pane) {
+ // Attempt to initialize the folder path text field with a default path
+ try {
+ String defaultFolderPath = QPEx.buildPathInProject("Tiles");
+ logger.info("Default folder path: {}", defaultFolderPath);
+ folderField.setText(defaultFolderPath);
+ } catch (Exception e) {
+ // If the default path cannot be set, probably due to no project being open
+ logger.info("Error setting default folder path, usually due to no project being open", e);
+ }
+
+ // Configure the action for the folder selection button
+ folderButton.setOnAction(e -> {
+ try {
+ DirectoryChooser dirChooser = new DirectoryChooser();
+ dirChooser.setTitle("Select Folder");
+
+ // Get the initial directory path from the text field
+ String initialDirPath = folderField.getText();
+ File initialDir = new File(initialDirPath);
+
+ // Set the initial directory in the directory chooser if it exists
+ if (initialDir.exists() && initialDir.isDirectory()) {
+ dirChooser.setInitialDirectory(initialDir);
+ } else {
+ logger.warn("Initial directory does not exist or is not a directory: {}", initialDir.getAbsolutePath());
+ }
+
+ // Show the directory chooser dialog and update the text field with the selected directory
+ File selectedDir = dirChooser.showDialog(null); // Replace null with your stage if available
+ if (selectedDir != null) {
+ folderField.setText(selectedDir.getAbsolutePath());
+ logger.info("Selected folder path: {}", selectedDir.getAbsolutePath());
+ }
+ } catch (Exception ex) {
+ // Log an error if there is an issue during folder selection
+ logger.error("Error selecting folder", ex);
+ }
+ });
+
+ // Add the folder label and text field to the GridPane
+ addToGrid(pane, folderLabel as Node, folderField as Node);
+
+ // Retrieve the row index for placing the folder button and add it to the GridPane
+ Integer rowIndex = guiElementPositions.get(folderLabel);
+ if (rowIndex != null) {
+ pane.add(folderButton, 2, rowIndex); // Place the button next to the text field
+ } else {
+ // Log an error if the row index for the folder button is not found
+ logger.error("Row index not found for folderButton");
+ }
+ }
+
+//TODO populate with a list of compression types
+/**
+ * Adds compression selection components to the specified GridPane.
+ * This method configures a combo box with options for different types of image compression
+ * and adds it to the grid along with a label. A tooltip is also set for the label and
+ * the combo box to provide additional information to the user.
+ *
+ * @param pane The GridPane to which the compression components are to be added.
+ */
+ private static void addCompressionComponents(GridPane pane) {
+ // Clear any existing items and add new compression options to the combo box
+ def compressionTypes = getCompressionTypeList()
+ compressionBox.getItems().clear();
+ compressionBox.getItems().addAll(compressionTypes);
+
+ // Set the default value for the combo box
+ compressionBox.setValue("J2K_LOSSY");
+
+ // Create and set a tooltip for additional information
+ Tooltip compressionTooltip = new Tooltip("Select the type of image compression.");
+ compressionLabel.setTooltip(compressionTooltip);
+ compressionBox.setTooltip(compressionTooltip);
+
+ // Add the compression label and combo box to the GridPane
+ addToGrid(pane, compressionLabel as Node, compressionBox as Node);
+ }
+
+
+/**
+ * Adds pixel size input components to the specified GridPane.
+ * This method adds a label and a text field for entering the pixel size to the grid.
+ *
+ * @param pane The GridPane to which the pixel size components are to be added.
+ */
+ private static void addPixelSizeComponents(GridPane pane) {
+ // Add the pixel size label and text field to the GridPane
+ addToGrid(pane, pixelSizeLabel as Node, pixelSizeField as Node);
+ }
+
+
+/**
+ * Adds downsample input components to the specified GridPane.
+ * This method adds a label and a text field for entering the downsample value to the grid.
+ * A tooltip is also set for the label and the text field to provide additional information.
+ *
+ * @param pane The GridPane to which the downsample components are to be added.
+ */
+ private static void addDownsampleComponents(GridPane pane) {
+ // Create and set a tooltip for additional information
+ Tooltip downsampleTooltip = new Tooltip("The amount by which the highest resolution plane will be initially downsampled.");
+ downsampleLabel.setTooltip(downsampleTooltip);
+ downsampleField.setTooltip(downsampleTooltip);
+
+ // Add the downsample label and text field to the GridPane
+ addToGrid(pane, downsampleLabel as Node, downsampleField as Node);
+ }
+
+
+/**
+ * Adds matching string input components to the specified GridPane.
+ * This method adds a label and a text field for entering the matching string to the grid.
+ *
+ * @param pane The GridPane to which the matching string components are to be added.
+ */
+ private static void addMatchStringComponents(GridPane pane) {
+ // Add the matching string label and text field to the GridPane
+ addToGrid(pane, matchStringLabel as Node, matchStringField as Node);
+ }
+
+
+/**
+ * Updates the visibility of certain GUI components based on the current selection
+ * in the stitching method combo box. Specifically, it hides or shows the pixel size
+ * field and label based on the selected stitching method.
+ *
+ * @param pane The GridPane containing the components to be updated.
+ */
+ private static void updateComponentsBasedOnSelection(GridPane pane) {
+ // Determine whether to hide the pixel size field and label
+ boolean hidePixelSize = stitchingGridBox.getValue().equals("Vectra multiplex tif") ||
+ stitchingGridBox.getValue().equals("Coordinates in TileCoordinates.txt file");
+ pixelSizeLabel.setVisible(!hidePixelSize);
+ pixelSizeField.setVisible(!hidePixelSize);
+
+ // Adjust the layout of the GridPane to reflect the visibility changes
+ adjustLayout(pane);
+ }
+
+
+/**
+ * Adjusts the layout of the GridPane based on the current positions specified in the guiElementPositions map.
+ * This method iterates through each GUI element in the map and updates its row index in the GridPane.
+ * The adjustment ensures that the GUI elements are displayed in the correct order and position,
+ * especially after any visibility changes.
+ *
+ * @param pane The GridPane whose layout is to be adjusted.
+ */
+ private static void adjustLayout(GridPane pane) {
+ // Iterate through each entry in the guiElementPositions map
+ for (Map.Entry entry : guiElementPositions.entrySet()) {
+ Node node = entry.getKey(); // The GUI element (Node)
+ Integer newRow = entry.getValue(); // The new row index for the element
+
+ // Check if the node is a part of the GridPane's children
+ if (pane.getChildren().contains(node)) {
+ // Update the node's row index in the GridPane
+ GridPane.setRowIndex(node, newRow);
+ }
+ }
+ }
+
+
+}
diff --git a/src/main/groovy/qupath/ext/basicstitching/stitching/StitchingImplementations.groovy b/src/main/groovy/qupath/ext/basicstitching/stitching/StitchingImplementations.groovy
new file mode 100644
index 0000000..559ac74
--- /dev/null
+++ b/src/main/groovy/qupath/ext/basicstitching/stitching/StitchingImplementations.groovy
@@ -0,0 +1,650 @@
+package qupath.ext.basicstitching.stitching
+
+import org.slf4j.LoggerFactory
+import qupath.ext.basicstitching.utilities.UtilityFunctions
+import qupath.lib.common.GeneralTools
+import qupath.lib.gui.QuPathGUI
+import qupath.lib.gui.dialogs.Dialogs
+import qupath.lib.images.servers.ImageServerProvider
+import qupath.lib.images.servers.ImageServers
+import qupath.lib.images.servers.SparseImageServer
+import qupath.lib.images.writers.ome.OMEPyramidWriter
+import qupath.lib.regions.ImageRegion
+
+import javax.imageio.ImageIO
+import javax.imageio.plugins.tiff.BaselineTIFFTagSet
+import javax.imageio.plugins.tiff.TIFFDirectory
+import java.awt.image.BufferedImage
+import java.nio.file.Files
+import java.nio.file.Path
+import java.nio.file.Paths
+
+import static qupath.lib.scripting.QP.getLogger;
+
+//TODO Is there a way to apply the downsample when accessing the image regions so the full res image region doesn't need to be stored in memory?
+// Maybe downsample after acquiring the region as a second step?
+
+// Interface for stitching strategies
+interface StitchingStrategy {
+ List