diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..a0a2781
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,8 @@
+## v0.4.0
+
+* Support for QuPath v0.5.0
+
+
+## v0.3.0
+
+* First version after extracting extension from QuPath's main repo.
\ No newline at end of file
diff --git a/LICENSE.txt b/LICENSE
similarity index 100%
rename from LICENSE.txt
rename to LICENSE
diff --git a/LICENSE.md b/LICENSE.md
deleted file mode 100644
index 2fb2e74..0000000
--- a/LICENSE.md
+++ /dev/null
@@ -1,675 +0,0 @@
-### GNU GENERAL PUBLIC LICENSE
-
-Version 3, 29 June 2007
-
-Copyright (C) 2007 Free Software Foundation, Inc.
-
-
-Everyone is permitted to copy and distribute verbatim copies of this
-license document, but changing it is not allowed.
-
-### Preamble
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-#### 13. Use with the GNU Affero General Public License.
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-#### 14. Revised Versions of this License.
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-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
-CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
-ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
-NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
-LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
-TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
-PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-
-#### 17. Interpretation of Sections 15 and 16.
-
-If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-END OF TERMS AND CONDITIONS
-
-### How to Apply These Terms to Your New Programs
-
-If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these
-terms.
-
-To do so, attach the following notices to the program. It is safest to
-attach them to the start of each source file to most effectively state
-the exclusion of warranty; and each file should have at least the
-"copyright" line and a pointer to where the full notice is found.
-
-
- Copyright (C)
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper
-mail.
-
-If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands \`show w' and \`show c' should show the
-appropriate parts of the General Public License. Of course, your
-program's commands might be different; for a GUI interface, you would
-use an "about box".
-
-You should also get your employer (if you work as a programmer) or
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary. For more information on this, and how to apply and follow
-the GNU GPL, see .
-
-The GNU General Public License does not permit incorporating your
-program into proprietary programs. If your program is a subroutine
-library, you may consider it more useful to permit linking proprietary
-applications with the library. If this is what you want to do, use the
-GNU Lesser General Public License instead of this License. But first,
-please read .
diff --git a/build.gradle b/build.gradle
index 631ee5c..64190b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,12 +1,13 @@
plugins {
- id 'java-library'
- // To create a shadow/fat jar, including dependencies
- // (not very useful here)
- id 'com.github.johnrengelman.shadow' version '7.0.0'
+ id 'java-library'
+ // To create a shadow/fat jar, including dependencies
+ // (not very useful here)
+ id 'com.github.johnrengelman.shadow' version '8.1.1'
+ id 'org.openjfx.javafxplugin' version '0.1.0'
}
repositories {
-// mavenLocal()
+
mavenCentral()
maven {
@@ -21,17 +22,21 @@ repositories {
ext.moduleName = 'qupath.extension.align'
-description = 'QuPath extension for interactive image alignment'
-
-version = "0.3.0"
+base {
+ description = 'QuPath extension for interactive image alignment'
+ version = "0.4.0"
+ group = "io.github.qupath"
+}
+ext.qupathVersion = gradle.ext.qupathVersion
+ext.qupathJavaVersion = 17
dependencies {
- shadow "io.github.qupath:qupath-gui-fx:0.3.0"
+ shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
shadow "org.slf4j:slf4j-api:1.7.30"
}
processResources {
- from ("${projectDir}/LICENSE.txt") {
+ from ("${projectDir}/LICENSE") {
into 'licenses/'
}
}
@@ -43,15 +48,9 @@ task copyDependencies(type: Copy) {
}
java {
- def version = project.findProperty('toolchain')
- if (!version)
- version = 11
- else if (version.strip() == 'skip')
- version = null
- if (version != null) {
- logger.quiet("Setting toolchain to {}", version)
- toolchain {
- languageVersion = JavaLanguageVersion.of(version)
- }
+ toolchain {
+ languageVersion = JavaLanguageVersion.of(qupathJavaVersion)
}
+ withSourcesJar()
+ withJavadocJar()
}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index e708b1c..7f93135 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 69a9715..1af9e09 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,7 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
index 4f906e0..1aa94a4 100755
--- a/gradlew
+++ b/gradlew
@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
#
-# Copyright 2015 the original author or authors.
+# 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.
@@ -17,67 +17,99 @@
#
##############################################################################
-##
-## Gradle start up script for UN*X
-##
+#
+# 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/HEAD/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
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
+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
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
warn () {
echo "$*"
-}
+} >&2
die () {
echo
echo "$*"
echo
exit 1
-}
+} >&2
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
esac
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -87,9 +119,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
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="$JAVA_HOME/jre/sh/java"
+ JAVACMD=$JAVA_HOME/jre/sh/java
else
- JAVACMD="$JAVA_HOME/bin/java"
+ JAVACMD=$JAVA_HOME/bin/java
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -98,88 +130,120 @@ Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+ JAVACMD=java
+ if ! command -v java >/dev/null 2>&1
+ then
+ die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
+ fi
fi
# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+ # shellcheck disable=SC2039,SC3045
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+ # shellcheck disable=SC2039,SC3045
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
fi
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-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 [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
+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
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
+ 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
- i=`expr $i + 1`
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
done
- case $i in
- 0) set -- ;;
- 1) set -- "$args0" ;;
- 2) set -- "$args0" "$args1" ;;
- 3) set -- "$args0" "$args1" "$args2" ;;
- 4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
fi
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=`save "$@"`
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+# 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"'
+
+# Collect all arguments for the java command:
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+# and any embedded shellness will be escaped.
+# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+# treated as '${Hostname}' itself on the command line.
+
+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
index ac1b06f..6689b85 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -14,7 +14,7 @@
@rem limitations under the License.
@rem
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
@rem ##########################################################################
@rem
@rem Gradle startup script for Windows
@@ -25,7 +25,8 @@
if "%OS%"=="Windows_NT" setlocal
set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
@@ -40,7 +41,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
+if %ERRORLEVEL% equ 0 goto execute
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -75,13 +76,15 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
:end
@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+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!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+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
diff --git a/settings.gradle b/settings.gradle
index dda3b69..ad8f915 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -1 +1,28 @@
rootProject.name = 'qupath-extension-align'
+
+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 hosted
+ maven {
+ url "https://maven.scijava.org/content/repositories/releases"
+ }
+
+ maven {
+ url "https://maven.scijava.org/content/repositories/snapshots"
+ }
+
+ }
+}
diff --git a/src/main/java/qupath/ext/align/AlignExtension.java b/src/main/java/qupath/ext/align/AlignExtension.java
index f3ecf49..1fdd6ba 100644
--- a/src/main/java/qupath/ext/align/AlignExtension.java
+++ b/src/main/java/qupath/ext/align/AlignExtension.java
@@ -2,7 +2,7 @@
* #%L
* This file is part of QuPath.
* %%
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
* %%
* QuPath is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
@@ -25,10 +25,10 @@
import qupath.ext.align.gui.InteractiveImageAlignmentCommand;
import qupath.lib.common.Version;
-import qupath.lib.gui.ActionTools;
-import qupath.lib.gui.ActionTools.ActionDescription;
-import qupath.lib.gui.ActionTools.ActionMenu;
+import qupath.lib.gui.actions.ActionTools;
+import qupath.lib.gui.actions.annotations.ActionConfig;
import qupath.lib.gui.QuPathGUI;
+import qupath.lib.gui.actions.annotations.ActionMenu;
import qupath.lib.gui.extensions.GitHubProject;
import qupath.lib.gui.extensions.QuPathExtension;
@@ -36,13 +36,11 @@
* Extension to make more experimental commands present in the GUI.
*/
public class AlignExtension implements QuPathExtension, GitHubProject {
-
- @SuppressWarnings("javadoc")
- public class ExperimentalCommands {
-
- @ActionMenu("Analyze>Interactive image alignment")
- @ActionDescription("Experimental command to interactively align images using an Affine transform. "
- + "This is currently not terribly useful in itself, but may be helpful as part of more complex scripting workflows.")
+
+ public static class ExperimentalCommands {
+
+ @ActionConfig(value = "alignAction", bundle = "qupath/ext/align/strings")
+ @ActionMenu("Menu.Analyze>Alignment")
public final Action actionInteractiveAlignment;
private ExperimentalCommands(QuPathGUI qupath) {
@@ -55,6 +53,7 @@ private ExperimentalCommands(QuPathGUI qupath) {
@Override
public void installExtension(QuPathGUI qupath) {
+
qupath.installActions(ActionTools.getAnnotatedActions(new ExperimentalCommands(qupath)));
}
@@ -75,7 +74,7 @@ public GitHubRepo getRepository() {
@Override
public Version getQuPathVersion() {
- return Version.parse("0.3.0-rc2");
+ return Version.parse("0.5.0");
}
}
diff --git a/src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java b/src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java
index d63cc57..180e9a7 100644
--- a/src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java
+++ b/src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java
@@ -2,7 +2,7 @@
* #%L
* This file is part of QuPath.
* %%
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
* %%
* QuPath is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
@@ -570,7 +570,8 @@ void promptToAddImages() {
// Read annotations from any data file
try {
// Try to get data from an open viewer first, if possible
- for (var viewer : qupath.getViewers()) {
+
+ for (var viewer : qupath.getAllViewers()) {
var tempData = viewer.getImageData();
if (tempData != null && temp.equals(project.getEntry(viewer.getImageData()))) {
imageData = tempData;
@@ -1018,4 +1019,4 @@ protected void updateItem(ImageData item, boolean empty) {
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/qupath/ext/align/gui/ImageServerOverlay.java b/src/main/java/qupath/ext/align/gui/ImageServerOverlay.java
index 34870ab..c4ff3c3 100644
--- a/src/main/java/qupath/ext/align/gui/ImageServerOverlay.java
+++ b/src/main/java/qupath/ext/align/gui/ImageServerOverlay.java
@@ -2,7 +2,7 @@
* #%L
* This file is part of QuPath.
* %%
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
* %%
* QuPath is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
diff --git a/src/main/java/qupath/ext/align/gui/InteractiveImageAlignmentCommand.java b/src/main/java/qupath/ext/align/gui/InteractiveImageAlignmentCommand.java
index 4516dc5..88d46d4 100644
--- a/src/main/java/qupath/ext/align/gui/InteractiveImageAlignmentCommand.java
+++ b/src/main/java/qupath/ext/align/gui/InteractiveImageAlignmentCommand.java
@@ -2,7 +2,7 @@
* #%L
* This file is part of QuPath.
* %%
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
* %%
* QuPath is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
diff --git a/src/main/resources/.gitkeep b/src/main/resources/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/src/main/resources/qupath/ext/align/strings.properties b/src/main/resources/qupath/ext/align/strings.properties
new file mode 100644
index 0000000..39d8643
--- /dev/null
+++ b/src/main/resources/qupath/ext/align/strings.properties
@@ -0,0 +1,3 @@
+alignAction = Interactive image alignment
+alignAction.description = Experimental command to interactively align images using an Affine transform. \
+ This is currently not terribly useful in itself, but may be helpful as part of more complex scripting workflows