Commit 7da50da5 authored by danyfel80's avatar danyfel80

update of gradle build file

remove gradle wrapper
now throws exception on fail of point RANSAC correspondence search
parent b9df6aa4
......@@ -4,3 +4,4 @@
/build/
.classpath
.project
/ecbuild/
println "ICY_HOME=${System.env.ICY_HOME}"
apply plugin: 'java-library'
apply plugin: 'eclipse'
version = '1.0.1'
println "ICY_HOME=${System.env.ICY_HOME}"
println project.name + " " + version
configurations {
extraLibs // configuration that holds jars to include in the jar
implementation.extendsFrom(extraLibs)
}
// In this section you declare where to find the dependencies of your project
......@@ -18,24 +20,38 @@ repositories {
dependencies {
extraLibs 'org.apache.commons:commons-math3:3.0' // Apache Math
configurations.implementation.extendsFrom(configurations.extraLibs)
implementation files("${System.env.ICY_HOME}/lib/bioformats.jar") // Bioformats
implementation files("${System.env.ICY_HOME}/lib/jai_core.jar") // JAI
implementation files("${System.env.ICY_HOME}/icy.jar") // Icy
implementation files("${System.env.ICY_HOME}/plugins/adufour/ezplug/EzPlug.jar") // EzPlug
implementation files("${System.env.ICY_HOME}/plugins/adufour/blocks/Blocks.jar") // Blocks
implementation files("${System.env.ICY_HOME}/plugins/adufour/protocols/Protocols.jar") // Protocols
implementation files("${System.env.ICY_HOME}/lib/bioformats.jar") // Bioformats
implementation files("${System.env.ICY_HOME}/lib/jai_core.jar") // JAI
testImplementation 'junit:junit:4.12'
testImplementation 'org.hamcrest:hamcrest-all:1.3' // Hamcrest
}
eclipse {
classpath.downloadJavadoc = true
project {
natures += ['icy.icy4eclipse.core.icynature']
}
classpath{
defaultOutputDir = file("ecbuild")
file.whenMerged {
entries.each {
source ->
// This seems kludgy. If the second test is omitted, it fails processing a 'Project Dependency' entry
if (source.kind == 'src' && source.toString().contains('output')) {
source.output = 'ecbuild'
}
}
}
downloadJavadoc = true
}
project {
natures += ['icy.icy4eclipse.core.icynature']
//natures += ['org.eclipse.buildship.core.gradleprojectnature']
//buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
}
}
jar {
......
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-4.3-bin.zip
#!/usr/bin/env sh
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# 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"`"/$link"
fi
done
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >/dev/null
APP_HOME="`pwd -P`"
cd "$SAVED" >/dev/null
APP_NAME="Gradle"
APP_BASE_NAME=`basename "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS=""
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn () {
echo "$*"
}
die () {
echo
echo "$*"
echo
exit 1
}
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
case "`uname`" in
CYGWIN* )
cygwin=true
;;
Darwin* )
darwin=true
;;
MINGW* )
msys=true
;;
NONSTOP* )
nonstop=true
;;
esac
CLASSPATH=$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" = "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
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
# For Cygwin, switch paths to Windows format before running java
if $cygwin ; then
APP_HOME=`cygpath --path --mixed "$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
# 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`="\"$arg\""
fi
i=$((i+1))
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"
# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
cd "$(dirname "$0")"
fi
exec "$JAVACMD" "$@"
@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 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=
@rem Find java.exe
if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
if "%ERRORLEVEL%" == "0" goto init
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 init
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
:init
@rem Get command-line arguments, handling Windows variants
if not "%OS%" == "Windows_NT" goto win9xME_args
:win9xME_args
@rem Slurp the command line arguments.
set CMD_LINE_ARGS=
set _SKIP=2
:win9xME_args_slurp
if "x%~1" == "x" goto execute
set CMD_LINE_ARGS=%*
: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 %CMD_LINE_ARGS%
:end
@rem End local scope for the variables with windows NT shell
if "%ERRORLEVEL%"=="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
:mainEnd
if "%OS%"=="Windows_NT" endlocal
:omega
......@@ -71,7 +71,7 @@ public class SurfMatcher {
this.ransacMinNumInliers = ransacMinNumInliers;
}
public void compute() throws InterruptedException {
public void compute() throws InterruptedException, RuntimeException {
createClosestDescriptorMatches();
cleanIdenticalMatches();
filterCorrelatedMatches();
......@@ -159,7 +159,7 @@ public class SurfMatcher {
matches = new ArrayList<>(new HashSet<>(matches));
}
private void filterCorrelatedMatches() {
private void filterCorrelatedMatches() throws RuntimeException {
try {
RansacAffineTransformationCalculator calculator = new RansacAffineTransformationCalculator.Builder(matches)
.setMaxNumIterations(ransacMaxNumIterations).setNumInliersThreshold(ransacMinNumInliers)
......@@ -167,10 +167,12 @@ public class SurfMatcher {
calculator.compute();
matches = calculator.getFilteredMatches();
} catch (RansacAffineTransformationCalculatorException e) {
e.printStackTrace();
System.err.println("RANSAC failed to compute a correct affine transformation. Giving raw matches instead");
// e.printStackTrace();
// System.err.println("RANSAC failed to compute a correct affine transformation. Giving raw matches instead");
throw new RuntimeException("RANSAC failed to compute a correct affine transformation.", e);
} catch (IllegalArgumentException e) {
System.err.format("Insufficient matches to compute RANSAC (%d). Giving raw matches instead\n", matches.size());
//System.err.format("Insufficient matches to compute RANSAC (%d). Giving raw matches instead\n", matches.size());
throw new RuntimeException(String.format("Insufficient matches to compute RANSAC (%d).", matches.size()), e);
}
}
......
......@@ -189,6 +189,9 @@ public class MatchSurfFeatures extends EzPlug implements Block, EzStoppable {
System.out.printf("Computation time: %d milliseconds\n", endTime - startTime);
} catch (InterruptedException e) {
throw getInterruptionException();
} catch (Exception e) {
e.printStackTrace();
throw new IcyHandledException(e);
}
createResult();
......
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