diff --git a/RandomGenerators/.gitignore b/RandomGenerators/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..f6ca8576ca690724d82e7ac4722a46cc332040c8 --- /dev/null +++ b/RandomGenerators/.gitignore @@ -0,0 +1,6 @@ +/.gradle/ +/bin/ +/build/ +/.settings/ +/.classpath +/.project diff --git a/RandomGenerators/build.gradle b/RandomGenerators/build.gradle new file mode 100644 index 0000000000000000000000000000000000000000..505d4c6ff69849620a8784001a17f7b13569ff62 --- /dev/null +++ b/RandomGenerators/build.gradle @@ -0,0 +1,44 @@ +apply plugin: 'java-library' +apply plugin: 'eclipse' + +version = '0.1.0' +repositories { + jcenter() +} + +println "Project=" + project.name +println "ICY_HOME=${System.env.ICY_HOME}" +dependencies { + testImplementation 'org.hamcrest:hamcrest-all:1.3' + testImplementation 'junit:junit:4.12' + + implementation files("${System.env.ICY_HOME}/icy.jar") // Icy core + 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}/plugins/danyfel80/var/BlockVars.jar") // Block vars +} + +eclipse { + classpath.downloadJavadoc = true + classpath.defaultOutputDir = file("bin") + project { + natures += ['icy.icy4eclipse.core.icynature'] + } +} + +task sourcesJar(type: Jar, dependsOn: classes) { + classifier = 'sources' + from sourceSets.main.output + from sourceSets.main.java +} + +task javadocJar(type: Jar, dependsOn: javadoc) { + classifier = 'javadoc' + from javadoc.destinationDir +} + +artifacts { + archives sourcesJar + archives javadocJar +} diff --git a/RandomGenerators/gradle/wrapper/gradle-wrapper.jar b/RandomGenerators/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000000000000000000000000000000000000..27768f1bbac3ce2d055b20d521f12da78d331e8e Binary files /dev/null and b/RandomGenerators/gradle/wrapper/gradle-wrapper.jar differ diff --git a/RandomGenerators/gradle/wrapper/gradle-wrapper.properties b/RandomGenerators/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000000000000000000000000000000000000..92165eede80f1d94536089f202478c7adc36a7a3 --- /dev/null +++ b/RandomGenerators/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +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 diff --git a/RandomGenerators/gradlew b/RandomGenerators/gradlew new file mode 100644 index 0000000000000000000000000000000000000000..cccdd3d517fc5249beaefa600691cf150f2fa3e6 --- /dev/null +++ b/RandomGenerators/gradlew @@ -0,0 +1,172 @@ +#!/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" "$@" diff --git a/RandomGenerators/gradlew.bat b/RandomGenerators/gradlew.bat new file mode 100644 index 0000000000000000000000000000000000000000..f9553162f122c71b34635112e717c3e733b5b212 --- /dev/null +++ b/RandomGenerators/gradlew.bat @@ -0,0 +1,84 @@ +@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 diff --git a/RandomGenerators/settings.gradle b/RandomGenerators/settings.gradle new file mode 100644 index 0000000000000000000000000000000000000000..308515d3208372655a78a75fe10cfb9636e26cdf --- /dev/null +++ b/RandomGenerators/settings.gradle @@ -0,0 +1,18 @@ +/* + * This settings file was generated by the Gradle 'init' task. + * + * The settings file is used to specify which projects to include in your build. + * In a single project build this file can be empty or even removed. + * + * Detailed information about configuring a multi-project build in Gradle can be found + * in the user guide at https://docs.gradle.org/4.3/userguide/multi_project_builds.html + */ + +/* +// To declare projects as part of a multi-project build use the 'include' method +include 'shared' +include 'api' +include 'services:webservice' +*/ + +rootProject.name = 'RandomGenerators' diff --git a/RandomGenerators/src/main/java/plugins/danyfel80/image/generator/RandomSubimageGenerator.java b/RandomGenerators/src/main/java/plugins/danyfel80/image/generator/RandomSubimageGenerator.java new file mode 100644 index 0000000000000000000000000000000000000000..2fb461ebd4f0332b14374f0a2a3fe178f64de1c9 --- /dev/null +++ b/RandomGenerators/src/main/java/plugins/danyfel80/image/generator/RandomSubimageGenerator.java @@ -0,0 +1,97 @@ +/* + * Copyright 2010-2018 Institut Pasteur. + * + * This file is part of Icy. + * + * Icy 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. + * + * Icy 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 Icy. If not, see <http://www.gnu.org/licenses/>. + */ +package plugins.danyfel80.image.generator; + +import java.awt.Dimension; + +import icy.plugin.abstract_.Plugin; +import icy.plugin.interface_.PluginLibrary; +import icy.roi.ROI; +import icy.sequence.Sequence; +import icy.sequence.SequenceUtil; +import icy.type.point.Point5D; +import icy.type.rectangle.Rectangle5D; +import icy.type.rectangle.Rectangle5D.Integer; +import plugins.adufour.blocks.lang.Block; +import plugins.adufour.blocks.util.VarList; +import plugins.adufour.vars.lang.VarSequence; +import vars.geom.VarDimension; + +/** + * @author Daniel Felipe Gonzalez Obando + */ +public class RandomSubimageGenerator extends Plugin implements PluginLibrary, Block { + + VarSequence varInputSequence; + VarDimension varPaddingDimension; + VarSequence varOutputSequence; + + @Override + public void declareInput(VarList inputMap) { + varInputSequence = new VarSequence("Sequence", null); + varPaddingDimension = new VarDimension("Padding dimension", new Dimension(0, 0)); + inputMap.add(varInputSequence.getName(), varInputSequence); + inputMap.add(varPaddingDimension.getName(), varPaddingDimension); + } + + @Override + public void declareOutput(VarList outputMap) { + varOutputSequence = new VarSequence("sub image", null); + outputMap.add(varOutputSequence.getName(), varOutputSequence); + } + + @Override + public void run() { + Sequence inputSequence = varInputSequence.getValue(true); + Dimension padding = varPaddingDimension.getValue(true); + + Rectangle5D.Integer region = getRandomRegion(inputSequence, padding); + Sequence outputSequence = generateSubSequence(inputSequence, region); + varOutputSequence.setValue(outputSequence); + } + + private Integer getRandomRegion(Sequence inputSequence, Dimension padding) { + int x = (int) ((padding.width * 2) * Math.random()); + int y = (int) ((padding.height * 2) * Math.random()); + int sizeX = inputSequence.getSizeX() - (padding.width * 2); + int sizeY = inputSequence.getSizeY() - (padding.width * 2); + + return new Rectangle5D.Integer(x, y, 0, 0, 0, sizeX, sizeY, inputSequence.getSizeZ(), inputSequence.getSizeT(), + inputSequence.getSizeC()); + } + + private Sequence generateSubSequence(Sequence inputSequence, Integer region) { + Sequence subSequence = SequenceUtil.getSubSequence(inputSequence, region); + for (ROI roi: inputSequence.getROIs()) { + if (region.intersects(roi.getBounds5D())) { + ROI roiCopy = roi.getCopy(); + Point5D copyPosition = roi.getPosition5D(); + copyPosition.setX(copyPosition.getX() - region.getX()); + copyPosition.setY(copyPosition.getY() - region.getY()); + copyPosition.setZ(copyPosition.getZ() - region.getZ()); + copyPosition.setT(copyPosition.getT() - region.getT()); + copyPosition.setC(copyPosition.getC() - region.getC()); + roiCopy.setPosition5D(copyPosition); + subSequence.addROI(roiCopy); + } + } + return subSequence; + } + +} diff --git a/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomDouble.java b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomDouble.java new file mode 100644 index 0000000000000000000000000000000000000000..3ec84990e480e9c74c75c57dcd6b61e208b80b2a --- /dev/null +++ b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomDouble.java @@ -0,0 +1,66 @@ +/* + * Copyright 2010-2018 Institut Pasteur. + * + * This file is part of Icy. + * + * Icy 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. + * + * Icy 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 Icy. If not, see <http://www.gnu.org/licenses/>. + */ +package plugins.danyfel80.numbers.generator; + +import java.util.Random; + +import icy.plugin.abstract_.Plugin; +import icy.plugin.interface_.PluginLibrary; +import plugins.adufour.blocks.lang.Block; +import plugins.adufour.blocks.util.VarList; +import plugins.adufour.vars.lang.VarDouble; + +/** + * This block plugin allows users to obtain a random real value within given + * minimum (inclusive) and maximum (exclusive) values. + * + * @author Daniel Felipe Gonzalez Obando + */ +public class GenerateRandomDouble extends Plugin implements PluginLibrary, Block { + + private static Random RANDOM_GENERATOR = new Random(); + + private VarDouble inVarMin; + private VarDouble inVarMax; + + private VarDouble outVarValue; + + @Override + public void declareInput(VarList inputMap) { + inVarMin = new VarDouble("Minimum value", 0d); + inVarMax = new VarDouble("Maximum value", 1d); + inputMap.add(inVarMin.getName(), inVarMin); + inputMap.add(inVarMax.getName(), inVarMax); + } + + @Override + public void declareOutput(VarList outputMap) { + outVarValue = new VarDouble("Value", 0d); + outputMap.add(outVarValue.getName(), outVarValue); + } + + @Override + public void run() { + Double min = inVarMin.getValue(true); + Double max = inVarMax.getValue(true); + Double value = min + ((max - min) * RANDOM_GENERATOR.nextDouble()); + outVarValue.setValue(value); + } + +} diff --git a/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomInteger.java b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomInteger.java new file mode 100644 index 0000000000000000000000000000000000000000..50d8b7fa84244a68339aa9c31029793f34b14885 --- /dev/null +++ b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/GenerateRandomInteger.java @@ -0,0 +1,66 @@ +/* + * Copyright 2010-2018 Institut Pasteur. + * + * This file is part of Icy. + * + * Icy 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. + * + * Icy 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 Icy. If not, see <http://www.gnu.org/licenses/>. + */ +package plugins.danyfel80.numbers.generator; + +import java.util.Random; + +import icy.plugin.abstract_.Plugin; +import icy.plugin.interface_.PluginLibrary; +import plugins.adufour.blocks.lang.Block; +import plugins.adufour.blocks.util.VarList; +import plugins.adufour.vars.lang.VarInteger; + +/** + * This block plugin allows users to obtain a random integer value within given + * minimum (inclusive) and maximum (exclusive) values. + * + * @author Daniel Felipe Gonzalez Obando + */ +public class GenerateRandomInteger extends Plugin implements PluginLibrary, Block { + + private static Random RANDOM_GENERATOR = new Random(); + + private VarInteger inVarMin; + private VarInteger inVarMax; + + private VarInteger outVarValue; + + @Override + public void declareInput(VarList inputMap) { + inVarMin = new VarInteger("Minimum value", 0); + inVarMax = new VarInteger("Maximum value", 100); + inputMap.add(inVarMin.getName(), inVarMin); + inputMap.add(inVarMax.getName(), inVarMax); + } + + @Override + public void declareOutput(VarList outputMap) { + outVarValue = new VarInteger("Value", 0); + outputMap.add(outVarValue.getName(), outVarValue); + } + + @Override + public void run() { + Integer min = inVarMin.getValue(true); + Integer max = inVarMax.getValue(true); + Integer value = min + (RANDOM_GENERATOR.nextInt(max - min)); + outVarValue.setValue(value); + } + +} diff --git a/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/RandomGenerators.java b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/RandomGenerators.java new file mode 100644 index 0000000000000000000000000000000000000000..cca07d735faa6affa2a38a2272f725bd50857141 --- /dev/null +++ b/RandomGenerators/src/main/java/plugins/danyfel80/numbers/generator/RandomGenerators.java @@ -0,0 +1,16 @@ +package plugins.danyfel80.numbers.generator; + +import icy.plugin.abstract_.Plugin; +import icy.plugin.interface_.PluginLibrary; + +/** + * Random generator plugins. When installed, this plugin allows access to the + * following blocks: + * <ul> + * <li>GenerateRandomInteger: Generator for random integer values.</li> + * <li>GenerateRandomDouble: Generator for random double values.</li> + * </ul> + * + * @author Daniel Felipe Gonzalez Obando + */ +public class RandomGenerators extends Plugin implements PluginLibrary {}