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Merge pull request #8 from ebremer/develop
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Revamp pyramid selector
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@ebremer
ebremer authored May 19, 2023
2 parents 13e7ebc + 01ac4fe commit cc4d219
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Showing 13 changed files with 199 additions and 3,292 deletions.
88 changes: 55 additions & 33 deletions dependency-reduced-pom.xml
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Expand Up @@ -10,7 +10,7 @@
<groupId>com.ebremer</groupId>
<artifactId>Halcyon</artifactId>
<name>Halcyon</name>
<version>0.2.1</version>
<version>0.3.1</version>
<description>A whole slide image annotation, management, and visualization system</description>
<issueManagement>
<system>github</system>
Expand Down Expand Up @@ -117,6 +117,25 @@
<groupId>org.panteleyev</groupId>
<artifactId>jpackage-maven-plugin</artifactId>
<version>1.6.0</version>
<configuration>
<name>Halcyon</name>
<appVersion>${project.version}</appVersion>
<vendor>Wing-n-Beak LLC</vendor>
<copyright>Copyright 2022 Erich Bremer - Stony Brook University</copyright>
<licenseFile>LICENSE</licenseFile>
<input>target</input>
<mainJar>Halcyon-0.3.1.jar</mainJar>
<verbose>true</verbose>
<description>Whole Slide Imaging and Feature Management</description>
<installDir>\Halcyon</installDir>
<icon>src\main\resources\META-INF\halcyon.ico</icon>
<destination>target/dist</destination>
<type>dmg</type>
<javaOptions>
<option>--enable-preview</option>
<option>-Dfile.encoding=UTF-8</option>
</javaOptions>
</configuration>
</plugin>
</plugins>
</build>
Expand Down Expand Up @@ -167,12 +186,20 @@
</plugin>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.2.1</version>
<configuration>
<rules>
<dependencyConvergence />
</rules>
</configuration>
<version>3.3.0</version>
<executions>
<execution>
<id>enforce</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<banDuplicatePomDependencyVersions />
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
Expand Down Expand Up @@ -611,55 +638,61 @@
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket-core</artifactId>
<version>9.12.0</version>
<version>9.13.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket-devutils</artifactId>
<version>9.12.0</version>
<version>9.13.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket-extensions</artifactId>
<version>9.12.0</version>
<version>9.13.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-tdb</artifactId>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-querybuilder</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-permissions</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-shacl</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-fuseki-main</artifactId>
<version>4.6.1</version>
<version>4.8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
Expand All @@ -671,7 +704,7 @@
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
<version>6.10.0</version>
<version>6.13.0</version>
<scope>provided</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -741,7 +774,7 @@
<dependency>
<groupId>com.ebremer</groupId>
<artifactId>BeakGraph</artifactId>
<version>0.1.0</version>
<version>0.2.0</version>
<scope>provided</scope>
</dependency>
<dependency>
Expand All @@ -762,12 +795,6 @@
<version>0.24.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-tdb</artifactId>
<version>4.6.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
Expand All @@ -786,12 +813,6 @@
<version>0.11.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.26</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
Expand Down Expand Up @@ -877,19 +898,20 @@
<java.version>17</java.version>
<resteasy.version>4.7.4.Final</resteasy.version>
<maven.compiler.source>17</maven.compiler.source>
<wicket.ver>9.12.0</wicket.ver>
<jena.version>4.8.0</jena.version>
<wicket.ver>9.13.0</wicket.ver>
<infinispan.version>13.0.12.Final</infinispan.version>
<embeddedkeycloak.ver>8.0.0</embeddedkeycloak.ver>
<dcm4che.ver>5.29.2</dcm4che.ver>
<jgroups.version>4.2.21.Final</jgroups.version>
<titanium-json-ld.ver>1.3.0</titanium-json-ld.ver>
<maven.compiler.target>17</maven.compiler.target>
<hilbert.ver>0.2.2</hilbert.ver>
<jena.ver>4.6.1</jena.ver>
<beakgraph.version>0.2.0</beakgraph.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<commons-pool2.ver>2.11.1</commons-pool2.ver>
<keycloak.ver>18.0.2</keycloak.ver>
<jakarta.json.version>2.0.1</jakarta.json.version>
<bioformats.ver>6.10.0</bioformats.ver>
<bioformats.ver>6.13.0</bioformats.ver>
</properties>
</project>
39 changes: 34 additions & 5 deletions pom.xml
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Expand Up @@ -68,7 +68,7 @@
<wicket.ver>9.13.0</wicket.ver>
<keycloak.ver>18.0.2</keycloak.ver>
<embeddedkeycloak.ver>8.0.0</embeddedkeycloak.ver>
<bioformats.ver>6.10.0</bioformats.ver>
<bioformats.ver>6.13.0</bioformats.ver>
<hilbert.ver>0.2.2</hilbert.ver>
<commons-pool2.ver>2.11.1</commons-pool2.ver>
<jakarta.json.version>2.0.1</jakarta.json.version>
Expand Down Expand Up @@ -191,6 +191,25 @@
<groupId>org.panteleyev</groupId>
<artifactId>jpackage-maven-plugin</artifactId>
<version>1.6.0</version>
<configuration>
<name>Halcyon</name>
<appVersion>${project.version}</appVersion>
<vendor>Wing-n-Beak LLC</vendor>
<copyright>Copyright 2022 Erich Bremer - Stony Brook University</copyright>
<licenseFile>LICENSE</licenseFile>
<input>target</input>
<mainJar>Halcyon-0.3.1.jar</mainJar>
<verbose>true</verbose>
<description>Whole Slide Imaging and Feature Management</description>
<installDir>\Halcyon</installDir>
<icon>src\main\resources\META-INF\halcyon.ico</icon>
<destination>target/dist</destination>
<type>dmg</type>
<javaOptions>
<option>--enable-preview</option>
<option>-Dfile.encoding=UTF-8</option>
</javaOptions>
</configuration>
</plugin>
</plugins>
</build>
Expand Down Expand Up @@ -233,10 +252,20 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.2.1</version>
<configuration>
<rules><dependencyConvergence/></rules>
</configuration>
<version>3.3.0</version>
<executions>
<execution>
<id>enforce</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<banDuplicatePomDependencyVersions/>
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<resources>
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/com/ebremer/halcyon/converters/HeatMap2OA.java
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Expand Up @@ -57,7 +57,7 @@ public HeatMap2OA(int cores) {
public void shutdown() {
System.out.println("All jobs submitted.");
int totaljobs = engine.getQueue().size()+engine.getActiveCount();
while (engine.getActiveCount()>0) {
while (!engine.isTerminated()) {
int c = engine.getQueue().size()+engine.getActiveCount();
long ram = (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/1024L/1024L;
System.out.println("jobs completed : "+(totaljobs-c)+" remaining jobs: "+c+" Total RAM used : "+ram+"MB Maximum RAM : "+(Runtime.getRuntime().maxMemory()/1024L/1024L)+"MB");
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2 changes: 2 additions & 0 deletions src/main/java/com/ebremer/halcyon/datum/DataCore.java
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Expand Up @@ -5,6 +5,7 @@
import static com.ebremer.halcyon.datum.DataCore.Level.CLOSED;
import com.ebremer.halcyon.filesystem.FileManager;
import com.ebremer.ns.HAL;
import org.apache.jena.assembler.Assembler;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
import org.apache.jena.query.Query;
Expand All @@ -15,6 +16,7 @@
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.riot.RDFDataMgr;
import org.apache.jena.riot.RDFFormat;
import org.apache.jena.tdb2.TDB2Factory;
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/com/ebremer/halcyon/imagebox/ImageServer.java
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Expand Up @@ -95,8 +95,8 @@ protected void doGet( HttpServletRequest request, HttpServletResponse response )
i.h = nt.GetHeight()-i.y;
}
}
String fileType = target.substring(target.lastIndexOf('.') + 1);
originalImage = nt.FetchImage(i.x, i.y, i.w, i.h, i.tx, i.tx, fileType);
//String fileType = target.substring(target.lastIndexOf('.') + 1);
originalImage = nt.FetchImage(i.x, i.y, i.w, i.h, i.tx, i.tx);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ServletOutputStream sos = response.getOutputStream();
if (i.imageformat == ImageFormat.JPG) {
Expand Down
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