Merge branch 'ebremer:master' into master

SBU-BMI · May 18, 2023 · c5e12ca · c5e12ca
2 parents 68fb6c3 + 7b36400
commit c5e12ca
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Hatch
+# Hatch 3.0.0
 
 This tool converts the largest image in a VSI, SVS, or TIF image into a new TIFF image with a freshly created image pyramid with each scaling 1/2 dimensions each scale.
 
@@ -12,15 +12,16 @@ Features:
 
 Usage:
 ```
-hatch <src> <dest>
+hatch -src <src> -dest <dest>
+
+or see
+
+hatch -help
 ```
 
 Credits and Acknowledgements:
 Many of the core files are modified files from the OME Bioformats Projects (https://github.com/ome/bioformats) such as (but not limited to):
 CellSensReader
-OMETiffWriter
 TiffCompression
 TiffParser
-TiffSaver
-TiffWriter
 
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>edu.stonybrook.bmi</groupId>
  <artifactId>hatch</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0</version>
  <build>
  <resources>
  <resource>
@@ -29,11 +29,19 @@
  <plugin>
  <artifactId>maven-enforcer-plugin</artifactId>
  <version>3.3.0</version>
- <configuration>
- <rules>
- <dependencyConvergence />
- </rules>
- </configuration>
+ <executions>
+ <execution>
+ <id>enforce</id>
+ <goals>
+ <goal>enforce</goal>
+ </goals>
+ <configuration>
+ <rules>
+ <banDuplicatePomDependencyVersions />
+ </rules>
+ </configuration>
+ </execution>
+ </executions>
  </plugin>
  <plugin>
  <artifactId>maven-shade-plugin</artifactId>
@@ -108,23 +116,21 @@
  <id>build-native</id>
  <phase>package</phase>
  <goals>
- <goal>build</goal>
+ <goal>compile-no-fork</goal>
  </goals>
  </execution>
  </executions>
  <configuration>
  <imageName>hatch</imageName>
  <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
  <debug>true</debug>
- <skipNativeBuild>true</skipNativeBuild>
  <skipNativeTests>true</skipNativeTests>
  <verbose>true</verbose>
  <buildArgs>
  <buildArg>--no-fallback</buildArg>
  <buildArg>-H:ConfigurationFileDirectories=config</buildArg>
  <buildArg>--enable-url-protocols=https</buildArg>
  <buildArg>-H:+AddAllCharsets</buildArg>
- <buildArg>--static</buildArg>
  </buildArgs>
  </configuration>
  </plugin>

diff --git a/ha.txt b/ha.txt
@@ -0,0 +1,63 @@
+[INFO] edu.stonybrook.bmi:hatch:jar:3.0.0
+[INFO] +- ome:formats-gpl:jar:6.12.0:compile
+[INFO] | +- org.openmicroscopy:ome-common:jar:6.0.14:compile
+[INFO] | | +- io.minio:minio:jar:5.0.2:compile
+[INFO] | | | +- com.google.http-client:google-http-client-xml:jar:1.20.0:compile
+[INFO] | | | | +- com.google.http-client:google-http-client:jar:1.20.0:compile
+[INFO] | | | | | \- org.apache.httpcomponents:httpclient:jar:4.0.1:compile
+[INFO] | | | | | \- org.apache.httpcomponents:httpcore:jar:4.0.1:compile
+[INFO] | | | | \- xpp3:xpp3:jar:1.1.4c:compile
+[INFO] | | | +- com.squareup.okhttp3:okhttp:jar:3.7.0:compile
+[INFO] | | | \- com.squareup.okio:okio:jar:1.12.0:compile
+[INFO] | | +- com.fasterxml.jackson.core:jackson-databind:jar:2.14.1:compile
+[INFO] | | | \- com.fasterxml.jackson.core:jackson-core:jar:2.14.1:compile
+[INFO] | | +- com.fasterxml.jackson.core:jackson-annotations:jar:2.14.1:compile
+[INFO] | | +- com.google.guava:guava:jar:29.0-jre:compile
+[INFO] | | | +- com.google.guava:failureaccess:jar:1.0.1:compile
+[INFO] | | | +- com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava:compile
+[INFO] | | | +- com.google.code.findbugs:jsr305:jar:3.0.2:compile
+[INFO] | | | +- org.checkerframework:checker-qual:jar:2.11.1:compile
+[INFO] | | | +- com.google.errorprone:error_prone_annotations:jar:2.3.4:compile
+[INFO] | | | \- com.google.j2objc:j2objc-annotations:jar:1.3:compile
+[INFO] | | +- xalan:serializer:jar:2.7.2:runtime
+[INFO] | | \- xalan:xalan:jar:2.7.2:runtime
+[INFO] | +- org.openmicroscopy:ome-xml:jar:6.3.2:compile
+[INFO] | | \- org.openmicroscopy:specification:jar:6.3.2:compile
+[INFO] | +- ome:formats-bsd:jar:6.12.0:compile
+[INFO] | | +- org.openmicroscopy:ome-codecs:jar:0.4.4:compile
+[INFO] | | | +- org.openmicroscopy:ome-jai:jar:0.1.3:compile
+[INFO] | | | \- io.airlift:aircompressor:jar:0.21:compile
+[INFO] | | +- ome:turbojpeg:jar:6.12.0:compile
+[INFO] | | +- org.scijava:native-lib-loader:jar:2.1.4:compile
+[INFO] | | +- com.jgoodies:jgoodies-forms:jar:1.7.2:compile
+[INFO] | | | \- com.jgoodies:jgoodies-common:jar:1.7.0:compile
+[INFO] | | +- commons-lang:commons-lang:jar:2.6:compile
+[INFO] | | +- org.perf4j:perf4j:jar:0.9.16:compile
+[INFO] | | +- cisd:jhdf5:jar:19.04.0:compile
+[INFO] | | | +- cisd:base:jar:18.09.0:compile
+[INFO] | | | +- commons-io:commons-io:jar:2.7:compile
+[INFO] | | | \- org.apache.commons:commons-lang3:jar:3.10:compile
+[INFO] | | +- com.drewnoakes:metadata-extractor:jar:2.18.0:compile
+[INFO] | | | \- com.adobe.xmp:xmpcore:jar:6.1.11:compile
+[INFO] | | +- ome:jxrlib-all:jar:0.2.4:compile
+[INFO] | | +- xerces:xercesImpl:jar:2.12.2:compile
+[INFO] | | +- xml-apis:xml-apis:jar:1.4.01:compile
+[INFO] | | \- org.yaml:snakeyaml:jar:1.32:compile
+[INFO] | +- ome:formats-api:jar:6.12.0:compile
+[INFO] | +- org.openmicroscopy:ome-mdbtools:jar:5.3.2:compile
+[INFO] | +- org.openmicroscopy:metakit:jar:5.3.5:compile
+[INFO] | +- org.openmicroscopy:ome-poi:jar:5.3.7:compile
+[INFO] | | \- commons-logging:commons-logging:jar:1.2:compile
+[INFO] | +- org.slf4j:slf4j-api:jar:1.7.30:compile
+[INFO] | +- woolz:JWlz:jar:1.4.0:compile
+[INFO] | +- joda-time:joda-time:jar:2.2:compile
+[INFO] | +- com.esotericsoftware:kryo:jar:4.0.2:compile
+[INFO] | | +- com.esotericsoftware:reflectasm:jar:1.11.3:compile
+[INFO] | | | \- org.ow2.asm:asm:jar:5.0.4:compile
+[INFO] | | +- com.esotericsoftware:minlog:jar:1.3.0:compile
+[INFO] | | \- org.objenesis:objenesis:jar:2.5.1:compile
+[INFO] | +- org.json:json:jar:20090211:compile
+[INFO] | \- org.xerial:sqlite-jdbc:jar:3.28.0:compile
+[INFO] +- com.beust:jcommander:jar:1.82:compile
+[INFO] \- com.github.jai-imageio:jai-imageio-jpeg2000:jar:1.4.0:compile
+[INFO] \- com.github.jai-imageio:jai-imageio-core:jar:1.4.0:compile
diff --git a/nbactions-hatchjar.xml b/nbactions-hatchjar.xml
@@ -12,7 +12,7 @@
  <properties>
  <exec.vmArgs></exec.vmArgs>
  <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
- <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
+ <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
  <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
  <exec.executable>java</exec.executable>
  </properties>
@@ -29,7 +29,7 @@
  <properties>
  <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
  <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
- <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
+ <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
  <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
  <exec.executable>java</exec.executable>
  <jpda.listen>true</jpda.listen>
@@ -49,7 +49,7 @@
  <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
  <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
  <exec.executable>java</exec.executable>
- <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
+ <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
  </properties>
  </action>
  </actions>
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>edu.stonybrook.bmi</groupId>
  <artifactId>hatch</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0</version>
  <packaging>jar</packaging>
  <properties>
  <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -29,12 +29,23 @@
  <artifactId>jcommander</artifactId>
  <version>1.82</version>
  </dependency>
+ <!--
  <dependency>
  <groupId>org.apache.jena</groupId>
  <artifactId>jena-core</artifactId>
- <version>4.7.0</version>
+ <version>4.8.0</version>
  <type>jar</type>
+ </dependency> 
+ <dependency>
+ <groupId>com.github.jai-imageio</groupId>
+ <artifactId>jai-imageio-core</artifactId>
+ <version>1.4.0</version>
  </dependency>
+ <dependency>
+ <groupId>com.github.jai-imageio</groupId>
+ <artifactId>jai-imageio-jpeg2000</artifactId>
+ <version>1.4.0</version>
+ </dependency>-->
  </dependencies>
  <build>
  <resources>
@@ -76,9 +87,19 @@
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-enforcer-plugin</artifactId>
  <version>3.3.0</version>
- <configuration>
- <rules><dependencyConvergence/></rules>
- </configuration>
+ <executions>
+ <execution>
+ <id>enforce</id>
+ <goals>
+ <goal>enforce</goal>
+ </goals>
+ <configuration>
+ <rules>
+ <banDuplicatePomDependencyVersions/>
+ </rules>
+ </configuration>
+ </execution>
+ </executions>
  </plugin>
  <plugin>
  <groupId>org.apache.maven.plugins</groupId>
@@ -131,7 +152,7 @@
  <execution>
  <id>build-native</id>
  <goals>
- <goal>build</goal>
+ <goal>compile-no-fork</goal>
  </goals>
  <phase>package</phase>
  </execution>
@@ -140,7 +161,6 @@
  <imageName>hatch</imageName>
  <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
  <debug>true</debug>
- <skipNativeBuild>true</skipNativeBuild>
  <skipNativeTests>true</skipNativeTests>
  <verbose>true</verbose>
  <buildArgs>

diff --git a/src/main/java/edu/stonybrook/bmi/hatch/BaseTiffReader.java b/src/main/java/edu/stonybrook/bmi/hatch/BaseTiffReader.java
@@ -95,6 +95,11 @@ protected void initMetadata() throws FormatException, IOException {
  initStandardMetadata();
  initMetadataStore();
  }
+
+ @Override
+ public IFDList getIFDs() {
+ return ifds;
+ }
 
  /**
  * Parses standard metadata.

diff --git a/src/main/java/edu/stonybrook/bmi/hatch/Bug2022.java b/src/main/java/edu/stonybrook/bmi/hatch/Bug2022.java
@@ -1,7 +1,3 @@
-/*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
- */
 package edu.stonybrook.bmi.hatch;
 
 /**