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StephanPreibischStephanPreibisch
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Merge branch 'main' of github.com:JaneliaSciComp/BigStitcher-Spark
2 parents 1144bcc + 44aa470 commit 2a6d219

29 files changed

+1179
-1016
lines changed

‎install

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Original file line numberDiff line numberDiff line change
@@ -81,7 +81,7 @@ else
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fi
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VERSION="0.0.2-SNAPSHOT"
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VERSION="0.1.0-SNAPSHOT"
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INSTALL_DIR=$(pwd)
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#INSTALL_DIR=${1:-$(pwd)}
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@@ -129,6 +129,7 @@ install_command nonrigid-fusion "net.preibisch.bigstitcher.spark.SparkNonRigidFu
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echo 'Installing utils ...'
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install_command split-images "net.preibisch.bigstitcher.spark.SplitDatasets"
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install_command downsample "net.preibisch.bigstitcher.spark.SparkDownsample"
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install_command clear-interestpoints "net.preibisch.bigstitcher.spark.ClearInterestPoints"
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install_command clear-registrations "net.preibisch.bigstitcher.spark.ClearRegistrations"

‎pom.xml

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@@ -6,13 +6,13 @@
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
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<version>37.0.0</version>
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<version>39.0.0</version>
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<relativePath/>
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</parent>
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<groupId>net.preibisch</groupId>
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<artifactId>BigStitcher-Spark</artifactId>
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<version>0.0.2-SNAPSHOT</version>
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<version>0.1.0-SNAPSHOT</version>
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<name>BigStitcher Spark</name>
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<description>Spark-based parallel BigStitcher project.</description>
@@ -83,9 +83,31 @@
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<package-name>net.preibisch.bigstitcher.spark</package-name>
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<!-- <scijava.jvm.version>1.8</scijava.jvm.version> -->
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<license.licenseName>gpl_v2</license.licenseName>
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<license.licenseName>bsd</license.licenseName>
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<license.copyrightOwners>Developers.</license.copyrightOwners>
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<!--
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<imglib2.version>7.1.2</imglib2.version>
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<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
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<imglib2-cache.version>1.0.0-beta-19</imglib2-cache.version>
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<imglib2-algorithm.version>0.16.0</imglib2-algorithm.version>
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<imglib2-roi.version>0.15.1</imglib2-roi.version>
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<n5-imglib2.version>7.0.2</n5-imglib2.version>
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<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
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<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
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-->
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<!-- <n5-zarr.version>1.3.5</n5-zarr.version> -->
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<bigdataviewer-core.version>10.6.3</bigdataviewer-core.version>
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<spim_data.version>2.3.5</spim_data.version>
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<multiview-reconstruction.version>5.0.0</multiview-reconstruction.version>
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<BigStitcher.version>2.3.0</BigStitcher.version>
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<!--for the old bioformats to work properly (compared with old main branch to find out)-->
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<ome-codecs.version>0.3.0</ome-codecs.version>
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</properties>
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<repositories>
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<!-- NB: for project parent -->
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<repository>
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>bigdataviewer-core</artifactId>
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<version>10.4.6</version>
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<!-- <version>10.4.6</version> -->
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</dependency>
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>bigdataviewer-vistools</artifactId>
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<version>1.0.0-beta-32</version>
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<!-- <version>1.0.0-beta-32</version> -->
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2-cache</artifactId>
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<version>1.0.0-beta-17</version>
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<!-- <version>1.0.0-beta-17</version> -->
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2</artifactId>
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<version>6.3.0</version>
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<!-- <version>6.3.0</version> -->
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2-algorithm</artifactId>
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<version>0.15.0</version>
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<!-- <version>0.15.0</version> -->
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</dependency>
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<dependency>
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<groupId>org.bigdataviewer</groupId>
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<artifactId>bigdataviewer-n5</artifactId>
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<version>1.0.1</version>
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<exclusions>
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<exclusion>
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<groupId>javax.annotation</groupId>
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<artifactId>javax.annotation-api</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>spim_data</artifactId>
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</dependency>
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<dependency>
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<!-- <dependency>
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<groupId>com.amazonaws</groupId>
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<artifactId>aws-java-sdk-s3</artifactId>
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<version>${aws-java-sdk-s3.version}</version>
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</dependency>
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<dependency>
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</dependency> -->
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<!-- <dependency>
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<groupId>org.bigdataviewer</groupId>
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<artifactId>bigdataviewer-omezarr</artifactId>
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<version>0.2.3</version>
139-
</dependency>
172+
</dependency> -->
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5</artifactId>
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<version>3.1.3</version>
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</dependency>
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5-zarr</artifactId>
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<version>1.2.1</version>
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</dependency>
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5-aws-s3</artifactId>
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<version>4.0.0</version>
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<!-- <version>4.0.0</version> -->
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</dependency>
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<!-- Scala is sensitive to fasterxml version -->
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<dependency>
@@ -227,7 +258,6 @@
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<dependency>
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<groupId>net.preibisch</groupId>
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<artifactId>multiview-reconstruction</artifactId>
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<version>3.2.12</version>
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<exclusions>
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<exclusion>
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<groupId>ch.epfl.biop</groupId>
@@ -268,12 +298,11 @@
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5-hdf5</artifactId>
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<version>2.0.0</version>
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<!-- <version>2.0.0</version> -->
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</dependency>
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5-imglib2</artifactId>
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<version>5.0.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/net.java.dev.jna/jna needed for M1 native library loading -->
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<dependency>
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<dependency>
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<groupId>net.preibisch</groupId>
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<artifactId>BigStitcher</artifactId>
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<version>1.2.11</version>
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<exclusions>
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<exclusion>
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<groupId>ch.epfl.biop</groupId>
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308336
</exclusion>
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</exclusions>
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</dependency>
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<!-- old bioformats -->
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<dependency>
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<groupId>org.openmicroscopy</groupId>

‎src/main/java/net/preibisch/bigstitcher/spark/ClearInterestPoints.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -105,7 +105,7 @@ public Void call() throws Exception
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System.out.println( "Saving XML (metadata only) ..." );
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dataGlobal.getViewInterestPoints().getViewInterestPoints().clear();
108-
new XmlIoSpimData2( null ).save( dataGlobal, xmlPath );
108+
new XmlIoSpimData2().save( dataGlobal, xmlURI );
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System.out.println( "Removing interest point directory '" + file + "' ... " );
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‎src/main/java/net/preibisch/bigstitcher/spark/ClearRegistrations.java

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Original file line numberDiff line numberDiff line change
@@ -101,7 +101,7 @@ else if ( keep != null )
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if ( !dryRun )
102102
{
103103
System.out.println( "Saving XML ..." );
104-
new XmlIoSpimData2( null ).save( dataGlobal, xmlPath );
104+
new XmlIoSpimData2().save( dataGlobal, xmlURI );
105105
}
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return null;

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