Skip to content

Support for OME-ZARR input #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 21 commits into
base: main
Choose a base branch
from
Open

Support for OME-ZARR input #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
21 commits
Select commit Hold shift + click to select a range
1ede79e
A first attempt to partition 5d array
cgoina Jun 26, 2025
f0568a8
Refactored the CSV writing to output the correct channel and timepoin…
cgoina Jun 26, 2025
f92e550
suppress warnings
cgoina Jun 26, 2025
80fc18b
docker recipe; bump up version
cgoina Jun 26, 2025
a02fd8f
formatting
cgoina Jun 26, 2025
abc8d77
fixed condition
cgoina Jun 26, 2025
d7863f1
added comment
cgoina Jun 26, 2025
12b7e9b
message to be able to track the processing block easier
cgoina Jun 26, 2025
5813a18
updated jar reference in the README
cgoina Jun 26, 2025
cd5c5b3
use versions from pom-scijava-40.0.0
cgoina Jun 26, 2025
18ca964
use OME NGFF metadata to get axis info
cgoina Jun 30, 2025
d298dc6
update git hash in docker image
cgoina Jun 30, 2025
7603887
parameters for time and channel intervals
cgoina Jun 30, 2025
a06db09
parameter to exclude channels from RS-FISH
cgoina Jun 30, 2025
0a368ab
exclude log4j backends from dependencies
cgoina Jul 8, 2025
e1a45d0
add parameter for processed channels
cgoina Jul 11, 2025
f5cad2d
Added per channel RadialSym parameters
cgoina Sep 5, 2025
63f5b7b
updated build docker script
cgoina Sep 5, 2025
6a7f522
parameter for intensityMethod
cgoina Sep 5, 2025
991935b
changed the lookup to return the options not the index
cgoina Sep 5, 2025
ded148b
Short flag for intensityMethod; RadialSymParamsGroup made package pro…
cgoina Sep 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
.idea
target
dependency-reduced-pom.xml
23 changes: 23 additions & 0 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
ARG SPARK_VERSION=3.3.2-scala2.12-java17-ubuntu24.04
ARG RS_FISH_SPARK_GIT_HASH=a06db09

FROM ghcr.io/janeliascicomp/spark:${SPARK_VERSION}
ARG RS_FISH_SPARK_GIT_HASH

LABEL \
org.opencontainers.image.title="RS-FISH Spark" \
org.opencontainers.image.description="Spark version of RS-FISH" \
org.opencontainers.image.authors="[email protected],[email protected],[email protected]" \
org.opencontainers.image.licenses="GPL-2.0" \
org.opencontainers.image.version=${RS_FISH_SPARK_GIT_HASH}

USER root

RUN apt update -y; \
apt-get install -y \
libblosc1 libblosc-dev \
libzstd1 libzstd-dev libhdf5-dev;

WORKDIR /app
COPY LICENSE.txt /app/LICENSE.txt
COPY target/RS-FISH-Spark-0.0.2-SNAPSHOT-with-dependencies.jar /app/app.jar
6 changes: 3 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ The code to run the distributed, [Spark](http://spark.apache.org)-based RS-FISH
### Local execution <a name="local">
</a>

For **local execution** (comparable to efficient multi-threading), compile the repository using `mvn clean package`, which will create a **farjar** in the target directory called `RS-Fish-jar-with-dependencies.jar`. You can then execute the [RS-FISH class](https://github.com/PreibischLab/RS-FISH-Spark/blob/main/src/main/java/net/preibisch/rsfish/spark/SparkRSFISH.java) (for large volumes) or the [RS-FISH-IJ class](https://github.com/PreibischLab/RS-FISH-Spark/blob/main/src/main/java/net/preibisch/rsfish/spark/SparkRSFISH_IJ.java) (for many smaller images), for example:
For **local execution** (comparable to efficient multi-threading), compile the repository using `mvn clean package`, which will create a **farjar** in the target directory called `RS-FISH-Spark-0.0.2-SNAPSHOT-with-dependencies.jar`. You can then execute the [RS-FISH class](https://github.com/PreibischLab/RS-FISH-Spark/blob/main/src/main/java/net/preibisch/rsfish/spark/SparkRSFISH.java) (for large volumes) or the [RS-FISH-IJ class](https://github.com/PreibischLab/RS-FISH-Spark/blob/main/src/main/java/net/preibisch/rsfish/spark/SparkRSFISH_IJ.java) (for many smaller images), for example:

`java -cp target/RS-Fish-jar-with-dependencies.jar -Xmx20G -Dspark.master=local[8] net.preibisch.rsfish.spark.SparkRSFISH --image=/home/test.n5 --dataset=/N2/s0 --minIntensity=0 --maxIntensity=4096 --anisotropy=0.7 --output=points.csv`
`java -cp target/RS-FISH-Spark-0.0.2-SNAPSHOT-with-dependencies.jar -Xmx20G -Dspark.master=local[8] net.preibisch.rsfish.spark.SparkRSFISH --image=/home/test.n5 --dataset=/N2/s0 --minIntensity=0 --maxIntensity=4096 --anisotropy=0.7 --output=points.csv`

*Alternatively, you can import the project into Eclipse and run it from there.*

Expand Down Expand Up @@ -121,7 +121,7 @@ Click on Create cluster from the EMR dashboard.
* Spark-submit options: --class
* for N5 input: net.preibisch.rsfish.spark.aws.AWSSparkRSFISH
* For multiple tifs: net.preibisch.rsfish.spark.aws.RunAWSSparkRSFISHIJ
* Application location*: s3://preibischlab-release-jars/RS-Fish-jar-with-dependencies.jar
* Application location*: s3://preibischlab-release-jars/RS-FISH-Spark-0.0.2-SNAPSHOT-with-dependencies.jar
* Arguments: minimum task arguments for default params:
-i =< N5 container path in s3, e.g. -i s3://bucket-name/smFish.n5 -o, --output= output CSV file in S3, e.g. -o s3://rs-fish/embryo_5_ch0.csv -p, --path= The path of the input Data inside bucket e.g. -p N2-702-ch0/c0/s0 -pk, --publicKey= User public key (*previously created) -pp, --privateKey= User private key

Expand Down
25 changes: 25 additions & 0 deletions build-local-docker-image.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
#!/bin/bash

# Run this using `./build-docker-image.sh docker|podman --load|--push`

BUILD_CONTAINER_TOOL=$1
shift
GIT_HASH=f5cad2d

echo "Build RS-FISH:${GIT_HASH} container using ${BUILD_CONTAINER_TOOL}"

if [[ "${BUILD_CONTAINER_TOOL}" == "podman" ]] ; then
podman build \
--platform linux/arm64,linux/amd64 \
--tag ghcr.io/janeliascicomp/rs-fish-spark:${GIT_HASH} \
--build-arg RS_FISH_SPARK_GIT_HASH=${GIT_HASH} \
. \
$*
else
docker buildx build \
--platform linux/arm64,linux/amd64 \
--tag ghcr.io/janeliascicomp/rs-fish-spark:${GIT_HASH} \
--build-arg RS_FISH_SPARK_GIT_HASH=${GIT_HASH} \
. \
$*
fi
142 changes: 107 additions & 35 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>RS-FISH-Spark</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.0.2-SNAPSHOT</version>

<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>39.0.0</version>
<version>40.0.0</version>
<relativePath/>
</parent>

Expand Down Expand Up @@ -92,6 +92,7 @@
<!-- <scijava.jvm.version>1.8</scijava.jvm.version> -->
<license.licenseName>gpl_v2</license.licenseName>
<license.copyrightOwners>Developers.</license.copyrightOwners>

</properties>
<repositories>
<!-- NB: for project parent -->
Expand All @@ -118,12 +119,26 @@
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
</exclusion>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-universe</artifactId>
<!-- <version>1.4.1</version> -->
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-universe</artifactId>
<version>2.1.0</version>
<exclusions>
<exclusion>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
Expand All @@ -136,7 +151,16 @@
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-aws-s3</artifactId>
<!-- <version>4.0.0</version> -->
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
Expand All @@ -145,18 +169,18 @@
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.6.5</version>
<version>2.13.4</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<version>2.4.7</version>
<!-- Spark 3.3.2 comes with scala 2.12.15 -->
<artifactId>spark-core_2.12</artifactId>
<version>3.3.2</version>
<exclusions>
<exclusion>
<artifactId>netty-all</artifactId>
<artifactId>netty</artifactId>
<groupId>io.netty</groupId>
</exclusion>

<exclusion>
<artifactId>jcl-over-slf4j</artifactId>
<groupId>org.slf4j</groupId>
Expand All @@ -169,6 +193,10 @@
<artifactId>slf4j-log4j12</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>log4j-slf4j-impl</artifactId>
<groupId>org.apache.logging.log4j</groupId>
</exclusion>
<exclusion>
<artifactId>aopalliance-repackaged</artifactId>
<groupId>org.glassfish.hk2.external</groupId>
Expand All @@ -181,6 +209,10 @@
<artifactId>jersey-client</artifactId>
<groupId>org.glassfish.jersey.core</groupId>
</exclusion>
<exclusion>
<artifactId>jersey-core</artifactId>
<groupId>com.sun.jersey</groupId>
</exclusion>
<exclusion>
<artifactId>lz4</artifactId>
<groupId>net.jpountz.lz4</groupId>
Expand All @@ -196,48 +228,88 @@
</exclusions>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.12.15</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-all</artifactId>
<version>4.1.17.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty</artifactId>
<version>3.9.9.Final</version>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
</dependencies>
<groupId>net.preibisch</groupId>
<build>
<finalName>RS-Fish</finalName>
<plugins>

<!-- other Maven plugins ... -->

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>

<artifactId>maven-shade-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<shadedClassifierName>with-dependencies</shadedClassifierName>
<shadedArtifactAttached>true</shadedArtifactAttached>
<!-- Do not minimize for now to speed up packaging. -->
<transformers combine.children="append">
<transformer
implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/json/org.janelia.saalfeldlab.n5.Compression$CompressionType</resource>
</transformer>
</transformers>
<!--<minimizeJar>true</minimizeJar> -->
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>Angle0.tif</exclude>
<exclude>LICENSE</exclude>
<exclude>LICENSE.txt</exclude>
<exclude>META-INF/DEPENDENCIES</exclude>
<exclude>META-INF/LICENSE</exclude>
<exclude>META-INF/NOTICE</exclude>
<exclude>META-INF/BSDL</exclude>
<exclude>META-INF/COPYING</exclude>
<exclude>META-INF/LEGAL</exclude>
<exclude>META-INF/LICENSE.RUBY</exclude>
<exclude>META-INF/json/org.scijava.plugin.Plugin</exclude>
<exclude>META-INF/*.MF</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/*.txt</exclude>
<exclude>module-info.class</exclude>
<exclude>plugins.config</exclude>
<exclude>META-INF/versions/9/module-info.class</exclude>
<exclude>META-INF/okio.kotlin_module</exclude>
<exclude>META-INF/services/com.fasterxml.jackson.core.JsonFactory</exclude>
</excludes>
</filter>
</filters>
<!-- Additional configuration. -->
<artifactSet>
<excludes>
<exclude>xpp3:xpp3</exclude>
</excludes>
</artifactSet>
<relocations>
<relocation>
<pattern>org.apache.commons.compress</pattern>
<shadedPattern>org.janelia.saalfeldlab.org.apache.commons.compress</shadedPattern>
</relocation>
<!-- Protect newer gson version from the old one preloaded by spark -->
<relocation>
<pattern>com.google.gson</pattern>
<shadedPattern>org.janelia.saalfeldlab.com.google.gson</shadedPattern>
</relocation>
</relocations>
</configuration>

<!-- binds by default to package phase -->
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
<goal>shade</goal>
</goals>
</execution>
</executions>

</plugin>
</plugins>
</build>
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/net/preibisch/rsfish/spark/Block.java
View file
Open in desktop
Copy link
Member

@StephanPreibisch StephanPreibisch Jun 26, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hi @cgoina, I do not think changes to this class are necessary. We simply need to use Views.hyperslice() in the SparkRSFISH class ...

Copy link
Author

@cgoina cgoina Jun 26, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I had it like that initially but IMO these made the code in SparkRSFISH cleaner

Copy link
Member

@StephanPreibisch StephanPreibisch Jun 27, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why?

What I do not like is that statements like if ( d < 3 ) and return min.length > 3 ? Arrays.copyOf(min, 3) : min; do some "magic" depending on the input and are very fragile. What happens when I select a block size in c & t > 1?

I would like to keep it the way it is because a Block is a unit that computation is done on, which is either 2D or 3D.

Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ public static ArrayList< Block > splitIntoBlocks( final Interval interval, final
min.add( pos );
max.add( pos + Math.min( bs - 1, interval.max( d ) - pos ) );

pos += bs - 2; // one overlap, starts at the max - 2 since the most outer pixels are not evaluated with DoG
pos += bs - 2; // one overlap, starts at the max - 2 since the most outer pixels are not evaluated with DoG
++numBlocks[ d ];
}

Expand Down Expand Up @@ -92,7 +92,7 @@ public static void main( String[] args )
{
ArrayList< Block > blocks = splitIntoBlocks( new FinalInterval( new long[] { 19, -5 }, new long[] { 1000, 100 } ), new int[] { 100, 100 } );

for ( final Block b : blocks )
System.out.println( Util.printInterval( b.createInterval() ) );
for ( final Block b : blocks )
System.out.println( Util.printInterval( b.createInterval() ) );
}
}
Loading