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[wip] OpenOrganelle demo #518

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[wip] OpenOrganelle demo #518

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f4bfc8e
[wip] OpenOrganelle demo, super not working yet
kephale Jun 13, 2023
1e5b9d7
Merge branch 'master' into openorganelle-demo
kephale Jun 15, 2023
ed52d8a
Merge branch 'master' into openorganelle-demo
kephale Jun 15, 2023
8eb98af
Gradle: Bump scenery to 0.9.0, pom-scijava to 35.1.1, fix snakeyaml t…
skalarproduktraum Jun 16, 2023
174e8cb
Adjust for changed APIs in scenery 0.9.0
skalarproduktraum Jun 16, 2023
370c8da
SwingSwapchain/REPLPane: Do UI initialisation on EDT, initialise REPL…
smlpt Jun 16, 2023
9336272
Gradle: Bump to latest staging repo for scenery
skalarproduktraum Jun 16, 2023
bc95ffa
SwingNodePropertyEditor: Add TransferFunctionEditor for volumes
skalarproduktraum Jun 16, 2023
d119572
Merge branch 'master' into scenery-0.9.0
kephale Jun 17, 2023
f8df1ea
Merge branch 'openorganelle-demo' into scenery-0.9.0
kephale Jun 17, 2023
7ad8a24
[wip] Exception with OpenOrganelle, memory overflow
kephale Jun 18, 2023
38fd97c
Add Java demo, this is where the actual demo is being developed
kephale Jun 18, 2023
523f5ed
Still exit code = 134, but add conversion to UnsignedShortType
kephale Jun 18, 2023
5a3d0ea
[wip] trying Converters stuck on bug
kephale Jun 19, 2023
abb16a0
Add Tobi's conversion method
kephale Jun 20, 2023
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48 changes: 33 additions & 15 deletions build.gradle.kts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ import java.net.URL
import sciview.*

plugins {
val ktVersion = "1.8.20"
val ktVersion = "1.8.22"
val dokkaVersion = "1.8.20"

java
Expand All @@ -25,43 +25,50 @@ java {
}

repositories {
if(project.properties["useMavenLocal"] == "true") {
logger.warn("Using local Maven repository as source")
mavenLocal()
}

mavenCentral()
maven("https://oss.sonatype.org/content/repositories/graphicsscenery-1222")
maven("https://maven.scijava.org/content/groups/public")
mavenLocal()
}

dependencies {
val ktVersion = "1.8.20"
implementation(platform("org.scijava:pom-scijava:31.1.0"))
val ktVersion = "1.8.22"
implementation(platform("org.scijava:pom-scijava:35.1.1"))

// Graphics dependencies

annotationProcessor("org.scijava:scijava-common:2.90.0")
kapt("org.scijava:scijava-common:2.90.0") { // MANUAL version increment
// Attention! Manual version increment necessary here!
val scijavaCommonVersion = "2.94.1"
annotationProcessor("org.scijava:scijava-common:$scijavaCommonVersion")
kapt("org.scijava:scijava-common:$scijavaCommonVersion") {
exclude("org.lwjgl")
}

val sceneryVersion = "0.8.0"
val sceneryVersion = "0.9.0"
api("graphics.scenery:scenery:$sceneryVersion") {
version { strictly(sceneryVersion) }
exclude("org.biojava.thirdparty", "forester")
exclude("null", "unspecified")
}

implementation("com.fasterxml.jackson.core:jackson-databind:2.13.4.2")
implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.13.4")
implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.4")
implementation("org.msgpack:jackson-dataformat-msgpack:0.9.3")
implementation("net.java.dev.jna:jna-platform:5.11.0")
implementation("net.clearvolume:cleargl")
implementation("org.janelia.saalfeldlab:n5")
implementation("org.janelia.saalfeldlab:n5-imglib2")
implementation("org.apache.logging.log4j:log4j-api:2.20.0")
implementation("org.apache.logging.log4j:log4j-1.2-api:2.20.0")

implementation("com.formdev:flatlaf:2.6")
implementation("com.formdev:flatlaf")

// SciJava dependencies

implementation("org.yaml:snakeyaml") {
version { strictly("1.33") }
}
implementation("org.scijava:scijava-common")
implementation("org.scijava:ui-behaviour")
implementation("org.scijava:script-editor")
Expand All @@ -84,8 +91,9 @@ dependencies {
implementation("io.scif:scifio-bf-compat")

// ImgLib2 dependencies
implementation("net.imglib2:imglib2")
implementation("net.imglib2:imglib2:6.2.0")
implementation("net.imglib2:imglib2-roi")
implementation("net.imglib2:imglib2-algorithm:0.14.0")

// XDG support
implementation("dev.dirs:directories:26")
Expand All @@ -110,15 +118,23 @@ dependencies {
// implementation(n5.imglib2)
implementation("org.janelia.saalfeldlab:n5")
implementation("org.janelia.saalfeldlab:n5-hdf5")
implementation("org.janelia.saalfeldlab:n5-ij:3.2.4-SNAPSHOT")
implementation("org.janelia.saalfeldlab:n5-imglib2:5.0.0")
implementation("org.janelia.saalfeldlab:n5-viewer_fiji:5.3.0")
//implementation("com.github.saalfeldlab:n5-viewer:ec0b177")
implementation("org.janelia.saalfeldlab:n5-aws-s3")
implementation("org.janelia.saalfeldlab:n5-google-cloud")
implementation("org.janelia.saalfeldlab:n5-blosc")
implementation("org.janelia.saalfeldlab:n5-zarr")
implementation("sc.fiji:spim_data")

implementation(platform(kotlin("bom")))
implementation(kotlin("stdlib-jdk8"))
testImplementation(kotlin("test-junit"))
testImplementation("org.slf4j:slf4j-simple:1.7.36")

implementation("sc.fiji:bigdataviewer-core")
implementation("sc.fiji:bigdataviewer-vistools")
implementation("sc.fiji:bigdataviewer-core:10.4.7")
implementation("sc.fiji:bigdataviewer-vistools:1.0.0-beta-32")

// OME
implementation("ome:formats-bsd")
Expand Down Expand Up @@ -435,5 +451,7 @@ artifacts {
archives(dokkaHtmlJar)
}



java.withSourcesJar()

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