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Curtis Rueden ctrueden

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@ctrueden
ctrueden / notes.groovy
Created Oct 15, 2020
2020-10-15 ImageJ2.js meeting notes
View notes.groovy
#@ CommandService cs
#@ ModuleService ms
#@ ScriptService ss
modules = ms.getModules() // get all modules!
future = ms.run(modules[0], true, listOrMapOfArguments)
// if you want to block till completion:
m = future.get()
outputs = m.getOutputs() // is a dict
View imagej-js.pom
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 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>
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>29.2.0</version>
<relativePath />
</parent>
View gh-pages-packages.log
$ conda create -n gh-pages rb-github-pages
...
$ conda activate gh-pages
$ conda list
# packages in environment at /usr/local/miniconda3/envs/gh-pages:
#
# Name Version Build Channel
ca-certificates 2019.6.16 hecc5488_0 conda-forge
gdbm 1.18 h0da4bb5_1 conda-forge
gettext 0.19.8.1 h46ab8bc_1002 conda-forge
View obsolete-N5-files.txt
jars/api-common-1.8.1.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/api-common-1.9.0.jar)
jars/auto-value-annotations-1.7.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/auto-value-annotations-1.7.jar)
jars/aws-java-sdk-core-1.11.719.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/aws-java-sdk-core-1.11.796.jar)
jars/aws-java-sdk-kms-1.11.719.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/aws-java-sdk-kms-1.11.796.jar)
jars/aws-java-sdk-s3-1.11.719.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/aws-java-sdk-s3-1.11.796.jar)
jars/commons-compress-1.19.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/commons-compress-1.20.jar)
jars/error_prone_annotations-2.3.4.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/error_prone_annotations-2.3.4.jar)
jars/gax-1.54.0.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/gax-1.56.0.jar)
jars/gax-httpjson-0.71.0.jar -- IS OBSOLETE (Java-8 file is: Fiji-Pristine.app/jars/gax-httpjson-0.73.
@ctrueden
ctrueden / failures.txt
Last active Jul 15, 2020
Full scan of all JARs on update.imagej.net, update.fiji.sc and sites.imagej.net
View failures.txt
2 ca.mcgill:Sholl_Analysis:3.6.13
1 ca.mcgill:Sholl_Analysis:3.6.2
1 ca.mcgill:Sholl_Analysis:3.7.4
1 ca.mcgill:Sholl_Analysis:4.0.1
1 ch.unibas.biozentrum.imcf:imcf-fiji-toolbars:2.0.2
24 com.github.jeanollion.bacmman:bacmman-core:2.2.4
2 com.github.jeanollion.bacmman:bacmman-core:2.2.5
5 com.github.jeanollion.bacmman:bacmman-core:2.2.9
2 com.github.jeanollion.bacmman:bacmman-core:v2.2.1
1 com.github.jeanollion.bacmman:bacmman-core:v2.2.2
@ctrueden
ctrueden / a.diff
Created Jul 14, 2020
mega-melt discrepancies
View a.diff
diff --git a/curtis-deps.txt b/tobias-deps.txt
index 11c28a1..cd26f14 100644
--- a/curtis-deps.txt
+++ b/tobias-deps.txt
@@ -111,6 +111,71 @@
[INFO] +- net.imagej:imagej-notebook:jar:0.7.1:compile
[INFO] | \- org.knowm.xchart:xchart:jar:3.5.4:compile
[INFO] | \- de.erichseifert.vectorgraphics2d:VectorGraphics2D:jar:0.13:compile
+[INFO] +- net.imagej:imagej-omero:jar:0.8.1:compile
+[INFO] | \- omero:blitz:jar:5.4.9-ice36-b101:compile
@ctrueden
ctrueden / LUT_Detection.groovy
Created Jun 23, 2020
Which LUTs is my image using?
View LUT_Detection.groovy
#@ LUTService lut
#@ DatasetView dv
#@ boolean verbose
def printColorTable = { t ->
if (t == null) {
println(" null")
return
}
for (comp = 0; comp < t.getComponentCount(); comp++) {
@ctrueden
ctrueden / locations.txt
Last active Jun 19, 2020
Where is libjvm in various JDKs?
View locations.txt
$ for f in *.tar.gz
do
echo
echo "[$f]"
result=$(tar tf "$f" | grep -i 'jvm\.\(dll\|dylib\|so\)$')
test "$result" && echo "$result" || echo "--> NOTHING FOUND"
done; for f in *.zip
do
echo
echo "[$f]"
@ctrueden
ctrueden / adoptopenjdk-11-1-JVMCI.log
Last active Jun 16, 2020
net.imglib2.img.DirtyVolatileBenchmark
View adoptopenjdk-11-1-JVMCI.log
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.openjdk.jmh.util.Utils (file:/Users/curtis/code/imglib/imglib2/target/dependency/jmh-core-1.19.jar) to field java.io.PrintStream.charOut
WARNING: Please consider reporting this to the maintainers of org.openjdk.jmh.util.Utils
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
# JMH version: 1.19
# VM version: JDK 11.0.2, VM 11.0.2+9
# VM invoker: /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home/bin/java
# VM options: -XX:+UnlockExperimentalVMOptions -XX:+EnableJVMCI -XX:+UseJVMCICompiler
# Warmup: 4 iterations, 200 ms each
@ctrueden
ctrueden / scifio.py
Last active Aug 31, 2020
Open images as numpy arrays using SCIFIO and Bio-Formats
View scifio.py
#!/usr/bin/env python
#
# scifio.py - Open images as numpy arrays using SCIFIO and Bio-Formats.
#
# -- Settings --
max_mem_mb = '6144'
scifio_lifesci = False
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