Category: Uncategorized

After you cloned this repository:

git@github.com:scijava/scijava-scripts.git

The following sequence of steps will make you happy:

ssh code.imagej.net

Then I stopped this because I had no user on code.imagej.net. So sad!

Annoyed by mvn throwing tons of javadoc errors? Some of those might be fixed with:

Removing mail addresses from @author:
sed -i '' -e 's/\(@author .*\) [<(].*[)>] *$/\1/' $(git grep -l '@author')
sed -i '' -e 's/\(@author .*\) &lt;.*&gt; *$/\1/' $(git grep -l '@author')

This is mostly a not to self… please do not expect a human-readable post… 😉

To prevent the decay of knowledge my brain is suffering I note here how things should run:

• Follow instructions from README here: https://github.com/knime/knime-sdk-setup
  • Once you double click KNIME.target, add the following update sites and select KNIME Image Processing in both of them
    • http://update.knime.org/community-contributions/trusted/3.4
    • http://update.knime.org/community-contributions/3.4
  • Wait until workspace is built (see bottom right in Eclipse), then click ‘Set as Target Platform’ on the top right.
  • In Arguments tab, set a more reasonable value for Xmx (default is 2G).
• We then cloned and imported https://github.com/knime-ip/knip into Eclipse.
  • Here the clone URL: git@github.com:knime-ip/knip.git
  • Then import all projects within this repo into Eclipse.

Here some notes on how to implement on Clear Volume from this setup:

• Import imglib-clearvolume into eclipse. This is easy, its a Maven plugin.
• You need to also install clearvolume, cleargl, and clearcuda. This is harder since those are Gradle projects…
  • One option is to first install the Eclipse Gradle plugin, if you installed Eclipse 3.4, it would be on this update site: http://download.eclipse.org/buildship/updates/e46/releases/2.x
  • Then you can import Existing Gradle Projects (the ones named above).
  • Since this Gradle Eclipse plugin sucked for me I used this: http://www.thejavageek.com/2015/05/22/create-eclipse-project-with-gradle/
    • Loic supported it already I guess since gradle eclipse just did the right thing.
    • After it you can import project as existing Eclipse project.
• Gradle magic to remember
  • Use the gradlew script instead of cradle itself. This is how it works is what I’ve been told…
  • ./gradlew clean build -Preleasebuild … building ClearVolume release version
  • ./gradlew collectDependencies … does what you would expect. Can then be found in ./build/dependecies
• Maven magic to remember
  • `mvn dependency:copy-dependencies` allows you to collect all dependencies of a given maven project.
    • note: this needs you to add the `maven-dependency-plugin` to the pom.xml (google it).

This post will grow within the next couple of weeks.

After the DAIS Learnathon 2017 it will contain a list of links to teaching material, tutorials, and examples.

Best,
your DAIS team