search

embl-cba / cats

Other
1 stars 2 forks source link

Using Java API in FIJI Windows #3

Open davodogster opened 5 years ago

davodogster commented 5 years ago

I tried to run the JAVA01API.java and the other scripts in that folder but the console always throws an error: No javac.jar found (looked in C:\Users\sam\Desktop\FIJI\FIJI-W~1\Fiji.app\jars)!

tischi commented 5 years ago

Yes, this is normal, because one cannot run Java code in Fiji anymore (this used to be possible some years back). If you are still interested in the scripting option I would have to make some Groovy or Jython examples for you. Shall i do it?

davodogster commented 5 years ago

So the Java code you wrote is meant to be run in an IDE and then I import the ImageJ modules/packages? A bit of Jython Script would be awesome. Sam

tischi commented 5 years ago

Ok. I will do it!

davodogster commented 5 years ago

How do I efficiently train a classifier on multiple images. E.g a 4 channel stack for 8 different images.

Another suggestion which would be extremely helpful - allow the user to have an RGB image as the first layer in the multi layer stack so that they can annotate it with confidence ( annotating an HSB/LAB stack etc can be difficult without colour ) But when computing the features, obviously don’t compute the features for the first layer because it’s not in grayscale. I hope you understand what I mean here as I think something like this will be really helpful.

Regards,

Sam

Get Outlook for iOShttps://aka.ms/o0ukef

From: tischi notifications@github.com Sent: Thursday, May 9, 2019 9:00:42 PM To: embl-cba/fiji-plugin-cats Cc: Sam Davidson; Author Subject: Re: [embl-cba/fiji-plugin-cats] Using Java API in FIJI Windows (#3)

Ok. I will do it!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/embl-cba/fiji-plugin-cats/issues/3#issuecomment-490820272, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK7R4HFXL7OCIWWISK3MKDDPUPR3VANCNFSM4HLDMUAA.

tischi commented 5 years ago

Hi Sam, I opened new issues for your two new requests. Could you please do the same in the future. I have so many projects, I really have to try to be organised to keep track :-)

tischi commented 5 years ago

Hi Sam,

Please

  1. update your Fiji, and
  2. try using below groovy script:

https://raw.githubusercontent.com/embl-cba/fiji-plugin-cats/master/src/test/java/headless/RunHeadlessBatchClassificationCommand.groovy

davodogster commented 5 years ago

Thanks a lot will give it a go. Yes will raise new issues in the future.

Sam