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Problem with Photomonitoring Plugin on Fiji

by silvanhi | September 24, 2014 18:51 | 2,176 views | 8 comments | #11182 | 2,176 views | 8 comments | #11182 24 Sep 18:51

Read more: publiclab.org/n/11182


What I want to do

I'd like to import the .lut files of Ned Hornings PhotoMonitoring plugin on my mac.

My attempt and results

I want to produce and analyse NDVI images. I did manage to run the plugin on windows but I changed to Mac recently.

Questions and next steps

In the Photo monitoring description it says that I have to copy the files into the proper file directory of the "fiji.app". Unfortunately I cant find this directory on my Mac. Also the app itself is named as "fiji" and not as "fiji.app". Can somebody help me on that subject?


8 Comments

I created a directory in my root and put everything there, then opened Fiji and registered the plugins manually:

Plugins -> Install Plugin -> 'file'.

The files are Photo_Monitoring.jar, metadata-extractor-2.6.2.jar, and xmpcore.jar. I registered each separately. I guess someday I should figure out where the installer puts everything.

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But the .lut files aren't included in your approach, are they?

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Good question. There are some luts in a separate directory on Github that I didn't grab. Once you install the plugins you'll see an added option 'Photo Monitoring' under Plugins, in Fiji. There are four options: 'Create dual image list', 'Dual image image processing', 'Single image index processing from directory', Single image index processing from displayed image'.

Put your NIR and RGB images in separate directories (don't ask me why, it just likes it that way) and run 'Create dual image list'. This writes a text file with paths to the two images. Next, run 'Dual image index processing', which asks you where the text file created in step 1 is. This loads the file and in that step you'll be presented with a screen that provides a dozen or so luts for processing, in a drop down. There's a bunch of other options in that screen so you'll need to look for it.

I didn't need to download the luts from Github. This suggests (again) that I should probably figure out where the installer puts everything since I'd like to have them.

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Thanks for your response.. I did manage it to work it like you describe. my only problem is that I want to use the "NDVIblue2red.lut" which is in the folder from github. In the readme file it says that I have to copy the lut file into the lut-folder of fiji. but exactly that folder I'm unable to localize on my mac..

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/Applications/Fiji.app/luts

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Thank you! now it works! :)

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Glad it's working. Here is the look up table (lut) I have been using recently.
.

NDVI_VGYRM_lutAy.jpg
A legend for the new colormap.
.
After another few weeks of trials, I think it is the most useful one I have used. I describe it here, but could not link to it until Jeff taught me how at LEAFFEST. I hope this works and you can download this...

NDVI_VGYRM.lut

This should be copied to the C:\Program Files (x86)\Fiji\Fiji.app\luts directory or something like that on Windows, and I guess to .../Applications/Fiji.app/luts on Mac. I will have to ask Ned to include this in the package at Github.

Chris

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Thanks Chris, I got your lookup table working now, sweet!

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