Multiple images at once

[yechp]

Hi.
I'm working on a research process. I need to process a large amount of images. Like, a lot. Is there any form within Nefi2 to feed multiple inputs at once?

yechp

[tastyminerals]

Have you tried python3 nefi2.py --help?

usage: nefi2.py [-h] [-p PIPELINE] [-d DIR] [-f FILE] [-o OUT]

optional arguments:
  -h, --help            show this help message and exit
  -p PIPELINE, --pipeline PIPELINE
                        Specify a saved pipeline xml file.
  -d DIR, --dir DIR     Specify a directory with images for batch processing.
  -f FILE, --file FILE  Specify an image file to process.
  -o OUT, --out OUT     Specify output directory.

PIPELINE is a json file that contains a list of algorithms and settings for processing:

cat nefi2/default_pipelines/a_junius.json 
  [
    ["Watershed DE Adaptive",{"Foreground Iteration":0, "Background Iteration":0,"Threshold Block Size":11,"Threshold Constant":1, "type":"Segmentation", "store_image":false}],
    ["Median Blur",{"channel1":true,"channel2":true,"channel3":true,"kernelsize":2, "type":"Preprocessing", "store_image":false}],
    ["Guo Hall Thinning",{"store_image":false,"type":"Thinning"}],
    ["Guo Hall Graph Detection",{"store_image":false,"type":"Graph Detection"}],
    ["Keep only LCC",{"store_image":false,"type":"Graph Filtering"}],
    ["Simple Cycle",{"store_image":false,"type":"Graph Filtering"}]
  ]

you can find a set of default pipelines under nefi2/default_pipelines dir.

[yechp]

Ok... I'm sorry but I just started with python. I come from R and NetLogo. Probably this question is going a very ignorant one but... where do I run this code?

[tastyminerals]

You need a Linux, where you can open console, navigate to nefi directory and run nefi2.py.
For example:

git clone https://github.com/05dirnbe/nefi.git
cd nefi/
python3 nefi2.py -p nefi2/default_pipelines/a_junius.json -d dir_with_images -o processed_images

I cannot test if current nefi2 version is working on Windows unfortunately.

[yechp]

Ok! Thank you very much!