plantit.yaml

name: DIRT\mu
author: Peter Pietrzyk
public: True
doi: 10.1002/essoar.10508833.1
shell: bash
image: docker://computationalplantscience/dirtmu
logo: DIRTX-mu.png
commands: python3 /opt/code/hairyroots.py -i $INPUT -o $OUTPUT --n_levels $N_LEVELS --w_mind $W_MIND --w_len $W_LEN --w_curve $W_CURVE --id_root $ID_ROOT --id_background $ID_BACKGROUND --id_roothair $ID_ROOTHAIR -p --pixel_size $PIXEL_SIZE
jobqueue:
  walltime: "24:00:00"
  memory: "32GB"
  processes: 1
  cores: 1
input:
  kind: files
  filetypes:
    - tif
    - tiff
output:
  include:
    patterns:
      - csv                             # include csv files
      - png                             # and png files
  exclude:
    patterns:
      - pkl                             # don't include pickle files
params:
  - name: n_levels                      # number of levels for simulated annealing
    type: number
    default: 1000
    step: 100
    min: 100
    max: 2000
  - name: w_mind                        # weight for minimum distance
    type: number
    default: 1
    step: 1
    min: 0
    max: 100
  - name: w_len                         # weight for length (=completeness)
    type: number
    default: 1
    step: 1
    min: 0
    max: 100
  - name: w_curve                       # weight for curvature
    type: number
    default: 1
    step: 1
    min: 0
    max: 100
  - name: id_root                       # index for root pixels
    type: number
    default: 3
    step: 1
    min: 0
    max: 255
  - name: id_background                 # index for image background
    type: number
    default: 2
    step: 1
    min: 0
    max: 255
  - name: id_roothair                   # index for root hair pixels
    type: number
    default: 1
    step: 1
    min: 0
    max: 255
  - name: pixel_size                    # scale of microscopy image
    type: number
    default: 1
    step: 0.01
    min: 0.01
    max: 10