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Ostu threshold

Goal

Wrap the crop step as a Common Workflow Language CommandLineTool and exectute it with a CWL runner.

CWL CommandLineTool wrapping the step

The CWL document below shows the crop step wrapped as a CWL CommandLineTool:

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cwlVersion: v1.0

class: CommandLineTool
id: otsu
requirements:
  InlineJavascriptRequirement: {}
  EnvVarRequirement:
    envDef:
      PATH: /opt/conda/envs/env_otsu/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
      PYTHONPATH: /app
  ResourceRequirement:
    coresMax: 1
    ramMax: 512
hints:
  DockerRequirement:
    dockerPull: localhost/otsu:latest 
baseCommand: ["python", "-m", "app"]
arguments: []
inputs:
  raster:
    type: File
    inputBinding:
      position: 1
outputs:
  binary_mask_item:
    outputBinding:
      glob: '*.tif'
    type: File

Steps

Run the CWL document using the cwltool CWL runner to execute the otsu step with:

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cwltool \
    --podman \
    --outdir /workspace/runs \
    ${WORKSPACE}/cwl-cli/otsu.cwl \
    --raster \
    /workspace/runs/norm_diff.tif

sh -x ${WORKSPACE}/scripts/cwl-cli-otsu.sh

Expected outcome

The folder /workspace/runs contains: 

(base) jovyan@coder-mrossi:~/runs$ tree .
.
├── crop_green.tif
├── crop_nir.tif
├── norm_diff.tif
└── otsu.tif

0 directories, 4 files