nacpl_workflow_basic-old

# NACpipeline Argo workflow
# Aaron Curtis
# Concurrency rules: Write files as temporary, then move to intended dest. Check for existing output before starting.

apiVersion: argoproj.io/v1alpha1
kind: Workflow
metadata:
  generateName: nac-stereo-
spec:
  entrypoint: nac-mosaic
  volumes:
    - name: nac-volume
      hostPath:
        path: /c/nacpldata4
        type: DirectoryOrCreate
  arguments:
    parameters:
      - name: west
      - name: east
      - name: south
      - name: north

  templates:
  # Dummy template with reusable parts for references in stereo templates. Not to be run.
  - name: dummy-stereo-template
    inputs: &right-left-inps
      parameters:
        - name: right-prod-id
        - name: left-prod-id
    container: &nacpl-container
      image: lmmp-local/lmmp-container
      imagePullPolicy: IfNotPresent
      volumeMounts:
        - name: nac-volume
          mountPath: /data/nac
  - name: dummy-stereo-dag-template
    inputs: *right-left-inps
    dag:
      tasks:
        - name: dummy-task
          template: dummy-stereo-template
          arguments: &left-right-arguments-from-inputs
            parameters:
            - name: right-prod-id
              value: "{{inputs.parameters.right-prod-id}}"
            - name: left-prod-id
              value: "{{inputs.parameters.left-prod-id}}"

  # Dummy template with reusable parts for references in mosaic templates. Not to be run.
  - name: dummy-mosaic-template
    inputs: &bounding-box-arguments-from-inputs
      parameters:
        - name: west
          value: "{{workflow.parameters.west}}"
        - name: east
          value: "{{workflow.parameters.east}}"
        - name: south
          value: "{{workflow.parameters.south}}"
        - name: north
          value: "{{workflow.parameters.north}}"
    container: *nacpl-container

  # Given a bounding box {{west}}, {{east}}, {{south}}, {{north}} find appropriate NAC stereo pairs and create:
  # - stereo DEM mosaic covering the box at /data/nac/{{west}}_{{east}}_{{south}}_{{north}}DEM-mosaic.tif
  # - orthophoto mosaic covering the box at /data/nac/{{west}}_{{east}}_{{south}}_{{north}}DRG-mosaic.tif
  # - list of NAC pairs to use at /data/nac/{{west}}_{{east}}_{{south}}_{{north}}pairs.txt
  - name: nac-mosaic
    inputs: *bounding-box-arguments-from-inputs
    parallelism: 3
    steps:
      - - name: find-pairs
          template: find-pairs
          arguments: *bounding-box-arguments-from-inputs
      - - name: nac-stereo
          template: nac-stereo
          arguments:
            parameters:
              - name: left-prod-id
                value: "{{item.left}}"
              - name: right-prod-id
                value: "{{item.right}}"
          withParam: "{{steps.find-pairs.outputs.result}}"
          continueOn:
            failed: true
      - - name: merge-dems
          template: merge-dems
          arguments:
            parameters:
              - name: pair-ids
                value: "{{steps.find-pairs.outputs.result}}"
      - - name: color-hillshade
          template: color-hillshade
          arguments:
            artifacts:
              - name: dem
                from: "{{steps.merge-dems.outputs.artifacts.dem}}"
        - name: merge-orthoimages # TODO don't need to wait for hillshade or dem
          template: merge-orthoimages
          arguments:
            parameters:
              - name: pair-ids
                value: "{{steps.find-pairs.outputs.result}}"

  - name: find-pairs
    inputs: *bounding-box-arguments-from-inputs
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        . activate NAC_pl_env_py3
        python /nacpl/find_stereo_pairs.py \
        --west={{inputs.parameters.west}} \
        --east={{inputs.parameters.east}} \
        --south={{inputs.parameters.south}} \
        --north={{inputs.parameters.north}} \
        --find-covering=True



  # Given two nac product ids, right-prod-id and left-prod-id, initiate workflow to create:
  # - stereo DEM at /data/nac/{{left-prod-id}}xx{{right-prod-id}}-median-DEM.tif
  # - orthophoto at /data/nac/{{left-prod-id}}xx{{right-prod-id}}-median-DRG.tif
  # Also create some useful extra products:
  # - Downloaded .IMG files in /data/nac/
  # - ISIS-ingested .cub files in /data/nac/
  # - Intermediate data products in /data/nac/{{left-prod-id}}xx{{right-prod-id}}
  - name: nac-stereo
    parallelism: 3
    inputs: *left-right-arguments-from-inputs
    dag:
      tasks:
      - name: dl-ingest-right
        template: dl-ingest-nac
        arguments:
          parameters: [{name: prod-id, value: "{{inputs.parameters.right-prod-id}}"}]
      - name: dl-ingest-left
        template: dl-ingest-nac
        arguments:
          parameters: [{name: prod-id, value: "{{inputs.parameters.left-prod-id}}"}]
      - name: map-project
        template: map-project
        arguments: *left-right-arguments-from-inputs
        dependencies: [dl-ingest-right, dl-ingest-left]
      - name: stereo
        template: stereo
        arguments: *left-right-arguments-from-inputs
        dependencies: [map-project]
      - name: download-lola
        template: download-lola
        arguments: *left-right-arguments-from-inputs
        dependencies: [map-project]
      - name: align
        template: align
        arguments: *left-right-arguments-from-inputs
        dependencies: [stereo, download-lola]

  # Before this point, intermediate data products are considered re-usable and should be stored in a common location to
  # prevent re-processing in future mosaics

      - name: generate-DEM-and-orthoimages
        template: generate-DEM-and-orthoimages
        arguments: *left-right-arguments-from-inputs
        dependencies: [align]

  # Given a nac product id prod-id, initiate workflow download and ingest NAC into ISIS, creating:
  # - Downloaded .IMG file in /data/nac/{{prod-id}}
  # - ISIS-ingested .cub file in /data/nac/{{prod-id}}
  - name: dl-ingest-nac
    inputs:
      parameters:
        - name: prod-id
    dag:
      tasks:
      - name: download-nac
        template: download-nac
        arguments:
          parameters:
            - name: prod-id
              value: "{{inputs.parameters.prod-id}}"
      - name: img2cub
        template: img2cub
        arguments:
          parameters:
            - name: prod-id
              value: "{{inputs.parameters.prod-id}}"
        dependencies: [download-nac]
      - name: calibrate
        template: calibrate
        arguments:
          parameters:
            - name: prod-id
              value: "{{inputs.parameters.prod-id}}"
        dependencies: [img2cub]

  # Download a NAC image if doesn't exist and store to /data/nac on NFS
  # Script downloads to a temporary file and then moves it into place
  - name: download-nac
    inputs:
      parameters:
        - name: prod-id
    retryStrategy:
      limit: 3
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        . activate NAC_pl_env_py3
        if ! test -f /data/nac/{{inputs.parameters.prod-id}}.IMG
        then
          python /nacpl/download_NAC.py {{inputs.parameters.prod-id}} /data/nac
        else
          echo "Skipping step because output file already exists"
        fi

  # Download LOLA data for NAC image if it hasn't already been downloaded
  # Saves image at /data/nac/[right-prod-id]xx[left-prod-id]_lola.csv
  # TODO see if can use abs paths and avoid cd
  # NOTE breaks concurrency rule but write time for file is short enough that collision unlikely
  - name: download-lola
    inputs: *right-left-inps
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if ! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/*_lola.csv
        then
          . activate NAC_pl_env_py3
          cd /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}
          python /nacpl/download_LOLA.py \
          map-{{inputs.parameters.left-prod-id}}.map.cub map-{{inputs.parameters.right-prod-id}}.map.cub \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}
        else
          echo "Skipping step because output file already exists"
        fi

  # Convert IMG to ISIS cube if the cube doesn't already exist
  - name: img2cub
    inputs:
      parameters:
        - name: prod-id
    retryStrategy:
      limit: 3

    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if ! test -f /data/nac/{{inputs.parameters.prod-id}}.cub
        then
          mkdir -p /data/nac/tmp/
          echo "Running lronac2isis FROM=/data/nac/{{inputs.parameters.prod-id}}.IMG TO=/data/nac/tmp/{{inputs.parameters.prod-id}}.cub"
          lronac2isis -v FROM=/data/nac/{{inputs.parameters.prod-id}}.IMG TO=/data/nac/tmp/{{inputs.parameters.prod-id}}.cub
          mv /data/nac/tmp/{{inputs.parameters.prod-id}}.cub /data/nac/
        else
          echo "Skipping step because output file already exists"
        fi

  # Run spiceinit, lronaccal, and lronacecho and produce a .cal.cub if one doesn't already exist
  - name: calibrate
    inputs:
      parameters:
        - name: prod-id
    retryStrategy:
      limit: 3
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if ! test -f /data/nac/{{inputs.parameters.prod-id}}.cal.cub
        then
          spiceinit FROM=/data/nac/{{inputs.parameters.prod-id}}.cub web=yes
          lronaccal FROM=/data/nac/{{inputs.parameters.prod-id}}.cub TO=/tmp/{{inputs.parameters.prod-id}}.cal.cub
          lronacecho FROM=/tmp/{{inputs.parameters.prod-id}}.cal.cub TO=/data/nac/tmp/{{inputs.parameters.prod-id}}.cal.cub
          mv /data/nac/tmp/{{inputs.parameters.prod-id}}.cal.cub /data/nac/{{inputs.parameters.prod-id}}.cal.cub
        else
          echo "Skipping step because output file already exists"
        fi

  # Project the images to the best common resolution
  - name: map-project
    inputs: *right-left-inps
    retryStrategy:
      limit: 3
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if (! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map-{{inputs.parameters.left-prod-id}}.map.cub && \
            ! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map-{{inputs.parameters.right-prod-id}}.map.cub)
        then
          . activate NAC_pl_env_py3
          cd /StereoPipeline-2.6.2-2019-06-17-x86_64-Linux/bin
          cam2map4stereo.py \
              --prefix=/data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map \
              /data/nac/{{inputs.parameters.left-prod-id}}.cal.cub \
              /data/nac/{{inputs.parameters.right-prod-id}}.cal.cub
          mkdir -p /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/
          mv /data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map*map.cub \
             /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/
        else
          echo "Skipping step because output file already exists"
        fi

  # Do stereo reconstruction between the pairs if a stereo point cloud doesn't exist yet for them
  - name: stereo
    inputs: *right-left-inps
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if ! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/stereo-PC.tif
        then
          parallel_stereo \
          --processes=10 \
          --threads-singleprocess=10 \
          --alignment-method=none \
          --individually-normalize \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map-{{inputs.parameters.right-prod-id}}.map.cub \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map-{{inputs.parameters.left-prod-id}}.map.cub \
          /data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/stereo
          mv /data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/* \
             /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/
        else
          echo "Skipping step because output file already exists"
        fi

  # Align the point cloud to LOLA
  - name: align
    inputs: *right-left-inps
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if ! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/pc_align-trans_reference.tif
        then
          pc_align \
          --max-displacement 1200 \
          --csv-format '1:lon 2:lat 3:height_above_datum' \
          --save-inv-transformed-reference-points \
          --threads 10 \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/stereo-PC.tif \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/map-{{inputs.parameters.left-prod-id}}xxmap-{{inputs.parameters.right-prod-id}}_lola.csv \
          -o /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/tmp/pc_align
          mv /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/tmp/pc_align*.tif \
             /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/
        else
          echo "Skipping step because output file already exists"
        fi

  # Convert the point cloud to a DEM and an orthoimage
  - name: generate-DEM-and-orthoimages
    inputs: *right-left-inps
    retryStrategy:
      limit: 3
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        if (! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}*DEM.tif && \
            ! test -f /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}*DRG.tif)
        then
          point2dem \
          -o /data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}} \
          --t_srs http://spatialreference.org/ref/iau2000/30100/  \
          --nodata -9999 \
          --filter median \
          --median-filter-params 40 20 \
          --tif-compress LZW \
          --threads 10 \
          --orthoimage \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/stereo-L.tif \
          /data/nac/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}/pc_align-trans_reference.tif
          mv /data/nac/tmp/{{inputs.parameters.left-prod-id}}xx{{inputs.parameters.right-prod-id}}*.tif \
             /data/nac/
        else
          echo "Skipping step because output file already exists"
        fi

  # Template to merge DEMs
  # mosaic_merge.py calls ASP dem_mosaic
  - name: merge-dems
    inputs:
      parameters:
        - name: pair-ids
    script:
      <<: *nacpl-container
      command: [bash]
      #TODO tidy up following section, maybe get rid of bash substitution
      source: |
        . activate NAC_pl_env_py3
        mkdir -p /data/nac/merged
        python /nacpl/mosaic_merge.py $'{{inputs.parameters.pair-ids}}' DEM /data/nac /tmp/

        # Copy to shared storage, ending the DEM with DEM.tif instead of tile-0.tif
        DEM_FILENAME=( /tmp/*tile-0.tif )
        DEM_FILENAME_CORRECTED=${DEM_FILENAME/tile-0/DEM}
        cp /tmp/*tile-0.tif /data/nac/merged/${DEM_FILENAME_CORRECTED/\/tmp/}

        # Move the file so it can be output as an artifact
        mv /tmp/*tile-0.tif /tmp/merged_DEM.tif
    outputs:
      artifacts:
      - name: dem
        path: /tmp/merged_DEM.tif

  # Template to render a color hillshade
  - name: color-hillshade
    inputs:
      artifacts:
        - name: dem
          path: /tmp/merged_DEM.tif
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        . activate NAC_pl_env_py3
        gdalwarp -s_srs "EPSG:104903" \
          -t_srs "+proj=eqc +lat_ts={{workflow.parameters.north}} +lat_0={{workflow.parameters.north}}  +lon_0={{workflow.parameters.west}} +x_0=0 +y_0=0 +a=1737400 +b=1737400 +units=m +no_defs" \
          /tmp/merged_DEM.tif /tmp/merged_DEM_eqc.tif
        gdaldem hillshade /tmp/merged_DEM_eqc.tif /tmp/merged_hillshade.tif
        gdaldem color-relief /tmp/merged_DEM_eqc.tif /nacpl/elevation_colors.txt /tmp/merged_color-relief.tif
        hsv_merge -o /tmp/color_hillshade.tif /tmp/merged_color-relief.tif /tmp/merged_hillshade.tif
    outputs:
      artifacts:
        - name: color-hillshade
          path: /tmp/ #TODO save in volume?

  # Template to merge orthophotos (digital raster graphics, DRGs)
  # mosaic_merge.py calls Orfeo Toolbox Mosaic (otbcli_Mosaic)
  - name: merge-orthoimages
    inputs:
      parameters:
        - name: pair-ids
    script:
      <<: *nacpl-container
      command: [bash]
      source: |
        . activate NAC_pl_env_py3
        mkdir -p /data/nac/merged
        export OTB_MAX_RAM_HINT=1024
        python /nacpl/mosaic_merge.py $'{{inputs.parameters.pair-ids}}' DRG /data/nac /tmp
    outputs:
      artifacts:
        - name: orthoimage
          path: /tmp/ #TODO save in volume?