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cwerner
/
deadtrees
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dvc.yaml 3.2 KB
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  1. # dvc project pipeline
    2. 

  2. 

  3. # NOTE: see scripts/README.MD for preprocessing from raw data up to the first
    4. 

  4. # tracked stage `createtiles`
    5. 

  5. 

  6. stages:
    7. 

  7.   createtiles:
    8. 

  8.     foreach:
    9. 

  9.       - 2017
    10. 

  10.       - 2018
    11. 

  11.       - 2019
    12. 

  12.       - 2020
    13. 

  13.     do:
    14. 

  14.       cmd: >-
    15. 

  15.         mkdir -p data/processed.images.${item};
    16. 

  16.         gdal_retile.py 
    17. 

  17.         -csv locations.csv 
    18. 

  18.         -v -ps ${source_dim} ${source_dim}
    19. 

  19.         -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "ALPHA=NO" -co "NUM_THREADS=ALL_CPUS"
    20. 

  20.         -targetDir data/processed.images.${item} 
    21. 

  21.         data/raw/ortho_ms_${item}_EPSG3044.tif
    22. 

  22.       deps:
    23. 

  23.       - data/raw/ortho_ms_${item}_EPSG3044.tif
    24. 

  24.       params:
    25. 

  25.       - source_dim
    26. 

  26.       outs:
    27. 

  27.       - data/processed.images.${item}
    28. 

  28. 

  29.   computestats:
    30. 

  30.     cmd: >-
    31. 

  31.       python scripts/computestats.py --frac 0.1
    32. 

  32.       data/processed.images.2017  
    33. 

  33.       data/processed.images.2018  
    34. 

  34.       data/processed.images.2019 
    35. 

  35.       data/processed.images.2020 
    36. 

  36.     deps:
    37. 

  37.       - data/processed.images.2017
    38. 

  38.       - data/processed.images.2018
    39. 

  39.       - data/processed.images.2019
    40. 

  40.       - data/processed.images.2020 
    41. 

  41.     outs:
    42. 

  42.       - data/processed.images.stats.json
    43. 

  43.   
    44. 

  44.   createmasks:
    45. 

  45.     cmd: >-
    46. 

  46.       python scripts/createmasks.py 
    47. 

  47.       data/processed.images.2019 
    48. 

  48.       data/processed.masks.2019 
    49. 

  49.       data/raw/shapefiles/deadtrees_2019/deadtrees_2019.shp
    50. 

  50.       --negativesample data/raw/shapefiles/deadtrees_notdead/deadtrees_notdead.shp
    51. 

  51.     deps:
    52. 

  52.     - data/processed.images.2019
    53. 

  53.     - data/raw/shapefiles/deadtrees_2019
    54. 

  54.     - data/raw/shapefiles/deadtrees_notdead
    55. 

  55.     outs:
    56. 

  56.     - data/processed.masks.2019
    57. 

  57.     - data/processed.masks.2019.neg_sample
    58. 

  58. 

  59.   createdataset:
    60. 

  60.     cmd: >-
    61. 

  61.       python scripts/createdataset.py 
    62. 

  62.       data/processed.images.2019 
    63. 

  63.       data/processed.masks.2019 
    64. 

  64.       data/dataset 
    65. 

  65.       --source_dim ${source_dim}
    66. 

  66.       --tile_size ${createdataset.tile_size}
    67. 

  67.       --format ${file_type}
    68. 

  68.     deps:
    69. 

  69.     - data/processed.images.2019
    70. 

  70.     - data/processed.masks.2019 
    71. 

  71.     - data/processed.masks.2019.neg_sample 
    72. 

  72.     params:
    73. 

  73.     - source_dim
    74. 

  74.     - createdataset.tile_size
    75. 

  75.     - file_type
    76. 

  76.     outs:
    77. 

  77.     - data/dataset/train
    78. 

  78.     - data/dataset/stats.csv 
    79. 

  79. 

  80.   # train: do this manually
    81. 

  81. 

  82.   # inference
    83. 

  83.   inference:
    84. 

  84.     foreach:
    85. 

  85.       - 2017
    86. 

  86.       - 2018
    87. 

  87.       - 2019
    88. 

  88.       - 2020
    89. 

  89.     do:
    90. 

  90.       cmd: >-
    91. 

  91.         mkdir -p data/predicted.${item};
    92. 

  92.         stdbuf -i0 -o0 -e0 python scripts/inference.py --all --nopreview -o data/predicted.${item} data/processed.images.${item};
    93. 

  93.         gdal_merge.py 
    94. 

  94.         -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "NUM_THREADS=ALL_CPUS"
    95. 

  95.         -o data/predicted_mosaic_${item}.tif 
    96. 

  96.         data/predicted.${item}/ortho_ms_${item}_EPSG3044_*
    97. 

  97.       deps:
    98. 

  98.       - data/processed.images.${item}
    99. 

  99.       - checkpoints/bestmodel.ckpt
    100. 

  100.       outs:
    101. 

  101.       - data/predicted.${item}
    102. 

  102.       - data/predicted_mosaic_${item}.tif
    103. 

  103. 

  104.       
    105. 

  105.   computestatsinference:
    106. 

  106.     cmd: >-
    107. 

  107.       python scripts/computestats_inference.py
    108. 

  108.       data/predicted.2017  
    109. 

  109.       data/predicted.2018  
    110. 

  110.       data/predicted.2019 
    111. 

  111.       data/predicted.2020  
    112. 

  112.     deps:
    113. 

  113.       - data/predicted.2017
    114. 

  114.       - data/predicted.2018
    115. 

  115.       - data/predicted.2019
    116. 

  116.       - data/predicted.2020  
    117. 

  117.     outs:
    118. 

  118.       - data/predicted.stats.csv
    119.
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