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avatar vdanilov
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oct_segmentation
connected to https://github.com/ViacheslavDanilov/oct_segmentation.git

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  1. schema: '2.0'
    2. 

  2. stages:
    3. 

  3.   extract_metadata:
    4. 

  4.     cmd:
    5. 

  5.     - echo "STAGE I"
    6. 

  6.     - rm data/dcm_metadata.csv || true
    7. 

  7.     - python src/data/extract_metadata.py
    8. 

  8.     deps:
    9. 

  9.     - path: data/dcm
    10. 

  10.       hash: md5
    11. 

  11.       md5: 776e4b24b55ef408ffd324a3e6cfcd57.dir
    12. 

  12.       size: 51636608570
    13. 

  13.       nfiles: 210
    14. 

  14.     - path: src/data/extract_metadata.py
    15. 

  15.       hash: md5
    16. 

  16.       md5: 93221105e879233bdb1dd812630b7b9b
    17. 

  17.       size: 4190
    18. 

  18.     outs:
    19. 

  19.     - path: data/dcm_metadata.csv
    20. 

  20.       hash: md5
    21. 

  21.       md5: 9b30138a835d12cfee681a96dfc0715e
    22. 

  22.       size: 35809
    23. 

  23.   convert_dicoms:
    24. 

  24.     cmd:
    25. 

  25.     - rm -rf data/sly_input_rgb || true
    26. 

  26.     - rm -rf data/sly_input_gray || true
    27. 

  27.     - python src/data/convert_dicoms.py to_gray=false save_dir=data/sly_input_rgb
    28. 

  28.     - python src/data/convert_dicoms.py to_gray=true save_dir=data/sly_input_gray
    29. 

  29.     deps:
    30. 

  30.     - path: data/dcm_metadata.csv
    31. 

  31.       hash: md5
    32. 

  32.       md5: 9b30138a835d12cfee681a96dfc0715e
    33. 

  33.       size: 35809
    34. 

  34.     - path: src/data/convert_dicoms.py
    35. 

  35.       hash: md5
    36. 

  36.       md5: 9bbc4995c7ea6c1b6c330f27d6783b2b
    37. 

  37.       size: 4496
    38. 

  38.     outs:
    39. 

  39.     - path: data/sly_input_gray
    40. 

  40.       hash: md5
    41. 

  41.       md5: df209b549a4c8d5726c2ac792a9c0c2e.dir
    42. 

  42.       size: 6279185933
    43. 

  43.       nfiles: 25698
    44. 

  44.     - path: data/sly_input_rgb
    45. 

  45.       hash: md5
    46. 

  46.       md5: 405e97e95a7138500e771dd69d56519b.dir
    47. 

  47.       size: 23240758188
    48. 

  48.       nfiles: 25698
    49. 

  49.   stack_images:
    50. 

  50.     cmd:
    51. 

  51.     - rm -rf data/sly_input || true
    52. 

  52.     - python src/data/stack_images.py output_type=video save_dir=data/sly_input
    53. 

  53.     deps:
    54. 

  54.     - path: data/sly_input_gray
    55. 

  55.       hash: md5
    56. 

  56.       md5: df209b549a4c8d5726c2ac792a9c0c2e.dir
    57. 

  57.       size: 6279185933
    58. 

  58.       nfiles: 25698
    59. 

  59.     - path: data/sly_input_rgb
    60. 

  60.       hash: md5
    61. 

  61.       md5: 405e97e95a7138500e771dd69d56519b.dir
    62. 

  62.       size: 23240758188
    63. 

  63.       nfiles: 25698
    64. 

  64.     - path: src/data/stack_images.py
    65. 

  65.       hash: md5
    66. 

  66.       md5: 72f001c3e0758d0d93f89d4dc5e03978
    67. 

  67.       size: 4802
    68. 

  68.     outs:
    69. 

  69.     - path: data/sly_input
    70. 

  70.       hash: md5
    71. 

  71.       md5: 80703f3dc0b23aec771aa09c9af38f42.dir
    72. 

  72.       size: 2161471795
    73. 

  73.       nfiles: 103
    74. 

  74.   convert_sly_to_int:
    75. 

  75.     cmd:
    76. 

  76.     - echo "STAGE II"
    77. 

  77.     - rm -rf data/interim || true
    78. 

  78.     - python src/data/convert_sly_to_int.py
    79. 

  79.     deps:
    80. 

  80.     - path: data/sly_output
    81. 

  81.       hash: md5
    82. 

  82.       md5: b4d6ab6210bd854d2a0c2130354dac0c.dir
    83. 

  83.       size: 1369637974
    84. 

  84.       nfiles: 82
    85. 

  85.     - path: src/data/convert_sly_to_int.py
    86. 

  86.       hash: md5
    87. 

  87.       md5: a681d7b0c341fc751440ec014e31d60a
    88. 

  88.       size: 9027
    89. 

  89.     outs:
    90. 

  90.     - path: data/interim
    91. 

  91.       hash: md5
    92. 

  92.       md5: 3cd4ea60168e604607f13b6db9ff886a.dir
    93. 

  93.       size: 9001243860
    94. 

  94.       nfiles: 10206
    95. 

  95.   convert_int_to_cv:
    96. 

  96.     cmd:
    97. 

  97.     - rm -rf data/cv || true
    98. 

  98.     - python src/data/convert_int_to_cv.py
    99. 

  99.     deps:
    100. 

  100.     - path: data/interim
    101. 

  101.       hash: md5
    102. 

  102.       md5: 3cd4ea60168e604607f13b6db9ff886a.dir
    103. 

  103.       size: 9001243860
    104. 

  104.       nfiles: 10206
    105. 

  105.     - path: data/interim/metadata.csv
    106. 

  106.       hash: md5
    107. 

  107.       md5: 96bb34c8ee68e5def961bfb26f3a6075
    108. 

  108.       size: 18915180
    109. 

  109.     - path: src/data/convert_int_to_cv.py
    110. 

  110.       hash: md5
    111. 

  111.       md5: 6ae9ec66137413ae3860e45eda051409
    112. 

  112.       size: 9765
    113. 

  113.     outs:
    114. 

  114.     - path: data/cv
    115. 

  115.       hash: md5
    116. 

  116.       md5: 1365e990781fd9f57fa37bdcbacfa782.dir
    117. 

  117.       size: 22540760453
    118. 

  118.       nfiles: 109351
    119.
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