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


  
1

	
2

	
3

	
4

	
5

	
6

	
7

	
8

	
9

	
10

	
11

	
12

	
13

	
14

	
15

	
16

	
17

	
18

	
19

	
20

	
21

	
22

	
23

	
24

	
25

	
26

	
27

	
28

	
29

	
30

	
31

	
32

	
33

	
34

	
35

	
36

	
37

	
38

	
39

	
40

	
41

	
42

	
43

	
44

	
45

	
46

	
47

	
48

	
49

	
50

	
51

	
52

	
53

	
54

	
55

	
56

	
57

	
58

	
59

	
60

	
61

	
62

	
            stages:

  # STAGE I
  extract_metadata:
    cmd:
    - echo "STAGE I"
    - rm data/dcm_metadata.csv || true
    - python src/data/extract_metadata.py
    deps:
    - src/data/extract_metadata.py
    - data/dcm
    outs:
    - data/dcm_metadata.csv

  convert_dicoms:
    cmd:
    - rm -rf data/sly_input_rgb || true
    - rm -rf data/sly_input_gray || true
    - python src/data/convert_dicoms.py to_gray=false save_dir=data/sly_input_rgb
    - python src/data/convert_dicoms.py to_gray=true save_dir=data/sly_input_gray
    deps:
    - src/data/convert_dicoms.py
    - data/dcm_metadata.csv
    outs:
    - data/sly_input_rgb:
        cache: false
    - data/sly_input_gray:
        cache: false

  stack_images:
    cmd:
    - rm -rf data/sly_input || true
    - python src/data/stack_images.py output_type=video save_dir=data/sly_input
    deps:
    - src/data/stack_images.py
    - data/sly_input_rgb
    - data/sly_input_gray
    outs:
    - data/sly_input

  # STAGE II
  convert_sly_to_int:
    cmd:
    - echo "STAGE II"
    - rm -rf data/interim || true
    - python src/data/convert_sly_to_int.py
    deps:
    - src/data/convert_sly_to_int.py
    - data/sly_output
    outs:
    - data/interim

  convert_int_to_cv:
    cmd:
    - rm -rf data/cv || true
    - python src/data/convert_int_to_cv.py
    deps:
    - src/data/convert_int_to_cv.py
    - data/interim
    - data/interim/metadata.csv
    outs:
    - data/cv