Question about Vessel VTK

[braininahat]

I tried replicating results from the paper on the DeepVesselNet synthetic dataset but my predictions look weird. Even what I'm assuming is the ground truth graph for a volume doesn't really seem to match when I visualize them. My first point of uncertainty with regard to data loading is as follows:

The VTK archive once unpacked looks like this:

vtk
    ├── 0
    │   ├── 1_arteries_final_1.vtk
    │   ├── 1_arteries_final_2.vtk
    │   ├── 1_arteries_final_3.vtk
    │   ├── 1_arteries_final_4.vtk
    │   ├── 1_arteries_final_5.vtk
    │   ├── 1_arteries_final_6.vtk
    │   ├── 1_arteries_final_7.vtk
    │   └── 1_arteries_final_8.vtk
    ├── 1
    │   ├── 1_arteries_final_10.vtk
    │   ├── 1_arteries_final_11.vtk
    │   ├── 1_arteries_final_12.vtk
    │   ├── 1_arteries_final_13.vtk
    │   ├── 1_arteries_final_14.vtk
    │   ├── 1_arteries_final_15.vtk
    │   ├── 1_arteries_final_16.vtk
    │   ├── 1_arteries_final_1.vtk
    │   ├── 1_arteries_final_2.vtk
    │   ├── 1_arteries_final_3.vtk
    │   ├── 1_arteries_final_4.vtk
    │   ├── 1_arteries_final_5.vtk
    │   ├── 1_arteries_final_6.vtk
    │   ├── 1_arteries_final_7.vtk
    │   ├── 1_arteries_final_8.vtk
    │   └── 1_arteries_final_9.vtk
    ├── 2
    │   ├── 1_arteries_final_10.vtk
    │   ├── 1_arteries_final_11.vtk
    │   ├── 1_arteries_final_12.vtk
    │   ├── 1_arteries_final_13.vtk
    │   ├── 1_arteries_final_14.vtk
    │   ├── 1_arteries_final_15.vtk
    │   ├── 1_arteries_final_16.vtk
    │   ├── 1_arteries_final_1.vtk
    │   ├── 1_arteries_final_2.vtk
    │   ├── 1_arteries_final_3.vtk
    │   ├── 1_arteries_final_4.vtk
    │   ├── 1_arteries_final_5.vtk
    │   ├── 1_arteries_final_6.vtk
    │   ├── 1_arteries_final_7.vtk
    │   ├── 1_arteries_final_8.vtk
    │   └── 1_arteries_final_9.vtk
    ├── 3
    │   ├── .
    │   ├── . 
    │   ├── .

The raw and seg files, however don't follow the same nested folder structure, instead being unpacked like this:

├── raw
│   ├── 100.nii.gz
│   ├── 101.nii.gz
│   ├── 102.nii.gz
│   ├── 103.nii.gz
│   ├── 104.nii.gz
│   ├── .
│   ├── . 
│   ├── .

Owing to this, the dataset preparation code in generate_data.py

    DATA_PATH = "./data/vessel_data/"

    img_folder = os.path.join(DATA_PATH, "raw")
    seg_folder = os.path.join(DATA_PATH, "seg")
    vtk_folder = os.path.join(DATA_PATH, "vtk")

    raw_files = []
    seg_files = []
    vtk_files = []

    for file_ in os.listdir(seg_folder):
        file_ = file_[:-7]
        raw_files.append(os.path.join(img_folder, file_+'.nii.gz'))
        seg_files.append(os.path.join(seg_folder, file_+'.nii.gz'))
        print(file_)
        vtk_files.append(os.path.join(vtk_folder, file_+'.vtk'))

fails for the VTK files since it doesn't account for the nested folder structure.

How I got around this is by doing:

    raw_files = natsorted(glob(f"{os.path.join(DATA_PATH, 'raw')}/*.nii.gz"))
    seg_files = natsorted(glob(f"{os.path.join(DATA_PATH, 'seg')}/*.nii.gz"))
    vtk_files = natsorted(
        glob(f"{os.path.join(DATA_PATH, 'vtk')}/*/*.vtk", recursive=True)
    )

What this gives me is:

[
    ('./data/vessel_data/raw/1.nii.gz', './data/vessel_data/seg/1.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_1.vtk'),
    ('./data/vessel_data/raw/2.nii.gz', './data/vessel_data/seg/2.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_2.vtk'),
    ('./data/vessel_data/raw/3.nii.gz', './data/vessel_data/seg/3.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_3.vtk'),
    ('./data/vessel_data/raw/4.nii.gz', './data/vessel_data/seg/4.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_4.vtk'),
    ('./data/vessel_data/raw/5.nii.gz', './data/vessel_data/seg/5.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_5.vtk'),
    ('./data/vessel_data/raw/6.nii.gz', './data/vessel_data/seg/6.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_6.vtk'),
    ('./data/vessel_data/raw/7.nii.gz', './data/vessel_data/seg/7.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_7.vtk'),
    ('./data/vessel_data/raw/8.nii.gz', './data/vessel_data/seg/8.nii.gz', './data/vessel_data/vtk/0/1_arteries_final_8.vtk'),
    ('./data/vessel_data/raw/9.nii.gz', './data/vessel_data/seg/9.nii.gz', './data/vessel_data/vtk/1/1_arteries_final_1.vtk'),
    ('./data/vessel_data/raw/10.nii.gz', './data/vessel_data/seg/10.nii.gz', './data/vessel_data/vtk/1/1_arteries_final_2.vtk'),
    .
    .
    .
]

I wanted to check if this is this is what the expected triplets of files would be?

[huangchieh]

At least the number of files in the vtk folder matches the raw folder. Did you figure it out? @braininahat Thank you.