soorena62
66 lines
1.9 KiB
Python
66 lines
1.9 KiB
Python
from dagster import job, op, In
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import SimpleITK as sitk
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from pathlib import Path
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from app.features.pysera_node import run_pysera
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# Write Your Codes Here:
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ARTIFACTS_DIR = Path("artifacts")
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ARTIFACTS_DIR.mkdir(parents=True, exist_ok=True)
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@op(config_schema={"image_file": str})
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def image_reader(context):
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# The Image File Is Read From Config.
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image_file = context.op_config["image_file"]
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input_path = Path("data/images") / image_file
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img = sitk.ReadImage(str(input_path))
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out_path = ARTIFACTS_DIR / "image_reader.nii.gz"
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sitk.WriteImage(img, str(out_path))
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return str(out_path)
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@op(config_schema={"mask_file": str})
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def mask_reader(context):
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mask_file = context.op_config["mask_file"]
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mask_path = Path("data/masks") / mask_file
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mask = sitk.ReadImage(str(mask_path))
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out_path = ARTIFACTS_DIR / "mask_reader.nii.gz"
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sitk.WriteImage(mask, str(out_path))
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return str(out_path)
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@op
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def image_registration(image_path: str):
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img = sitk.ReadImage(image_path)
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out_path = ARTIFACTS_DIR / "registered.nii.gz"
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sitk.WriteImage(img, str(out_path))
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return str(out_path)
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@op
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def image_filter(registered_path: str):
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img = sitk.ReadImage(registered_path)
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filtered = sitk.DiscreteGaussian(img, variance=1.5)
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out_path = ARTIFACTS_DIR / "filtered.nii.gz"
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sitk.WriteImage(filtered, str(out_path))
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return str(out_path)
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@op
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def pysera_extract(filtered_path: str, mask_path: str):
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features = run_pysera(filtered_path, mask_path)
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out_path = ARTIFACTS_DIR / "features.json"
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out_path.write_text(str(features))
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return str(out_path)
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@op
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def image_writer(filtered_path: str):
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final_path = ARTIFACTS_DIR / "final_output.nii.gz"
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final_path.write_bytes(Path(filtered_path).read_bytes())
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return str(final_path)
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@job
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def radiuma_job():
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img = image_reader()
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mask = mask_reader()
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reg = image_registration(img)
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filt = image_filter(reg)
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pysera_extract(filt, mask)
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image_writer(filt)
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