Add All Folders

2026-02-08 04:38:10 +03:30
commit 9bb57e4799
191 changed files with 8469 additions and 0 deletions
@@ -0,0 +1,54 @@
+from pathlib import Path
+import numpy as np
+import SimpleITK as sitk
+
+ARTIFACTS = Path("app/storage/artifacts")
+ARTIFACTS.mkdir(parents=True, exist_ok=True)
+
+def image_reader_fn(state):
+    # Decide input file (DICOM series or NIfTI)
+    input_image_path = Path("data/images/CT_AVM.nii.gz")  # adapt as needed
+    img = sitk.ReadImage(str(input_image_path))
+    out_path = ARTIFACTS / "image_reader.nii.gz"
+    sitk.WriteImage(img, str(out_path))
+    return {"image_path": str(out_path)}
+
+def image_registration_fn(state):
+    fixed_path = state.get_outputs("image_reader").get("image_path")
+    moving_path = fixed_path  # demo: register image to itself; replace with real moving image
+    fixed = sitk.ReadImage(fixed_path)
+    moving = sitk.ReadImage(moving_path)
+
+    # Simple rigid registration (demo)
+    registration_method = sitk.ImageRegistrationMethod()
+    registration_method.SetMetricAsMeanSquares()
+    registration_method.SetOptimizerAsRegularStepGradientDescent(
+        learningRate=1.0, minStep=1e-4, numberOfIterations=100
+    )
+    registration_method.SetInterpolator(sitk.sitkLinear)
+    initial_transform = sitk.CenteredTransformInitializer(
+        fixed, moving, sitk.Euler3DTransform(), sitk.CenteredTransformInitializerFilter.GEOMETRY
+    )
+    registration_method.SetInitialTransform(initial_transform, inPlace=False)
+    final_transform = registration_method.Execute(fixed, moving)
+
+    resampled = sitk.Resample(moving, fixed, final_transform, sitk.sitkLinear, 0.0, moving.GetPixelID())
+    out_path = ARTIFACTS / "registered.nii.gz"
+    sitk.WriteImage(resampled, str(out_path))
+    return {"registered_path": str(out_path), "transform": "euler3d"}
+
+def image_filter_fn(state):
+    reg_path = state.get_outputs("image_registration").get("registered_path")
+    img = sitk.ReadImage(reg_path)
+    # Example filter: Gaussian smoothing
+    filtered = sitk.DiscreteGaussian(img, variance=1.5)
+    out_path = ARTIFACTS / "filtered.nii.gz"
+    sitk.WriteImage(filtered, str(out_path))
+    return {"filtered_path": str(out_path)}
+
+def image_writer_fn(state):
+    # Writer here is just saving; already done by previous steps; simulate final export
+    filtered_path = state.get_outputs("image_filter").get("filtered_path")
+    final_path = ARTIFACTS / "final_output.nii.gz"
+    Path(final_path).write_bytes(Path(filtered_path).read_bytes())
+    return {"final_output_path": str(final_path)}