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Replace itk with sitk bc of itk/torch mess #2

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Replace itk with sitk bc of itk/torch mess #2

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8 changes: 4 additions & 4 deletions cbctmc/speedup/inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
from pathlib import Path
from typing import Tuple

import itk
import SimpleITK as sitk
import numpy as np
import torch
from ipmi.common.logger import init_fancy_logging
Expand Down Expand Up @@ -85,12 +85,12 @@ def _execute(

@staticmethod
def _load_image(filepath: PathLike) -> Tuple[np.ndarray, dict]:
image = itk.imread(filepath)
image = sitk.ReadImage(filepath)
spacing = image.GetSpacing()
origin = image.GetOrigin()
direction = image.GetDirection()

image = itk.array_from_image(image)
image = sitk.GetArrayFromImage(image)

meta = {
"spacing": spacing,
Expand Down Expand Up @@ -125,7 +125,7 @@ def execute(
batch_size=batch_size,
)

sample = itk.image_from_array(sample)
sample = sitk.GetImageFromArray(sample)
sample.SetSpacing(meta["spacing"])
sample.SetOrigin(meta["origin"])
sample.SetDirection(meta["direction"])
Expand Down
8 changes: 4 additions & 4 deletions scripts/run_mc_simulations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
import click
import numpy as np
import pkg_resources
import SimpleITK
import SimpleITK as sitk
import torch
import yaml
from ipmi.common.logger import init_fancy_logging
Expand Down Expand Up @@ -44,11 +44,11 @@
from cbctmc.speedup.models import FlexUNet

_DEFAULT_SEGMENTER_WEIGHTS = Path(
pkg_resources.resource_filename("cbctmc", f"assets/models/segmenter/default.pth")
pkg_resources.resource_filename("cbctmc", f"assets/weights/segmenter/default.pth")
)

_DEFAULT_SPEEDUP_WEIGHTS = Path(
pkg_resources.resource_filename("cbctmc", f"assets/models/speedup/default.pth")
pkg_resources.resource_filename("cbctmc", f"assets/weights/speedup/default.pth")
)


Expand Down Expand Up @@ -584,7 +584,7 @@ def run(
/ config_name
/ "projections_total_normalized_speedup.mha"
)
itk.imwrite(speedup_projections, str(speedup_projections_filepath))
sitk.WriteImage(speedup_projections, str(speedup_projections_filepath))

if not dry_run:
reconstruct_4d = is_4d and reconstruct_4d
Expand Down