armcrop
This package contains a machine learning model that can crop a CT scan to any of the following classes:
- clavicle
- scapula
- humerus
- radius_ulna
- hand
It can do both axis aligned cropping and oriented bounding box (obb) cropping. The obb cropping allows for rigid registration of CT scans.
This model was trained on arm only scans and proximal half chest scans. A limitation of this model is that when using a full chest CT where the spine is present the model will struggle to differentiate between it and the scapula.
Installation
To use CPU execution install with:
pip install armcrop
To use CUDA execution you will need to also install torch and onnxruntime-gpu.
Usage
import armcrop
import SimpleITK as sitk
# load CT scan
volume = sitk.ReadImage("path/to/ct_scan.nrrd")
# Oriented Bounding Box Cropping
cropper = armcrop.CropOrientedBoundingBox(volume)
cropped_images = cropper.process(bone="humerus")
for i, img in enumerate(cropped_images):
sitk.WriteImage(img, f"aligned_humerus-{i}.nrrd")
# Bounding Box Cropping
cropper = armcrop.Crop(volume)
output = cropper.process(bone="scapula")
for i, img in enumerate(output):
sitk.WriteImage(img, f"cropped_scapula-{i}.nrrd")
1 maintainer
Metadata
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Release files for armcrop 1.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| armcrop-1.2.1.tar.gz | 14.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| armcrop-1.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 31.6 kB
Release files / armcrop-1.2.1.tar.gz
| Download URL | armcrop-1.2.1.tar.gz |
|---|---|
| Size | 14.6 kB |
| Tags | Source |
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Release files / armcrop-1.2.1-py3-none-any.whl
| Download URL | armcrop-1.2.1-py3-none-any.whl |
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| Size | 17.0 kB |
| Tags | Python 3 |
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