2. NIfTI I/O¶

Load an aligned NIfTI dose and structure set, check their geometry, and inspect both containers and raw array data.

In [1]:

from dosemetrics import Dose
from dosemetrics.io import detect_folder_format, load_structure_set, load_volume
from dosemetrics.utils import download_example_data, dose_statistics_table, plot_dose_slice

study_dir = download_example_data("test_subject")
dose = Dose.from_nifti(study_dir / "Dose.nii.gz", name="Clinical")
structures = load_structure_set(study_dir, format="nifti")

print(f"Format: {detect_folder_format(study_dir)}")
print(f"Dose grid: {dose.shape}, spacing={dose.spacing} mm")
print(f"Structures: {len(structures)}")

from dosemetrics import Dose from dosemetrics.io import detect_folder_format, load_structure_set, load_volume from dosemetrics.utils import download_example_data, dose_statistics_table, plot_dose_slice study_dir = download_example_data("test_subject") dose = Dose.from_nifti(study_dir / "Dose.nii.gz", name="Clinical") structures = load_structure_set(study_dir, format="nifti") print(f"Format: {detect_folder_format(study_dir)}") print(f"Dose grid: {dose.shape}, spacing={dose.spacing} mm") print(f"Structures: {len(structures)}")

Format: nifti
Dose grid: (128, 128, 128), spacing=(2.0, 2.0, 2.0) mm
Structures: 16

Check dose and contour alignment¶

In [2]:

plot_dose_slice(
    dose,
    structures=structures,
    structure_names=["PTV", "Brainstem", "Chiasm"],
    contour_colors={"PTV": "white", "Brainstem": "lime", "Chiasm": "cyan"},
    cmap="turbo",
);

plot_dose_slice( dose, structures=structures, structure_names=["PTV", "Brainstem", "Chiasm"], contour_colors={"PTV": "white", "Brainstem": "lime", "Chiasm": "cyan"}, cmap="turbo", );

Summarize several structures¶

In [3]:

dose_statistics_table(dose, structures, ["PTV", "Brainstem", "Chiasm"]).round(2)

dose_statistics_table(dose, structures, ["PTV", "Brainstem", "Chiasm"]).round(2)

Out[3]:

	Volume (cc)	Mean dose (Gy)	Minimum dose (Gy)	Maximum dose (Gy)	D98 (Gy)	D95 (Gy)	D50 (Gy)	D02 (Gy)
Structure
PTV	343.03	58.13	31.72	63.90	45.08	48.17	59.81	61.48
Brainstem	31.06	58.42	41.11	61.65	47.93	50.66	60.00	61.19
Chiasm	0.96	54.46	43.19	60.52	43.86	45.23	56.66	59.81

Access a raw array¶

Use load_volume when you need the array and spatial metadata without a Dose container.

In [4]:

volume, spacing, origin = load_volume(study_dir / "Dose.nii.gz")
print(f"Array: shape={volume.shape}, dtype={volume.dtype}")
print(f"Spacing: {spacing} mm; origin: {origin} mm")

volume, spacing, origin = load_volume(study_dir / "Dose.nii.gz") print(f"Array: shape={volume.shape}, dtype={volume.dtype}") print(f"Spacing: {spacing} mm; origin: {origin} mm")

Array: shape=(128, 128, 128), dtype=float32
Spacing: (2.0, 2.0, 2.0) mm; origin: (92.70909881591797, 80.26853942871094, 52.468624114990234) mm