small_animal.py

import pymirc.viewer as pv
import pymirc.fileio as pf
import numpy as np
import pynemaiqpet.nema_smallanimal as nsa

from scipy.ndimage import find_objects

import argparse

parser = argparse.ArgumentParser(description="NEMA small animal IQ scan analyzer")
parser.add_argument("dcm_dir", help="absolute path of input dicom directory")
parser.add_argument(
    "--phantom",
    help="phantom version",
    choices=["standard", "mini"],
    default="standard",
)
args = parser.parse_args()

# read the PET volume from dicom
dcm = pf.DicomVolume(args.dcm_dir)
vol = dcm.get_data()

# align the PET volume to "standard" space (a digitial version of the phantom)
vol_aligned = nsa.align_nema_2008_small_animal_iq_phantom(
    vol, dcm.voxsize, version=args.phantom
)

# generate the ROI label volume
roi_vol = nsa.nema_2008_small_animal_pet_rois(
    vol_aligned, dcm.voxsize, phantom=args.phantom
)

# generate the report
nsa.nema_2008_small_animal_iq_phantom_report(vol_aligned, roi_vol)

# show the aligned volume and the ROI volume (cropped versions)
th = 0.3 * np.percentile(vol_aligned, 99.9)
bbox = find_objects(vol_aligned > th)[0]
vi = pv.ThreeAxisViewer(
    [vol_aligned[bbox], vol_aligned[bbox]],
    [None, roi_vol[bbox] ** 0.1],
    voxsize=dcm.voxsize,
    ls="",
)