Scripts/OM_reg_flexres_om.py

"""

OM_reg_flexres_om.py — Full-resolution registration using OMorpher.



Drop-in replacement for OM_reg_flexres.py.  Produces identical outputs but

uses OMorpher instead of DeformDDPM + STN + standalone apply_ddf().



Usage:

    python Scripts/OM_reg_flexres_om.py -C Config/config_om.yaml

"""

import os
import sys
import argparse

# Add project root to path so imports work from Scripts/
sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))

import numpy as np
import torch
import torch.nn.functional as F
import nibabel as nib
import yaml
import SimpleITK as sitk
from tqdm import tqdm

import utils
from Dataloader.dataLoader import OminiDataset_inference_w_all, reverse_axis_order
from OMorpher import OMorpher

# ========== CLI ==========

parser = argparse.ArgumentParser()
parser.add_argument(
    "--config", "-C",
    help="Path for the config file",
    type=str,
    default="Config/config_om.yaml",
    required=False,
)
args = parser.parse_args()

# ========== Config ==========

with open(args.config, "r") as file:
    hyp_parameters = yaml.safe_load(file)
    print(hyp_parameters)

if not os.path.exists(hyp_parameters["aug_img_savepath"]):
    os.makedirs(hyp_parameters["aug_img_savepath"])
if not os.path.exists(hyp_parameters["aug_msk_savepath"]):
    os.makedirs(hyp_parameters["aug_msk_savepath"])
if not os.path.exists(hyp_parameters["aug_ddf_savepath"]):
    os.makedirs(hyp_parameters["aug_ddf_savepath"])
print(hyp_parameters["aug_img_savepath"])

hyp_parameters["batchsize"] = 1
model_img_sz = hyp_parameters["img_size"]

# ========== Dataset (unchanged — used only for filtering/metadata) ==========

label_keys = ["brain"]
database = ["Brats2019"]

dataset = OminiDataset_inference_w_all(
    transform=None, min_crop_ratio=1.0, label_key=label_keys, database=database,
)

# ========== OMorpher setup ==========

epoch = f'{hyp_parameters["model_id_str"]}_{hyp_parameters["data_name"]}_{hyp_parameters["net_name"]}'
model_save_path = os.path.join(
    f'Models/{hyp_parameters["data_name"]}_{hyp_parameters["net_name"]}/',
    str(epoch) + ".pth",
)
print("Loading model from:", model_save_path)

om = OMorpher(
    config=hyp_parameters,
    checkpoint_path=model_save_path,
    device=str(hyp_parameters.get("device", "cpu")),
)
print(om)

# ========== Output directories ==========

reg_img_savepath_fullres = hyp_parameters["reg_img_savepath"].rstrip("/") + "_fullres/"
reg_msk_savepath_fullres = hyp_parameters["reg_msk_savepath"].rstrip("/") + "_fullres/"
reg_ddf_savepath_fullres = hyp_parameters["reg_ddf_savepath"].rstrip("/") + "_fullres/"

for p in [
    hyp_parameters["reg_img_savepath"],
    hyp_parameters["reg_msk_savepath"],
    hyp_parameters["reg_ddf_savepath"],
    reg_img_savepath_fullres,
    reg_msk_savepath_fullres,
    reg_ddf_savepath_fullres,
]:
    os.makedirs(p, exist_ok=True)


# ========== Helper: load full-res data (same as original) ==========

def center_pad_to_cube(volume):
    """Pad volume to a cube using the max dimension, with symmetric (center) padding."""
    max_dim = max(volume.shape[:3])
    pad_width = []
    for s in volume.shape[:3]:
        total_pad = max_dim - s
        pad_before = total_pad // 2
        pad_after = total_pad - pad_before
        pad_width.append((pad_before, pad_after))
    for _ in range(volume.ndim - 3):
        pad_width.append((0, 0))
    return np.pad(volume, pad_width, mode="constant", constant_values=0)


def load_fullres_volume(key, ds):
    """Load original-resolution volume: axis reorder, clamp, normalize, center-pad to cube."""
    volume = sitk.ReadImage(key)
    volume = sitk.GetArrayFromImage(volume)
    volume = reverse_axis_order(volume)
    if volume.ndim == 4:
        channel_ids = ds.get_channel_ids(key)
        channel_id = channel_ids[0] if len(channel_ids) > 0 else 0
        volume = volume[:, :, :, channel_id]
    if ds.clamp_range is not None:
        modality = ds.ALLdata_filtered[key].get("Modality", None)
        if modality == "CT":
            volume = np.clip(volume, ds.clamp_range[0], ds.clamp_range[1])
    volume = ds.normalize(volume)
    volume = center_pad_to_cube(volume)
    return volume


def load_fullres_label(key, ds, label_key):
    """Load original-resolution label: axis reorder, center-pad to cube."""
    label_path_dict = ds.ALLdata_filtered[key].get("Label_path", {})
    task_labels = label_path_dict.get("segmentation", {})
    if label_key not in task_labels:
        return None
    label = sitk.ReadImage(task_labels[label_key])
    label = sitk.GetArrayFromImage(label)
    label = reverse_axis_order(label)
    if label.ndim > 3:
        channel_ids = ds.get_channel_ids(key)
        if len(channel_ids) != 0:
            label = label[..., channel_ids]
    label = center_pad_to_cube(label)
    return label


# ========== Main inference loop ==========

keys = list(dataset.ALLdata_filtered.keys())
print("total num of images:", len(keys))
device = om.device

for e, key in enumerate(tqdm(keys)):
    pid = e
    print(f"Processing patient {pid}, image {e}, key: {key}")

    # --- Load & standardize volume via OMorpher ---
    fullres_vol = load_fullres_volume(key, dataset)
    om.set_init_img(fullres_vol)
    img = om._init_img                    # [1, 1, model_sz, model_sz, model_sz]
    fullres_img_tensor = om._init_img_raw  # [1, 1, D, H, W] full-res tensor
    orig_sz = list(fullres_img_tensor.shape[2:])
    print(f"  Full-res padded shape: {orig_sz}")

    # --- Load & standardize labels via OMorpher ---
    masks_model = []
    masks_fullres = []
    for lk in label_keys:
        lab = load_fullres_label(key, dataset, lk)
        model_t, fullres_t = om._standardize_label(lab)   # None → -1 placeholder
        masks_model.append(model_t)
        masks_fullres.append(fullres_t)

    if masks_model:
        mask = torch.cat(masks_model, dim=1)                # [1, C_total, S, S, S]
        fullres_msk_tensor = torch.cat(masks_fullres, dim=1)  # [1, C_total, D, H, W]
    else:
        mask = None
        fullres_msk_tensor = None

    # --- Save target conditioning image (first subject) ---
    if e <= 0:
        target_img = img.clone().detach()

    # --- Save original images at model resolution ---
    image_original = img.cpu().numpy()
    nib.save(
        utils.converet_to_nibabel(image_original, ndims=hyp_parameters["ndims"]),
        os.path.join(hyp_parameters["reg_img_savepath"],
                     utils.get_barcode([pid, e]) + ".nii.gz"),
    )
    if mask is not None:
        mask_original = mask.cpu().numpy()
        nib.save(
            utils.converet_to_nibabel(mask_original, ndims=hyp_parameters["ndims"]),
            os.path.join(hyp_parameters["reg_msk_savepath"],
                         utils.get_barcode([pid, e]) + "_GT.nii.gz"),
        )

    # --- Save original at full-res ---
    nib.save(
        utils.converet_to_nibabel(fullres_img_tensor, ndims=hyp_parameters["ndims"]),
        os.path.join(reg_img_savepath_fullres,
                     utils.get_barcode([pid, e]) + ".nii.gz"),
    )
    if fullres_msk_tensor is not None:
        nib.save(
            utils.converet_to_nibabel(fullres_msk_tensor, ndims=hyp_parameters["ndims"]),
            os.path.join(reg_msk_savepath_fullres,
                         utils.get_barcode([pid, e]) + "_GT.nii.gz"),
        )

    # --- Diffusion recovery via OMorpher ---
    noise_step = hyp_parameters["start_noise_step"]
    with torch.no_grad():
        for im in range(1):
            print(
                f"  Generating -> Subject-{pid}, Scan-{e} "
                f'({im}/{hyp_parameters["aug_coe"]})',
                end="\r",
            )

            # Set up OMorpher inputs
            om.set_init_img(img)
            om.set_cond_img(target_img.clone().detach())

            # Run diffusion recovery
            # T=[None, timesteps] in original means: no initial noise, full reverse diffusion
            om.predict(
                T=[None, hyp_parameters["timesteps"]],
                proc_type=hyp_parameters["condition_type"],
            )

            ddf_comp = om.get_def()

            # Reconstruct images at model resolution using OMorpher
            img_rec = om.apply_def(img=img, ddf=ddf_comp, padding_mode="zeros")

            # --- Save model-resolution results ---
            denoise_imgs = img_rec.cpu().numpy()

            nib.save(
                utils.converet_to_nibabel(denoise_imgs, ndims=hyp_parameters["ndims"]),
                os.path.join(
                    hyp_parameters["reg_img_savepath"],
                    utils.get_barcode([pid, e, im, noise_step]) + ".nii.gz",
                ),
            )

            if mask is not None:
                msk_rec = om.apply_def(
                    img=mask, ddf=ddf_comp,
                    padding_mode="zeros", resample_mode="nearest",
                )
                denoise_msks = msk_rec.cpu().numpy()
                nib.save(
                    utils.converet_to_nibabel(denoise_msks, ndims=hyp_parameters["ndims"]),
                    os.path.join(
                        hyp_parameters["reg_msk_savepath"],
                        utils.get_barcode([pid, e, im, noise_step]) + "_GT.nii.gz",
                    ),
                )

            # --- Upscale DDF and apply at full resolution via OMorpher ---
            img_rec_fullres = om.apply_def(
                img=fullres_img_tensor, ddf=ddf_comp, padding_mode="border",
            )

            if fullres_msk_tensor is not None:
                msk_rec_fullres = om.apply_def(
                    img=fullres_msk_tensor, ddf=ddf_comp,
                    padding_mode="zeros", resample_mode="nearest",
                )

            # Upscale DDF for saving
            ddf_fullres = F.interpolate(
                ddf_comp, size=orig_sz, mode="trilinear", align_corners=False,
            )

            # --- Save full-res results ---
            nib.save(
                utils.converet_to_nibabel(img_rec_fullres, ndims=hyp_parameters["ndims"]),
                os.path.join(
                    reg_img_savepath_fullres,
                    utils.get_barcode([pid, e, im, noise_step]) + ".nii.gz",
                ),
            )

            if fullres_msk_tensor is not None:
                nib.save(
                    utils.converet_to_nibabel(msk_rec_fullres, ndims=hyp_parameters["ndims"]),
                    os.path.join(
                        reg_msk_savepath_fullres,
                        utils.get_barcode([pid, e, im, noise_step]) + "_GT.nii.gz",
                    ),
                )

            nib.save(
                utils.converet_to_nibabel(ddf_fullres, ndims=hyp_parameters["ndims"]),
                os.path.join(
                    reg_ddf_savepath_fullres,
                    utils.get_barcode([pid, e, im, noise_step]) + ".nii.gz",
                ),
            )

            if (im - hyp_parameters["start_noise_step"]) % 2 == 0:
                noise_step = noise_step + hyp_parameters["noise_step"]

    if e > 5:
        break