Source code for ivadomed.testing

import os

import nibabel as nib
import numpy as np
import torch
import torch.backends.cudnn as cudnn
from import DataLoader
from tqdm import tqdm

from ivadomed import metrics as imed_metrics
from ivadomed import utils as imed_utils
from ivadomed.loader import utils as imed_loader_utils
from ivadomed.object_detection import utils as imed_obj_detect
from import get_metadata
from ivadomed.postprocessing import threshold_predictions

cudnn.benchmark = True

[docs]def test(model_params, dataset_test, testing_params, log_directory, device, cuda_available=True, metric_fns=None): """Main command to test the network. Args: model_params (dict): Model's parameters. dataset_test (imed_loader): Testing dataset. testing_params (dict): Testing parameters. log_directory (str): Folder where predictions are saved. device (torch.device): Indicates the CPU or GPU ID. cuda_available (bool): If True, CUDA is available. metric_fns (list): List of metrics, see :mod:`ivadomed.metrics`. Returns: dict: result metrics. """ # DATA LOADER test_loader = DataLoader(dataset_test, batch_size=testing_params["batch_size"], shuffle=False, pin_memory=True, collate_fn=imed_loader_utils.imed_collate, num_workers=0) # LOAD TRAIN MODEL fname_model = os.path.join(log_directory, "") print('\nLoading model: {}'.format(fname_model)) model = torch.load(fname_model, map_location=device) if cuda_available: model.cuda() model.eval() # CREATE OUTPUT FOLDER path_3Dpred = os.path.join(log_directory, 'pred_masks') if not os.path.isdir(path_3Dpred): os.makedirs(path_3Dpred) # METRIC MANAGER metric_mgr = imed_metrics.MetricManager(metric_fns) # UNCERTAINTY SETTINGS if (testing_params['uncertainty']['epistemic'] or testing_params['uncertainty']['aleatoric']) and \ testing_params['uncertainty']['n_it'] > 0: n_monteCarlo = testing_params['uncertainty']['n_it'] testing_params['uncertainty']['applied'] = True print('\nComputing model uncertainty over {} iterations.'.format(n_monteCarlo)) else: testing_params['uncertainty']['applied'] = False n_monteCarlo = 1 for i_monteCarlo in range(n_monteCarlo): preds_npy, gt_npy = run_inference(test_loader, model, model_params, testing_params, path_3Dpred, cuda_available, i_monteCarlo) metric_mgr(preds_npy, gt_npy) # COMPUTE UNCERTAINTY MAPS if n_monteCarlo > 1: imed_utils.run_uncertainty(ifolder=path_3Dpred) metrics_dict = metric_mgr.get_results() metric_mgr.reset() print(metrics_dict) return metrics_dict
[docs]def run_inference(test_loader, model, model_params, testing_params, ofolder, cuda_available, i_monte_carlo=None): """Run inference on the test data and save results as nibabel files. Args: test_loader (torch DataLoader): model (nn.Module): model_params (dict): testing_params (dict): ofolder (str): Folder where predictions are saved. cuda_available (bool): If True, CUDA is available. i_monte_carlo (int): i_th Monte Carlo iteration. Returns: ndarray, ndarray: Prediction, Ground-truth of shape n_sample, n_label, h, w, d. """ # INIT STORAGE VARIABLES preds_npy_list, gt_npy_list = [], [] pred_tmp_lst, z_tmp_lst, fname_tmp = [], [], '' volume = None weight_matrix = None for i, batch in enumerate(tqdm(test_loader, desc="Inference - Iteration " + str(i_monte_carlo))): with torch.no_grad(): # GET SAMPLES # input_samples: list of batch_size tensors, whose size is n_channels X height X width X depth # gt_samples: idem with n_labels # batch['*_metadata']: list of batch_size lists, whose size is n_channels or n_labels if model_params["name"] == "HeMISUnet": input_samples = imed_utils.cuda(imed_utils.unstack_tensors(batch["input"]), cuda_available) else: input_samples = imed_utils.cuda(batch["input"], cuda_available) gt_samples = imed_utils.cuda(batch["gt"], cuda_available, non_blocking=True) # EPISTEMIC UNCERTAINTY if testing_params['uncertainty']['applied'] and testing_params['uncertainty']['epistemic']: for m in model.modules(): if m.__class__.__name__.startswith('Dropout'): m.train() # RUN MODEL if model_params["name"] in ["HeMISUnet", "FiLMedUnet"]: metadata = get_metadata(batch["input_metadata"], model_params) preds = model(input_samples, metadata) else: preds = model(input_samples) if model_params["name"] == "HeMISUnet": # Reconstruct image with only one modality input_samples = batch['input'][0] if model_params["name"] == "UNet3D" and model_params["attention"]: imed_utils.save_feature_map(batch, "attentionblock2", os.path.dirname(ofolder), model, input_samples, slice_axis=test_loader.dataset.slice_axis) # PREDS TO CPU preds_cpu = preds.cpu() # RECONSTRUCT 3D IMAGE last_batch_bool = (i == len(test_loader) - 1) slice_axis = imed_utils.AXIS_DCT[testing_params['slice_axis']] # LOOP ACROSS SAMPLES for smp_idx in range(len(preds_cpu)): if "bounding_box" in batch['input_metadata'][smp_idx][0]: imed_obj_detect.adjust_undo_transforms(testing_params["undo_transforms"].transforms, batch, smp_idx) if not model_params["name"].endswith('3D'): last_sample_bool = (last_batch_bool and smp_idx == len(preds_cpu) - 1) # undo transformations preds_idx_undo, metadata_idx = testing_params["undo_transforms"](preds_cpu[smp_idx], batch['gt_metadata'][smp_idx], data_type='gt') # preds_idx_undo is a list n_label arrays preds_idx_arr = np.array(preds_idx_undo) # TODO: gt_filenames should not be a list fname_ref = metadata_idx[0]['gt_filenames'][0] # NEW COMPLETE VOLUME if pred_tmp_lst and (fname_ref != fname_tmp or last_sample_bool): # save the completely processed file as a nifti file fname_pred = os.path.join(ofolder, fname_tmp.split('/')[-1]) fname_pred = fname_pred.split(testing_params['target_suffix'][0])[0] + '_pred.nii.gz' # If Uncertainty running, then we save each simulation result if testing_params['uncertainty']['applied']: fname_pred = fname_pred.split('.nii.gz')[0] + '_' + str(i_monte_carlo).zfill(2) + '.nii.gz' output_nii = imed_utils.pred_to_nib(data_lst=pred_tmp_lst, z_lst=z_tmp_lst, fname_ref=fname_tmp, fname_out=fname_pred, slice_axis=slice_axis, kernel_dim='2d', bin_thr=0.9 if testing_params["binarize_prediction"] else -1) # TODO: Adapt to multilabel preds_npy_list.append(output_nii.get_fdata()[:, :, :, 0]) gt_npy_list.append(nib.load(fname_tmp).get_fdata()) output_nii_shape = output_nii.get_fdata().shape if len(output_nii_shape) == 4 and output_nii_shape[-1] > 1: imed_utils.save_color_labels(np.stack(pred_tmp_lst, -1), testing_params["binarize_prediction"], fname_tmp, fname_pred.split(".nii.gz")[0] + '_color.nii.gz', imed_utils.AXIS_DCT[testing_params['slice_axis']]) # re-init pred_stack_lst pred_tmp_lst, z_tmp_lst = [], [] # add new sample to pred_tmp_lst, of size n_label X h X w ... pred_tmp_lst.append(preds_idx_arr) # TODO: slice_index should be stored in gt_metadata as well z_tmp_lst.append(int(batch['input_metadata'][smp_idx][0]['slice_index'])) fname_tmp = fname_ref else: pred_undo, metadata, last_sample_bool, volume, weight_matrix = \ imed_utils.volume_reconstruction(batch, preds_cpu, testing_params['undo_transforms'], smp_idx, volume, weight_matrix) fname_ref = metadata[0]['gt_filenames'][0] # Indicator of last batch if last_sample_bool: pred_undo = np.array(pred_undo) fname_pred = os.path.join(ofolder, fname_ref.split('/')[-1]) fname_pred = fname_pred.split(testing_params['target_suffix'][0])[0] + '_pred.nii.gz' # If uncertainty running, then we save each simulation result if testing_params['uncertainty']['applied']: fname_pred = fname_pred.split('.nii.gz')[0] + '_' + str(i_monte_carlo).zfill(2) + '.nii.gz' # Choose only one modality output_nii = imed_utils.pred_to_nib(data_lst=[pred_undo], z_lst=[], fname_ref=fname_ref, fname_out=fname_pred, slice_axis=slice_axis, kernel_dim='3d', bin_thr=0.5 if testing_params["binarize_prediction"] else -1) preds_npy_list.append(output_nii.get_fdata().transpose(3, 0, 1, 2)) gt_lst = [] for gt in metadata[0]['gt_filenames']: # For multi-label, if all labels are not in every image if gt is not None: gt_lst.append(nib.load(gt).get_fdata()) else: gt_lst.append(np.zeros(gt_lst[0].shape)) gt_npy_list.append(np.array(gt_lst)) # Save merged labels with color if pred_undo.shape[0] > 1: imed_utils.save_color_labels(pred_undo, testing_params['binarize_prediction'], batch['input_metadata'][smp_idx][0]['input_filenames'], fname_pred.split(".nii.gz")[0] + '_color.nii.gz', slice_axis) return preds_npy_list, gt_npy_list