def run_inference(pred_folder,
im_lst,
thr_pred,
gt_folder,
target_suf,
param_eval,
unc_name=None,
thr_unc=None):
# init df
df_results = pd.DataFrame()
# loop across images
for fname_pref in im_lst:
if not any(elem is None for elem in [unc_name, thr_unc]):
logger.debug(thr_unc)
# uncertainty map
fname_unc = os.path.join(pred_folder,
fname_pref + unc_name + '.nii.gz')
im = nib.load(fname_unc)
data_unc = im.get_data()
del im
# list MC samples
data_pred_lst = np.array([
nib.load(os.path.join(pred_folder, f)).get_data()
for f in os.listdir(pred_folder) if fname_pref + '_pred_' in f
])
else:
data_pred_lst = np.array([
nib.load(os.path.join(pred_folder, f)).get_data()
for f in os.listdir(pred_folder) if fname_pref + '_pred.' in f
])
# ground-truth fname
fname_gt = os.path.join(gt_folder,
fname_pref.split('_')[0], 'anat',
fname_pref + target_suf + '.nii.gz')
nib_gt = nib.load(fname_gt)
data_gt = nib_gt.get_data()
# soft prediction
data_soft = np.mean(data_pred_lst, axis=0)
if not any(elem is None for elem in [unc_name, thr_unc]):
logger.debug("thr")
# discard uncertain lesions from data_soft
data_soft[data_unc > thr_unc] = 0
data_hard = imed_postpro.threshold_predictions(
data_soft, thr=thr_pred).astype(np.uint8)
eval = imed_utils.Evaluation3DMetrics(
data_pred=data_hard,
data_gt=data_gt,
dim_lst=nib_gt.header['pixdim'][1:4],
params=param_eval)
results_pred, _ = eval.run_eval()
# save results of this fname_pred
results_pred['image_id'] = fname_pref.split('_')[0]
df_results = df_results.append(results_pred, ignore_index=True)
return df_results
def run_experiment(level, unc_name, thr_unc_lst, thr_pred_lst, gt_folder,
pred_folder, im_lst, target_suf, param_eval):
# init results
tmp_lst = [[] for _ in range(len(thr_pred_lst))]
res_init_lst = [deepcopy(tmp_lst) for _ in range(len(thr_unc_lst))]
res_dct = {
'tpr': deepcopy(res_init_lst),
'fdr': deepcopy(res_init_lst),
'retained_elt': [[] for _ in range(len(thr_unc_lst))]
}
# loop across images
for fname_pref in im_lst:
# uncertainty map
fname_unc = os.path.join(pred_folder,
fname_pref + unc_name + '.nii.gz')
im = nib.load(fname_unc)
data_unc = im.get_data()
del im
# list MC samples
data_pred_lst = np.array([
nib.load(os.path.join(pred_folder, f)).get_data()
for f in os.listdir(pred_folder) if fname_pref + '_pred_' in f
])
# ground-truth fname
fname_gt = os.path.join(gt_folder,
fname_pref.split('_')[0], 'anat',
fname_pref + target_suf + '.nii.gz')
if os.path.isfile(fname_gt):
nib_gt = nib.load(fname_gt)
data_gt = nib_gt.get_data()
logger.debug(np.sum(data_gt))
# soft prediction
data_soft = np.mean(data_pred_lst, axis=0)
if np.any(data_soft):
for i_unc, thr_unc in enumerate(thr_unc_lst):
# discard uncertain lesions from data_soft
data_soft_thrUnc = deepcopy(data_soft)
data_soft_thrUnc[data_unc > thr_unc] = 0
cmpt = count_retained(
(data_soft > 0).astype(np.int),
(data_soft_thrUnc > 0).astype(np.int), level)
res_dct['retained_elt'][i_unc].append(cmpt)
logger.debug(f"{thr_unc} {cmpt}")
for i_pred, thr_pred in enumerate(thr_pred_lst):
data_hard = imed_postpro.threshold_predictions(deepcopy(data_soft_thrUnc), thr=thr_pred)\
.astype(np.uint8)
eval = imed_utils.Evaluation3DMetrics(
data_pred=data_hard,
data_gt=data_gt,
dim_lst=nib_gt.header['pixdim'][1:4],
params=param_eval)
if level == 'vox':
tpr = imed_metrics.recall_score(eval.data_pred,
eval.data_gt,
err_value=np.nan)
fdr = 100. - imed_metrics.precision_score(
eval.data_pred, eval.data_gt, err_value=np.nan)
else:
tpr, _ = eval.get_ltpr()
fdr = eval.get_lfdr()
logger.debug(
f"{thr_pred} {np.count_nonzero(deepcopy(data_soft_thrUnc))} "
f"{np.count_nonzero(data_hard)} {tpr} {fdr}")
res_dct['tpr'][i_unc][i_pred].append(tpr / 100.)
res_dct['fdr'][i_unc][i_pred].append(fdr / 100.)
return res_dct