print("Saving ensemble predicted images . . .")
save_img(Y=Y_test_ensemble,
mask_dir=ens_no_bin_dir_per_image,
prefix="test_out_ens_no_bin")
save_img(Y=(Y_test_ensemble > 0.5).astype(np.uint8),
mask_dir=ens_bin_dir_per_image,
prefix="test_out_smo")
print("Calculate metrics (ensemble + per subvolume). . .")
ens_iou_per_image = jaccard_index_numpy(Y_test, (Y_test_ensemble > 0.5).astype(
np.uint8))
ens_ov_iou_per_image = voc_calculation(Y_test, (Y_test_ensemble > 0.5).astype(
np.uint8), ens_iou_per_image)
print("~~~~ Z-Filtering (per image) ~~~~")
zfil_preds_test = calculate_z_filtering(preds_test)
print("Saving Z-filtered images . . .")
save_img(Y=zfil_preds_test,
mask_dir=zfil_dir_per_image,
prefix="test_out_zfil")
print("Calculate metrics (Z-filtering + per crop) . . .")
zfil_iou_per_image = jaccard_index_numpy(
Y_test, (zfil_preds_test > 0.5).astype(np.uint8))
zfil_ov_iou_per_image = voc_calculation(Y_test, (zfil_preds_test > 0.5).astype(
np.uint8), zfil_iou_per_image)
del zfil_preds_test
print("~~~~ Ensemble + Z-Filtering (per subvolume) ~~~~")
ens_zfil_preds_test = calculate_z_filtering(Y_test_ensemble)
save_img(Y=(Y_test_blending > 0.5).astype(np.uint8),
mask_dir=smo_bin_dir_per_image,
prefix="test_out_smo")
print("Calculate metrics (smooth + per crop) . . .")
smo_score_per_image = jaccard_index_numpy(
Y_test, (Y_test_blending > 0.5).astype(np.uint8))
smo_ov_iou_per_image = voc_calculation(Y_test, (Y_test_blending > 0.5).astype(
np.uint8), smo_score_per_image)
smo_det_per_image = DET_calculation(Y_test,
(Y_test_blending > 0.5).astype(np.uint8),
det_eval_ge_path, det_eval_post_path,
det_bin, n_dig, args.job_id)
print("~~~~ Z-Filtering (per image) ~~~~")
zfil_preds_test = calculate_z_filtering(preds_test)
print("Saving Z-filtered images . . .")
save_img(Y=zfil_preds_test,
mask_dir=zfil_dir_per_image,
prefix="test_out_zfil")
print("Calculate metrics (Z-filtering + per crop) . . .")
zfil_score_per_image = jaccard_index_numpy(
Y_test, (zfil_preds_test > 0.5).astype(np.uint8))
zfil_ov_iou_per_image = voc_calculation(Y_test, (zfil_preds_test > 0.5).astype(
np.uint8), zfil_score_per_image)
zfil_det_per_image = DET_calculation(Y_test,
(zfil_preds_test > 0.5).astype(np.uint8),
det_eval_ge_path, det_eval_post_path,
det_bin, n_dig, args.job_id)
os.makedirs(ens_no_bin_dir_per_image, exist_ok=True)
aux = np.expand_dims(orig_preds_test.astype(np.uint8), 1)
f = os.path.join(ens_no_bin_dir_per_image, f_name)
imsave(f, aux, imagej=True, metadata={'axes': 'ZCYXS'})
print("Calculate metrics (ensemble + per subvolume). . .")
j = jaccard_index_numpy(orig_Y_test,
(orig_preds_test > 0.5).astype(np.uint8))
v = voc_calculation(orig_Y_test, (orig_preds_test > 0.5).astype(np.uint8),
j)
print("Image {} ; Foreground IoU: {} ; Overall IoU: {}".format(i, j, v))
iou += j
ov_iou += v
print("~~~~ Z-Filtering (per image) ~~~~")
zfil_preds_test = calculate_z_filtering(orig_preds_test)
zfil_preds_test = zfil_preds_test.astype(np.float32)
print("Saving Z-filtered images . . .")
os.makedirs(zfil_dir_per_image, exist_ok=True)
aux = np.expand_dims(zfil_preds_test.astype(np.uint8), 1)
f = os.path.join(zfil_dir_per_image, f_name)
imsave(f, aux, imagej=True, metadata={'axes': 'ZCYXS'})
print("Calculate metrics (Z-filtering + per crop) . . .")
j = jaccard_index_numpy(orig_Y_test,
(zfil_preds_test > 0.5).astype(np.uint8))
v = voc_calculation(orig_Y_test, (zfil_preds_test > 0.5).astype(np.uint8),
j)
print("Image {} ; Foreground IoU: {} ; Overall IoU: {}".format(i, j, v))
iou_z += j
print("Saving smooth predicted images . . .")
save_img(Y=Y_test_blending,
mask_dir=smo_no_bin_dir_per_image,
prefix="test_out_smo_no_bin")
save_img(Y=(Y_test_blending > 0.5).astype(np.uint8),
mask_dir=smo_bin_dir_per_image,
prefix="test_out_smo")
print("Calculate metrics (smooth + per crop) . . .")
smo_iou_per_image = jaccard_index_numpy(Y_test, (Y_test_blending > 0.5).astype(
np.uint8))
smo_ov_iou_per_image = voc_calculation(Y_test, (Y_test_blending > 0.5).astype(
np.uint8), smo_iou_per_image)
print("~~~~ Z-Filtering (per image) ~~~~")
zfil_preds_test = calculate_z_filtering(preds_test)
print("Saving Z-filtered images . . .")
save_img(Y=zfil_preds_test,
mask_dir=zfil_dir_per_image,
prefix="test_out_zfil")
print("Calculate metrics (Z-filtering + per crop) . . .")
zfil_iou_per_image = jaccard_index_numpy(
Y_test, (zfil_preds_test > 0.5).astype(np.uint8))
zfil_ov_iou_per_image = voc_calculation(Y_test, (zfil_preds_test > 0.5).astype(
np.uint8), zfil_iou_per_image)
del zfil_preds_test, preds_test
print("~~~~ Blending + Z-Filtering (per image) ~~~~")
smo_zfil_preds_test = calculate_z_filtering(Y_test_blending)
save_img(Y=Y_test_ensemble,
mask_dir=smo_no_bin_dir_full,
prefix="test_out_ens_no_bin")
save_img(Y=(Y_test_ensemble > 0.5).astype(np.uint8),
mask_dir=smo_bin_dir_full,
prefix="test_out_ens")
print("Calculate metrics (8-Ensemble + full image) . . .")
smo_iou_full = jaccard_index_numpy(Y_test,
(Y_test_ensemble > 0.5).astype(np.uint8))
smo_ov_iou_full = voc_calculation(Y_test,
(Y_test_ensemble > 0.5).astype(np.uint8),
smo_iou_full)
print("~~~~ 8-Ensemble + Z-Filtering (full image) ~~~~")
zfil_preds_test = calculate_z_filtering(Y_test_ensemble)
print("Saving Z-filtered images . . .")
save_img(Y=zfil_preds_test, mask_dir=zfil_dir_full, prefix="test_out_zfil")
print("Calculate metrics (8-Ensemble + Z-filtering + full image) . . .")
zfil_iou_full = jaccard_index_numpy(Y_test,
(zfil_preds_test > 0.5).astype(np.uint8))
zfil_ov_iou_full = voc_calculation(Y_test,
(zfil_preds_test > 0.5).astype(np.uint8),
zfil_iou_full)
del zfil_preds_test, Y_test_ensemble
####### OZTEL POST-PROCESSING #######
print("~~~~ Spurious Detection (full image) ~~~~")
