def run_seg_qc(args):
seg_qc.main(args)
def main(args):
"""
Segment hippocampus using a trained CNN
:param args: subj_dir, subj, t1, out, bias, force
:return: prediction (segmentation file)
"""
parser = parsefn()
subj_dir, subj, t1, out, bias, ign_ort, num_mc, force = parse_inputs(
parser, args)
pred_name = 'T1acq_hipp_pred' if hasattr(args, 'subj') else 'hipp_pred'
if out is None:
prediction = os.path.join(subj_dir, "%s_%s.nii.gz" % (subj, pred_name))
else:
prediction = out
if os.path.exists(prediction) and force is False:
print("\n %s already exists" % prediction)
else:
start_time = datetime.now()
hfb = os.path.realpath(__file__)
hyper_dir = str(Path(hfb).parents[2])
model_json = os.path.join(hyper_dir, 'models', 'hipp_model.json')
model_weights = os.path.join(hyper_dir, 'models',
'hipp_model_weights.h5')
assert os.path.exists(
model_weights
), "%s model does not exist ... please download and rerun script" % model_weights
# pred preprocess dir
pred_dir = os.path.join('%s' % os.path.abspath(subj_dir),
'pred_process')
if not os.path.exists(pred_dir):
os.mkdir(pred_dir)
training_mod = "t1"
if bias is True:
t1_bias = os.path.join(
subj_dir, "%s_nu.nii.gz" % os.path.basename(t1).split('.')[0])
biascorr.main(["-i", "%s" % t1, "-o", "%s" % t1_bias])
in_ort = t1_bias
else:
in_ort = t1
# check orientation
r_orient = 'RPI'
l_orient = 'LPI'
t1_ort = os.path.join(
subj_dir,
"%s_std_orient.nii.gz" % os.path.basename(t1).split('.')[0])
if ign_ort is False:
check_orient(in_ort, r_orient, l_orient, t1_ort)
# threshold at 10 percentile of non-zero voxels
thresh_file = os.path.join(
pred_dir,
"%s_thresholded.nii.gz" % os.path.basename(t1).split('.')[0])
in_thresh = t1_ort if os.path.exists(t1_ort) else t1
threshold_img(in_thresh, training_mod, 10, thresh_file)
# standardize
std_file = os.path.join(
pred_dir, "%s_thresholded_standardized.nii.gz" %
os.path.basename(t1).split('.')[0])
standard_img(thresh_file, std_file)
# resample images
t1_img = nib.load(std_file)
res = resample(t1_img, [160, 160, 128])
res_file = os.path.join(
pred_dir, "%s_thresholded_resampled.nii.gz" %
os.path.basename(t1).split('.')[0])
res.to_filename(res_file)
std = nib.load(res_file)
test_data = np.zeros((1, 1, 160, 160, 128),
dtype=t1_img.get_data_dtype())
test_data[0, 0, :, :, :] = std.get_data()
print(
colored("\n predicting initial hippocampus segmentation", 'green'))
pred = run_test_case(test_data=test_data,
model_json=model_json,
model_weights=model_weights,
affine=res.affine,
output_label_map=True,
labels=1)
# resample back
pred_res = resample_to_img(pred, t1_img)
pred_th = math_img('img > 0.5', img=pred_res)
# largest conn comp
init_pred_name = os.path.join(pred_dir,
"%s_hipp_init_pred.nii.gz" % subj)
get_largest_two_comps(pred_th, init_pred_name)
# trim seg to size
trim_seg = os.path.join(pred_dir,
"%s_hipp_init_pred_trimmed.nii.gz" % subj)
trim_img_to_size(init_pred_name, trim_seg)
# trim t1
t1_zoom = os.path.join(pred_dir, "%s_hipp_region.nii.gz" % subj)
trim_like.main(
['-i %s' % thresh_file,
'-r %s' % trim_seg,
'-o %s' % t1_zoom])
# --------------
# 2nd model
# --------------
pred_shape = [112, 112, 64]
t1_zoom_img = nib.load(t1_zoom)
test_zoom_data = np.zeros(
(1, 1, pred_shape[0], pred_shape[1], pred_shape[2]),
dtype=t1_zoom_img.get_data_dtype())
# standardize
std_file_trim = os.path.join(
pred_dir, "%s_trimmed_thresholded_standardized.nii.gz" %
os.path.basename(t1).split('.')[0])
standard_img(t1_zoom, std_file_trim)
# resample images
t1_img = nib.load(std_file_trim)
res_zoom = resample(t1_img, pred_shape)
res_file = os.path.join(
pred_dir,
"%s_trimmed_resampled.nii.gz" % os.path.basename(t1).split('.')[0])
res_zoom.to_filename(res_file)
test_zoom_data[0, 0, :, :, :] = res_zoom.get_data()
model_zoom_json = os.path.join(hyper_dir, 'models',
'hipp_zoom_mcdp_model.json')
model_zoom_weights = os.path.join(hyper_dir, 'models',
'hipp_zoom_mcdp_model_weights.h5')
assert os.path.exists(
model_zoom_weights
), "%s model does not exits ... please download and rerun script" % model_zoom_weights
print(
colored(
"\n predicting hippocampus segmentation using MC Dropout with %s samples"
% num_mc, 'green'))
pred_zoom_s = np.zeros(
(num_mc, pred_shape[0], pred_shape[1], pred_shape[2]),
dtype=res_zoom.get_data_dtype())
for sample_id in range(num_mc):
pred = run_test_case(test_data=test_zoom_data,
model_json=model_zoom_json,
model_weights=model_zoom_weights,
affine=res_zoom.affine,
output_label_map=True,
labels=1)
pred_zoom_s[sample_id, :, :, :] = pred.get_data()
nib.save(pred,
os.path.join(pred_dir, "hipp_pred_%s.nii.gz" % sample_id))
# computing mean
pred_zoom_mean = pred_zoom_s.mean(axis=0)
# pred_zoom_mean = np.median(pred_zoom_s, axis=0)
pred_zoom = nib.Nifti1Image(pred_zoom_mean, res_zoom.affine)
# resample back
pred_zoom_res = resample_to_img(pred_zoom, t1_zoom_img)
pred_zoom_name = os.path.join(
pred_dir, "%s_trimmed_hipp_pred_mean_prob.nii.gz" % subj)
nib.save(pred_zoom_res, pred_zoom_name)
# reslice like
t1_ref = t1_ort if os.path.exists(t1_ort) else t1
pred_zoom_res_t1 = os.path.join(
pred_dir, "%s_%s_hipp_pred_mean.nii.gz" % (subj, pred_name))
reslice_like(pred_zoom_name, t1_ref, pred_zoom_res_t1)
# thr
pred_zoom_res_t1_img = nib.load(pred_zoom_res_t1)
pred_zoom_th = math_img('img > 0.5', img=pred_zoom_res_t1_img)
# largest 2 conn comp
# comb_comps_zoom_bin_cmp = os.path.join(pred_dir, "%s_hipp_pred_mean_bin.nii.gz" % subj)
bin_prediction = os.path.join(subj_dir,
"%s_%s_bin.nii.gz" % (subj, pred_name))
get_largest_two_comps(pred_zoom_th, bin_prediction)
# split seg sides
split_seg_sides(bin_prediction, prediction)
print(colored("\n generating mosaic image for qc", 'green'))
seg_qc.main([
'-i',
'%s' % t1_ref, '-s',
'%s' % prediction, '-d', '1', '-g', '3'
])
endstatement.main(
'Hippocampus prediction (Using MC Dropout) and mosaic generation',
'%s' % (datetime.now() - start_time))