def main():
options = parse_inputs()
c = color_codes()
experimental = options['experimental']
exp_s = c['b'] + '(experimental %d)' % experimental if experimental else c[
'b'] + '(baseline)'
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
'Starting cross-validation ' + exp_s + c['nc'])
# N-fold cross validation main loop (we'll do 2 training iterations with testing for each patient)
data_names, label_names = get_names_from_path(options)
folds = len(data_names)
fold_generator = izip(
nfold_cross_validation(data_names, label_names, n=folds),
xrange(folds))
dsc_results = list()
for (train_data, train_labels, test_data,
test_labels), i in fold_generator:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] +
'Fold %d/%d: ' % (i + 1, folds) + c['g'] +
'Number of training/testing images (%d=%d/%d)' %
(len(train_data), len(train_labels), len(test_data)) + c['nc'])
# Prepare the data relevant to the leave-one-out (subtract the patient from the dataset and set the path)
# Also, prepare the network
if not check_image_list(test_data, options):
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] +
c['g'] + 'Training' + c['nc'])
net = train_net(i, train_data, train_labels, options)
else:
net = None
# Then we test the net.
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] +
c['g'] + 'Testing' + c['nc'])
for p, gt_name in zip(test_data, test_labels):
image, gt = test_net(net, p, gt_name, options)
p_name = '-'.join(
p[0].rsplit('/')[-1].rsplit('.')[0].rsplit('-')[:-1])
vals = np.unique(gt.flatten())
gt_mask = np.sum(map(
lambda (l, val): np.array(gt == val, dtype=np.uint8) * l,
enumerate(vals)),
axis=0)
results = (str.capitalize(p_name), dsc_seg(gt_mask == 1,
image == 1),
dsc_seg(gt_mask == 2,
image == 2), dsc_seg(gt_mask == 3, image == 3))
dsc_results.append(results)
print('%s DSC: %f/%f/%f' % results)
dsc_results = sorted(dsc_results,
cmp=lambda x, y: int(x[0][8:]) - int(y[0][8:]))
for results in dsc_results:
print(c['c'] + '%s DSC: \033[32;1m%f/%f/%f' % results + c['nc'])
f_dsc = tuple(
np.asarray([results[1:] for results in dsc_results]).mean(axis=0))
print(c['c'] + 'Final results DSC: \033[32;1m%f/%f/%f' % f_dsc + c['nc'])
def get_lesion_metrics(gt_lesion_mask,
lesion_unet,
spacing,
metric_file,
patient,
general_flag=True,
fold=1):
if general_flag:
dist = average_surface_distance(gt_lesion_mask, lesion_unet, spacing)
tpfv = tp_fraction_seg(gt_lesion_mask, lesion_unet)
fpfv = fp_fraction_seg(gt_lesion_mask, lesion_unet)
dscv = dsc_seg(gt_lesion_mask, lesion_unet)
tpfl = tp_fraction_det(gt_lesion_mask, lesion_unet)
fpfl = fp_fraction_det(gt_lesion_mask, lesion_unet)
dscl = dsc_det(gt_lesion_mask, lesion_unet)
tp = true_positive_det(lesion_unet, gt_lesion_mask)
gt_d = num_regions(gt_lesion_mask)
lesion_s = num_voxels(lesion_unet)
gt_s = num_voxels(gt_lesion_mask)
pdsc = probabilistic_dsc_seg(gt_lesion_mask, lesion_unet)
if metric_file:
metric_file.write(
'%s;%s;%s;%f;%f;%f;%f;%f;%f;%f;%d;%d;%d;%d\n' %
(patient + 'gt', patient + 'pd', str(fold), dist, tpfv, fpfv,
dscv, tpfl, fpfl, dscl, tp, gt_d, lesion_s, gt_s))
else:
print('SurfDist TPFV FPFV DSCV '
'TPFL FPFL DSCL '
'TPL GTL Voxels GTV PrDSC')
print('%f %f %f %f %f %f %f %d %d %d %d %f' %
(dist, tpfv, fpfv, dscv, tpfl, fpfl, dscl, tp, gt_d,
lesion_s, gt_s, pdsc))
return dscv
else:
sizes = [3, 11, 51]
tpf, fpf, dscd, dscs = analysis_by_sizes(gt_lesion_mask, lesion_unet,
sizes)
names = '%s;%s;' % (patient + 'gt', patient + 'pd')
measures = ';'.join([
'%f;%f;%f;%f' % (tpf_i, fpf_i, dscd_i, dscs_i)
for tpf_i, fpf_i, dscd_i, dscs_i in zip(tpf, fpf, dscd, dscs)
])
if metric_file:
metric_file.write(names + measures + '\n')
else:
intervals = [
'\t\t[%d-%d)\t\t|' % (mins, maxs)
for mins, maxs in zip(sizes[:-1], sizes[1:])
]
intervals = ''.join(intervals) + \
'\t\t[%d-inf)\t|' % sizes[-1]
measures_s = 'TPF\tFPF\tDSCd\tDSCs\t|' * len(sizes)
measures = ''.join([
'%.2f\t%.2f\t%.2f\t%.2f\t|' % (tpf_i, fpf_i, dscd_i, dscs_i)
for tpf_i, fpf_i, dscd_i, dscs_i in zip(tpf, fpf, dscd, dscs)
])
print(intervals)
print(measures_s)
print(measures)
def label_level_evaluation(
path='/media/lele/DATA/brain/Brats17TrainingData/HGG7/'):
patients = os.listdir(path)
print len(patients)
pixel_accuracy_instance = []
mean_IU_instance = []
mean_accuracy_insintance = []
frequency_weighted_IU_instance = []
label0 = 0
label1 = 0
label2 = 0
label4 = 0
dsc = []
for patient in patients:
if patient[0] != 'B':
continue
p_name = patient
patient = path + patient + '/'
fs = os.listdir(patient)
if len(fs) == 5:
continue
gt_path = patient
seg_path = patient
no_file = 0
for f in fs:
if f[-10:-7] == 'seg':
gt_path = gt_path + f
if f[-10:-7] == 'est' and '.e6.' in f:
seg_path = seg_path + f
no_file = 1
if no_file == 0:
continue
seg_3d = nii2np(seg_path)
gt_3d = nii2np(gt_path)
labels = np.unique(gt_3d.flatten())
results = (p_name, ) + tuple(
[dsc_seg(gt_3d == l, seg_3d == l) for l in labels])
text = 'Subject %s DSC: ' + '/'.join(['%f' for _ in labels[1:]])
# print(text % results)
if results[4] + results[2] + results[3] > 0.1:
dsc.append(results[1:])
for i in range(len(dsc)):
# print dsc[i]\
label0 += dsc[i][0]
label1 += dsc[i][1]
label2 += dsc[i][2]
label4 += dsc[i][3]
label0 = label0 / len(dsc)
label1 = label1 / len(dsc)
label2 = label2 / len(dsc)
label4 = label4 / len(dsc)
print label0
print label1
print label2
print label4
def main():
options = parse_inputs()
c = color_codes()
# Prepare the net architecture parameters
sequential = options['sequential']
dfactor = options['dfactor']
# Prepare the net hyperparameters
num_classes = 5
epochs = options['epochs']
padding = options['padding']
patch_width = options['patch_width']
patch_size = (patch_width, patch_width, patch_width)
batch_size = options['batch_size']
dense_size = options['dense_size']
conv_blocks = options['conv_blocks']
n_filters = options['n_filters']
filters_list = n_filters if len(n_filters) > 1 else n_filters * conv_blocks
conv_width = options['conv_width']
kernel_size_list = conv_width if isinstance(
conv_width, list) else [conv_width] * conv_blocks
balanced = options['balanced']
# Data loading parameters
preload = options['preload']
queue = options['queue']
# Prepare the sufix that will be added to the results for the net and images
path = options['dir_name']
filters_s = 'n'.join(['%d' % nf for nf in filters_list])
conv_s = 'c'.join(['%d' % cs for cs in kernel_size_list])
s_s = '.s' if sequential else '.f'
ub_s = '.ub' if not balanced else ''
params_s = (ub_s, dfactor, s_s, patch_width, conv_s, filters_s, dense_size,
epochs, padding)
sufix = '%s.D%d%s.p%d.c%s.n%s.d%d.e%d.pad_%s.' % params_s
n_channels = np.count_nonzero([
options['use_flair'], options['use_t2'], options['use_t1'],
options['use_t1ce']
])
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
'Starting cross-validation' + c['nc'])
# N-fold cross validation main loop (we'll do 2 training iterations with testing for each patient)
data_names, label_names = get_names_from_path(options)
folds = options['folds']
fold_generator = izip(
nfold_cross_validation(data_names, label_names, n=folds,
val_data=0.25), xrange(folds))
dsc_results = list()
for (train_data, train_labels, val_data, val_labels, test_data,
test_labels), i in fold_generator:
print(
c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] +
'Fold %d/%d: ' % (i + 1, folds) + c['g'] +
'Number of training/validation/testing images (%d=%d/%d=%d/%d)' %
(len(train_data), len(train_labels), len(val_data),
len(val_labels), len(test_data)) + c['nc'])
# Prepare the data relevant to the leave-one-out (subtract the patient from the dataset and set the path)
# Also, prepare the network
net_name = os.path.join(
path, 'baseline-brats2017.fold%d' % i + sufix + 'mdl')
# First we check that we did not train for that patient, in order to save time
try:
# net_name_before = os.path.join(path,'baseline-brats2017.fold0.D500.f.p13.c3c3c3c3c3.n32n32n32n32n32.d256.e1.pad_valid.mdl')
net = keras.models.load_model(net_name)
except IOError:
print '==============================================================='
# NET definition using Keras
train_centers = get_cnn_centers(train_data[:, 0],
train_labels,
balanced=balanced)
val_centers = get_cnn_centers(val_data[:, 0],
val_labels,
balanced=balanced)
train_samples = len(train_centers) / dfactor
val_samples = len(val_centers) / dfactor
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'Creating and compiling the model ' + c['b'] +
'(%d samples)' % train_samples + c['nc'])
train_steps_per_epoch = -(-train_samples / batch_size)
val_steps_per_epoch = -(-val_samples / batch_size)
input_shape = (n_channels, ) + patch_size
# This architecture is based on the functional Keras API to introduce 3 output paths:
# - Whole tumor segmentation
# - Core segmentation (including whole tumor)
# - Whole segmentation (tumor, core and enhancing parts)
# The idea is to let the network work on the three parts to improve the multiclass segmentation.
# merged_inputs = Input(shape=(4,) + patch_size, name='merged_inputs')
# flair = merged_inputs
model = Sequential()
model.add(
Conv3D(64, (3, 3, 3),
strides=1,
padding='same',
activation='relu',
data_format='channels_first',
input_shape=(4, options['patch_width'],
options['patch_width'],
options['patch_width'])))
model.add(
Conv3D(64, (3, 3, 3),
strides=1,
padding='same',
activation='relu',
data_format='channels_first'))
model.add(
MaxPooling3D(pool_size=(3, 3, 3),
strides=2,
data_format='channels_first'))
model.add(
Conv3D(128, (3, 3, 3),
strides=1,
padding='same',
activation='relu',
data_format='channels_first'))
model.add(
Conv3D(128, (3, 3, 3),
strides=1,
padding='same',
activation='relu',
data_format='channels_first'))
model.add(
MaxPooling3D(pool_size=(3, 3, 3),
strides=2,
data_format='channels_first'))
model.add(Flatten())
model.add(Dense(256, activation='relu'))
model.add(Dropout(0.5))
model.add(Dense(num_classes, activation='softmax'))
net = model
# net_name_before = os.path.join(path,'baseline-brats2017.fold0.D500.f.p13.c3c3c3c3c3.n32n32n32n32n32.d256.e1.pad_valid.mdl')
# net = keras.models.load_model(net_name_before)
net.compile(optimizer='sgd',
loss='categorical_crossentropy',
metrics=['accuracy'])
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'Training the model with a generator for ' + c['b'] +
'(%d parameters)' % net.count_params() + c['nc'])
print(net.summary())
net.fit_generator(
generator=load_patch_batch_train(
image_names=train_data,
label_names=train_labels,
centers=train_centers,
batch_size=batch_size,
size=patch_size,
# fc_shape = patch_size,
nlabels=num_classes,
dfactor=dfactor,
preload=preload,
split=not sequential,
datatype=np.float32),
validation_data=load_patch_batch_train(
image_names=val_data,
label_names=val_labels,
centers=val_centers,
batch_size=batch_size,
size=patch_size,
# fc_shape = patch_size,
nlabels=num_classes,
dfactor=dfactor,
preload=preload,
split=not sequential,
datatype=np.float32),
# workers=queue,
steps_per_epoch=train_steps_per_epoch,
validation_steps=val_steps_per_epoch,
max_q_size=queue,
epochs=epochs)
net.save(net_name)
# Then we test the net.
for p, gt_name in zip(test_data, test_labels):
p_name = p[0].rsplit('/')[-2]
patient_path = '/'.join(p[0].rsplit('/')[:-1])
outputname = os.path.join(patient_path,
'deep-brats17' + sufix + 'test.nii.gz')
gt_nii = load_nii(gt_name)
gt = np.copy(gt_nii.get_data()).astype(dtype=np.uint8)
try:
load_nii(outputname)
except IOError:
roi_nii = load_nii(p[0])
roi = roi_nii.get_data().astype(dtype=np.bool)
centers = get_mask_voxels(roi)
test_samples = np.count_nonzero(roi)
image = np.zeros_like(roi).astype(dtype=np.uint8)
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Creating the probability map ' + c['b'] + p_name +
c['nc'] + c['g'] + ' (%d samples)>' % test_samples +
c['nc'])
test_steps_per_epoch = -(-test_samples / batch_size)
y_pr_pred = net.predict_generator(
generator=load_patch_batch_generator_test(
image_names=p,
centers=centers,
batch_size=batch_size,
size=patch_size,
preload=preload,
),
steps=test_steps_per_epoch,
max_q_size=queue)
[x, y, z] = np.stack(centers, axis=1)
if not sequential:
tumor = np.argmax(y_pr_pred[0], axis=1)
y_pr_pred = y_pr_pred[-1]
roi = np.zeros_like(roi).astype(dtype=np.uint8)
roi[x, y, z] = tumor
roi_nii.get_data()[:] = roi
roiname = os.path.join(
patient_path,
'deep-brats17' + sufix + 'test.roi.nii.gz')
roi_nii.to_filename(roiname)
y_pred = np.argmax(y_pr_pred, axis=1)
image[x, y, z] = y_pred
# Post-processing (Basically keep the biggest connected region)
image = get_biggest_region(image)
labels = np.unique(gt.flatten())
results = (p_name, ) + tuple(
[dsc_seg(gt == l, image == l) for l in labels[1:]])
text = 'Subject %s DSC: ' + '/'.join(
['%f' for _ in labels[1:]])
print(text % results)
dsc_results.append(results)
print(c['g'] + ' -- Saving image ' + c['b'] +
outputname + c['nc'])
roi_nii.get_data()[:] = image
roi_nii.to_filename(outputname)
def check_dsc(gt_name, image, nlabels):
gt_nii = load_nii(gt_name)
gt = np.minimum(gt_nii.get_data(), nlabels - 1).astype(dtype=np.uint8)
labels = np.unique(gt.flatten())
gt_nii.uncache()
return [dsc_seg(gt == l, image == l) for l in labels[1:]]
def main():
options = parse_inputs()
c = color_codes()
# Prepare the net architecture parameters
register = options['register']
multi = options['multi']
defo = options['deformation']
layers = ''.join(options['layers'])
greenspan = options['greenspan']
freeze = options['freeze']
balanced = options['balanced'] if not freeze else False
# Prepare the net hyperparameters
epochs = options['epochs']
padding = options['padding']
patch_width = options['patch_width']
patch_size = (32, 32) if greenspan else (patch_width, patch_width, patch_width)
pool_size = options['pool_size']
batch_size = options['batch_size']
dense_size = options['dense_size']
conv_blocks = options['conv_blocks']
n_filters = options['number_filters']
n_filters = n_filters if len(n_filters) > 1 else n_filters*conv_blocks
conv_width = options['conv_width']
conv_size = conv_width if isinstance(conv_width, list) else [conv_width]*conv_blocks
# Prepare the sufix that will be added to the results for the net and images
use_flair = options['use_flair']
use_pd = options['use_pd']
use_t2 = options['use_t2']
flair_name = 'flair' if use_flair else None
pd_name = 'pd' if use_pd else None
t2_name = 't2' if use_t2 else None
images = filter(None, [flair_name, pd_name, t2_name])
reg_s = '.reg' if register else ''
filters_s = 'n'.join(['%d' % nf for nf in n_filters])
conv_s = 'c'.join(['%d' % cs for cs in conv_size])
im_s = '.'.join(images)
mc_s = '.mc' if multi else ''
d_s = 'd%d.' % (conv_blocks*2+defo) if defo else ''
sufix = '.greenspan' if greenspan else '%s.%s%s%s.p%d.c%s.n%s.d%d.e%d.pad_%s' %\
(mc_s, d_s, im_s, reg_s, patch_width, conv_s, filters_s, dense_size, epochs, padding)
# Prepare the data names
mask_name = options['mask']
wm_name = options['wm_mask']
sub_folder = options['sub_folder']
sub_name = options['flair_sub']
dir_name = options['dir_name']
patients = [f for f in sorted(os.listdir(dir_name))
if os.path.isdir(os.path.join(dir_name, f))]
n_patients = len(patients)
names = get_names_from_path(dir_name, options, patients)
defo_names = get_defonames_from_path(dir_name, options, patients) if defo else None
defo_width = conv_blocks*2+defo if defo else None
defo_size = (defo_width, defo_width, defo_width)
# Random initialisation
seed = np.random.randint(np.iinfo(np.int32).max)
# Metrics output
metrics_file = os.path.join(dir_name, 'metrics' + sufix)
with open(metrics_file, 'w') as f:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + 'Starting leave-one-out' + c['nc'])
# Leave-one-out main loop (we'll do 2 training iterations with testing for each patient)
for i in range(0, n_patients):
# Prepare the data relevant to the leave-one-out (subtract the patient from the dataset and set the path)
# Also, prepare the network
case = patients[i]
path = os.path.join(dir_name, case)
names_lou = np.concatenate([names[:, :i], names[:, i + 1:]], axis=1)
defo_names_lou = np.concatenate([defo_names[:, :i], defo_names[:, i + 1:]], axis=1) if defo else None
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] + 'Patient ' + c['b'] + case + c['nc'] +
c['g'] + ' (%d/%d)' % (i+1, n_patients))
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Running iteration ' + c['b'] + '1' + c['nc'] + c['g'] + '>' + c['nc'])
net_name = os.path.join(path, 'deep-longitudinal.init' + sufix + '.')
if greenspan:
net = create_cnn_greenspan(
input_channels=names.shape[0]/2,
patience=25,
name=net_name,
epochs=500
)
images = ['axial', 'coronal', 'sagital']
else:
if multi:
net = create_cnn3d_det_string(
cnn_path=layers,
input_shape=(None, names.shape[0], patch_width, patch_width, patch_width),
convo_size=conv_size,
padding=padding,
dense_size=dense_size,
pool_size=2,
number_filters=n_filters,
patience=10,
multichannel=True,
name=net_name,
epochs=100
)
else:
net = create_cnn3d_longitudinal(
convo_blocks=conv_blocks,
input_shape=(None, names.shape[0], patch_width, patch_width, patch_width),
images=images,
convo_size=conv_size,
pool_size=pool_size,
dense_size=dense_size,
number_filters=n_filters,
padding=padding,
drop=0.5,
register=register,
defo=defo,
patience=10,
name=net_name,
epochs=100
)
names_test = get_names_from_path(path, options)
defo_names_test = get_defonames_from_path(path, options) if defo else None
outputname1 = os.path.join(path, 't' + case + sufix + '.iter1.nii.gz') if not greenspan else os.path.join(
path, 't' + case + sufix + '.nii.gz')
# First we check that we did not train for that patient, in order to save time
try:
net.load_params_from(net_name + 'model_weights.pkl')
except IOError:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
c['g'] + 'Loading the data for ' + c['b'] + 'iteration 1' + c['nc'])
# Data loading. Most of it is based on functions from data_creation that load the data.
# But we also need to prepare the name list to load the leave-one-out data.
paths = [os.path.join(dir_name, p) for p in np.concatenate([patients[:i], patients[i+1:]])]
mask_names = [os.path.join(p_path, mask_name) for p_path in paths]
wm_names = [os.path.join(p_path, wm_name) for p_path in paths]
pr_names = [os.path.join(p_path, sub_folder, sub_name) for p_path in paths]
x_train, y_train = load_lesion_cnn_data(
names=names_lou,
mask_names=mask_names,
defo_names=defo_names_lou,
roi_names=wm_names,
pr_names=pr_names,
patch_size=patch_size,
defo_size=defo_size,
random_state=seed
)
# Afterwards we train. Check the relevant training function.
if greenspan:
x_train = np.swapaxes(x_train, 1, 2)
train_greenspan(net, x_train, y_train, images)
else:
train_net(net, x_train, y_train, images)
with open(net_name + 'layers.pkl', 'wb') as fnet:
pickle.dump(net.layers, fnet, -1)
# Then we test the net. Again we save time by checking if we already tested that patient.
try:
image_nii = load_nii(outputname1)
image1 = image_nii.get_data()
except IOError:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Creating the probability map ' + c['b'] + '1' + c['nc'] + c['g'] + '>' + c['nc'])
image_nii = load_nii(os.path.join(path, options['image_folder'], options['flair_f']))
mask_nii = load_nii(os.path.join(path, wm_name))
if greenspan:
image1 = test_greenspan(
net,
names_test,
mask_nii.get_data(),
batch_size,
patch_size,
image_nii.get_data().shape,
images
)
else:
image1 = test_net(
net,
names_test,
mask_nii.get_data(),
batch_size,
patch_size,
defo_size,
image_nii.get_data().shape,
images,
defo_names_test
)
image_nii.get_data()[:] = image1
image_nii.to_filename(outputname1)
if greenspan:
# Since Greenspan did not use two iterations, we must get the final mask here.
outputname_final = os.path.join(path, 't' + case + sufix + '.final.nii.gz')
mask_nii.get_data()[:] = (image1 > 0.5).astype(dtype=np.int8)
mask_nii.to_filename(outputname_final)
else:
# If not, we test the net with the training set to look for misclassified negative with a high
# probability of being positives according to the net.
# These voxels will be the input of the second training iteration.
''' Here we get the seeds '''
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
c['g'] + '<Looking for seeds for the final iteration>' + c['nc'])
patients_names = zip(np.rollaxis(names_lou, 1), np.rollaxis(defo_names_lou, 1)) if defo\
else np.rollaxis(names_lou, 1)
for patient in patients_names:
if defo:
patient, d_patient = patient
else:
d_patient = None
patient_path = '/'.join(patient[0].rsplit('/')[:-1])
outputname = os.path.join(patient_path, 't' + case + sufix + '.nii.gz')
mask_nii = load_nii(os.path.join('/'.join(patient[0].rsplit('/')[:-3]), wm_name))
try:
load_nii(outputname)
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
c['g'] + ' Patient ' + patient[0].rsplit('/')[-4] + ' already done' + c['nc'])
except IOError:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
c['g'] + ' Testing with patient ' + c['b'] + patient[0].rsplit('/')[-4] + c['nc'])
image_nii = load_nii(patient[0])
image = test_net(
net,
patient,
mask_nii.get_data(),
batch_size,
patch_size,
defo_size,
image_nii.get_data().shape,
images,
d_patient
)
print(c['g'] + ' -- Saving image ' + c['b'] + outputname + c['nc'])
image_nii.get_data()[:] = image
image_nii.to_filename(outputname)
''' Here we perform the last iteration '''
# Finally we perform the final iteration. After refactoring the code, the code looks almost exactly
# the same as the training of the first iteration.
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Running iteration ' + c['b'] + '2' + c['nc'] + c['g'] + '>' + c['nc'])
f_s = '.f' if freeze else ''
ub_s = '.ub' if not balanced else ''
final_s = f_s + ub_s
outputname2 = os.path.join(path, 't' + case + final_s + sufix + '.iter2.nii.gz')
net_name = os.path.join(path, 'deep-longitudinal.final' + final_s + sufix + '.')
if multi:
net = create_cnn3d_det_string(
cnn_path=layers,
input_shape=(None, names.shape[0], patch_width, patch_width, patch_width),
convo_size=conv_size,
padding=padding,
pool_size=2,
dense_size=dense_size,
number_filters=n_filters,
patience=50,
multichannel=True,
name=net_name,
epochs=epochs
)
else:
if not freeze:
net = create_cnn3d_longitudinal(
convo_blocks=conv_blocks,
input_shape=(None, names.shape[0], patch_width, patch_width, patch_width),
images=images,
convo_size=conv_size,
pool_size=pool_size,
dense_size=dense_size,
number_filters=n_filters,
padding=padding,
drop=0.5,
register=register,
defo=defo,
patience=50,
name=net_name,
epochs=epochs
)
else:
net.max_epochs = epochs
net.on_epoch_finished[0].name = net_name + 'model_weights.pkl'
for layer in net.get_all_layers():
if not isinstance(layer, DenseLayer):
for param in layer.params:
layer.params[param].discard('trainable')
try:
net.load_params_from(net_name + 'model_weights.pkl')
except IOError:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
c['g'] + 'Loading the data for ' + c['b'] + 'iteration 2' + c['nc'])
roi_paths = ['/'.join(name.rsplit('/')[:-1]) for name in names_lou[0, :]]
paths = [os.path.join(dir_name, p) for p in np.concatenate([patients[:i], patients[i + 1:]])]
ipr_names = [os.path.join(p_path, sub_folder, sub_name) for p_path in paths] if freeze else None
pr_names = [os.path.join(p_path, 't' + case + sufix + '.nii.gz') for p_path in roi_paths]
mask_names = [os.path.join(p_path, mask_name) for p_path in paths]
wm_names = [os.path.join(p_path, wm_name) for p_path in paths]
x_train, y_train = load_lesion_cnn_data(
names=names_lou,
mask_names=mask_names,
defo_names=defo_names_lou,
roi_names=wm_names,
init_pr_names=ipr_names,
pr_names=pr_names,
patch_size=patch_size,
defo_size=defo_size,
random_state=seed,
balanced=balanced
)
train_net(net, x_train, y_train, images)
with open(net_name + 'layers.pkl', 'wb') as fnet:
pickle.dump(net.layers, fnet, -1)
try:
image_nii = load_nii(outputname2)
image2 = image_nii.get_data()
except IOError:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Creating the probability map ' + c['b'] + '2' + c['nc'] + c['g'] + '>' + c['nc'])
image_nii = load_nii(os.path.join(path, options['image_folder'], options['flair_f']))
mask_nii = load_nii(os.path.join(path, wm_name))
image2 = test_net(
net,
names_test,
mask_nii.get_data(),
batch_size,
patch_size,
defo_size,
image_nii.get_data().shape,
images,
defo_names_test
)
image_nii.get_data()[:] = image2
image_nii.to_filename(outputname2)
image = image1 * image2
image_nii.get_data()[:] = image
outputname_mult = os.path.join(path, 't' + case + final_s + sufix + '.iter1_x_2.nii.gz')
image_nii.to_filename(outputname_mult)
image = (image1 * image2) > 0.5
image_nii.get_data()[:] = image
outputname_final = os.path.join(path, 't' + case + final_s + sufix + '.final.nii.gz')
image_nii.to_filename(outputname_final)
# Finally we compute some metrics that are stored in the metrics file defined above.
# I plan on replicating Challenge's 2008 evaluation measures here.
gt = load_nii(os.path.join(path, mask_name)).get_data().astype(dtype=np.bool)
seg1 = image1 > 0.5
if not greenspan:
seg2 = image2 > 0.5
dsc1 = dsc_seg(gt, seg1)
if not greenspan:
dsc2 = dsc_seg(gt, seg2)
if not greenspan:
dsc_final = dsc_seg(gt, image)
else:
dsc_final = dsc1
tpf1 = tp_fraction_seg(gt, seg1)
if not greenspan:
tpf2 = tp_fraction_seg(gt, seg2)
if not greenspan:
tpf_final = tp_fraction_seg(gt, image)
fpf1 = fp_fraction_seg(gt, seg1)
if not greenspan:
fpf2 = fp_fraction_seg(gt, seg2)
if not greenspan:
fpf_final = fp_fraction_seg(gt, image)
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<DSC ' + c['c'] + case + c['g'] + ' = ' + c['b'] + str(dsc_final) + c['nc'] + c['g'] + '>' + c['nc'])
f.write('%s;Test 1; %f;%f;%f\n' % (case, dsc1, tpf1, fpf1))
if not greenspan:
f.write('%s;Test 2; %f;%f;%f\n' % (case, dsc2, tpf2, fpf2))
if not greenspan:
f.write('%s;Final; %f;%f;%f\n' % (case, dsc_final, tpf_final, fpf_final))
def main():
options = parse_inputs()
c = color_codes()
# Prepare the net hyperparameters
epochs = options['epochs']
patch_width = options['patch_width']
patch_size = (patch_width, patch_width, patch_width)
dense_size = options['dense_size']
conv_blocks = options['conv_blocks']
n_filters = options['n_filters']
filters_list = n_filters if len(n_filters) > 1 else n_filters * conv_blocks
conv_width = options['conv_width']
kernel_size_list = conv_width if isinstance(conv_width, list) else [conv_width] * conv_blocks
balanced = options['balanced']
# Data loading parameters
downsample = options['downsample']
preload = options['preload']
shuffle = options['shuffle']
# Prepare the sufix that will be added to the results for the net and images
filters_s = 'n'.join(['%d' % nf for nf in filters_list])
conv_s = 'c'.join(['%d' % cs for cs in kernel_size_list])
unbalanced_s = '.ub' if not balanced else ''
shuffle_s = '.s' if shuffle else ''
params_s = (unbalanced_s, shuffle_s, patch_width, conv_s, filters_s, dense_size, downsample)
sufix = '%s%s.p%d.c%s.n%s.d%d.D%d' % params_s
preload_s = ' (with %spreloading%s%s)' % (c['b'], c['nc'], c['c']) if preload else ''
print('%s[%s] Starting training%s%s' % (c['c'], strftime("%H:%M:%S"), preload_s, c['nc']))
train_data, _ = get_names_from_path(options)
test_data, test_labels = get_names_from_path(options, False)
input_shape = (train_data.shape[1],) + patch_size
dsc_results = list()
dsc_results_pr = list()
train_data, train_labels = get_names_from_path(options)
centers_s = np.random.permutation(
get_cnn_centers(train_data[:, 0], train_labels, balanced=balanced)
)[::downsample]
x_seg, y_seg = load_patches_ganseg_by_batches(
image_names=train_data,
label_names=train_labels,
source_centers=centers_s,
size=patch_size,
nlabels=2,
preload=preload,
)
for i, (p, gt_name) in enumerate(zip(test_data, test_labels)):
p_name = p[0].rsplit('/')[-3]
patient_path = '/'.join(p[0].rsplit('/')[:-1])
print('%s[%s] %sCase %s%s%s%s%s (%d/%d):%s' % (
c['c'], strftime("%H:%M:%S"), c['nc'],
c['c'], c['b'], p_name, c['nc'],
c['c'], i + 1, len(test_data), c['nc']
))
# NO DSC objective
image_cnn_name = os.path.join(patient_path, p_name + '.cnn.test%s.e%d' % (shuffle_s, epochs))
image_gan_name = os.path.join(patient_path, p_name + '.gan.test%s.e%d' % (shuffle_s, epochs))
# DSC objective
image_cnn_dsc_name = os.path.join(patient_path, p_name + '.dsc-cnn.test%s.e%d' % (shuffle_s, epochs))
image_gan_dsc_name = os.path.join(patient_path, p_name + '.dsc-gan.test%s.e%d' % (shuffle_s, epochs))
try:
# NO DSC objective
image_cnn = load_nii(image_cnn_name + '.nii.gz').get_data()
image_cnn_pr = load_nii(image_cnn_name + '.pr.nii.gz').get_data()
image_gan = load_nii(image_gan_name + '.nii.gz').get_data()
image_gan_pr = load_nii(image_gan_name + '.pr.nii.gz').get_data()
# DSC objective
image_cnn_dsc = load_nii(image_cnn_dsc_name + '.nii.gz').get_data()
image_cnn_dsc_pr = load_nii(image_cnn_dsc_name + '.pr.nii.gz').get_data()
image_gan_dsc = load_nii(image_gan_dsc_name + '.nii.gz').get_data()
image_gan_dsc_pr = load_nii(image_gan_dsc_name + '.pr.nii.gz').get_data()
except IOError:
# Lesion segmentation
adversarial_w = K.variable(0)
# NO DSC objective
cnn, gan, gan_test = get_wmh_nets(
input_shape=input_shape,
filters_list=filters_list,
kernel_size_list=kernel_size_list,
dense_size=dense_size,
lambda_var=adversarial_w
)
# DSC objective
cnn_dsc, gan_dsc, gan_dsc_test = get_wmh_nets(
input_shape=input_shape,
filters_list=filters_list,
kernel_size_list=kernel_size_list,
dense_size=dense_size,
lambda_var=adversarial_w,
dsc_obj=True
)
train_nets(
gan=gan,
gan_dsc=gan_dsc,
cnn=cnn,
cnn_dsc=cnn_dsc,
p=p,
x=x_seg,
y=y_seg,
name='wmh2017' + sufix,
adversarial_w=adversarial_w
)
# NO DSC objective
image_cnn = test_net(cnn, p, image_cnn_name)
image_cnn_pr = load_nii(image_cnn_name + '.pr.nii.gz').get_data()
image_gan = test_net(gan_test, p, image_gan_name)
image_gan_pr = load_nii(image_gan_name + '.pr.nii.gz').get_data()
# DSC objective
image_cnn_dsc = test_net(cnn_dsc, p, image_cnn_dsc_name)
image_cnn_dsc_pr = load_nii(image_cnn_dsc_name + '.pr.nii.gz').get_data()
image_gan_dsc = test_net(gan_dsc_test, p, image_gan_dsc_name)
image_gan_dsc_pr = load_nii(image_gan_dsc_name + '.pr.nii.gz').get_data()
# NO DSC objective
seg_cnn = image_cnn.astype(np.bool)
seg_gan = image_gan.astype(np.bool)
# DSC objective
seg_cnn_dsc = image_cnn_dsc.astype(np.bool)
seg_gan_dsc = image_gan_dsc.astype(np.bool)
seg_gt = load_nii(gt_name).get_data()
not_roi = np.logical_not(seg_gt == 2)
results_cnn_dsc = dsc_seg(seg_gt == 1, np.logical_and(seg_cnn_dsc, not_roi))
results_cnn_dsc_pr = probabilistic_dsc_seg(seg_gt == 1, image_cnn_dsc_pr * not_roi)
results_cnn = dsc_seg(seg_gt == 1, np.logical_and(seg_cnn, not_roi))
results_cnn_pr = probabilistic_dsc_seg(seg_gt == 1, image_cnn_pr * not_roi)
results_gan_dsc = dsc_seg(seg_gt == 1, np.logical_and(seg_gan_dsc, not_roi))
results_gan_dsc_pr = probabilistic_dsc_seg(seg_gt == 1, image_gan_dsc_pr * not_roi)
results_gan = dsc_seg(seg_gt == 1, np.logical_and(seg_gan, not_roi))
results_gan_pr = probabilistic_dsc_seg(seg_gt == 1, image_gan_pr * not_roi)
whites = ''.join([' '] * 14)
print('%sCase %s%s%s%s %sCNN%s vs %sGAN%s DSC: %s%f%s (%s%f%s) vs %s%f%s (%s%f%s)' % (
whites, c['c'], c['b'], p_name, c['nc'],
c['lgy'], c['nc'],
c['y'], c['nc'],
c['lgy'], results_cnn_dsc, c['nc'],
c['lgy'], results_cnn, c['nc'],
c['y'], results_gan_dsc, c['nc'],
c['y'], results_gan, c['nc']
))
print('%sCase %s%s%s%s %sCNN%s vs %sGAN%s DSC Pr: %s%f%s (%s%f%s) vs %s%f%s (%s%f%s)' % (
whites, c['c'], c['b'], p_name, c['nc'],
c['lgy'], c['nc'],
c['y'], c['nc'],
c['lgy'], results_cnn_dsc_pr, c['nc'],
c['lgy'], results_cnn_pr, c['nc'],
c['y'], results_gan_dsc_pr, c['nc'],
c['y'], results_gan_pr, c['nc']
))
dsc_results.append((results_cnn_dsc, results_cnn, results_gan_dsc, results_gan))
dsc_results_pr.append((results_cnn_dsc_pr, results_cnn_pr, results_gan_dsc_pr, results_gan_pr))
final_dsc = tuple(np.mean(dsc_results, axis=0))
final_dsc_pr = tuple(np.mean(dsc_results_pr, axis=0))
print('Final results DSC: %s%f%s (%s%f%s) vs %s%f%s (%s%f%s)' % (
c['lgy'], final_dsc[0], c['nc'],
c['lgy'], final_dsc[1], c['nc'],
c['y'], final_dsc[2], c['nc'],
c['y'], final_dsc[3], c['nc']
))
print('Final results DSC Pr: %s%f%s (%s%f%s) vs %s%f%s (%s%f%s)' % (
c['lgy'], final_dsc_pr[0], c['nc'],
c['lgy'], final_dsc_pr[1], c['nc'],
c['y'], final_dsc_pr[2], c['nc'],
c['y'], final_dsc_pr[3], c['nc']
))
def train_test_seg(net_name, n_folds, val_split=0.1):
# Init
c = color_codes()
options = parse_inputs()
depth = options['blocks']
filters = options['filters']
d_path = options['loo_dir']
unc_path = os.path.join(d_path, 'uncertainty')
if not os.path.isdir(unc_path):
os.mkdir(unc_path)
seg_path = os.path.join(d_path, 'segmentation')
if not os.path.isdir(seg_path):
os.mkdir(seg_path)
patients = get_dirs(d_path)
cbica = filter(lambda p: 'CBICA' in p, patients)
tcia = filter(lambda p: 'TCIA' in p, patients)
tmc = filter(lambda p: 'TMC' in p, patients)
b2013 = filter(lambda p: '2013' in p, patients)
for i in range(n_folds):
print(
'%s[%s] %sFold %s(%s%d%s%s/%d)%s' % (
c['c'], strftime("%H:%M:%S"), c['g'],
c['c'], c['b'], i + 1, c['nc'], c['c'], n_folds, c['nc']
)
)
# Training itself
# Data split (using the patient names) for train and validation.
# We also compute the number of batches for both training and
# validation according to the batch size.
''' Training '''
ini_cbica = len(cbica) * i / n_folds
end_cbica = len(cbica) * (i + 1) / n_folds
fold_cbica = cbica[:ini_cbica] + cbica[end_cbica:]
n_fold_cbica = len(fold_cbica)
n_cbica = int(n_fold_cbica * (1 - val_split))
ini_tcia = len(tcia) * i / n_folds
end_tcia = len(tcia) * (i + 1) / n_folds
fold_tcia = tcia[:ini_tcia] + tcia[end_tcia:]
n_fold_tcia = len(fold_tcia)
n_tcia = int(n_fold_tcia * (1 - val_split))
ini_tmc = len(tmc) * i / n_folds
end_tmc = len(tmc) * (i + 1) / n_folds
fold_tmc = tmc[:ini_tmc] + tmc[end_tmc:]
n_fold_tmc = len(fold_tmc)
n_tmc = int(n_fold_tmc * (1 - val_split))
ini_b2013 = len(b2013) * i / n_folds
end_b2013 = len(b2013) * (i + 1) / n_folds
fold_b2013 = b2013[:ini_b2013] + b2013[end_b2013:]
n_fold_b2013 = len(fold_b2013)
n_b2013 = int(n_fold_b2013 * (1 - val_split))
training_n = n_fold_cbica + n_fold_tcia + n_fold_tmc + n_fold_b2013
testing_n = len(patients) - training_n
print(
'Training / testing samples = %d / %d' % (
training_n, testing_n
)
)
# Training
train_cbica = fold_cbica[:n_cbica]
train_tcia = fold_tcia[:n_tcia]
train_tmc = fold_tmc[:n_tmc]
train_b2013 = fold_b2013[:n_b2013]
train_patients = train_cbica + train_tcia + train_tmc + train_b2013
# Validation
val_cbica = fold_cbica[n_cbica:]
val_tcia = fold_tcia[n_tcia:]
val_tmc = fold_tmc[n_tmc:]
val_b2013 = fold_b2013[n_b2013:]
val_patients = val_cbica + val_tcia + val_tmc + val_b2013
model_name = '%s-f%d.mdl' % (net_name, i)
net = BratsSegmentationNet(depth=depth, filters=filters)
# train_seg(net, model_name, train_patients, val_patients)
train_seg(
net, model_name, train_patients, val_patients, dropout=0
)
# model_name = '%s-f%d-R.mdl' % (net_name, i)
# train_seg(
# net, model_name, train_patients, val_patients,
# refine=True, dropout=0.5, lr=1e-2
# )
# Testing data (with GT)
test_cbica = cbica[ini_cbica:end_cbica]
test_tcia = tcia[ini_tcia:end_tcia]
test_tmc = tmc[ini_tmc:end_tmc]
test_b2013 = b2013[ini_b2013:end_b2013]
test_patients = test_cbica + test_tcia + test_tmc + test_b2013
patient_paths = map(lambda p: os.path.join(d_path, p), test_patients)
_, test_x = get_images(test_patients)
print(
'Testing patients (with GT) = %d' % (
len(test_patients)
)
)
# The sub-regions considered for evaluation are:
# 1) the "enhancing tumor" (ET)
# 2) the "tumor core" (TC)
# 3) the "whole tumor" (WT)
#
# The provided segmentation labels have values of 1 for NCR & NET,
# 2 for ED, 4 for ET, and 0 for everything else.
# The participants are called to upload their segmentation labels
# as a single multi-label file in nifti (.nii.gz) format.
#
# The participants are called to upload 4 nifti (.nii.gz) volumes
# (3 uncertainty maps and 1 multi-class segmentation volume from
# Task 1) onto CBICA's Image Processing Portal format. For example,
# for each ID in the dataset, participants are expected to upload
# following 4 volumes:
# 1. {ID}.nii.gz (multi-class label map)
# 2. {ID}_unc_whole.nii.gz (Uncertainty map associated with whole tumor)
# 3. {ID}_unc_core.nii.gz (Uncertainty map associated with tumor core)
# 4. {ID}_unc_enhance.nii.gz (Uncertainty map associated with enhancing tumor)
for p, (path_i, p_i, test_i) in enumerate(zip(
patient_paths, test_patients, test_x
)):
pred_i = net.segment([test_i])[0]
# unc_i = net.uncertainty([test_i], steps=25)[0]
# whole_i = np.sum(unc_i[1:])
# core_i = unc_i[1] + unc_i[-1]
# enhance_i = unc_i[-1]
seg_i = np.argmax(pred_i, axis=0)
seg_i[seg_i == 3] = 4
# seg_unc_i = np.argmax(unc_i, axis=0)
# seg_unc_i[seg_unc_i == 3] = 4
# tumor_mask = remove_small_regions(
# seg_i.astype(np.bool), min_size=30
# )
#
# seg_i[log_not(tumor_mask)] = 0
# seg_unc_i[log_not(tumor_mask)] = 0
#
# whole_i *= tumor_mask.astype(np.float32)
# core_i *= tumor_mask.astype(np.float32)
# enhance_i *= tumor_mask.astype(np.float32)
niiname = os.path.join(path_i, p_i + '_seg.nii.gz')
nii = load_nii(niiname)
seg = nii.get_data()
dsc = map(
lambda label: dsc_seg(seg == label, seg_i == label),
[1, 2, 4]
)
# dsc_unc = map(
# lambda label: dsc_seg(seg == label, seg_unc_i == label),
# [1, 2, 4]
# )
nii.get_data()[:] = seg_i
save_nii(nii, os.path.join(seg_path, p_i + '.nii.gz'))
# nii.get_data()[:] = seg_unc_i
# save_nii(nii, os.path.join(unc_path, p_i + '.nii.gz'))
# niiname = os.path.join(d_path, p_i, p_i + '_flair.nii.gz')
# nii = load_nii(niiname)
# nii.get_data()[:] = whole_i
# save_nii(nii, os.path.join(unc_path, p_i + '_unc_whole.nii.gz'))
# nii.get_data()[:] = core_i
# save_nii(nii, os.path.join(unc_path, p_i + '_unc_core.nii.gz'))
# nii.get_data()[:] = enhance_i
# save_nii(nii, os.path.join(unc_path, p_i + '_unc_enhance.nii.gz'))
print(
'Segmentation - Patient %s (%d/%d): %s' % (
p_i, p, len(test_x), ' / '.join(map(str, dsc))
)
)
def main():
options = parse_inputs()
c = color_codes()
# Prepare the net architecture parameters
sequential = options['sequential']
dfactor = options['dfactor']
# Prepare the net hyperparameters
num_classes = 5
epochs = options['epochs']
padding = options['padding']
patch_width = options['patch_width']
patch_size = (patch_width, patch_width, patch_width)
batch_size = options['batch_size']
dense_size = options['dense_size']
conv_blocks = options['conv_blocks']
n_filters = options['n_filters']
filters_list = n_filters if len(n_filters) > 1 else n_filters * conv_blocks
conv_width = options['conv_width']
kernel_size_list = conv_width if isinstance(
conv_width, list) else [conv_width] * conv_blocks
balanced = options['balanced']
recurrent = options['recurrent']
# Data loading parameters
preload = options['preload']
queue = options['queue']
# Prepare the sufix that will be added to the results for the net and images
path = options['dir_name']
filters_s = 'n'.join(['%d' % nf for nf in filters_list])
conv_s = 'c'.join(['%d' % cs for cs in kernel_size_list])
s_s = '.s' if sequential else '.f'
ub_s = '.ub' if not balanced else ''
params_s = (ub_s, dfactor, s_s, patch_width, conv_s, filters_s, dense_size,
epochs, padding)
sufix = '%s.D%d%s.p%d.c%s.n%s.d%d.e%d.pad_%s.' % params_s
n_channels = np.count_nonzero([
options['use_flair'], options['use_t2'], options['use_t1'],
options['use_t1ce']
])
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' +
'Starting cross-validation' + c['nc'])
# N-fold cross validation main loop (we'll do 2 training iterations with testing for each patient)
data_names, label_names = get_names_from_path(options)
folds = options['folds']
fold_generator = izip(
nfold_cross_validation(data_names, label_names, n=folds,
val_data=0.25), xrange(folds))
dsc_results = list()
for (train_data, train_labels, val_data, val_labels, test_data,
test_labels), i in fold_generator:
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['nc'] +
'Fold %d/%d: ' % (i + 1, folds) + c['g'] +
'Number of training/validation/testing images (%d=%d/%d=%d/%d)' %
(len(train_data), len(train_labels), len(val_data),
len(val_labels), len(test_data)) + c['nc'])
# Prepare the data relevant to the leave-one-out (subtract the patient from the dataset and set the path)
# Also, prepare the network
net_name = os.path.join(
path, 'baseline-brats2017.fold%d' % i + sufix + 'mdl')
# First we check that we did not train for that patient, in order to save time
try:
net = keras.models.load_model(net_name)
except IOError:
# NET definition using Keras
train_centers = get_cnn_centers(train_data[:, 0],
train_labels,
balanced=balanced)
val_centers = get_cnn_centers(val_data[:, 0],
val_labels,
balanced=balanced)
train_samples = len(train_centers) / dfactor
val_samples = len(val_centers) / dfactor
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'Creating and compiling the model ' + c['b'] +
'(%d samples)' % train_samples + c['nc'])
train_steps_per_epoch = -(-train_samples / batch_size)
val_steps_per_epoch = -(-val_samples / batch_size)
input_shape = (n_channels, ) + patch_size
if sequential:
# Sequential model that merges all 4 images. This architecture is just a set of convolutional blocks
# that end in a dense layer. This is supposed to be an original baseline.
net = Sequential()
net.add(
Conv3D(filters_list[0],
kernel_size=kernel_size_list[0],
input_shape=input_shape,
activation='relu',
data_format='channels_first'))
for filters, kernel_size in zip(filters_list[1:],
kernel_size_list[1:]):
net.add(Dropout(0.5))
net.add(
Conv3D(filters,
kernel_size=kernel_size,
activation='relu',
data_format='channels_first'))
net.add(Dropout(0.5))
net.add(Flatten())
net.add(Dense(dense_size, activation='relu'))
net.add(Dropout(0.5))
net.add(Dense(num_classes, activation='softmax'))
else:
# This architecture is based on the functional Keras API to introduce 3 output paths:
# - Whole tumor segmentation
# - Core segmentation (including whole tumor)
# - Whole segmentation (tumor, core and enhancing parts)
# The idea is to let the network work on the three parts to improve the multiclass segmentation.
merged_inputs = Input(shape=(4, ) + patch_size,
name='merged_inputs')
flair = Reshape((1, ) + patch_size)(Lambda(
lambda l: l[:, 0, :, :, :],
output_shape=(1, ) + patch_size)(merged_inputs), )
t2 = Reshape((1, ) + patch_size)(Lambda(
lambda l: l[:, 1, :, :, :],
output_shape=(1, ) + patch_size)(merged_inputs))
t1 = Lambda(lambda l: l[:, 2:, :, :, :],
output_shape=(2, ) + patch_size)(merged_inputs)
for filters, kernel_size in zip(filters_list,
kernel_size_list):
flair = Conv3D(filters,
kernel_size=kernel_size,
activation='relu',
data_format='channels_first')(flair)
t2 = Conv3D(filters,
kernel_size=kernel_size,
activation='relu',
data_format='channels_first')(t2)
t1 = Conv3D(filters,
kernel_size=kernel_size,
activation='relu',
data_format='channels_first')(t1)
flair = Dropout(0.5)(flair)
t2 = Dropout(0.5)(t2)
t1 = Dropout(0.5)(t1)
# We only apply the RCNN to the multioutput approach (we keep the simple one, simple)
if recurrent:
flair = Conv3D(dense_size,
kernel_size=(1, 1, 1),
activation='relu',
data_format='channels_first',
name='fcn_flair')(flair)
flair = Dropout(0.5)(flair)
t2 = concatenate([flair, t2], axis=1)
t2 = Conv3D(dense_size,
kernel_size=(1, 1, 1),
activation='relu',
data_format='channels_first',
name='fcn_t2')(t2)
t2 = Dropout(0.5)(t2)
t1 = concatenate([t2, t1], axis=1)
t1 = Conv3D(dense_size,
kernel_size=(1, 1, 1),
activation='relu',
data_format='channels_first',
name='fcn_t1')(t1)
t1 = Dropout(0.5)(t1)
flair = Dropout(0.5)(flair)
t2 = Dropout(0.5)(t2)
t1 = Dropout(0.5)(t1)
lstm_instance = LSTM(dense_size,
implementation=1,
name='rf_layer')
flair = lstm_instance(
Permute((2, 1))(Reshape((dense_size, -1))(flair)))
t2 = lstm_instance(
Permute((2, 1))(Reshape((dense_size, -1))(t2)))
t1 = lstm_instance(
Permute((2, 1))(Reshape((dense_size, -1))(t1)))
else:
flair = Flatten()(flair)
t2 = Flatten()(t2)
t1 = Flatten()(t1)
flair = Dense(dense_size, activation='relu')(flair)
flair = Dropout(0.5)(flair)
t2 = concatenate([flair, t2])
t2 = Dense(dense_size, activation='relu')(t2)
t2 = Dropout(0.5)(t2)
t1 = concatenate([t2, t1])
t1 = Dense(dense_size, activation='relu')(t1)
t1 = Dropout(0.5)(t1)
tumor = Dense(2, activation='softmax', name='tumor')(flair)
core = Dense(3, activation='softmax', name='core')(t2)
enhancing = Dense(num_classes,
activation='softmax',
name='enhancing')(t1)
net = Model(inputs=merged_inputs,
outputs=[tumor, core, enhancing])
net.compile(optimizer='adadelta',
loss='categorical_crossentropy',
metrics=['accuracy'])
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'Training the model with a generator for ' + c['b'] +
'(%d parameters)' % net.count_params() + c['nc'])
print(net.summary())
net.fit_generator(
generator=load_patch_batch_train(image_names=train_data,
label_names=train_labels,
centers=train_centers,
batch_size=batch_size,
size=patch_size,
nlabels=num_classes,
dfactor=dfactor,
preload=preload,
split=not sequential,
datatype=np.float32),
validation_data=load_patch_batch_train(image_names=val_data,
label_names=val_labels,
centers=val_centers,
batch_size=batch_size,
size=patch_size,
nlabels=num_classes,
dfactor=dfactor,
preload=preload,
split=not sequential,
datatype=np.float32),
steps_per_epoch=train_steps_per_epoch,
validation_steps=val_steps_per_epoch,
max_q_size=queue,
epochs=epochs)
net.save(net_name)
# Then we test the net.
use_gt = options['use_gt']
for p, gt_name in zip(test_data, test_labels):
p_name = p[0].rsplit('/')[-2]
patient_path = '/'.join(p[0].rsplit('/')[:-1])
outputname = os.path.join(patient_path,
'deep-brats17' + sufix + 'test.nii.gz')
try:
load_nii(outputname)
except IOError:
roi_nii = load_nii(p[0])
roi = roi_nii.get_data().astype(dtype=np.bool)
centers = get_mask_voxels(roi)
test_samples = np.count_nonzero(roi)
image = np.zeros_like(roi).astype(dtype=np.uint8)
print(c['c'] + '[' + strftime("%H:%M:%S") + '] ' + c['g'] +
'<Creating the probability map ' + c['b'] + p_name +
c['nc'] + c['g'] + ' (%d samples)>' % test_samples +
c['nc'])
test_steps_per_epoch = -(-test_samples / batch_size)
y_pr_pred = net.predict_generator(
generator=load_patch_batch_generator_test(
image_names=p,
centers=centers,
batch_size=batch_size,
size=patch_size,
preload=preload,
),
steps=test_steps_per_epoch,
max_q_size=queue)
[x, y, z] = np.stack(centers, axis=1)
if not sequential:
tumor = np.argmax(y_pr_pred[0], axis=1)
y_pr_pred = y_pr_pred[-1]
roi = np.zeros_like(roi).astype(dtype=np.uint8)
roi[x, y, z] = tumor
roi_nii.get_data()[:] = roi
roiname = os.path.join(
patient_path,
'deep-brats17' + sufix + 'test.roi.nii.gz')
roi_nii.to_filename(roiname)
y_pred = np.argmax(y_pr_pred, axis=1)
image[x, y, z] = y_pred
# Post-processing (Basically keep the biggest connected region)
image = get_biggest_region(image)
if use_gt:
gt_nii = load_nii(gt_name)
gt = np.copy(gt_nii.get_data()).astype(dtype=np.uint8)
labels = np.unique(gt.flatten())
results = (p_name, ) + tuple(
[dsc_seg(gt == l, image == l) for l in labels[1:]])
text = 'Subject %s DSC: ' + '/'.join(
['%f' for _ in labels[1:]])
print(text % results)
dsc_results.append(results)
print(c['g'] + ' -- Saving image ' + c['b'] +
outputname + c['nc'])
roi_nii.get_data()[:] = image
roi_nii.to_filename(outputname)
def check_dsc(gt_name, image):
gt_nii = load_nii(gt_name)
gt = np.copy(gt_nii.get_data()).astype(dtype=np.uint8)
labels = np.unique(gt.flatten())
return [dsc_seg(gt == l, image == l) for l in labels[1:]]