Refactor the model utils functions (download weight files, get weight files path, and load models)
dc4b749
import os, sys | |
# currentdir = os.path.dirname(os.path.realpath(__file__)) | |
# parentdir = os.path.dirname(currentdir) | |
# sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing | |
# | |
# PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True' | |
import tensorflow as tf | |
import voxelmorph as vxm | |
from voxelmorph.tf.modelio import LoadableModel, store_config_args | |
from tensorflow.keras.layers import UpSampling3D | |
class WeaklySupervised(LoadableModel): | |
def __init__(self, inshape, all_labels: [list, tuple], nb_unet_features=None, int_steps=5, bidir=False, | |
int_downsize=1, outshape=None, **kwargs): | |
""" | |
Parameters: | |
inshape: Input shape. e.g. (192, 192, 192) | |
all_labels: List of all labels included in training segmentations. | |
hot_labels: List of labels to output as one-hot maps. | |
nb_unet_features: Unet convolutional features. See VxmDense documentation for more information. | |
int_steps: Number of flow integration steps. The warp is non-diffeomorphic when this value is 0. | |
int_downsize: Dowsampling of the displacement map. Integer | |
kwargs: Forwarded to the internal VxmDense model. | |
""" | |
mov_segm = tf.keras.Input((*inshape, len(all_labels)), name='mov_segmentations_input') | |
fix_img = tf.keras.Input((*inshape, 1), name='fix_image_input') | |
mov_img = tf.keras.Input((*inshape, 1), name='mov_image_input') | |
input_model = tf.keras.Model(inputs=[mov_img, fix_img], outputs=[mov_img, fix_img]) | |
vxm_model = vxm.networks.VxmDense(inshape=inshape, | |
nb_unet_features=nb_unet_features, | |
input_model=input_model, | |
int_steps=int_steps, | |
bidir=bidir, | |
int_downsize=int_downsize, | |
**kwargs) | |
pred_segm = vxm.layers.SpatialTransformer(interp_method='linear', indexing='ij', name='interp_segm')( | |
[mov_segm, vxm_model.references.pos_flow]) | |
inputs = [mov_img, fix_img, mov_segm] # mov_img, mov_segm, fix_segm | |
model_outputs = vxm_model.outputs | |
if outshape is not None: | |
scale_factors = [o//i for i, o in zip(inshape, outshape)] | |
upsampling_layer = UpSampling3D(scale_factors) # Doesn't perform trilinear, only nearest | |
# Image | |
model_outputs[0] = upsampling_layer(model_outputs[0]) | |
# Segmentation | |
pred_segm = upsampling_layer(pred_segm) | |
# Displacement map | |
model_outputs[1] = upsampling_layer(scale_factors)(model_outputs[1]) | |
model_outputs[1] = tf.multiply(model_outputs[1], tf.cast(scale_factors, model_outputs[1].dtype)) | |
# Just renaming | |
pred_fix_image = tf.identity(model_outputs[0], name='pred_fix_image') | |
pred_dm = tf.identity(model_outputs[1], name='pred_dm') | |
pred_segm = tf.identity(pred_segm, name='pred_fix_segm') | |
outputs = [pred_fix_image, pred_segm, pred_dm] | |
self.references = LoadableModel.ReferenceContainer() | |
self.references.pred_segm = pred_segm | |
self.references.pred_img = vxm_model.outputs[0] | |
self.references.pos_flow = vxm_model.references.pos_flow | |
super(WeaklySupervised, self).__init__(inputs=inputs, outputs=outputs) | |
def get_registration_model(self): | |
return tf.keras.Model(self.inputs, self.references.pos_flow) | |
def register(self, mov_img, mov_segm, fix_segm): | |
return self.get_registration_model().predict([mov_segm, fix_segm, mov_img]) | |
def apply_transform(self, mov_img, mov_segm, fix_segm, interp_method='linear'): | |
warp_model = self.get_registration_model() | |
img_input = tf.keras.Input(shape=mov_img.shape[1:], name='input_img') | |
pred_img = vxm.layers.SpatialTransformer(interp_method=interp_method)([img_input, warp_model.output]) | |
return tf.keras.Model(warp_model.inputs, pred_img).predict([mov_segm, fix_segm, mov_img]) | |