--- a +++ b/DigiPathAI/models/densenet.py @@ -0,0 +1,165 @@ +""" + github cite: +""" + +from __future__ import absolute_import +from __future__ import division +from __future__ import print_function + +from datetime import datetime +import os +import glob +import random + +import imgaug +from imgaug import augmenters as iaa +from PIL import Image +from tqdm import tqdm +import matplotlib.pyplot as plt + + +import numpy as np +import tensorflow as tf +from tensorflow.keras import backend as K +from tensorflow.keras.models import Model +from tensorflow.keras.layers import (Input, BatchNormalization, Conv2D, MaxPooling2D, AveragePooling2D, ZeroPadding2D, concatenate, + Concatenate, UpSampling2D, Activation, Lambda) +from tensorflow.keras.losses import categorical_crossentropy +from tensorflow.keras.optimizers import Adam +from tensorflow.keras.callbacks import ModelCheckpoint, LearningRateScheduler, TensorBoard +from tensorflow.keras import metrics + + +# Densenet Model +bn_axis = 3 +channel_axis = bn_axis + +def conv_block(prev, num_filters, kernel=(3, 3), strides=(1, 1), act='relu', prefix=None): + name = None + if prefix is not None: + name = prefix + '_conv' + conv = Conv2D(num_filters, kernel, padding='same', kernel_initializer='he_normal', strides=strides, name=name)(prev) + if prefix is not None: + name = prefix + '_norm' + conv = BatchNormalization(name=name, axis=bn_axis)(conv) + if prefix is not None: + name = prefix + '_act' + conv = Activation(act, name=name)(conv) + return conv + +def dense_conv_block(x, growth_rate, name): + """A building block for a dense block. + # Arguments + x: input tensor. + growth_rate: float, growth rate at dense layers. + name: string, block label. + # Returns + Output tensor for the block. + """ + bn_axis = 3 + x1 = BatchNormalization(axis=bn_axis, + epsilon=1.001e-5, + name=name + '_0_bn')(x) + x1 = Activation('relu', name=name + '_0_relu')(x1) + x1 = Conv2D(4 * growth_rate, 1, + use_bias=False, + name=name + '_1_conv')(x1) + x1 = BatchNormalization(axis=bn_axis, epsilon=1.001e-5, + name=name + '_1_bn')(x1) + x1 = Activation('relu', name=name + '_1_relu')(x1) + x1 = Conv2D(growth_rate, 3, + padding='same', + use_bias=False, + name=name + '_2_conv')(x1) + x = Concatenate(axis=bn_axis, name=name + '_concat')([x, x1]) + return x + +def dense_block(x, blocks, name): + """A dense block. + # Arguments + x: input tensor. + blocks: integer, the number of building blocks. + name: string, block label. + # Returns + output tensor for the block. + """ + for i in range(blocks): + x = dense_conv_block(x, 32, name=name + '_block' + str(i + 1)) + return x + + +def transition_block(x, reduction, name): + """A transition block. + # Arguments + x: input tensor. + reduction: float, compression rate at transition layers. + name: string, block label. + # Returns + output tensor for the block. + """ + bn_axis = 3 + x = BatchNormalization(axis=bn_axis, epsilon=1.001e-5, + name=name + '_bn')(x) + x = Activation('relu', name=name + '_relu')(x) + x = Conv2D(int(K.int_shape(x)[bn_axis] * reduction), 1, + use_bias=False, + name=name + '_conv')(x) + x = AveragePooling2D(2, strides=2, name=name + '_pool')(x) + return x + +def unet_densenet121(input_shape, weights='imagenet'): + blocks = [6, 12, 24, 16] + n_channel = 3 + n_class = 2 + img_input = Input(input_shape + (n_channel,)) + + x = ZeroPadding2D(padding=((3, 3), (3, 3)))(img_input) + x = Conv2D(64, 7, strides=2, use_bias=False, name='conv1/conv')(x) + x = BatchNormalization(axis=bn_axis, epsilon=1.001e-5, + name='conv1/bn')(x) + x = Activation('relu', name='conv1/relu')(x) + conv1 = x + x = ZeroPadding2D(padding=((1, 1), (1, 1)))(x) + x = MaxPooling2D(3, strides=2, name='pool1')(x) + x = dense_block(x, blocks[0], name='conv2') + conv2 = x + x = transition_block(x, 0.5, name='pool2') + x = dense_block(x, blocks[1], name='conv3') + conv3 = x + x = transition_block(x, 0.5, name='pool3') + x = dense_block(x, blocks[2], name='conv4') + conv4 = x + x = transition_block(x, 0.5, name='pool4') + x = dense_block(x, blocks[3], name='conv5') + x = BatchNormalization(axis=bn_axis, epsilon=1.001e-5, + name='bn')(x) + conv5 = x + + conv6 = conv_block(UpSampling2D()(conv5), 320) + conv6 = concatenate([conv6, conv4], axis=-1) + conv6 = conv_block(conv6, 320) + + conv7 = conv_block(UpSampling2D()(conv6), 256) + conv7 = concatenate([conv7, conv3], axis=-1) + conv7 = conv_block(conv7, 256) + + conv8 = conv_block(UpSampling2D()(conv7), 128) + conv8 = concatenate([conv8, conv2], axis=-1) + conv8 = conv_block(conv8, 128) + + conv9 = conv_block(UpSampling2D()(conv8), 96) + conv9 = concatenate([conv9, conv1], axis=-1) + conv9 = conv_block(conv9, 96) + + conv10 = conv_block(UpSampling2D()(conv9), 64) + conv10 = conv_block(conv10, 64) + res = Conv2D(n_class, (1, 1), activation='softmax')(conv10) + model = Model(img_input, res) + + return model +#model = unet_densenet121(input_shape=(256,256), weights=None) +#model.summary() + + +# In[6]: +