# %% importing packages

import numpy as np

import tensorflow as tf

from tensorflow import keras

from tensorflow.keras import layers

from tensorflow.keras import mixed_precision

from tensorflow.python.ops.numpy_ops import np_config

np_config.enable_numpy_behavior()

from skimage import measure

import cv2 as cv

import os

import matplotlib.pyplot as plt

plt.rcParams['figure.figsize'] = [10, 15]

# %% Citations

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# https://www.tensorflow.org/guide/keras/functional

# https://www.tensorflow.org/tutorials/customization/custom_layers

# https://keras.io/examples/keras_recipes/tfrecord/

# https://arxiv.org/abs/1505.04597

# https://www.tensorflow.org/guide/gpu

# Defining Functions

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def parse_tf_elements(element):

    '''This function is the mapper function for retrieving examples from the

       tfrecord'''

    # create placeholders for all the features in each example

    data = {

        'height' : tf.io.FixedLenFeature([],tf.int64),

        'width' : tf.io.FixedLenFeature([],tf.int64),

        'raw_image' : tf.io.FixedLenFeature([],tf.string),

        'raw_seg' : tf.io.FixedLenFeature([],tf.string),

        'bbox_x' : tf.io.VarLenFeature(tf.float32),

        'bbox_y' : tf.io.VarLenFeature(tf.float32),

        'bbox_height' : tf.io.VarLenFeature(tf.float32),

        'bbox_width' : tf.io.VarLenFeature(tf.float32)

    }

    # pull out the current example

    content = tf.io.parse_single_example(element, data)

    # pull out each feature from the example 

    height = content['height']

    width = content['width']

    raw_seg = content['raw_seg']

    raw_image = content['raw_image']

    bbox_x = content['bbox_x']

    bbox_y = content['bbox_y']

    bbox_height = content['bbox_height']

    bbox_width = content['bbox_width']

    # convert the images to uint8, and reshape them accordingly

    image = tf.io.parse_tensor(raw_image, out_type=tf.uint8)

    image = tf.reshape(image,shape=[height,width,3])

    segmentation = tf.io.parse_tensor(raw_seg, out_type=tf.uint8)

    segmentation = tf.reshape(segmentation,shape=[height,width,1])

    one_hot_seg = tf.one_hot(tf.squeeze(segmentation),7,axis=-1)

    # there currently is a bug with returning the bbox, but isn't necessary

    # to fix for creating the initial uNet for segmentation exploration

    # bbox = [bbox_x,bbox_y,bbox_height,bbox_width]

    return(image,one_hot_seg)

#############################################################

class EncoderBlock(layers.Layer):

    '''This function returns an encoder block with two convolutional layers and 

       an option for returning both a max-pooled output with a stride and pool 

       size of (2,2) and the output of the second convolution for skip 

       connections implemented later in the network during the decoding 

       section. All padding is set to "same" for cleanliness.

       When initializing it receives the number of filters to be used in both

       of the convolutional layers as well as the kernel size and stride for 

       those same layers. It also receives the trainable variable for use with

       the batch normalization layers.'''

    def __init__(self,

                 filters,

                 kernel_size=(3,3),

                 strides=(1,1),

                 trainable=True,

                 name='encoder_block',

                 **kwargs):

        super(EncoderBlock,self).__init__(trainable, name, **kwargs)

        # When initializing this object receives a trainable parameter for

        # freezing the convolutional layers. 

        # including the image normalization within the network for easier image

        # processing during inference

        self.image_normalization = layers.Normalization()

        # below creates the first of two convolutional layers

        self.conv1 = layers.Conv2D(filters=filters,

                      kernel_size=kernel_size,

                      strides=strides,

                      padding='same',

                      name='encoder_conv1',

                      trainable=trainable)

        # second of two convolutional layers

        self.conv2 = layers.Conv2D(filters=filters,

                      kernel_size=kernel_size,

                      strides=strides,

                      padding='same',

                      name='encoder_conv2',

                      trainable=trainable)

        # creates the max-pooling layer for downsampling the image.

        self.enc_pool = layers.MaxPool2D(pool_size=(2,2),

                                    strides=(2,2),

                                    padding='same',

                                    name='enc_pool')

        # ReLU layer for activations.

        self.ReLU = layers.ReLU()

        # both batch normalization layers for use with their corresponding

        # convolutional layers.

        self.batch_norm1 = tf.keras.layers.BatchNormalization()

        self.batch_norm2 = tf.keras.layers.BatchNormalization()

    def call(self,input,training=True,include_pool=True):

        # first conv of the encoder block

        x = self.image_normalization(input)

        x = self.conv1(x)

        x = self.batch_norm1(x,training=training)

        x = self.ReLU(x)

        # second conv of the encoder block

        x = self.conv2(x)

        x = self.batch_norm2(x,training=training)

        x = self.ReLU(x)

        # calculate and include the max pooling layer if include_pool is true.

        # This output is used for the skip connections later in the network.

        if include_pool:

            pooled_x = self.enc_pool(x)

            return(x,pooled_x)

        else:

            return(x)

#############################################################

class DecoderBlock(layers.Layer):

    '''This function returns a decoder block that when called receives both an

       input and a "skip connection". The input is passed to the 

       "up convolution" or transpose conv layer to double the dimensions before

       being concatenated with its associated skip connection from the encoder

       section of the network. All padding is set to "same" for cleanliness. 

       The decoder block also has an option for including an additional 

       "segmentation" layer, which is a (1,1) convolution with 4 filters, which

       produces the logits for the one-hot encoded ground truth. 

       When initializing it receives the number of filters to be used in the

       up convolutional layer as well as the other two forward convolutions. 

       The received kernel_size and stride is used for the forward convolutions,

       with the up convolution kernel and stride set to be (2,2).'''

    def __init__(self,

                 filters,

                 trainable=True,

                 kernel_size=(3,3),

                 strides=(1,1),

                 name='DecoderBlock',

                 **kwargs):

        super(DecoderBlock,self).__init__(trainable, name, **kwargs)

        # creating the up convolution layer

        self.up_conv = layers.Conv2DTranspose(filters=filters,

                                              kernel_size=(2,2),

                                              strides=(2,2),

                                              padding='same',

                                              name='decoder_upconv',

                                              trainable=trainable)

        # the first of two forward convolutional layers

        self.conv1 = layers.Conv2D(filters=filters,

                                   kernel_size=kernel_size,

                                   strides=strides,

                                   padding='same',

                                   name ='decoder_conv1',

                                   trainable=trainable)

        # second convolutional layer

        self.conv2 = layers.Conv2D(filters=filters,

                                   kernel_size=kernel_size,

                                   strides=strides,

                                   padding='same',

                                   name ='decoder_conv2',

                                   trainable=trainable)

        # this creates the output prediction logits layer.

        self.seg_out = layers.Conv2D(filters=7,

                        kernel_size=(1,1),

                        name='conv_feature_map')

        # ReLU for activation of all above layers

        self.ReLU = layers.ReLU()

        # the individual batch normalization layers for their respective 

        # convolutional layers.

        self.batch_norm1 = tf.keras.layers.BatchNormalization()

        self.batch_norm2 = tf.keras.layers.BatchNormalization()

    def call(self,input,skip_conn,training=True,segmentation=False):

        up = self.up_conv(input) # perform image up convolution

        # concatenate the input and the skip_conn along the features axis

        concatenated = layers.concatenate([up,skip_conn],axis=-1)

        # first convolution 

        x = self.conv1(concatenated)

        x = self.batch_norm1(x,training=training)

        x = self.ReLU(x)

        # second convolution

        x = self.conv2(x)

        x = self.batch_norm2(x,training=training)

        x = self.ReLU(x)

        # if segmentation is True, then run the segmentation (1,1) convolution

        # and use the Softmax to produce a probability distribution.

        if segmentation:

            seg = self.seg_out(x)

            # deliberately set as "float32" to ensure proper calculation if 

            # switching to mixed precision for efficiency

            prob = layers.Softmax(dtype='float32')(seg)

            return(prob)

        else:

            return(x)

#############################################################

class uNet(keras.Model):

    '''This is a sub-classed model that uses the encoder and decoder blocks

       defined above to create a custom unet. The differences from the original 

       paper include a variable filter scalar (filter_multiplier), batch 

       normalization between each convolutional layer and the associated ReLU 

       activation, as well as feature normalization implemented in the first 

       layer of the network.'''

    def __init__(self,filter_multiplier=2,**kwargs):

        super(uNet,self).__init__()

        # Defining encoder blocks

        self.encoder_block1 = EncoderBlock(filters=2*filter_multiplier,

                                           name='Enc1')

        self.encoder_block2 = EncoderBlock(filters=4*filter_multiplier,

                                           name='Enc2')

        self.encoder_block3 = EncoderBlock(filters=8*filter_multiplier,

                                           name='Enc3')

        self.encoder_block4 = EncoderBlock(filters=16*filter_multiplier,

                                           name='Enc4')

        self.encoder_block5 = EncoderBlock(filters=32*filter_multiplier,

                                           name='Enc5')

        self.encoder_block6 = EncoderBlock(filters=64*filter_multiplier,

                                           name='Enc6')

        # Defining decoder blocks. The names are in reverse order to make it 

        # (hopefully) easier to understand which skip connections are associated

        # with which decoder layers.

        self.decoder_block5 = DecoderBlock(filters=32*filter_multiplier,

                                           name='Dec5')

        self.decoder_block4 = DecoderBlock(filters=16*filter_multiplier,

                                           name='Dec4')

        self.decoder_block3 = DecoderBlock(filters=8*filter_multiplier,

                                           name='Dec3')

        self.decoder_block2 = DecoderBlock(filters=4*filter_multiplier,

                                           name='Dec2')

        self.decoder_block1 = DecoderBlock(filters=2*filter_multiplier,

                                           name='Dec1')

    def call(self,inputs,training):

        # encoder    

        enc1,enc1_pool = self.encoder_block1(input=inputs,training=training)

        enc2,enc2_pool = self.encoder_block2(input=enc1_pool,training=training)

        enc3,enc3_pool = self.encoder_block3(input=enc2_pool,training=training)

        enc4,enc4_pool = self.encoder_block4(input=enc3_pool,training=training)

        enc5,enc5_pool = self.encoder_block5(input=enc4_pool,training=training)

        enc6 = self.encoder_block6(input=enc5_pool,

                                   include_pool=False,

                                   training=training)

        # decoder

        dec5 = self.decoder_block5(input=enc6,skip_conn=enc5,training=training)

        dec4 = self.decoder_block4(input=dec5,skip_conn=enc4,training=training)

        dec3 = self.decoder_block3(input=dec4,skip_conn=enc3,training=training)

        dec2 = self.decoder_block2(input=dec3,skip_conn=enc2,training=training)

        seg_logits_out = self.decoder_block1(input=dec2,

                                             skip_conn=enc1,

                                             segmentation=True,

                                             training=training)

        return(seg_logits_out)

#############################################################

def load_dataset(file_names):

    '''Receives a list of file names from a folder that contains tfrecord files

       compiled previously. Takes these names and creates a tensorflow dataset

       from them.'''

    ignore_order = tf.data.Options()

    ignore_order.experimental_deterministic = False

    dataset = tf.data.TFRecordDataset(file_names)

    # you can shard the dataset if you like to reduce the size when necessary

    dataset = dataset.shard(num_shards=3,index=1)

    # order in the file names doesn't really matter, so ignoring it

    dataset = dataset.with_options(ignore_order)

    # mapping the dataset using the parse_tf_elements function defined earlier

    dataset = dataset.map(parse_tf_elements,num_parallel_calls=1)

    return(dataset)

#############################################################

def get_dataset(file_names,batch_size):

    '''Receives a list of file names of tfrecord shards from a dataset as well

       as a batch size for the dataset.'''

    # uses the load_dataset function to retrieve the files and put them into a 

    # dataset.

    dataset = load_dataset(file_names)

    # creates a shuffle buffer of 1000. Number was arbitrarily chosen, feel free

    # to alter as fits your hardware.

    dataset = dataset.shuffle(1000)

    # adding the batch size to the dataset

    dataset = dataset.batch(batch_size=batch_size)

    return(dataset)

#############################################################

def weighted_cce_loss(y_true,y_pred):

    '''Yes, this function essentially does what the "fit" argument 

       "class_weight" does when training a network. I had to create this 

       separate custom loss function because aparently when using tfrecord files

       for reading your dataset a check is performed comparing the input, ground

       truth, and weights values to each other. However, a comparison between 

       the empty None that is passed during the build call of the model and the

       weight array/dictionary returns an error. Thus, here is a custom loss 

       function that applies a weighting to the different classes based on the 

       distribution of the classes within the entire dataset. For thoroughness'

       sake future iteration of the dataset will only base the weights on the 

       dataset used for training, not the whole dataset.'''

    # weights for each class, as background, connective, muscle, and vasculature

    weights = [0,10.52735078, 2.3808943, 2.44062288, 250.61600774,  8,  20]

    # create a weight for each of the images in the current batch (because the

    # weighting for categorical crossentropy needs one per input)

    for idx,weight in enumerate(weights):

        # making the input a numpy array and not an eager tensor to allow for

        # binary index masking.

        current_weights = np.asarray(tf.argmax(y_true,axis=-1)).copy().astype(

                                                                    np.float64)

        # create a mask for the current class that then becomes the value of the

        # weight. This is then passed to the loss function to apply to each

        # pixel.

        mask = current_weights==idx

        current_weights[mask] = weight

    cce = tf.keras.losses.CategoricalCrossentropy()

    cce_loss = cce(y_true,y_pred,current_weights)

    return(cce_loss)

#############################################################

#############################################################

# %% Setting up the GPU, and setting memory growth to true so that it is easier

# to see how much memory the training process is taking up exactly. This code is

# from a tensorflow tutorial. 

gpus = tf.config.list_physical_devices('GPU')

if gpus:

  try:

    for gpu in gpus:

      tf.config.experimental.set_memory_growth(gpu, True)

    logical_gpus = tf.config.list_logical_devices('GPU')

    print(len(gpus), "Physical GPUs,", len(logical_gpus), "Logical GPUs")

  except RuntimeError as e:

    print(e)

# use this to set mixed precision for higher efficiency later if you would like

# mixed_precision.set_global_policy('mixed_float16')

# %% setting up datasets and building model

# directory where the dataset shards are stored

shard_dataset_directory = '/home/briancottle/Research/Semantic_Segmentation/dataset_shards'

os.chdir(shard_dataset_directory)

# only get the file names that follow the shard naming convention

file_names = tf.io.gfile.glob(shard_dataset_directory + \

                              "/shard_*_of_*.tfrecords")

# first 70% of names go to the training dataset. Following 20% go to the val

# dataset, followed by last 10% go to the testing dataset.

val_split_idx = int(0.7*len(file_names))

test_split_idx = int(0.9*len(file_names))

# separate the file names out

train_files, val_files, test_files = file_names[:val_split_idx],\

                                     file_names[val_split_idx:test_split_idx],\

                                     file_names[test_split_idx:]

# create the datasets. Because of how batches are run for training, we set

# the dataset to repeat() because the batches and epochs are altered from 

# standard practice to fit on graphics cards and provide more meaningful and 

# frequent updates to the console.

training_dataset = get_dataset(train_files,batch_size=3)

training_dataset = training_dataset.repeat()

validation_dataset = get_dataset(val_files,batch_size = 2)

# testing has a batch size of 1 to facilitate visualization of predictions

testing_dataset = get_dataset(test_files,batch_size=1)

# explicitly puts the model on the GPU to show how large it is. 

gpus = tf.config.list_logical_devices('GPU')

with tf.device(gpus[0].name):

    # filter multiplier provided creates largest filter depth of 256 with a 

    # multiplier of 8. 

    sample_data = np.zeros((1,1024,1024,3)).astype(np.int8)

    unet = uNet(filter_multiplier=32)

    # build with input image size of 512*512

    out = unet(sample_data)

    unet.summary()

# %%

# running network eagerly because it allows us to use convert a tensor to a

# numpy array to help with the weighted loss calculation.

unet.compile(

    optimizer=tf.keras.optimizers.Adam(learning_rate=0.00008),

    loss=weighted_cce_loss,

    run_eagerly=True,

    metrics=[tf.keras.metrics.Precision(name='precision'),

                tf.keras.metrics.Recall(name='recall')]

)

# %%

# creating callbacks

reduce_lr = tf.keras.callbacks.ReduceLROnPlateau(monitor='val_recall',

                                                 mode='max',

                                                 factor=0.8,

                                                 patience=3,

                                                 min_lr=0.000001,

                                                 verbose=True)

checkpoint_cb = tf.keras.callbacks.ModelCheckpoint('unet_seg_subclassed.h5',

                                                   save_best_only=True,

                                                   save_weights_only=True,

                                                   monitor='val_precision',

                                                   mode='max',

                                                   verbose=True)

early_stopping_cb = tf.keras.callbacks.EarlyStopping(patience=8,

                                                     monitor='val_recall',

                                                     mode='max',

                                                     restore_best_weights=True,

                                                     verbose=True)

# setting the number of batches to iterate through each epoch to a value much

# lower than what it normaly would be so that we can actually see what is going

# on with the network, as well as have a meaningful early stopping.

num_steps = 250

# fit the network!

history = unet.fit(training_dataset,

                   epochs=70,

                   steps_per_epoch=num_steps,

                   validation_data=validation_dataset,

                   callbacks=[checkpoint_cb,

                              early_stopping_cb,

                              reduce_lr])

# %%

# %%

# evaluate the network after loading the weights

unet.load_weights('./unet_seg_subclassed.h5')

results = unet.evaluate(testing_dataset)

# %%

# extracting loss vs epoch

loss = history.history['loss']

val_loss = history.history['val_loss']

# extracting precision vs epoch

precision = history.history['precision']

val_precision = history.history['val_precision']

# extracting recall vs epoch

recall = history.history['recall']

val_recall = history.history['val_recall']

epochs = range(len(loss))

figs, axes = plt.subplots(3,1)

# plotting loss and validation loss

axes[0].plot(epochs,loss)

axes[0].plot(epochs,val_loss)

axes[0].legend(['loss','val_loss'])

axes[0].set(xlabel='epochs',ylabel='crossentropy loss')

# plotting precision and validation precision

axes[1].plot(epochs,precision)

axes[1].plot(epochs,val_precision)

axes[1].legend(['precision','val_precision'])

axes[1].set(xlabel='epochs',ylabel='precision')

# plotting recall validation recall

axes[2].plot(epochs,recall)

axes[2].plot(epochs,val_recall)

axes[2].legend(['recall','val_recall'])

axes[2].set(xlabel='epochs',ylabel='recall')

# %% exploring the predictions to better understand what the network is doing

images = []

gt = []

predictions = []

# taking out 10 of the next samples from the testing dataset and iterating 

# through them

for sample in testing_dataset.take(10):

    # make sure it is producing the correct dimensions

    print(sample[0].shape)

    # take the image and convert it back to RGB, store in list

    image = sample[0]

    image = cv.cvtColor(np.squeeze(np.asarray(image).copy()),cv.COLOR_BGR2RGB)

    images.append(image)

    # extract the ground truth and store in list

    ground_truth = sample[1]

    gt.append(ground_truth)

    # perform inference

    out = unet.predict(sample[0])

    predictions.append(out)

    # show the original input image

    plt.imshow(image)

    plt.show()

    # flatten the ground truth from one-hot encoded along the last axis, and 

    # show the resulting image

    squeezed_gt = tf.argmax(ground_truth,axis=-1)

    squeezed_prediction = tf.argmax(out,axis=-1)

    plt.imshow(squeezed_gt[0,:,:],vmin=0, vmax=6)

    # print the number of classes in this tile

    print(np.unique(squeezed_gt))

    plt.show()

    # show the flattened predictions

    plt.imshow(squeezed_prediction[0,:,:],vmin=0, vmax=6)

    print(np.unique(squeezed_prediction))

    plt.show()

# %%

# select one of the images cycled through above to investigate further

image_to_investigate = 6

# show the original image

plt.imshow(images[image_to_investigate])

plt.show()

# show the ground truth for this tile

squeezed_gt = tf.argmax(gt[image_to_investigate],axis=-1)

plt.imshow(squeezed_gt[0,:,:])

# print the number of unique classes in the ground truth

print(np.unique(squeezed_gt))

plt.show()

 # flatten the prediction and show the probability distribution

squeezed_prediction = tf.argmax(predictions[image_to_investigate],axis=-1)

plt.imshow(predictions[image_to_investigate][0,:,:,3])

plt.show()

# show the flattened image

plt.imshow(squeezed_prediction[0,:,:])

print(np.unique(squeezed_prediction))

plt.show()

# %%