From 3bfda0567f6997d7c19ba5c4da6ac66bc3bd0295 Mon Sep 17 00:00:00 2001
From: Debojyoti Pal <62235947+Dynamo13@users.noreply.github.com>
Date: Fri, 1 Sep 2023 16:10:16 -0500
Subject: [PATCH] Add files via upload

---
 SE_UResNet_tf.ipynb | 84 +++++++++++++++++++++++++++++++++++++++++++++
 dataloader.py       | 33 ++++++++++++++++++
 main.py             | 65 +++++++++++++++++++++++++++++++++++
 model.py            | 68 ++++++++++++++++++++++++++++++++++++
 utils.py            | 55 +++++++++++++++++++++++++++++
 5 files changed, 305 insertions(+)
 create mode 100644 SE_UResNet_tf.ipynb
 create mode 100644 dataloader.py
 create mode 100644 main.py
 create mode 100644 model.py
 create mode 100644 utils.py

diff --git a/SE_UResNet_tf.ipynb b/SE_UResNet_tf.ipynb
new file mode 100644
index 0000000..a409b77
--- /dev/null
+++ b/SE_UResNet_tf.ipynb
@@ -0,0 +1,84 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c0744c9f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from dataloader import *\n",
+    "from model import *\n",
+    "from main import *\n",
+    "from utils import *\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "04766fc7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "image_height=256\n",
+    "image_width=256\n",
+    "image_channel=3"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dbd05bca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "img_dir='E:/Data_test/images'\n",
+    "mask_dir='E:/Data_test/mask'\n",
+    "weight_dir='E:/Data_test/weights'\n",
+    "\n",
+    "main(img_dir,mask_dir,weight_dir)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f8393f0f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "\n",
+    "path = r'E:\\Data_test\\images\\CHNCXR_0001_0.png'\n",
+    "model=SE_UResNet((image_height,image_width,image_channel),num_classes, dropout_rate=0.0, batch_norm=True)\n",
+    "model.compile(optimizer='adam',loss='binary_crossentropy',metrics=['accuracy'])\n",
+    "model.load_weights(str(weight_dir)+'/weights.h5')\n",
+    "\n",
+    "test_image = cv2.resize(cv2.imread(path),(image_height,image_width))\n",
+    "predicted_image=model.predict(test_image.reshape(1,image_height,image_width,image_channel))\n",
+    "plt.imshow(predicted_image[0]>0.5,cmap='gray')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.17"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/dataloader.py b/dataloader.py
new file mode 100644
index 0000000..76cfbfb
--- /dev/null
+++ b/dataloader.py
@@ -0,0 +1,33 @@
+import keras
+import numpy as np
+import cv2
+
+class Loader(keras.utils.Sequence):
+    """Helper to iterate over the data (as Numpy arrays)."""
+
+    def __init__(self, batch_size, img_size, input_img_paths, mask_img_paths,image_channel,num_classes):
+        self.batch_size = batch_size
+        self.img_size = img_size
+        self.input_img_paths = input_img_paths
+        self.mask_img_paths = mask_img_paths
+        self.num_classes = num_classes
+        self.image_channel=image_channel
+
+
+    def __len__(self):
+        return len(self.mask_img_paths) // self.batch_size
+
+    def __getitem__(self, idx):
+        """Returns tuple (input, target) correspond to batch #idx."""
+        i = idx * self.batch_size
+        batch_input_img_paths = self.input_img_paths[i : i + self.batch_size]
+        batch_mask_img_paths = self.mask_img_paths[i : i + self.batch_size]
+        x = np.zeros((self.batch_size,) + self.img_size +(self.image_channel,) , dtype="uint8")
+        for j, path in enumerate(batch_input_img_paths):
+            img = cv2.resize(cv2.imread(path),self.img_size)
+            x[j]=img
+        y = np.zeros((self.batch_size,) + self.img_size + (self.num_classes,), dtype="uint8")
+        for j, path in enumerate(batch_mask_img_paths):
+            msk = cv2.resize(cv2.imread(path),self.img_size)
+            y[j]=np.expand_dims((msk[:,:,0]/255).astype('uint8'),axis=-1)
+        return x, y
\ No newline at end of file
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..0d74799
--- /dev/null
+++ b/main.py
@@ -0,0 +1,65 @@
+from dataloader import*
+from model import*
+import random
+import os
+def main(input_dir, mask_dir,weight_dir,
+    image_height=256,
+    image_width=256,
+    image_channel=3,
+    img_size = (256,256),
+    num_classes = 1,
+    batch_size = 8,
+    epochs=100,
+    val_samples = 40,):
+
+    img_size = (image_height,image_width)
+    input_img_paths = sorted(
+    [
+        os.path.join(input_dir, fname)
+        for fname in os.listdir(input_dir)
+    ]
+    )
+    mask_img_paths = sorted(
+    [
+        os.path.join(mask_dir, fname)
+        for fname in os.listdir(mask_dir)
+    ]
+    )
+    random.Random(1337).shuffle(input_img_paths)
+    random.Random(1337).shuffle(mask_img_paths)
+    train_input_img_paths = input_img_paths[:-val_samples]
+    train_mask_img_paths = mask_img_paths[:-val_samples]
+    val_input_img_paths = input_img_paths[-val_samples:]
+    val_mask_img_paths = mask_img_paths[-val_samples:]
+
+    # Instantiate data Sequences for each split
+    train_gen = Loader(
+        batch_size, img_size, train_input_img_paths, train_mask_img_paths,image_channel,num_classes
+    )
+    val_gen = Loader(batch_size, img_size, val_input_img_paths, val_mask_img_paths,image_channel,num_classes)
+    
+    model=SE_UResNet((image_height,image_width,image_channel),num_classes, dropout_rate=0.0, batch_norm=True)
+
+    model.compile(optimizer='adam',loss='binary_crossentropy',metrics=['accuracy'])
+    checkpoint_callback = tf.keras.callbacks.ModelCheckpoint(
+    filepath=weight_dir+"\\weights.h5",
+    save_weights_only=True,
+    monitor='val_loss',
+    mode='min',
+    save_best_only=True
+    )
+    rlp =tf.keras.callbacks.ReduceLROnPlateau(
+    monitor='val_loss',
+    factor=0.001,
+    patience=10,
+    verbose=1,
+    mode='auto',
+    min_delta=0.00005)
+    #es=tf.keras.callbacks.EarlyStopping(monitor='val_loss', mode='min', verbose=1, patience=15)
+    history = model.fit(train_gen,validation_data=val_gen,epochs=epochs,callbacks=[checkpoint_callback,rlp])
+
+if __name__ == "__main__":
+    img_dir = sys.argv[1]
+    mask_dir = sys.argv[2]
+    weight_dir = sys.argv[3]
+    main(img_dir,mask_dir,weight_dir)
\ No newline at end of file
diff --git a/model.py b/model.py
new file mode 100644
index 0000000..635398a
--- /dev/null
+++ b/model.py
@@ -0,0 +1,68 @@
+from utils import *
+import tensorflow as tf
+def SE_UResNet(input_shape, NUM_CLASSES=1, dropout_rate=0.0, batch_norm=True):
+    '''
+    Attention UNet, 
+    
+    '''
+    # network structure
+    FILTER_NUM = 32 # number of basic filters for the first layer
+    FILTER_SIZE = 3 # size of the convolutional filter
+    UP_SAMP_SIZE = 2 # size of upsampling filters
+    
+    inputs = layers.Input(input_shape, dtype=tf.float32)
+
+    # Downsampling layers
+    # DownRes 1, convolution + pooling
+    conv_128 = conv_block(inputs, FILTER_SIZE, FILTER_NUM, 0.2, 1, batch_norm)
+    pool_64 = layers.MaxPooling2D(pool_size=(2,2))(conv_128)
+    # DownRes 2
+    conv_64 = conv_block(pool_64, FILTER_SIZE, 2*FILTER_NUM, 0.2, 2, batch_norm)
+    pool_32 = layers.MaxPooling2D(pool_size=(2,2))(conv_64)
+    # DownRes 3
+    conv_32 = conv_block(pool_32, FILTER_SIZE, 4*FILTER_NUM,0.2, 3, batch_norm)
+    pool_16 = layers.MaxPooling2D(pool_size=(2,2))(conv_32)
+    # DownRes 4
+    conv_16 = conv_block(pool_16, FILTER_SIZE, 8*FILTER_NUM,0.2,4, batch_norm)
+    pool_8 = layers.MaxPooling2D(pool_size=(2,2))(conv_16)
+    # DownRes 5, convolution only
+    conv_8 = conv_block(pool_8, FILTER_SIZE, 16*FILTER_NUM, 0.2,5, batch_norm)
+    
+    # W-net layers
+    attw_16 = se_block(conv_16, 8*FILTER_NUM)
+    upw_16 = layers.UpSampling2D(size=(UP_SAMP_SIZE, UP_SAMP_SIZE), data_format="channels_last")(conv_8)
+    upw_16 = layers.concatenate([upw_16, attw_16], axis=3)
+    up_convw_16 = resb(upw_16, FILTER_SIZE, 8*FILTER_NUM, 0.2,6, batch_norm)
+
+    poolw_8 = layers.MaxPooling2D(pool_size=(2,2))(up_convw_16)
+    convw_16 = conv_block(poolw_8, FILTER_SIZE, 16*FILTER_NUM, 0.2,7, batch_norm)
+    
+    # UpRes 6, attention gated concatenation + upsampling + double residual convolution
+    att_16 = se_block(up_convw_16, 8*FILTER_NUM)
+    up_16 = layers.UpSampling2D(size=(UP_SAMP_SIZE, UP_SAMP_SIZE), data_format="channels_last")(convw_16)
+    up_16 = layers.concatenate([up_16, att_16], axis=3)
+    up_conv_16 = conv_block(up_16, FILTER_SIZE, 8*FILTER_NUM, 0.2,8, batch_norm)
+    # UpRes 7
+    att_32 = se_block(conv_32,  4*FILTER_NUM)
+    up_32 = layers.UpSampling2D(size=(UP_SAMP_SIZE, UP_SAMP_SIZE), data_format="channels_last")(up_conv_16)
+    up_32 = layers.concatenate([up_32, att_32], axis=3)
+    up_conv_32 =conv_block(up_32, FILTER_SIZE, 4*FILTER_NUM, dropout_rate,9, batch_norm)
+    # UpRes 8
+    att_64 = se_block(conv_64,  2*FILTER_NUM)
+    up_64 = layers.UpSampling2D(size=(UP_SAMP_SIZE, UP_SAMP_SIZE), data_format="channels_last")(up_conv_32)
+    up_64 = layers.concatenate([up_64, att_64], axis=3)
+    up_conv_64 = conv_block(up_64, FILTER_SIZE, 2*FILTER_NUM, 0.2,10, batch_norm)
+    # UpRes 9
+    att_128 = se_block(conv_128,  FILTER_NUM)
+    up_128 = layers.UpSampling2D(size=(UP_SAMP_SIZE, UP_SAMP_SIZE), data_format="channels_last")(up_conv_64)
+    up_128 = layers.concatenate([up_128, att_128], axis=3)
+    up_conv_128 = conv_block(up_128, FILTER_SIZE, FILTER_NUM, 0.2,11, batch_norm)
+
+    # 1*1 convolutional layers
+    conv_final = layers.Conv2D(NUM_CLASSES, kernel_size=(1,1))(up_conv_128)
+    conv_final = layers.BatchNormalization(axis=3)(conv_final)
+    conv_final = layers.Activation('sigmoid')(conv_final)  #Change to softmax for multichannel
+
+    # Model integration
+    model = models.Model(inputs, conv_final, name="Attention_UWNet")
+    return model
\ No newline at end of file
diff --git a/utils.py b/utils.py
new file mode 100644
index 0000000..f23b35e
--- /dev/null
+++ b/utils.py
@@ -0,0 +1,55 @@
+from tensorflow.keras import models, layers, regularizers
+from tensorflow.keras import backend as K
+import tensorflow as tf
+
+def conv_block(x, filter_size, size, dropout,num, batch_norm=False):
+    
+    conv = layers.Conv2D(size, (filter_size, filter_size), padding="same")(x)
+    if batch_norm is True:
+        conv = layers.BatchNormalization(axis=3)(conv)
+    conv = layers.Activation("relu")(conv)
+
+    conv = layers.Conv2D(size, (filter_size, filter_size), padding="same",name="conv"+str(num))(conv)
+    if batch_norm is True:
+        conv = layers.BatchNormalization(axis=3)(conv)
+    conv = layers.Activation("relu")(conv)
+    
+    if dropout > 0:
+        conv = layers.Dropout(dropout)(conv)
+
+    return conv
+
+def se_block(x,r):
+    copy=x
+    gap=layers.GlobalAveragePooling2D()(x)
+    flat=layers.Flatten()(gap)
+    dense=layers.Dense(flat.shape[-1]//r, activation = 'relu')(gap)
+    dense=layers.Dense(flat.shape[-1], activation = 'sigmoid')(dense)
+    m =layers.multiply([dense,copy])
+    return m
+
+def resb(x, filter_size, size, dropout,num, batch_norm=False):
+    # copy tensor to variable called x_skip
+    x_skip = x
+    x_skip=layers.Conv2D(1, (1, 1), padding="same")(x_skip)
+    print(x_skip.shape)
+    # Layer 1
+    x = layers.Conv2D(size, (filter_size, filter_size), padding="same")(x)
+    if batch_norm is True:
+        x = layers.BatchNormalization(axis=3)(x)
+    x = layers.Activation("relu")(x)
+    if dropout > 0:
+        x = layers.Dropout(dropout)(x)
+    print(x.shape)
+    # Layer 2
+    x = layers.Conv2D(size, (filter_size, filter_size), padding="same")(x)
+    if batch_norm is True:
+        x = layers.BatchNormalization(axis=3)(x)
+    x = layers.Activation("relu")(x)
+    if dropout > 0:
+        x = layers.Dropout(dropout)(x)
+    print(x.shape)
+    # Add Residue
+    x = tf.keras.layers.Add()([x, x_skip])     
+    x = tf.keras.layers.Activation('relu')(x)
+    return x
\ No newline at end of file