From 6b6bd4a7a6a5180d1274f20df9cc652655c12cd6 Mon Sep 17 00:00:00 2001
From: Liu <20925537+Fab-Liu@users.noreply.github.com>
Date: Sun, 7 Apr 2024 18:41:36 +0800
Subject: [PATCH 1/3] fix

---
 data.py  | 229 +++++++++++++++++++++++++++++++++++--------------------
 main.py  |  34 +++++----
 model.py | 122 ++++++++++++++++++++---------
 3 files changed, 251 insertions(+), 134 deletions(-)

diff --git a/data.py b/data.py
index 956497d3f..4ef677622 100644
--- a/data.py
+++ b/data.py
@@ -1,124 +1,189 @@
 from __future__ import print_function
 from keras.preprocessing.image import ImageDataGenerator
-import numpy as np 
+import numpy as np
 import os
 import glob
+import cv2
 import skimage.io as io
+from PIL import Image
 import skimage.transform as trans
 
-Sky = [128,128,128]
-Building = [128,0,0]
-Pole = [192,192,128]
-Road = [128,64,128]
-Pavement = [60,40,222]
-Tree = [128,128,0]
-SignSymbol = [192,128,128]
-Fence = [64,64,128]
-Car = [64,0,128]
-Pedestrian = [64,64,0]
-Bicyclist = [0,128,192]
-Unlabelled = [0,0,0]
-
-COLOR_DICT = np.array([Sky, Building, Pole, Road, Pavement,
-                          Tree, SignSymbol, Fence, Car, Pedestrian, Bicyclist, Unlabelled])
-
-
-def adjustData(img,mask,flag_multi_class,num_class):
-    if(flag_multi_class):
+Sky = [128, 128, 128]
+Building = [128, 0, 0]
+Pole = [192, 192, 128]
+Road = [128, 64, 128]
+Pavement = [60, 40, 222]
+Tree = [128, 128, 0]
+SignSymbol = [192, 128, 128]
+Fence = [64, 64, 128]
+Car = [64, 0, 128]
+Pedestrian = [64, 64, 0]
+Bicyclist = [0, 128, 192]
+Unlabelled = [0, 0, 0]
+
+COLOR_DICT = np.array(
+    [
+        Sky,
+        Building,
+        Pole,
+        Road,
+        Pavement,
+        Tree,
+        SignSymbol,
+        Fence,
+        Car,
+        Pedestrian,
+        Bicyclist,
+        Unlabelled,
+    ]
+)
+
+
+def adjustData(img, mask, flag_multi_class, num_class):
+    if flag_multi_class:
         img = img / 255
-        mask = mask[:,:,:,0] if(len(mask.shape) == 4) else mask[:,:,0]
+        mask = mask[:, :, :, 0] if (len(mask.shape) == 4) else mask[:, :, 0]
         new_mask = np.zeros(mask.shape + (num_class,))
         for i in range(num_class):
-            #for one pixel in the image, find the class in mask and convert it into one-hot vector
-            #index = np.where(mask == i)
-            #index_mask = (index[0],index[1],index[2],np.zeros(len(index[0]),dtype = np.int64) + i) if (len(mask.shape) == 4) else (index[0],index[1],np.zeros(len(index[0]),dtype = np.int64) + i)
-            #new_mask[index_mask] = 1
-            new_mask[mask == i,i] = 1
-        new_mask = np.reshape(new_mask,(new_mask.shape[0],new_mask.shape[1]*new_mask.shape[2],new_mask.shape[3])) if flag_multi_class else np.reshape(new_mask,(new_mask.shape[0]*new_mask.shape[1],new_mask.shape[2]))
+            # for one pixel in the image, find the class in mask and convert it into one-hot vector
+            # index = np.where(mask == i)
+            # index_mask = (index[0],index[1],index[2],np.zeros(len(index[0]),dtype = np.int64) + i) if (len(mask.shape) == 4) else (index[0],index[1],np.zeros(len(index[0]),dtype = np.int64) + i)
+            # new_mask[index_mask] = 1
+            new_mask[mask == i, i] = 1
+        new_mask = (
+            np.reshape(
+                new_mask,
+                (
+                    new_mask.shape[0],
+                    new_mask.shape[1] * new_mask.shape[2],
+                    new_mask.shape[3],
+                ),
+            )
+            if flag_multi_class
+            else np.reshape(
+                new_mask, (new_mask.shape[0] * new_mask.shape[1], new_mask.shape[2])
+            )
+        )
         mask = new_mask
-    elif(np.max(img) > 1):
+    elif np.max(img) > 1:
         img = img / 255
-        mask = mask /255
+        mask = mask / 255
         mask[mask > 0.5] = 1
         mask[mask <= 0.5] = 0
-    return (img,mask)
-
-
-
-def trainGenerator(batch_size,train_path,image_folder,mask_folder,aug_dict,image_color_mode = "grayscale",
-                    mask_color_mode = "grayscale",image_save_prefix  = "image",mask_save_prefix  = "mask",
-                    flag_multi_class = False,num_class = 2,save_to_dir = None,target_size = (256,256),seed = 1):
-    '''
+    return (img, mask)
+
+
+def trainGenerator(
+    batch_size,
+    train_path,
+    image_folder,
+    mask_folder,
+    aug_dict,
+    image_color_mode="grayscale",
+    mask_color_mode="grayscale",
+    image_save_prefix="image",
+    mask_save_prefix="mask",
+    flag_multi_class=False,
+    num_class=2,
+    save_to_dir=None,
+    target_size=(256, 256),
+    seed=1,
+):
+    """
     can generate image and mask at the same time
     use the same seed for image_datagen and mask_datagen to ensure the transformation for image and mask is the same
     if you want to visualize the results of generator, set save_to_dir = "your path"
-    '''
+    """
     image_datagen = ImageDataGenerator(**aug_dict)
     mask_datagen = ImageDataGenerator(**aug_dict)
     image_generator = image_datagen.flow_from_directory(
         train_path,
-        classes = [image_folder],
-        class_mode = None,
-        color_mode = image_color_mode,
-        target_size = target_size,
-        batch_size = batch_size,
-        save_to_dir = save_to_dir,
-        save_prefix  = image_save_prefix,
-        seed = seed)
+        classes=[image_folder],
+        class_mode=None,
+        color_mode=image_color_mode,
+        target_size=target_size,
+        batch_size=batch_size,
+        save_to_dir=save_to_dir,
+        save_prefix=image_save_prefix,
+        seed=seed,
+    )
     mask_generator = mask_datagen.flow_from_directory(
         train_path,
-        classes = [mask_folder],
-        class_mode = None,
-        color_mode = mask_color_mode,
-        target_size = target_size,
-        batch_size = batch_size,
-        save_to_dir = save_to_dir,
-        save_prefix  = mask_save_prefix,
-        seed = seed)
+        classes=[mask_folder],
+        class_mode=None,
+        color_mode=mask_color_mode,
+        target_size=target_size,
+        batch_size=batch_size,
+        save_to_dir=save_to_dir,
+        save_prefix=mask_save_prefix,
+        seed=seed,
+    )
     train_generator = zip(image_generator, mask_generator)
-    for (img,mask) in train_generator:
-        img,mask = adjustData(img,mask,flag_multi_class,num_class)
-        yield (img,mask)
-
-
-
-def testGenerator(test_path,num_image = 30,target_size = (256,256),flag_multi_class = False,as_gray = True):
+    for img, mask in train_generator:
+        img, mask = adjustData(img, mask, flag_multi_class, num_class)
+        yield (img, mask)
+
+
+def testGenerator(
+    test_path,
+    num_image=30,
+    target_size=(256, 256),
+    flag_multi_class=False,
+    as_gray=True,
+):
     for i in range(num_image):
-        img = io.imread(os.path.join(test_path,"%d.png"%i),as_gray = as_gray)
+        img = io.imread(os.path.join(test_path, "%d.png" % i), as_gray=as_gray)
         img = img / 255
-        img = trans.resize(img,target_size)
-        img = np.reshape(img,img.shape+(1,)) if (not flag_multi_class) else img
-        img = np.reshape(img,(1,)+img.shape)
+        img = trans.resize(img, target_size)
+        img = np.reshape(img, img.shape + (1,)) if (not flag_multi_class) else img
+        img = np.reshape(img, (1,) + img.shape)
         yield img
 
 
-def geneTrainNpy(image_path,mask_path,flag_multi_class = False,num_class = 2,image_prefix = "image",mask_prefix = "mask",image_as_gray = True,mask_as_gray = True):
-    image_name_arr = glob.glob(os.path.join(image_path,"%s*.png"%image_prefix))
+def geneTrainNpy(
+    image_path,
+    mask_path,
+    flag_multi_class=False,
+    num_class=2,
+    image_prefix="image",
+    mask_prefix="mask",
+    image_as_gray=True,
+    mask_as_gray=True,
+):
+    image_name_arr = glob.glob(os.path.join(image_path, "%s*.png" % image_prefix))
     image_arr = []
     mask_arr = []
-    for index,item in enumerate(image_name_arr):
-        img = io.imread(item,as_gray = image_as_gray)
-        img = np.reshape(img,img.shape + (1,)) if image_as_gray else img
-        mask = io.imread(item.replace(image_path,mask_path).replace(image_prefix,mask_prefix),as_gray = mask_as_gray)
-        mask = np.reshape(mask,mask.shape + (1,)) if mask_as_gray else mask
-        img,mask = adjustData(img,mask,flag_multi_class,num_class)
+    for index, item in enumerate(image_name_arr):
+        img = io.imread(item, as_gray=image_as_gray)
+        img = np.reshape(img, img.shape + (1,)) if image_as_gray else img
+        mask = io.imread(
+            item.replace(image_path, mask_path).replace(image_prefix, mask_prefix),
+            as_gray=mask_as_gray,
+        )
+        mask = np.reshape(mask, mask.shape + (1,)) if mask_as_gray else mask
+        img, mask = adjustData(img, mask, flag_multi_class, num_class)
         image_arr.append(img)
         mask_arr.append(mask)
     image_arr = np.array(image_arr)
     mask_arr = np.array(mask_arr)
-    return image_arr,mask_arr
+    return image_arr, mask_arr
 
 
-def labelVisualize(num_class,color_dict,img):
-    img = img[:,:,0] if len(img.shape) == 3 else img
+def labelVisualize(num_class, color_dict, img):
+    img = img[:, :, 0] if len(img.shape) == 3 else img
     img_out = np.zeros(img.shape + (3,))
     for i in range(num_class):
-        img_out[img == i,:] = color_dict[i]
+        img_out[img == i, :] = color_dict[i]
     return img_out / 255
 
 
-
-def saveResult(save_path,npyfile,flag_multi_class = False,num_class = 2):
-    for i,item in enumerate(npyfile):
-        img = labelVisualize(num_class,COLOR_DICT,item) if flag_multi_class else item[:,:,0]
-        io.imsave(os.path.join(save_path,"%d_predict.png"%i),img)
\ No newline at end of file
+def saveResult(save_path, npyfile, flag_multi_class=False, num_class=2):
+    for i, item in enumerate(npyfile):
+        img = (
+            labelVisualize(num_class, COLOR_DICT, item)
+            if flag_multi_class
+            else item[:, :, 0]
+        )
+        img = (img > 0.5).astype(np.uint8)  # .reshape(256, 256)
+        img = img * 255
+        cv2.imwrite(os.path.join(save_path, "%d_predict.png" % i), img)
diff --git a/main.py b/main.py
index f6041b875..6bfeefc0c 100644
--- a/main.py
+++ b/main.py
@@ -1,22 +1,28 @@
 from model import *
 from data import *
 
-#os.environ["CUDA_VISIBLE_DEVICES"] = "0"
+# os.environ["CUDA_VISIBLE_DEVICES"] = "0"
 
 
-data_gen_args = dict(rotation_range=0.2,
-                    width_shift_range=0.05,
-                    height_shift_range=0.05,
-                    shear_range=0.05,
-                    zoom_range=0.05,
-                    horizontal_flip=True,
-                    fill_mode='nearest')
-myGene = trainGenerator(2,'data/membrane/train','image','label',data_gen_args,save_to_dir = None)
+data_gen_args = dict(
+    rotation_range=0.2,
+    width_shift_range=0.05,
+    height_shift_range=0.05,
+    shear_range=0.05,
+    zoom_range=0.05,
+    horizontal_flip=True,
+    fill_mode="nearest",
+)
+myGene = trainGenerator(
+    2, "./data/membrane/train", "image", "label", data_gen_args, save_to_dir=None
+)
 
 model = unet()
-model_checkpoint = ModelCheckpoint('unet_membrane.hdf5', monitor='loss',verbose=1, save_best_only=True)
-model.fit_generator(myGene,steps_per_epoch=300,epochs=1,callbacks=[model_checkpoint])
+model_checkpoint = ModelCheckpoint(
+    "unet_membrane.hdf5", monitor="loss", verbose=1, save_best_only=True
+)
+model.fit_generator(myGene, steps_per_epoch=300, epochs=1, callbacks=[model_checkpoint])
 
-testGene = testGenerator("data/membrane/test")
-results = model.predict_generator(testGene,30,verbose=1)
-saveResult("data/membrane/test",results)
\ No newline at end of file
+testGene = testGenerator("./data/membrane/test")
+results = model.predict_generator(testGene, 30, verbose=1)
+saveResult("./data/membrane/test", results)
diff --git a/model.py b/model.py
index 7df5b6889..51f86142a 100644
--- a/model.py
+++ b/model.py
@@ -1,4 +1,4 @@
-import numpy as np 
+import numpy as np
 import os
 import skimage.io as io
 import skimage.transform as trans
@@ -10,57 +10,103 @@
 from keras import backend as keras
 
 
-def unet(pretrained_weights = None,input_size = (256,256,1)):
+def unet(pretrained_weights=None, input_size=(256, 256, 1)):
     inputs = Input(input_size)
-    conv1 = Conv2D(64, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(inputs)
-    conv1 = Conv2D(64, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv1)
+    conv1 = Conv2D(
+        64, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(inputs)
+    conv1 = Conv2D(
+        64, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv1)
     pool1 = MaxPooling2D(pool_size=(2, 2))(conv1)
-    conv2 = Conv2D(128, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(pool1)
-    conv2 = Conv2D(128, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv2)
+    conv2 = Conv2D(
+        128, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(pool1)
+    conv2 = Conv2D(
+        128, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv2)
     pool2 = MaxPooling2D(pool_size=(2, 2))(conv2)
-    conv3 = Conv2D(256, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(pool2)
-    conv3 = Conv2D(256, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv3)
+    conv3 = Conv2D(
+        256, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(pool2)
+    conv3 = Conv2D(
+        256, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv3)
     pool3 = MaxPooling2D(pool_size=(2, 2))(conv3)
-    conv4 = Conv2D(512, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(pool3)
-    conv4 = Conv2D(512, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv4)
+    conv4 = Conv2D(
+        512, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(pool3)
+    conv4 = Conv2D(
+        512, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv4)
     drop4 = Dropout(0.5)(conv4)
     pool4 = MaxPooling2D(pool_size=(2, 2))(drop4)
 
-    conv5 = Conv2D(1024, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(pool4)
-    conv5 = Conv2D(1024, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv5)
+    conv5 = Conv2D(
+        1024, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(pool4)
+    conv5 = Conv2D(
+        1024, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv5)
     drop5 = Dropout(0.5)(conv5)
 
-    up6 = Conv2D(512, 2, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(UpSampling2D(size = (2,2))(drop5))
-    merge6 = concatenate([drop4,up6], axis = 3)
-    conv6 = Conv2D(512, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(merge6)
-    conv6 = Conv2D(512, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv6)
-
-    up7 = Conv2D(256, 2, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(UpSampling2D(size = (2,2))(conv6))
-    merge7 = concatenate([conv3,up7], axis = 3)
-    conv7 = Conv2D(256, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(merge7)
-    conv7 = Conv2D(256, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv7)
+    up6 = Conv2D(
+        512, 2, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(UpSampling2D(size=(2, 2))(drop5))
+    merge6 = concatenate([drop4, up6], axis=3)
+    conv6 = Conv2D(
+        512, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(merge6)
+    conv6 = Conv2D(
+        512, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv6)
 
-    up8 = Conv2D(128, 2, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(UpSampling2D(size = (2,2))(conv7))
-    merge8 = concatenate([conv2,up8], axis = 3)
-    conv8 = Conv2D(128, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(merge8)
-    conv8 = Conv2D(128, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv8)
+    up7 = Conv2D(
+        256, 2, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(UpSampling2D(size=(2, 2))(conv6))
+    merge7 = concatenate([conv3, up7], axis=3)
+    conv7 = Conv2D(
+        256, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(merge7)
+    conv7 = Conv2D(
+        256, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv7)
 
-    up9 = Conv2D(64, 2, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(UpSampling2D(size = (2,2))(conv8))
-    merge9 = concatenate([conv1,up9], axis = 3)
-    conv9 = Conv2D(64, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(merge9)
-    conv9 = Conv2D(64, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv9)
-    conv9 = Conv2D(2, 3, activation = 'relu', padding = 'same', kernel_initializer = 'he_normal')(conv9)
-    conv10 = Conv2D(1, 1, activation = 'sigmoid')(conv9)
+    up8 = Conv2D(
+        128, 2, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(UpSampling2D(size=(2, 2))(conv7))
+    merge8 = concatenate([conv2, up8], axis=3)
+    conv8 = Conv2D(
+        128, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(merge8)
+    conv8 = Conv2D(
+        128, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv8)
 
-    model = Model(input = inputs, output = conv10)
+    up9 = Conv2D(
+        64, 2, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(UpSampling2D(size=(2, 2))(conv8))
+    merge9 = concatenate([conv1, up9], axis=3)
+    conv9 = Conv2D(
+        64, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(merge9)
+    conv9 = Conv2D(
+        64, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv9)
+    conv9 = Conv2D(
+        2, 3, activation="relu", padding="same", kernel_initializer="he_normal"
+    )(conv9)
+    conv10 = Conv2D(1, 1, activation="sigmoid")(conv9)
 
-    model.compile(optimizer = Adam(lr = 1e-4), loss = 'binary_crossentropy', metrics = ['accuracy'])
-    
-    #model.summary()
+    model = Model(inputs=inputs, outputs=conv10)
 
-    if(pretrained_weights):
-    	model.load_weights(pretrained_weights)
+    model.compile(
+        optimizer=Adam(lr=1e-4), loss="binary_crossentropy", metrics=["accuracy"]
+    )
 
-    return model
+    # model.summary()
 
+    if pretrained_weights:
+        model.load_weights(pretrained_weights)
 
+    return model

From cab1dce1e014e6833e418d75611c1ad432fdef88 Mon Sep 17 00:00:00 2001
From: Liu <SWE2009510@xmu.edu.my>
Date: Mon, 8 Apr 2024 08:18:10 +0800
Subject: [PATCH 2/3] Create pylint.yml

---
 .github/workflows/pylint.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 .github/workflows/pylint.yml

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
new file mode 100644
index 000000000..383e65cd0
--- /dev/null
+++ b/.github/workflows/pylint.yml
@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

From 8a55db158d04057f0c06228470347398c661fb43 Mon Sep 17 00:00:00 2001
From: Liu <20925537+Fab-Liu@users.noreply.github.com>
Date: Wed, 10 Apr 2024 10:30:35 +0800
Subject: [PATCH 3/3] Create readme

---
 readme | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 readme

diff --git a/readme b/readme
new file mode 100644
index 000000000..f7be52778
--- /dev/null
+++ b/readme
@@ -0,0 +1,19 @@
+1、TypeError: ('Keyword argument not understood:', 'input')
+A: Model文件里面的input修改为
+model = Model(inputs=inputs, outputs=conv10)
+
+2、cannot write mode F as PNG
+A: 参见问题3，修改saveResult
+
+3、训练完结果是黑色的/白色的
+A: 训练的轮数太少了，loss不下降 / saveResult 函数没有改过来
+
+for i, item in enumerate(npyfile):
+        img = (
+            labelVisualize(num_class, COLOR_DICT, item)
+            if flag_multi_class
+            else item[:, :, 0]
+        )
+        img = (img > 0.5).astype(np.uint8)  # .reshape(256, 256)
+        img = img * 255
+        cv2.imwrite(os.path.join(save_path, "%d_predict.png" % i), img)
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