From 7e71fc4a31c4aff2894e5d09947b355fb1a2947e Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 12:31:06 +0530
Subject: [PATCH 01/12] Update .gitignore

---
 .gitignore | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index ebf1ca1b7..f9e3453de 100755
--- a/.gitignore
+++ b/.gitignore
@@ -105,4 +105,8 @@ ENV/
 .ropeproject
 
 # VSCode settings
-.vscode/
\ No newline at end of file
+.vscode/
+.idea/image-segmentation-keras.iml
+.idea/inspectionProfiles/profiles_settings.xml
+.idea/modules.xml
+.idea/inspectionProfiles/Project_Default.xml

From f1d3f8d2175f5d8e16895475dc3601439cfbcbdf Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 12:51:29 +0530
Subject: [PATCH 02/12] Update README.md

Added the usage of loss function
---
 README.md | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index c31213855..ef6ccbbea 100644
--- a/README.md
+++ b/README.md
@@ -170,10 +170,14 @@ from keras_segmentation.models.unet import vgg_unet
 
 model = vgg_unet(n_classes=51 ,  input_height=416, input_width=608  )
 
+def custom_fun():
+    #some loss function
+    pass
+
 model.train(
     train_images =  "dataset1/images_prepped_train/",
     train_annotations = "dataset1/annotations_prepped_train/",
-    checkpoints_path = "/tmp/vgg_unet_1" , epochs=5
+    checkpoints_path = "/tmp/vgg_unet_1" , epochs=5, loss_fun = custom_fun() #dice or soft_dice
 )
 
 out = model.predict_segmentation(
@@ -186,9 +190,14 @@ plt.imshow(out)
 
 # evaluating the model 
 print(model.evaluate_segmentation( inp_images_dir="dataset1/images_prepped_test/"  , annotations_dir="dataset1/annotations_prepped_test/" ) )
-
 ```
+### Custom loss function
 
+#### Available loss function:
+    
+- Dice loss (usage: `loss_fun = dice`)
+- Soft Dice Loss (usage: `loss_fun = soft_dice`)
+- and others available in [Losses](https://keras.io/api/losses/)
 
 ## Usage via command line
 You can also use the tool just using command line
@@ -229,6 +238,7 @@ python -m keras_segmentation train \
  --input_height=320 \
  --input_width=640 \
  --model_name="vgg_unet"
+ --loss_fun= "dice" or "soft_dice"
 ```
 
 Choose model_name from the table above

From 68968ff7add610af324ad208a50e7f650c75fcf8 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 13:39:13 +0530
Subject: [PATCH 03/12] Update train.py

Added the implementation of dice coefficient, dice loss, soft dice loss
---
 keras_segmentation/train.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/keras_segmentation/train.py b/keras_segmentation/train.py
index 6306f719d..b1a479f99 100755
--- a/keras_segmentation/train.py
+++ b/keras_segmentation/train.py
@@ -7,9 +7,40 @@
 from keras.callbacks import Callback
 from tensorflow.keras.callbacks import ModelCheckpoint
 import tensorflow as tf
+from tensorflow.keras import backend as K
 import glob
 import sys
 
+
+def dice_coef(y_true, y_pred):
+    """
+    Function to calculate dice coefficient
+
+    Parameters
+    ----------
+    y_true : numpy array of actual masks
+    y_pred : numpy array of predicted masks
+
+    Returns
+    -------
+    dice coefficient
+    """
+    y_true_f = K.flatten(y_true)
+    y_pred_f = K.flatten(y_pred)
+    intersection = K.sum(y_true_f * y_pred_f)
+    return  (2. * intersection + K.epsilon()) / (K.sum(y_true_f) + K.sum(y_pred_f) + K.epsilon())
+
+
+def dice_coef_loss(y_true, y_pred):
+    return 1-dice_coef(y_true, y_pred)
+
+def soft_dice_loss(y_true, y_pred, axis=(1, 2, 3)):
+    dice_numerator = 2. * K.sum(y_true * y_pred, axis=axis) + 0.00001
+    dice_denominator = K.sum(y_true ** 2, axis=axis) + K.sum(y_pred ** 2, axis=axis) + 0.00001
+    dice_loss = 1 - K.mean((dice_numerator) / (dice_denominator))
+    return dice_loss
+
+
 def find_latest_checkpoint(checkpoints_path, fail_safe=True):
 
     # This is legacy code, there should always be a "checkpoint" file in your directory

From b41a5eb3f2a29a07ca659372b7e30e6883069c74 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 13:41:25 +0530
Subject: [PATCH 04/12] Update README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ef6ccbbea..22cc81103 100644
--- a/README.md
+++ b/README.md
@@ -177,7 +177,7 @@ def custom_fun():
 model.train(
     train_images =  "dataset1/images_prepped_train/",
     train_annotations = "dataset1/annotations_prepped_train/",
-    checkpoints_path = "/tmp/vgg_unet_1" , epochs=5, loss_fun = custom_fun() #dice or soft_dice
+    checkpoints_path = "/tmp/vgg_unet_1" , epochs=5, loss_fun = custom_fun() #dice or soft_dice, default = 'categorical_crossentropy'
 )
 
 out = model.predict_segmentation(
@@ -238,7 +238,7 @@ python -m keras_segmentation train \
  --input_height=320 \
  --input_width=640 \
  --model_name="vgg_unet"
- --loss_fun= "dice" or "soft_dice"
+ --loss_fun= "dice" or "soft_dice" #default = 'categorical_crossentropy'
 ```
 
 Choose model_name from the table above

From 09cb3f8f520071a69f4355a0f59299273a9e27e2 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:02:06 +0530
Subject: [PATCH 05/12] Updated the metrics

Added the Jaccard Index metrics
---
 keras_segmentation/metrics.py | 21 +++++++++++++++++++++
 keras_segmentation/train.py   | 26 ++++----------------------
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/keras_segmentation/metrics.py b/keras_segmentation/metrics.py
index 0162dd9ce..ea1bfc750 100644
--- a/keras_segmentation/metrics.py
+++ b/keras_segmentation/metrics.py
@@ -1,4 +1,5 @@
 import numpy as np
+from tensorflow.keras import backend as K
 
 EPS = 1e-12
 
@@ -11,3 +12,23 @@ def get_iou(gt, pr, n_classes):
         iou = float(intersection)/(union + EPS)
         class_wise[cl] = iou
     return class_wise
+
+def dice_coef(y_true, y_pred):
+
+    y_true_f = K.flatten(y_true)
+    y_pred_f = K.flatten(y_pred)
+    intersection = K.sum(y_true_f * y_pred_f)
+    return  (2. * intersection + EPS) / (K.sum(y_true_f) + K.sum(y_pred_f) + EPS)
+
+# def dice_coef(y_true, y_pre, smooth=1):
+#     # Dice Coefficient is 2 * the Area of Overlap divided by the total number of pixels in both images
+#     y_true = np.asarray(y_true, 'bool')
+#     y_pre = np.asarray(y_pre, 'bool')
+#     inter = np.sum(y_true * y_pre)
+#     uni = np.sum(y_true) + np.sum(y_pre)
+#
+#     return (2 * inter + smooth) / (uni + smooth)
+
+
+def jacard_index(dice):
+    return dice / (2 - dice)
diff --git a/keras_segmentation/train.py b/keras_segmentation/train.py
index b1a479f99..c2d1ec36c 100755
--- a/keras_segmentation/train.py
+++ b/keras_segmentation/train.py
@@ -10,26 +10,7 @@
 from tensorflow.keras import backend as K
 import glob
 import sys
-
-
-def dice_coef(y_true, y_pred):
-    """
-    Function to calculate dice coefficient
-
-    Parameters
-    ----------
-    y_true : numpy array of actual masks
-    y_pred : numpy array of predicted masks
-
-    Returns
-    -------
-    dice coefficient
-    """
-    y_true_f = K.flatten(y_true)
-    y_pred_f = K.flatten(y_pred)
-    intersection = K.sum(y_true_f * y_pred_f)
-    return  (2. * intersection + K.epsilon()) / (K.sum(y_true_f) + K.sum(y_pred_f) + K.epsilon())
-
+from metrics import dice_coef
 
 def dice_coef_loss(y_true, y_pred):
     return 1-dice_coef(y_true, y_pred)
@@ -109,6 +90,7 @@ def train(model,
           gen_use_multiprocessing=False,
           ignore_zero_class=False,
           optimizer_name='adam',
+          loss_fun ='categorical_crossentropy',
           do_augment=False,
           augmentation_name="aug_all",
           callbacks=None,
@@ -145,11 +127,11 @@ def train(model,
         if ignore_zero_class:
             loss_k = masked_categorical_crossentropy
         else:
-            loss_k = 'categorical_crossentropy'
+            loss_k = loss_fun #'categorical_crossentropy'
 
         model.compile(loss=loss_k,
                       optimizer=optimizer_name,
-                      metrics=['accuracy'])
+                      metrics=['accuracy',dice_coef])
 
     if checkpoints_path is not None:
         config_file = checkpoints_path + "_config.json"

From bfaec91c807747c846f0fc688bd259c3dcf34c13 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:12:55 +0530
Subject: [PATCH 06/12] Update train.py

---
 keras_segmentation/train.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/keras_segmentation/train.py b/keras_segmentation/train.py
index c2d1ec36c..2f00bbcec 100755
--- a/keras_segmentation/train.py
+++ b/keras_segmentation/train.py
@@ -10,7 +10,14 @@
 from tensorflow.keras import backend as K
 import glob
 import sys
-from metrics import dice_coef
+
+
+def dice_coef(y_true, y_pred):
+
+    y_true_f = K.flatten(y_true)
+    y_pred_f = K.flatten(y_pred)
+    intersection = K.sum(y_true_f * y_pred_f)
+    return (2. * intersection + K.epsilon()) / (K.sum(y_true_f) + K.sum(y_pred_f) + K.epsilon())
 
 def dice_coef_loss(y_true, y_pred):
     return 1-dice_coef(y_true, y_pred)

From 342cd37ca0aa3e3217b70d1297d73789df23c2a0 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:20:58 +0530
Subject: [PATCH 07/12] Update pretrained.py

---
 keras_segmentation/pretrained.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/keras_segmentation/pretrained.py b/keras_segmentation/pretrained.py
index 647e8cd9f..e52d7ceb8 100644
--- a/keras_segmentation/pretrained.py
+++ b/keras_segmentation/pretrained.py
@@ -1,4 +1,5 @@
-import keras
+# import keras
+import tensorflow.keras as keras
 
 from .models.all_models import model_from_name
 

From 991f9f26046d6313d29eaf4cc62811ef596d61d6 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:29:43 +0530
Subject: [PATCH 08/12] updated the tf and keras import module

---
 keras_segmentation/models/mobilenet.py | 4 ++--
 keras_segmentation/models/resnet50.py  | 2 +-
 keras_segmentation/models/vgg16.py     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/keras_segmentation/models/mobilenet.py b/keras_segmentation/models/mobilenet.py
index f8a34f5d7..2d70af4f0 100644
--- a/keras_segmentation/models/mobilenet.py
+++ b/keras_segmentation/models/mobilenet.py
@@ -1,7 +1,7 @@
 from keras.models import *
 from keras.layers import *
-import keras.backend as K
-import keras
+import tensorflow.keras.backend as K
+import tensorflow.keras as keras
 
 from .config import IMAGE_ORDERING
 
diff --git a/keras_segmentation/models/resnet50.py b/keras_segmentation/models/resnet50.py
index 5bbb3368f..ee13ed8c4 100644
--- a/keras_segmentation/models/resnet50.py
+++ b/keras_segmentation/models/resnet50.py
@@ -1,4 +1,4 @@
-import keras
+import tensorflow.keras as keras
 from keras.models import *
 from keras.layers import *
 from keras import layers
diff --git a/keras_segmentation/models/vgg16.py b/keras_segmentation/models/vgg16.py
index 922682121..79a763960 100644
--- a/keras_segmentation/models/vgg16.py
+++ b/keras_segmentation/models/vgg16.py
@@ -1,4 +1,4 @@
-import keras
+import tensorflow.keras as keras
 from keras.models import *
 from keras.layers import *
 

From 85ca9dd7c7561a9b8b37bf92e3d22c47e03efcf9 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:38:18 +0530
Subject: [PATCH 09/12] Update model_compression.py

---
 keras_segmentation/model_compression.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/keras_segmentation/model_compression.py b/keras_segmentation/model_compression.py
index a461aa7c4..cb96ee28a 100644
--- a/keras_segmentation/model_compression.py
+++ b/keras_segmentation/model_compression.py
@@ -1,4 +1,4 @@
-import keras
+import tensorflow.keras as keras
 import tensorflow as tf
 
 from tqdm import tqdm 

From 93327d50c8a9d30311d0bd5ac0f32bcafb0ff232 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:40:01 +0530
Subject: [PATCH 10/12] Update model_compression.py

---
 keras_segmentation/model_compression.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/keras_segmentation/model_compression.py b/keras_segmentation/model_compression.py
index cb96ee28a..cb58d0e52 100644
--- a/keras_segmentation/model_compression.py
+++ b/keras_segmentation/model_compression.py
@@ -11,7 +11,7 @@
 from .data_utils.data_loader import image_segmentation_generator
 from .train import CheckpointsCallback 
 
-from keras.models import Model 
+from tensorflow.keras.models import Model
 
 
 

From 13450361fca7aab9bb3a939d867b9c4d3b5990f4 Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Wed, 1 Dec 2021 16:16:56 +0530
Subject: [PATCH 11/12] fixed tenforflow and keras import issue

Update import keras to import tensorflow.keras
---
 keras_segmentation/models/_pspnet_2.py    | 8 ++++----
 keras_segmentation/models/basic_models.py | 6 +++---
 keras_segmentation/models/fcn.py          | 4 ++--
 keras_segmentation/models/mobilenet.py    | 4 ++--
 keras_segmentation/models/model_utils.py  | 6 +++---
 keras_segmentation/models/pspnet.py       | 8 ++++----
 keras_segmentation/models/resnet50.py     | 6 +++---
 keras_segmentation/models/segnet.py       | 4 ++--
 keras_segmentation/models/unet.py         | 4 ++--
 keras_segmentation/models/vgg16.py        | 4 ++--
 10 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/keras_segmentation/models/_pspnet_2.py b/keras_segmentation/models/_pspnet_2.py
index 145ab99b2..dad61cd9b 100644
--- a/keras_segmentation/models/_pspnet_2.py
+++ b/keras_segmentation/models/_pspnet_2.py
@@ -2,11 +2,11 @@
 
 from math import ceil
 from sys import exit
-from keras import layers
-from keras.layers import Conv2D, MaxPooling2D, AveragePooling2D
-from keras.layers import BatchNormalization, Activation,\
+from tensorflow.keras import layers
+from tensorflow.keras.layers import Conv2D, MaxPooling2D, AveragePooling2D
+from tensorflow.keras.layers import BatchNormalization, Activation,\
     Input, Dropout, ZeroPadding2D
-from keras.layers.merge import Concatenate, Add
+from tensorflow.keras.layers.merge import Concatenate, Add
 import tensorflow as tf
 
 from .config import IMAGE_ORDERING
diff --git a/keras_segmentation/models/basic_models.py b/keras_segmentation/models/basic_models.py
index a9405b91a..2bca106ce 100644
--- a/keras_segmentation/models/basic_models.py
+++ b/keras_segmentation/models/basic_models.py
@@ -1,6 +1,6 @@
-from keras.models import *
-from keras.layers import *
-import keras.backend as K
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
+import tensorflow.keras.backend as K
 
 from .config import IMAGE_ORDERING
 
diff --git a/keras_segmentation/models/fcn.py b/keras_segmentation/models/fcn.py
index 6b2f347d6..de417d3b9 100644
--- a/keras_segmentation/models/fcn.py
+++ b/keras_segmentation/models/fcn.py
@@ -1,5 +1,5 @@
-from keras.models import *
-from keras.layers import *
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
 
 from .config import IMAGE_ORDERING
 from .model_utils import get_segmentation_model
diff --git a/keras_segmentation/models/mobilenet.py b/keras_segmentation/models/mobilenet.py
index 2d70af4f0..f9a618d0c 100644
--- a/keras_segmentation/models/mobilenet.py
+++ b/keras_segmentation/models/mobilenet.py
@@ -1,5 +1,5 @@
-from keras.models import *
-from keras.layers import *
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
 import tensorflow.keras.backend as K
 import tensorflow.keras as keras
 
diff --git a/keras_segmentation/models/model_utils.py b/keras_segmentation/models/model_utils.py
index 8232f5e03..367f93143 100644
--- a/keras_segmentation/models/model_utils.py
+++ b/keras_segmentation/models/model_utils.py
@@ -1,8 +1,8 @@
 from types import MethodType
 
-from keras.models import *
-from keras.layers import *
-import keras.backend as K
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
+import tensorflow.keras.backend as K
 from tqdm import tqdm
 
 from .config import IMAGE_ORDERING
diff --git a/keras_segmentation/models/pspnet.py b/keras_segmentation/models/pspnet.py
index a0c82c158..a347a95f1 100755
--- a/keras_segmentation/models/pspnet.py
+++ b/keras_segmentation/models/pspnet.py
@@ -1,8 +1,8 @@
 import numpy as np
-import keras
-from keras.models import *
-from keras.layers import *
-import keras.backend as K
+import tensorflow.keras as keras
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
+import tensorflow.keras.backend as K
 
 from .config import IMAGE_ORDERING
 from .model_utils import get_segmentation_model, resize_image
diff --git a/keras_segmentation/models/resnet50.py b/keras_segmentation/models/resnet50.py
index ee13ed8c4..4ce21fbe3 100644
--- a/keras_segmentation/models/resnet50.py
+++ b/keras_segmentation/models/resnet50.py
@@ -1,7 +1,7 @@
 import tensorflow.keras as keras
-from keras.models import *
-from keras.layers import *
-from keras import layers
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
+from tensorflow.keras import layers
 
 # Source:
 # https://github.com/fchollet/deep-learning-models/blob/master/resnet50.py
diff --git a/keras_segmentation/models/segnet.py b/keras_segmentation/models/segnet.py
index 6a9ad431e..142a74892 100755
--- a/keras_segmentation/models/segnet.py
+++ b/keras_segmentation/models/segnet.py
@@ -1,5 +1,5 @@
-from keras.models import *
-from keras.layers import *
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
 
 from .config import IMAGE_ORDERING
 from .model_utils import get_segmentation_model
diff --git a/keras_segmentation/models/unet.py b/keras_segmentation/models/unet.py
index ba5d5e3be..1ee16f5a6 100755
--- a/keras_segmentation/models/unet.py
+++ b/keras_segmentation/models/unet.py
@@ -1,5 +1,5 @@
-from keras.models import *
-from keras.layers import *
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
 
 from .config import IMAGE_ORDERING
 from .model_utils import get_segmentation_model
diff --git a/keras_segmentation/models/vgg16.py b/keras_segmentation/models/vgg16.py
index 79a763960..25198c27a 100644
--- a/keras_segmentation/models/vgg16.py
+++ b/keras_segmentation/models/vgg16.py
@@ -1,6 +1,6 @@
 import tensorflow.keras as keras
-from keras.models import *
-from keras.layers import *
+from tensorflow.keras.models import *
+from tensorflow.keras.layers import *
 
 from .config import IMAGE_ORDERING
 

From 9d27c752b9d40f9730ec7f4de6fae03bf320b9dc Mon Sep 17 00:00:00 2001
From: Sushant Agarwal <41518238+sushantag9@users.noreply.github.com>
Date: Sat, 1 Jan 2022 20:30:59 +0530
Subject: [PATCH 12/12] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 22cc81103..95e46b553 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 [![Downloads](https://pepy.tech/badge/keras-segmentation)](https://pepy.tech/project/keras-segmentation)
 [![Build Status](https://travis-ci.org/divamgupta/image-segmentation-keras.png)](https://travis-ci.org/divamgupta/image-segmentation-keras)
 [![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](http://perso.crans.org/besson/LICENSE.html)
-[![Twitter](https://img.shields.io/twitter/url.svg?label=Follow%20%40divamgupta&style=social&url=https%3A%2F%2Ftwitter.com%2Fdivamgupta)](https://twitter.com/divamgupta)
+[![Twitter](https://img.shields.io/twitter/url.svg?label=Follow%20%40sushantag9&style=social&url=https%3A%2F%2Ftwitter.com%2Fdivamgupta)](https://twitter.com/sushantag9)