msd-seg.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n",
      "  from ._conv import register_converters as _register_converters\n",
      "Using TensorFlow backend.\n"
     ]
    }
   ],
   "source": [
    "import keras\n",
    "from keras.layers import Input, Conv2D, Conv2DTranspose, MaxPooling2D, Cropping2D, Concatenate, BatchNormalization, Activation, Flatten\n",
    "from keras.models import Model\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "input_image = Input(shape=(None,None,4))\n",
    "\n",
    "layers=3\n",
    "scale_depth=5\n",
    "feature_maps = [64,128,256,512,1024]\n",
    "bottleneck=16"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "encoding_layers = [ [ None for y in range( layers ) ] for x in range( scale_depth ) ]\n",
    "\n",
    "x = BatchNormalization()(input_image)\n",
    "x = Activation('relu')(x)\n",
    "encoding_layers[0][0] = Conv2D(feature_maps[0], (3, 3), padding='same')(x)\n",
    "\n",
    "for i in range(1,scale_depth):\n",
    "    x = BatchNormalization()(encoding_layers[i-1][0])\n",
    "    x = Activation('relu')(x)\n",
    "    encoding_layers[i][0] = Conv2D(feature_maps[i], (3, 3), strides=2, padding='same')(x)\n",
    "    \n",
    "\n",
    "#MSD\n",
    "for scale in range(scale_depth):\n",
    "    for layer in range(1,layers):\n",
    "        if scale == 0:\n",
    "            # layer 1 (2nd layer) layer only has one previous input, so no need to concatenate\n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(encoding_layers[scale][0])\n",
    "            else:\n",
    "                to_concatenate = [encoding_layers[scale][i] for i in (range(layer))] #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            encoding_layers[scale][layer] = Conv2D(feature_maps[scale], (3, 3), padding='same')(x)\n",
    "        else:\n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(encoding_layers[scale-1][0])\n",
    "            else:\n",
    "                to_concatenate_prev = [encoding_layers[scale-1][i] for i in (range(layer))]  #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate_prev)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            out_previous = Conv2D(feature_maps[scale], (3, 3), strides=2,padding='same')(x)\n",
    "            \n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(encoding_layers[scale][0])\n",
    "            else:\n",
    "                to_concatenate = [encoding_layers[scale][i] for i in (range(layer))] #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            out_current = Conv2D(feature_maps[scale], (3, 3), padding='same')(x)\n",
    "\n",
    "            encoding_layers[scale][layer] = Concatenate()([out_previous, out_current])\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "decoding_layers = [ [ None for y in range( layers ) ] for x in range( scale_depth ) ]\n",
    "\n",
    "for i in range(scale_depth):\n",
    "    decoding_layers[i][0] = encoding_layers[i][-1]\n",
    "    \n",
    "for scale in range(scale_depth)[::-1]:\n",
    "    for layer in range(1,layers):\n",
    "        if scale == scale_depth-1:\n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(decoding_layers[scale][0])\n",
    "            else:\n",
    "                to_concatenate = [decoding_layers[scale][i] for i in (range(layer))] #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            decoding_layers[scale][layer] = Conv2D(feature_maps[scale], (3, 3), padding='same')(x)\n",
    "        else:\n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(decoding_layers[scale+1][0])\n",
    "            else:\n",
    "                to_concatenate_prev = [decoding_layers[scale+1][i] for i in (range(layer))]  #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate_prev)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            out_previous = Conv2DTranspose(feature_maps[scale], (3, 3), strides=2,padding='same')(x)\n",
    "            \n",
    "            if layer == 1:\n",
    "                x = BatchNormalization()(decoding_layers[scale][0])\n",
    "            else:\n",
    "                to_concatenate = [decoding_layers[scale][i] for i in (range(layer))] #TODO: pass as reference\n",
    "                x = Concatenate()(to_concatenate)\n",
    "                x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            x = Conv2D(bottleneck, (1, 1), padding='same')(x) #TODO: bottleneck\n",
    "            x = BatchNormalization()(x)\n",
    "            x = Activation('relu')(x)\n",
    "            out_current = Conv2D(feature_maps[scale], (3, 3), padding='same')(x)\n",
    "\n",
    "            decoding_layers[scale][layer] = Concatenate()([out_previous, out_current])\n",
    "\n",
    "for i in range(scale_depth-1):\n",
    "    x = BatchNormalization()(decoding_layers[i+1][-1])\n",
    "    x = Activation('relu')(x)\n",
    "    x = Conv2DTranspose(feature_maps[i], (3, 3), strides=2, padding='same')(x)\n",
    "    decoding_layers[i][-1] = Concatenate()([decoding_layers[i][-1],x])\n",
    "\n",
    "x = BatchNormalization()(decoding_layers[0][-1])\n",
    "x = Activation('relu')(x)\n",
    "x = Conv2D(bottleneck, (3, 3), padding='same')(x)\n",
    "x = BatchNormalization()(x)\n",
    "x = Activation('relu')(x)\n",
    "mask = Conv2D(1, (1, 1), padding='same', activation='sigmoid')(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "model = Model(inputs=input_image, outputs=mask)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "__________________________________________________________________________________________________\n",
      "Layer (type)                    Output Shape         Param #     Connected to                     \n",
      "==================================================================================================\n",
      "input_1 (InputLayer)            (None, None, None, 3 0                                            \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_1 (BatchNor (None, None, None, 3 12          input_1[0][0]                    \n",
      "__________________________________________________________________________________________________\n",
      "activation_1 (Activation)       (None, None, None, 3 0           batch_normalization_1[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_1 (Conv2D)               (None, None, None, 6 1792        activation_1[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_2 (BatchNor (None, None, None, 6 256         conv2d_1[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "activation_2 (Activation)       (None, None, None, 6 0           batch_normalization_2[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_2 (Conv2D)               (None, None, None, 1 73856       activation_2[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_3 (BatchNor (None, None, None, 1 512         conv2d_2[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "activation_3 (Activation)       (None, None, None, 1 0           batch_normalization_3[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_3 (Conv2D)               (None, None, None, 2 295168      activation_3[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_4 (BatchNor (None, None, None, 2 1024        conv2d_3[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "activation_4 (Activation)       (None, None, None, 2 0           batch_normalization_4[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_4 (Conv2D)               (None, None, None, 5 1180160     activation_4[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_10 (BatchNo (None, None, None, 6 256         conv2d_1[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_12 (BatchNo (None, None, None, 1 512         conv2d_2[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_18 (BatchNo (None, None, None, 1 512         conv2d_2[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_20 (BatchNo (None, None, None, 2 1024        conv2d_3[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_26 (BatchNo (None, None, None, 2 1024        conv2d_3[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_28 (BatchNo (None, None, None, 5 2048        conv2d_4[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_6 (BatchNor (None, None, None, 6 256         conv2d_1[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "activation_10 (Activation)      (None, None, None, 6 0           batch_normalization_10[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_12 (Activation)      (None, None, None, 1 0           batch_normalization_12[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_18 (Activation)      (None, None, None, 1 0           batch_normalization_18[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_20 (Activation)      (None, None, None, 2 0           batch_normalization_20[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_26 (Activation)      (None, None, None, 2 0           batch_normalization_26[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_28 (Activation)      (None, None, None, 5 0           batch_normalization_28[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_6 (Activation)       (None, None, None, 6 0           batch_normalization_6[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_10 (Conv2D)              (None, None, None, 1 1040        activation_10[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_12 (Conv2D)              (None, None, None, 1 2064        activation_12[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_18 (Conv2D)              (None, None, None, 1 2064        activation_18[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_20 (Conv2D)              (None, None, None, 1 4112        activation_20[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_26 (Conv2D)              (None, None, None, 1 4112        activation_26[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_28 (Conv2D)              (None, None, None, 1 8208        activation_28[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_6 (Conv2D)               (None, None, None, 1 1040        activation_6[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_11 (BatchNo (None, None, None, 1 64          conv2d_10[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_13 (BatchNo (None, None, None, 1 64          conv2d_12[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_19 (BatchNo (None, None, None, 1 64          conv2d_18[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_21 (BatchNo (None, None, None, 1 64          conv2d_20[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_27 (BatchNo (None, None, None, 1 64          conv2d_26[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_29 (BatchNo (None, None, None, 1 64          conv2d_28[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_7 (BatchNor (None, None, None, 1 64          conv2d_6[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "activation_11 (Activation)      (None, None, None, 1 0           batch_normalization_11[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_13 (Activation)      (None, None, None, 1 0           batch_normalization_13[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_19 (Activation)      (None, None, None, 1 0           batch_normalization_19[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_21 (Activation)      (None, None, None, 1 0           batch_normalization_21[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_27 (Activation)      (None, None, None, 1 0           batch_normalization_27[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_29 (Activation)      (None, None, None, 1 0           batch_normalization_29[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_7 (Activation)       (None, None, None, 1 0           batch_normalization_7[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_11 (Conv2D)              (None, None, None, 1 18560       activation_11[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_13 (Conv2D)              (None, None, None, 1 18560       activation_13[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_19 (Conv2D)              (None, None, None, 2 37120       activation_19[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_21 (Conv2D)              (None, None, None, 2 37120       activation_21[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_27 (Conv2D)              (None, None, None, 5 74240       activation_27[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_29 (Conv2D)              (None, None, None, 5 74240       activation_29[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_7 (Conv2D)               (None, None, None, 6 9280        activation_7[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_2 (Concatenate)     (None, None, None, 2 0           conv2d_11[0][0]                  \n",
      "                                                                 conv2d_13[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_6 (Concatenate)     (None, None, None, 5 0           conv2d_19[0][0]                  \n",
      "                                                                 conv2d_21[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_10 (Concatenate)    (None, None, None, 1 0           conv2d_27[0][0]                  \n",
      "                                                                 conv2d_29[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_3 (Concatenate)     (None, None, None, 1 0           conv2d_1[0][0]                   \n",
      "                                                                 conv2d_7[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_4 (Concatenate)     (None, None, None, 3 0           conv2d_2[0][0]                   \n",
      "                                                                 concatenate_2[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_7 (Concatenate)     (None, None, None, 3 0           conv2d_2[0][0]                   \n",
      "                                                                 concatenate_2[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_8 (Concatenate)     (None, None, None, 7 0           conv2d_3[0][0]                   \n",
      "                                                                 concatenate_6[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_11 (Concatenate)    (None, None, None, 7 0           conv2d_3[0][0]                   \n",
      "                                                                 concatenate_6[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_12 (Concatenate)    (None, None, None, 1 0           conv2d_4[0][0]                   \n",
      "                                                                 concatenate_10[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_14 (BatchNo (None, None, None, 1 512         concatenate_3[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_16 (BatchNo (None, None, None, 3 1536        concatenate_4[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_22 (BatchNo (None, None, None, 3 1536        concatenate_7[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_24 (BatchNo (None, None, None, 7 3072        concatenate_8[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_30 (BatchNo (None, None, None, 7 3072        concatenate_11[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_32 (BatchNo (None, None, None, 1 6144        concatenate_12[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "activation_14 (Activation)      (None, None, None, 1 0           batch_normalization_14[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_16 (Activation)      (None, None, None, 3 0           batch_normalization_16[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_22 (Activation)      (None, None, None, 3 0           batch_normalization_22[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_24 (Activation)      (None, None, None, 7 0           batch_normalization_24[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_30 (Activation)      (None, None, None, 7 0           batch_normalization_30[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_32 (Activation)      (None, None, None, 1 0           batch_normalization_32[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_14 (Conv2D)              (None, None, None, 1 2064        activation_14[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_16 (Conv2D)              (None, None, None, 1 6160        activation_16[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_22 (Conv2D)              (None, None, None, 1 6160        activation_22[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_24 (Conv2D)              (None, None, None, 1 12304       activation_24[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_30 (Conv2D)              (None, None, None, 1 12304       activation_30[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_32 (Conv2D)              (None, None, None, 1 24592       activation_32[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_15 (BatchNo (None, None, None, 1 64          conv2d_14[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_17 (BatchNo (None, None, None, 1 64          conv2d_16[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_23 (BatchNo (None, None, None, 1 64          conv2d_22[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_25 (BatchNo (None, None, None, 1 64          conv2d_24[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_1 (Concatenate)     (None, None, None, 1 0           conv2d_1[0][0]                   \n",
      "                                                                 conv2d_7[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_31 (BatchNo (None, None, None, 1 64          conv2d_30[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_33 (BatchNo (None, None, None, 1 64          conv2d_32[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_15 (Activation)      (None, None, None, 1 0           batch_normalization_15[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_17 (Activation)      (None, None, None, 1 0           batch_normalization_17[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_23 (Activation)      (None, None, None, 1 0           batch_normalization_23[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_25 (Activation)      (None, None, None, 1 0           batch_normalization_25[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_8 (BatchNor (None, None, None, 1 512         concatenate_1[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "activation_31 (Activation)      (None, None, None, 1 0           batch_normalization_31[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_33 (Activation)      (None, None, None, 1 0           batch_normalization_33[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_15 (Conv2D)              (None, None, None, 1 18560       activation_15[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_17 (Conv2D)              (None, None, None, 1 18560       activation_17[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_23 (Conv2D)              (None, None, None, 2 37120       activation_23[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_25 (Conv2D)              (None, None, None, 2 37120       activation_25[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "activation_8 (Activation)       (None, None, None, 1 0           batch_normalization_8[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_31 (Conv2D)              (None, None, None, 5 74240       activation_31[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_33 (Conv2D)              (None, None, None, 5 74240       activation_33[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_5 (Concatenate)     (None, None, None, 2 0           conv2d_15[0][0]                  \n",
      "                                                                 conv2d_17[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_9 (Concatenate)     (None, None, None, 5 0           conv2d_23[0][0]                  \n",
      "                                                                 conv2d_25[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_8 (Conv2D)               (None, None, None, 1 2064        activation_8[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_13 (Concatenate)    (None, None, None, 1 0           conv2d_31[0][0]                  \n",
      "                                                                 conv2d_33[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_62 (BatchNo (None, None, None, 5 2048        concatenate_9[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_64 (BatchNo (None, None, None, 2 1024        concatenate_5[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_9 (BatchNor (None, None, None, 1 64          conv2d_8[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_54 (BatchNo (None, None, None, 1 4096        concatenate_13[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_56 (BatchNo (None, None, None, 5 2048        concatenate_9[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "activation_62 (Activation)      (None, None, None, 5 0           batch_normalization_62[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_64 (Activation)      (None, None, None, 2 0           batch_normalization_64[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_9 (Activation)       (None, None, None, 1 0           batch_normalization_9[0][0]      \n",
      "__________________________________________________________________________________________________\n",
      "activation_54 (Activation)      (None, None, None, 1 0           batch_normalization_54[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_56 (Activation)      (None, None, None, 5 0           batch_normalization_56[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_58 (Conv2D)              (None, None, None, 1 8208        activation_62[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_59 (Conv2D)              (None, None, None, 1 4112        activation_64[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_9 (Conv2D)               (None, None, None, 6 9280        activation_9[0][0]               \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_52 (Conv2D)              (None, None, None, 1 16400       activation_54[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_53 (Conv2D)              (None, None, None, 1 8208        activation_56[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_63 (BatchNo (None, None, None, 1 64          conv2d_58[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_65 (BatchNo (None, None, None, 1 64          conv2d_59[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_70 (BatchNo (None, None, None, 2 1024        concatenate_5[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_72 (BatchNo (None, None, None, 6 256         conv2d_9[0][0]                   \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_55 (BatchNo (None, None, None, 1 64          conv2d_52[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_57 (BatchNo (None, None, None, 1 64          conv2d_53[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_63 (Activation)      (None, None, None, 1 0           batch_normalization_63[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_65 (Activation)      (None, None, None, 1 0           batch_normalization_65[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_70 (Activation)      (None, None, None, 2 0           batch_normalization_70[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_72 (Activation)      (None, None, None, 6 0           batch_normalization_72[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_55 (Activation)      (None, None, None, 1 0           batch_normalization_55[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_57 (Activation)      (None, None, None, 1 0           batch_normalization_57[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_5 (Conv2DTrans (None, None, None, 1 18560       activation_63[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_60 (Conv2D)              (None, None, None, 1 18560       activation_65[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_64 (Conv2D)              (None, None, None, 1 4112        activation_70[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_65 (Conv2D)              (None, None, None, 1 1040        activation_72[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_3 (Conv2DTrans (None, None, None, 2 37120       activation_55[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_54 (Conv2D)              (None, None, None, 2 37120       activation_57[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_27 (Concatenate)    (None, None, None, 2 0           conv2d_transpose_5[0][0]         \n",
      "                                                                 conv2d_60[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_71 (BatchNo (None, None, None, 1 64          conv2d_64[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_73 (BatchNo (None, None, None, 1 64          conv2d_65[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_23 (Concatenate)    (None, None, None, 5 0           conv2d_transpose_3[0][0]         \n",
      "                                                                 conv2d_54[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_71 (Activation)      (None, None, None, 1 0           batch_normalization_71[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_73 (Activation)      (None, None, None, 1 0           batch_normalization_73[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_28 (Concatenate)    (None, None, None, 1 0           concatenate_9[0][0]              \n",
      "                                                                 concatenate_23[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_29 (Concatenate)    (None, None, None, 5 0           concatenate_5[0][0]              \n",
      "                                                                 concatenate_27[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_7 (Conv2DTrans (None, None, None, 6 9280        activation_71[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_66 (Conv2D)              (None, None, None, 6 9280        activation_73[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_66 (BatchNo (None, None, None, 1 4096        concatenate_28[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_68 (BatchNo (None, None, None, 5 2048        concatenate_29[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_31 (Concatenate)    (None, None, None, 1 0           conv2d_transpose_7[0][0]         \n",
      "                                                                 conv2d_66[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_66 (Activation)      (None, None, None, 1 0           batch_normalization_66[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_68 (Activation)      (None, None, None, 5 0           batch_normalization_68[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_32 (Concatenate)    (None, None, None, 5 0           concatenate_5[0][0]              \n",
      "                                                                 concatenate_27[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_33 (Concatenate)    (None, None, None, 1 0           conv2d_9[0][0]                   \n",
      "                                                                 concatenate_31[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_61 (Conv2D)              (None, None, None, 1 16400       activation_66[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_62 (Conv2D)              (None, None, None, 1 8208        activation_68[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_74 (BatchNo (None, None, None, 5 2048        concatenate_32[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_76 (BatchNo (None, None, None, 1 768         concatenate_33[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_67 (BatchNo (None, None, None, 1 64          conv2d_61[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_69 (BatchNo (None, None, None, 1 64          conv2d_62[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_74 (Activation)      (None, None, None, 5 0           batch_normalization_74[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_76 (Activation)      (None, None, None, 1 0           batch_normalization_76[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_67 (Activation)      (None, None, None, 1 0           batch_normalization_67[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_69 (Activation)      (None, None, None, 1 0           batch_normalization_69[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_67 (Conv2D)              (None, None, None, 1 8208        activation_74[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_68 (Conv2D)              (None, None, None, 1 3088        activation_76[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_6 (Conv2DTrans (None, None, None, 1 18560       activation_67[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_63 (Conv2D)              (None, None, None, 1 18560       activation_69[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_75 (BatchNo (None, None, None, 1 64          conv2d_67[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_77 (BatchNo (None, None, None, 1 64          conv2d_68[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_30 (Concatenate)    (None, None, None, 2 0           conv2d_transpose_6[0][0]         \n",
      "                                                                 conv2d_63[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_75 (Activation)      (None, None, None, 1 0           batch_normalization_75[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "activation_77 (Activation)      (None, None, None, 1 0           batch_normalization_77[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_78 (BatchNo (None, None, None, 2 1024        concatenate_30[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_8 (Conv2DTrans (None, None, None, 6 9280        activation_75[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_69 (Conv2D)              (None, None, None, 6 9280        activation_77[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "activation_78 (Activation)      (None, None, None, 2 0           batch_normalization_78[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_34 (Concatenate)    (None, None, None, 1 0           conv2d_transpose_8[0][0]         \n",
      "                                                                 conv2d_69[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_transpose_9 (Conv2DTrans (None, None, None, 6 147520      activation_78[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "concatenate_35 (Concatenate)    (None, None, None, 1 0           concatenate_34[0][0]             \n",
      "                                                                 conv2d_transpose_9[0][0]         \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_82 (BatchNo (None, None, None, 1 768         concatenate_35[0][0]             \n",
      "__________________________________________________________________________________________________\n",
      "activation_82 (Activation)      (None, None, None, 1 0           batch_normalization_82[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_70 (Conv2D)              (None, None, None, 1 27664       activation_82[0][0]              \n",
      "__________________________________________________________________________________________________\n",
      "batch_normalization_83 (BatchNo (None, None, None, 1 64          conv2d_70[0][0]                  \n",
      "__________________________________________________________________________________________________\n",
      "activation_83 (Activation)      (None, None, None, 1 0           batch_normalization_83[0][0]     \n",
      "__________________________________________________________________________________________________\n",
      "conv2d_71 (Conv2D)              (None, None, None, 1 17          activation_83[0][0]              \n",
      "==================================================================================================\n",
      "Total params: 2,662,957\n",
      "Trainable params: 2,639,623\n",
      "Non-trainable params: 23,334\n",
      "__________________________________________________________________________________________________\n"
     ]
    }
   ],
   "source": [
    "model.summary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import tensorflow as tf\n",
    "from keras import backend as K\n",
    "\n",
    "def mask_loss(y_true, y_pred, smooth = 1.):\n",
    "    #y_true_f = tf.convert_to_tensor(y_true) \n",
    "    intersection = tf.reduce_sum(y_true * y_pred)\n",
    "\n",
    "    dice = -tf.log(tf.constant(2.) * intersection + smooth) + \\\n",
    "        tf.log((tf.reduce_sum(y_true) + tf.reduce_sum(y_pred) + smooth))\n",
    "    \n",
    "    bce = K.mean(K.binary_crossentropy(y_true, y_pred), axis=-1)\n",
    "    \n",
    "    loss = bce + 1 - dice"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.compile(optimizer='rmsprop',\n",
    "              loss='mask_loss',\n",
    "              metrics=['accuracy'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def train():\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "import keras\n",
    "\n",
    "input_image = keras.layers.Input(shape=(100,100,4))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "TensorShape([Dimension(None), Dimension(100), Dimension(100), Dimension(16)])"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x = input_image\n",
    "x = keras.layers.Conv2D(16,(3,3),dilation_rate=2, padding='same')(x)\n",
    "x.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'Tensor' object has no attribute 'output'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-22-f570658b56b9>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m: 'Tensor' object has no attribute 'output'"
     ]
    }
   ],
   "source": [
    "x.output()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.14"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}