initial commit

Untitled.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "676fb056",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint8 = np.dtype([(\"qint8\", np.int8, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_quint8 = np.dtype([(\"quint8\", np.uint8, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint16 = np.dtype([(\"qint16\", np.int16, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_quint16 = np.dtype([(\"quint16\", np.uint16, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint32 = np.dtype([(\"qint32\", np.int32, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorflow\\python\\framework\\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  np_resource = np.dtype([(\"resource\", np.ubyte, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint8 = np.dtype([(\"qint8\", np.int8, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_quint8 = np.dtype([(\"quint8\", np.uint8, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint16 = np.dtype([(\"qint16\", np.int16, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_quint16 = np.dtype([(\"quint16\", np.uint16, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  _np_qint32 = np.dtype([(\"qint32\", np.int32, 1)])\n",
+      "C:\\ProgramData\\Anaconda3\\envs\\env-unets\\lib\\site-packages\\tensorboard\\compat\\tensorflow_stub\\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
+      "  np_resource = np.dtype([(\"resource\", np.ubyte, 1)])\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Default GPU Device:/device:GPU:0\n"
+     ]
+    }
+   ],
+   "source": [
+    "import tensorflow as tf \n",
+    "\n",
+    "if tf.test.gpu_device_name(): \n",
+    "\n",
+    "    print('Default GPU Device:{}'.format(tf.test.gpu_device_name()))\n",
+    "\n",
+    "else:\n",
+    "\n",
+    "   print(\"Please install GPU version of TF\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fb1acd79",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

configs/.ipynb_checkpoints/default_multiclass_unet-checkpoint.yml

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+general:
+#### General settings ####
+  dataset_dir: '/mnt/mbi/home/mbirdm/AI/data_ai/Richard/MultiClass/RI/Train'
+  model_dir: '/mnt/mbi/home/mbirdm/AI/data_ai/Richard/Networks_edge/RI/'
+  image_subfolder: 'Images'
+  ground_truth_subfolder: 'Masks'
+
+  # CPU/GPU settings
+  visible_gpu: None
+  use_cpu: False
+  for_prediction: False
+
+  #callbacks
+  reduce_LR_on_plateau: True
+  use_tensorboard: True
+  early_stopping: False
+
+  # File Saving
+  save_as_uint16: True
+
+model:
+#### Model parameters ####
+  filters: 16 # convolution filters
+  levels: 4 # for unet 
+  num_epochs: 100
+  val_split: 0.1
+  batch_size_per_GPU: 10
+
+  optimizer: 
+    optimizer_function: 'adam' #'sgd','rmsprop', 'adam'
+    learning_rate: 0.0001
+    decay: 0
+    momentum: 0.9
+    nesterov: True
+
+  loss: 'bce_dice_loss' #'bce_dice_loss', 'binary_crossentropy', 'categorical_crossentropy','jaccard_distance_loss','lovasz_hinge','dice_loss','sparse_categorical_crossentropy'
+  edge_enhance: False
+
+  metrics:
+    - 'categorical_accuracy' # 'binary_accuracy','categorical_accuracy'
+
+  dropout_value: 0.5
+  weight_regularizer: 0
+
+  initializer: 'he_normal'
+  strides: [1, 1]
+
+  activation:
+    activation_function: 'relu' #'relu', 'sigmoid','softmax', 'tanh'
+    final_activation: 'softmax' #'relu', 'sigmoid','softmax', 'tanh'
+
+  padding: 'same'
+
+images:
+#### Image/Ground truth settings ####
+  tile_size: [512,512] # h,w
+  tile_overlap_size: [0,0]
+  image_channel: 1
+  nb_classes: 3 
+  invert_ground_truth: False
+  use_binary_erosion: False
+  use_binary_dilation: False
+  use_binary_dilation_after_augmentation: False
+  disk_size: 1
+
+  # image normalization during dataset loading
+  percentile_normalization: True
+  percentile: [3, 99.8]
+
+  # patch normalization during test time
+  scale_input: False
+  mean_std_normalization: False
+  mean: 0
+  std: 0
+
+augmentation:
+#### Image augmentations settings ####
+  augmentation_library: 'albumentations'
+  num_augmented_images: 10
+  augmentations_p: 0.9
+
+  random_rotate: True
+  random_rotate_p: 0.9
+
+  flip: True
+  transpose: True
+
+  blur_group: False
+  blur_group_p: 0.3
+
+  motion_blur: False
+  motion_blur_p: 0.1
+  median_blur: False
+  median_blur_limit: 3
+  median_blur_p: 0.3
+  blur: False
+  blur_limit: 3
+  blur_p: 0.3
+
+  shift_scale_rotate: True
+  shift_scale_rotate_p: 0.3
+  shift_limit: 0.0625
+  scale_limit: 0.5
+  rotate_limit: 45
+
+  distortion_group: False
+  distortion_group_p: 0.2
+  optical_distortion: False
+  optical_distortion_p: 0.3
+  elastic_transform: False
+  elastic_transform_p: 0.3
+  grid_distortion: False
+  grid_distortion_p: 0.3
+
+  brightness_contrast_group: False
+  brightness_contrast_group_p: 0.3
+  clahe: False
+  sharpen: False
+  random_brightness_contrast: False
+
+callbacks:
+#### Callback settings ####
+  # Tensorboard settings
+  tensorboard:
+    write_graph: False
+    write_images: False
+    write_grads: False
+    histogram_freq: 0
+
+  reduceLR:
+  # Reduce LR on plateau settings
+    reduce_LR_monitor: 'val_loss'
+    reduce_LR_patience: 10
+    reduce_LR_factor: 0.5
+    reduce_LR_min_lr: 0.000001
+
+  earlystopping:
+  # Early stopping settings
+    early_stopping_monitor: 'val_loss'
+    early_stopping_patience: 20
+    early_stopping_min_delta: 0
+
+  modelcheckpoint:
+  # Model checkpoint settings
+    save_best_weights: True

configs/.ipynb_checkpoints/default_singleclass_unet-checkpoint.yml

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+general:
+#### General settings ####
+  dataset_dir: '/Users/cjt678/Desktop/Unets/Data/'
+  #dataset_dir: '/mnt/mbi/home/mbirdm/AI/data_ai/Anne/Unet_Noyau/train/'
+  model_dir: '/Users/cjt678/Desktop/Unets/Networks/'
+  image_subfolder: 'Images'
+  ground_truth_subfolder: 'Masks'
+
+  # CPU/GPU settings
+  visible_gpu: None
+  use_cpu: False
+  for_prediction: False
+
+  #callbacks
+  reduce_LR_on_plateau: True
+  use_tensorboard: True
+  early_stopping: False
+
+  # File Saving
+  save_as_uint16: True
+
+model:
+#### Model parameters ####
+  filters: 16 # convolution filters
+  levels: 4 # for unet 
+  num_epochs: 120
+  val_split: 0.1
+  batch_size_per_GPU: 6
+
+  optimizer: 
+    optimizer_function: 'adam' #'sgd','rmsprop', 'adam'
+    learning_rate: 0.0001
+    decay: 0
+    momentum: 0.9
+    nesterov: True
+
+  loss: 'dice_loss' #'bce_dice_loss', 'binary_crossentropy' 'categorical_crossentropy','jaccard_distance_loss','lovasz_hinge','dice_loss','sparse_categorical_crossentropy'
+  edge_enhance: True
+
+  metrics:
+    - 'IoU' # 'binary_accuracy','categorical_accuracy', 'IoU'
+
+  dropout_value: 0.5
+  weight_regularizer: 0
+
+  initializer: 'he_normal'
+  strides: [1, 1]
+
+  activation:
+    activation_function: 'relu' #'relu', 'sigmoid','softmax', 'tanh'
+    final_activation: 'sigmoid' #'relu', 'sigmoid','softmax', 'tanh'
+
+  padding: 'same'
+
+images:
+#### Image/Ground truth settings ####
+  tile_size: [512,512] # h,w,z
+  tile_overlap_size: [0,0]
+  image_channel: 1
+  nb_classes: 1 
+  invert_ground_truth: False
+  use_binary_erosion: False
+  use_binary_dilation: False
+  use_binary_dilation_after_augmentation: False
+  disk_size: 1
+
+  # image normalization during dataset loading
+  percentile_normalization: True
+  percentile: [3, 99.8]
+
+  # patch normalization during test time
+  scale_input: False
+  mean_std_normalization: False
+  mean: 0
+  std: 0
+
+augmentation:
+#### Image augmentations settings ####
+  augmentation_library: 'albumentations'
+  num_augmented_images: 10
+  augmentations_p: 0.9
+
+  random_rotate: True
+  random_rotate_p: 0.9
+
+  flip: True
+  transpose: True
+
+  blur_group: False
+  blur_group_p: 0.3
+
+  motion_blur: False
+  motion_blur_p: 0.1
+  median_blur: False
+  median_blur_limit: 3
+  median_blur_p: 0.3
+  blur: False
+  blur_limit: 3
+  blur_p: 0.3
+
+  shift_scale_rotate: True
+  shift_scale_rotate_p: 0.3
+  shift_limit: 0.0625
+  scale_limit: 0.5
+  rotate_limit: 45
+
+  distortion_group: False
+  distortion_group_p: 0.2
+  optical_distortion: False
+  optical_distortion_p: 0.3
+  elastic_transform: False
+  elastic_transform_p: 0.3
+  grid_distortion: False
+  grid_distortion_p: 0.3
+
+  brightness_contrast_group: False
+  brightness_contrast_group_p: 0.3
+  clahe: False
+  sharpen: False
+  random_brightness_contrast: False
+
+callbacks:
+#### Callback settings ####
+  # Tensorboard settings
+  tensorboard:
+    write_graph: False
+    write_images: False
+    write_grads: False
+    histogram_freq: 0
+
+  reduceLR:
+  # Reduce LR on plateau settings
+    reduce_LR_monitor: 'val_loss'
+    reduce_LR_patience: 10
+    reduce_LR_factor: 0.5
+    reduce_LR_min_lr: 0.000001
+
+  earlystopping:
+  # Early stopping settings
+    early_stopping_monitor: 'val_loss'
+    early_stopping_patience: 20
+    early_stopping_min_delta: 0
+
+  modelcheckpoint:
+  # Model checkpoint settings
+    save_best_weights: True