{"cells":[{"metadata":{},"cell_type":"markdown","source":"# About\n\nThis kernel is based on [this kernel](https://www.kaggle.com/wrrosa/tpu-enet-b7-densenet).\n\nExperiments:\n\nIncreased the score:\n* The LR schedule defined in [this kernel](https://www.kaggle.com/mgornergoogle/five-flowers-with-keras-and-xception-on-tpu) from the [TPU Documentation](https://www.kaggle.com/docs/tpu).\n* Skip validation and add the validation dataset to the training dataset.\n\nLowered the score:\n* Reducing image size to 224x224 from 512x512"},{"metadata":{},"cell_type":"markdown","source":"<font size=4 color='red'> If you find this kernel useful, please don't forget to upvote. Thank you. </font>"},{"metadata":{},"cell_type":"markdown","source":"# Utilities"},{"metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true},"cell_type":"code","source":"import re\n\nimport numpy as np\n\nfrom matplotlib import pyplot as plt\n\nfrom sklearn.metrics import f1_score, precision_score, recall_score, confusion_matrix","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Tensorflow 2.1"},{"metadata":{"trusted":true},"cell_type":"code","source":"import tensorflow as tf\n\nprint(\"Tensorflow version \" + tf.__version__)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# TPU Configurations"},{"metadata":{"trusted":true},"cell_type":"code","source":"# This is basically -1\nAUTO = tf.data.experimental.AUTOTUNE\nAUTO","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"# Cluster Resolver for Google Cloud TPUs.\ntpu = tf.distribute.cluster_resolver.TPUClusterResolver()\n\n# Connects to the given cluster.\ntf.config.experimental_connect_to_cluster(tpu)\n\n# Initialize the TPU devices.\ntf.tpu.experimental.initialize_tpu_system(tpu)\n\n# TPU distribution strategy implementation.\nstrategy = tf.distribute.experimental.TPUStrategy(tpu)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Model Configurations"},{"metadata":{"trusted":true},"cell_type":"code","source":"IMAGE_SIZE = [512, 512]\nEPOCHS = 20\nBATCH_SIZE = 16 * strategy.num_replicas_in_sync","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Custom LR schedule\n\nAs in [this kernel](https://www.kaggle.com/mgornergoogle/five-flowers-with-keras-and-xception-on-tpu) from the [TPU Documentation](https://www.kaggle.com/docs/tpu)."},{"metadata":{"trusted":true},"cell_type":"code","source":"# Learning rate schedule for TPU, GPU and CPU.\n# Using an LR ramp up because fine-tuning a pre-trained model.\n# Starting with a high LR would break the pre-trained weights.\n\nLR_START = 0.00001\nLR_MAX = 0.00005 * strategy.num_replicas_in_sync\nLR_MIN = 0.00001\nLR_RAMPUP_EPOCHS = 5\nLR_SUSTAIN_EPOCHS = 0\nLR_EXP_DECAY = .8\n\ndef lrfn(epoch):\n    if epoch < LR_RAMPUP_EPOCHS:\n        lr = (LR_MAX - LR_START) / LR_RAMPUP_EPOCHS * epoch + LR_START\n    elif epoch < LR_RAMPUP_EPOCHS + LR_SUSTAIN_EPOCHS:\n        lr = LR_MAX\n    else:\n        lr = (LR_MAX - LR_MIN) * LR_EXP_DECAY**(epoch - LR_RAMPUP_EPOCHS - LR_SUSTAIN_EPOCHS) + LR_MIN\n    return lr\n    \nlr_callback = tf.keras.callbacks.LearningRateScheduler(lrfn, verbose=True)\n\nrng = [i for i in range(EPOCHS)]\ny = [lrfn(x) for x in rng]\nplt.plot(rng, y)\nprint(\"Learning rate schedule: {:.3g} to {:.3g} to {:.3g}\".format(y[0], max(y), y[-1]))","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Kaggle Datasets Access"},{"metadata":{"trusted":true},"cell_type":"code","source":"# As TPUs require access to the GCS path\n\nfrom kaggle_datasets import KaggleDatasets\n\nGCS_DS_PATH = KaggleDatasets().get_gcs_path()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"GCS_PATH_SELECT = { # available image sizes\n    192: GCS_DS_PATH + '/tfrecords-jpeg-192x192',\n    224: GCS_DS_PATH + '/tfrecords-jpeg-224x224',\n    331: GCS_DS_PATH + '/tfrecords-jpeg-331x331',\n    512: GCS_DS_PATH + '/tfrecords-jpeg-512x512'\n}\nGCS_PATH = GCS_PATH_SELECT[IMAGE_SIZE[0]]\n\nTRAINING_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/train/*.tfrec')\nVALIDATION_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/val/*.tfrec')\nTEST_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/test/*.tfrec') # predictions on this dataset should be submitted for the competition","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Skip Validation?"},{"metadata":{"trusted":true},"cell_type":"code","source":"SKIP_VALIDATION = True\n\nif SKIP_VALIDATION:\n    TRAINING_FILENAMES = TRAINING_FILENAMES + VALIDATION_FILENAMES","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# CLASSES"},{"metadata":{"trusted":true,"_kg_hide-input":true},"cell_type":"code","source":"CLASSES = ['pink primrose',    'hard-leaved pocket orchid', 'canterbury bells', 'sweet pea',     'wild geranium',     'tiger lily',           'moon orchid',              'bird of paradise', 'monkshood',        'globe thistle',         # 00 - 09\n           'snapdragon',       \"colt's foot\",               'king protea',      'spear thistle', 'yellow iris',       'globe-flower',         'purple coneflower',        'peruvian lily',    'balloon flower',   'giant white arum lily', # 10 - 19\n           'fire lily',        'pincushion flower',         'fritillary',       'red ginger',    'grape hyacinth',    'corn poppy',           'prince of wales feathers', 'stemless gentian', 'artichoke',        'sweet william',         # 20 - 29\n           'carnation',        'garden phlox',              'love in the mist', 'cosmos',        'alpine sea holly',  'ruby-lipped cattleya', 'cape flower',              'great masterwort', 'siam tulip',       'lenten rose',           # 30 - 39\n           'barberton daisy',  'daffodil',                  'sword lily',       'poinsettia',    'bolero deep blue',  'wallflower',           'marigold',                 'buttercup',        'daisy',            'common dandelion',      # 40 - 49\n           'petunia',          'wild pansy',                'primula',          'sunflower',     'lilac hibiscus',    'bishop of llandaff',   'gaura',                    'geranium',         'orange dahlia',    'pink-yellow dahlia',    # 50 - 59\n           'cautleya spicata', 'japanese anemone',          'black-eyed susan', 'silverbush',    'californian poppy', 'osteospermum',         'spring crocus',            'iris',             'windflower',       'tree poppy',            # 60 - 69\n           'gazania',          'azalea',                    'water lily',       'rose',          'thorn apple',       'morning glory',        'passion flower',           'lotus',            'toad lily',        'anthurium',             # 70 - 79\n           'frangipani',       'clematis',                  'hibiscus',         'columbine',     'desert-rose',       'tree mallow',          'magnolia',                 'cyclamen ',        'watercress',       'canna lily',            # 80 - 89\n           'hippeastrum ',     'bee balm',                  'pink quill',       'foxglove',      'bougainvillea',     'camellia',             'mallow',                   'mexican petunia',  'bromelia',         'blanket flower',        # 90 - 99\n           'trumpet creeper',  'blackberry lily',           'common tulip',     'wild rose']                                                                                                                                               # 100 - 102","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Helper Functions\n## Visualization"},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"def display_confusion_matrix(cmat, score, precision, recall):\n    plt.figure(figsize=(15,15))\n    ax = plt.gca()\n    ax.matshow(cmat, cmap='Reds')\n    ax.set_xticks(range(len(CLASSES)))\n    ax.set_xticklabels(CLASSES, fontdict={'fontsize': 7})\n    plt.setp(ax.get_xticklabels(), rotation=45, ha=\"left\", rotation_mode=\"anchor\")\n    ax.set_yticks(range(len(CLASSES)))\n    ax.set_yticklabels(CLASSES, fontdict={'fontsize': 7})\n    plt.setp(ax.get_yticklabels(), rotation=45, ha=\"right\", rotation_mode=\"anchor\")\n    titlestring = \"\"\n    if score is not None:\n        titlestring += 'f1 = {:.3f} '.format(score)\n    if precision is not None:\n        titlestring += '\\nprecision = {:.3f} '.format(precision)\n    if recall is not None:\n        titlestring += '\\nrecall = {:.3f} '.format(recall)\n    if len(titlestring) > 0:\n        ax.text(101, 1, titlestring, fontdict={'fontsize': 18, 'horizontalalignment':'right', 'verticalalignment':'top', 'color':'#804040'})\n    plt.show()\n    \ndef display_training_curves(training, validation, title, subplot):\n    if subplot%10==1: # set up the subplots on the first call\n        plt.subplots(figsize=(10,10), facecolor='#F0F0F0')\n        plt.tight_layout()\n    ax = plt.subplot(subplot)\n    ax.set_facecolor('#F8F8F8')\n    ax.plot(training)\n    ax.plot(validation)\n    ax.set_title('model '+ title)\n    ax.set_ylabel(title)\n    #ax.set_ylim(0.28,1.05)\n    ax.set_xlabel('epoch')\n    ax.legend(['train', 'valid.'])","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Datasets Functions"},{"metadata":{"_uuid":"d629ff2d2480ee46fbb7e2d37f6b5fab8052498a","_cell_guid":"79c7e3d0-c299-4dcb-8224-4455121ee9b0","trusted":true,"_kg_hide-input":true},"cell_type":"code","source":"def decode_image(image_data):\n    image = tf.image.decode_jpeg(image_data, channels=3)\n    image = tf.cast(image, tf.float32) / 255.0  # convert image to floats in [0, 1] range\n    image = tf.reshape(image, [*IMAGE_SIZE, 3]) # explicit size needed for TPU\n    return image\n\ndef read_labeled_tfrecord(example):\n    LABELED_TFREC_FORMAT = {\n        \"image\": tf.io.FixedLenFeature([], tf.string), # tf.string means bytestring\n        \"class\": tf.io.FixedLenFeature([], tf.int64),  # shape [] means single element\n    }\n    example = tf.io.parse_single_example(example, LABELED_TFREC_FORMAT)\n    image = decode_image(example['image'])\n    label = tf.cast(example['class'], tf.int32)\n    return image, label # returns a dataset of (image, label) pairs\n\ndef read_unlabeled_tfrecord(example):\n    UNLABELED_TFREC_FORMAT = {\n        \"image\": tf.io.FixedLenFeature([], tf.string), # tf.string means bytestring\n        \"id\": tf.io.FixedLenFeature([], tf.string),  # shape [] means single element\n        # class is missing, this competitions's challenge is to predict flower classes for the test dataset\n    }\n    example = tf.io.parse_single_example(example, UNLABELED_TFREC_FORMAT)\n    image = decode_image(example['image'])\n    idnum = example['id']\n    return image, idnum # returns a dataset of image(s)\n\ndef load_dataset(filenames, labeled=True, ordered=False):\n    # Read from TFRecords. For optimal performance, reading from multiple files at once and\n    # disregarding data order. Order does not matter since we will be shuffling the data anyway.\n\n    ignore_order = tf.data.Options()\n    if not ordered:\n        ignore_order.experimental_deterministic = False # disable order, increase speed\n\n    dataset = tf.data.TFRecordDataset(filenames, num_parallel_reads=AUTO) # automatically interleaves reads from multiple files\n    dataset = dataset.with_options(ignore_order) # uses data as soon as it streams in, rather than in its original order\n    dataset = dataset.map(read_labeled_tfrecord if labeled else read_unlabeled_tfrecord, num_parallel_calls=AUTO)\n    # returns a dataset of (image, label) pairs if labeled=True or (image, id) pairs if labeled=False\n    return dataset\n\ndef data_augment(image, label):\n    # data augmentation. Thanks to the dataset.prefetch(AUTO) statement in the next function (below),\n    # this happens essentially for free on TPU. Data pipeline code is executed on the \"CPU\" part\n    # of the TPU while the TPU itself is computing gradients.\n    image = tf.image.random_flip_left_right(image)\n    #image = tf.image.random_saturation(image, 0, 2)\n    return image, label   \n\ndef get_training_dataset():\n    dataset = load_dataset(TRAINING_FILENAMES, labeled=True)\n    dataset = dataset.map(data_augment, num_parallel_calls=AUTO)\n    dataset = dataset.repeat() # the training dataset must repeat for several epochs\n    dataset = dataset.shuffle(2048)\n    dataset = dataset.batch(BATCH_SIZE)\n    dataset = dataset.prefetch(AUTO) # prefetch next batch while training (autotune prefetch buffer size)\n    return dataset\n\ndef get_validation_dataset(ordered=False):\n    dataset = load_dataset(VALIDATION_FILENAMES, labeled=True, ordered=ordered)\n    dataset = dataset.batch(BATCH_SIZE)\n    dataset = dataset.cache()\n    dataset = dataset.prefetch(AUTO) # prefetch next batch while training (autotune prefetch buffer size)\n    return dataset\n\ndef get_test_dataset(ordered=False):\n    dataset = load_dataset(TEST_FILENAMES, labeled=False, ordered=ordered)\n    dataset = dataset.batch(BATCH_SIZE)\n    dataset = dataset.prefetch(AUTO) # prefetch next batch while training (autotune prefetch buffer size)\n    return dataset\n\ndef count_data_items(filenames):\n    # the number of data items is written in the name of the .tfrec files, i.e. flowers00-230.tfrec = 230 data items\n    n = [int(re.compile(r\"-([0-9]*)\\.\").search(filename).group(1)) for filename in filenames]\n    return np.sum(n)\n\nNUM_TRAINING_IMAGES = count_data_items(TRAINING_FILENAMES)\n\nNUM_VALIDATION_IMAGES = 0 if SKIP_VALIDATION else count_data_items(VALIDATION_FILENAMES)\n\nNUM_TEST_IMAGES = count_data_items(TEST_FILENAMES)\nSTEPS_PER_EPOCH = NUM_TRAINING_IMAGES // BATCH_SIZE\n\nprint('Dataset: {} training images, {} validation images, {} unlabeled test images'.format(NUM_TRAINING_IMAGES, NUM_VALIDATION_IMAGES, NUM_TEST_IMAGES))","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Models"},{"metadata":{"trusted":true},"cell_type":"code","source":"models = []\nhistories = []","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## EfficientNetB7"},{"metadata":{"trusted":true},"cell_type":"code","source":"!pip install -q efficientnet\n\nimport efficientnet.tfkeras as efn","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"# Need this line so Google will recite some incantations\n# for Turing to magically load the model onto the TPU\nwith strategy.scope():\n    enet = efn.EfficientNetB7(\n        input_shape=(IMAGE_SIZE[0], IMAGE_SIZE[1], 3),\n        weights='imagenet',\n        include_top=False\n    )\n    \n    enet.trainable = True\n\n    model = tf.keras.Sequential([\n        enet,\n        tf.keras.layers.GlobalAveragePooling2D(),\n        tf.keras.layers.Dense(len(CLASSES), activation='softmax')\n    ])\n            \nmodel.compile(\n    optimizer=tf.keras.optimizers.Adam(lr=0.0001),\n    loss = 'sparse_categorical_crossentropy',\n    metrics=['sparse_categorical_accuracy']\n)\n\nmodel.summary()\n\nmodels.append(model)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"history = model.fit(\n    get_training_dataset(), \n    steps_per_epoch=STEPS_PER_EPOCH,\n    epochs=EPOCHS,\n    callbacks=[lr_callback],\n    validation_data=None if SKIP_VALIDATION else get_validation_dataset()\n)\n\nhistories.append(history)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"if not SKIP_VALIDATION:\n    display_training_curves(history.history['loss'], history.history['val_loss'], 'loss', 211)\n    display_training_curves(history.history['sparse_categorical_accuracy'], history.history['val_sparse_categorical_accuracy'], 'accuracy', 212)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## DenseNet201:"},{"metadata":{"trusted":true},"cell_type":"code","source":"from tensorflow.keras.applications import DenseNet201","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"with strategy.scope():\n    rnet = DenseNet201(\n        input_shape=(IMAGE_SIZE[0], IMAGE_SIZE[1], 3),\n        weights='imagenet',\n        include_top=False\n    )\n    \n    rnet.trainable = True\n\n    model = tf.keras.Sequential([\n        rnet,\n        tf.keras.layers.GlobalAveragePooling2D(),\n        tf.keras.layers.Dense(len(CLASSES), activation='softmax')\n    ])\n        \nmodel.compile(\n    optimizer=tf.keras.optimizers.Adam(lr=0.0001),\n    loss = 'sparse_categorical_crossentropy',\n    metrics=['sparse_categorical_accuracy']\n)\n\nmodel.summary()\n\nmodels.append(model)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"history = model.fit(\n    get_training_dataset(), \n    steps_per_epoch=STEPS_PER_EPOCH,\n    epochs=EPOCHS, \n    callbacks=[lr_callback],\n    validation_data=None if SKIP_VALIDATION else get_validation_dataset()\n)\n\nhistories.append(history)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"if not SKIP_VALIDATION:\n    display_training_curves(history.history['loss'], history.history['val_loss'], 'loss', 211)\n    display_training_curves(history.history['sparse_categorical_accuracy'], history.history['val_sparse_categorical_accuracy'], 'accuracy', 212)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Confusion matrix"},{"metadata":{"trusted":true},"cell_type":"code","source":"if not SKIP_VALIDATION:\n    cmdataset = get_validation_dataset(ordered=True) # since we are splitting the dataset and iterating separately on images and labels, order matters.\n    images_ds = cmdataset.map(lambda image, label: image)\n    labels_ds = cmdataset.map(lambda image, label: label).unbatch()\n    cm_correct_labels = next(iter(labels_ds.batch(NUM_VALIDATION_IMAGES))).numpy() # get everything as one batch\n    cm_probabilities = (models[0].predict(images_ds) + models[1].predict(images_ds)) / 2\n    cm_predictions = np.argmax(cm_probabilities, axis=-1)\n    print(\"Correct   labels: \", cm_correct_labels.shape, cm_correct_labels)\n    print(\"Predicted labels: \", cm_predictions.shape, cm_predictions)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"if not SKIP_VALIDATION:\n    cmat = confusion_matrix(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)))\n    score = f1_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)), average='macro')\n    precision = precision_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)), average='macro')\n    recall = recall_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)), average='macro')\n    display_confusion_matrix(cmat, score, precision, recall)\n    print('f1 score: {:.3f}, precision: {:.3f}, recall: {:.3f}'.format(score, precision, recall))","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"if not SKIP_VALIDATION:\n    cmat_norm = (cmat.T / cmat.sum(axis=1)).T # normalized\n    display_confusion_matrix(cmat_norm, score, precision, recall)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"# Predictions"},{"metadata":{"trusted":true},"cell_type":"code","source":"test_ds = get_test_dataset(ordered=True) # since we are splitting the dataset and iterating separately on images and ids, order matters.\n\nprint('Computing predictions...')\ntest_images_ds = test_ds.map(lambda image, idnum: image)\nprobabilities = (models[0].predict(test_images_ds) + models[1].predict(test_images_ds)) / 2\npredictions = np.argmax(probabilities, axis=-1)\nprint(predictions)\n\nprint('Generating submission.csv file...')\ntest_ids_ds = test_ds.map(lambda image, idnum: idnum).unbatch()\ntest_ids = next(iter(test_ids_ds.batch(NUM_TEST_IMAGES))).numpy().astype('U') # all in one batch\n\nnp.savetxt('submission.csv', np.rec.fromarrays([test_ids, predictions]), fmt=['%s', '%d'], delimiter=',', header='id,label', comments='')","execution_count":null,"outputs":[]}],"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat":4,"nbformat_minor":1}