Kaggle competition: Petals to the Metal - Flower Classification on TPU
<SOS> metric: macrofscore Kaggle data source: petals-to-the-metal-flower-classification-on-tpu<categorify>
print("TF version " + tf.__version__)
 AUTO = tf.data.experimental.AUTOTUNE
le=LabelEncoder()
for col in newdata.columns:
if not _check_numberic(newdata[col]):
le.fit(newdata[col])
 newdata[col]=le.transform(newdata[col] )<filter>
try:
tpu = tf.distribute.cluster_resolver.TPUClusterResolver()
print('Running on TPU ', tpu.master())
 except ValueError:
tpu = None
if tpu:
tf.config.experimental_connect_to_cluster(tpu)
 tf.tpu.experimental.initialize_tpu_system(tpu)
 strategy = tf.distribute.experimental.TPUStrategy(tpu)
 else:
strategy = tf.distribute.get_strategy()
print("REPLICAS: ", strategy.num_replicas_in_sync )
test_data=newdata.loc[newdata.SalePrice.isna() ,:]<filter>
IMAGE_SIZE = [224, 224]
EPOCHS = 35
BATCH_SIZE = 16 * strategy.num_replicas_in_sync
SEED = 752
SKIP_VALIDATION = False
TTA_NUM = 5
random.seed(SEED)
 np.random.seed(SEED)
 tf.random.set_seed(SEED )
train_data=newdata.loc[newdata.SalePrice.notna() ,:]<compute_test_metric>
GCS_DS_PATH = KaggleDatasets().get_gcs_path('tpu-getting-started')
 GCS_DS_PATH_EXT = KaggleDatasets().get_gcs_path('tf-flower-photo-tfrec')
 GCS_PATH_SELECT = {
192: GCS_DS_PATH + '/tfrecords-jpeg-192x192',
224: GCS_DS_PATH + '/tfrecords-jpeg-224x224',
331: GCS_DS_PATH + '/tfrecords-jpeg-331x331',
512: GCS_DS_PATH + '/tfrecords-jpeg-512x512'
}
GCS_PATH = GCS_PATH_SELECT[IMAGE_SIZE[0]]
GCS_PATH_SELECT_EXT = {
192: '/tfrecords-jpeg-192x192',
224: '/tfrecords-jpeg-224x224',
331: '/tfrecords-jpeg-331x331',
512: '/tfrecords-jpeg-512x512'
}
GCS_PATH_EXT = GCS_PATH_SELECT_EXT[IMAGE_SIZE[0]]
IMAGENET_FILES = tf.io.gfile.glob(GCS_DS_PATH_EXT + '/imagenet' + GCS_PATH_EXT + '/*.tfrec')
 INATURELIST_FILES = tf.io.gfile.glob(GCS_DS_PATH_EXT + '/inaturalist' + GCS_PATH_EXT + '/*.tfrec')
 OPENIMAGE_FILES = tf.io.gfile.glob(GCS_DS_PATH_EXT + '/openimage' + GCS_PATH_EXT + '/*.tfrec')
 OXFORD_FILES = tf.io.gfile.glob(GCS_DS_PATH_EXT + '/oxford_102' + GCS_PATH_EXT + '/*.tfrec')
 TENSORFLOW_FILES = tf.io.gfile.glob(GCS_DS_PATH_EXT + '/tf_flowers' + GCS_PATH_EXT + '/*.tfrec')
 ADDITIONAL_TRAINING_FILENAMES = IMAGENET_FILES + INATURELIST_FILES + OPENIMAGE_FILES + OXFORD_FILES + TENSORFLOW_FILES
CLASSES = ['pink primrose', 'hard-leaved pocket orchid', 'canterbury bells', 'sweet pea', 'wild geranium', 'tiger lily', 'moon orchid', 'bird of paradise', 'monkshood', 'globe thistle',
'snapdragon', "colt's foot", 'king protea', 'spear thistle', 'yellow iris', 'globe-flower', 'purple coneflower', 'peruvian lily', 'balloon flower', 'giant white arum lily',
'fire lily', 'pincushion flower', 'fritillary', 'red ginger', 'grape hyacinth', 'corn poppy', 'prince of wales feathers', 'stemless gentian', 'artichoke', 'sweet william',
'carnation', 'garden phlox', 'love in the mist', 'cosmos', 'alpine sea holly', 'ruby-lipped cattleya', 'cape flower', 'great masterwort', 'siam tulip', 'lenten rose',
'barberton daisy', 'daffodil', 'sword lily', 'poinsettia', 'bolero deep blue', 'wallflower', 'marigold', 'buttercup', 'daisy', 'common dandelion',
'petunia', 'wild pansy', 'primula', 'sunflower', 'lilac hibiscus', 'bishop of llandaff', 'gaura', 'geranium', 'orange dahlia', 'pink-yellow dahlia',
'cautleya spicata', 'japanese anemone', 'black-eyed susan', 'silverbush', 'californian poppy', 'osteospermum', 'spring crocus', 'iris', 'windflower', 'tree poppy',
'gazania', 'azalea', 'water lily', 'rose', 'thorn apple', 'morning glory', 'passion flower', 'lotus', 'toad lily', 'anthurium',
'frangipani', 'clematis', 'hibiscus', 'columbine', 'desert-rose', 'tree mallow', 'magnolia', 'cyclamen ', 'watercress', 'canna lily',
'hippeastrum ', 'bee balm', 'pink quill', 'foxglove', 'bougainvillea', 'camellia', 'mallow', 'mexican petunia', 'bromelia', 'blanket flower',
'trumpet creeper', 'blackberry lily', 'common tulip', 'wild rose']
TRAINING_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/train/*.tfrec')
 VALIDATION_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/val/*.tfrec')
 TEST_FILENAMES = tf.io.gfile.glob(GCS_PATH + '/test/*.tfrec')
 TRAINING_FILENAMES = TRAINING_FILENAMES + ADDITIONAL_TRAINING_FILENAMES
def rmsle(y, y_pred):
assert len(y)== len(y_pred)
 terms_to_sum = [(math.log(y_pred[i] + 1)- math.log(y[i] + 1)) ** 2.0 for i,pred in enumerate(y_pred)]
return(sum(terms_to_sum)*(1.0/len(y)))** 0.5<import_modules>
np.set_printoptions(threshold=15, linewidth=80)
 def batch_to_numpy_images_and_labels(data):
images, labels = data
numpy_images = images.numpy()
numpy_labels = labels.numpy()
if numpy_labels.dtype == object:
numpy_labels = [None for _ in enumerate(numpy_images)]
return numpy_images, numpy_labels
def title_from_label_and_target(label, correct_label):
if correct_label is None:
return CLASSES[label], True
correct =(label == correct_label)
 return "{} [{}{}{}]".format(CLASSES[label], 'OK' if correct else 'NO', u"\u2192" if not correct else '',
CLASSES[correct_label] if not correct else ''), correct
def display_one_flower(image, title, subplot, red=False, titlesize=16):
plt.subplot(*subplot)
 plt.axis('off')
 plt.imshow(image)
 if len(title)> 0:
plt.title(title, fontsize=int(titlesize)if not red else int(titlesize/1.2), color='red' if red else 'black', fontdict={'verticalalignment':'center'}, pad=int(titlesize/1.5))
return(subplot[0], subplot[1], subplot[2]+1)
 def display_batch_of_images(databatch, predictions=None):

 images, labels = batch_to_numpy_images_and_labels(databatch)
 if labels is None:
labels = [None for _ in enumerate(images)]
rows = int(math.sqrt(len(images)))
 cols = len(images)//rows
FIGSIZE = 13.0
SPACING = 0.1
subplot=(rows,cols,1)
 if rows < cols:
plt.figure(figsize=(FIGSIZE,FIGSIZE/cols*rows))
else:
plt.figure(figsize=(FIGSIZE/rows*cols,FIGSIZE))
for i,(image, label)in enumerate(zip(images[:rows*cols], labels[:rows*cols])) :
title = '' if label is None else CLASSES[label]
correct = True
if predictions is not None:
title, correct = title_from_label_and_target(predictions[i], label)
 dynamic_titlesize = FIGSIZE*SPACING/max(rows,cols)*40+3
subplot = display_one_flower(image, title, subplot, not correct, titlesize=dynamic_titlesize)
 plt.tight_layout()
if label is None and predictions is None:
plt.subplots_adjust(wspace=0, hspace=0)
 else:
plt.subplots_adjust(wspace=SPACING, hspace=SPACING)
 plt.show()
def display_confusion_matrix(cmat, score, precision, recall):
plt.figure(figsize=(15,15))
ax = plt.gca()
ax.matshow(cmat, cmap='Reds')
 ax.set_xticks(range(len(CLASSES)))
 ax.set_xticklabels(CLASSES, fontdict={'fontsize': 7})
 plt.setp(ax.get_xticklabels() , rotation=45, ha="left", rotation_mode="anchor")
 ax.set_yticks(range(len(CLASSES)))
 ax.set_yticklabels(CLASSES, fontdict={'fontsize': 7})
 plt.setp(ax.get_yticklabels() , rotation=45, ha="right", rotation_mode="anchor")
 titlestring = ""
if score is not None:
titlestring += 'f1 = {:.3f} '.format(score)
 if precision is not None:
titlestring += '
precision = {:.3f} '.format(precision)
 if recall is not None:
titlestring += '
recall = {:.3f} '.format(recall)
 if len(titlestring)> 0:
ax.text(101, 1, titlestring, fontdict={'fontsize': 18, 'horizontalalignment':'right', 'verticalalignment':'top', 'color':'
plt.show()
def display_training_curves(training, validation, title, subplot):
if subplot%10==1:
plt.subplots(figsize=(10,10), facecolor='
plt.tight_layout()
ax = plt.subplot(subplot)
 ax.set_facecolor('
ax.plot(training)
 ax.plot(validation)
 ax.set_title('model '+ title)
 ax.set_ylabel(title)
 ax.set_xlabel('epoch')
 ax.legend(['train', 'valid.'] )
from sklearn.model_selection import train_test_split<import_modules>
def random_blockout(img, sl=0.1, sh=0.2, rl=0.4):
p=random.random()
if p>=0.25:
w, h, c = IMAGE_SIZE[0], IMAGE_SIZE[1], 3
origin_area = tf.cast(h*w, tf.float32)
 e_size_l = tf.cast(tf.round(tf.sqrt(origin_area * sl * rl)) , tf.int32)
 e_size_h = tf.cast(tf.round(tf.sqrt(origin_area * sh / rl)) , tf.int32)
 e_height_h = tf.minimum(e_size_h, h)
 e_width_h = tf.minimum(e_size_h, w)
 erase_height = tf.random.uniform(shape=[], minval=e_size_l, maxval=e_height_h, dtype=tf.int32)
 erase_width = tf.random.uniform(shape=[], minval=e_size_l, maxval=e_width_h, dtype=tf.int32)
 erase_area = tf.zeros(shape=[erase_height, erase_width, c])
 erase_area = tf.cast(erase_area, tf.uint8)
 pad_h = h - erase_height
pad_top = tf.random.uniform(shape=[], minval=0, maxval=pad_h, dtype=tf.int32)
 pad_bottom = pad_h - pad_top
pad_w = w - erase_width
pad_left = tf.random.uniform(shape=[], minval=0, maxval=pad_w, dtype=tf.int32)
 pad_right = pad_w - pad_left
erase_mask = tf.pad([erase_area], [[0,0],[pad_top, pad_bottom], [pad_left, pad_right], [0,0]], constant_values=1)
 erase_mask = tf.squeeze(erase_mask, axis=0)
 erased_img = tf.multiply(tf.cast(img,tf.float32), tf.cast(erase_mask, tf.float32))
return tf.cast(erased_img, img.dtype)
 else:
return tf.cast(img, img.dtype )
from sklearn.model_selection import train_test_split<drop_column>
def decode_image(image_data):
image = tf.image.decode_jpeg(image_data, channels=3)
 image = tf.cast(image, tf.float32)/ 255.0
image = tf.reshape(image, [*IMAGE_SIZE, 3])
 return image
def read_labeled_tfrecord(example):
LABELED_TFREC_FORMAT = {
"image": tf.io.FixedLenFeature([], tf.string),
"class": tf.io.FixedLenFeature([], tf.int64),
}
example = tf.io.parse_single_example(example, LABELED_TFREC_FORMAT)
 image = decode_image(example['image'])
 label = tf.cast(example['class'], tf.int32)
 return image, label
def read_unlabeled_tfrecord(example):
UNLABELED_TFREC_FORMAT = {
"image": tf.io.FixedLenFeature([], tf.string),
"id": tf.io.FixedLenFeature([], tf.string),
}
example = tf.io.parse_single_example(example, UNLABELED_TFREC_FORMAT)
 image = decode_image(example['image'])
 idnum = example['id']
return image, idnum
def load_dataset(filenames, labeled=True, ordered=False):
ignore_order = tf.data.Options()
if not ordered:
ignore_order.experimental_deterministic = False
dataset = tf.data.TFRecordDataset(filenames, num_parallel_reads=AUTO)
 dataset = dataset.with_options(ignore_order)
 dataset = dataset.map(read_labeled_tfrecord if labeled else read_unlabeled_tfrecord, num_parallel_calls=AUTO)
 return dataset
def data_augment(image, label):
image = tf.image.random_flip_left_right(image, seed=SEED)
 image = random_blockout(image)
 return image, label
def get_training_dataset() :
dataset = load_dataset(TRAINING_FILENAMES, labeled=True)
 dataset = dataset.map(data_augment, num_parallel_calls=AUTO)
 dataset = dataset.repeat()
dataset = dataset.shuffle(2048)
 dataset = dataset.batch(BATCH_SIZE)
 dataset = dataset.prefetch(AUTO)
 return dataset
def get_validation_dataset(ordered=False):
dataset = load_dataset(VALIDATION_FILENAMES, labeled=True, ordered=ordered)
 dataset = dataset.batch(BATCH_SIZE)
 dataset = dataset.cache()
dataset = dataset.prefetch(AUTO)
 return dataset
def get_test_dataset(ordered=False):
dataset = load_dataset(TEST_FILENAMES, labeled=False, ordered=ordered)
 dataset = dataset.batch(BATCH_SIZE)
 dataset = dataset.prefetch(AUTO)
 return dataset
def count_data_items(filenames):
n = [int(re.compile(r"-([0-9]*)\." ).search(filename ).group(1)) for filename in filenames]
return np.sum(n)
 NUM_TRAINING_IMAGES = count_data_items(TRAINING_FILENAMES)
 NUM_VALIDATION_IMAGES = count_data_items(VALIDATION_FILENAMES)
 NUM_TEST_IMAGES = count_data_items(TEST_FILENAMES)
 STEPS_PER_EPOCH = NUM_TRAINING_IMAGES // BATCH_SIZE
print('Dataset: {} training images, {} validation images, {} unlabeled test images'.format(NUM_TRAINING_IMAGES, NUM_VALIDATION_IMAGES, NUM_TEST_IMAGES))
features.remove('Id')
 features.remove('SalePrice' )<prepare_x_and_y>
if SKIP_VALIDATION:
TRAINING_FILENAMES = TRAINING_FILENAMES + VALIDATION_FILENAMES
train=train_data[features].values
train_y=train_data['SalePrice']<normalization>
print("Training data shapes:")
 for image, label in get_training_dataset().take(3):
print(image.numpy().shape, label.numpy().shape)
 print("Training data label examples:", label.numpy())
 print("Validation data shapes:")
 for image, label in get_validation_dataset().take(3):
print(image.numpy().shape, label.numpy().shape)
 print("Validation data label examples:", label.numpy())
 print("Test data shapes:")
 for image, idnum in get_test_dataset().take(3):
print(image.numpy().shape, idnum.numpy().shape)
 print("Test data IDs:", idnum.numpy().astype('U'))
sc= RobustScaler()
sc.fit(train)
 train=sc.transform(train )<import_modules>
training_dataset = get_training_dataset()
training_dataset = training_dataset.unbatch().batch(20)
 train_batch = iter(training_dataset )
from sklearn.model_selection import train_test_split<import_modules>
display_batch_of_images(next(train_batch))
from sklearn.model_selection import train_test_split<split>
test_dataset = get_test_dataset()
test_dataset = test_dataset.unbatch().batch(20)
 test_batch = iter(test_dataset )
x_train,x_test,y_train,y_test=train_test_split(train,train_y,test_size=0.2 )<train_model>
display_batch_of_images(next(test_batch))
rf = RandomForestRegressor(n_estimators = 120, random_state = 42 )<train_model>
LR_START = 0.00001
LR_MAX = 0.00005 * strategy.num_replicas_in_sync
LR_MIN = 0.00001
LR_RAMPUP_EPOCHS = 5
LR_SUSTAIN_EPOCHS = 0
LR_EXP_DECAY =.8
def lrfn(epoch):
if epoch < LR_RAMPUP_EPOCHS:
lr =(LR_MAX - LR_START)/ LR_RAMPUP_EPOCHS * epoch + LR_START
elif epoch < LR_RAMPUP_EPOCHS + LR_SUSTAIN_EPOCHS:
lr = LR_MAX
else:
lr =(LR_MAX - LR_MIN)* LR_EXP_DECAY**(epoch - LR_RAMPUP_EPOCHS - LR_SUSTAIN_EPOCHS)+ LR_MIN
return lr
lr_callback = tf.keras.callbacks.LearningRateScheduler(lrfn, verbose = True)
 rng = [i for i in range(25 if EPOCHS<25 else EPOCHS)]
y = [lrfn(x)for x in rng]
plt.plot(rng, y)
 print("Learning rate schedule: {:.3g} to {:.3g} to {:.3g}".format(y[0], max(y), y[-1]))
rf.fit(x_train, y_train )<predict_on_test>
!pip install -q efficientnet
predictions=rf.predict(x_test)
 rmsle(y_test.to_list() ,predictions )<import_modules>
with strategy.scope() :
enet = efn.EfficientNetB7(input_shape=[*IMAGE_SIZE, 3], weights='noisy-student', include_top=False)
 enet.trainable = True
model1 = tf.keras.Sequential([
enet,
tf.keras.layers.GlobalAveragePooling2D() ,
tf.keras.layers.Dense(len(CLASSES), activation='softmax')
 ])
 model1.compile(
 optimizer=tf.keras.optimizers.Adam() ,
loss = 'sparse_categorical_crossentropy',
metrics=['sparse_categorical_accuracy'] 
)
 model1.summary()
from sklearn.metrics import mean_squared_error<import_modules>
if not SKIP_VALIDATION:
history1 = model1.fit(get_training_dataset() ,
steps_per_epoch=STEPS_PER_EPOCH,
epochs=EPOCHS,
validation_data=get_validation_dataset() ,
callbacks = [lr_callback])
 else:
history1 = model1.fit(get_training_dataset() ,
steps_per_epoch=STEPS_PER_EPOCH,
epochs=EPOCHS,
callbacks = [lr_callback] )
from sklearn.metrics import mean_squared_error<import_modules>
with strategy.scope() :
densenet = tf.keras.applications.DenseNet201(input_shape=[*IMAGE_SIZE, 3], weights='imagenet', include_top=False)
 densenet.trainable = True
model2 = tf.keras.Sequential([
densenet,
tf.keras.layers.GlobalAveragePooling2D() ,
tf.keras.layers.Dense(len(CLASSES), activation='softmax')
 ])
 model2.compile(
 optimizer=tf.keras.optimizers.Adam() ,
loss = 'sparse_categorical_crossentropy',
metrics=['sparse_categorical_accuracy'] 
)
 model2.summary()
import xgboost as xgb<choose_model_class>
if not SKIP_VALIDATION:
history2 = model2.fit(get_training_dataset() ,
steps_per_epoch=STEPS_PER_EPOCH,
epochs=EPOCHS,
validation_data=get_validation_dataset() ,
callbacks = [lr_callback])
 else:
history2 = model2.fit(get_training_dataset() ,
steps_per_epoch=STEPS_PER_EPOCH,
epochs=EPOCHS,
callbacks = [lr_callback] )
model=xgb.XGBRegressor(base_score=0.5, booster='gbtree', colsample_bylevel=1,
colsample_bynode=1, colsample_bytree=0.4603, gamma=0.0468,
importance_type='split', learning_rate=0.05, max_delta_step=0,
max_depth=20, min_child_weight=1.7817, missing=None,
n_estimators=1024, n_jobs=1, nthread=-1, objective='reg:squarederror',
random_state=7, reg_alpha=0.464, reg_lambda=0.8571,
scale_pos_weight=1, seed=None, silent=1, subsample=0.5213,
verbosity=1 )<train_model>
if not SKIP_VALIDATION:
cmdataset = get_validation_dataset(ordered=True)
 images_ds = cmdataset.map(lambda image, label: image)
 labels_ds = cmdataset.map(lambda image, label: label ).unbatch()
cm_correct_labels = next(iter(labels_ds.batch(NUM_VALIDATION_IMAGES)) ).numpy()
m1 = model1.predict(images_ds)
 m2 = model2.predict(images_ds)
 scores = []
for alpha in np.linspace(0,1,100):
cm_probabilities = alpha*m1+(1-alpha)*m2
cm_predictions = np.argmax(cm_probabilities, axis=-1)
 scores.append(f1_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)) , average='macro'))
best_alpha = np.argmax(scores)/100
else:
best_alpha = 0.51
print('Best alpha: ' + str(best_alpha))
model.fit(x_train,y_train )<predict_on_test>
if not SKIP_VALIDATION:
cm_probabilities = best_alpha*m1 +(1-best_alpha)*m2
cm_predictions = np.argmax(cm_probabilities, axis=-1)
 cmat = confusion_matrix(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)))
 score = f1_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)) , average='macro')
 precision = precision_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)) , average='macro')
 recall = recall_score(cm_correct_labels, cm_predictions, labels=range(len(CLASSES)) , average='macro')
 display_confusion_matrix(cmat, score, precision, recall)
 print('f1 score: {:.3f}, precision: {:.3f}, recall: {:.3f}'.format(score, precision, recall))
predictions=model.predict(x_test)
 rmsle(y_test.to_list() ,predictions )<choose_model_class>
def predict_tta(model, n_iter):
probs = []
for i in range(n_iter):
test_ds = get_test_dataset(ordered=True)
 test_images_ds = test_ds.map(lambda image, idnum: image)
 probs.append(model.predict(test_images_ds,verbose=0))
return probs
<compute_train_metric><EOS> 
test_ds = get_test_dataset(ordered=True)
 print('Calculating predictions...')
 test_images_ds = test_ds.map(lambda image, idnum: image)
 probs1 = np.mean(predict_tta(model1, TTA_NUM), axis=0)
 probs2 = np.mean(predict_tta(model2, TTA_NUM), axis=0)
 probabilities = best_alpha*probs1 +(1-best_alpha)*probs2
predictions = np.argmax(probabilities, axis=-1)
 print('Generating submission file...')
 test_ids_ds = test_ds.map(lambda image, idnum: idnum ).unbatch()
test_ids = next(iter(test_ids_ds.batch(NUM_TEST_IMAGES)) ).numpy().astype('U')
 np.savetxt('submission.csv', np.rec.fromarrays([test_ids, predictions]), fmt=['%s', '%d'], delimiter=',', header='id,label', comments='' )