Kaggle competition: Plant Pathology 2020 - FGVC7
<SOS> metric: MCAUC Kaggle data source: plant-pathology-2020-fgvc7<define_variables>
!pip install -q efficientnet
VERBOSE = 2
DISPLAY_PLOT = False
skf = KFold(n_splits=FOLDS,shuffle=True,random_state=SEED)
 oof_pred = []; oof_tar = []; oof_val = []; oof_names = []; oof_folds = []
preds = np.zeros(( count_data_items(files_test),1))
for fold,(idxT,idxV)in enumerate(skf.split(np.arange(15))):
if DEVICE=='TPU':
if tpu: tf.tpu.experimental.initialize_tpu_system(tpu)
 print('
print(' 
(IMG_SIZES[fold],BATCH_SIZES[fold]*REPLICAS))
files_train = tf.io.gfile.glob([GCS_PATH[fold] + '/train%.2i*.tfrec'%x for x in idxT])
 if INC2019[fold]:
files_train += tf.io.gfile.glob([GCS_PATH2[fold] + '/train%.2i*.tfrec'%x for x in idxT*2+1])
 print('
if INC2018[fold]:
files_train += tf.io.gfile.glob([GCS_PATH2[fold] + '/train%.2i*.tfrec'%x for x in idxT*2])
 print('
np.random.shuffle(files_train); print('
files_valid = tf.io.gfile.glob([GCS_PATH[fold] + '/train%.2i*.tfrec'%x for x in idxV])
 files_test = np.sort(np.array(tf.io.gfile.glob(GCS_PATH[fold] + '/test*.tfrec')))
 K.clear_session()
with strategy.scope() :
model = build_model(dim=IMG_SIZES[fold],ef=EFF_NETS[fold])
 sv = tf.keras.callbacks.ModelCheckpoint(
 'fold-%i.h5'%fold, monitor='val_loss', verbose=0, save_best_only=True,
save_weights_only=True, mode='min', save_freq='epoch')
 print('Training...')
 history = model.fit(
 get_dataset(files_train, augment=True, shuffle=True, repeat=True,
dim=IMG_SIZES[fold], batch_size = BATCH_SIZES[fold]),
epochs=EPOCHS[fold], callbacks = [sv,get_lr_callback(BATCH_SIZES[fold])],
steps_per_epoch=count_data_items(files_train)/BATCH_SIZES[fold]//REPLICAS,
validation_data=get_dataset(files_valid,augment=False,shuffle=False,
repeat=False,dim=IMG_SIZES[fold]),
verbose=VERBOSE 
)
 print('Loading best model...')
 model.load_weights('fold-%i.h5'%fold)
 print('Predicting OOF with TTA...')
 ds_valid = get_dataset(files_valid,labeled=False,return_image_names=False,augment=True,
repeat=True,shuffle=False,dim=IMG_SIZES[fold],batch_size=BATCH_SIZES[fold]*4)
 ct_valid = count_data_items(files_valid); STEPS = TTA * ct_valid/BATCH_SIZES[fold]/4/REPLICAS
pred = model.predict(ds_valid,steps=STEPS,verbose=VERBOSE)[:TTA*ct_valid,]
oof_pred.append(np.mean(pred.reshape(( ct_valid,TTA),order='F'),axis=1))
ds_valid = get_dataset(files_valid, augment=False, repeat=False, dim=IMG_SIZES[fold],
labeled=True, return_image_names=True)
 oof_tar.append(np.array([target.numpy() for img, target in iter(ds_valid.unbatch())]))
oof_folds.append(np.ones_like(oof_tar[-1],dtype='int8')*fold)
 ds = get_dataset(files_valid, augment=False, repeat=False, dim=IMG_SIZES[fold],
labeled=False, return_image_names=True)
 oof_names.append(np.array([img_name.numpy().decode("utf-8")for img, img_name in iter(ds.unbatch())]))
print('Predicting Test with TTA...')
 ds_test = get_dataset(files_test,labeled=False,return_image_names=False,augment=True,
repeat=True,shuffle=False,dim=IMG_SIZES[fold],batch_size=BATCH_SIZES[fold]*4)
 ct_test = count_data_items(files_test); STEPS = TTA * ct_test/BATCH_SIZES[fold]/4/REPLICAS
pred = model.predict(ds_test,steps=STEPS,verbose=VERBOSE)[:TTA*ct_test,]
preds[:,0] += np.mean(pred.reshape(( ct_test,TTA),order='F'),axis=1)* WGTS[fold]
auc = roc_auc_score(oof_tar[-1],oof_pred[-1])
 oof_val.append(np.max(history.history['val_auc']))
print('
if DISPLAY_PLOT:
plt.figure(figsize=(15,5))
plt.plot(np.arange(EPOCHS[fold]),history.history['auc'],'-o',label='Train AUC',color='
plt.plot(np.arange(EPOCHS[fold]),history.history['val_auc'],'-o',label='Val AUC',color='
x = np.argmax(history.history['val_auc']); y = np.max(history.history['val_auc'])
 xdist = plt.xlim() [1] - plt.xlim() [0]; ydist = plt.ylim() [1] - plt.ylim() [0]
plt.scatter(x,y,s=200,color='
%.2f'%y,size=14)
 plt.ylabel('AUC',size=14); plt.xlabel('Epoch',size=14)
 plt.legend(loc=2)
 plt2 = plt.gca().twinx()
plt2.plot(np.arange(EPOCHS[fold]),history.history['loss'],'-o',label='Train Loss',color='
plt2.plot(np.arange(EPOCHS[fold]),history.history['val_loss'],'-o',label='Val Loss',color='
x = np.argmin(history.history['val_loss']); y = np.min(history.history['val_loss'])
 ydist = plt.ylim() [1] - plt.ylim() [0]
plt.scatter(x,y,s=200,color='
plt.ylabel('Loss',size=14)
 plt.title('FOLD %i - Image Size %i, InceptionResNetV2, inc2019=%i, inc2018=%i'% 
(fold+1,IMG_SIZES[fold],INC2019[fold],INC2018[fold]),size=18)
 plt.legend(loc=3)
 plt.show()<save_to_csv>
import numpy as np
import pandas as pd
import os
import tensorflow as tf
import keras
import efficientnet.tfkeras as efn
from kaggle_datasets import KaggleDatasets
from tensorflow.keras.models import Sequential
import tensorflow.keras.layers as L
from tensorflow.keras.applications import InceptionResNetV2
from tensorflow.keras.layers import Dense, GlobalAveragePooling2D
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from sklearn.model_selection import train_test_split
import matplotlib.pyplot as plt
oof = np.concatenate(oof_pred); true = np.concatenate(oof_tar);
names = np.concatenate(oof_names); folds = np.concatenate(oof_folds)
 auc = roc_auc_score(true,oof)
 print('Overall OOF AUC with TTA = %.3f'%auc)
 df_oof = pd.DataFrame(dict(
 image_name = names, target=true, pred = oof, fold=folds))
df_oof.to_csv('oof.csv',index=False)
 df_oof.head()<create_dataframe>
AUTO = tf.data.experimental.AUTOTUNE
tpu = tf.distribute.cluster_resolver.TPUClusterResolver()
tf.config.experimental_connect_to_cluster(tpu)
 tf.tpu.experimental.initialize_tpu_system(tpu)
 strategy = tf.distribute.experimental.TPUStrategy(tpu)
 GCS_DS_PATH = KaggleDatasets().get_gcs_path()
EPOCHS = 40
BATCH_SIZE = 16 * strategy.num_replicas_in_sync
ds = get_dataset(files_test, augment=False, repeat=False, dim=IMG_SIZES[fold],
labeled=False, return_image_names=True)
 image_names = np.array([img_name.numpy().decode("utf-8")
 for img, img_name in iter(ds.unbatch())] )<save_to_csv>
def format_path(st):
return GCS_DS_PATH + '/images/' + st + '.jpg'
submission = pd.DataFrame(dict(image_name=image_names, target=preds[:,0]))
submission = submission.sort_values('image_name')
 submission.to_csv('submission.csv', index=False)
 submission.head()<load_from_csv>
train = pd.read_csv('/kaggle/input/plant-pathology-2020-fgvc7/train.csv')
 test = pd.read_csv('/kaggle/input/plant-pathology-2020-fgvc7/test.csv')
 sub = pd.read_csv('/kaggle/input/plant-pathology-2020-fgvc7/sample_submission.csv')
 train_paths = train.image_id.apply(format_path ).values
test_paths = test.image_id.apply(format_path ).values
train_labels = train.loc[:, 'healthy':].values
train = pd.read_csv('.. /input/siim-isic-melanoma-classification/train.csv')
 print('Examples WITH Melanoma')
 imgs = train.loc[train.target==1].sample(10 ).image_name.values
plt.figure(figsize=(20,8))
for i,k in enumerate(imgs):
img = cv2.imread('.. /input/jpeg-melanoma-128x128/train/%s.jpg'%k)
 img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
 plt.subplot(2,5,i+1); plt.axis('off')
 plt.imshow(img)
 plt.show()
print('Examples WITHOUT Melanoma')
 imgs = train.loc[train.target==0].sample(10 ).image_name.values
plt.figure(figsize=(20,8))
for i,k in enumerate(imgs):
img = cv2.imread('.. /input/jpeg-melanoma-128x128/train/%s.jpg'%k)
 img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
 plt.subplot(2,5,i+1); plt.axis('off')
 plt.imshow(img)
 plt.show()<install_modules>
image_size = 850
!pip install -q efficientnet >> /dev/null<import_modules>
def decode_image(filename, label=None, image_size=(image_size, image_size)) :
bits = tf.io.read_file(filename)
 image = tf.image.decode_jpeg(bits, channels=3)
 image = tf.cast(image, tf.float32)/ 255.0
image = tf.image.resize(image, image_size)
 if label is None:
return image
else:
return image, label
def data_augment(image, label=None):
image = tf.image.random_flip_left_right(image)
 image = tf.image.random_flip_up_down(image)
 if label is None:
return image
else:
return image, label
import pandas as pd, numpy as np
from kaggle_datasets import KaggleDatasets
import tensorflow as tf, re, math
import tensorflow.keras.backend as K
import efficientnet.tfkeras as efn
from sklearn.model_selection import KFold
from sklearn.metrics import roc_auc_score
import matplotlib.pyplot as plt<define_search_space>
train_dataset =(
 tf.data.Dataset 
.from_tensor_slices(( train_paths, train_labels)) 
.map(decode_image, num_parallel_calls=AUTO)
.cache() 
.map(data_augment, num_parallel_calls=AUTO)
.repeat() 
.shuffle(512)
.batch(BATCH_SIZE)
.prefetch(AUTO)
)
 train_dataset_1 =(
 tf.data.Dataset 
.from_tensor_slices(( train_paths, train_labels)) 
.map(decode_image, num_parallel_calls=AUTO)
.cache() 
.map(data_augment, num_parallel_calls=AUTO)
.repeat() 
.shuffle(512)
.batch(64)
.prefetch(AUTO)
)
 test_dataset =(
 tf.data.Dataset 
.from_tensor_slices(test_paths)
.map(decode_image, num_parallel_calls=AUTO)
.batch(BATCH_SIZE)
 )
DEVICE = "TPU"
SEED = 42
FOLDS = 5
IMG_SIZES = [512]*FOLDS
INC2019 = [1]*FOLDS
INC2018 = [1,1,1,1,1]
M1 = [1]*5
M2 = [1]*5
M3 = [1]*5
M4 = [1]*5
MS = [1]*5
BATCH_SIZES = [32]*FOLDS
EPOCHS = [5,5,5,5,5]
EFF_NETS = [6,6,6,6,6]
WGTS = [1/FOLDS]*FOLDS
TTA = 11<choose_model_class>
LR_START = 0.0001
LR_MAX = 0.00005 * strategy.num_replicas_in_sync
LR_MIN = 0.0001
LR_RAMPUP_EPOCHS = 4
LR_SUSTAIN_EPOCHS = 6
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(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]))
if DEVICE == "TPU":
print("connecting to TPU...")
 try:
tpu = tf.distribute.cluster_resolver.TPUClusterResolver()
print('Running on TPU ', tpu.master())
 except ValueError:
print("Could not connect to TPU")
 tpu = None
if tpu:
try:
print("initializing TPU...")
 tf.config.experimental_connect_to_cluster(tpu)
 tf.tpu.experimental.initialize_tpu_system(tpu)
 strategy = tf.distribute.experimental.TPUStrategy(tpu)
 print("TPU initialized")
 except _:
print("failed to initialize TPU")
 else:
DEVICE = "GPU"
if DEVICE != "TPU":
print("Using default strategy for CPU and single GPU")
 strategy = tf.distribute.get_strategy()
if DEVICE == "GPU":
print("Num GPUs Available: ", len(tf.config.experimental.list_physical_devices('GPU')))
 AUTO = tf.data.experimental.AUTOTUNE
REPLICAS = strategy.num_replicas_in_sync
print(f'REPLICAS: {REPLICAS}' )<define_variables>
class SoftProbField(Layer):
def __init__(self, **kwargs):
super(SoftProbField, self ).__init__(**kwargs)
 def build(self, input_shape):
super(SoftProbField, self ).build(input_shape)
 def call(self, x):
h = x[:, 0]
s = x[:, 1]
r = x[:, 2]
m = s*r*(1-h)
 s = s*(1-h)*(1-m)
 r = r*(1-h)*(1-m)
 return tf.stack([h, m, r, s], axis=-1)
 def compute_output_shape(self, input_shape):
return(input_shape[0], 4 )
GCS_PATH = [None]*FOLDS; GCS_PATH2 = [None]*FOLDS; GCS_PATH3 = [None]*FOLDS; GCS_PATH4 = [None]*FOLDS
for i,k in enumerate(IMG_SIZES[:FOLDS]):
GCS_PATH[i] = KaggleDatasets().get_gcs_path('melanoma-%ix%i'%(k,k))
GCS_PATH2[i] = KaggleDatasets().get_gcs_path('isic2019-%ix%i'%(k,k))
GCS_PATH3[i] = KaggleDatasets().get_gcs_path('malignant-v2-%ix%i'%(k,k))
for i,k in enumerate(IMG_SIZES[:FOLDS]):
GCS_PATH4[i] = KaggleDatasets().get_gcs_path('unknowndatas')
 files_train = np.sort(np.array(tf.io.gfile.glob(GCS_PATH[0] + '/train*.tfrec')))
 files_test = np.sort(np.array(tf.io.gfile.glob(GCS_PATH[0] + '/test*.tfrec')) )<define_variables>
with strategy.scope() :
model = tf.keras.Sequential([
InceptionResNetV2(
 input_shape=(image_size, image_size, 3),
weights='imagenet',
include_top=False 
),
L.GlobalAveragePooling2D() ,
L.Dense(3, activation='sigmoid'),
SoftProbField()
])
 model.compile(
 optimizer = 'adam',
loss = 'categorical_crossentropy',
metrics=['categorical_accuracy'] 
)
 model.summary()
ROT_ = 180.0
SHR_ = 2.0
HZOOM_ = 8.0
WZOOM_ = 8.0
HSHIFT_ = 8.0
WSHIFT_ = 8.0<normalization>
STEPS_PER_EPOCH = train_labels.shape[0] // BATCH_SIZE
history = model.fit(
 train_dataset,
epochs=EPOCHS,
callbacks=[lr_callback],
steps_per_epoch=STEPS_PER_EPOCH,
)
def get_mat(rotation, shear, height_zoom, width_zoom, height_shift, width_shift):
rotation = math.pi * rotation / 180.
 shear = math.pi * shear / 180.
 def get_3x3_mat(lst):
return tf.reshape(tf.concat([lst],axis=0), [3,3])
 c1 = tf.math.cos(rotation)
 s1 = tf.math.sin(rotation)
 one = tf.constant([1],dtype='float32')
 zero = tf.constant([0],dtype='float32')
 rotation_matrix = get_3x3_mat([c1, s1, zero,
-s1, c1, zero,
zero, zero, one])
 c2 = tf.math.cos(shear)
 s2 = tf.math.sin(shear)
 shear_matrix = get_3x3_mat([one, s2, zero,
zero, c2, zero,
zero, zero, one])
 zoom_matrix = get_3x3_mat([one/height_zoom, zero, zero,
zero, one/width_zoom, zero,
zero, zero, one])
 shift_matrix = get_3x3_mat([one, zero, height_shift,
zero, one, width_shift,
zero, zero, one])
 return K.dot(K.dot(rotation_matrix, shear_matrix),
K.dot(zoom_matrix, shift_matrix))
def transform(image, DIM=256):
XDIM = DIM%2
rot = ROT_ * tf.random.normal([1], dtype='float32')
 shr = SHR_ * tf.random.normal([1], dtype='float32')
 h_zoom = 1.0 + tf.random.normal([1], dtype='float32')/ HZOOM_
w_zoom = 1.0 + tf.random.normal([1], dtype='float32')/ WZOOM_
h_shift = HSHIFT_ * tf.random.normal([1], dtype='float32')
 w_shift = WSHIFT_ * tf.random.normal([1], dtype='float32')
 m = get_mat(rot,shr,h_zoom,w_zoom,h_shift,w_shift)
 x = tf.repeat(tf.range(DIM//2, -DIM//2,-1), DIM)
 y = tf.tile(tf.range(-DIM//2, DIM//2), [DIM])
 z = tf.ones([DIM*DIM], dtype='int32')
 idx = tf.stack([x,y,z])
 idx2 = K.dot(m, tf.cast(idx, dtype='float32'))
idx2 = K.cast(idx2, dtype='int32')
 idx2 = K.clip(idx2, -DIM//2+XDIM+1, DIM//2)
 idx3 = tf.stack([DIM//2-idx2[0,], DIM//2-1+idx2[1,]])
 d = tf.gather_nd(image, tf.transpose(idx3))
return tf.reshape(d,[DIM, DIM,3] )<prepare_x_and_y>
with strategy.scope() :
model2 = tf.keras.Sequential([
efn.EfficientNetB7(
 input_shape=(image_size, image_size, 3),
weights='noisy-student',
include_top=False 
),
L.GlobalAveragePooling2D() ,
L.Dense(3, activation='sigmoid'),
SoftProbField()
])
 model2.compile(
 optimizer = 'adam',
loss = 'categorical_crossentropy',
metrics=['categorical_accuracy'] 
)
 model2.summary()
def read_labeled_tfrecord(example):
tfrec_format = {
'image' : tf.io.FixedLenFeature([], tf.string),
'image_name' : tf.io.FixedLenFeature([], tf.string),
'patient_id' : tf.io.FixedLenFeature([], tf.int64),
'sex' : tf.io.FixedLenFeature([], tf.int64),
'age_approx' : tf.io.FixedLenFeature([], tf.int64),
'anatom_site_general_challenge': tf.io.FixedLenFeature([], tf.int64),
'target' : tf.io.FixedLenFeature([], tf.int64)
 }
example = tf.io.parse_single_example(example, tfrec_format)
 return example['image'], example['target']
def read_unlabeled_tfrecord(example, return_image_name):
tfrec_format = {
'image' : tf.io.FixedLenFeature([], tf.string),
'image_name' : tf.io.FixedLenFeature([], tf.string),
}
example = tf.io.parse_single_example(example, tfrec_format)
 return example['image'], example['image_name'] if return_image_name else 0
def prepare_image(img, augment=True, dim=256):
img = tf.image.decode_jpeg(img, channels=3)
 img = tf.cast(img, tf.float32)/ 255.0
if augment:
img = transform(img,DIM=dim)
 img = tf.image.random_flip_left_right(img)
 img = tf.image.random_saturation(img, 0.7, 1.3)
 img = tf.image.random_contrast(img, 0.8, 1.2)
 img = tf.image.random_brightness(img, 0.1)
 img = tf.reshape(img, [dim,dim, 3])
 return img
def count_data_items(filenames):
n = [int(re.compile(r"-([0-9]*)\." ).search(filename ).group(1))
for filename in filenames]
return np.sum(n )<create_dataframe>
STEPS_PER_EPOCH = train_labels.shape[0] // 64
history = model2.fit(
 train_dataset_1,
epochs=EPOCHS,
callbacks=[lr_callback],
steps_per_epoch=STEPS_PER_EPOCH,
)
<train_model><EOS> 
probs1 = model.predict(test_dataset, verbose=1)
 probs2 = model2.predict(test_dataset, verbose=1)
 probs_avg =(probs1+probs2)/2
sub.loc[:, 'healthy':] = probs_avg
sub.to_csv('submission.csv', index=False)
 sub.head()