Kaggle competition: Cassava Leaf Disease Classification
<SOS> metric: CategorizationAccuracy Kaggle data source: cassava-leaf-disease-classification<count_values>
!pip install --quiet /kaggle/input/kerasapplications
!pip install --quiet /kaggle/input/efficientnet-git
train['status'].value_counts()<filter>
def seed_everything(seed=0):
random.seed(seed)
 np.random.seed(seed)
 tf.random.set_seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 os.environ['TF_DETERMINISTIC_OPS'] = '1'
seed = 0
seed_everything(seed)
 warnings.filterwarnings('ignore')
train.loc[train['status'] == "Rumored"][['status','revenue']]<count_values>
BATCH_SIZE = 32 * REPLICAS
HEIGHT = 512
WIDTH = 512
CHANNELS = 3
N_CLASSES = 5
TTA_STEPS = 8
test['status'].value_counts()<load_from_csv>
def data_augment(image, label):
p_spatial = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 p_rotate = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 p_pixel_1 = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 p_pixel_2 = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 p_pixel_3 = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 p_crop = tf.random.uniform([], 0, 1.0, dtype=tf.float32)
 image = tf.image.random_flip_left_right(image)
 image = tf.image.random_flip_up_down(image)
 if p_spatial >.75:
image = tf.image.transpose(image)
 if p_rotate >.75:
image = tf.image.rot90(image, k=3)
 elif p_rotate >.5:
image = tf.image.rot90(image, k=2)
 elif p_rotate >.25:
image = tf.image.rot90(image, k=1)
 if p_pixel_1 >=.4:
image = tf.image.random_saturation(image, lower=.7, upper=1.3)
 if p_pixel_2 >=.4:
image = tf.image.random_contrast(image, lower=.8, upper=1.2)
 if p_pixel_3 >=.4:
image = tf.image.random_brightness(image, max_delta=.1)
 if p_crop >.7:
if p_crop >.9:
image = tf.image.central_crop(image, central_fraction=.7)
 elif p_crop >.8:
image = tf.image.central_crop(image, central_fraction=.8)
 else:
image = tf.image.central_crop(image, central_fraction=.9)
 elif p_crop >.4:
crop_size = tf.random.uniform([], int(HEIGHT*.8), HEIGHT, dtype=tf.int32)
 image = tf.image.random_crop(image, size=[crop_size, crop_size, CHANNELS])
 return image, label
trainAdditionalFeatures = pd.read_csv('.. /input/tmdb-competition-additional-features/TrainAdditionalFeatures.csv')
 testAdditionalFeatures = pd.read_csv('.. /input/tmdb-competition-additional-features/TestAdditionalFeatures.csv')
 train = pd.merge(train, trainAdditionalFeatures, how='left', on=['imdb_id'])
 test = pd.merge(test, testAdditionalFeatures, how='left', on=['imdb_id'] )<count_missing_values>
def get_name(file_path):
parts = tf.strings.split(file_path, os.path.sep)
 name = parts[-1]
return name
def decode_image(image_data):
image = tf.image.decode_jpeg(image_data, channels=3)
 image = tf.cast(image, tf.float32)/ 255.0
return image
def center_crop(image):
image = tf.reshape(image, [600, 800, CHANNELS])
 h, w = image.shape[0], image.shape[1]
if h > w:
image = tf.image.crop_to_bounding_box(image,(h - w)// 2, 0, w, w)
 else:
image = tf.image.crop_to_bounding_box(image, 0,(w - h)// 2, h, h)
 image = tf.image.resize(image, [HEIGHT, WIDTH])
 return image
def resize_image(image, label):
image = tf.image.resize(image, [HEIGHT, WIDTH])
 image = tf.reshape(image, [HEIGHT, WIDTH, CHANNELS])
 return image, label
def process_path(file_path):
name = get_name(file_path)
 img = tf.io.read_file(file_path)
 img = decode_image(img)
 return img, name
def get_dataset(files_path, shuffled=False, tta=False, extension='jpg'):
dataset = tf.data.Dataset.list_files(f'{files_path}*{extension}', shuffle=shuffled)
 dataset = dataset.map(process_path, num_parallel_calls=AUTO)
 if tta:
dataset = dataset.map(data_augment, num_parallel_calls=AUTO)
 dataset = dataset.map(resize_image, num_parallel_calls=AUTO)
 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 )
print("Missing rating in Train set", train['rating'].isna().sum())
 print("Missing total Votes in Train set", train['totalVotes'].isna().sum())
 print("")
 print("Missing rating in Test set", test['rating'].isna().sum())
 print("Missing total Votes in Test set", test['totalVotes'].isna().sum() )<data_type_conversions>
model_path_list = glob.glob('/kaggle/input/cassava-leaf-disease-training-with-tpu-v2-pods/*.h5')
 model_path_list.sort()
print('Models to predict:')
 print(*model_path_list, sep='
' )
train['rating'] = train['rating'].fillna(1.5)
 train['totalVotes'] = train['totalVotes'].fillna(6)
 test['rating'] = test['rating'].fillna(1.5)
 test['totalVotes'] = test['totalVotes'].fillna(6 )<feature_engineering>
def model_fn(input_shape, N_CLASSES):
inputs = L.Input(shape=input_shape, name='input_image')
 base_model = efn.EfficientNetB4(input_tensor=inputs,
include_top=False,
weights=None,
pooling='avg')
 x = L.Dropout (.5 )(base_model.output)
 output = L.Dense(N_CLASSES, activation='softmax', name='output' )(x)
 model = Model(inputs=inputs, outputs=output)
 return model
with strategy.scope() :
model = model_fn(( None, None, CHANNELS), N_CLASSES)
 model.summary()
def prepare(df):
global json_cols
global train_dict
df[['release_month','release_day','release_year']]=df['release_date'].str.split('/',expand=True ).replace(np.nan, 0 ).astype(int)
 df['release_year'] = df['release_year']
df.loc[(df['release_year'] <= 19)&(df['release_year'] < 100), "release_year"] += 2000
df.loc[(df['release_year'] > 19)&(df['release_year'] < 100), "release_year"] += 1900
releaseDate = pd.to_datetime(df['release_date'])
 df['release_dayofweek'] = releaseDate.dt.dayofweek
df['release_quarter'] = releaseDate.dt.quarter
rating_na = df.groupby(["release_year","original_language"])['rating'].mean().reset_index()
df[df.rating.isna() ]['rating'] = df.merge(rating_na, how = 'left' ,on = ["release_year","original_language"])
 vote_count_na = df.groupby(["release_year","original_language"])['totalVotes'].mean().reset_index()
df[df.totalVotes.isna() ]['totalVotes'] = df.merge(vote_count_na, how = 'left' ,on = ["release_year","original_language"])
 df['weightedRating'] =(df['rating']*df['totalVotes'] + 6.367 * 1000)/(df['totalVotes'] + 1000)
 df['originalBudget'] = df['budget']
df['inflationBudget'] = df['budget'] + df['budget']*1.8/100*(2018-df['release_year'])
 df['budget'] = np.log1p(df['budget'])
 df['genders_0_crew'] = df['crew'].apply(lambda x: sum([1 for i in x if i['gender'] == 0]))
df['genders_1_crew'] = df['crew'].apply(lambda x: sum([1 for i in x if i['gender'] == 1]))
df['genders_2_crew'] = df['crew'].apply(lambda x: sum([1 for i in x if i['gender'] == 2]))
df['_collection_name'] = df['belongs_to_collection'].apply(lambda x: x[0]['name'] if x != {} else 0)
 le = LabelEncoder()
le.fit(list(df['_collection_name'].fillna('')))
 df['_collection_name'] = le.transform(df['_collection_name'].fillna('' ).astype(str))
df['_num_Keywords'] = df['Keywords'].apply(lambda x: len(x)if x != {} else 0)
 df['_num_cast'] = df['cast'].apply(lambda x: len(x)if x != {} else 0)
 df['_popularity_mean_year'] = df['popularity'] / df.groupby("release_year")["popularity"].transform('mean')
 df['_budget_runtime_ratio'] = df['budget']/df['runtime']
df['_budget_popularity_ratio'] = df['budget']/df['popularity']
df['_budget_year_ratio'] = df['budget']/(df['release_year']*df['release_year'])
 df['_releaseYear_popularity_ratio'] = df['release_year']/df['popularity']
df['_releaseYear_popularity_ratio2'] = df['popularity']/df['release_year']
df['_popularity_totalVotes_ratio'] = df['totalVotes']/df['popularity']
df['_rating_popularity_ratio'] = df['rating']/df['popularity']
df['_rating_totalVotes_ratio'] = df['totalVotes']/df['rating']
df['_totalVotes_releaseYear_ratio'] = df['totalVotes']/df['release_year']
df['_budget_rating_ratio'] = df['budget']/df['rating']
df['_runtime_rating_ratio'] = df['runtime']/df['rating']
df['_budget_totalVotes_ratio'] = df['budget']/df['totalVotes']
df['has_homepage'] = 1
df.loc[pd.isnull(df['homepage']),"has_homepage"] = 0
df['isbelongs_to_collectionNA'] = 0
df.loc[pd.isnull(df['belongs_to_collection']),"isbelongs_to_collectionNA"] = 1
df['isTaglineNA'] = 0
df.loc[df['tagline'] == 0 ,"isTaglineNA"] = 1
df['isOriginalLanguageEng'] = 0
df.loc[ df['original_language'] == "en" ,"isOriginalLanguageEng"] = 1
df['isTitleDifferent'] = 1
df.loc[ df['original_title'] == df['title'] ,"isTitleDifferent"] = 0
df['isMovieReleased'] = 1
df.loc[ df['status'] != "Released" ,"isMovieReleased"] = 0
df['collection_id'] = df['belongs_to_collection'].apply(lambda x : np.nan if len(x)==0 else x[0]['id'])
 df['original_title_letter_count'] = df['original_title'].str.len()
df['original_title_word_count'] = df['original_title'].str.split().str.len()
df['title_word_count'] = df['title'].str.split().str.len()
df['overview_word_count'] = df['overview'].str.split().str.len()
df['tagline_word_count'] = df['tagline'].str.split().str.len()
df['production_countries_count'] = df['production_countries'].apply(lambda x : len(x))
df['production_companies_count'] = df['production_companies'].apply(lambda x : len(x))
df['cast_count'] = df['cast'].apply(lambda x : len(x))
df['crew_count'] = df['crew'].apply(lambda x : len(x))
df['meanruntimeByYear'] = df.groupby("release_year")["runtime"].aggregate('mean')
 df['meanPopularityByYear'] = df.groupby("release_year")["popularity"].aggregate('mean')
 df['meanBudgetByYear'] = df.groupby("release_year")["budget"].aggregate('mean')
 df['meantotalVotesByYear'] = df.groupby("release_year")["totalVotes"].aggregate('mean')
 df['meanTotalVotesByRating'] = df.groupby("rating")["totalVotes"].aggregate('mean')
 df['medianBudgetByYear'] = df.groupby("release_year")["budget"].aggregate('median')
 for col in ['genres', 'production_countries', 'spoken_languages', 'production_companies'] :
df[col] = df[col].map(lambda x: sorted(list(set([n if n in train_dict[col] else col+'_etc' for n in [d['name'] for d in x]])))).map(lambda x: ','.join(map(str, x)))
 temp = df[col].str.get_dummies(sep=',')
 df = pd.concat([df, temp], axis=1, sort=False)
 df.drop(['genres_etc'], axis = 1, inplace = True)
 df = df.drop(['id', 'revenue','belongs_to_collection','genres','homepage','imdb_id','overview','runtime'
,'poster_path','production_companies','production_countries','release_date','spoken_languages'
,'status','title','Keywords','cast','crew','original_language','original_title','tagline', 'collection_id'
],axis=1)
 df.fillna(value=0.0, inplace = True)
 return df
train = pd.read_csv('.. /input/tmdb-box-office-prediction/train.csv')
 train.loc[train['id'] == 16,'revenue'] = 192864
train.loc[train['id'] == 90,'budget'] = 30000000
train.loc[train['id'] == 118,'budget'] = 60000000
train.loc[train['id'] == 149,'budget'] = 18000000
train.loc[train['id'] == 313,'revenue'] = 12000000
train.loc[train['id'] == 451,'revenue'] = 12000000
train.loc[train['id'] == 464,'budget'] = 20000000
train.loc[train['id'] == 470,'budget'] = 13000000
train.loc[train['id'] == 513,'budget'] = 930000
train.loc[train['id'] == 797,'budget'] = 8000000
train.loc[train['id'] == 819,'budget'] = 90000000
train.loc[train['id'] == 850,'budget'] = 90000000
train.loc[train['id'] == 1007,'budget'] = 2
train.loc[train['id'] == 1112,'budget'] = 7500000
train.loc[train['id'] == 1131,'budget'] = 4300000
train.loc[train['id'] == 1359,'budget'] = 10000000
train.loc[train['id'] == 1542,'budget'] = 1
train.loc[train['id'] == 1570,'budget'] = 15800000
train.loc[train['id'] == 1571,'budget'] = 4000000
train.loc[train['id'] == 1714,'budget'] = 46000000
train.loc[train['id'] == 1721,'budget'] = 17500000
train.loc[train['id'] == 1865,'revenue'] = 25000000
train.loc[train['id'] == 1885,'budget'] = 12
train.loc[train['id'] == 2091,'budget'] = 10
train.loc[train['id'] == 2268,'budget'] = 17500000
train.loc[train['id'] == 2491,'budget'] = 6
train.loc[train['id'] == 2602,'budget'] = 31000000
train.loc[train['id'] == 2612,'budget'] = 15000000
train.loc[train['id'] == 2696,'budget'] = 10000000
train.loc[train['id'] == 2801,'budget'] = 10000000
train.loc[train['id'] == 335,'budget'] = 2
train.loc[train['id'] == 348,'budget'] = 12
train.loc[train['id'] == 470,'budget'] = 13000000
train.loc[train['id'] == 513,'budget'] = 1100000
train.loc[train['id'] == 640,'budget'] = 6
train.loc[train['id'] == 696,'budget'] = 1
train.loc[train['id'] == 797,'budget'] = 8000000
train.loc[train['id'] == 850,'budget'] = 1500000
train.loc[train['id'] == 1199,'budget'] = 5
train.loc[train['id'] == 1282,'budget'] = 9
train.loc[train['id'] == 1347,'budget'] = 1
train.loc[train['id'] == 1755,'budget'] = 2
train.loc[train['id'] == 1801,'budget'] = 5
train.loc[train['id'] == 1918,'budget'] = 592
train.loc[train['id'] == 2033,'budget'] = 4
train.loc[train['id'] == 2118,'budget'] = 344
train.loc[train['id'] == 2252,'budget'] = 130
train.loc[train['id'] == 2256,'budget'] = 1
train.loc[train['id'] == 2696,'budget'] = 10000000
test = pd.read_csv('.. /input/tmdb-box-office-prediction/test.csv')
 test.loc[test['id'] == 6733,'budget'] = 5000000
test.loc[test['id'] == 3889,'budget'] = 15000000
test.loc[test['id'] == 6683,'budget'] = 50000000
test.loc[test['id'] == 5704,'budget'] = 4300000
test.loc[test['id'] == 6109,'budget'] = 281756
test.loc[test['id'] == 7242,'budget'] = 10000000
test.loc[test['id'] == 7021,'budget'] = 17540562
test.loc[test['id'] == 5591,'budget'] = 4000000
test.loc[test['id'] == 4282,'budget'] = 20000000
test.loc[test['id'] == 3033,'budget'] = 250
test.loc[test['id'] == 3051,'budget'] = 50
test.loc[test['id'] == 3084,'budget'] = 337
test.loc[test['id'] == 3224,'budget'] = 4
test.loc[test['id'] == 3594,'budget'] = 25
test.loc[test['id'] == 3619,'budget'] = 500
test.loc[test['id'] == 3831,'budget'] = 3
test.loc[test['id'] == 3935,'budget'] = 500
test.loc[test['id'] == 4049,'budget'] = 995946
test.loc[test['id'] == 4424,'budget'] = 3
test.loc[test['id'] == 4460,'budget'] = 8
test.loc[test['id'] == 4555,'budget'] = 1200000
test.loc[test['id'] == 4624,'budget'] = 30
test.loc[test['id'] == 4645,'budget'] = 500
test.loc[test['id'] == 4709,'budget'] = 450
test.loc[test['id'] == 4839,'budget'] = 7
test.loc[test['id'] == 3125,'budget'] = 25
test.loc[test['id'] == 3142,'budget'] = 1
test.loc[test['id'] == 3201,'budget'] = 450
test.loc[test['id'] == 3222,'budget'] = 6
test.loc[test['id'] == 3545,'budget'] = 38
test.loc[test['id'] == 3670,'budget'] = 18
test.loc[test['id'] == 3792,'budget'] = 19
test.loc[test['id'] == 3881,'budget'] = 7
test.loc[test['id'] == 3969,'budget'] = 400
test.loc[test['id'] == 4196,'budget'] = 6
test.loc[test['id'] == 4221,'budget'] = 11
test.loc[test['id'] == 4222,'budget'] = 500
test.loc[test['id'] == 4285,'budget'] = 11
test.loc[test['id'] == 4319,'budget'] = 1
test.loc[test['id'] == 4639,'budget'] = 10
test.loc[test['id'] == 4719,'budget'] = 45
test.loc[test['id'] == 4822,'budget'] = 22
test.loc[test['id'] == 4829,'budget'] = 20
test.loc[test['id'] == 4969,'budget'] = 20
test.loc[test['id'] == 5021,'budget'] = 40
test.loc[test['id'] == 5035,'budget'] = 1
test.loc[test['id'] == 5063,'budget'] = 14
test.loc[test['id'] == 5119,'budget'] = 2
test.loc[test['id'] == 5214,'budget'] = 30
test.loc[test['id'] == 5221,'budget'] = 50
test.loc[test['id'] == 4903,'budget'] = 15
test.loc[test['id'] == 4983,'budget'] = 3
test.loc[test['id'] == 5102,'budget'] = 28
test.loc[test['id'] == 5217,'budget'] = 75
test.loc[test['id'] == 5224,'budget'] = 3
test.loc[test['id'] == 5469,'budget'] = 20
test.loc[test['id'] == 5840,'budget'] = 1
test.loc[test['id'] == 5960,'budget'] = 30
test.loc[test['id'] == 6506,'budget'] = 11
test.loc[test['id'] == 6553,'budget'] = 280
test.loc[test['id'] == 6561,'budget'] = 7
test.loc[test['id'] == 6582,'budget'] = 218
test.loc[test['id'] == 6638,'budget'] = 5
test.loc[test['id'] == 6749,'budget'] = 8
test.loc[test['id'] == 6759,'budget'] = 50
test.loc[test['id'] == 6856,'budget'] = 10
test.loc[test['id'] == 6858,'budget'] = 100
test.loc[test['id'] == 6876,'budget'] = 250
test.loc[test['id'] == 6972,'budget'] = 1
test.loc[test['id'] == 7079,'budget'] = 8000000
test.loc[test['id'] == 7150,'budget'] = 118
test.loc[test['id'] == 6506,'budget'] = 118
test.loc[test['id'] == 7225,'budget'] = 6
test.loc[test['id'] == 7231,'budget'] = 85
test.loc[test['id'] == 5222,'budget'] = 5
test.loc[test['id'] == 5322,'budget'] = 90
test.loc[test['id'] == 5350,'budget'] = 70
test.loc[test['id'] == 5378,'budget'] = 10
test.loc[test['id'] == 5545,'budget'] = 80
test.loc[test['id'] == 5810,'budget'] = 8
test.loc[test['id'] == 5926,'budget'] = 300
test.loc[test['id'] == 5927,'budget'] = 4
test.loc[test['id'] == 5986,'budget'] = 1
test.loc[test['id'] == 6053,'budget'] = 20
test.loc[test['id'] == 6104,'budget'] = 1
test.loc[test['id'] == 6130,'budget'] = 30
test.loc[test['id'] == 6301,'budget'] = 150
test.loc[test['id'] == 6276,'budget'] = 100
test.loc[test['id'] == 6473,'budget'] = 100
test.loc[test['id'] == 6842,'budget'] = 30
test['revenue'] = np.nan
train = pd.merge(train, pd.read_csv('.. /input/tmdb-competition-additional-features/TrainAdditionalFeatures.csv'), how='left', on=['imdb_id'])
 test = pd.merge(test, pd.read_csv('.. /input/tmdb-competition-additional-features/TestAdditionalFeatures.csv'), how='left', on=['imdb_id'])
 additionalTrainData = pd.read_csv('.. /input/tmdb-box-office-prediction-more-training-data/additionalTrainData.csv')
 additionalTrainData['release_date'] = additionalTrainData['release_date'].astype('str')
 additionalTrainData['release_date'] = additionalTrainData['release_date'].str.replace('-', '/')
 train = pd.concat([train, additionalTrainData])
 print(train.columns)
 print(train.shape)
 train['revenue'] = np.log1p(train['revenue'])
 y = train['revenue'].values
json_cols = ['genres', 'production_companies', 'production_countries', 'spoken_languages', 'Keywords', 'cast', 'crew']
def get_dictionary(s):
try:
d = eval(s)
 except:
d = {}
return d
for col in tqdm(json_cols + ['belongs_to_collection']):
train[col] = train[col].apply(lambda x : get_dictionary(x))
test[col] = test[col].apply(lambda x : get_dictionary(x))
def get_json_dict(df):
global json_cols
result = dict()
for e_col in json_cols :
d = dict()
rows = df[e_col].values
for row in rows :
if row is None : continue
for i in row :
if i['name'] not in d :
d[i['name']] = 0
d[i['name']] += 1
result[e_col] = d
return result
train_dict = get_json_dict(train)
 test_dict = get_json_dict(test)
 for col in json_cols :
remove = []
train_id = set(list(train_dict[col].keys()))
test_id = set(list(test_dict[col].keys()))
remove += list(train_id - test_id)+ list(test_id - train_id)
 for i in train_id.union(test_id)- set(remove):
if train_dict[col][i] < 10 or i == '' :
remove += [i]
for i in remove :
if i in train_dict[col] :
del train_dict[col][i]
if i in test_dict[col] :
del test_dict[col][i]
all_data = prepare(pd.concat([train, test] ).reset_index(drop = True))
train = all_data.loc[:train.shape[0] - 1,:]
test = all_data.loc[train.shape[0]:,:]<choose_model_class>
files_path = f'{database_base_path}test_images/'
test_size = len(os.listdir(files_path))
test_preds = np.zeros(( test_size, N_CLASSES))
for model_path in model_path_list:
print(model_path)
 K.clear_session()
model.load_weights(model_path)
 if TTA_STEPS > 0:
test_ds = get_dataset(files_path, tta=True ).repeat()
ct_steps = TTA_STEPS *(( test_size/BATCH_SIZE)+ 1)
 preds = model.predict(test_ds, steps=ct_steps, verbose=1)[:(test_size * TTA_STEPS)]
preds = np.mean(preds.reshape(test_size, TTA_STEPS, N_CLASSES, order='F'), axis=1)
 test_preds += preds / len(model_path_list)
 else:
test_ds = get_dataset(files_path, tta=False)
 x_test = test_ds.map(lambda image, image_name: image)
 test_preds += model.predict(x_test)/ len(model_path_list)
 test_preds = np.argmax(test_preds, axis=-1)
 test_names_ds = get_dataset(files_path)
 image_names = [img_name.numpy().decode('utf-8')for img, img_name in iter(test_names_ds.unbatch())]
<train_model><EOS> 
submission = pd.DataFrame({'image_id': image_names, 'label': test_preds})
 submission.to_csv('submission.csv', index=False)
 display(submission.head() )