External data

Helper functions used to download and extract common time series datasets.


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decompress_from_url

 decompress_from_url (url, target_dir=None, verbose=False)

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download_data

 download_data (url, fname=None, c_key='archive', force_download=False,
                timeout=4, verbose=False)

Download url to fname.


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get_UCR_univariate_list

 get_UCR_univariate_list ()

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get_UCR_multivariate_list

 get_UCR_multivariate_list ()

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get_UCR_data

 get_UCR_data (dsid, path='.', parent_dir='data/UCR', on_disk=True,
               mode='c', Xdtype='float32', ydtype=None, return_split=True,
               split_data=True, force_download=False, verbose=False)
from fastai.data.transforms import get_files
PATH = Path('.')
dsids = ['ECGFiveDays', 'AtrialFibrillation'] # univariate and multivariate
for dsid in dsids:
    print(dsid)
    tgt_dir = PATH/f'data/UCR/{dsid}'
    if os.path.isdir(tgt_dir): shutil.rmtree(tgt_dir)
    test_eq(len(get_files(tgt_dir)), 0) # no file left
    X_train, y_train, X_valid, y_valid = get_UCR_data(dsid)
    test_eq(len(get_files(tgt_dir, '.npy')), 6)
    test_eq(len(get_files(tgt_dir, '.npy')), len(get_files(tgt_dir))) # test no left file/ dir
    del X_train, y_train, X_valid, y_valid
    X_train, y_train, X_valid, y_valid = get_UCR_data(dsid)
    test_eq(X_train.ndim, 3)
    test_eq(y_train.ndim, 1)
    test_eq(X_valid.ndim, 3)
    test_eq(y_valid.ndim, 1)
    test_eq(len(get_files(tgt_dir, '.npy')), 6)
    test_eq(len(get_files(tgt_dir, '.npy')), len(get_files(tgt_dir))) # test no left file/ dir
    test_eq(X_train.ndim, 3)
    test_eq(y_train.ndim, 1)
    test_eq(X_valid.ndim, 3)
    test_eq(y_valid.ndim, 1)
    test_eq(X_train.dtype, np.float32)
    test_eq(X_train.__class__.__name__, 'memmap')
    del X_train, y_train, X_valid, y_valid
    X_train, y_train, X_valid, y_valid = get_UCR_data(dsid, on_disk=False)
    test_eq(X_train.__class__.__name__, 'ndarray')
    del X_train, y_train, X_valid, y_valid
ECGFiveDays
AtrialFibrillation
X_train, y_train, X_valid, y_valid = get_UCR_data('natops')
dsid = 'natops' 
X_train, y_train, X_valid, y_valid = get_UCR_data(dsid, verbose=True)
X, y, splits = get_UCR_data(dsid, split_data=False)
test_eq(X[splits[0]], X_train)
test_eq(y[splits[1]], y_valid)
test_eq(X[splits[0]], X_train)
test_eq(y[splits[1]], y_valid)
test_type(X, X_train)
test_type(y, y_train)
Dataset: NATOPS
X_train: (180, 24, 51)
y_train: (180,)
X_valid: (180, 24, 51)
y_valid: (180,) 

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check_data

 check_data (X, y=None, splits=None, show_plot=True)
dsid = 'ECGFiveDays'
X, y, splits = get_UCR_data(dsid, split_data=False, on_disk=False, force_download=False)
check_data(X, y, splits)
check_data(X[:, 0], y, splits)
y = y.astype(np.float32)
check_data(X, y, splits)
y[:10] = np.nan
check_data(X[:, 0], y, splits)
X, y, splits = get_UCR_data(dsid, split_data=False, on_disk=False, force_download=False)
splits = get_splits(y, 3)
check_data(X, y, splits)
check_data(X[:, 0], y, splits)
y[:5]= np.nan
check_data(X[:, 0], y, splits)
X, y, splits = get_UCR_data(dsid, split_data=False, on_disk=False, force_download=False)
X      - shape: [884 samples x 1 features x 136 timesteps]  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:<U1  n_classes: 2 (442 samples per class) ['1', '2']  isnan: False
splits - n_splits: 2 shape: [23, 861]  overlap: False
X      - shape: (884, 136)  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:<U1  n_classes: 2 (442 samples per class) ['1', '2']  isnan: False
splits - n_splits: 2 shape: [23, 861]  overlap: False
X      - shape: [884 samples x 1 features x 136 timesteps]  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:float32  isnan: 0
splits - n_splits: 2 shape: [23, 861]  overlap: False
X      - shape: (884, 136)  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:float32  isnan: 10
splits - n_splits: 2 shape: [23, 861]  overlap: False
X      - shape: [884 samples x 1 features x 136 timesteps]  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:<U1  n_classes: 2 (442 samples per class) ['1', '2']  isnan: False
splits - n_splits: 3 shape: [[589, 295], [589, 295], [590, 294]]  overlap: [False, False, False]
X      - shape: (884, 136)  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:<U1  n_classes: 2 (442 samples per class) ['1', '2']  isnan: False
splits - n_splits: 3 shape: [[589, 295], [589, 295], [590, 294]]  overlap: [False, False, False]
X      - shape: (884, 136)  type: ndarray  dtype:float32  isnan: 0
y      - shape: (884,)  type: ndarray  dtype:<U1  n_classes: 3 (294 samples per class) ['1', '2', 'n']  isnan: False
splits - n_splits: 3 shape: [[589, 295], [589, 295], [590, 294]]  overlap: [False, False, False]

/var/folders/42/4hhwknbd5kzcbq48tmy_gbp00000gn/T/ipykernel_70492/278801922.py:23: UserWarning: y contains nan values
  warnings.warn('y contains nan values')


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get_Monash_regression_list

 get_Monash_regression_list ()

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get_Monash_regression_data

 get_Monash_regression_data (dsid, path='./data/Monash', on_disk=True,
                             mode='c', Xdtype='float32', ydtype=None,
                             split_data=True, force_download=False,
                             verbose=False, timeout=4)
dsid = "Covid3Month"
X_train, y_train, X_valid, y_valid = get_Monash_regression_data(dsid, on_disk=False, split_data=True, force_download=False)
X, y, splits = get_Monash_regression_data(dsid, on_disk=True, split_data=False, force_download=False, verbose=True)
if X_train is not None: 
    test_eq(X_train.shape, (140, 1, 84))
if X is not None: 
    test_eq(X.shape, (201, 1, 84))
Dataset: Covid3Month
X      : (201, 1, 84)
y      : (201,)
splits : (#140) [0,1,2,3,4,5,6,7,8,9...] (#61) [140,141,142,143,144,145,146,147,148,149...] 

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get_forecasting_list

 get_forecasting_list ()

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get_forecasting_time_series

 get_forecasting_time_series (dsid, path='./data/forecasting/',
                              force_download=False, verbose=True,
                              **kwargs)
ts = get_forecasting_time_series("sunspots", force_download=False)
test_eq(len(ts), 2820)
ts
Dataset: Sunspots
downloading data...
...done. Path = data/forecasting/Sunspots.csv
Sunspots
Month
1749-01-31 58.0
1749-02-28 62.6
1749-03-31 70.0
1749-04-30 55.7
1749-05-31 85.0
... ...
1983-08-31 71.8
1983-09-30 50.3
1983-10-31 55.8
1983-11-30 33.3
1983-12-31 33.4

2820 rows × 1 columns

ts = get_forecasting_time_series("weather", force_download=False)
if ts is not None: 
    test_eq(len(ts), 70091)
    display(ts)
Dataset: Weather
downloading data...
...done. Path = data/forecasting/Weather.csv.zip
p (mbar) T (degC) Tpot (K) Tdew (degC) rh (%) VPmax (mbar) VPact (mbar) VPdef (mbar) sh (g/kg) H2OC (mmol/mol) rho (g/m**3) Wx Wy max Wx max Wy Day sin Day cos Year sin Year cos
0 996.50 -8.05 265.38 -8.78 94.40 3.33 3.14 0.19 1.96 3.15 1307.86 -0.204862 -0.046168 -0.614587 -0.138503 -1.776611e-12 1.000000 0.009332 0.999956
1 996.62 -8.88 264.54 -9.77 93.20 3.12 2.90 0.21 1.81 2.91 1312.25 -0.245971 -0.044701 -0.619848 -0.112645 2.588190e-01 0.965926 0.010049 0.999950
2 996.84 -8.81 264.59 -9.66 93.50 3.13 2.93 0.20 1.83 2.94 1312.18 -0.175527 0.039879 -0.614344 0.139576 5.000000e-01 0.866025 0.010766 0.999942
3 996.99 -9.05 264.34 -10.02 92.60 3.07 2.85 0.23 1.78 2.85 1313.61 -0.050000 -0.086603 -0.190000 -0.329090 7.071068e-01 0.707107 0.011483 0.999934
4 997.46 -9.63 263.72 -10.65 92.20 2.94 2.71 0.23 1.69 2.71 1317.19 -0.368202 0.156292 -0.810044 0.343843 8.660254e-01 0.500000 0.012199 0.999926
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
70086 1002.18 -0.98 272.01 -5.36 72.00 5.69 4.09 1.59 2.54 4.08 1280.70 -0.855154 -0.160038 -1.336792 -0.250174 -9.990482e-01 0.043619 0.006183 0.999981
70087 1001.40 -1.40 271.66 -6.84 66.29 5.51 3.65 1.86 2.27 3.65 1281.87 -0.716196 -0.726267 -1.348134 -1.367090 -9.537170e-01 0.300706 0.006900 0.999976
70088 1001.19 -2.75 270.32 -6.90 72.90 4.99 3.64 1.35 2.26 3.63 1288.02 -0.661501 0.257908 -1.453438 0.566672 -8.433914e-01 0.537300 0.007617 0.999971
70089 1000.65 -2.89 270.22 -7.15 72.30 4.93 3.57 1.37 2.22 3.57 1288.03 -0.280621 -0.209169 -0.545207 -0.406385 -6.755902e-01 0.737277 0.008334 0.999965
70090 1000.11 -3.93 269.23 -8.09 72.60 4.56 3.31 1.25 2.06 3.31 1292.41 -0.516998 -0.215205 -0.923210 -0.384295 -4.617486e-01 0.887011 0.009050 0.999959

70091 rows × 19 columns


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convert_tsf_to_dataframe

 convert_tsf_to_dataframe (full_file_path_and_name,
                           replace_missing_vals_with='NaN',
                           value_column_name='series_value')

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get_Monash_forecasting_data

 get_Monash_forecasting_data (dsid, path='./data/forecasting/',
                              force_download=False,
                              remove_from_disk=False, add_timestamp=True,
                              verbose=True)

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get_fcst_horizon

 get_fcst_horizon (frequency, dsid)

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preprocess_Monash_df

 preprocess_Monash_df (df, frequency)
dsid = 'covid_deaths_dataset'
df = get_Monash_forecasting_data(dsid, force_download=False)
if df is not None: 
    test_eq(df.shape, (56392, 3))
Dataset: covid_deaths_dataset
downloading data...
...data downloaded
decompressing data...
...data decompressed
converting data to dataframe...
...done

freq                   : daily
forecast_horizon       : 30
contain_missing_values : False
contain_equal_length   : True

exploding dataframe...
...done


data.shape: (56392, 3)

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download_all_long_term_forecasting_data

 download_all_long_term_forecasting_data
                                          (target_dir='./data/long_forecas
                                          ting/', force_download=False,
                                          remove_zip=False,
                                          c_key='archive', timeout=4,
                                          verbose=True)

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unzip_file

 unzip_file (file, target_dir)

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get_long_term_forecasting_data

 get_long_term_forecasting_data (dsid,
                                 target_dir='./data/long_forecasting/',
                                 task='M', fcst_horizon=None,
                                 fcst_history=None, preprocess=True,
                                 force_download=False, remove_zip=False,
                                 return_df=True, show_plot=True,
                                 dtype=<class 'numpy.float32'>,
                                 verbose=True, **kwargs)

Downloads (and preprocess) a pandas dataframe with the requested long-term forecasting dataset

Type Default Details
dsid ID of the dataset to be used for long-term forecasting.
target_dir str ./data/long_forecasting/ Directory where the long-term forecasting data will be saved.
task str M ‘M’ for multivariate, ‘S’ for univariate and ‘MS’ for multivariate input with univariate output
fcst_horizon NoneType None # historical steps used as input. If None, the default is applied.
fcst_history NoneType None # steps forecasted into the future. If None, the minimum default is applied.
preprocess bool True Flag that indicates whether if the data is preprocessed before saving.
force_download bool False Flag that indicates if the data should be downloaded again even if directory exists.
remove_zip bool False Flag that indicates if the zip file should be removed after extracting the data.
return_df bool True Flag that indicates whether a dataframe (True) or X and and y arrays (False) are returned.
show_plot bool True plot the splits
dtype type float32
verbose bool True Flag tto indicate the verbosity.
kwargs
dsid = "ILI"
try:
    df = get_long_term_forecasting_data(dsid, target_dir='./data/forecasting/', force_download=False)
    print(f"{dsid:15}: {str(df.shape):15}")
    del df; gc.collect()
    remove_dir('./data/forecasting/', False)
except Exception as e:
    print(f"{dsid:15}: {str(e):15}")
100.01% [54001664/53995526 00:09<00:00]
/Users/nacho/opt/anaconda3/envs/py39t20/lib/python3.9/site-packages/fastai/tabular/core.py:23: UserWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version. A strict version of it is now the default, see https://pandas.pydata.org/pdeps/0004-consistent-to-datetime-parsing.html. You can safely remove this argument.
  df[date_field] = pd.to_datetime(df[date_field], infer_datetime_format=True)
ILI            : (966, 8)       
dsid = "ILI"
try:
    X, y, splits, stats = get_long_term_forecasting_data(dsid, target_dir='./data/forecasting/', force_download=False, return_df=False, show_plot=False)
    print(f"{dsid:15} -  X.shape: {str(X.shape):20}  y.shape: {str(y.shape):20}  splits: {str([len(s) for s in splits]):25}  \
stats: {str([s.shape for s in stats]):30}")
    del X, y, splits, stats
    gc.collect()
    remove_dir('./data/forecasting/', False)
except Exception as e:
    print(f"{dsid:15}: {str(e):15}")
100.01% [54001664/53995526 00:09<00:00]
/Users/nacho/opt/anaconda3/envs/py39t20/lib/python3.9/site-packages/fastai/tabular/core.py:23: UserWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version. A strict version of it is now the default, see https://pandas.pydata.org/pdeps/0004-consistent-to-datetime-parsing.html. You can safely remove this argument.
  df[date_field] = pd.to_datetime(df[date_field], infer_datetime_format=True)
ILI             -  X.shape: (839, 7, 104)         y.shape: (839, 7, 24)          splits: [549, 74, 170]             stats: [(1, 7, 1), (1, 7, 1)]