"""Automatically download MLdata datasets.""" # Copyright (c) 2011 Pietro Berkes # License: BSD 3 clause import os from os.path import join, exists import re import numbers try: # Python 2 from urllib2 import HTTPError from urllib2 import quote from urllib2 import urlopen except ImportError: # Python 3+ from urllib.error import HTTPError from urllib.parse import quote from urllib.request import urlopen import numpy as np import scipy as sp from scipy import io from shutil import copyfileobj from .base import get_data_home, Bunch MLDATA_BASE_URL = "http://mldata.org/repository/data/download/matlab/%s" def mldata_filename(dataname): """Convert a raw name for a data set in a mldata.org filename.""" dataname = dataname.lower().replace(' ', '-') return re.sub(r'[().]', '', dataname) def fetch_mldata(dataname, target_name='label', data_name='data', transpose_data=True, data_home=None): """Fetch an mldata.org data set If the file does not exist yet, it is downloaded from mldata.org . mldata.org does not have an enforced convention for storing data or naming the columns in a data set. The default behavior of this function works well with the most common cases: 1) data values are stored in the column 'data', and target values in the column 'label' 2) alternatively, the first column stores target values, and the second data values 3) the data array is stored as `n_features x n_samples` , and thus needs to be transposed to match the `sklearn` standard Keyword arguments allow to adapt these defaults to specific data sets (see parameters `target_name`, `data_name`, `transpose_data`, and the examples below). mldata.org data sets may have multiple columns, which are stored in the Bunch object with their original name. Parameters ---------- dataname: Name of the data set on mldata.org, e.g.: "leukemia", "Whistler Daily Snowfall", etc. The raw name is automatically converted to a mldata.org URL . target_name: optional, default: 'label' Name or index of the column containing the target values. data_name: optional, default: 'data' Name or index of the column containing the data. transpose_data: optional, default: True If True, transpose the downloaded data array. data_home: optional, default: None Specify another download and cache folder for the data sets. By default all scikit learn data is stored in '~/scikit_learn_data' subfolders. Returns ------- data : Bunch Dictionary-like object, the interesting attributes are: 'data', the data to learn, 'target', the classification labels, 'DESCR', the full description of the dataset, and 'COL_NAMES', the original names of the dataset columns. Examples -------- Load the 'iris' dataset from mldata.org: >>> from sklearn.datasets.mldata import fetch_mldata >>> import tempfile >>> test_data_home = tempfile.mkdtemp() >>> iris = fetch_mldata('iris', data_home=test_data_home) >>> iris.target.shape (150,) >>> iris.data.shape (150, 4) Load the 'leukemia' dataset from mldata.org, which needs to be transposed to respects the scikit-learn axes convention: >>> leuk = fetch_mldata('leukemia', transpose_data=True, ... data_home=test_data_home) >>> leuk.data.shape (72, 7129) Load an alternative 'iris' dataset, which has different names for the columns: >>> iris2 = fetch_mldata('datasets-UCI iris', target_name=1, ... data_name=0, data_home=test_data_home) >>> iris3 = fetch_mldata('datasets-UCI iris', ... target_name='class', data_name='double0', ... data_home=test_data_home) >>> import shutil >>> shutil.rmtree(test_data_home) """ # normalize dataset name dataname = mldata_filename(dataname) # check if this data set has been already downloaded data_home = get_data_home(data_home=data_home) data_home = join(data_home, 'mldata') if not exists(data_home): os.makedirs(data_home) matlab_name = dataname + '.mat' filename = join(data_home, matlab_name) # if the file does not exist, download it if not exists(filename): urlname = MLDATA_BASE_URL % quote(dataname) try: mldata_url = urlopen(urlname) except HTTPError as e: if e.code == 404: e.msg = "Dataset '%s' not found on mldata.org." % dataname raise # store Matlab file try: with open(filename, 'w+b') as matlab_file: copyfileobj(mldata_url, matlab_file) except: os.remove(filename) raise mldata_url.close() # load dataset matlab file with open(filename, 'rb') as matlab_file: matlab_dict = io.loadmat(matlab_file, struct_as_record=True) # -- extract data from matlab_dict # flatten column names col_names = [str(descr[0]) for descr in matlab_dict['mldata_descr_ordering'][0]] # if target or data names are indices, transform then into names if isinstance(target_name, numbers.Integral): target_name = col_names[target_name] if isinstance(data_name, numbers.Integral): data_name = col_names[data_name] # rules for making sense of the mldata.org data format # (earlier ones have priority): # 1) there is only one array => it is "data" # 2) there are multiple arrays # a) copy all columns in the bunch, using their column name # b) if there is a column called `target_name`, set "target" to it, # otherwise set "target" to first column # c) if there is a column called `data_name`, set "data" to it, # otherwise set "data" to second column dataset = {'DESCR': 'mldata.org dataset: %s' % dataname, 'COL_NAMES': col_names} # 1) there is only one array => it is considered data if len(col_names) == 1: data_name = col_names[0] dataset['data'] = matlab_dict[data_name] # 2) there are multiple arrays else: for name in col_names: dataset[name] = matlab_dict[name] if target_name in col_names: del dataset[target_name] dataset['target'] = matlab_dict[target_name] else: del dataset[col_names[0]] dataset['target'] = matlab_dict[col_names[0]] if data_name in col_names: del dataset[data_name] dataset['data'] = matlab_dict[data_name] else: del dataset[col_names[1]] dataset['data'] = matlab_dict[col_names[1]] # set axes to scikit-learn conventions if transpose_data: dataset['data'] = dataset['data'].T if 'target' in dataset: if not sp.sparse.issparse(dataset['target']): dataset['target'] = dataset['target'].squeeze() return Bunch(**dataset) # The following is used by nosetests to setup the docstring tests fixture def setup_module(module): # setup mock urllib2 module to avoid downloading from mldata.org from sklearn.utils.testing import install_mldata_mock install_mldata_mock({ 'iris': { 'data': np.empty((150, 4)), 'label': np.empty(150), }, 'datasets-uci-iris': { 'double0': np.empty((150, 4)), 'class': np.empty((150,)), }, 'leukemia': { 'data': np.empty((72, 7129)), }, }) def teardown_module(module): from sklearn.utils.testing import uninstall_mldata_mock uninstall_mldata_mock()