GPy/GPy/util/datasets.py

import os
import numpy as np
import GPy
import scipy.io
import cPickle as pickle
import zipfile
import tarfile
import datetime
import json
ipython_available=True
try:
    import IPython
except ImportError:
    ipython_available=False


import sys, urllib2

def reporthook(a,b,c):
    # ',' at the end of the line is important!
    #print "% 3.1f%% of %d bytes\r" % (min(100, float(a * b) / c * 100), c),
    #you can also use sys.stdout.write
    sys.stdout.write("\r% 3.1f%% of %d bytes" % (min(100, float(a * b) / c * 100), c))
    sys.stdout.flush()

# Global variables
data_path = os.path.join(os.path.dirname(__file__), 'datasets')
default_seed = 10000
overide_manual_authorize=False
neil_url = 'http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/dataset_mirror/'

# Read data resources from json file.
# Don't do this when ReadTheDocs is scanning as it breaks things
on_rtd = os.environ.get('READTHEDOCS', None) == 'True' #Checks if RTD is scanning
if not (on_rtd):
    path = os.path.join(os.path.dirname(__file__), 'data_resources.json')
    json_data=open(path).read()
    data_resources = json.loads(json_data)


def prompt_user(prompt):
    """Ask user for agreeing to data set licenses."""
    # raw_input returns the empty string for "enter"
    yes = set(['yes', 'y'])
    no = set(['no','n'])

    try:
        print(prompt)
        choice = raw_input().lower()
        # would like to test for exception here, but not sure if we can do that without importing IPython
    except:
        print('Stdin is not implemented.')
        print('You need to set')
        print('overide_manual_authorize=True')
        print('to proceed with the download. Please set that variable and continue.')
        raise


    if choice in yes:
        return True
    elif choice in no:
        return False
    else:
        print("Your response was a " + choice)
        print("Please respond with 'yes', 'y' or 'no', 'n'")
        #return prompt_user()


def data_available(dataset_name=None):
    """Check if the data set is available on the local machine already."""
    for file_list in data_resources[dataset_name]['files']:
        for file in file_list:
            if not os.path.exists(os.path.join(data_path, dataset_name, file)):
                return False
    return True

def download_url(url, store_directory, save_name = None, messages = True, suffix=''):
    """Download a file from a url and save it to disk."""
    i = url.rfind('/')
    file = url[i+1:]
    print file
    dir_name = os.path.join(data_path, store_directory)
    save_name = os.path.join(dir_name, file)
    print "Downloading ", url, "->", os.path.join(store_directory, file)
    if not os.path.exists(dir_name):
        os.makedirs(dir_name)
    try:
        response = urllib2.urlopen(url+suffix)
    except urllib2.URLError, e:
        if not hasattr(e, "code"):
            raise
        response = e
        if response.code > 399 and response.code<500:
            raise ValueError('Tried url ' + url + suffix + ' and received client error ' + str(response.code))
        elif response.code > 499:
            raise ValueError('Tried url ' + url + suffix + ' and received server error ' + str(response.code))
    # if we wanted to get more sophisticated maybe we should check the response code here again even for successes.
    with open(save_name, 'wb') as f:
        f.write(response.read())

    #urllib.urlretrieve(url+suffix, save_name, reporthook)

def authorize_download(dataset_name=None):
    """Check with the user that the are happy with terms and conditions for the data set."""
    print('Acquiring resource: ' + dataset_name)
    # TODO, check resource is in dictionary!
    print('')
    dr = data_resources[dataset_name]
    print('Details of data: ')
    print(dr['details'])
    print('')
    if dr['citation']:
        print('Please cite:')
        print(dr['citation'])
        print('')
    if dr['size']:
        print('After downloading the data will take up ' + str(dr['size']) + ' bytes of space.')
        print('')
    print('Data will be stored in ' + os.path.join(data_path, dataset_name) + '.')
    print('')
    if overide_manual_authorize:
        if dr['license']:
            print('You have agreed to the following license:')
            print(dr['license'])
            print('')
        return True
    else:
        if dr['license']:
            print('You must also agree to the following license:')
            print(dr['license'])
            print('')
        return prompt_user('Do you wish to proceed with the download? [yes/no]')

def download_data(dataset_name=None):
    """Check with the user that the are happy with terms and conditions for the data set, then download it."""

    dr = data_resources[dataset_name]
    if not authorize_download(dataset_name):
        raise Exception("Permission to download data set denied.")

    if dr.has_key('suffices'):
        for url, files, suffices in zip(dr['urls'], dr['files'], dr['suffices']):
            for file, suffix in zip(files, suffices):
                download_url(os.path.join(url,file), dataset_name, dataset_name, suffix=suffix)
    else:
        for url, files in zip(dr['urls'], dr['files']):
            for file in files:
                download_url(os.path.join(url,file), dataset_name, dataset_name)
    return True

def data_details_return(data, data_set):
    """Update the data component of the data dictionary with details drawn from the data_resources."""
    data.update(data_resources[data_set])
    return data


def cmu_urls_files(subj_motions, messages = True):
    '''
    Find which resources are missing on the local disk for the requested CMU motion capture motions.
    '''
    dr = data_resources['cmu_mocap_full']
    cmu_url = dr['urls'][0]

    subjects_num = subj_motions[0]
    motions_num = subj_motions[1]

    resource = {'urls' : [], 'files' : []}
    # Convert numbers to strings
    subjects = []
    motions = [list() for _ in range(len(subjects_num))]
    for i in range(len(subjects_num)):
        curSubj = str(int(subjects_num[i]))
        if int(subjects_num[i]) < 10:
            curSubj = '0' + curSubj
        subjects.append(curSubj)
        for j in range(len(motions_num[i])):
            curMot = str(int(motions_num[i][j]))
            if int(motions_num[i][j]) < 10:
                curMot = '0' + curMot
            motions[i].append(curMot)

    all_skels = []

    assert len(subjects) == len(motions)

    all_motions = []

    for i in range(len(subjects)):
        skel_dir = os.path.join(data_path, 'cmu_mocap')
        cur_skel_file = os.path.join(skel_dir, subjects[i] + '.asf')

        url_required = False
        file_download = []
        if not os.path.exists(cur_skel_file):
            # Current skel file doesn't exist.
            if not os.path.isdir(skel_dir):
                os.mkdir(skel_dir)
            # Add skel file to list.
            url_required = True
            file_download.append(subjects[i] + '.asf')
        for j in range(len(motions[i])):
            file_name = subjects[i] + '_' + motions[i][j] + '.amc'
            cur_motion_file = os.path.join(skel_dir, file_name)
            if not os.path.exists(cur_motion_file):
                url_required = True
                file_download.append(subjects[i] + '_' + motions[i][j] + '.amc')
        if url_required:
            resource['urls'].append(cmu_url + '/' + subjects[i] + '/')
            resource['files'].append(file_download)
    return resource

try:
    import gpxpy
    import gpxpy.gpx
    gpxpy_available = True

except ImportError:
    gpxpy_available = False

if gpxpy_available:
    def epomeo_gpx(data_set='epomeo_gpx', sample_every=4):
        if not data_available(data_set):
            download_data(data_set)
        files = ['endomondo_1', 'endomondo_2', 'garmin_watch_via_endomondo','viewranger_phone', 'viewranger_tablet']

        X = []
        for file in files:
            gpx_file = open(os.path.join(data_path, 'epomeo_gpx', file + '.gpx'), 'r')

            gpx = gpxpy.parse(gpx_file)
            segment = gpx.tracks[0].segments[0]
            points = [point for track in gpx.tracks for segment in track.segments for point in segment.points]
            data = [[(point.time-datetime.datetime(2013,8,21)).total_seconds(), point.latitude, point.longitude, point.elevation] for point in points]
            X.append(np.asarray(data)[::sample_every, :])
            gpx_file.close()
        return data_details_return({'X' : X, 'info' : 'Data is an array containing time in seconds, latitude, longitude and elevation in that order.'}, data_set)

#del gpxpy_available



# Some general utilities.
def sample_class(f):
    p = 1. / (1. + np.exp(-f))
    c = np.random.binomial(1, p)
    c = np.where(c, 1, -1)
    return c

def boston_housing(data_set='boston_housing'):
    if not data_available(data_set):
        download_data(data_set)
    all_data = np.genfromtxt(os.path.join(data_path, data_set, 'housing.data'))
    X = all_data[:, 0:13]
    Y = all_data[:, 13:14]
    return data_details_return({'X' : X, 'Y': Y}, data_set)

def brendan_faces(data_set='brendan_faces'):
    if not data_available(data_set):
        download_data(data_set)
    mat_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'frey_rawface.mat'))
    Y = mat_data['ff'].T
    return data_details_return({'Y': Y}, data_set)

def della_gatta_TRP63_gene_expression(data_set='della_gatta', gene_number=None):
    if not data_available(data_set):
        download_data(data_set)
    mat_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'DellaGattadata.mat'))
    X = np.double(mat_data['timepoints'])
    if gene_number == None:
        Y = mat_data['exprs_tp53_RMA']
    else:
        Y = mat_data['exprs_tp53_RMA'][:, gene_number]
        if len(Y.shape) == 1:
            Y = Y[:, None]
    return data_details_return({'X': X, 'Y': Y, 'gene_number' : gene_number}, data_set)



# The data sets
def oil(data_set='three_phase_oil_flow'):
    """The three phase oil data from Bishop and James (1993)."""
    if not data_available(data_set):
        download_data(data_set)
    oil_train_file = os.path.join(data_path, data_set, 'DataTrn.txt')
    oil_trainlbls_file = os.path.join(data_path, data_set, 'DataTrnLbls.txt')
    oil_test_file = os.path.join(data_path, data_set, 'DataTst.txt')
    oil_testlbls_file = os.path.join(data_path, data_set, 'DataTstLbls.txt')
    oil_valid_file = os.path.join(data_path, data_set, 'DataVdn.txt')
    oil_validlbls_file = os.path.join(data_path, data_set, 'DataVdnLbls.txt')
    fid = open(oil_train_file)
    X = np.fromfile(fid, sep='\t').reshape((-1, 12))
    fid.close()
    fid = open(oil_test_file)
    Xtest = np.fromfile(fid, sep='\t').reshape((-1, 12))
    fid.close()
    fid = open(oil_valid_file)
    Xvalid = np.fromfile(fid, sep='\t').reshape((-1, 12))
    fid.close()
    fid = open(oil_trainlbls_file)
    Y = np.fromfile(fid, sep='\t').reshape((-1, 3)) * 2. - 1.
    fid.close()
    fid = open(oil_testlbls_file)
    Ytest = np.fromfile(fid, sep='\t').reshape((-1, 3)) * 2. - 1.
    fid.close()
    fid = open(oil_validlbls_file)
    Yvalid = np.fromfile(fid, sep='\t').reshape((-1, 3)) * 2. - 1.
    fid.close()
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'Xtest' : Xtest, 'Xvalid': Xvalid, 'Yvalid': Yvalid}, data_set)
    #else:
    # throw an error

def oil_100(seed=default_seed, data_set = 'three_phase_oil_flow'):
    np.random.seed(seed=seed)
    data = oil()
    indices = np.random.permutation(1000)
    indices = indices[0:100]
    X = data['X'][indices, :]
    Y = data['Y'][indices, :]
    return data_details_return({'X': X, 'Y': Y, 'info': "Subsample of the full oil data extracting 100 values randomly without replacement, here seed was " + str(seed)}, data_set)

def pumadyn(seed=default_seed, data_set='pumadyn-32nm'):
    if not data_available(data_set):
        download_data(data_set)
        path = os.path.join(data_path, data_set)
        tar = tarfile.open(os.path.join(path, 'pumadyn-32nm.tar.gz'))
        print('Extracting file.')
        tar.extractall(path=path)
        tar.close()
    # Data is variance 1, no need to normalize.
    data = np.loadtxt(os.path.join(data_path, data_set, 'pumadyn-32nm', 'Dataset.data.gz'))
    indices = np.random.permutation(data.shape[0])
    indicesTrain = indices[0:7168]
    indicesTest = indices[7168:-1]
    indicesTrain.sort(axis=0)
    indicesTest.sort(axis=0)
    X = data[indicesTrain, 0:-2]
    Y = data[indicesTrain, -1][:, None]
    Xtest = data[indicesTest, 0:-2]
    Ytest = data[indicesTest, -1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'seed': seed}, data_set)

def robot_wireless(data_set='robot_wireless'):
    # WiFi access point strengths on a tour around UW Paul Allen building.
    if not data_available(data_set):
        download_data(data_set)
    file_name = os.path.join(data_path, data_set, 'uw-floor.txt')
    all_time = np.genfromtxt(file_name, usecols=(0))
    macaddress = np.genfromtxt(file_name, usecols=(1), dtype='string')
    x = np.genfromtxt(file_name, usecols=(2))
    y = np.genfromtxt(file_name, usecols=(3))
    strength = np.genfromtxt(file_name, usecols=(4))
    addresses = np.unique(macaddress)
    times = np.unique(all_time)
    addresses.sort()
    times.sort()
    allY = np.zeros((len(times), len(addresses)))
    allX = np.zeros((len(times), 2))
    allY[:]=-92.
    strengths={}
    for address, j in zip(addresses, range(len(addresses))):
        ind = np.nonzero(address==macaddress)
        temp_strengths=strength[ind]
        temp_x=x[ind]
        temp_y=y[ind]
        temp_times = all_time[ind]
        for time in temp_times:
            vals = time==temp_times
            if any(vals):
                ind2 = np.nonzero(vals)
                i = np.nonzero(time==times)
                allY[i, j] = temp_strengths[ind2]
                allX[i, 0] = temp_x[ind2]
                allX[i, 1] = temp_y[ind2]
    allY = (allY + 85.)/15.

    X = allX[0:215, :]
    Y = allY[0:215, :]

    Xtest = allX[215:, :]
    Ytest = allY[215:, :]
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'addresses' : addresses, 'times' : times}, data_set)

def silhouette(data_set='ankur_pose_data'):
    # Ankur Agarwal and Bill Trigg's silhoutte data.
    if not data_available(data_set):
        download_data(data_set)
    mat_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'ankurDataPoseSilhouette.mat'))
    inMean = np.mean(mat_data['Y'])
    inScales = np.sqrt(np.var(mat_data['Y']))
    X = mat_data['Y'] - inMean
    X = X / inScales
    Xtest = mat_data['Y_test'] - inMean
    Xtest = Xtest / inScales
    Y = mat_data['Z']
    Ytest = mat_data['Z_test']
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest}, data_set)

def decampos_digits(data_set='decampos_characters', which_digits=[0,1,2,3,4,5,6,7,8,9]):
    if not data_available(data_set):
        download_data(data_set)
    path = os.path.join(data_path, data_set)
    digits = np.load(os.path.join(path, 'digits.npy'))
    digits = digits[which_digits,:,:,:]
    num_classes, num_samples, height, width = digits.shape
    Y = digits.reshape((digits.shape[0]*digits.shape[1],digits.shape[2]*digits.shape[3]))
    lbls = np.array([[l]*num_samples for l in which_digits]).reshape(Y.shape[0], 1)
    str_lbls = np.array([[str(l)]*num_samples for l in which_digits])
    return data_details_return({'Y': Y, 'lbls': lbls, 'str_lbls' : str_lbls, 'info': 'Digits data set from the de Campos characters data'}, data_set)
    
def ripley_synth(data_set='ripley_prnn_data'):
    if not data_available(data_set):
        download_data(data_set)
    train = np.genfromtxt(os.path.join(data_path, data_set, 'synth.tr'), skip_header=1)
    X = train[:, 0:2]
    y = train[:, 2:3]
    test = np.genfromtxt(os.path.join(data_path, data_set, 'synth.te'), skip_header=1)
    Xtest = test[:, 0:2]
    ytest = test[:, 2:3]
    return data_details_return({'X': X, 'Y': y, 'Xtest': Xtest, 'Ytest': ytest, 'info': 'Synthetic data generated by Ripley for a two class classification problem.'}, data_set)

def mauna_loa(data_set='mauna_loa', num_train=543, refresh_data=False):
    path = os.path.join(data_path, data_set)
    if data_available(data_set) and not refresh_data:
        print 'Using cached version of the data set, to use latest version set refresh_data to True'
    else:
        download_data(data_set)
    data = np.loadtxt(os.path.join(data_path, data_set, 'co2_mm_mlo.txt'))
    print 'Most recent data observation from month ', data[-1, 1], ' in year ', data[-1, 0]
    allX = data[data[:, 3]!=-99.99, 2:3]
    allY = data[data[:, 3]!=-99.99, 3:4]
    X = allX[:num_train, 0:1]
    Xtest = allX[num_train:, 0:1]
    Y = allY[:num_train, 0:1]
    Ytest = allY[num_train:, 0:1]
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'info': "Mauna Loa data with " + str(num_train) + " values used as training points."}, data_set)
    

def boxjenkins_airline(data_set='boxjenkins_airline', num_train=96):
    path = os.path.join(data_path, data_set)
    if not data_available(data_set):
        download_data(data_set)
    data = np.loadtxt(os.path.join(data_path, data_set, 'boxjenkins_airline.csv'), delimiter=',')
    Y = data[:num_train, 1:2]
    X = data[:num_train, 0:1]
    Xtest = data[num_train:, 0:1]
    Ytest = data[num_train:, 1:2]
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'info': "Montly airline passenger data from Box & Jenkins 1976."}, data_set)
    

def osu_run1(data_set='osu_run1', sample_every=4):
    path = os.path.join(data_path, data_set)
    if not data_available(data_set):
        download_data(data_set)
        zip = zipfile.ZipFile(os.path.join(data_path, data_set, 'run1TXT.ZIP'), 'r')
        for name in zip.namelist():
            zip.extract(name, path)
    Y, connect = GPy.util.mocap.load_text_data('Aug210106', path)
    Y = Y[0:-1:sample_every, :]
    return data_details_return({'Y': Y, 'connect' : connect}, data_set)

def swiss_roll_generated(num_samples=1000, sigma=0.0):
    with open(os.path.join(data_path, 'swiss_roll.pickle')) as f:
        data = pickle.load(f)
    Na = data['Y'].shape[0]
    perm = np.random.permutation(np.r_[:Na])[:num_samples]
    Y = data['Y'][perm, :]
    t = data['t'][perm]
    c = data['colors'][perm, :]
    so = np.argsort(t)
    Y = Y[so, :]
    t = t[so]
    c = c[so, :]
    return {'Y':Y, 't':t, 'colors':c}

def swiss_roll_1000():
    return swiss_roll(num_samples=1000)

def swiss_roll(num_samples=3000, data_set='swiss_roll'):
    if not data_available(data_set):
        download_data(data_set)
    mat_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'swiss_roll_data.mat'))
    Y = mat_data['X_data'][:, 0:num_samples].transpose()
    return data_details_return({'Y': Y, 'X': mat_data['X_data'], 'info': "The first " + str(num_samples) + " points from the swiss roll data of Tennenbaum, de Silva and Langford (2001)."}, data_set)

def isomap_faces(num_samples=698, data_set='isomap_face_data'):
    if not data_available(data_set):
        download_data(data_set)
    mat_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'face_data.mat'))
    Y = mat_data['images'][:, 0:num_samples].transpose()
    return data_details_return({'Y': Y, 'poses' : mat_data['poses'], 'lights': mat_data['lights'], 'info': "The first " + str(num_samples) + " points from the face data of Tennenbaum, de Silva and Langford (2001)."}, data_set)

def simulation_BGPLVM():
    mat_data = scipy.io.loadmat(os.path.join(data_path, 'BGPLVMSimulation.mat'))
    Y = np.array(mat_data['Y'], dtype=float)
    S = np.array(mat_data['initS'], dtype=float)
    mu = np.array(mat_data['initMu'], dtype=float)
    #return data_details_return({'S': S, 'Y': Y, 'mu': mu}, data_set)
    return {'Y': Y, 'S': S,
            'mu' : mu,
            'info': "Simulated test dataset generated in MATLAB to compare BGPLVM between python and MATLAB"}

def toy_rbf_1d(seed=default_seed, num_samples=500):
    """
    Samples values of a function from an RBF covariance with very small noise for inputs uniformly distributed between -1 and 1.

    :param seed: seed to use for random sampling.
    :type seed: int
    :param num_samples: number of samples to sample in the function (default 500).
    :type num_samples: int

    """
    np.random.seed(seed=seed)
    num_in = 1
    X = np.random.uniform(low= -1.0, high=1.0, size=(num_samples, num_in))
    X.sort(axis=0)
    rbf = GPy.kern.RBF(num_in, variance=1., lengthscale=np.array((0.25,)))
    white = GPy.kern.White(num_in, variance=1e-2)
    kernel = rbf + white
    K = kernel.K(X)
    y = np.reshape(np.random.multivariate_normal(np.zeros(num_samples), K), (num_samples, 1))
    return {'X':X, 'Y':y, 'info': "Sampled " + str(num_samples) + " values of a function from an RBF covariance with very small noise for inputs uniformly distributed between -1 and 1."}

def toy_rbf_1d_50(seed=default_seed):
    np.random.seed(seed=seed)
    data = toy_rbf_1d()
    indices = np.random.permutation(data['X'].shape[0])
    indices = indices[0:50]
    indices.sort(axis=0)
    X = data['X'][indices, :]
    Y = data['Y'][indices, :]
    return {'X': X, 'Y': Y, 'info': "Subsamples the toy_rbf_sample with 50 values randomly taken from the original sample.", 'seed' : seed}


def toy_linear_1d_classification(seed=default_seed):
    np.random.seed(seed=seed)
    x1 = np.random.normal(-3, 5, 20)
    x2 = np.random.normal(3, 5, 20)
    X = (np.r_[x1, x2])[:, None]
    return {'X': X, 'Y':  sample_class(2.*X), 'F': 2.*X, 'seed' : seed}

def olivetti_glasses(data_set='olivetti_glasses', num_training=200, seed=default_seed):
    path = os.path.join(data_path, data_set)
    if not data_available(data_set):
        download_data(data_set)
    y = np.load(os.path.join(path, 'has_glasses.np'))
    y = np.where(y=='y',1,0).reshape(-1,1)
    faces = scipy.io.loadmat(os.path.join(path, 'olivettifaces.mat'))['faces'].T
    np.random.seed(seed=seed)
    index = np.random.permutation(faces.shape[0])
    X = faces[index[:num_training],:]
    Xtest = faces[index[num_training:],:]
    Y = y[index[:num_training],:]
    Ytest = y[index[num_training:]]
    return data_details_return({'X': X, 'Y': Y, 'Xtest': Xtest, 'Ytest': Ytest, 'seed' : seed, 'info': "ORL Faces with labels identifiying who is wearing glasses and who isn't. Data is randomly partitioned according to given seed. Presence or absence of glasses was labelled by James Hensman."}, 'olivetti_faces')
    
def olivetti_faces(data_set='olivetti_faces'):
    path = os.path.join(data_path, data_set)
    if not data_available(data_set):
        download_data(data_set)
        zip = zipfile.ZipFile(os.path.join(path, 'att_faces.zip'), 'r')
        for name in zip.namelist():
            zip.extract(name, path)
    Y = []
    lbls = []
    for subject in range(40):
        for image in range(10):
            image_path = os.path.join(path, 'orl_faces', 's'+str(subject+1), str(image+1) + '.pgm')
            Y.append(GPy.util.netpbmfile.imread(image_path).flatten())
            lbls.append(subject)
    Y = np.asarray(Y)
    lbls = np.asarray(lbls)[:, None]
    return data_details_return({'Y': Y, 'lbls' : lbls, 'info': "ORL Faces processed to 64x64 images."}, data_set)

def xw_pen(data_set='xw_pen'):
    if not data_available(data_set):
        download_data(data_set)
    Y = np.loadtxt(os.path.join(data_path, data_set, 'xw_pen_15.csv'), delimiter=',')
    X = np.arange(485)[:, None]
    return data_details_return({'Y': Y, 'X': X, 'info': "Tilt data from a personalized digital assistant pen. Plot in original paper showed regression between time steps 175 and 275."}, data_set)


def download_rogers_girolami_data(data_set='rogers_girolami_data'):
    if not data_available('rogers_girolami_data'):
        download_data(data_set)
        path = os.path.join(data_path, data_set)
        tar_file = os.path.join(path, 'firstcoursemldata.tar.gz')
        tar = tarfile.open(tar_file)
        print('Extracting file.')
        tar.extractall(path=path)
        tar.close()

def olympic_100m_men(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['male100']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Olympic sprint times for 100 m men from 1896 until 2008. Example is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_100m_women(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['female100']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Olympic sprint times for 100 m women from 1896 until 2008. Example is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_200m_women(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['female200']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Olympic 200 m winning times for women from 1896 until 2008. Data is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_200m_men(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['male200']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Male 200 m winning times for women from 1896 until 2008. Data is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_400m_women(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['female400']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Olympic 400 m winning times for women until 2008. Data is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_400m_men(data_set='rogers_girolami_data'):
    download_rogers_girolami_data()
    olympic_data = scipy.io.loadmat(os.path.join(data_path, data_set, 'data', 'olympics.mat'))['male400']

    X = olympic_data[:, 0][:, None]
    Y = olympic_data[:, 1][:, None]
    return data_details_return({'X': X, 'Y': Y, 'info': "Male 400 m winning times for women until 2008. Data is from Rogers and Girolami's First Course in Machine Learning."}, data_set)

def olympic_marathon_men(data_set='olympic_marathon_men'):
    if not data_available(data_set):
        download_data(data_set)
    olympics = np.genfromtxt(os.path.join(data_path, data_set, 'olympicMarathonTimes.csv'), delimiter=',')
    X = olympics[:, 0:1]
    Y = olympics[:, 1:2]
    return data_details_return({'X': X, 'Y': Y}, data_set)

def olympic_sprints(data_set='rogers_girolami_data'):
    """All olympics sprint winning times for multiple output prediction."""
    X = np.zeros((0, 2))
    Y = np.zeros((0, 1))
    for i, dataset in enumerate([olympic_100m_men,
                              olympic_100m_women,
                              olympic_200m_men,
                              olympic_200m_women,
                              olympic_400m_men,
                              olympic_400m_women]):
        data = dataset()
        year = data['X']
        time = data['Y']
        X = np.vstack((X, np.hstack((year, np.ones_like(year)*i))))
        Y = np.vstack((Y, time))
    data['X'] = X
    data['Y'] = Y
    data['info'] = "Olympics sprint event winning for men and women to 2008. Data is from Rogers and Girolami's First Course in Machine Learning."
    return data_details_return({
        'X': X,
        'Y': Y,
        'info': "Olympics sprint event winning for men and women to 2008. Data is from Rogers and Girolami's First Course in Machine Learning.",
        'output_info': {
          0:'100m Men',
          1:'100m Women',
          2:'200m Men',
          3:'200m Women',
          4:'400m Men',
          5:'400m Women'}
        }, data_set)

# def movielens_small(partNo=1,seed=default_seed):
#     np.random.seed(seed=seed)

#     fileName = os.path.join(data_path, 'movielens', 'small', 'u' + str(partNo) + '.base')
#     fid = open(fileName)
#     uTrain = np.fromfile(fid, sep='\t', dtype=np.int16).reshape((-1, 4))
#     fid.close()
#     maxVals = np.amax(uTrain, axis=0)
#     numUsers = maxVals[0]
#     numFilms = maxVals[1]
#     numRatings = uTrain.shape[0]

#     Y = scipy.sparse.lil_matrix((numFilms, numUsers), dtype=np.int8)
#     for i in range(numUsers):
#         ind = pb.mlab.find(uTrain[:, 0]==i+1)
#         Y[uTrain[ind, 1]-1, i] = uTrain[ind, 2]

#     fileName = os.path.join(data_path, 'movielens', 'small', 'u' + str(partNo) + '.test')
#     fid = open(fileName)
#     uTest = np.fromfile(fid, sep='\t', dtype=np.int16).reshape((-1, 4))
#     fid.close()
#     numTestRatings = uTest.shape[0]

#     Ytest = scipy.sparse.lil_matrix((numFilms, numUsers), dtype=np.int8)
#     for i in range(numUsers):
#         ind = pb.mlab.find(uTest[:, 0]==i+1)
#         Ytest[uTest[ind, 1]-1, i] = uTest[ind, 2]

#     lbls = np.empty((1,1))
#     lblstest = np.empty((1,1))
#     return {'Y':Y, 'lbls':lbls, 'Ytest':Ytest, 'lblstest':lblstest}


def crescent_data(num_data=200, seed=default_seed):
    """
Data set formed from a mixture of four Gaussians. In each class two of the Gaussians are elongated at right angles to each other and offset to form an approximation to the crescent data that is popular in semi-supervised learning as a toy problem.

    :param num_data_part: number of data to be sampled (default is 200).
    :type num_data: int
    :param seed: random seed to be used for data generation.
    :type seed: int

    """
    np.random.seed(seed=seed)
    sqrt2 = np.sqrt(2)
    # Rotation matrix
    R = np.array([[sqrt2 / 2, -sqrt2 / 2], [sqrt2 / 2, sqrt2 / 2]])
    # Scaling matrices
    scales = []
    scales.append(np.array([[3, 0], [0, 1]]))
    scales.append(np.array([[3, 0], [0, 1]]))
    scales.append([[1, 0], [0, 3]])
    scales.append([[1, 0], [0, 3]])
    means = []
    means.append(np.array([4, 4]))
    means.append(np.array([0, 4]))
    means.append(np.array([-4, -4]))
    means.append(np.array([0, -4]))

    Xparts = []
    num_data_part = []
    num_data_total = 0
    for i in range(0, 4):
        num_data_part.append(round(((i + 1) * num_data) / 4.))
        num_data_part[i] -= num_data_total
        part = np.random.normal(size=(num_data_part[i], 2))
        part = np.dot(np.dot(part, scales[i]), R) + means[i]
        Xparts.append(part)
        num_data_total += num_data_part[i]
    X = np.vstack((Xparts[0], Xparts[1], Xparts[2], Xparts[3]))

    Y = np.vstack((np.ones((num_data_part[0] + num_data_part[1], 1)), -np.ones((num_data_part[2] + num_data_part[3], 1))))
    return {'X':X, 'Y':Y, 'info': "Two separate classes of data formed approximately in the shape of two crescents."}

def creep_data(data_set='creep_rupture'):
    """Brun and Yoshida's metal creep rupture data."""
    if not data_available(data_set):
        download_data(data_set)
        path = os.path.join(data_path, data_set)
        tar_file = os.path.join(path, 'creeprupt.tar')
        tar = tarfile.open(tar_file)
        print('Extracting file.')
        tar.extractall(path=path)
        tar.close()
    all_data = np.loadtxt(os.path.join(data_path, data_set, 'taka'))
    y = all_data[:, 1:2].copy()
    features = [0]
    features.extend(range(2, 31))
    X = all_data[:, features].copy()
    return data_details_return({'X': X, 'y': y}, data_set)

def cmu_mocap_49_balance(data_set='cmu_mocap'):
    """Load CMU subject 49's one legged balancing motion that was used by Alvarez, Luengo and Lawrence at AISTATS 2009."""
    train_motions = ['18', '19']
    test_motions = ['20']
    data = cmu_mocap('49', train_motions, test_motions, sample_every=4, data_set=data_set)
    data['info'] = "One legged balancing motions from CMU data base subject 49. As used in Alvarez, Luengo and Lawrence at AISTATS 2009. It consists of " + data['info']
    return data

def cmu_mocap_35_walk_jog(data_set='cmu_mocap'):
    """Load CMU subject 35's walking and jogging motions, the same data that was used by Taylor, Roweis and Hinton at NIPS 2007. but without their preprocessing. Also used by Lawrence at AISTATS 2007."""
    train_motions = ['01', '02', '03', '04', '05', '06',
                '07', '08', '09', '10', '11', '12',
                '13', '14', '15', '16', '17', '19',
                '20', '21', '22', '23', '24', '25',
                '26', '28', '30', '31', '32', '33', '34']
    test_motions = ['18', '29']
    data = cmu_mocap('35', train_motions, test_motions, sample_every=4, data_set=data_set)
    data['info'] = "Walk and jog data from CMU data base subject 35. As used in Tayor, Roweis and Hinton at NIPS 2007, but without their pre-processing (i.e. as used by Lawrence at AISTATS 2007). It consists of " + data['info']
    return data

def cmu_mocap(subject, train_motions, test_motions=[], sample_every=4, data_set='cmu_mocap'):
    """Load a given subject's training and test motions from the CMU motion capture data."""
    # Load in subject skeleton.
    subject_dir = os.path.join(data_path, data_set)

    # Make sure the data is downloaded.
    all_motions = train_motions + test_motions
    resource = cmu_urls_files(([subject], [all_motions]))
    data_resources[data_set] = data_resources['cmu_mocap_full'].copy()
    data_resources[data_set]['files'] = resource['files']
    data_resources[data_set]['urls'] = resource['urls']
    if resource['urls']:
        download_data(data_set)

    skel = GPy.util.mocap.acclaim_skeleton(os.path.join(subject_dir, subject + '.asf'))

    # Set up labels for each sequence
    exlbls = np.eye(len(train_motions))

    # Load sequences
    tot_length = 0
    temp_Y = []
    temp_lbls = []
    for i in range(len(train_motions)):
        temp_chan = skel.load_channels(os.path.join(subject_dir, subject + '_' + train_motions[i] + '.amc'))
        temp_Y.append(temp_chan[::sample_every, :])
        temp_lbls.append(np.tile(exlbls[i, :], (temp_Y[i].shape[0], 1)))
        tot_length += temp_Y[i].shape[0]

    Y = np.zeros((tot_length, temp_Y[0].shape[1]))
    lbls = np.zeros((tot_length, temp_lbls[0].shape[1]))

    end_ind = 0
    for i in range(len(temp_Y)):
        start_ind = end_ind
        end_ind += temp_Y[i].shape[0]
        Y[start_ind:end_ind, :] = temp_Y[i]
        lbls[start_ind:end_ind, :] = temp_lbls[i]
    if len(test_motions) > 0:
        temp_Ytest = []
        temp_lblstest = []

        testexlbls = np.eye(len(test_motions))
        tot_test_length = 0
        for i in range(len(test_motions)):
            temp_chan = skel.load_channels(os.path.join(subject_dir, subject + '_' + test_motions[i] + '.amc'))
            temp_Ytest.append(temp_chan[::sample_every, :])
            temp_lblstest.append(np.tile(testexlbls[i, :], (temp_Ytest[i].shape[0], 1)))
            tot_test_length += temp_Ytest[i].shape[0]

        # Load test data
        Ytest = np.zeros((tot_test_length, temp_Ytest[0].shape[1]))
        lblstest = np.zeros((tot_test_length, temp_lblstest[0].shape[1]))

        end_ind = 0
        for i in range(len(temp_Ytest)):
            start_ind = end_ind
            end_ind += temp_Ytest[i].shape[0]
            Ytest[start_ind:end_ind, :] = temp_Ytest[i]
            lblstest[start_ind:end_ind, :] = temp_lblstest[i]
    else:
        Ytest = None
        lblstest = None

    info = 'Subject: ' + subject + '. Training motions: '
    for motion in train_motions:
        info += motion + ', '
    info = info[:-2]
    if len(test_motions) > 0:
        info += '. Test motions: '
        for motion in test_motions:
            info += motion + ', '
        info = info[:-2] + '.'
    else:
        info += '.'
    if sample_every != 1:
        info += ' Data is sub-sampled to every ' + str(sample_every) + ' frames.'
    return data_details_return({'Y': Y, 'lbls' : lbls, 'Ytest': Ytest, 'lblstest' : lblstest, 'info': info, 'skel': skel}, data_set)