コード例 #1
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def regresswithpca(data, modelfile, regressmode):
    """Perform univariate regression,
    followed by principal components analysis
    to reduce dimensionality

    :param data: RDD of data points as key value pairs
    :param modelfile: model parameters (string with file location, array, or tuple)
    :param regressmode: form of regression ("linear" or "bilinear")

    :return stats: statistics of the fit
    :return comps: compoents from PCA
    :return scores: scores from PCA
    :return latent: latent variances from PCA
    """
    # create model
    model = RegressionModel.load(modelfile, regressmode)

    # do regression
    betas, stats, resid = model.fit(data)

    # do principal components analysis
    scores, latent, comps = svd(betas, 2)

    # compute trajectories from raw data
    traj = model.fit(data, comps)

    return stats, comps, latent, scores, traj
コード例 #2
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ファイル: tuning.py プロジェクト: CheMcCandless/thunder
def tuning(data, tuningmodelfile, tuningmode, regressmodelfile=None, regressmode=None):
    """Estimate parameters of a tuning curve model,
    optionally preceeded by regression

    :param data: RDD of data points as key value pairs
    :param tuningmodelfile: model parameters for tuning (string with file location, array, or tuple)
    :param: tuningmode: form of tuning ("gaussian" or "circular")
    :param regressmodelfile: model parameters for regression (default=None)
    :param regressmode: form of regression ("linear" or "bilinear") (default=None)

    :return params: tuning curve parameters
    """
    # create tuning model
    tuningmodel = TuningModel.load(tuningmodelfile, tuningmode)

    # get tuning curves
    if regressmodelfile is not None:
        # use regression results
        regressmodel = RegressionModel.load(regressmodelfile, regressmode)
        betas, stats, resid = regressmodel.fit(data)
        params = tuningmodel.fit(betas)
    else:
        # use data
        params = tuningmodel.fit(data)

    return params
コード例 #3
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ファイル: tuning.py プロジェクト: arunesh-mittal/thunder
def tuning(data,
           tuningmodelfile,
           tuningmode,
           regressmodelfile=None,
           regressmode=None):
    """Estimate parameters of a tuning curve model,
    optionally preceeded by regression

    :param data: RDD of data points as key value pairs
    :param tuningmodelfile: model parameters for tuning (string with file location, array, or tuple)
    :param: tuningmode: form of tuning ("gaussian" or "circular")
    :param regressmodelfile: model parameters for regression (default=None)
    :param regressmode: form of regression ("linear" or "bilinear") (default=None)

    :return params: tuning curve parameters
    """
    # create tuning model
    tuningmodel = TuningModel.load(tuningmodelfile, tuningmode)

    # get tuning curves
    if regressmodelfile is not None:
        # use regression results
        regressmodel = RegressionModel.load(regressmodelfile, regressmode)
        betas, stats, resid = regressmodel.fit(data)
        params = tuningmodel.fit(betas)
    else:
        # use data
        params = tuningmodel.fit(data)

    return params
コード例 #4
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ファイル: regress.py プロジェクト: fairymane/thunder
def regress(data, modelfile, regressmode):
    """perform mass univariate regression,
    followed by principal components analysis
    to reduce dimensionality

    arguments:
    data - RDD of data points
    modelfile - model parameters (string with file location, array, or tuple)
    regressmode - form of regression ("linear" or "bilinear")

    returns:
    stats - statistics of the fit
    comps, latent, scores, traj - results of principal components analysis
    """
    # create model
    model = RegressionModel.load(modelfile, regressmode)

    # do regression
    betas, stats, resid = model.fit(data)

    # do principal components analysis
    scores, latent, comps = svd(betas, 2)

    # compute trajectories from raw data
    traj = model.fit(data, comps)

    return stats, comps, latent, scores, traj
コード例 #5
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ファイル: tuning.py プロジェクト: errord/thunder
def tuning(data, tuningmodelfile, tuningmode, regressmodelfile=None, regressmode=None):
    """estimate parameters of a tuning curve model,
    optionally preceeded by regression

    arguments:
    data - RDD of data points
    tuningmodelfile - model parameters (string with file location, array, or tuple)
    tuningmode - form of tuning ("gaussian" or "circular")
    regressmodelfile - model parameters (default=None)
    regressmode - form of regression ("linear" or "bilinear") (default=None)

    returns:
    params - tuning curve parameters
    """
    # create tuning model
    tuningmodel = TuningModel.load(tuningmodelfile, tuningmode)

    # get tuning curves
    if regressmodelfile is not None:
        # use regression results
        regressmodel = RegressionModel.load(regressmodelfile, regressmode)
        betas, stats, resid = regressmodel.fit(data)
        params = tuningmodel.fit(betas)
    else:
        # use data
        params = tuningmodel.fit(data)

    return params
コード例 #6
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def regresswithpca(data, modelfile, regressmode, k=2):
    """Perform univariate regression,
    followed by principal components analysis
    to reduce dimensionality

    :param data: RDD of data points as key value pairs
    :param modelfile: model parameters (string with file location, array, or tuple)
    :param regressmode: form of regression ("linear" or "bilinear")
    :param k: number of principal components to compute

    :return stats: statistics of the fit
    :return comps: compoents from PCA
    :return scores: scores from PCA
    :return latent: latent variances from PCA
    """
    # create model
    model = RegressionModel.load(modelfile, regressmode)

    # do regression
    betas, stats, resid = model.fit(data)

    # do principal components analysis
    scores, latent, comps = svd(betas, k)

    # compute trajectories from raw data
    traj = model.fit(data, comps)

    return stats, comps, latent, scores, traj
コード例 #7
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 def test_blinear_regress(self):
     data = self.sc.parallelize([(1, array([1.5, 2.3, 6.2, 5.1, 3.4,
                                            2.1]))])
     x1 = array([array([1, 0, 1, 0, 1, 0]), array([0, 1, 0, 1, 0, 1])])
     x2 = array([
         array([1, 1, 0, 0, 0, 0]),
         array([0, 0, 1, 1, 0, 0]),
         array([0, 0, 0, 0, 1, 1])
     ])
     model = RegressionModel.load((x1, x2), "bilinear")
     betas, stats, resid = model.fit(data)
     tol = 1E-4  # to handle rounding errors
     assert (allclose(betas.map(lambda (_, v): v).collect()[0],
                      array([-3.1249, 5.6875, 0.4375]),
                      atol=tol))
コード例 #8
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    def test_linear_regress(self):
        data = self.sc.parallelize([(1, array([1.5, 2.3, 6.2, 5.1, 3.4, 2.1]))])
        x = array([array([1, 0, 0, 0, 0, 0]), array([0, 1, 0, 0, 0, 0])])
        model = RegressionModel.load(x, "linear")
        betas, stats, resid = model.fit(data)
        assert allclose(betas.map(lambda (_, v): v).collect()[0], array([-2.7, -1.9]))
        assert allclose(stats.map(lambda (_, v): v).collect()[0], array([0.42785299]))
        assert allclose(resid.map(lambda (_, v): v).collect()[0], array([0, 0, 2, 0.9, -0.8, -2.1]))

        stats, betas = regress(data, x, "linear")
        stats.collect()
        betas.collect()

        stats, comps, latent, scores, traj = regresswithpca(data, x, "linear")
        stats.collect()
        scores.collect()
コード例 #9
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ファイル: regress.py プロジェクト: arunesh-mittal/thunder
def regress(data, modelfile, regressmode):
    """Perform mass univariate regression

    :param data: RDD of data points as key value pairs
    :param modelfile: model parameters (string with file location, array, or tuple)
    :param regressmode: form of regression ("linear" or "bilinear")

    :return stats: statistics of the fit
    :return betas: regression coefficients
    """
    # create model
    model = RegressionModel.load(modelfile, regressmode)

    # do regression
    betas, stats, resid = model.fit(data)

    return stats, betas
コード例 #10
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ファイル: regress.py プロジェクト: arunesh-mittal/thunder
def regress(data, modelfile, regressmode):
    """Perform mass univariate regression

    :param data: RDD of data points as key value pairs
    :param modelfile: model parameters (string with file location, array, or tuple)
    :param regressmode: form of regression ("linear" or "bilinear")

    :return stats: statistics of the fit
    :return betas: regression coefficients
    """
    # create model
    model = RegressionModel.load(modelfile, regressmode)

    # do regression
    betas, stats, resid = model.fit(data)

    return stats, betas
コード例 #11
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    def test_blinear_regress(self):
        data = self.sc.parallelize([(1, array([1.5, 2.3, 6.2, 5.1, 3.4, 2.1]))])
        x1 = array([array([1, 0, 1, 0, 1, 0]), array([0, 1, 0, 1, 0, 1])])
        x2 = array([array([1, 1, 0, 0, 0, 0]), array([0, 0, 1, 1, 0, 0]), array([0, 0, 0, 0, 1, 1])])
        model = RegressionModel.load((x1, x2), "bilinear")
        betas, stats, resid = model.fit(data)
        tol = 1e-4  # to handle rounding errors
        assert allclose(betas.map(lambda (_, v): v).collect()[0], array([-3.1249, 5.6875, 0.4375]), atol=tol)
        assert allclose(stats.map(lambda (_, v): v).collect()[0], array([0.6735]), tol)
        assert allclose(resid.map(lambda (_, v): v).collect()[0], array([0, -0.8666, 0, 1.9333, 0, -1.0666]), atol=tol)

        stats, betas = regress(data, (x1, x2), "bilinear")
        stats.collect()
        betas.collect()

        stats, comps, latent, scores, traj = regresswithpca(data, (x1, x2), "bilinear")
        stats.collect()
        scores.collect()
コード例 #12
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    def test_linear_regress(self):
        data = self.sc.parallelize([(1, array([1.5, 2.3, 6.2, 5.1, 3.4,
                                               2.1]))])
        x = array([array([1, 0, 0, 0, 0, 0]), array([0, 1, 0, 0, 0, 0])])
        model = RegressionModel.load(x, "linear")
        betas, stats, resid = model.fit(data)
        assert (allclose(
            betas.map(lambda (_, v): v).collect()[0], array([-2.7, -1.9])))
        assert (allclose(
            stats.map(lambda (_, v): v).collect()[0], array([0.42785299])))
        assert (allclose(
            resid.map(lambda (_, v): v).collect()[0],
            array([0, 0, 2, 0.9, -0.8, -2.1])))

        stats, betas = regress(data, x, "linear")
        stats.collect()
        betas.collect()

        stats, comps, latent, scores, traj = regresswithpca(data, x, "linear")
        stats.collect()
        scores.collect()
コード例 #13
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 def runtest(self):
     model = RegressionModel.load(os.path.join(self.modelfile, "linear"), "linear")
     betas, stats, resid = model.fit(self.rdd)
     result = stats.map(lambda (_, v): float16(v)).collect()
     savemat(self.savefile + "tmp.mat", mdict={"tmp": result}, oned_as='column')
コード例 #14
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 def runtest(self):
     model = RegressionModel.load(os.path.join(self.modelfile, "linear"), "linear")
     betas, stats, resid = model.fit(self.rdd)
     stats.count()