コード例 #1
0
def main(root, pattern='68/*block03/*trial00', frames=10, start=27.5, stop=38.5):
    _, jac = jacobian(root, pattern, frames)
    n = int(np.sqrt(len(jac.columns) / 9))

    pca = lmj.pca.PCA(filename=PCA_FILE)
    for v in (0.5, 0.8, 0.9, 0.95, 0.98, 0.99, 0.995, 0.998, 0.999):
        print('variance', v, 'components', pca.num_components(v))

    if os.path.exists(MODEL):
        dl = pickle.load(open(MODEL, 'rb'))
    else:
        dl = sklearn.decomposition.MiniBatchSparsePCA(
            n_components=100, alpha=0.0001, verbose=10)
        dl.fit(pca.encode(jac.dropna().values, retain=0.999))
        pickle.dump(dl, open(MODEL, 'wb'), -1)

    df = pd.DataFrame(pca.decode(dl.components_, retain=0.999), columns=jac.columns)

    enc = sklearn.decomposition.sparse_encode(
        pca.encode(jac.dropna().loc[start:stop, :], retain=0.999),
        dl.components_,
        algorithm='omp',
        alpha=0.0001,
    )

    kw = dict(vmin=-10, vmax=10, cmap='RdBu')
    lmj.plot.create_axes(111, spines=False).imshow(enc.T, **kw)
    lmj.plot.show()

    enc = sklearn.decomposition.sparse_encode(
        jac.dropna().loc[start:stop, :],
        pca.vecs.T[:len(dl.components_)],
        algorithm='omp',
        alpha=0.0001,
    )

    kw = dict(vmin=-10, vmax=10, cmap='RdBu')
    lmj.plot.create_axes(111, spines=False).imshow(enc.T, **kw)
    lmj.plot.show()

    def find(i, g, b):
        cs = [c for c in jac.columns if '{}/'.format(g) in c and c.endswith(b)]
        return df[cs].loc[i, :].values.reshape((n, n))

    def plot(where, i, g, b):
        ax = lmj.plot.create_axes(where, spines=False)
        ax.imshow(find(i, g, b), cmap='RdBu')

    for i in range(10):
        plot(331, i, 'x', 'x')
        plot(332, i, 'x', 'y')
        plot(333, i, 'x', 'z')
        plot(334, i, 'y', 'x')
        plot(335, i, 'y', 'y')
        plot(336, i, 'y', 'z')
        plot(337, i, 'z', 'x')
        plot(338, i, 'z', 'y')
        plot(339, i, 'z', 'z')
        lmj.plot.gcf().subplots_adjust(left=0, right=1, bottom=0, top=1, wspace=0, hspace=0)
        lmj.plot.show()
コード例 #2
0
def fill(dfs, rank, window):
    '''Complete missing marker data using linear interpolation.

    This method alters the given `dfs` in-place.

    Parameters
    ----------
    dfs : list of pd.DataFrame
        Frames of source data. The frames will be stacked into a single large
        frame and interpolated linearly, either in the data space or (if rank is
        not None) in principal component space.
    rank : float
        Number of principal components (if >1) or fraction of variance (if in
        (0, 1)) to retain in the encoded data.
    window : int
        Model windows of this many consecutive frames.
    '''
    df = lmj.cubes.fill.stack(dfs, window)
    centers = lmj.cubes.fill.center(df)
    if rank is None:
        prediction, _, _ = lmj.cubes.fill.window(df, window, True)
    else:
        if not 0 < rank < 1:
            rank = int(rank)
        pca = lmj.pca.PCA()
        pos, _, _ = lmj.cubes.fill.window(df, window, None)
        pca.fit(pos)
        enc = pd.DataFrame(pca.encode(pos, retain=rank))
        lin = enc.interpolate().ffill().bfill().values
        prediction = pca.decode(lin, retain=rank)
    lmj.cubes.fill.update(df, prediction, window)
    lmj.cubes.fill.restore(df, centers)
    lmj.cubes.fill.unstack(df, dfs)
コード例 #3
0
def fill(dfs, rank, window):
    """Complete missing marker data using linear interpolation.

    This method alters the given `dfs` in-place.

    Parameters
    ----------
    dfs : list of pd.DataFrame
        Frames of source data. The frames will be stacked into a single large
        frame and interpolated linearly, either in the data space or (if rank is
        not None) in principal component space.
    rank : float
        Number of principal components (if >1) or fraction of variance (if in
        (0, 1)) to retain in the encoded data.
    window : int
        Model windows of this many consecutive frames.
    """
    df = lmj.cubes.fill.stack(dfs, window)
    centers = lmj.cubes.fill.center(df)
    if rank is None:
        prediction, _, _ = lmj.cubes.fill.window(df, window, True)
    else:
        if not 0 < rank < 1:
            rank = int(rank)
        pca = lmj.pca.PCA()
        pos, _, _ = lmj.cubes.fill.window(df, window, None)
        pca.fit(pos)
        enc = pd.DataFrame(pca.encode(pos, retain=rank))
        lin = enc.interpolate().ffill().bfill().values
        prediction = pca.decode(lin, retain=rank)
    lmj.cubes.fill.update(df, prediction, window)
    lmj.cubes.fill.restore(df, centers)
    lmj.cubes.fill.unstack(df, dfs)
コード例 #4
0
def main(root,
         pattern='68/*block03/*trial00',
         frames=10,
         start=27.5,
         stop=38.5):
    _, jac = jacobian(root, pattern, frames)
    n = int(np.sqrt(len(jac.columns) / 9))

    pca = lmj.pca.PCA(filename=PCA_FILE)
    for v in (0.5, 0.8, 0.9, 0.95, 0.98, 0.99, 0.995, 0.998, 0.999):
        print('variance', v, 'components', pca.num_components(v))

    if os.path.exists(MODEL):
        dl = pickle.load(open(MODEL, 'rb'))
    else:
        dl = sklearn.decomposition.MiniBatchSparsePCA(n_components=100,
                                                      alpha=0.0001,
                                                      verbose=10)
        dl.fit(pca.encode(jac.dropna().values, retain=0.999))
        pickle.dump(dl, open(MODEL, 'wb'), -1)

    df = pd.DataFrame(pca.decode(dl.components_, retain=0.999),
                      columns=jac.columns)

    enc = sklearn.decomposition.sparse_encode(
        pca.encode(jac.dropna().loc[start:stop, :], retain=0.999),
        dl.components_,
        algorithm='omp',
        alpha=0.0001,
    )

    kw = dict(vmin=-10, vmax=10, cmap='RdBu')
    lmj.plot.create_axes(111, spines=False).imshow(enc.T, **kw)
    lmj.plot.show()

    enc = sklearn.decomposition.sparse_encode(
        jac.dropna().loc[start:stop, :],
        pca.vecs.T[:len(dl.components_)],
        algorithm='omp',
        alpha=0.0001,
    )

    kw = dict(vmin=-10, vmax=10, cmap='RdBu')
    lmj.plot.create_axes(111, spines=False).imshow(enc.T, **kw)
    lmj.plot.show()

    def find(i, g, b):
        cs = [c for c in jac.columns if '{}/'.format(g) in c and c.endswith(b)]
        return df[cs].loc[i, :].values.reshape((n, n))

    def plot(where, i, g, b):
        ax = lmj.plot.create_axes(where, spines=False)
        ax.imshow(find(i, g, b), cmap='RdBu')

    for i in range(10):
        plot(331, i, 'x', 'x')
        plot(332, i, 'x', 'y')
        plot(333, i, 'x', 'z')
        plot(334, i, 'y', 'x')
        plot(335, i, 'y', 'y')
        plot(336, i, 'y', 'z')
        plot(337, i, 'z', 'x')
        plot(338, i, 'z', 'y')
        plot(339, i, 'z', 'z')
        lmj.plot.gcf().subplots_adjust(left=0,
                                       right=1,
                                       bottom=0,
                                       top=1,
                                       wspace=0,
                                       hspace=0)
        lmj.plot.show()