def test_tga_check_list():
# Test that the projection by TGA on list data is correct
X = [[1.0, 0.0], [0.0, 1.0]]
X_transformed = TGA(n_components=1,
random_state=0).fit(X).transform(X)
assert_equal(X_transformed.shape, (2, 1))
assert_almost_equal(X_transformed.mean(), 0.00, 2)
assert_almost_equal(X_transformed.std(), 0.71, 2)
def test_tga_inverse():
# Test that the projection of data can be inverted
rng = np.random.RandomState(0)
n, p = 50, 3
X = rng.randn(n, p) # spherical data
X[:, 1] *= .00001 # make middle component relatively small
X += [5, 4, 3] # make a large mean
# same check that we can find the original data from the transformed
# signal (since the data is almost of rank n_components)
tga = TGA(n_components=2).fit(X)
Y = tga.transform(X)
Y_inverse = tga.inverse_transform(Y)
assert_almost_equal(X, Y_inverse, decimal=3)
ax.cla()
ax.imshow(img.reshape(shape), cmap="gray", interpolation="nearest")
ax.set_xticklabels([])
ax.set_yticklabels([])
if __name__ == "__main__":
import sys
import glob
import matplotlib.pyplot as pl
use_data = str(sys.argv[1])
M, shape = bitmap_to_mat(glob.glob(use_data + "/*.bmp")[:2000:2])
print(M.shape)
tga = TGA(n_components=5, random_state=1)
start_time = time.time()
tga.fit(M)
print("fitted, time taken {0}s".format(time.time() - start_time))
start_time = time.time()
transformed = tga.transform(M)
L = tga.inverse_transform(transformed)
print('calculated L, time taken {0}s'.format(time.time() - start_time))
S = M - L
if not os.path.exists('results_tga'):
os.makedirs('results_tga')
directory = "results_tga/" + use_data
if not os.path.exists(directory):
os.makedirs(directory)
def test_tga_median():
# TGA on dense arrays
tga = TGA(n_components=2, random_state=1, centering='median')
X = iris.data
X_r = tga.fit(X).transform(X)
assert_equal(X_r.shape[1], 2)
tga = TGA(n_components=2, random_state=1, centering='median')
X_r2 = tga.fit_transform(X)
assert_array_almost_equal(X_r, X_r2)
tga = TGA(random_state=1, centering='median')
tga.fit(X)
X_r = tga.transform(X)
tga = TGA(random_state=1, centering='median')
X_r2 = tga.fit_transform(X)
assert_array_almost_equal(X_r, X_r2)
def test_pca_error():
X = [[0, 1], [1, 0]]
for n_components in [-1, 3]:
assert_raises(ValueError, TGA(n_components).fit, X)
for trim_p in [-0.1, 0.6]:
assert_raises(ValueError, TGA(trim_proportion=trim_p).fit, X)
assert_raises(ValueError, TGA(centering='invalid').fit, X)
def test_tga_dim():
# Check automated dimensionality setting
rng = np.random.RandomState(0)
n, p = 100, 5
X = rng.randn(n, p) * .1
tga = TGA().fit(X)
assert_equal(tga.components_.shape[0], 5)
def test_tga_check_projection():
# Test that the projection by RandomizedPCA on dense data is correct
rng = np.random.RandomState(0)
n, p = 100, 3
X = rng.randn(n, p) * .1
X[:10] += np.array([3, 4, 5])
Xt = 0.1 * rng.randn(1, p) + np.array([3, 4, 5])
Yt = TGA(n_components=2, random_state=0).fit(X).transform(Xt)
Yt /= np.sqrt((Yt ** 2).sum())
assert_almost_equal(np.abs(Yt[0][0]), 1., 1)
'sepnmf':
lambda args: NimfaWrapper(nimfa.SepNMF, args.dims),
'spca':
lambda args: SparsePCA(
n_components=args.dims, n_jobs=args.njobs, normalize_components=True),
'spca-batch':
lambda args: MiniBatchSparsePCA(
n_components=args.dims, n_jobs=args.njobs, normalize_components=True),
'spectral':
lambda args: SpectralEmbedding(n_components=args.dims, n_jobs=args.njobs),
'snmf':
lambda args: NimfaWrapper(nimfa.Snmf, args.dims),
'srp':
lambda args: SparseRandomProjection(n_components=args.dims),
'tga':
lambda args: TGA(n_components=args.dims)
if TGA_AVAILABLE else _embedding_error(),
'tsvd':
lambda args: TruncatedSVD(n_components=args.dims),
'tsne':
lambda args: TSNE(n_components=args.dims),
'umap':
lambda args: umap.UMAP(n_components=args.dims)
if UMAP_AVAILABLE else _embedding_error(),
'vpac':
lambda args: VpacWrapper(args.dims)
if VPAC_AVAILABLE else _embedding_error(),
'vasc':
lambda args: VascWrapper(args.dims)
if VPAC_AVAILABLE else _embedding_error(),
'zifa':