def add_tree():
# construct the matrices to be used for the eigendecomposition
lfdo = ProofDecoration.tree_string_to_LFDO(g_tree_string)
lfdi = ProofDecoration.LFDO_to_LFDI(lfdo)
# we need the ordered ids themselves to to construct the edges
tree = NewickIO.parse(g_tree_string, FelTree.NewickTree)
ordered_ids = ProofDecoration.tree_to_leaf_first_ids(tree)
index_edges = get_index_edges(tree, ordered_ids)
# define the points
X, Y, Z = get_grant_proposal_points_b(lfdi)
# draw the image
draw_3d_tree(X, Y, Z, index_edges)
draw_crossings(X, Y, Z, index_edges)
def add_tree():
# construct the matrices to be used for the eigendecomposition
lfdo = ProofDecoration.tree_string_to_LFDO(g_tree_string)
lfdi = ProofDecoration.LFDO_to_LFDI(lfdo)
# we need the ordered ids themselves to to construct the edges
tree = NewickIO.parse(g_tree_string, FelTree.NewickTree)
ordered_ids = ProofDecoration.tree_to_leaf_first_ids(tree)
index_edges = get_index_edges(tree, ordered_ids)
# define the points
X, Y, Z = get_grant_proposal_points_b(lfdi)
# draw the image
draw_3d_tree(X, Y, Z, index_edges)
draw_crossings(X, Y, Z, index_edges)
def get_grant_proposal_points_b(lfdi):
M, p, q = lfdi.M, lfdi.p, lfdi.q
G = -.5 * M
GQ, GX, GXT, GP = ProofDecoration.get_corners(G, q, p)
# Get the eigendecomposition of the leaf-only Gower matrix.
ws, vs = EigUtil.eigh(GQ)
S = np.diag(ws)
U = np.vstack(vs).T
USUT = np.dot(np.dot(U, S), U.T)
if not np.allclose(USUT, GQ):
raise ValueError('eigenfail')
S_sqrt = np.diag(np.sqrt(ws))
X = np.dot(U, S_sqrt)
# Find the imputed internal points.
S_sqrt_pinv = np.linalg.pinv(S_sqrt)
#W = np.dot(np.dot(S_sqrt_pinv, GX.T), U)
try:
W = np.dot(np.dot(GX.T, U), S_sqrt_pinv)
except ValueError as e:
arr = [GX.shape, U.shape, S_sqrt_pinv.shape]
raise ValueError(', '.join(str(x) for x in arr))
# put them together and get only the first coordinates
full_points = np.vstack([X, W])
X = full_points.T[0]
Y = full_points.T[1]
Z = full_points.T[2]
return X, Y, Z
def get_response_content(fs):
# define the requested physical size of the images (in pixels)
physical_size = (640, 480)
# construct the matrices to be used for the eigendecomposition
lfdo = ProofDecoration.tree_string_to_LFDO(fs.tree_string)
lfdi = ProofDecoration.LFDO_to_LFDI(lfdo)
# we need the ordered ids themselves to to construct the edges
tree = NewickIO.parse(fs.tree_string, FelTree.NewickTree)
ordered_ids = ProofDecoration.tree_to_leaf_first_ids(tree)
index_edges = get_index_edges(tree, ordered_ids)
# define the points
points = get_grant_proposal_points_b(lfdi)
# draw the image
ext = Form.g_imageformat_to_ext[fs.imageformat]
return get_animation_frame(ext, physical_size, fs.scale, index_edges,
points)
def get_grant_proposal_points_b(lfdi):
M, p, q = lfdi.M, lfdi.p, lfdi.q
G = -.5 * M
GQ, GX, GXT, GP = ProofDecoration.get_corners(G, q, p)
# Get the eigendecomposition of the leaf-only Gower matrix.
ws, vs = EigUtil.eigh(GQ)
S = np.diag(ws)
U = np.vstack(vs).T
USUT = np.dot(np.dot(U, S), U.T)
if not np.allclose(USUT, GQ):
raise ValueError('eigenfail')
S_sqrt = np.diag(np.sqrt(ws))
X = np.dot(U, S_sqrt)
# Find the imputed internal points.
S_sqrt_pinv = np.linalg.pinv(S_sqrt)
#W = np.dot(np.dot(S_sqrt_pinv, GX.T), U)
try:
W = np.dot(np.dot(GX.T, U), S_sqrt_pinv)
except ValueError as e:
arr = [
GX.shape,
U.shape,
S_sqrt_pinv.shape]
msg = ', '.join(str(x) for x in arr)
raise ValueError(msg)
# put them together and get only the first coordinates
full_points = np.vstack([X, W])
points = full_points.T[:2].T
return points
def get_response_content(fs):
# define the requested physical size of the images (in pixels)
physical_size = (640, 480)
# construct the matrices to be used for the eigendecomposition
lfdo = ProofDecoration.tree_string_to_LFDO(fs.tree_string)
lfdi = ProofDecoration.LFDO_to_LFDI(lfdo)
# we need the ordered ids themselves to to construct the edges
tree = NewickIO.parse(fs.tree_string, FelTree.NewickTree)
ordered_ids = ProofDecoration.tree_to_leaf_first_ids(tree)
index_edges = get_index_edges(tree, ordered_ids)
# define the points
points = get_grant_proposal_points_b(lfdi)
# draw the image
ext = Form.g_imageformat_to_ext[fs.imageformat]
return get_animation_frame(ext, physical_size, fs.scale,
index_edges, points)
