def get_response_content(fs):
flags = get_flags(fs)
nseconds = 5
tm = time.time()
rejected_s = None
nerrors = 0
nchecked = 0
while time.time() < tm + nseconds and not rejected_s:
nchecked += 1
# Sample a Newick tree.
true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
true_s = NewickIO.get_newick_string(true_f)
true_tree = Newick.parse(true_s, Newick.NewickTree)
# Get the leaf and internal vertex ids for the true tree.
internal_ids = set(id(x) for x in true_tree.gen_internal_nodes())
leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(leaf_ids)
# Get the harmonic valuations for all vertices of the tree.
id_to_full_val_list = [
Harmonic.get_harmonic_valuations(true_tree, i)
for i in range(1, nleaves)
]
# Check for small valuations at the leaves.
try:
for id_to_full_val in id_to_full_val_list:
for x in leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise CheckTreeError('the true tree is too symmetric')
except CheckTreeError as e:
nerrors += 1
continue
# Assign the leaf values and assign None to internal values.
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in leaf_ids:
s = -1 if id_to_full_val[x] < 0 else 1
d[x] = s
for x in internal_ids:
d[x] = None
id_to_val_list.append(d)
# Define the topology in a different format.
id_to_adj = get_id_to_adj(true_tree)
# Check the tree for self-compatibility under the given conditions.
id_to_vals = SeekEigenLacing.rec_eigen(id_to_adj, id_to_val_list,
flags)
if not id_to_vals:
rejected_s = true_s
# make the report
out = StringIO()
if rejected_s:
print >> out, 'rejected a true tree:'
print >> out, rejected_s
else:
print >> out, 'no true tree was rejected'
print >> out
print >> out, nchecked, 'trees were sampled total'
print >> out, nerrors, 'trees were too symmetric'
return out.getvalue()
def get_response_content(fs):
flags = get_flags(fs)
nseconds = 5
tm = time.time()
rejected_s = None
nerrors = 0
nchecked = 0
while time.time() < tm + nseconds and not rejected_s:
nchecked += 1
# Sample a Newick tree.
true_f = TreeSampler.sample_tree(fs.nleaves, 0, 1.0)
true_s = NewickIO.get_newick_string(true_f)
true_tree = Newick.parse(true_s, Newick.NewickTree)
# Get the leaf and internal vertex ids for the true tree.
internal_ids = set(id(x) for x in true_tree.gen_internal_nodes())
leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(leaf_ids)
# Get the harmonic valuations for all vertices of the tree.
id_to_full_val_list = [Harmonic.get_harmonic_valuations(
true_tree, i) for i in range(1, nleaves)]
# Check for small valuations at the leaves.
try:
for id_to_full_val in id_to_full_val_list:
for x in leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise CheckTreeError('the true tree is too symmetric')
except CheckTreeError as e:
nerrors += 1
continue
# Assign the leaf values and assign None to internal values.
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in leaf_ids:
s = -1 if id_to_full_val[x] < 0 else 1
d[x] = s
for x in internal_ids:
d[x] = None
id_to_val_list.append(d)
# Define the topology in a different format.
id_to_adj = get_id_to_adj(true_tree)
# Check the tree for self-compatibility under the given conditions.
id_to_vals = SeekEigenLacing.rec_eigen(
id_to_adj, id_to_val_list, flags)
if not id_to_vals:
rejected_s = true_s
# make the report
out = StringIO()
if rejected_s:
print >> out, 'rejected a true tree:'
print >> out, rejected_s
else:
print >> out, 'no true tree was rejected'
print >> out
print >> out, nchecked, 'trees were sampled total'
print >> out, nerrors, 'trees were too symmetric'
return out.getvalue()
def check_tree_pair(true_tree, test_tree, data):
"""
Do this for every pair of sampled trees.
The returned array has three zeros and a one.
The position of the one shows
whether the test tree was accepted or rejected
with respect to the true tree
for the pair of methods.
@param true_tree: a true Newick tree
@param test_tree: a test Newick tree
@param data: keeps some running data about the search
"""
# Get a list of maps from node id to harmonic extension.
true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(true_tree_leaf_ids)
id_to_full_val_list = [
Harmonic.get_harmonic_valuations(true_tree, i)
for i in range(1, nleaves)
]
id_map = get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
test_id_to_adj = get_id_to_adj(test_tree)
test_id_to_name = get_id_to_name(test_tree)
# Get the list of id to val maps with respect to leaf ids of the test tree.
test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
# Fill out the acceptance pair.
acceptance_pair = []
for i, flags in enumerate((data.flags_a, data.flags_b)):
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in true_tree_leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise CheckTreeError('the true tree is too symmetric')
elif value < 0:
s = -1
else:
s = 1
d[id_map[x]] = s
for x in test_tree_internal_ids:
d[x] = None
id_to_val_list.append(d)
id_to_vals = SeekEigenLacing.rec_eigen(test_id_to_adj, id_to_val_list,
flags)
acceptance_pair.append(1 if id_to_vals else 0)
data.add_acceptances(acceptance_pair)
found_example = acceptance_pair[0] != acceptance_pair[1]
if found_example and (data.report is None):
s = StringIO()
print >> s, 'true tree:'
print >> s, true_tree.get_newick_string()
print >> s
print >> s, 'test tree:'
print >> s, test_tree.get_newick_string()
data.report = s.getvalue()
return found_example
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
id_to_v1 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx1)
id_to_v2 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx2)
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_single_tree_image(
tree, (640, 480), ext, id_to_v1, id_to_v2)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
id_to_v1 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx1)
id_to_v2 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx2)
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_single_tree_image(tree, (640, 480), ext,
id_to_v1, id_to_v2)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def check_tree_pair(true_tree, test_tree, data):
"""
Do this for every pair of sampled trees.
The returned array has three zeros and a one.
The position of the one shows
whether the test tree was accepted or rejected
with respect to the true tree
for the pair of methods.
@param true_tree: a true Newick tree
@param test_tree: a test Newick tree
@param data: keeps some running data about the search
"""
# Get a list of maps from node id to harmonic extension.
true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(true_tree_leaf_ids)
id_to_full_val_list = [Harmonic.get_harmonic_valuations(
true_tree, i) for i in range(1, nleaves)]
id_map = get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
test_id_to_adj = get_id_to_adj(test_tree)
test_id_to_name = get_id_to_name(test_tree)
# Get the list of id to val maps with respect to leaf ids of the test tree.
test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
# Fill out the acceptance pair.
acceptance_pair = []
for i, flags in enumerate((data.flags_a, data.flags_b)):
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in true_tree_leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise CheckTreeError('the true tree is too symmetric')
elif value < 0:
s = -1
else:
s = 1
d[id_map[x]] = s
for x in test_tree_internal_ids:
d[x] = None
id_to_val_list.append(d)
id_to_vals = SeekEigenLacing.rec_eigen(
test_id_to_adj, id_to_val_list, flags)
acceptance_pair.append(1 if id_to_vals else 0)
data.add_acceptances(acceptance_pair)
found_example = acceptance_pair[0] != acceptance_pair[1]
if found_example and (data.report is None):
s = StringIO()
print >> s, 'true tree:'
print >> s, true_tree.get_newick_string()
print >> s
print >> s, 'test tree:'
print >> s, test_tree.get_newick_string()
data.report = s.getvalue()
return found_example
def get_response_content(fs):
# Read the newick trees.
true_tree = Newick.parse(fs.true_tree, Newick.NewickTree)
test_tree = Newick.parse(fs.test_tree, Newick.NewickTree)
flags = get_flags(fs)
# Get a list of maps from node id to harmonic extension.
true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(true_tree_leaf_ids)
id_to_full_val_list = [
Harmonic.get_harmonic_valuations(true_tree, i)
for i in range(1, nleaves)
]
id_map = get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
test_id_to_adj = get_id_to_adj(test_tree)
test_id_to_name = get_id_to_name(test_tree)
# Get the list of id to val maps with respect to leaf ids of the test tree.
test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in true_tree_leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise ValueError('the true tree is too symmetric')
elif value < 0:
s = -1
else:
s = 1
d[id_map[x]] = s
for x in test_tree_internal_ids:
d[x] = None
id_to_val_list.append(d)
# Attempt to find a sign assignment.
id_to_vals = SeekEigenLacing.rec_eigen(test_id_to_adj, id_to_val_list,
flags)
# Reorder the leaf and the internal node ids according to name order.
leaf_pair = sorted((test_id_to_name[x], x) for x in test_tree_leaf_ids)
internal_pair = sorted(
(test_id_to_name[x], x) for x in test_tree_internal_ids)
reordered_leaf_ids = zip(*leaf_pair)[1]
reordered_internal_ids = zip(*internal_pair)[1]
# Check for a failure to find a certificate.
if not id_to_vals:
return 'no non-rejection certificate was found'
# Start writing the response.
out = StringIO()
print >> out, 'leaf sign valuations:'
for x in reordered_leaf_ids:
print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
print >> out
print >> out, 'vertex sign compatible internal vertex valuations:'
for x in reordered_internal_ids:
print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
return out.getvalue()
def get_response_content(fs):
# Read the newick trees.
true_tree = Newick.parse(fs.true_tree, Newick.NewickTree)
test_tree = Newick.parse(fs.test_tree, Newick.NewickTree)
flags = get_flags(fs)
# Get a list of maps from node id to harmonic extension.
true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
nleaves = len(true_tree_leaf_ids)
id_to_full_val_list = [Harmonic.get_harmonic_valuations(
true_tree, i) for i in range(1, nleaves)]
id_map = get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
test_id_to_adj = get_id_to_adj(test_tree)
test_id_to_name = get_id_to_name(test_tree)
# Get the list of id to val maps with respect to leaf ids of the test tree.
test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
id_to_val_list = []
for id_to_full_val in id_to_full_val_list:
d = {}
for x in true_tree_leaf_ids:
value = id_to_full_val[x]
if abs(value) < 1e-8:
raise ValueError('the true tree is too symmetric')
elif value < 0:
s = -1
else:
s = 1
d[id_map[x]] = s
for x in test_tree_internal_ids:
d[x] = None
id_to_val_list.append(d)
# Attempt to find a sign assignment.
id_to_vals = SeekEigenLacing.rec_eigen(
test_id_to_adj, id_to_val_list, flags)
# Reorder the leaf and the internal node ids according to name order.
leaf_pair = sorted(
(test_id_to_name[x], x) for x in test_tree_leaf_ids)
internal_pair = sorted(
(test_id_to_name[x], x) for x in test_tree_internal_ids)
reordered_leaf_ids = zip(*leaf_pair)[1]
reordered_internal_ids = zip(*internal_pair)[1]
# Check for a failure to find a certificate.
if not id_to_vals:
return 'no non-rejection certificate was found'
# Start writing the response.
out = StringIO()
print >> out, 'leaf sign valuations:'
for x in reordered_leaf_ids:
print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
print >> out
print >> out, 'vertex sign compatible internal vertex valuations:'
for x in reordered_internal_ids:
print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
return out.getvalue()
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
valuations = [Harmonic.get_harmonic_valuations(
tree, i) for i in range(fs.first_index, fs.last_index+1)]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_forest_image(
tree, (640, 480), ext, valuations,
fs.draw_background, fs.draw_vertices, fs.draw_labels)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# read the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
# get ids
leaf_ids = [id(x) for x in tree.gen_tips()]
internal_ids = [id(x) for x in tree.gen_internal_nodes()]
nleaves = len(leaf_ids)
ninternal = len(internal_ids)
# get map from id to name
id_to_name = get_id_to_name(tree)
# Reorder the leaf and the internal node ids according to name order.
leaf_pair = sorted(
(id_to_name[x], x) for x in leaf_ids)
internal_pair = sorted(
(id_to_name[x], x) for x in internal_ids)
leaf_ids = zip(*leaf_pair)[1]
internal_ids = zip(*internal_pair)[1]
# compute the harmonic extensions
id_to_val_list = []
eigenvalues = []
for i in range(nleaves-1):
index = i+1
w, d = Harmonic.get_eigenvalue_and_harmonic_valuations(tree, index)
id_to_val_list.append(d)
eigenvalues.append(w)
# write the report
out = StringIO()
print >> out, 'valuations:'
print >> out
for i, (w, id_to_val) in enumerate(zip(eigenvalues, id_to_val_list)):
index = i+1
print >> out, index, '(1 is Fiedler)'
print >> out, 'eigenvalue:', w
print >> out, 'leaves:'
for x in leaf_ids:
print >> out, id_to_name[x], id_to_val[x]
print >> out, 'internal vertices:'
for x in internal_ids:
print >> out, id_to_name[x], id_to_val[x]
print >> out
return out.getvalue()
def get_response_content(fs):
# read the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
# get ids
leaf_ids = [id(x) for x in tree.gen_tips()]
internal_ids = [id(x) for x in tree.gen_internal_nodes()]
nleaves = len(leaf_ids)
ninternal = len(internal_ids)
# get map from id to name
id_to_name = get_id_to_name(tree)
# Reorder the leaf and the internal node ids according to name order.
leaf_pair = sorted((id_to_name[x], x) for x in leaf_ids)
internal_pair = sorted((id_to_name[x], x) for x in internal_ids)
leaf_ids = zip(*leaf_pair)[1]
internal_ids = zip(*internal_pair)[1]
# compute the harmonic extensions
id_to_val_list = []
eigenvalues = []
for i in range(nleaves - 1):
index = i + 1
w, d = Harmonic.get_eigenvalue_and_harmonic_valuations(tree, index)
id_to_val_list.append(d)
eigenvalues.append(w)
# write the report
out = StringIO()
print >> out, 'valuations:'
print >> out
for i, (w, id_to_val) in enumerate(zip(eigenvalues, id_to_val_list)):
index = i + 1
print >> out, index, '(1 is Fiedler)'
print >> out, 'eigenvalue:', w
print >> out, 'leaves:'
for x in leaf_ids:
print >> out, id_to_name[x], id_to_val[x]
print >> out, 'internal vertices:'
for x in internal_ids:
print >> out, id_to_name[x], id_to_val[x]
print >> out
return out.getvalue()
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
valuations = [
Harmonic.get_harmonic_valuations(tree, i)
for i in range(fs.first_index, fs.last_index + 1)
]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
physical_size = (fs.width, fs.height)
return DrawEigenLacing.get_forest_image_revised(
tree, physical_size, ext, valuations, fs.draw_background,
fs.draw_labels, fs.inner_margin, fs.outer_margin, fs.reflect_trees)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)