def pyquest(data,params):
"""
Runs the questionnaire on data with params.
params is a PyQuestParams object.
"""
if params.init_aff_type == INIT_AFF_COS_SIM:
init_row_aff = affinity.mutual_cosine_similarity(
data.T,False,0,threshold=params.init_aff_threshold)
elif params.init_aff_type == INIT_AFF_GAUSSIAN:
init_row_aff = affinity.gaussian_euclidean(
data.T, params.init_aff_knn, params.init_aff_epsilon)
#Initial row tree
if params.tree_type == TREE_TYPE_BINARY:
init_row_tree = bin_tree_build.bin_tree_build(init_row_aff,'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
init_row_tree = flex_tree_build.flex_tree_diffusion(init_row_aff,
params.tree_constant)
dual_col_trees = []
dual_row_trees = [init_row_tree]
row_tree_descs = ["Initial tree"]
col_tree_descs = []
for i in xrange(params.n_iters):
message = "Iteration {}: calculating column affinity...".format(i)
#print "Beginning iteration {}".format(i)
if params.col_affinity_type == DUAL_EMD:
col_emd = dual_affinity.calc_emd(data,dual_row_trees[-1],
params.col_alpha,params.col_beta)
col_aff = dual_affinity.emd_dual_aff(col_emd)
elif params.col_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
if params.tree_type == TREE_TYPE_BINARY:
col_tree = bin_tree_build.bin_tree_build(col_aff,'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
col_tree = flex_tree_build.flex_tree_diffusion(col_aff,
params.tree_constant)
dual_col_trees.append(col_tree)
col_tree_descs.append("Iteration {}".format(i))
message = "Iteration {}: calculating row affinity...".format(i)
if params.row_affinity_type == DUAL_EMD:
row_emd = dual_affinity.calc_emd(data.T,dual_col_trees[-1],
params.row_alpha,params.row_beta)
row_aff = dual_affinity.emd_dual_aff(row_emd)
elif params.row_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating row tree...".format(i)
if params.tree_type == TREE_TYPE_BINARY:
row_tree = bin_tree_build.bin_tree_build(row_aff,'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
row_tree = flex_tree_build.flex_tree_diffusion(row_aff,
params.tree_constant)
dual_row_trees.append(row_tree)
row_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
return PyQuestRun(quest_run_desc,dual_row_trees,dual_col_trees,
row_tree_descs,col_tree_descs,params)
def pyquest3d(data3d, params):
"""
Runs the 3d questionnaire on data with params.
params is a PyQuest3DParams object.
Order of analysis is initialization for rows and columns
and then iterating over channels (3rd dimension), rows and columns.
"""
nrows, ncols, nchans = data3d.shape
data_Y = np.reshape(data3d, (nrows, ncols * nchans), order='F')
data_X = np.reshape(np.transpose(data3d, (0, 2, 1)),
(nrows * nchans, ncols),
order='F')
if params.init_aff_type == INIT_AFF_COS_SIM:
init_row_aff = affinity.mutual_cosine_similarity(
data_Y.T, False, 0, threshold=params.init_aff_threshold)
init_col_aff = affinity.mutual_cosine_similarity(
data_X, False, 0, threshold=params.init_aff_threshold)
elif params.init_aff_type == INIT_AFF_GAUSSIAN:
init_row_aff = affinity.gaussian_euclidean(data_Y.T,
params.init_aff_knn,
params.init_aff_epsilon)
init_col_aff = affinity.gaussian_euclidean(data_X, params.init_aff_knn,
params.init_aff_epsilon)
#Initial row tree
if params.row_tree_type == TREE_TYPE_BINARY:
init_row_tree = bin_tree_build.bin_tree_build(
init_row_aff, 'r_dyadic', params.row_tree_bal_constant)
elif params.row_tree_type == TREE_TYPE_FLEXIBLE:
init_row_tree = flex_tree_build.flex_tree_diffusion(
init_row_aff, params.row_tree_constant)
# initial column tree
if params.col_tree_type == TREE_TYPE_BINARY:
init_col_tree = bin_tree_build.bin_tree_build(
init_col_aff, 'r_dyadic', params.col_tree_bal_constant)
elif params.col_tree_type == TREE_TYPE_FLEXIBLE:
init_col_tree = flex_tree_build.flex_tree_diffusion(
init_col_aff, params.col_tree_constant)
# data structure for trees. All trees calculated in the process are exported
dual_row_trees = [init_row_tree]
dual_col_trees = [init_col_tree]
dual_chan_trees = []
row_tree_descs = ["Initial tree"]
col_tree_descs = ["Initial tree"]
chan_tree_descs = []
# iterate over the questionnaire starting with channels and then rows and cols in each iteration
for i in xrange(params.n_iters):
message = "Iteration {}: calculating channel affinity...".format(i)
# calculating channel affinity based on row and col trees
#print "Beginning iteration {}".format(i)
if params.chan_affinity_type == DUAL_EMD:
chan_emd2d = dual_affinity.calc_2demd(data3d,
init_row_tree,
init_col_tree,
row_alpha=params.row_alpha,
row_beta=params.row_beta,
col_alpha=params.col_alpha,
col_beta=params.col_beta)
chan_aff = dual_affinity.emd_dual_aff(chan_emd2d)
chan_tree = flex_tree_build.flex_tree_diffusion(
chan_aff, params.chan_tree_constant)
elif params.chan_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
# constructing channel tree
if params.chan_tree_type == TREE_TYPE_BINARY:
chan_tree = bin_tree_build.bin_tree_build(
chan_aff, 'r_dyadic', params.chan_tree_bal_constant)
elif params.chan_tree_type == TREE_TYPE_FLEXIBLE:
chan_tree = flex_tree_build.flex_tree_diffusion(
chan_aff, params.chan_tree_constant)
dual_chan_trees.append(chan_tree)
chan_tree_descs.append("Iteration {}".format(i))
# channel tree finished, now starting with rows
message = "Iteration {}: calculating row affinity...".format(i)
# calculate row affinity based on column and channel trees
if params.row_affinity_type == DUAL_EMD:
row_emd2d = dual_affinity.calc_2demd(np.transpose(
data3d, (1, 2, 0)),
dual_col_trees[-1],
dual_chan_trees[-1],
row_alpha=params.col_alpha,
row_beta=params.col_beta,
col_alpha=params.chan_alpha,
col_beta=params.chan_beta)
row_aff = dual_affinity.emd_dual_aff(row_emd2d)
elif params.row_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating row tree...".format(i)
# constructing row tree
if params.row_tree_type == TREE_TYPE_BINARY:
row_tree = bin_tree_build.bin_tree_build(
row_aff, 'r_dyadic', params.row_tree_bal_constant)
elif params.row_tree_type == TREE_TYPE_FLEXIBLE:
row_tree = flex_tree_build.flex_tree_diffusion(
row_aff, params.row_tree_constant)
dual_row_trees.append(row_tree)
row_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
# calculate column affinity based on row and channel trees
if params.col_affinity_type == DUAL_EMD:
col_emd2d = dual_affinity.calc_2demd(np.transpose(
data3d, (0, 2, 1)),
dual_row_trees[-1],
dual_chan_trees[-1],
row_alpha=params.row_alpha,
row_beta=params.row_beta,
col_alpha=params.chan_alpha,
col_beta=params.chan_beta)
col_aff = dual_affinity.emd_dual_aff(col_emd2d)
elif params.col_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
# constructing column tree
if params.col_tree_type == TREE_TYPE_BINARY:
col_tree = bin_tree_build.bin_tree_build(
col_aff, 'r_dyadic', params.col_tree_bal_constant)
elif params.col_tree_type == TREE_TYPE_FLEXIBLE:
col_tree = flex_tree_build.flex_tree_diffusion(
col_aff, params.col_tree_constant)
dual_col_trees.append(col_tree)
col_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
# iterations have finished, outputting structures of the tree,
# parameters
return PyQuest3DRun(quest_run_desc, dual_row_trees, dual_col_trees,
dual_chan_trees, row_tree_descs, col_tree_descs,
chan_tree_descs, params, init_col_aff, init_row_aff,
row_aff, col_aff, chan_aff)
def pyquest(data,params):
#params should be a PyQuestParams object
Publisher.sendMessage("status.bar", "Calculating initial affinity...")
if params.init_aff_type == INIT_AFF_COS_SIM:
init_row_aff = affinity.mutual_cosine_similarity(
data.T,False,0,threshold=params.init_aff_threshold)
elif params.init_aff_type == INIT_AFF_GAUSSIAN:
#add KNN to the page
init_row_aff = affinity.gaussian_euclidean(
data.T, 5, params.init_aff_epsilon)
#Compute diffusion embedding of initial affinities
init_row_vecs,init_row_vals = markov.markov_eigs(init_row_aff, 12)
init_row_vals[np.isnan(init_row_vals)] = 0.0
row_embedding = init_row_vecs.dot(np.diag(init_row_vals))
row_distances = spsp.distance.squareform(spsp.distance.pdist(row_embedding))
row_affinity = np.max(row_distances) - row_distances
#Generate initial tree
#print "call1 tree_constant:{}".format(tree_constant)
Publisher.sendMessage("status.bar", "Calculating initial row tree...")
if params.tree_type == TREE_TYPE_BINARY:
init_row_tree = bintree_construct.median_tree(
init_row_vecs,init_row_vals,max_levels=12)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
# init_row_tree = tree_building.make_tree_embedding(
# row_affinity,params.tree_constant)
init_row_tree = tree_building.make_tree_embedding(
row_affinity,params.tree_constant)
dual_col_trees = []
dual_row_trees = [init_row_tree]
row_tree_descs = ["Initial tree"]
col_tree_descs = []
for i in xrange(params.n_iters):
message = "Iteration {}: calculating column affinity...".format(i)
Publisher.sendMessage("status.bar", message)
#print "Beginning iteration {}".format(i)
if params.col_affinity_type == DUAL_EMD:
col_emd = dual_affinity.calc_emd(data,dual_row_trees[-1],
params.col_alpha,params.col_beta)
col_aff = dual_affinity.emd_dual_aff(col_emd)
elif params.col_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
Publisher.sendMessage("status.bar", message)
if params.tree_type == TREE_TYPE_BINARY:
col_tree = bintree_construct.eigen_tree(data,dual_row_trees[-1],
params.col_alpha,params.col_beta,params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
col_tree = tree_building.make_tree_embedding(col_aff,
params.tree_constant)
dual_col_trees.append(col_tree)
col_tree_descs.append("Iteration {}".format(i))
message = "Iteration {}: calculating row affinity...".format(i)
Publisher.sendMessage("status.bar", message)
if params.row_affinity_type == DUAL_EMD:
row_emd = dual_affinity.calc_emd(data.T,dual_col_trees[-1],
params.row_alpha,params.row_beta)
row_aff = dual_affinity.emd_dual_aff(row_emd)
elif params.row_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating row tree...".format(i)
Publisher.sendMessage("status.bar", message)
if params.tree_type == TREE_TYPE_BINARY:
row_tree = bintree_construct.eigen_tree(data.T,dual_col_trees[-1],
params.row_alpha,params.row_beta,params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
row_tree = tree_building.make_tree_embedding(row_aff,
params.tree_constant)
dual_row_trees.append(row_tree)
row_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
return PyQuestRun(quest_run_desc,dual_row_trees,dual_col_trees,
row_tree_descs,col_tree_descs,params)
def pyquest(data, params):
"""
Runs the questionnaire on data with params. params is a PyQuestParams object.
Starts by constructing the initial affinity on the rows of the matrix (default).
"""
# construct row affinity
if params.init_aff_type == INIT_AFF_COS_SIM:
init_row_aff = affinity.mutual_cosine_similarity(
data.T, False, 0, threshold=params.init_aff_threshold)
elif params.init_aff_type == INIT_AFF_GAUSSIAN:
init_row_aff = affinity.gaussian_euclidean(data.T, params.init_aff_knn,
params.init_aff_epsilon)
#Initial row tree
if params.row_tree_type == TREE_TYPE_BINARY:
init_row_tree = bin_tree_build.bin_tree_build(
init_row_aff, 'r_dyadic', params.row_tree_bal_constant)
elif params.row_tree_type == TREE_TYPE_FLEXIBLE:
init_row_tree = flex_tree_build.flex_tree_diffusion(
init_row_aff, params.row_tree_constant)
# data structure for trees. All trees calculated in the process are exported
dual_row_trees = [init_row_tree]
dual_col_trees = []
row_tree_descs = ["Initial tree"]
col_tree_descs = []
# iterate over the questionnaire starting with columns and then rows in each iteration
for i in xrange(params.n_iters):
message = "Iteration {}: calculating column affinity...".format(i)
print message
# calculating column affinity based on row tree
#print "Beginning iteration {}".format(i)
if params.col_affinity_type == DUAL_EMD:
if params.col_weighted == True:
print "weighted emd"
row_coefs = tree_util.tree_transform_mat(
dual_row_trees[-1]).dot(data)
row_weights = np.sqrt(np.sum(row_coefs**2, axis=1))
col_emd = dual_affinity.calc_emd(data,
dual_row_trees[-1],
alpha=0,
beta=0,
weights=row_weights)
else:
col_emd = dual_affinity.calc_emd(data, dual_row_trees[-1],
params.col_alpha,
params.col_beta)
col_aff = dual_affinity.emd_dual_aff(col_emd)
elif params.col_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
print message
# constructing column tree
if params.col_tree_type == TREE_TYPE_BINARY:
col_tree = bin_tree_build.bin_tree_build(
col_aff, 'r_dyadic', params.col_tree_bal_constant)
elif params.col_tree_type == TREE_TYPE_FLEXIBLE:
col_tree = flex_tree_build.flex_tree_diffusion(
col_aff, params.col_tree_constant)
dual_col_trees.append(col_tree)
col_tree_descs.append("Iteration {}".format(i))
# column tree finished, now starting with rows
message = "Iteration {}: calculating row affinity...".format(i)
print message
# calculate row affinity based on column tree
if params.row_affinity_type == DUAL_EMD:
if params.row_weighted == True:
print "weighted emd"
col_coefs = tree_util.tree_transform_mat(
dual_col_trees[-1]).dot(data.T)
col_weights = np.sqrt(np.sum(col_coefs**2, axis=1))
row_emd = dual_affinity.calc_emd(data.T,
dual_col_trees[-1],
alpha=0,
beta=0,
weights=col_weights)
else:
row_emd = dual_affinity.calc_emd(data.T, dual_col_trees[-1],
params.row_alpha,
params.row_beta)
row_aff = dual_affinity.emd_dual_aff(row_emd)
elif params.row_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating row tree...".format(i)
print message
# constructing row tree
if params.row_tree_type == TREE_TYPE_BINARY:
row_tree = bin_tree_build.bin_tree_build(
row_aff, 'r_dyadic', params.row_tree_bal_constant)
elif params.row_tree_type == TREE_TYPE_FLEXIBLE:
row_tree = flex_tree_build.flex_tree_diffusion(
row_aff, params.row_tree_constant)
dual_row_trees.append(row_tree)
row_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
# iterations have finished, outputting structures of the tree,
# parameters
return PyQuestRun(quest_run_desc, dual_row_trees, dual_col_trees,
row_tree_descs, col_tree_descs, params)
def pyquest(data, params):
"""
Runs the questionnaire on data with params.
params is a PyQuestParams object.
"""
if params.init_aff_type == INIT_AFF_COS_SIM:
init_row_aff = affinity.mutual_cosine_similarity(
data.T, False, 0, threshold=params.init_aff_threshold)
elif params.init_aff_type == INIT_AFF_GAUSSIAN:
init_row_aff = affinity.gaussian_euclidean(data.T, params.init_aff_knn,
params.init_aff_epsilon)
#Initial row tree
if params.tree_type == TREE_TYPE_BINARY:
init_row_tree = bin_tree_build.bin_tree_build(init_row_aff, 'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
init_row_tree = flex_tree_build.flex_tree_diffusion(
init_row_aff, params.tree_constant)
dual_col_trees = []
dual_row_trees = [init_row_tree]
row_tree_descs = ["Initial tree"]
col_tree_descs = []
for i in xrange(params.n_iters):
message = "Iteration {}: calculating column affinity...".format(i)
#print "Beginning iteration {}".format(i)
if params.col_affinity_type == DUAL_EMD:
col_emd = dual_affinity.calc_emd(data, dual_row_trees[-1],
params.col_alpha, params.col_beta)
col_aff = dual_affinity.emd_dual_aff(col_emd)
elif params.col_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating column tree...".format(i)
if params.tree_type == TREE_TYPE_BINARY:
col_tree = bin_tree_build.bin_tree_build(col_aff, 'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
col_tree = flex_tree_build.flex_tree_diffusion(
col_aff, params.tree_constant)
dual_col_trees.append(col_tree)
col_tree_descs.append("Iteration {}".format(i))
message = "Iteration {}: calculating row affinity...".format(i)
if params.row_affinity_type == DUAL_EMD:
row_emd = dual_affinity.calc_emd(data.T, dual_col_trees[-1],
params.row_alpha, params.row_beta)
row_aff = dual_affinity.emd_dual_aff(row_emd)
elif params.row_affinity_type == DUAL_GAUSSIAN:
print "Gaussian dual affinity not supported at the moment."
return None
message = "Iteration {}: calculating row tree...".format(i)
if params.tree_type == TREE_TYPE_BINARY:
row_tree = bin_tree_build.bin_tree_build(row_aff, 'r_dyadic',
params.tree_bal_constant)
elif params.tree_type == TREE_TYPE_FLEXIBLE:
row_tree = flex_tree_build.flex_tree_diffusion(
row_aff, params.tree_constant)
dual_row_trees.append(row_tree)
row_tree_descs.append("Iteration {}".format(i))
quest_run_desc = "{}".format(datetime.datetime.now())
return PyQuestRun(quest_run_desc, dual_row_trees, dual_col_trees,
row_tree_descs, col_tree_descs, params)
