Sphere and swissroll with noise = 0.01

%matplotlib inline

# Not really required
import sys
sys.path.insert(0, '../../..')

from pyLDLE2 import datasets
from pyLDLE2 import buml_, util_

matplotlib.get_backend() =  module://matplotlib_inline.backend_inline

save_dir_root = '../data/pyLDLE2/sphere_and_swissoll/'

X, labelsMat, ddX = datasets.Datasets().sphere_and_swissroll()

X.shape =  (5000, 3)
X.shape =  (5207, 3)
X.shape =  (10207, 3)

# The supplied options would override the default options
buml_obj = buml_.BUML(local_opts={'algo':'LDLE'},
                      intermed_opts={'algo':'best', 'eta_min': 5},
                      vis_opts={'c': labelsMat[:,0], 'save_dir': save_dir_root},
                      verbose=True, debug=True)

local_opts['k_nn0'] = 700 is created.
Options provided:
local_opts:
{
    "Atilde_method": "LDLE_1",
    "N": 100,
    "U_method": "k_nn",
    "algo": "LDLE",
    "alpha": 1,
    "debug": true,
    "delta": 0.9,
    "gl_type": "unnorm",
    "k": 28,
    "k_nn": 49,
    "k_nn0": 700,
    "k_tune": 7,
    "lambda1_decay": 0.75,
    "lambda1_init": 8,
    "lambda1_min": 0.001,
    "max_iter": 300,
    "max_sparsity": 0.9,
    "metric": "euclidean",
    "n_proc": 32,
    "p": 0.99,
    "power": 5,
    "pp_n_thresh": 32,
    "radius": 0.5,
    "reg": 0.0,
    "scale_by": "gamma",
    "tau": 50,
    "to_postprocess": true,
    "verbose": true
}
intermed_opts:
{
    "algo": "best",
    "debug": true,
    "eta_max": 25,
    "eta_min": 5,
    "len_S_thresh": 256,
    "local_algo": "LDLE",
    "metric": "euclidean",
    "n_proc": 32,
    "n_times": 4,
    "verbose": true
}
global_opts:
{
    "add_dim": false,
    "align_transform": "rigid",
    "align_w_parent_only": true,
    "alpha": 0.3,
    "beta": {
        "align": null,
        "repel": 1
    },
    "color_tear": true,
    "compute_error": false,
    "debug": true,
    "eps": 1e-08,
    "err_tol": 0.0001,
    "far_off_points_type": "reuse_fixed",
    "init_algo_name": "procrustes",
    "k": 28,
    "max_internal_iter": 100,
    "max_iter": 20,
    "metric": "euclidean",
    "n_proc": 32,
    "n_repel": 0,
    "nu": 3,
    "patience": 5,
    "refine_algo_name": "rgd",
    "repel_by": 0.0,
    "to_tear": true,
    "verbose": true,
    "vis_before_init": false
}

buml_obj.fit(X=X)

Computing local views using LDLE
Constructing unnorm graph Laplacian + its eigendecomposition.
Done.
##############################
Time elapsed from last time log: 3.8 seconds
Total time elapsed: 3.8 seconds
##############################
Computing Atilde: Inner Prod of Grad of EigFuncs.
FEM for Atilde.
Atilde: 0 points processed...
Atilde: 2551 points processed...
Atilde: 5102 points processed...
Atilde: 7653 points processed...
Atilde: 10204 points processed...
Atilde: all points processed...
Done.
##############################
Time elapsed from last time log: 0.7 seconds
Total time elapsed: 4.6 seconds
##############################
Computing LDLE.
local_param: all 10207 points processed...
max distortion is 1201.183123
Done.
##############################
Time elapsed from last time log: 1.7 seconds
Total time elapsed: 6.3 seconds
##############################
Posprocessing local parameterizations.
#Param replaced: 9688, max distortion: 116.956648
#Param replaced: 4868, max distortion: 69.101870
#Param replaced: 1902, max distortion: 69.101870
#Param replaced: 963, max distortion: 69.101870
#Param replaced: 721, max distortion: 63.102186
#Param replaced: 436, max distortion: 63.102186
#Param replaced: 112, max distortion: 63.102186
#Param replaced: 46, max distortion: 63.102186
#Param replaced: 10, max distortion: 63.102186
#Param replaced: 8, max distortion: 63.102186
#Param replaced: 9, max distortion: 63.102186
#Param replaced: 0, max distortion: 63.102186
Max local distortion after postprocessing: 63.10218619922525
Done.
##############################
Time elapsed from last time log: 9.3 seconds
Total time elapsed: 15.6 seconds
##############################
Max local distortion = 63.10218619922525
Constructing intermediate views.
eta = 2.
#non-empty views with sz < 2 = 10207
#nodes in views with sz < 2 = 10207
Costs computed when eta = 2.
##############################
Time elapsed from last time log: 9.7 seconds
Total time elapsed: 10.6 seconds
##############################
ctr=7794, total_len_S=50233, avg_len_S=6.445
Remaining #nodes in views with sz < 2 = 0
Done with eta = 2.
##############################
Time elapsed from last time log: 163.3 seconds
Total time elapsed: 173.9 seconds
##############################
eta = 3.
#non-empty views with sz < 3 = 642
#nodes in views with sz < 3 = 1284
Costs computed when eta = 3.
##############################
Time elapsed from last time log: 1.9 seconds
Total time elapsed: 175.8 seconds
##############################
ctr=1103, total_len_S=20221, avg_len_S=18.333
Remaining #nodes in views with sz < 3 = 0
Done with eta = 3.
##############################
Time elapsed from last time log: 11.8 seconds
Total time elapsed: 187.6 seconds
##############################
eta = 4.
#non-empty views with sz < 4 = 429
#nodes in views with sz < 4 = 1287
Costs computed when eta = 4.
##############################
Time elapsed from last time log: 1.8 seconds
Total time elapsed: 189.4 seconds
##############################
ctr=1147, total_len_S=30453, avg_len_S=26.550
Remaining #nodes in views with sz < 4 = 0
Done with eta = 4.
##############################
Time elapsed from last time log: 16.1 seconds
Total time elapsed: 205.5 seconds
##############################
eta = 5.
#non-empty views with sz < 5 = 322
#nodes in views with sz < 5 = 1288
Costs computed when eta = 5.
##############################
Time elapsed from last time log: 1.7 seconds
Total time elapsed: 207.2 seconds
##############################
ctr=1122, total_len_S=37592, avg_len_S=33.504
Remaining #nodes in views with sz < 5 = 0
Done with eta = 5.
##############################
Time elapsed from last time log: 20.6 seconds
Total time elapsed: 227.8 seconds
##############################
Pruning and cleaning up.
Done.
##############################
Time elapsed from last time log: 0.9 seconds
Total time elapsed: 228.8 seconds
##############################
After clustering, max distortion is 92.094365
Using rigid transforms for alignment.
Computing laterations scores for overlaps b/w intermed views
Done
##############################
Time elapsed from last time log: 1.7 seconds
Total time elapsed: 1.7 seconds
##############################
Computing a lateration.
Seq of intermediate views and their predecessors computed.
No. of connected components = 2
Multiple connected components detected
Done.
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 1.8 seconds
##############################
Computing initial embedding using: procrustes algorithm
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 1.8 seconds
##############################
Initial alignment of 303 views completed
Initial alignment of 303 views completed
Initial alignment of 606 views completed
Embedding initialized.
##############################
Time elapsed from last time log: 1.0 seconds
Total time elapsed: 2.8 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 0
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 10.3 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.9 seconds
Total time elapsed: 18.2 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 1
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 23.2 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.8 seconds
Total time elapsed: 31.1 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 2
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 35.2 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.7 seconds
Total time elapsed: 42.9 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 3
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 47.3 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.7 seconds
Total time elapsed: 55.0 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 4
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 59.2 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.8 seconds
Total time elapsed: 67.0 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 5
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 71.7 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.0 seconds
Total time elapsed: 79.7 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 6
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 83.7 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.3 seconds
Total time elapsed: 91.9 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 7
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 96.3 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.9 seconds
Total time elapsed: 104.2 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 8
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 109.4 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.2 seconds
Total time elapsed: 117.6 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 9
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 121.5 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 9.7 seconds
Total time elapsed: 131.2 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 10
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 135.2 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.4 seconds
Total time elapsed: 143.5 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 11
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 148.4 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.9 seconds
Total time elapsed: 156.2 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 12
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 161.3 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.8 seconds
Total time elapsed: 169.1 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 13
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 172.9 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 9.9 seconds
Total time elapsed: 182.8 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 14
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 186.6 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.1 seconds
Total time elapsed: 194.7 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 15
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 199.9 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.9 seconds
Total time elapsed: 207.8 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 16
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 212.5 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.2 seconds
Total time elapsed: 220.7 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 17
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 224.6 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 9.3 seconds
Total time elapsed: 233.9 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 18
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 238.3 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 8.5 seconds
Total time elapsed: 246.8 seconds
##############################

Refining with rgd algorithm for 100 iterations.
Refinement iteration: 19
##############################
Time elapsed from last time log: 0.0 seconds
Total time elapsed: 251.1 seconds
##############################
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Descent starts
Done.
##############################
Time elapsed from last time log: 7.8 seconds
Total time elapsed: 258.9 seconds
##############################
Computing error.
min and max weights: 1.0 1.0
Computing Pseudoinverse of a matrix of L of size 10207 + 1213 multiplied with B
Computing svd
Done
Alignment error: 15.493539
##############################
Time elapsed from last time log: 5.1 seconds
Total time elapsed: 263.9 seconds
##############################

array([[-0.24955428, -0.23055957],
       [-0.24665172, -0.24239243],
       [-0.26277892, -0.23021224],
       ...,
       [ 2.13479731,  0.30073441],
       [ 2.14975114,  0.29813219],
       [ 2.13405762,  0.27891651]])

buml_obj.GlobalViews.vis_embedding(buml_obj.GlobalViews.y_final, buml_obj.vis, buml_obj.vis_opts,
                                   buml_obj.GlobalViews.color_of_pts_on_tear_final,
                                   title='Final global embedding', )

util_.save(save_dir_root, 'ldle.dat', [X, labelsMat, buml_obj])