In [1]:
import pickle
import src.bottleneck as bottleneck
# Load data from pickle file
with open('results/dragon_complexes.pkl', 'rb') as f:
complex_res = pickle.load(f)
for sample_name in list(complex_res.keys()):
sample_complexes = complex_res[sample_name]
print(f"\n{'='*80}")
print(f"BOTTLENECK DISTANCES FOR {sample_name.upper()}")
print(f"{'='*80}")
distances = bottleneck.compute_bottleneck_distances(sample_complexes)
mds_results = bottleneck.compute_mds(distances)
bottleneck.visualize_bottleneck_distances(mds_results, sample_complexes.keys())
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 500 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00679752 0.00679752 0.00679752 0.00679752 0.00679752 0.00679752 0.00679752 cech 0.00679752 0.000 0.00000000 0.00339876 0.00339876 0.00002310 0.00002310 0.00005313 delaunay_cech 0.00679752 0.00000000 0.000 0.00339876 0.00339876 0.00002310 0.00002310 0.00005313 alpha 0.00679752 0.00339876 0.00339876 0.000 0.00000000 0.00339876 0.00339876 0.00339876 delaunay_alpha 0.00679752 0.00339876 0.00339876 0.00000000 0.000 0.00339876 0.00339876 0.00339876 witness 0.00679752 0.00002310 0.00002310 0.00339876 0.00339876 0.000 0.00000000 0.00005313 relaxed_witness 0.00679752 0.00002310 0.00002310 0.00339876 0.00339876 0.00000000 0.000 0.00005313 strong_witness 0.00679752 0.00005313 0.00005313 0.00339876 0.00339876 0.00005313 0.00005313 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf 0.00425640 inf 0.00425640 inf 0.00425640 0.00425640 cech inf 0.000 inf 0.01020214 inf inf inf inf delaunay_cech 0.00425640 inf 0.000 inf 0.00246345 inf 0.00015595 0.00018729 alpha inf 0.01020214 inf 0.000 inf inf inf inf delaunay_alpha 0.00425640 inf 0.00246345 inf 0.000 inf 0.00246345 0.00246345 witness inf inf inf inf inf 0.000 inf inf relaxed_witness 0.00425640 inf 0.00015595 inf 0.00246345 inf 0.000 0.00015603 strong_witness 0.00425640 inf 0.00018729 inf 0.00246345 inf 0.00015603 0.000 Using replacement value for infinity intervals in dimension 1: 0.032675883505129455 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.01021854 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00632185 0.00021858 inf inf alpha inf 0.01021854 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00632185 inf 0.000 0.00632185 inf inf witness inf inf 0.00021858 inf 0.00632185 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 2: 0.03541411138860276
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 1000 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00528380 0.00528380 0.00528380 0.00528380 0.00528380 0.00528380 0.00528380 cech 0.00528380 0.000 0.00000000 0.00264190 0.00264190 0.00001396 0.00001396 0.00002849 delaunay_cech 0.00528380 0.00000000 0.000 0.00264190 0.00264190 0.00001396 0.00001396 0.00002849 alpha 0.00528380 0.00264190 0.00264190 0.000 0.00000000 0.00264190 0.00264190 0.00264190 delaunay_alpha 0.00528380 0.00264190 0.00264190 0.00000000 0.000 0.00264190 0.00264190 0.00264190 witness 0.00528380 0.00001396 0.00001396 0.00264190 0.00264190 0.000 0.00000000 0.00002849 relaxed_witness 0.00528380 0.00001396 0.00001396 0.00264190 0.00264190 0.00000000 0.000 0.00002849 strong_witness 0.00528380 0.00002849 0.00002849 0.00264190 0.00264190 0.00002849 0.00002849 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00760415 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00270284 inf 0.00010490 inf alpha inf 0.00760415 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00270284 inf 0.000 inf 0.00270284 inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf 0.00010490 inf 0.00270284 inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.027238812436306097 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00761862 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00696125 0.00021607 inf inf alpha inf 0.00761862 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00696125 inf 0.000 0.00696125 inf inf witness inf inf 0.00021607 inf 0.00696125 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 0.00009190 strong_witness inf inf inf inf inf inf 0.00009190 0.000 Using replacement value for infinity intervals in dimension 2: 0.033721059177937635
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 1501 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00423837 0.00423837 0.00423837 0.00423837 0.00423837 0.00423837 0.00423837 cech 0.00423837 0.000 0.00000000 0.00211918 0.00211918 0.00000898 0.00000898 0.00002768 delaunay_cech 0.00423837 0.00000000 0.000 0.00211918 0.00211918 0.00000898 0.00000898 0.00002768 alpha 0.00423837 0.00211918 0.00211918 0.000 0.00000000 0.00211918 0.00211918 0.00211918 delaunay_alpha 0.00423837 0.00211918 0.00211918 0.00000000 0.000 0.00211918 0.00211918 0.00211918 witness 0.00423837 0.00000898 0.00000898 0.00211918 0.00211918 0.000 0.00000000 0.00002768 relaxed_witness 0.00423837 0.00000898 0.00000898 0.00211918 0.00211918 0.00000000 0.000 0.00002768 strong_witness 0.00423837 0.00002768 0.00002768 0.00211918 0.00211918 0.00002768 0.00002768 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00614140 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00311728 inf inf inf alpha inf 0.00614140 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00311728 inf 0.000 inf inf inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.02771711829641324 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf 0.01309256 0.01301792 cech inf 0.000 inf 0.00613580 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00721874 0.00021837 inf inf alpha inf 0.00613580 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00721874 inf 0.000 0.00721874 inf inf witness inf inf 0.00021837 inf 0.00721874 0.000 inf inf relaxed_witness 0.01309256 inf inf inf inf inf 0.000 0.00008880 strong_witness 0.01301792 inf inf inf inf inf 0.00008880 0.000 Using replacement value for infinity intervals in dimension 2: 0.03351575254836972
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 2000 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00382158 0.00382158 0.00382158 0.00382158 0.00382158 0.00382158 0.00382158 cech 0.00382158 0.000 0.00000000 0.00191079 0.00191079 0.00000730 0.00000730 0.00002432 delaunay_cech 0.00382158 0.00000000 0.000 0.00191079 0.00191079 0.00000730 0.00000730 0.00002432 alpha 0.00382158 0.00191079 0.00191079 0.000 0.00000000 0.00191079 0.00191079 0.00191079 delaunay_alpha 0.00382158 0.00191079 0.00191079 0.00000000 0.000 0.00191079 0.00191079 0.00191079 witness 0.00382158 0.00000730 0.00000730 0.00191079 0.00191079 0.000 0.00000000 0.00002432 relaxed_witness 0.00382158 0.00000730 0.00000730 0.00191079 0.00191079 0.00000000 0.000 0.00002432 strong_witness 0.00382158 0.00002432 0.00002432 0.00191079 0.00191079 0.00002432 0.00002432 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00549064 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00333262 inf inf inf alpha inf 0.00549064 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00333262 inf 0.000 inf inf inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.025297357823818086 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00548992 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00827169 0.00023280 inf inf alpha inf 0.00548992 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00827169 inf 0.000 0.00827169 inf inf witness inf inf 0.00023280 inf 0.00827169 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 0.00004304 strong_witness inf inf inf inf inf inf 0.00004304 0.000 Using replacement value for infinity intervals in dimension 2: 0.03351575254836972
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 3002 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00302919 0.00302919 0.00302919 0.00302919 0.00302919 0.00302919 0.00302919 cech 0.00302919 0.000 0.00000000 0.00151459 0.00151459 0.00000459 0.00000459 0.00001719 delaunay_cech 0.00302919 0.00000000 0.000 0.00151459 0.00151459 0.00000459 0.00000459 0.00001719 alpha 0.00302919 0.00151459 0.00151459 0.000 0.00000000 0.00151459 0.00151459 0.00151459 delaunay_alpha 0.00302919 0.00151459 0.00151459 0.00000000 0.000 0.00151459 0.00151459 0.00151459 witness 0.00302919 0.00000459 0.00000459 0.00151459 0.00151459 0.000 0.00000000 0.00001719 relaxed_witness 0.00302919 0.00000459 0.00000459 0.00151459 0.00151459 0.00000000 0.000 0.00001719 strong_witness 0.00302919 0.00001719 0.00001719 0.00151459 0.00151459 0.00001719 0.00001719 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00447035 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00315005 inf inf inf alpha inf 0.00447035 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00315005 inf 0.000 inf inf inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.01987790418560008 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf 0.00960040 cech inf 0.000 inf 0.00448437 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00874656 0.00023680 inf inf alpha inf 0.00448437 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00874656 inf 0.000 0.00874656 inf inf witness inf inf 0.00023680 inf 0.00874656 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness 0.00960040 inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 2: 0.03342454617542934
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 3476 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00306256 0.00306256 0.00306256 0.00306256 0.00306256 0.00306256 0.00306256 cech 0.00306256 0.000 0.00000000 0.00153128 0.00153128 0.00000469 0.00000469 0.00001345 delaunay_cech 0.00306256 0.00000000 0.000 0.00153128 0.00153128 0.00000469 0.00000469 0.00001345 alpha 0.00306256 0.00153128 0.00153128 0.000 0.00000000 0.00153128 0.00153128 0.00153128 delaunay_alpha 0.00306256 0.00153128 0.00153128 0.00000000 0.000 0.00153128 0.00153128 0.00153128 witness 0.00306256 0.00000469 0.00000469 0.00153128 0.00153128 0.000 0.00000000 0.00001345 relaxed_witness 0.00306256 0.00000469 0.00000469 0.00153128 0.00153128 0.00000000 0.000 0.00001345 strong_witness 0.00306256 0.00001345 0.00001345 0.00153128 0.00153128 0.00001345 0.00001345 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf 0.00894296 cech inf 0.000 inf 0.00418528 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00305947 inf inf inf alpha inf 0.00418528 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00305947 inf 0.000 inf inf inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness 0.00894296 inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.027581578598318775 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00418471 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00882740 0.00023637 inf inf alpha inf 0.00418471 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00882740 inf 0.000 0.00882740 inf inf witness inf inf 0.00023637 inf 0.00882740 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 2: 0.03332338137116013
================================================================================ BOTTLENECK DISTANCES FOR DRAGON 4000 ================================================================================ Computing dimension 0... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 0.00271259 0.00271259 0.00271259 0.00271259 0.00271259 0.00271259 0.00271259 cech 0.00271259 0.000 0.00000000 0.00135629 0.00135629 0.00000368 0.00000368 0.00001235 delaunay_cech 0.00271259 0.00000000 0.000 0.00135629 0.00135629 0.00000368 0.00000368 0.00001235 alpha 0.00271259 0.00135629 0.00135629 0.000 0.00000000 0.00135629 0.00135629 0.00135629 delaunay_alpha 0.00271259 0.00135629 0.00135629 0.00000000 0.000 0.00135629 0.00135629 0.00135629 witness 0.00271259 0.00000368 0.00000368 0.00135629 0.00135629 0.000 0.00000000 0.00001235 relaxed_witness 0.00271259 0.00000368 0.00000368 0.00135629 0.00135629 0.00000000 0.000 0.00001235 strong_witness 0.00271259 0.00001235 0.00001235 0.00135629 0.00135629 0.00001235 0.00001235 0.000 Computing dimension 1... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00393038 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00335759 inf inf inf alpha inf 0.00393038 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00335759 inf 0.000 inf inf inf witness inf inf inf inf inf 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 1: 0.028151630473491066 Computing dimension 2... Complex rips cech delaunay_cech alpha delaunay_alpha witness relaxed_witness strong_witness --------------------------------------------------------------------------------------------------------------------------------------------------------------------- rips 0.000 inf inf inf inf inf inf inf cech inf 0.000 inf 0.00393086 inf inf inf inf delaunay_cech inf inf 0.000 inf 0.00898840 0.00024000 inf inf alpha inf 0.00393086 inf 0.000 inf inf inf inf delaunay_alpha inf inf 0.00898840 inf 0.000 0.00898840 inf inf witness inf inf 0.00024000 inf 0.00898840 0.000 inf inf relaxed_witness inf inf inf inf inf inf 0.000 inf strong_witness inf inf inf inf inf inf inf 0.000 Using replacement value for infinity intervals in dimension 2: 0.03350828642183624
