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PD-PGA example #148

Merged
merged 20 commits into from
Sep 4, 2024
Merged

PD-PGA example #148

merged 20 commits into from
Sep 4, 2024

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MatPont
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@MatPont MatPont commented Apr 20, 2023

This PR adds the example for PD-PGA. It reproduces the figure 11 of the reference below:

Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)
Mathieu Pont, Jules Vidal, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2023.
https://arxiv.org/pdf/2207.10960.pdf

Here is a screenshot of the result on my desktop and laptop.
Screenshot from 2023-04-20 16-55-10

@julien-tierny
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Screenshot_20230421_174208

... snap...
the pink cluster is different on my system :(

@julien-tierny
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julien-tierny commented Apr 22, 2023

with my laptop, it looks closer to your screenshot:
Screenshot_20230422_061518
but still, in the 2D planar view, it seems that the spheres land in the middle of the quads, not on the vertices like in your screenshot.

@julien-tierny
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Screenshot_20230511_124420

it looks like the situation also improved on the pd-pga front with the projection fix (https://github.com/MatPont/ttk/tree/projFromTableFix)

the points are now correctly snapped on grid points (bottom right view).

for some reason, the dimensionality reduction is still different (especially the pink cluster) although the previous screenshot (without the fix) looked a bit closer to yours... :(

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I confirm I can reproduce your screenshot on my laptop.
I'll try again on my desktop (to confirm the variability or not).

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Screenshot_20230519_125140

it looks like I have the right thing on my desktop too now :)

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now it seems that my home desktop computer shows some variability for this example :(
Screenshot_20230526_160011

@julien-tierny
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on my home desktop, with paraview 5.12, this state file crashes:

julien@hal9000 /data/julien/Pro/git/github/mathieu/ttk-data $ paraview states/persistenceDiagramPGA.pvsm 
[Common]                            ▒▒▒▒▒▒▒▒▒▒▒▒▒▒░
[Common]                     ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░
[Common]                 ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒
[Common]              ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░▒░░░▒▒░░░▒▒▒▒▒▒▒
[Common]           ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░░░░   ░░░░░░░░░░░▒▒▒▒▒▒▒
[Common]         ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░                    ░░░░░░░▒▒▒
[Common]       ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░    ▒▒▒▒▒▒▒▒▒▒▒▒          ░▒▒ ░░▒▒▒
[Common]      ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░   ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░▒▒       ░░▒ ░░▒▒
[Common]     ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░  ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░▒▒    ░░░░▒ ░░▒▒
[Common]    ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░ ▒▒▒▒▒▒▒▒▒▒▒▒▄▓██▓█████▓▄▄░░░▒   ░░░░░░░░░▒
[Common]   ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░  ▒▒▒▒▒▒▒▒▒▓▓▓▀▀▀▀▀▀▀████▓▓▓▓▄░░   ░░░░░▒ ░░▒
[Common]  ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░ ▒▒▒▒▒▒▒▒▒           ░░░▀██▓▓▓▓▓░░    ░░░▒ ░░▒
[Common]  ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░ ▒▒▒▒▒▒                  ░▀██▓▓▓▓░    ░░░░▒ ░░░
[Common]  ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░▒░░ ▒▒▒                     ░░▀▓▓▓▓▒░    ░░░▒░░░▒
[Common]  ▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░ ▒▒                        ░▐▓▓▓▒▒    ░░░░▒ ░░
[Common]  ░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░                         ░░░▐▓▓▒▒▒ ░░░░░▒▒ ░░▒
[Common] ░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░                        ░░░▐▓▒▒▒░░░░░░░▒▒ ░░▒
[Common] ░░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░                   ░░░░░░▐▓▒▒▒░░░░░░░▒▒ ░░
[Common]   ░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░           ░░░░░░▒▒░▓▒▒▒░░░░░░░▒▒▒░░░
[Common]    ░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░░░░░░░░░░░░░ ▓▒▒░░░░░░▒▒▒▒▒░░░
[Common]     ░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░░░░░░▒░░░▓▒▒░▒░░▒▒▒▒▒▒▒░░░
[Common]      ░░▒▒▒▒▒▒▒▒▒▒▒▒▓▓▓▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░ ▓▒░ ▒▒▒▒▒▒▒▒▒▒▒░░▒
[Common]       ▒░░░▒▒▒▒▒▒▒▒▒▒▓▓▓▓▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░ ▒▒  ▒▒▒▒▒▒▒▒▒▒▒░░░
[Common]       ░░░░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░ ▒▒   ▒▒▒▒▒▒▒▒▒▒▒░░░
[Common]        ░░░░░░░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░░▒     ▒▒▒▒▒▒▒▒▒▒▒░░░
[Common]          ▒░░░░░░░░░░▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒░░░░░ ░       ░▒▒▒▒▒▒▒▒▒▒░░░
[Common]           ░░░░░░░░░░░░░░░░░░░░░░░░░░░            ▒▒▒▒▒▒▒▒▒▒░░░
[Common]             ░▒░░░░░░░░░░                       ▒▒▒▒▒▒▒▒▒▒░░░
[Common]               ░▒░░░░░░░░░░░░░░░░░░░░░░░░░░░░ ░▒▒▒▒▒▒▒▒░░░░
[Common]                  ░░▒░░░░░░░░░░░░░░░░░░░░░░░▒▒▒▒▒▒▒▒░░░░
[Common]                       ░░▒░░░░░░░░░░░░░░░▒▒▒▒▒▒░░░░░
[Common]                               ░░░░░░░░░░░░░▒░
[Common]  _____ _____ _  __                   __  __    ____   ___ ____  _  _
[Common] |_   _|_   _| |/ /                  / /__\ \  |___ \ / _ \___ \| || |
[Common]   | |   | | | ' /                  | |/ __| |   __) | | | |__) | || |_
[Common]   | |   | | | . \                  | | (__| |  / __/| |_| / __/|__   _|
[Common]   |_|   |_| |_|\_\                 | |\___| | |_____|\___/_____|  |_|
[Common]                                     \_\  /_/
[Common] Welcome!
^[[B[CinemaReader] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[CinemaReader] Database    : Isabel.cdb
[CinemaReader] FILE Columns: FILE      
[CinemaReader] =================================================================
[CinemaReader] Reading CSV file .................................. [0.001s|100%]
[CinemaReader] -----------------------------------------------------------------
[CinemaReader] Complete (#rows: 12) .............................. [0.001s|100%]
[CinemaReader] =================================================================
[CinemaProductReader] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[CinemaProductReader] #Files     : 12  
[CinemaProductReader] FILE Column: FILE
[CinemaProductReader] ==========================================================
[CinemaProductReader] Reading (1/12): "isabel_02.vti" ............ [0.003s|100%]
[CinemaProductReader] Reading (2/12): "isabel_03.vti" ............ [0.003s|100%]
[CinemaProductReader] Reading (3/12): "isabel_04.vti" ............ [0.002s|100%]
[CinemaProductReader] Reading (4/12): "isabel_05.vti" ............ [0.002s|100%]
[CinemaProductReader] Reading (5/12): "isabel_30.vti" ............ [0.002s|100%]
[CinemaProductReader] Reading (6/12): "isabel_31.vti" ............ [0.003s|100%]
[CinemaProductReader] Reading (7/12): "isabel_32.vti" ............ [0.003s|100%]
[CinemaProductReader] Reading (8/12): "isabel_33.vti" ............ [0.002s|100%]
[CinemaProductReader] Reading (9/12): "isabel_45.vti" ............ [0.002s|100%]
[CinemaProductReader] Reading (10/12): "isabel_46.vti" ........... [0.002s|100%]
[CinemaProductReader] Reading (11/12): "isabel_47.vti" ........... [0.003s|100%]
[CinemaProductReader] Reading (12/12): "isabel_48.vti" ........... [0.002s|100%]
[CinemaProductReader] ----------------------------------------------------------
[CinemaProductReader] Complete (#products: 12) ................... [0.031s|100%]
[CinemaProductReader] ==========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.007s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.028s|24T|100%]
[FTMTree] init ............................................... [0.005s|24T|100%]
[FTMTree] sort step .......................................... [0.002s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.018s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.019s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.003s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.003s|24T|100%]
[FTMTree] merge trees  ....................................... [0.025s|24T|100%]
[FTMTree] build tree ......................................... [0.025s|24T|100%]
[FTMTree] Total  ............................................. [0.032s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.087s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.005s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.015s|24T|100%]
[FTMTree] init ............................................... [0.019s|24T|100%]
[FTMTree] sort step .......................................... [0.001s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.016s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.002s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.044s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.002s|24T|100%]
[FTMTree] merge trees  ....................................... [0.049s|24T|100%]
[FTMTree] build tree ......................................... [0.049s|24T|100%]
[FTMTree] Total  ............................................. [0.069s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.092s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.008s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.015s|24T|100%]
[FTMTree] init ............................................... [0.010s|24T|100%]
[FTMTree] sort step .......................................... [0.001s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.010s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.003s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.039s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.002s|24T|100%]
[FTMTree] merge trees  ....................................... [0.045s|24T|100%]
[FTMTree] build tree ......................................... [0.045s|24T|100%]
[FTMTree] Total  ............................................. [0.055s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.077s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.004s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.016s|24T|100%]
[FTMTree] init ............................................... [0.007s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.012s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.004s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.050s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.002s|24T|100%]
[FTMTree] merge trees  ....................................... [0.054s|24T|100%]
[FTMTree] build tree ......................................... [0.054s|24T|100%]
[FTMTree] Total  ............................................. [0.062s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.087s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.010s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.011s|24T|100%]
[FTMTree] init ............................................... [0.007s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.034s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.006s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.040s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMTree] merge trees  ....................................... [0.048s|24T|100%]
[FTMTree] build tree ......................................... [0.048s|24T|100%]
[FTMTree] Total  ............................................. [0.056s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.090s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.004s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.018s|24T|100%]
[FTMTree] init ............................................... [0.002s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.041s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.046s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.004s|24T|100%]
[FTMTree] merge trees  ....................................... [0.053s|24T|100%]
[FTMTree] build tree ......................................... [0.053s|24T|100%]
[FTMTree] Total  ............................................. [0.056s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.094s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.004s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.017s|24T|100%]
[FTMTree] init ............................................... [0.001s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.045s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.047s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.006s|24T|100%]
[FTMTree] merge trees  ....................................... [0.056s|24T|100%]
[FTMTree] build tree ......................................... [0.056s|24T|100%]
[FTMTree] Total  ............................................. [0.057s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.096s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.004s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.017s|24T|100%]
[FTMTree] init ............................................... [0.003s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.041s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.047s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.006s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMTree] merge trees  ....................................... [0.055s|24T|100%]
[FTMTree] build tree ......................................... [0.055s|24T|100%]
[FTMTree] Total  ............................................. [0.058s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.096s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.012s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.018s|24T|100%]
[FTMTree] init ............................................... [0.012s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.045s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.048s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.006s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.008s|24T|100%]
[FTMTree] merge trees  ....................................... [0.058s|24T|100%]
[FTMTree] build tree ......................................... [0.058s|24T|100%]
[FTMTree] Total  ............................................. [0.071s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.128s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.016s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.018s|24T|100%]
[FTMTree] init ............................................... [0.016s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.040s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.044s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.006s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.004s|24T|100%]
[FTMTree] merge trees  ....................................... [0.050s|24T|100%]
[FTMTree] build tree ......................................... [0.050s|24T|100%]
[FTMTree] Total  ............................................. [0.067s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.104s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.004s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.018s|24T|100%]
[FTMTree] init ............................................... [0.002s|24T|100%]
[FTMTree] sort step .......................................... [0.000s|24T|100%]
[FTMTree] leafSearch ......................................... [0.002s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.049s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.051s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.005s|24T|100%]
[FTMTree] merge trees  ....................................... [0.061s|24T|100%]
[FTMTree] build tree ......................................... [0.061s|24T|100%]
[FTMTree] Total  ............................................. [0.063s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.233s|24T|100%]
[PersistenceDiagram] ===========================================================
[PersistenceDiagram] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] No pre-existing order for array:
[PersistenceDiagram] [WARNING]   `velocityMag`.
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] Initializing order array. ............... [0.026s|24T|100%]
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] [WARNING] TIP: run `ttkArrayPreconditioning` first
[PersistenceDiagram] [WARNING] for improved performances :)
[PersistenceDiagram] -----------------------------------------------------------
[PersistenceDiagram] ===========================================================
[FTMTree] ======================================================================
[FTMTree] number of threads : 24
[FTMTree] * debug lvl  : 3
[FTMTree] * tree type  : Join + Split
[FTMTree] ======================================================================
[FTMTree] alloc .............................................. [0.019s|24T|100%]
[FTMTree] init ............................................... [0.053s|24T|100%]
[FTMTree] sort step .......................................... [0.005s|24T|100%]
[FTMTree] leafSearch ......................................... [0.005s|24T|100%]
[FTMtree_MT] leafGrowth JT ................................... [0.045s|24T|100%]
[FTMtree_MT] trunk JT ........................................ [0.005s|24T|100%]
[FTMtree_MT] leafGrowth ST ................................... [0.053s|24T|100%]
[FTMtree_MT] trunk ST ........................................ [0.005s|24T|100%]
[FTMTree] merge trees  ....................................... [0.064s|24T|100%]
[FTMTree] build tree ......................................... [0.064s|24T|100%]
[FTMTree] Total  ............................................. [0.123s|24T|100%]
[PersistenceDiagram] Complete ................................ [0.170s|24T|100%]
[PersistenceDiagram] ===========================================================
[MergeTreePrincipalGeodesics] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeTreePrincipalGeodesics] Computation without normalized Wasserstein.
[MergeTreePrincipalGeodesics] 12 trees average [node: 103 / 207, depth: 1]
[MergeTreePrincipalGeodesics] Preprocessing .................. [0.008s|24T|100%]
[MergeTreePrincipalGeodesics] Barycenter ..................... [0.436s|24T|100%]
[MergeTreePrincipalGeodesics] tree [node: 245 / 490, depth: 1]
[MergeTreePrincipalGeodesics] ==================================================
[MergeTreePrincipalGeodesics] Compute geodesic 0
[MergeTreePrincipalGeodesics] Init ........................... [0.047s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 0
[MergeTreePrincipalGeodesics] Assignment ..................... [0.377s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 193.272
[MergeTreePrincipalGeodesics] Prop. cost  = 2.01948e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.374s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 1
[MergeTreePrincipalGeodesics] Assignment ..................... [0.382s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 151.869
[MergeTreePrincipalGeodesics] Prop. cost  = 2.90806e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.0871173
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.434s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 2
[MergeTreePrincipalGeodesics] Assignment ..................... [0.384s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 143.192
[MergeTreePrincipalGeodesics] Prop. cost  = 0
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.771735
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.396s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 3
[MergeTreePrincipalGeodesics] Assignment ..................... [0.393s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 147.701
[MergeTreePrincipalGeodesics] Prop. cost  = 5.16988e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.00910098
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.404s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 4
[MergeTreePrincipalGeodesics] Assignment ..................... [0.368s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 142.678
[MergeTreePrincipalGeodesics] Prop. cost  = 3.95819e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.0289967
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.393s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 5
[MergeTreePrincipalGeodesics] Assignment ..................... [0.386s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 140.821
[MergeTreePrincipalGeodesics] Prop. cost  = 8.07794e-28
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.0425623
[MergeTreePrincipalGeodesics] Update ......................... [0.001s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.461s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 6
[MergeTreePrincipalGeodesics] Assignment ..................... [0.391s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 140.273
[MergeTreePrincipalGeodesics] Prop. cost  = 1.16322e-25
[MergeTreePrincipalGeodesics] Ortho. cost = 0
[MergeTreePrincipalGeodesics] Map. cost   = 0.0486549
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Best energy is 140.273224 (iteration 6 / 6)
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Explained T-Variance            : 44.95 %
[MergeTreePrincipalGeodesics] Cumulative explained T-Variance : 44.95 %
[MergeTreePrincipalGeodesics] ==================================================
[MergeTreePrincipalGeodesics] Compute geodesic 1
[MergeTreePrincipalGeodesics] Init ........................... [0.046s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 0
[MergeTreePrincipalGeodesics] Assignment ..................... [0.407s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 103.386
[MergeTreePrincipalGeodesics] Prop. cost  = 2.90806e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 1.29247e-26
[MergeTreePrincipalGeodesics] Map. cost   = 0
[MergeTreePrincipalGeodesics] Update ......................... [0.043s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.339s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 1
[MergeTreePrincipalGeodesics] Assignment ..................... [0.410s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 95.1218
[MergeTreePrincipalGeodesics] Prop. cost  = 3.95819e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 6.54313e-26
[MergeTreePrincipalGeodesics] Map. cost   = 0.0700127
[MergeTreePrincipalGeodesics] Update ......................... [0.042s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.377s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 2
[MergeTreePrincipalGeodesics] Assignment ..................... [0.412s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 92.2288
[MergeTreePrincipalGeodesics] Prop. cost  = 8.07794e-28
[MergeTreePrincipalGeodesics] Ortho. cost = 8.07794e-28
[MergeTreePrincipalGeodesics] Map. cost   = 0.0640617
[MergeTreePrincipalGeodesics] Update ......................... [0.044s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.444s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 3
[MergeTreePrincipalGeodesics] Assignment ..................... [0.425s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 90.607
[MergeTreePrincipalGeodesics] Prop. cost  = 0
[MergeTreePrincipalGeodesics] Ortho. cost = 1.81754e-25
[MergeTreePrincipalGeodesics] Map. cost   = 0.107015
[MergeTreePrincipalGeodesics] Update ......................... [0.042s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.451s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 4
[MergeTreePrincipalGeodesics] Assignment ..................... [0.409s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 89.5898
[MergeTreePrincipalGeodesics] Prop. cost  = 9.7743e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 7.27014e-27
[MergeTreePrincipalGeodesics] Map. cost   = 0.0368838
[MergeTreePrincipalGeodesics] Update ......................... [0.041s|24T|100%]
[MergeTreePrincipalGeodesics] Projection ..................... [0.482s|24T|100%]
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Iteration 5
[MergeTreePrincipalGeodesics] Assignment ..................... [0.421s|24T|100%]
[MergeTreePrincipalGeodesics] Energy      = 89.3241
[MergeTreePrincipalGeodesics] Prop. cost  = 2.90806e-26
[MergeTreePrincipalGeodesics] Ortho. cost = 7.27014e-27
[MergeTreePrincipalGeodesics] Map. cost   = 0.122131
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Best energy is 89.324097 (iteration 5 / 5)
[MergeTreePrincipalGeodesics] --------------------------------------------------
[MergeTreePrincipalGeodesics] Explained T-Variance            : 18.61 %
[MergeTreePrincipalGeodesics] Cumulative explained T-Variance : 63.56 %
[MergeTreePrincipalGeodesics] ==================================================
[MergeTreePrincipalGeodesics] Total time .................... [10.551s|24T|100%]
[MergeTreePrincipalGeodesicsDecoding] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeTreePrincipalGeodesicsDecoding] Load parameters from field data.
[MergeTreePrincipalGeodesicsDecoding]  - epsilon1 = 100.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon2 = 95.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon3 = 90.000000
[MergeTreePrincipalGeodesicsDecoding]  - persistenceThreshold = 2.000000
[MergeTreePrincipalGeodesicsDecoding]  - branchDecomposition = 1.000000
[MergeTreePrincipalGeodesicsDecoding]  - normalizedWasserstein = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - keepSubtree = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - isPersistenceDiagram = 1.000000
[MergeTreePrincipalGeodesicsDecoding]  - deleteMultiPersPairs = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon1UseFarthestSaddle = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - mixtureCoefficient = 0.000000
[MergeTreePrincipalGeodesicsDecoding] Computation without normalized Wasserstein.
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Compute Geodesics Distance...
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Process Input Trees...
[MergeTreePrincipalGeodesicsDecoding] 12 trees average [node: 103 / 207, depth: 1]
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Reconstruct Input Trees...
[MergeTreePrincipalGeodesicsDecoding] 12 trees average [node: 103 / 207, depth: 1]
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Construct Geodesics Trees...
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Make output...
[MergeTreePrincipalGeodesicsDecoding] noInput     = 12
[MergeTreePrincipalGeodesicsDecoding] noReconst   = 12
[MergeTreePrincipalGeodesicsDecoding] noBary      = 1
[MergeTreePrincipalGeodesicsDecoding] noGeod      = 32
[MergeTreePrincipalGeodesicsDecoding] noEllipses  = 0
[MergeTreePrincipalGeodesicsDecoding] noRectangle = 0
[MergeTreePrincipalGeodesicsDecoding] noSurface   = 0
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.007s|24T|100%]
[IcospheresFromPoints] Moving 4 Icospheres (R: 3.700000) ..... [0.008s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.008s|24T|100%]
[IcospheresFromPoints] Moving 6 Icospheres (R: 3.700000) ..... [0.005s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.010s|24T|100%]
[IcospheresFromPoints] Moving 8 Icospheres (R: 3.700000) ..... [0.008s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.011s|24T|100%]
[IcospheresFromPoints] Moving 4 Icospheres (R: 3.700000) ..... [0.007s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.008s|24T|100%]
[IcospheresFromPoints] Moving 6 Icospheres (R: 3.700000) ..... [0.008s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.002s|24T|100%]
[IcospheresFromPoints] Moving 8 Icospheres (R: 3.700000) ..... [0.004s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.002s|24T|100%]
[IcospheresFromPoints] Moving 40 Icospheres (R: 1.850000) .... [0.005s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.003s|24T|100%]
[IcospheresFromPoints] Moving 266 Icospheres (R: 1.850000) ... [0.010s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.007s|24T|100%]
[IcospheresFromPoints] Moving 224 Icospheres (R: 1.850000) ... [0.007s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.008s|24T|100%]
[IcospheresFromPoints] Moving 408 Icospheres (R: 1.850000) ... [0.004s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.005s|24T|100%]
[IcospheresFromPoints] Moving 484 Icospheres (R: 1.850000) ... [0.005s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.006s|24T|100%]
[IcospheresFromPoints] Moving 482 Icospheres (R: 1.850000) ... [0.010s|24T|100%]
[MergeTreePrincipalGeodesicsDecoding] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeTreePrincipalGeodesicsDecoding] Load parameters from field data.
[MergeTreePrincipalGeodesicsDecoding]  - epsilon1 = 100.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon2 = 95.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon3 = 90.000000
[MergeTreePrincipalGeodesicsDecoding]  - persistenceThreshold = 2.000000
[MergeTreePrincipalGeodesicsDecoding]  - branchDecomposition = 1.000000
[MergeTreePrincipalGeodesicsDecoding]  - normalizedWasserstein = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - keepSubtree = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - isPersistenceDiagram = 1.000000
[MergeTreePrincipalGeodesicsDecoding]  - deleteMultiPersPairs = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - epsilon1UseFarthestSaddle = 0.000000
[MergeTreePrincipalGeodesicsDecoding]  - mixtureCoefficient = 0.000000
[MergeTreePrincipalGeodesicsDecoding] Computation without normalized Wasserstein.
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Compute Geodesics Distance...
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Construct Surface Trees...
[MergeTreePrincipalGeodesicsDecoding] ------------------------------------------
[MergeTreePrincipalGeodesicsDecoding] Make output...
[MergeTreePrincipalGeodesicsDecoding] noInput     = 0
[MergeTreePrincipalGeodesicsDecoding] noReconst   = 0
[MergeTreePrincipalGeodesicsDecoding] noBary      = 0
[MergeTreePrincipalGeodesicsDecoding] noGeod      = 0
[MergeTreePrincipalGeodesicsDecoding] noEllipses  = 0
[MergeTreePrincipalGeodesicsDecoding] noRectangle = 0
[MergeTreePrincipalGeodesicsDecoding] noSurface   = 256
[FlattenMultiBlock] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeTreeDistanceMatrix] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeTreeDistanceMatrix] Load parameters from field data.
[MergeTreeDistanceMatrix]  - epsilon1 = 100.000000
[MergeTreeDistanceMatrix]  - epsilon2 = 95.000000
[MergeTreeDistanceMatrix]  - epsilon3 = 90.000000
[MergeTreeDistanceMatrix]  - persistenceThreshold = 2.000000
[MergeTreeDistanceMatrix]  - branchDecomposition = 1.000000
[MergeTreeDistanceMatrix]  - normalizedWasserstein = 0.000000
[MergeTreeDistanceMatrix]  - keepSubtree = 0.000000
[MergeTreeDistanceMatrix]  - isPersistenceDiagram = 1.000000
[MergeTreeDistanceMatrix]  - deleteMultiPersPairs = 0.000000
[MergeTreeDistanceMatrix]  - epsilon1UseFarthestSaddle = 0.000000
[MergeTreeDistanceMatrix]  - mixtureCoefficient = 0.000000
[MergeTreeDistanceMatrix] Computation without normalized Wasserstein.
[MergeTreeDistanceMatrix] BranchDecomposition: 1
[MergeTreeDistanceMatrix] NormalizedWasserstein: 0
[MergeTreeDistanceMatrix] KeepSubtree: 0
[MergeTreeDistanceMatrix] 0 / 256
[MergeTreeDistanceMatrix] 250 / 256
[MergeTreeDistanceMatrix] 25 / 256
[MergeTreeDistanceMatrix] 225 / 256
[MergeTreeDistanceMatrix] 50 / 256
[MergeTreeDistanceMatrix] 75 / 256
[MergeTreeDistanceMatrix] 100 / 256
[MergeTreeDistanceMatrix] 125 / 256
[MergeTreeDistanceMatrix] 200 / 256
[MergeTreeDistanceMatrix] 150 / 256
[MergeTreeDistanceMatrix] 175 / 256
[DimensionReduction] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[DimensionReduction] Using backend `Multi-Dimensional Scaling`
[DimensionReduction] Loading Python script from: /usr/local/scripts/ttk
/usr/lib/python3.11/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/usr/lib/python3.11/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
/usr/lib/python3.11/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/usr/lib/python3.11/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
/usr/lib/python3.11/site-packages/sklearn/manifold/_mds.py:298: FutureWarning: The default value of `normalized_stress` will change to `'auto'` in version 1.4. To suppress this warning, manually set the value of `normalized_stress`.
  warnings.warn(
[DimensionReduction] Computed MDS ............................. [4.864s|1T|100%]
[GeometrySmoother] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[OneSkeleton] Built 705 edges ................................. [0.005s|1T|100%]
[ZeroSkeleton] Built 256 vertex neighbors ..................... [0.000s|1T|100%]
[GeometrySmoother] Smoothed 256 vertices ..................... [0.021s|24T|100%]
[FlattenMultiBlock] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[MergeBlockTables] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[ProjectionFromTable] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.003s|24T|100%]
[IcospheresFromPoints] Moving 1 Icospheres (R: 1.100000) ..... [0.007s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.002s|24T|100%]
[IcospheresFromPoints] Moving 12 Icospheres (R: 1.000000) .... [0.012s|24T|100%]
[IdentifyByScalarField] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IdentifyByScalarField] Computing Identifiers ................. [0.000s|1T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.005s|24T|100%]
[IcospheresFromPoints] Moving 2 Icospheres (R: 0.700000) ..... [0.004s|24T|100%]
[IdentifyByScalarField] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IdentifyByScalarField] Computing Identifiers ................. [0.000s|1T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.002s|24T|100%]
[IcospheresFromPoints] Moving 2 Icospheres (R: 0.700000) ..... [0.004s|24T|100%]
[IcospheresFromPoints] %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[IcospheresFromPoints] Computing Icosphere (S: 2) ............ [0.000s|24T|100%]
[IcospheresFromPoints] Computing Normals ..................... [0.007s|24T|100%]
[IcospheresFromPoints] Moving 256 Icospheres (R: 0.170000) ... [0.025s|24T|100%]
Segmentation fault

@julien-tierny
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julien-tierny commented Apr 23, 2024

(it seems to crash inMergeBlockTables)

@julien-tierny
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julien-tierny commented May 13, 2024

segfault fixed with topology-tool-kit/ttk#1027
(still variability on home desktop)
Screenshot_20240513_064102

@julien-tierny
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Screenshot_20240828_190858

here's the current status!

@MatPont
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MatPont commented Aug 29, 2024

Nice, we have the same screenshot.
I just pushed a commit to fix the surface camera and the arrows, here is what I have now:
Screenshot from 2024-08-29 14-21-55

@julien-tierny
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  • state file OK
  • python script OK
  • documentation OK

@julien-tierny julien-tierny merged commit 23a7469 into topology-tool-kit:dev Sep 4, 2024
@MatPont MatPont deleted the pd-pga branch September 9, 2024 12:46
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2 participants