Multiparameter simplextree, C++ part. by DavidLapous · Pull Request #976 · GUDHI/gudhi-devel

DavidLapous · 2023-09-28T16:11:45Z

Cpp part of PR #817.
List of changes :

new is_multi_parameter flag in the simplextree's options to deal with filtration values that behave as array-like instead of float-like.
Filtration values are now as const ref to prevent array-like copies
- This implies adding static members for trivial filtrations : null_value and inf_
new member filtration_mutable to have a non-const access to the filtration.
For multiparameter filtrations, deactivated the assign behavior of the insert to prevent unwanted behaviors (and stay 1-critical). The filtration property is no longer maintained.
New array-like structure as Filtration_value, child of std::vector with numpy-like pointwise operations, in Simplex_tree/multi_filtrations/Finitely_critical_multi_filtrations.h
The Simplex_tree/Simplex_tree_multi.h contains the options of a simplextree multi, functions that can convert a 1-parameter simplextree to a multiparameter simplextree and vice versa, aswell as useful functions to push filtration values on a discrete grid (for discrete computations.
I also copied the unit tests of the simplextree to apply them to this new structure.

Feel free to move files/functions if they don't follow Gudhi's standard, or commit if its moral changes.

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/box.h

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/finitely_critical_filtrations.h

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/line.h

src/Simplex_tree/test/simplex_tree_multi_unit_test.cpp

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/finitely_critical_filtrations.h

src/Simplex_tree/include/gudhi/Simplex_tree.h

VincentRouvreau · 2023-09-29T13:25:56Z

src/Simplex_tree/include/gudhi/Simplex_tree.h

    void assign_filtration(Filtration_value GUDHI_CHECK_code(f)) { GUDHI_CHECK(f == 0, "filtration value specified for a complex that does not store them"); }
-    Filtration_value filtration() const { return 0; }
+    const Filtration_value& filtration() const  { return null_value; }
+    static constexpr Filtration_value null_value={};


If we say:

struct MyOptions : Simplex_tree_options_multidimensional_filtration { // is_multi_parameter but not store_filtration static const bool store_filtration = false; }; Simplex_tree<MyOptions> stree;

We are facing the error:

gudhi-devel/src/Simplex_tree/include/gudhi/Simplex_tree.h:165:39: error: the type 'const Filtration_value' {aka 'const Gudhi::multiparameter::multi_filtrations::Finitely_critical_multi_filtration<float>'} of 'constexpr' variable 'Gudhi::Simplex_tree<MyOptions>::Filtration_simplex_base_dummy::null_value' is not literal static constexpr Filtration_value null_value={}; ^~~~~~~~~~

But maybe this error is normal ? I was wondering to see if we should static_assert some error in this weird case.

A static_assert could be a good idea, as the multi parameter tree only differentiate it self from the standard with its filtration values. If store_filtration == false, is_multi_parameter set to true makes no sense. But the problem could also be solved by removing null_value (see Issue #977), then we can just document that is_multi_parameter is ignored if store_filtration == false.

A simple fix is to do a static_assert(!store_filtration || is_multi_parameter). thoughts ?

I guess you meant static_assert(store_filtration || !is_multi_parameter) instead?

hschreiber · 2023-09-29T12:51:39Z

src/Simplex_tree/include/gudhi/Simplex_tree.h

+  static const Filtration_value& filtration(Simplex_handle sh){
    if (sh != null_simplex()) {
      return sh->second.filtration();
    } else {
-      return std::numeric_limits<Filtration_value>::infinity();
+      return inf_;
+    }
+  }
+  static Filtration_value& filtration_mutable(Simplex_handle sh){
+    if (sh != null_simplex()) {
+      return sh->second.filtration();
+    } else {
+      return inf_;


Already from the previous PR:

I am wondering if we could not just keep the version with the non const, as the validity of the filtration in the simplex tree is already responsibility of the user. This would avoid having to find a different name when it does exactly the same thing than filtration(). Or could there be performance issues when using non const references for numerical values (i.e., when the simplex tree is not multi)? If it is the case, an ugly way to solve this would be to return a std::conditional to switch between Filtration_value& and Filtration_value depending on the value of is_multi_parameter.

I don't have a fixed point of view on this. So its only a matter of what's the gudhi style of accessing a filtration value by reference.

If they really do the same thing, I am ok with filtration returning a non-const reference. But I wonder if filtration_mutable actually needs to return infinity for the null simplex. If we decided instead that filtration_mutable only accepts real simplices (GUDHI_CHECK that sh!=null_simplex()), it could make sense for it to be a separate function, and it would let us declare inf_ const.
IIRC (that was a while ago, so I am likely wrong), handling null_simplex was mostly for convenience for the output of persistent cohomology, not some fundamental reason.

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

hschreiber · 2023-09-29T13:02:59Z

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+#ifndef SIMPLEX_TREE_MULTI_H_


Simplex_tree_multi_utilities.h seems more precise and less misleading to me than Simplex_tree_multi.h. What do you think?

I'm not a big fan of the utilities name, but the name can be changed indeed. Let's fix the other issues and we'll decide that once the content of this file is fixed.

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

hschreiber · 2023-09-29T13:25:06Z

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

+		std::vector<int> simplex;
+		for (auto vertex : st_multi.simplex_vertex_range(simplex_handle))
+			simplex.push_back(vertex);
+		typename simplextree_multi::Options::value_type f = dimension >= 0 ? st_multi.filtration(simplex_handle)[dimension] : 0;


What is the use of dimension to possibly be negative?

put every filtration values of st to 0. May be useful to copy a simplextree when we don't care about filtration values.

Ok, I see. You should say this in the description of dimension, now that you added the doc.

hschreiber · 2023-09-29T13:26:00Z

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

+
+
+
+// Turns a multi-parameter simplextree into a 1-parameter simplextree


Should precise that the filtration values are not token over (which makes sense, but still). Could also add, that for the filtration values, linear_projection can be used.

I'm not sure what you mean, each flatten function take into account filtration values.

Huh? You are right, I think I completely missed a line here as I had the feeling that the filtration value was always put to 0. Which would also explain why I didn't understood the role of the dimension.

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/Finitely_critical_filtrations.h

src/Simplex_tree/example/simplex_tree_multi.cpp

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/Finitely_critical_filtrations.h

src/Simplex_tree/include/gudhi/Simplex_tree.h

Co-authored-by: hschreiber <48448038+hschreiber@users.noreply.github.com>

…dLapous/gudhi-devel-multi into Multiparameter-Simplextree-C++-part

src/Simplex_tree/include/gudhi/Simplex_tree.h

VincentRouvreau · 2023-09-29T14:33:45Z

src/Simplex_tree/include/gudhi/Simplex_tree.h

+    Filtration_simplex_base_real() : filt_{} {}
+    void assign_filtration(const Filtration_value& f) { filt_ = f; }
+    const Filtration_value& filtration() const { return filt_; }
+    Filtration_value& filtration() { return filt_; }


TBD, but I am not sure we should add this method.
And if we add it we should add it to the dummy one.

…Finitely_critical_filtrations.h Co-authored-by: hschreiber <48448038+hschreiber@users.noreply.github.com>

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

src/Simplex_tree/concept/FiltrationValue.h

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

…rsistence

…iparameter-Simplextree-C++-part

…istent with the other filtration classes

…rsistence

…iparameter-Simplextree-C++-part

VincentRouvreau reviewed Sep 29, 2023

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include fix

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hschreiber mentioned this pull request Sep 29, 2023

[Simplex tree] empty dummies with if constexpr #977

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fix

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DavidLapous and others added 3 commits September 29, 2023 16:15

Update src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_multi.h

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Co-authored-by: hschreiber <48448038+hschreiber@users.noreply.github.com>

doc

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Merge branch 'Multiparameter-Simplextree-C++-part' of github.com:Davi…

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…dLapous/gudhi-devel-multi into Multiparameter-Simplextree-C++-part

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indentation

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DavidLapous and others added 4 commits September 29, 2023 16:48

Filtration_value concept

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static assert setter for 1parameter sts

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Update src/Simplex_tree/include/gudhi/Simplex_tree/multi_filtrations/…

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…Finitely_critical_filtrations.h Co-authored-by: hschreiber <48448038+hschreiber@users.noreply.github.com>

find coord fix

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DavidLapous and others added 8 commits October 3, 2023 11:01

doc formatting

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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

typo (Thanks Vincent)

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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

inf and nan limits fix part 1

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part 2 nan + inf limits for multi-filtrations

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missing import

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Fix the auto-breakline breakages + remove python ptr interface

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fix numeric_limits with multi filtrations

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test fix

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hschreiber added 4 commits September 8, 2025 17:51

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second update

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third update

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fourth update

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hschreiber marked this pull request as draft September 8, 2025 16:22

hschreiber and others added 25 commits September 10, 2025 21:34

conversion methods

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windows fix?

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Merge remote-tracking branch 'origin/multi_filtrations' into multi_pe…

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…rsistence

more general minus infinity value

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upstream merge

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windows fix?

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typo

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Merge branch 'GUDHI:master' into multi_filtrations

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Merge remote-tracking branch 'origin/multi_filtrations' into multi_pe…

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…rsistence

Merge remote-tracking branch 'hschreiber/multi_persistence' into Mult…

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…iparameter-Simplextree-C++-part

most persistent cycle

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more general build_complex_from_simplex_tree

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Merge branch 'GUDHI:master' into multi_filtrations

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inverts first and second parameter for Degree_rips_filtration

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changes push_to and pull_to of Degree_rips_filtration to be more cons…

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…istent with the other filtration classes

Merge branch 'GUDHI:master' into multi_filtrations

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better bounds for factorize_* in Degree_rips_filtration

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Merge branch 'GUDHI:master' into multi_filtrations

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Merge branch 'GUDHI:master' into multi_filtrations

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change of behaviour for project_onto_grid

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Merge remote-tracking branch 'origin/multi_filtrations' into multi_pe…

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…rsistence

upstream merge

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add copy constructor for Slicer with different templates

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small fixes

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Merge remote-tracking branch 'hschreiber/multi_persistence' into Mult…

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…iparameter-Simplextree-C++-part




		// Turns a multi-parameter simplextree into a 1-parameter simplextree

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