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Fixed warnings in M2 1.23 per issue #1 #2

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Fixed warnings in M2 1.23 per issue #1 #2

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18 changes: 9 additions & 9 deletions CODE/common.m2
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Original file line number Diff line number Diff line change
Expand Up @@ -384,8 +384,8 @@ leverageScores = M -> (


-- indexes subsystem giving Jacobian rank
rowSelector = method(Options=>{Threshold=>1e-4})
rowSelector Matrix := o -> J0 -> (
rowSelectorPLMP = method(Options=>{Threshold=>1e-4})
rowSelectorPLMP Matrix := o -> J0 -> (
(m , n) := size J0;
J0' := J0^{0}; -- should technically check this is not identically zero
i := 1;
Expand All @@ -405,7 +405,7 @@ rowSelector Matrix := o -> J0 -> (

leverageScoreRowSelector = J0 -> (
sortedRows := (leverageScores J0)/last;
r := rowSelector J0^(sortedRows);
r := rowSelectorPLMP J0^(sortedRows);
sort(r/(i->sortedRows#i))
)

Expand Down Expand Up @@ -493,24 +493,24 @@ cpMatrix = t -> matrix{{0,-t_(2,0),t_(1,0)},{t_(2,0),0,-t_(0,0)},{-t_(1,0),t_(0,

essential = (R,t) -> R * cpMatrix t

pCompose = method()
pCompose (MutableHashTable, MutableHashTable) := (H1, H2) -> (
pCompose2 = method()
pCompose2 (MutableHashTable, MutableHashTable) := (H1, H2) -> (
new MutableHashTable from apply(keys H1,k-> if H2#?(H1#k) then k=> H2#(H1#k))
)

writePermutations = method(Options=>{})
writePermutations (HomotopyNode, String) := o -> (V, filename) -> (
writePermutationsPLMP = method(Options=>{})
writePermutationsPLMP (HomotopyNode, String) := o -> (V, filename) -> (
-- assume for now that G has 2 nodes
G := V.Graph;
V1 := first G.Vertices;
V2 := last G.Vertices;
E1 := toList V1.Edges;
-- "petal loops" based at V1
e1 := first E1;
perms := apply(drop(E1,1),e->values pCompose(e1.Correspondence12,e.Correspondence21));
perms := apply(drop(E1,1),e->values pCompose2(e1.Correspondence12,e.Correspondence21));
writePermutations(perms,filename);
)
writePermutations (List, String) := o -> (L, filename) -> (
writePermutationsPLMP (List, String) := o -> (L, filename) -> (
perms := L/(P->P/(i->i+1)); -- increment letters by 1 for GAP
file := openOut (currentFileDirectory | filename);
for i from 0 to #perms-1 do file << "p" << i << ":= PermList(" << toString(new Array from perms#i) << ");" << endl;
Expand Down
2 changes: 1 addition & 1 deletion CODE/monodromy_example.m2
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Expand Up @@ -77,4 +77,4 @@ concatenate ts
-- post-process the output of monodromySolver


writePermutations(V, "example" | ".txt")
writePermutationsPLMP(V, "example" | ".txt")
2 changes: 1 addition & 1 deletion CODE/numerical-problem-builder.m2
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Expand Up @@ -174,7 +174,7 @@ if (instance(Jpivots, Symbol) and JACOBIAN) then (
(M,N) = size J;
elapsedTime JGS = gateSystem(paramMatrix, varMatrix, transpose matrix{flatten entries J});
elapsedTime J0 = matrix(transpose evaluate(JGS,y,c),M,N);
elapsedTime Jpivots = rowSelector(J0,Threshold=>1e-6);
elapsedTime Jpivots = rowSelectorPLMP(J0,Threshold=>1e-6);
elapsedTime S = first SVD J0^Jpivots;
<< "pivot indices are " << toString Jpivots << endl;
)
Expand Down