The `perm`of `permutedims(A,perm)`


#1

@yuyichao So you’re saying perm necessarily has to be an ordered basis and cannot be a set?


#2

Well, that sounds reasonable because the unordered set is always the same anyway. I don’t remember when/where/in which context I said that though.


#3

You didn’t say it, but this is the context. If an ordered basis is the case, then permute_dims is ordered. I don’t understand what’s missing for permutedims() to work.


#4

I don’t think I mentioned anything about ordering at all. The input type is simply wrong.


#5

Right, I brought up ordering. The input type is the same as the one from permutedims() in this other block, which passes. Should both permutedims() not be Vector{Int}? I don’t understand why not, from the definition of perm below

help?> permutedims
search: permutedims permutedims! ipermutedims

  permutedims(A, perm)

  Permute the dimensions of array A. perm is a vector specifying a permutation
  of length ndims(A). This is a generalization of transpose for
  multi-dimensional arrays. Transpose is equivalent to permutedims(A, [2,1]).
```

#6

Well it isn’t.

Both should be.


#7

And this is also why I posted the code in the one of the replies showing that the type is wrong.


#8

Do you mean [Remain_dims,Remove_dims] is a 2x2 matrix? If yes, how do I turn it into an ordered vector? I’m sorry, thanks for the patience…


#9

No, it’s a Vector of Vector.

That’s exactly the code I posted, on the julia-users thread.

julia> [[1]]
1-element Array{Array{Int64,1},1}:
 [1]

julia> [[1];]
1-element Array{Int64,1}:
 1

And for more than one element to concatenate

julia> [[1]; [2, 3]]
3-element Array{Int64,1}:
 1
 2
 3

#10

Thanks, I switched it to [Remain_dims;Remove_dims]… but now I got this

julia> Pkg.test("BN")
INFO: Testing BN
WARNING: Method definition (::Type{BN.Factor})(Array{String, 1}, Array{Int64, 1}, Array{Float64, 1}) in module BN at /Users/Corvus/.julia/v0.5/BN/src/Factor.jl:9 overwritten at /Users/Corvus/.julia/v0.5/BN/src/Factor.jl:9.
Test Summary:                                             | 
  Define Factor arguments, create instances, permute Factor | No tests
Multiply and marginalize factor: Error During Test
  Got an exception of type ArgumentError outside of a @test
  ArgumentError: reduced dimension(s) must be integers
   in reduced_dims(::Tuple{Int64,Int64,Int64}, ::Array{UnitRange{Int64},1}) at ./reducedim.jl:39
   in reducedim_initarray(::Array{Float64,3}, ::Array{UnitRange{Int64},1}, ::Float64, ::Type{Float64}) at ./reducedim.jl:85
   in mapreducedim at ./reducedim.jl:253 [inlined]
   in sum at ./reducedim.jl:303 [inlined]
   in sum(::Array{Float64,3}, ::Array{UnitRange{Int64},1}) at ./reducedim.jl:305
   in FactorMargin(::BN.Factor, ::Array{String,1}, ::Array{String,1}, ::Array{Int64,1}, ::Array{Int64,1}) at /Users/Corvus/.julia/v0.5/BN/src/FactorOperations.jl:71
   in FactorDropMargin(::BN.Factor, ::Array{String,1}) at /Users/Corvus/.julia/v0.5/BN/src/FactorOperations.jl:87
   in macro expansion; at /Users/Corvus/.julia/v0.5/BN/test/runtests.jl:19 [inlined]
   in macro expansion; at ./test.jl:672 [inlined]
   in anonymous at ./<missing>:?
   in include_from_node1(::String) at ./loading.jl:488
   in include_from_node1(::String) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
   in process_options(::Base.JLOptions) at ./client.jl:262
   in _start() at ./client.jl:318
   in _start() at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
Test Summary:                   | Error  Total
  Multiply and marginalize factor |     1      1
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
 in finish(::Base.Test.DefaultTestSet) at ./test.jl:495
 in macro expansion; at ./test.jl:679 [inlined]
 in anonymous at ./<missing>:?
 in include_from_node1(::String) at ./loading.jl:488
 in include_from_node1(::String) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
 in process_options(::Base.JLOptions) at ./client.jl:262
 in _start() at ./client.jl:318
 in _start() at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?
while loading /Users/Corvus/.julia/v0.5/BN/test/runtests.jl, in expression starting on line 14
=================================[ ERROR: BN ]==================================

failed process: Process(`/Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia -Ccore2 -J/Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /Users/Corvus/.julia/v0.5/BN/test/runtests.jl`, ProcessExited(1)) [1]

================================================================================
ERROR: BN had test errors
 in #test#61(::Bool, ::Function, ::Array{AbstractString,1}) at ./pkg/entry.jl:740
 in (::Base.Pkg.Entry.#kw##test)(::Array{Any,1}, ::Base.Pkg.Entry.#test, ::Array{AbstractString,1}) at ./<missing>:0
 in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}})() at ./pkg/dir.jl:31
 in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}}, ::String) at ./file.jl:59
 in #cd#1(::Array{Any,1}, ::Function, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./pkg/dir.jl:31
 in (::Base.Pkg.Dir.#kw##cd)(::Array{Any,1}, ::Base.Pkg.Dir.#cd, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./<missing>:0
 in #test#3(::Bool, ::Function, ::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258
 in test(::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258

julia> 
```

[Factor.jl:9](https://github.com/hpoit/MLN.jl/blob/master/BN/src/Factor.jl#L9)
[FactorOperations.jl:71](https://github.com/hpoit/MLN.jl/blob/master/BN/src/FactorOperations.jl#L71)
[FactorOperations.jl:87](https://github.com/hpoit/MLN.jl/blob/master/BN/src/FactorOperations.jl#L87)

Your help is much appreciated, Yichao.

#11

The backtrace was printed for a reason and you should use it to figure out how you are using the functions wrong. The method signature printed in this function that’s the first Base function you called in the backtrace should show clearly that you are giving sum the wrong type as dims. Note that the same wrong parameter is also passed to squeeze below, which expects a tuple.


#12

Thanks Yichao. I’m not sure if I should just sum the permuted_valuespace by the Remain_dims to make sense. Factor marginalization here is just the sum over the relevant variables (Remain_var).

To me this makes more sense, but I’m not sure

# Factor marginalization: computes the factor without the non-relevant variables (Remove_var)

function FactorMargin(A::Factor, Remove_var::Vector{String}, Remain_var::Vector{String}, Remove_dims::Vector{Int}, Remain_dims::Vector{Int})
    Remain_card = A.card[Remain_dims]

    valuespace = reshape(A.value, A.card...)
    permute_dims = [Remain_dims;Remove_dims]
    permuted_valuespace = permutedims(valuespace, permute_dims)

    # squeeze_dims = [length(Remain_dims)+1:length(permute_dims)] (I would delete this line)

    sumvaluespace = sum(permuted_valuespace, Remain_dims) # changed for Remain_dims
    Remain_valuespace = squeeze(sumvaluespace, Remove_dims) # changed for Remove_dims

    Factor(Remain_var, Remain_card, Remain_valuespace[:])
end

This is my reference.

FactorProduct.m
IndexToAssignment.m
AssignmentToIndex.m


#13

Also, some days past I was having a bad one and I

julia> include("/Users/Corvus/.julia/v0.5/BN/src/BN.jl")
julia> include("/Users/Corvus/.julia/v0.5/BN/src/Factor.jl")
julia> include("/Users/Corvus/.julia/v0.5/BN/test/runtests.jl")

julia> Package.test("BN")
ERROR: UndefVarError: Package not defined
```
... even though the BN folder is already exists, in `.julia/v0.5/BN`. 

I don't know how to get back to using `.julia/v0.5/BN`.

#14

I’m pretty sure squeeze needs a tuple instead of a vector (and this operation is inherently type unstable if you pass in Vector as the dimensions)

Where did you get the Package from? Please read the actual error more carefully since I think this one should be pretty clear from the error message. The package module in base is called Pkg.
Using include like that also won’t do anything about Pkg.test. The tests are run in a script and has nothing to do with the calling process.


#15

Sorry, I didn’t pay attention to Package.

The tuple is a non-issue, I agree. Does the logic of any version of the function make sense to you?


#16

Sorry that’s not what I’m familiar with.


#17

That’s cool, thanks anyway!