[julia-users] how to read .raw 3D image files in Julia
How to read 3D image files with a .raw extension in Julia? Thanks.
[julia-users] Overlapping data in DArrays
Is it possible to construct DArrays such that they overlap? For example, given an array with 10 elements, and 2 processors, elements 1..6 should belong to processor 1, and 5..10 to processor 2. Thanks.
[julia-users] ijulia indentation
How do i customize the indentation in ijulia? For example, i would like the indentation to be 2 spaces instead of 4. I couldn't get the solution suggested at http://stackoverflow.com/questions/19068730/how-do-i-change-the-autoindent-to-2-space-in-ipython-notebook to work. Thanks.
[julia-users] convert a matrix of reals into an image
Could you give me an example to convert a matrix of reals into a grayscale image in julia? I read through the Images.jl documentation, but couldn't find a simple example to do this. Thanks.
[julia-users] Re: metaprogramming : modifying function arguments
Thanks. That works. On Saturday, May 16, 2015 at 7:38:49 PM UTC-4, David P. Sanders wrote: > > Apologies for the double (now triple) posting. Passing the function as an > argument as well, that becomes: > > function f1(f, args...) > @show args > new_args = [modify(arg) for arg in args] > f(new_args...) > end > > function f2(a, b) > @show a, b > end > > f1(f2, 2, 3.5) > > El sábado, 16 de mayo de 2015, 18:36:42 (UTC-5), David P. Sanders escribió: >> >> >> >> El sábado, 16 de mayo de 2015, 18:26:48 (UTC-5), Eka Palamadai escribió: >>> >>> I am trying to write a function f1 that takes a function f2 and >>> arguments of f2 as parameters, >>> modifies some arguments of f2, and calls f2 with the modified arguments. >>> >>> function f1(f2::Function, args...) >>> #iterate through the args and modify some of the contents of args >>> f2(args) >>> end >>> >> >> Depending on what you mean by "modifying", you don't need metaprogramming >> for this. >> For example: >> >> >> modify(x::Int) = 2x >> modify(x::Float64) = 3x >> >> function f1(args...) >> new_args = [modify(arg) for arg in args] >> f2(new_args...) >> end >> >> function f2(a, b) >> @show a, b >> end >> >> f1(2, 3.5) >> >> >> This gives >> >> (4,10.5) >> >> >> David. >> >> >> >> >> >>> >>> Any suggestions on how to do this? >>> >>> Thanks. >>> >>> >>> >>> >>> >>> >>> >>
[julia-users] metaprogramming : modifying function arguments
I am trying to write a function f1 that takes a function f2 and arguments of f2 as parameters, modifies some arguments of f2, and calls f2 with the modified arguments. function f1(f2::Function, args...) #iterate through the args and modify some of the contents of args f2(args) end Any suggestions on how to do this? Thanks.
Re: [julia-users] Re: Google Summer of Code: Your Project Suggestions
Chris, Just wanted to check about the progress you made about integrating PetSc in Julia. Could you pls let me know the status of this project? Thanks, Eka On Thursday, February 20, 2014 at 8:54:33 PM UTC-5, Christopher Fusting wrote: > > Great. I'm going to start poking around PETSc. Any guidance you have is > welcome :) > > _Chris > > On Wednesday, February 19, 2014 7:01:51 PM UTC-5, Jiahao Chen wrote: >> >> If no one else volunteers, it's quite likely that that responsibility >> will devolve to me. There's certainly plenty of work to do to improve >> the base numerical library, so any interest there is much welcomed. >> >> Thanks, >> >> Jiahao Chen, PhD >> Staff Research Scientist >> MIT Computer Science and Artificial Intelligence Laboratory >> >> >> On Wed, Feb 19, 2014 at 4:48 PM, Christopher Fusting >> wrote: >> > I may be interested in filling the student role of a project under >> > scalability of big data applications, specifically PETSc integration >> and >> > solvers for numerical linear alegbra. Has anyone expressed interest in >> > mentoring these projects? I've been developing software for years but >> have >> > recently returned to school to study mathematics. Could be lots of fun >> :) >> >
[julia-users] PetSc interface in Julia
Just wanted to check if any work has been done on integrating PetSc into Julia? I notice Stevenj has done some work on this, and there was some discussion about a student working on this last year as part of the google project. Would appreciate any updates. Thanks, Eka
Re: [julia-users] SymTridiagonal
Thanks.
Fortunately (or unfortunately) i have to use julia, and will have to make
noise
where something is confusing.
On Monday, November 17, 2014 1:26:09 PM UTC-5, Tim Holy wrote:
>
> Your best bet, then, is to decide as quickly as possible whether you want
> to
> use Julia. If you start reading here:
>
> http://docs.julialang.org/en/latest/manual/faq/#what-does-type-stable-mean
>
> you'll maximize your chances of quickly discovering other things that will
> likely annoy you :-). While only the section I directly linked to is
> necessary
> to understand why `ones(n,1)` can't return a Vector, you should also be
> sure
> to read the next 2 sections on DomainErrors and machine arithmetic, just
> to
> make sure you've drunk the full cup's worth of annoyance.
>
> Then you'll be in a good position to make an informed judgment about
> whether
> you want to accept the hassles in exchange for the benefits the type
> system
> provides.
>
> Best,
> --Tim
>
> On Monday, November 17, 2014 10:02:07 AM Eka Palamadai wrote:
> > I don't know what matlab does.
> >
> > As a user, ones(n,1) and ones(n) both return me a vector, and it is
> > confusing to find that ones(n,1) != ones(n).
> >
> > On Monday, November 17, 2014 12:53:25 PM UTC-5, Tim Holy wrote:
> > > What's intuitive is very dependent upon your background. If you're
> coming
> > > from
> > > Matlab, for example, "everything is a matrix" and Matlab does this
> > > extraordinarily-confusing thing:
> > >
> > > ones(3,3,3) gives me a 3d array;
> > > ones(3,3) gives me a 2d array;
> > > but
> > >
> > > >> ones(3)
> > >
> > > ans =
> > >
> > > 1 1 1
> > > 1 1 1
> > > 1 1 1
> > >
> > > Why the heck did it give me a 2d matrix when I asked for a
> 1-dimensional
> > > vector of 1s?
> > >
> > > Julia is much more consistent: the dimensionality of the created
> object is
> > > equal to the number of indices you supply. If you ask for something
> that's
> > > 3x1, that's the size you'll get out; perforce, that is a 2d array.
> > >
> > > --Tim
> > >
> > > On Monday, November 17, 2014 09:41:10 AM Eka Palamadai wrote:
> > > > "which I think is reasonable" is a subjective argument.
> > > > It would be helpful if the type system is intuitive and
> non-confusing to
> > > > programmers.
> > > >
> > > > On Monday, November 17, 2014 12:24:58 PM UTC-5, Andreas Noack wrote:
> > > > > Semantically, ones(n,1) creates a vector and not a matrix.
> > > > >
> > > > > I'd rather say that in MATLAB ones(n,1) creates a vector.
> > > > >
> > > > > This has been discussed many times on the list and in issues. In
> > > > > particular, see the famous
> > >
> > > https://github.com/JuliaLang/julia/issues/4774
> > >
> > > > > .
> > > > >
> > > > > In Julia, Vector{T} and Matrix{T} are aliases for Array{T,1} and
> > > > > Array{T,2} which I think is reasonable. The questions are to what
> > >
> > > extend a
> > >
> > > > > nx1 Matrix should work similarly to a Vector and a Vector should
> work
> > > > > similarly to a nx1 Matrix. That is the discussion in the issue
> > >
> > > mentioned,
> > >
> > > > > and it is actually more subtle than one would expect.
> > > > >
> > > > > 2014-11-17 12:04 GMT-05:00 Eka Palamadai > >
> > > >
> > >
> > > > >> Semantically, ones(n,1) creates a vector and not a matrix.
> > > > >> Why is ones(n,1) different from ones(n)?
> > > > >> The type system is very confusing and non-intuitive.
> > > > >>
> > > > >> On Sunday, November 16, 2014 7:28:28 PM UTC-5, Andreas Noack
> wrote:
> > > > >>> The input should be two Vectors, but your first argument is a
> Matrix
> > > > >>>
> > > > >>> 2014-11-16 19:25 GMT-05:00 Eka Palamadai :
> > > > >>>> SymTridiagonal does not seem to work properly.
> > > > >>>>
> > > > >>>> For e.g, the following snippet fails.
> > > > >>>>
> > > > >>>> julia> n=10 ;
> > > > >>>> A=SymTridiagonal(2*ones(n,1), -1*ones(n-1));
> > > > >>>> ERROR: `convert` has no method matching
> > > > >>>> convert(::Type{SymTridiagonal{T}},
> > > > >>>>
> > > > >>>> ::Array{Float64,2}, ::Array{Float64,1})
> > > > >>>>
> > > > >>>> in call at base.jl:34
> > > > >>>>
> > > > >>>> Any thoughts?
>
>
Re: [julia-users] SymTridiagonal
I don't know what matlab does.
As a user, ones(n,1) and ones(n) both return me a vector, and it is
confusing to find that ones(n,1) != ones(n).
On Monday, November 17, 2014 12:53:25 PM UTC-5, Tim Holy wrote:
>
> What's intuitive is very dependent upon your background. If you're coming
> from
> Matlab, for example, "everything is a matrix" and Matlab does this
> extraordinarily-confusing thing:
>
> ones(3,3,3) gives me a 3d array;
> ones(3,3) gives me a 2d array;
> but
>
> >> ones(3)
>
> ans =
>
> 1 1 1
> 1 1 1
> 1 1 1
>
> Why the heck did it give me a 2d matrix when I asked for a 1-dimensional
> vector of 1s?
>
> Julia is much more consistent: the dimensionality of the created object is
> equal to the number of indices you supply. If you ask for something that's
> 3x1, that's the size you'll get out; perforce, that is a 2d array.
>
> --Tim
>
>
>
> On Monday, November 17, 2014 09:41:10 AM Eka Palamadai wrote:
> > "which I think is reasonable" is a subjective argument.
> > It would be helpful if the type system is intuitive and non-confusing to
> > programmers.
> >
> > On Monday, November 17, 2014 12:24:58 PM UTC-5, Andreas Noack wrote:
> > > Semantically, ones(n,1) creates a vector and not a matrix.
> > >
> > > I'd rather say that in MATLAB ones(n,1) creates a vector.
> > >
> > > This has been discussed many times on the list and in issues. In
> > > particular, see the famous
> https://github.com/JuliaLang/julia/issues/4774
> > > .
> > >
> > > In Julia, Vector{T} and Matrix{T} are aliases for Array{T,1} and
> > > Array{T,2} which I think is reasonable. The questions are to what
> extend a
> > > nx1 Matrix should work similarly to a Vector and a Vector should work
> > > similarly to a nx1 Matrix. That is the discussion in the issue
> mentioned,
> > > and it is actually more subtle than one would expect.
> > >
> > > 2014-11-17 12:04 GMT-05:00 Eka Palamadai >
> > >
> > >> Semantically, ones(n,1) creates a vector and not a matrix.
> > >> Why is ones(n,1) different from ones(n)?
> > >> The type system is very confusing and non-intuitive.
> > >>
> > >> On Sunday, November 16, 2014 7:28:28 PM UTC-5, Andreas Noack wrote:
> > >>> The input should be two Vectors, but your first argument is a Matrix
> > >>>
> > >>> 2014-11-16 19:25 GMT-05:00 Eka Palamadai :
> > >>>> SymTridiagonal does not seem to work properly.
> > >>>>
> > >>>> For e.g, the following snippet fails.
> > >>>>
> > >>>> julia> n=10 ;
> > >>>> A=SymTridiagonal(2*ones(n,1), -1*ones(n-1));
> > >>>> ERROR: `convert` has no method matching
> > >>>> convert(::Type{SymTridiagonal{T}},
> > >>>>
> > >>>> ::Array{Float64,2}, ::Array{Float64,1})
> > >>>>
> > >>>> in call at base.jl:34
> > >>>>
> > >>>> Any thoughts?
>
>
Re: [julia-users] SymTridiagonal
"which I think is reasonable" is a subjective argument.
It would be helpful if the type system is intuitive and non-confusing to
programmers.
On Monday, November 17, 2014 12:24:58 PM UTC-5, Andreas Noack wrote:
>
> Semantically, ones(n,1) creates a vector and not a matrix.
>
> I'd rather say that in MATLAB ones(n,1) creates a vector.
>
> This has been discussed many times on the list and in issues. In
> particular, see the famous https://github.com/JuliaLang/julia/issues/4774
> .
>
> In Julia, Vector{T} and Matrix{T} are aliases for Array{T,1} and
> Array{T,2} which I think is reasonable. The questions are to what extend a
> nx1 Matrix should work similarly to a Vector and a Vector should work
> similarly to a nx1 Matrix. That is the discussion in the issue mentioned,
> and it is actually more subtle than one would expect.
>
> 2014-11-17 12:04 GMT-05:00 Eka Palamadai >
> :
>
>> Semantically, ones(n,1) creates a vector and not a matrix.
>> Why is ones(n,1) different from ones(n)?
>> The type system is very confusing and non-intuitive.
>>
>> On Sunday, November 16, 2014 7:28:28 PM UTC-5, Andreas Noack wrote:
>>>
>>> The input should be two Vectors, but your first argument is a Matrix
>>>
>>> 2014-11-16 19:25 GMT-05:00 Eka Palamadai :
>>>
>>>> SymTridiagonal does not seem to work properly.
>>>>
>>>> For e.g, the following snippet fails.
>>>>
>>>> julia> n=10 ;
>>>> A=SymTridiagonal(2*ones(n,1), -1*ones(n-1));
>>>> ERROR: `convert` has no method matching convert(::Type{SymTridiagonal{T}},
>>>> ::Array{Float64,2}, ::Array{Float64,1})
>>>> in call at base.jl:34
>>>>
>>>> Any thoughts?
>>>>
>>>
>>>
>
Re: [julia-users] SymTridiagonal
Semantically, ones(n,1) creates a vector and not a matrix.
Why is ones(n,1) different from ones(n)?
The type system is very confusing and non-intuitive.
On Sunday, November 16, 2014 7:28:28 PM UTC-5, Andreas Noack wrote:
>
> The input should be two Vectors, but your first argument is a Matrix
>
> 2014-11-16 19:25 GMT-05:00 Eka Palamadai >
> :
>
>> SymTridiagonal does not seem to work properly.
>>
>> For e.g, the following snippet fails.
>>
>> julia> n=10 ;
>> A=SymTridiagonal(2*ones(n,1), -1*ones(n-1));
>> ERROR: `convert` has no method matching
>> convert(::Type{SymTridiagonal{T}}, ::Array{Float64,2}, ::Array{Float64,1})
>> in call at base.jl:34
>>
>> Any thoughts?
>>
>
>
[julia-users] SymTridiagonal
SymTridiagonal does not seem to work properly.
For e.g, the following snippet fails.
julia> n=10 ;
A=SymTridiagonal(2*ones(n,1), -1*ones(n-1));
ERROR: `convert` has no method matching convert(::Type{SymTridiagonal{T}},
::Array{Float64,2}, ::Array{Float64,1})
in call at base.jl:34
Any thoughts?
Re: [julia-users] how to persist state in parallel computing
Thanks. Adding the global keyword to definition of d works.
Using remoteref also works.
Here is the snippet with remoteref
--
function foo()
d = zeros(5)
for i = 1:5
d [i] = i
end
r = RemoteRef()
put!(r, d)
r
end
function bar(r)
d = take!(r)
println ("d", d)
end
function test_parallel()
r1 = @spawnat 2 foo()
r2 = fetch(r1)
@spawnat 2 bar(r2)
end
--
Is there a limit on the number of RemoteRef() calls that can be made in a
given process?
Do 2 RemoteRef() calls in the same process yield 2 different remote
references?
Thanks.
On Wednesday, May 28, 2014 6:19:39 PM UTC-4, Jameson wrote:
>
> Right, but that's where you can return a remoteref wrapper instead of the
> entire array (or perhaps spawnat does this already? I don't recall exactly)
>
> On Wednesday, May 28, 2014, Stefan Karpinski
> >
> wrote:
>
>> I suspect that global variable is what Eka is after here. If you put
>> "global" in front of the definition of d, it will work. I would advise
>> against using globals, however. It's much better to return the array and
>> pass it to the other function as an argument.
>>
>> On May 28, 2014, at 5:24 PM, Jameson Nash wrote:
>>
>> A RemoteRef lets up pass around a variable without actually moving the
>> data (until you fetch)
>>
>> On Wednesday, May 28, 2014, Eka Palamadai wrote:
>>
>>> Is it possible to persist a variable across function calls?
>>>
>>> Consider 2 functions foo and bar shown below :
>>> -
>>> function foo()
>>> d = zeros(5)
>>> for i = 1:5
>>> d [i] = i
>>> end
>>> end
>>>
>>> function bar()
>>> println ("d", d)
>>> end
>>>
>>> function test_parallel()
>>>@spawnat 2 foo()
>>>@spawnat 2 bar()
>>> end
>>> -
>>> The code doesn't compile since d is not defined in function bar.
>>>
>>> foo defines array d but bar needs to use d as well.
>>>
>>> How could both foo and bar use d without passing d around?
>>>
>>> I could pass d back and forth, but i would like to avoid the
>>> communication overhead.
>>> Any ideas?
>>>
>>> Thanks.
>>>
>>>
>>>
>>>
[julia-users] how to persist state in parallel computing
Is it possible to persist a variable across function calls?
Consider 2 functions foo and bar shown below :
-
function foo()
d = zeros(5)
for i = 1:5
d [i] = i
end
end
function bar()
println ("d", d)
end
function test_parallel()
@spawnat 2 foo()
@spawnat 2 bar()
end
-
The code doesn't compile since d is not defined in function bar.
foo defines array d but bar needs to use d as well.
How could both foo and bar use d without passing d around?
I could pass d back and forth, but i would like to avoid the communication
overhead.
Any ideas?
Thanks.
Re: [julia-users] factorizing tridiagonal matrices
I need to extract L and U factors from a tridiagonal matrix factorization for my application. Would it be possible to have this feature? The matrix is diagonally dominant, so off-diagonal pivoting may not happen. (For the general case where off-diagonal pivoting may happen, a permutation could be returned as well) Thanks, Eka On Wednesday, December 18, 2013 3:12:12 AM UTC-5, Andreas Noack Jensen wrote: > > Extracting the factors of an tridiagonal LU factorisation is not > supported. You can see the names of the storage vectors by writing names(F) > and the U is easily constructed from those. L is more tricky because of > pivoting. > > Best > Andreas > > > 2013/12/18 Eka Palamadai > > >> How do i factorize a tridiagonal matrix in Julia? >> I tried F=lufact(A) as specified in the manual and it works. >> But i am not sure how to access the L and U factors from F. >> The manual specifies indexing as F[:L], but it doesn't work. >> >> Thanks, >> Eka >> >> > > > > -- > Med venlig hilsen > > Andreas Noack Jensen >
Re: [julia-users] Re: ipython error
Doing Pkg.build("IJulia") at the julia prompt gave a bunch of errors as
follows:
--
julia> Pkg.build("IJulia")
INFO: Building Homebrew
INFO: Cloning brew from https://github.com/staticfloat/homebrew.git
error: unknown option `single-branch'
usage: git clone [options] [--] []
-v, --verbose be more verbose
-q, --quiet be more quiet
--progressforce progress reporting
-n, --no-checkout don't create a checkout
--barecreate a bare repository
--mirror create a mirror repository (implies bare)
-l, --local to clone from a local repository
--no-hardlinksdon't use local hardlinks, always copy
-s, --shared setup as shared repository
--recursive initialize submodules in the clone
--recurse-submodules initialize submodules in the clone
--template
directory from which templates will be used
--reference reference repository
-o, --origin
use instead of 'origin' to track upstream
-b, --branch
checkout instead of the remote's HEAD
-u, --upload-pack
path to git-upload-pack on the remote
--depthcreate a shallow clone of that depth
--separate-git-dir
separate git dir from working tree
-c, --config
set config inside the new repository
==[ ERROR: Homebrew
]===
brew_prefix! not defined
while loading /Users/epn/.julia/Homebrew/src/Homebrew.jl, in expression
starting on line 196
while loading /Users/epn/.julia/Homebrew/deps/build.jl, in expression
starting on line 1
INFO: Building Nettle
===[ ERROR: Nettle
]
stack overflow
while loading /Users/epn/.julia/Nettle/deps/build.jl, in expression
starting on line 27
INFO: Building ZMQ
=[ ERROR: ZMQ
]=
stack overflow
while loading /Users/epn/.julia/ZMQ/deps/build.jl, in expression starting
on line 7
INFO: Building IJulia
Found IPython version 1.1.0 ... ok.
Creating julia profile in IPython...
(Existing KernelManager.kernel_cmd setting in ipython_config.py is
untouched.)
(Existing IPythonWidget.execute_on_complete_input setting in
ipython_qtconsole_config.py is untouched.)
(Existing NotebookApp.port setting in ipython_notebook_config.py is
untouched.)
(Existing ipynblogo.png file untouched.)
(Existing ipynblogo.svg file untouched.)
(Existing tooltip.js file untouched.)
(Existing custom.js file untouched.)
(Existing julia.js file untouched.)
[ BUILD ERRORS
]
WARNING: Nettle, ZMQ and Homebrew had build errors.
---
On Thursday, March 20, 2014 4:34:08 PM UTC-4, Stefan Karpinski wrote:
>
> Just a blind guess but in the past this has sometimes been fixed by doing
> `Pkg.build("IJulia")` at the Julia prompt.
>
>
> On Thu, Mar 20, 2014 at 4:28 PM, Jake Bolewski
>
> > wrote:
>
>> To get a backtrace of the potential problem, in the julia repl start up a
>> kernel by "import IJulia". If the kernel is crashing for some reason this
>> should provide more clues as to what is going on.
>>
>>
>>
>> On Thursday, March 20, 2014 4:21:35 PM UTC-4, Eka Palamadai wrote:
>>>
>>> I did a git pull today, then make clean and make in the julia directory.
>>>
>>> I killed and restarted ipython as
>>>
>>> ipython notebook --profile julia
>>>
>>> When i open a notebook on the browser,
>>> I get repeated error messages saying 'Kernel restarting - The kernel
>>> appears to have died. It will restart automatically.'
>>>
>>> Any idea how to fix this?
>>>
>>> Thanks,
>>> Eka
>>>
>>
>
[julia-users] Re: ipython error
When i did 'import IJulia' at the julia prompt, i got the following output "connect ipython with --existing profile-97310.json" I restarted ipython as ipython notebook --profile profile-97310.json When i try a simple code snippet in the browser notebook, i get the following message NameError Traceback (most recent call last) in () 1 n=10 > 2 a=ones(n)*2 3 #println(a) 4 b=ones(n-1)*-1 5 c=b NameError: name 'ones' is not defined It doesn't recognize julia builtin functions anymore. But i don't get the 'Kernel Restarting' error message. Thanks, Eka On Thursday, March 20, 2014 4:28:47 PM UTC-4, Jake Bolewski wrote: > > To get a backtrace of the potential problem, in the julia repl start up a > kernel by "import IJulia". If the kernel is crashing for some reason this > should provide more clues as to what is going on. > > > On Thursday, March 20, 2014 4:21:35 PM UTC-4, Eka Palamadai wrote: >> >> I did a git pull today, then make clean and make in the julia directory. >> >> I killed and restarted ipython as >> >> ipython notebook --profile julia >> >> When i open a notebook on the browser, >> I get repeated error messages saying 'Kernel restarting - The kernel >> appears to have died. It will restart automatically.' >> >> Any idea how to fix this? >> >> Thanks, >> Eka >> >
[julia-users] ipython error
I did a git pull today, then make clean and make in the julia directory. I killed and restarted ipython as ipython notebook --profile julia When i open a notebook on the browser, I get repeated error messages saying 'Kernel restarting - The kernel appears to have died. It will restart automatically.' Any idea how to fix this? Thanks, Eka
[julia-users] factorizing tridiagonal matrices
How do i factorize a tridiagonal matrix in Julia? I tried F=lufact(A) as specified in the manual and it works. But i am not sure how to access the L and U factors from F. The manual specifies indexing as F[:L], but it doesn't work. Thanks, Eka
