# Specific Domains

**URL:** https://discourse.julialang.org/c/domain/10.md?no_subcategories=false&page=415

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**Page:** 416

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## [Interest in single molecule localization microscopy?](https://discourse.julialang.org/t/interest-in-single-molecule-localization-microscopy/48227)

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**Author:** [@nboyd](https://discourse.julialang.org/u/nboyd)\
**Replies:** 3\
**Last updated:** [October 13, 2020, 10:08pm UTC](https://discourse.julialang.org/t/interest-in-single-molecule-localization-microscopy/48227 "2020-10-13T22:08:55Z")

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I’ve implemented a few algorithms for single molecule localization microscopy: a (quite) fast localizer for high density 2D SMLM and a drift correction algorithm for 2D and 3D localizations. My question is whether there…

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## [UndefVarError: t not defined](https://discourse.julialang.org/t/undefvarerror-t-not-defined/47987)

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**Author:** [@Arega\_Getaneh](https://discourse.julialang.org/u/Arega_Getaneh)\
**Replies:** 2\
**Last updated:** [October 13, 2020, 10:01pm UTC](https://discourse.julialang.org/t/undefvarerror-t-not-defined/47987 "2020-10-13T22:01:12Z")

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function DR\_Model\_MPEC(J,T,W,PS\_tw,D\_jtw,delta\_jcmax,C\_t,sigma\_w,M\_S,M\_P,M\_C,M\_T) m = Model(Gurobi.Optimizer) # Variables definition ################################# @variables(m, begin De…

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## [Global memory behavior explained](https://discourse.julialang.org/t/global-memory-behavior-explained/47422)

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**Author:** [@barrettp](https://discourse.julialang.org/u/barrettp)\
**Replies:** 9\
**Last updated:** [October 13, 2020, 2:58pm UTC](https://discourse.julialang.org/t/global-memory-behavior-explained/47422 "2020-10-13T14:58:27Z")

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Can anyone explain the following behavior? I am using CUDA and have a nested set of kernels, one first-level kernel and three second-level kernels. I’m performing three summations/reductions and storing the results in a…

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## [U.S. Counties Choropleth](https://discourse.julialang.org/t/u-s-counties-choropleth/20845)

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**Author:** [@mthelm85](https://discourse.julialang.org/u/mthelm85)\
**Replies:** 27\
**Last updated:** [October 13, 2020, 1:43pm UTC](https://discourse.julialang.org/t/u-s-counties-choropleth/20845 "2020-10-13T13:43:40Z")

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I can’t seem to find any info on how to create a choropleth map with U.S. counties in Julia. Is everyone using Python/R packages for this or is there a way to do it in Julia? It would be really nice if it was possible to…

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## [HPC / Julia, MPI / big data](https://discourse.julialang.org/t/hpc-julia-mpi-big-data/48236)

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**Author:** [@oddodaoddo](https://discourse.julialang.org/u/oddodaoddo)\
**Replies:** 15\
**Last updated:** [October 13, 2020, 1:37pm UTC](https://discourse.julialang.org/t/hpc-julia-mpi-big-data/48236 "2020-10-13T13:37:38Z")

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Hello. Many years ago I was in HPC (as in university/govt supercomputers). We used to write code in C/pthreads, MPI, PVM etc. Then I left and went to the private sector and then big data came with Spark, Scala and that w…

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## [A question about SCIP in Julia](https://discourse.julialang.org/t/a-question-about-scip-in-julia/35842)

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**Author:** [@abcde](https://discourse.julialang.org/u/abcde)\
**Replies:** 8\
**Last updated:** [October 13, 2020, 8:28am UTC](https://discourse.julialang.org/t/a-question-about-scip-in-julia/35842 "2020-10-13T08:28:41Z")

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Error: Error building \`SCIP\`: │ ERROR: LoadError: Unable to locate SCIP installation. │ Tried: │ scip.dll │ Note that this must be downloaded separately from scip.zib.de. │ Please set the environment variable SCI…

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## [How to start Partial Differential Equation (PDE) Solving in Julia for modified Wave Equation](https://discourse.julialang.org/t/how-to-start-partial-differential-equation-pde-solving-in-julia-for-modified-wave-equation/46555)

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**Author:** [@CosmoProf](https://discourse.julialang.org/u/CosmoProf)\
**Replies:** 50\
**Last updated:** [October 12, 2020, 11:40pm UTC](https://discourse.julialang.org/t/how-to-start-partial-differential-equation-pde-solving-in-julia-for-modified-wave-equation/46555 "2020-10-12T23:40:05Z")

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Hi, after working with ordinary differential equations so far, I now have to numerically solve a partial differential equation (PDE) in Julia, and I’m not sure where to start. My equation is like the usual wave equation…

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## [Saving vegalite plots takes very long time compared to plots.jl](https://discourse.julialang.org/t/saving-vegalite-plots-takes-very-long-time-compared-to-plots-jl/48232)

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**Author:** [@MackHarry](https://discourse.julialang.org/u/MackHarry)\
**Replies:** 10\
**Last updated:** [October 12, 2020, 9:41pm UTC](https://discourse.julialang.org/t/saving-vegalite-plots-takes-very-long-time-compared-to-plots-jl/48232 "2020-10-12T21:41:31Z")

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Hello everyone, first time poster here. I’m running into problems when trying to save vegalite plots as pdf, or anything other than html for that matter. The following script exemplifies this quite well: using VegaLit…

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## [Regression: fixed effects + quantiles](https://discourse.julialang.org/t/regression-fixed-effects-quantiles/45427)

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**Author:** [@danicaratelli](https://discourse.julialang.org/u/danicaratelli)\
**Replies:** 16\
**Last updated:** [October 12, 2020, 7:23pm UTC](https://discourse.julialang.org/t/regression-fixed-effects-quantiles/45427 "2020-10-12T19:23:00Z")

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I am trying to run a quantile regression with fixed effects. Does anyone know if a package for this exists? Thanks!

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## [How to find combination of linear transformations to recover original Matrix with wrap?](https://discourse.julialang.org/t/how-to-find-combination-of-linear-transformations-to-recover-original-matrix-with-wrap/48186)

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**Author:** [@Nosferican](https://discourse.julialang.org/u/Nosferican)\
**Replies:** 4\
**Last updated:** [October 12, 2020, 5:27pm UTC](https://discourse.julialang.org/t/how-to-find-combination-of-linear-transformations-to-recover-original-matrix-with-wrap/48186 "2020-10-12T17:27:39Z")

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Given obj::CircularArray{Bool,2,BitMatrix} that has undergone a combination of linear transformations circshift(A::AbstractMatrix, shifts::NTuple{2,\<:Integer}) rotl90(A::AbstractMatrix, k::Integer) reverse(A::Abstrac…

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## [Pass rcParams to pyplot() while using Plots.jl](https://discourse.julialang.org/t/pass-rcparams-to-pyplot-while-using-plots-jl/48058)

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**Author:** [@Gregstrq](https://discourse.julialang.org/u/Gregstrq)\
**Replies:** 1\
**Last updated:** [October 12, 2020, 3:56pm UTC](https://discourse.julialang.org/t/pass-rcparams-to-pyplot-while-using-plots-jl/48058 "2020-10-12T15:56:17Z")

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If one uses PyPlot.jl separately from Plots.jl, one can change all default settings by editing rcParams dictionary. Is there a way to edit rcParams if one uses PyPlot as a backend for Plots.jl? May be I can pass rcParam…

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## [Dynamically split DataFrame into bins](https://discourse.julialang.org/t/dynamically-split-dataframe-into-bins/48046)

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**Author:** [@fbanning](https://discourse.julialang.org/u/fbanning)\
**Replies:** 4\
**Last updated:** [October 12, 2020, 3:27pm UTC](https://discourse.julialang.org/t/dynamically-split-dataframe-into-bins/48046 "2020-10-12T15:27:45Z")

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I suppose this is a simple thing to do but I don’t quite know what to search for. I’m currently wondering how I can dynamically split a DataFrame into equal size bins. using DataFrames, StatsPlots df = DataFrame(a = ra…

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## [How to tackle 2D Poisson equation?](https://discourse.julialang.org/t/how-to-tackle-2d-poisson-equation/48185)

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**Author:** [@sw72](https://discourse.julialang.org/u/sw72)\
**Replies:** 3\
**Last updated:** [October 12, 2020, 11:27am UTC](https://discourse.julialang.org/t/how-to-tackle-2d-poisson-equation/48185 "2020-10-12T11:27:08Z")

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Can anyone point me in the right direction for solving a 2D Poisson equation in a circular region? I’m a little overwhelmed by the number of different Julia packages which a google search returns, and it can be hard to …

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## [Interpolations inaccuracy](https://discourse.julialang.org/t/interpolations-inaccuracy/48102)

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**Author:** [@OlafTeichert](https://discourse.julialang.org/u/OlafTeichert)\
**Replies:** 6\
**Last updated:** [October 12, 2020, 10:17am UTC](https://discourse.julialang.org/t/interpolations-inaccuracy/48102 "2020-10-12T10:17:11Z")

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While moving code from python, I noticed that linear interpolation in Julia is less accurate than the python numpy interp function, see MWE below. The error may seem tiny, but the value is integrated and adds up over ti…

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## [Makie not updating scene in Jupyter](https://discourse.julialang.org/t/makie-not-updating-scene-in-jupyter/48179)

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**Author:** [@Iulian.Cioarca](https://discourse.julialang.org/u/Iulian.Cioarca)\
**Replies:** 0\
**Last updated:** [October 11, 2020, 8:03pm UTC](https://discourse.julialang.org/t/makie-not-updating-scene-in-jupyter/48179 "2020-10-11T20:03:17Z")

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I want to update a plot in Jupyter notebook by clicking a button. I’m using Makie and Interact. Here is a minimal example: using Makie, AbstractPlotting, WGLMakie using Interact t=0:1e-3:1 y1 = sin.(2pi\*10\*t).\*exp.(-t/…

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## [When to use QRSHManager?](https://discourse.julialang.org/t/when-to-use-qrshmanager/47154)

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**Author:** [@jzr](https://discourse.julialang.org/u/jzr)\
**Replies:** 1\
**Last updated:** [October 11, 2020, 1:20pm UTC](https://discourse.julialang.org/t/when-to-use-qrshmanager/47154 "2020-10-11T13:20:36Z")

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@bjarthur mentioned that QRSHManager can increase reliability on some systems: Julia workers can frequently timeout waiting for the standard output files to appear. In this case, it’s better to use the QRSHManager, whi…

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## [Pairwise Alignment Score function: From Python to Julia. Suggestions](https://discourse.julialang.org/t/pairwise-alignment-score-function-from-python-to-julia-suggestions/48089)

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**Author:** [@aadam](https://discourse.julialang.org/u/aadam)\
**Replies:** 3\
**Last updated:** [October 10, 2020, 1:23pm UTC](https://discourse.julialang.org/t/pairwise-alignment-score-function-from-python-to-julia-suggestions/48089 "2020-10-10T13:23:24Z")

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I wanted a function to compute the Pairwise Alignment Score in Julia, but didn’t find any in the BioJulia repository. I submitted an issue, asking for some guidance, but no response till now. So, after waiting a long tim…

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## [Manual link does not work](https://discourse.julialang.org/t/manual-link-does-not-work/48083)

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**Author:** [@vaeli](https://discourse.julialang.org/u/vaeli)\
**Replies:** 0\
**Last updated:** [October 10, 2020, 1:28am UTC](https://discourse.julialang.org/t/manual-link-does-not-work/48083 "2020-10-10T01:28:33Z")

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http://juliagraphics.github.io/Gtk.jl/v0.17/doc/precompilation.md - building into local installation of Gtk does not work

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## [How to simulate a random signal sequence change](https://discourse.julialang.org/t/how-to-simulate-a-random-signal-sequence-change/47964)

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**Author:** [@aachener](https://discourse.julialang.org/u/aachener)\
**Replies:** 4\
**Last updated:** [October 10, 2020, 3:22am UTC](https://discourse.julialang.org/t/how-to-simulate-a-random-signal-sequence-change/47964 "2020-10-10T03:22:10Z")

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I have got a simple problem to calculate Posterior after some signal disturbances. Say the input signal is a sequence of 0 and 1 with 70% of chance is 1. And somehow we know that after the transmission, the output have …

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## [Adding a 3d curve to a 3d surface plot breaks the surface colourmap](https://discourse.julialang.org/t/adding-a-3d-curve-to-a-3d-surface-plot-breaks-the-surface-colourmap/48059)

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**Author:** [@Gregstrq](https://discourse.julialang.org/u/Gregstrq)\
**Replies:** 1\
**Last updated:** [October 9, 2020, 6:55pm UTC](https://discourse.julialang.org/t/adding-a-3d-curve-to-a-3d-surface-plot-breaks-the-surface-colourmap/48059 "2020-10-09T18:55:58Z")

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I am trying to add a 3d curve to a 3d surface plot. Without the curve, the surface plot functions as expected: it has different colours for different values along the z axis. However, if I try to add a 3d curve, the co…

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## [Pair of non-intersecting shortest paths on undirected graph](https://discourse.julialang.org/t/pair-of-non-intersecting-shortest-paths-on-undirected-graph/47988)

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**Author:** [@mastrof](https://discourse.julialang.org/u/mastrof)\
**Replies:** 6\
**Last updated:** [October 9, 2020, 5:30pm UTC](https://discourse.julialang.org/t/pair-of-non-intersecting-shortest-paths-on-undirected-graph/47988 "2020-10-09T17:30:24Z")

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Hello, I only have a very basic background in graph theory and don’t really know the ideas behind most of the algorithms that are used for path/cycle detection, yet I have somehow found myself in a position where I’m wo…

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## [Getting strange MV Normal samples based on sparse precision matrix](https://discourse.julialang.org/t/getting-strange-mv-normal-samples-based-on-sparse-precision-matrix/48001)

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**Author:** [@ElOceanografo](https://discourse.julialang.org/u/ElOceanografo)\
**Replies:** 5\
**Last updated:** [October 9, 2020, 4:02pm UTC](https://discourse.julialang.org/t/getting-strange-mv-normal-samples-based-on-sparse-precision-matrix/48001 "2020-10-09T16:02:37Z")

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I’ve noticed something odd while trying to generate Gaussian Markov random fields on an irregular mesh. In this model, a spatial field is a multivariate normal variable defined on the mesh nodes. The distribution is de…

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## [JuMP Container Benchmark](https://discourse.julialang.org/t/jump-container-benchmark/47844)

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**Author:** [@SonntagK](https://discourse.julialang.org/u/SonntagK)\
**Replies:** 3\
**Last updated:** [October 9, 2020, 1:41pm UTC](https://discourse.julialang.org/t/jump-container-benchmark/47844 "2020-10-09T13:41:29Z")

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Hello, we are Julia beginners. We want to use Julia for solving linear programs using JuMP and some external solver. For very large LP problems the model generation time can be significant. Since JuMP covers many differ…

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## [Defining binary operators inner product angle brackets](https://discourse.julialang.org/t/defining-binary-operators-inner-product-angle-brackets/48025)

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**Author:** [@kapple](https://discourse.julialang.org/u/kapple)\
**Replies:** 1\
**Last updated:** [October 9, 2020, 11:37am UTC](https://discourse.julialang.org/t/defining-binary-operators-inner-product-angle-brackets/48025 "2020-10-09T11:37:31Z")

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I’d like to define an inner product, and I’m wondering if it’s possible to call it using the angle brackets. using QuadGK # "Definition" (quote-unquote) ⟨u, v⟩ = quadgk(x -\> u(x)\*v(x), 0, 1, rtol = 1e-3) # Usage u(x) …

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## [Documentation of Clp.jl](https://discourse.julialang.org/t/documentation-of-clp-jl/48005)

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**Author:** [@JohnZ](https://discourse.julialang.org/u/JohnZ)\
**Replies:** 1\
**Last updated:** [October 8, 2020, 11:06pm UTC](https://discourse.julialang.org/t/documentation-of-clp-jl/48005 "2020-10-08T23:06:28Z")

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The documentation of the Julia wapper to the Clp solver is a bit out of date. Under options, “SolveType” is still listed but it looks like it has been replaced by “Algorithm”: https://github.com/jump-dev/Clp.jl Options …

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## [Using Z3.jl](https://discourse.julialang.org/t/using-z3-jl/48006)

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**Author:** [@Nosferican](https://discourse.julialang.org/u/Nosferican)\
**Replies:** 1\
**Last updated:** [October 8, 2020, 10:25pm UTC](https://discourse.julialang.org/t/using-z3-jl/48006 "2020-10-08T22:25:13Z")

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I am trying to use atleast and atmost to set up constraints but not sure how these work (type of the first argument). The method signature is # 1 method for generic function "atleast": \[1\] atleast(arg1::Union{CxxWrap.…

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## [Parallelism - Understanding pmap and the batch\_size parameter](https://discourse.julialang.org/t/parallelism-understanding-pmap-and-the-batch-size-parameter/15604)

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**Author:** [@mdsalerno](https://discourse.julialang.org/u/mdsalerno)\
**Replies:** 1\
**Last updated:** [October 8, 2020, 3:22pm UTC](https://discourse.julialang.org/t/parallelism-understanding-pmap-and-the-batch-size-parameter/15604 "2020-10-08T15:22:12Z")

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I am running something that looks like the following: addprocs(Sys.CPU\_THREADS) pmap(x -\> f(x, A, B, C), args) I have 48 CPU cores and thus 48 workers after running addprocs. A, B, and C are DataFrames, the largest h…

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## [ERROR: type DataType has no field optimizer\_constructor](https://discourse.julialang.org/t/error-type-datatype-has-no-field-optimizer-constructor/47920)

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**Author:** [@umbe](https://discourse.julialang.org/u/umbe)\
**Replies:** 3\
**Last updated:** [October 8, 2020, 2:54pm UTC](https://discourse.julialang.org/t/error-type-datatype-has-no-field-optimizer-constructor/47920 "2020-10-08T14:54:40Z")

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Hi everyone, I’m having a problem with JuMP/Juniper. For first I create an optimization model m = Model(Juniper.Optimizer) set\_optimizer\_attribute(m, "nl\_solver", Ipopt.Optimizer) set\_optimizer\_attribute(m…

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## [Recover MLE fit parameters in vector form](https://discourse.julialang.org/t/recover-mle-fit-parameters-in-vector-form/47972)

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**Author:** [@Albert\_Zevelev](https://discourse.julialang.org/u/Albert_Zevelev)\
**Replies:** 4\
**Last updated:** [October 8, 2020, 2:53pm UTC](https://discourse.julialang.org/t/recover-mle-fit-parameters-in-vector-form/47972 "2020-10-08T14:53:38Z")

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Suppose I fit some data using Distributions, Random; DGP\_True = LogNormal(0,1); Random.seed!(123); const d\_train = rand(DGP\_True, 1\_000); D1=Distributions.fit\_mle(LogNormal, d\_train) #Gives a fit distribution julia\> D1…

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## [How to read JSON from HTML?](https://discourse.julialang.org/t/how-to-read-json-from-html/3664)

<div class="topic-metadata">

**Author:** [@juliohm](https://discourse.julialang.org/u/juliohm)\
**Replies:** 8\
**Last updated:** [October 8, 2020, 10:20am UTC](https://discourse.julialang.org/t/how-to-read-json-from-html/3664 "2020-10-08T10:20:03Z")

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I know we can use Requests.jl to get the data, but I am not sure how we can parse the JSON with JSON.jl: using Requests, JSON r = get("https://api.github.com/users/juliohm") parse(r.data) # should JSON.Parser.parse wor…

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