sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
076f1f11155e400e64364114787d5458d1d23f9691e0acf6f05472bd5860fba5 | Julia | 3,790 | 65 | @testset "Orbital configuration" begin
# Test 1: Test conjugates
sym = Hamster.SymOrb()
def = Hamster.DefOrb()
mirr = Hamster.MirrOrb()
@test typeof(Hamster.conjugate(sym)) <: Hamster.SymOrb
@test typeof(Hamster.conjugate(def)) <: Hamster.MirrOrb
@test typeof(Hamster.conjugate(mirr)) <: Ha... |
2c933883716058b552c78fe588c19ea47dae5792b4f1a7a09908de7956467b2a | Julia | 3,922 | 109 | # uses Gaussian emission dist for mL - mR
struct HMM_ARTR_m_diff <: HiddenMarkovModels.AbstractHMM
transition_matrix::Matrix{Float64} # T[y,z] = P(y -> z)
μ::Vector{Float64}
σ::Vector{Float64}
pinit::Vector{Float64} # initial state probabilities
λreg::Vector{Float64} # regularization for μ
func... |
501a22b999bbc607c54f2ab5b889da606e24b8e5475400bf41b67626863aa701 | Julia | 3,923 | 109 | ### A Pluto.jl notebook ###
# v0.19.41
using Markdown
using InteractiveUtils
# ╔═╡ 1dc64219-66c6-44e8-8cba-bda286833f94
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 6ae0e2b3-16af-41c5-99d7-7bb4d5a5d7bb
using Statistics: mean, std, cov, cor
# ╔═╡ 5c8c9272-34dd-4aa0-a5e0-7df9eff2ba96
using DataFrame... |
28e45f5916a7795379a8e06c4c9bd264958b1ba2c1930883b7e8c95972b9d550 | Julia | 3,968 | 118 | ### A Pluto.jl notebook ###
# v0.19.41
using Markdown
using InteractiveUtils
# ╔═╡ d9d420e7-9df0-4aa5-8b18-b9ec77a9021e
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ be486509-c91a-49e9-b8ec-65fde601dab5
using Statistics: mean
# ╔═╡ a22b7e35-84ca-424a-b888-b933d5637436
using Distributions: Normal
#... |
57a4a1e5aefa7df99bc4c9af9bd5d910cfb0e40b64c3ab99d34bf9d1440845e7 | Julia | 4,015 | 114 | function brute_force_periodic_coulomb(
pos,
q,
box;
nimg::Int=3
)
N = length(pos)
phi = zeros(Float64, N)
E = 0.0
@views for i in 1:N
ri = pos[i]
for j in 1:N
rj = pos[j]
qj = q[j]
for nx in -nimg:nimg, ny in -nimg:nimg, nz in -nimg:... |
9624aa563798b40e24373933bde4360f64ec2a3424ce6d7bb769a924700f91b4 | Julia | 4,021 | 97 | using Colors
using DelimitedFiles
# RelaxationColorMap: acts in two ways:
# 1. generate a colormap to be used on display, given image type
# (which must be one of
# "T1","R1","T2","T2*","R2","R2*","T1rho","T1ρ","R1rho","R1ρ","t1","r1","t2","t2*","r2","r2*","t1rho","t1ρ","r1rho","r1ρ")
# and given t... |
edcaeb9bee2a6d5da075fdab6f51ff48d306484227f57e28de1d8ff450029f8c | Julia | 4,023 | 112 | mutable struct ZebrafishHMM_TN03 <: HiddenMarkovModels.AbstractHMM
#=
Truncated normal (TN) turning angle emissions (zero mean).
States are stored in this order:
1. Forward (forward bouts)
2. Left (left turning bouts)
3. Right (right turning bouts)
=#
const initial_probs::Vec... |
8c5d9371f0ab05c170184f2503cdb8f74f19f60fb9d4edfbb6fbe6f9fd59f3ca | Julia | 4,036 | 164 | # Kai Sandbrink, building off script by Johanni Brea
# 2023-01-31
# This script solves the Infobandit POMDP - OvB for the Pure Explore v. Pure Exploit Task
## LIBRARY IMPORT
using Pkg; Pkg.activate("."); Pkg.instantiate()
Pkg.add(["POMDPTools", "CSV"])
using POMDPs, POMDPTools, QuickPOMDPs, SARSOP, Statistics
using ... |
fd006f8bd187d5d453397d914c83307e27baa353cbd58353f62df63e24a87f4e | Julia | 4,050 | 101 | struct Gaze_ARTR_Emit
gaze::Normal{Float64} # Normal gaze distribution
logbias::Vector{Float64} # Fields for the ARTR neural activity
pseudocount::Float64 # regularize inference of fields
function Gaze_ARTR_Emit(gaze::Normal, logbias::AbstractVector{<:Real}, pseudocount::Real = 0.0)
@assert all(... |
7d0d0cbb4965c2b793af17986a720fdf429e094cf9a40e8aaac79202e8358480 | Julia | 4,115 | 89 | @testset "Optimization workflow for TB" begin
path = joinpath(@__DIR__, "test_files")
conf = get_config(filename = joinpath(path, "hconf"))
set_value!(conf, "poscar", joinpath(path, "POSCAR_gaas"))
set_value!(conf, "rllm_file", joinpath(path, "rllm.dat"))
set_value!(conf, "train_data", "Optimizer", ... |
6697c33864b502f1e92a4bb9f6d1c93f5c37e42b04e335baa8e562a08421556f | Julia | 4,197 | 85 | """
get_nearest_neighbors(r0, rs, Ts, point_grid::PointGrid; kNN=1, sorted=false)
Find the nearest neighbors (NN) of a given point `r0` within a set of points `rs` and translation vectors `Ts`.
# Arguments
- `r0::AbstractVector{T}`: The reference point in 3D space for which the nearest neighbors are to be found.
... |
ce8f38caac285979666824b59e7ff376b3fd8a2baad27e0055d80dae5ae10d81 | Julia | 4,204 | 85 | """
get_nearest_neighbors(r0, rs, Ts, point_grid::PointGrid; kNN=1, sorted=false)
Find the nearest neighbors (NN) of a given point `r0` within a set of points `rs` and translation vectors `Ts`.
# Arguments
- `r0::AbstractVector{T}`: The reference point in 3D space for which the nearest neighbors are to be found.
... |
1a72f8c67f6ad58bdcd0cffb7bf254274ee63846f007d424a0dc4cd10f52a21c | Julia | 4,211 | 82 | @testset "Fit model to GaAs eigenvalues" begin
path = joinpath(@__DIR__, "test_files")
conf = get_config(filename = joinpath(path, "hconf"))
set_value!(conf, "poscar", joinpath(path, "POSCAR_gaas"))
set_value!(conf, "rllm_file", joinpath(path, "rllm.dat"))
set_value!(conf, "train_data", "Optimizer",... |
93df88757c12aab06d1da629c9daae5d052e98697b0d20c38216c98eb004c2a6 | Julia | 4,232 | 92 | @testset "Optimization workflow for TB" begin
path = joinpath(@__DIR__, "test_files")
conf = get_config(filename = joinpath(path, "hconf"))
set_value!(conf, "poscar", joinpath(path, "POSCAR_gaas"))
set_value!(conf, "rllm_file", joinpath(path, "rllm.dat"))
set_value!(conf, "train_data", "Optimizer", ... |
d6733c03194ffce6830f235d2381599f20e5138bd06187958ff60472fd53602f | Julia | 4,241 | 78 | """
Structure
A data structure representing a crystal structure, including its lattice vectors, atomic positions, and a point grid for efficient neighbor searching.
# Fields
- `lattice::Matrix{Float64}`: A 3x3 matrix representing the lattice vectors of the crystal. Each column corresponds to a lattice vector.
- `... |
93e5305983172e1b065e1985ad612d702a7f4e24357cd4864f78dcd71c4914c1 | Julia | 4,254 | 130 | using Plots
using HDF5
using NaNStatistics
using Statistics
# MAIN PATH
DANDIPATH = "/Volumes/labs/dmclab/Pierre/NPX_Database/mPFC/Passive/" #"Your/Path/To/DandiSet/"
# FIGURE PATH
FIGPATH = "Your/path/to/figures"
# UTILS FUNCTIONS REQUIRED
include("Utils/simple_raster_units.jl")
include("Utils/simple_PSTH.jl")
# P... |
740e057df8430d3535b07bd7a9cc790aeca28dc87dc4f28b8b69b6410b5d08a0 | Julia | 4,259 | 101 | """
Ion
A mutable structure representing an ion in a crystal lattice.
# Fields
- `type::UInt8`: The type or species of the ion, denoted by its proton number.
- `pos::StaticArray{3, Float64}`: A 3D static array representing the position of the ion in Cartesian coordinates.
- `dist::StaticArray{3, Float64}`: A 3D s... |
31bcc309e495d0bc30101d77dd034165574a99ab7c1604d60998848c84c3cf0c | Julia | 4,279 | 140 | println("""
Welcome to
===========================================================================
|| _ _ _ _ _ ||
|| | | | | __ _ _ __ ___ ___ | |_ ___ _ __ (_) | | ||
|| | |_| | / _` | | '_ ` _ \\ / __| | __| / _ \\ | '__| | ... |
4c8b48321b71fac688edd52b4646c92a3d2d6406e8d0f30fd31270671ff47182 | Julia | 4,295 | 146 | using Plots
using ProgressMeter
using Glob
using HDF5
using Statistics
using Random
Random.seed!(42)
# MAIN PATH
ZENODOPATH = "Your/Path/To/Zenodo/Data"
DANDIPATH = "Your/Path/To/DandiSet/"
DANDIPATH2 = "Your/Path/To/DandiSet2/"
# FIGURE PATH
FIGPATH = "Your/path/to/figures"
# Hard-coded values used for the Nw Ww s... |
53897c50cb9a286a562eb5c51a974933f0ad45cc3963727fde3b0d1b1bb258dc | Julia | 4,333 | 117 | mutable struct ZebrafishHMM_TN04 <: HiddenMarkovModels.AbstractHMM
#=
Truncated normal (TN) turning angle emissions (zero mean). States are stored in this order:
1. Forward-Left (forward bouts, but last turn was left)
2. Forward-Right (forward bouts, but last turn was right)
3. Left (lef... |
25892bad05a12d4e0ae1c810ef4ce2d89aaa0d5ec5654fb34a4aec6d38867783 | Julia | 4,364 | 159 | module HHChannels
export Stim, run_hh
using Sundials
using Unitful
using Unitful.DefaultSymbols
struct HHParam
c_m # membrane spacific capacitance
gnabar # Na channel cross-membrane conductivity
gkbar # K channel cross-membrane conductivity
gl # Leak conductivity
ena # N... |
516827916eebd093838d770f325352f587bcd593e184bdd2338e4cff4d914481 | Julia | 4,374 | 97 | #––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
# MACAQUE VS MARMOSET - DISTRIBUTED WORKING MEMORY #
#––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
#––––––––––––––––––––––––––––––––––––––––––––––––––––#
# ... |
0f2778f4978777dd37bc5b7116cf2799863950eb34b7247f9edb442b871f1037 | Julia | 4,385 | 92 | """
get_translation_vectors(rs_ion, lattice, conf=get_empty_config(); Rmax=get_Rmax(lattice, conf), rcut=get_rcut(conf))
Generate a set of translation vectors based on ion positions `rs_ion`, the lattice vectors `lattice`, and optional configuration settings. The function returns the translation vectors that satis... |
731cef16b9fb7db2e7621222044da7838e496c9dc17143439d8e08433f95a56b | Julia | 4,385 | 92 | """
get_translation_vectors(rs_ion, lattice, conf=get_empty_config(); Rmax=get_Rmax(lattice, conf), rcut=get_rcut(conf))
Generate a set of translation vectors based on ion positions `rs_ion`, the lattice vectors `lattice`, and optional configuration settings. The function returns the translation vectors that satis... |
e97cc4d06c35e2e9aa6d29c5a2509572b13315578199fd0888cf0e7a449cce40 | Julia | 4,475 | 127 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using DelimitedFiles
usi... |
93883979075987aa6df1d65a76dbff38de0d3b30d5bf199412a312205846a5b3 | Julia | 4,489 | 131 | ### A Pluto.jl notebook ###
# v0.19.41
using Markdown
using InteractiveUtils
# ╔═╡ 32deac33-32dd-454f-96fd-1276e03d1a68
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ eca1a5cb-7862-4afe-b5ba-efeb864da254
using Statistics: mean
# ╔═╡ 54f44afc-9a47-4f55-a4fe-0e09769e86ac
using Distributions: Normal
#... |
684c974ce756d44d82ad8b78ea18d1c38f07fda9c149927d3b72eb7d2e6ebc57 | Julia | 4,495 | 119 | """
clear_hamster_output(; output_files=["hamster_out.h5", "hamster.out", "Es.dat", "vs.dat"])
Delete output files generated by Hamster.
# Keyword Arguments
- `output_files::Vector{String}`: List of filenames to remove. Defaults to
`["hamster_out.h5", "hamster.out", "Es.dat", "vs.dat"]`.
"""
function clear_hams... |
8c7c06cc92d47e612a67687c854540e66f0ed3ef7046e9c7bb9cdfa3b9406689 | Julia | 4,505 | 122 | #= Freeze some parameters of the model =#
struct HMM_ARTR_Log_Freeze <: HiddenMarkovModels.AbstractHMM
transition_matrix::Matrix{LogFloat64} # T[y,z] = P(y -> z)
h::Matrix{Float64} # h[:,z] = fields in hidden state 'z'
pinit::Vector{LogFloat64} # initial state probabilities
pseudocount::Float64 # pseudo... |
83c45fb0f377c6ee88763a8d2c4647122a2e8e0b923332cdeba6e24c99904e45 | Julia | 4,524 | 102 | const ê_z = Float64[0, 0, 1]
"""
get_sk_transform_matrix(r⃗₁, r⃗₂, axis, tmethod)
Returns a transformation matrix that aligns the z-axis along the vector connecting
`r⃗₁` and `r⃗₂`. The method of transformation depends on `tmethod`.
# Arguments
- `r⃗₁::AbstractVector`: The first position vector.
- `r⃗₂::Abstra... |
37fe11d8674ffe736879875274132f56d4294d7a48e3ae91abc2d846ebd08b90 | Julia | 4,585 | 124 | mutable struct ZebrafishHMM_G4 <: HiddenMarkovModels.AbstractHMM
#=
If allow_flipe == false, states are stored in this order:
1. Forward-Left (forward bouts, but last turn was left)
2. Forward-Right (forward bouts, but last turn was right)
3. Left (left turning bouts)
4. Right (r... |
0a0a4c10f15a9c6ca963c8fc278f7f0d96c8e9e792609a43620737e5071bc82e | Julia | 4,615 | 95 | """
run_calculation(::Val{:optimization}, comm, conf::Config; rank=0, nranks=1)
Runs the optimization process for an effective Hamiltonian model using the specified configuration.
# Arguments
- `conf::Config`: A configuration instance.
# Workflow
1. **Configuration Sampling**:
- Splits the configuration indice... |
06f884ff12a9de1924ebc41a29f8e506d6420ddeacd227eb03d42f78de101451 | Julia | 4,624 | 144 | """
**verbosity**=1
The `verbosity` parameter controls the amount of output printed to the console or written to output files.
A value of `0` disables most print statements.
Possible options:
- `0`: minimal output; most print statements are suppressed.
- `1`: normal output volume (default).
- `2`: increased output;... |
664780d592a021294e761f978e5da7992aaffd6a7aefbcd4e0bf3a821190df28 | Julia | 4,644 | 167 | module LVAChannels
export Stim, run_lva, LVAParam
using Sundials
using Unitful
using Unitful.DefaultSymbols
struct LVAParam
c_m # membrane spacific capacitance
gbar # Ca channel cross-membrane conductivity
eca # Ca channel reversal potential
gl # leak conductivity
el ... |
f201b9bff556c86b5a71f83b90260ee3b58efc2b8699aaba3a7d3d3528e21265 | Julia | 4,686 | 132 | mutable struct ZebrafishHMM_G3 <: HiddenMarkovModels.AbstractHMM
#=
States are stored in this order:
1. Forward (forward bouts)
2. Left (left turning bouts)
3. Right (right turning bouts)
In contrast to ZebrafishHMM_G4, Forward bouts have no memory of the last turning direction.
... |
f41be0f607c04962dcaeeaa71bcd6d4fa211da5e4b8d7de71a38b491af908394 | Julia | 4,747 | 98 | function wolf_eyes_data()
mat = matread(joinpath(wolf_eyes_data_dir(), "analysis.mat"))
return mat["D"]
end
#= Neural recordings corresponding to the eye gaze data =#
function wolf_eyes_artr_data_dir()
return artifact"Wolf_Eyes_ARTR_Data_20240313"
end
function wolf_eyes_artr_data()
left = matread(join... |
6a2252f3e367d50311168633d686495f747c7eac91bb873c95aece5081b0aad4 | Julia | 4,791 | 127 | """
Ion
A mutable structure representing an ion in a crystal lattice.
# Fields
- `type::UInt8`: The type or species of the ion, denoted by its proton number.
- `pos::StaticArray{3, Float64}`: A 3D static array representing the position of the ion in Cartesian coordinates.
- `dist::StaticArray{3, Float64}`: A 3D s... |
82c21bddf2201ac7511c30d48c08d2ec895d9a81992752ce948b368653fbd637 | Julia | 4,797 | 144 | using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
Pkg.instantiate() # download all the required packages
using FFTW
using LinearAlgebra
usi... |
26174a0d1d08c41798210effc23ddfd7d860e64f3be3c52d96d0e2d2e0866324 | Julia | 4,824 | 127 | mutable struct ZebrafishHMM_G3_Sym <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
const transition_matrix::Matrix{Float64} # T[i,j] = probability of transitions i -> j
σforw::Float64
turn::Gamma{Float64}
min_turn_alpha::Float64
function ZebrafishHMM_G3_Sym(
pinit_turn::Real,
... |
30f0355a5516a56ec7de1632245c712b7966d8e7a2fcbb7b329ff58947bab796 | Julia | 4,909 | 156 | # Constants used in modelling
#
# SI units are used in computations but we need to pay attention to some conventions between text files and computation
# Units used: s (second), m (meter), T (tesla), s/m^2, m^2/s, T/m
#
# In text files, e.g. bval, techo, tdelta and tsmalldel, units are s/mm^2 for b-values and ms for ti... |
6331ef8da9e4170d868e8020f7faaf2fc0142e065ff2116f1b2c527ecbacaf0d | Julia | 4,939 | 117 | @testset "DataLoader PC Eigs" begin
path = joinpath(@__DIR__, "test_files")
conf = get_empty_config()
kp, Es = Hamster.read_eigenval(joinpath(path, "EIGENVAL_gaas"), 8)
set_value!(conf, "train_data", "Optimizer", joinpath(path, "EIGENVAL_gaas"))
# Test 1: test PC training data with no validati... |
966f2bd01204323c7f000f0831cd438585f23316402858d3a1b71d99f2c01211 | Julia | 4,946 | 90 | #––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
# MACAQUE VS MARMOSET - DISTRIBUTED WORKING MEMORY #
#––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
#––––––––––––––––––––––––––––––––––––––––––––––––––––#
# ... |
972eaddc19f824d6b0defccd180edee869284506abbf0c742b432f7f650d896b | Julia | 4,946 | 114 | @testset "Profiler validation prints" begin
prof = HamsterProfiler(3)
# Test 1: verbosity > 0
val_print = @capture_out Hamster.print_val_start(prof, 1, verbosity=1)
@test val_print == " Validating model...\n"
#Test 2: verbosity = 0
val_print = @capture_out Hamster.print_val_start(prof, 1,... |
74e3d7763d19d12a380aa7da42c824387962c5b96ed3fe2199355d27354dc9cc | Julia | 4,960 | 119 | using Test: @test, @testset
using ZebrafishHMM2023: ZebrafishHMM_G3, ZebrafishHMM_G4, ZebrafishHMM_TN03, ZebrafishHMM_TN04,
ZebrafishHMM_TN3, ZebrafishHMM_TN4, ZebrafishHMM_G3_Sym, ZebrafishHMM_G4_Sym,
save_hmm, load_hmm, HMM_ARTR_Log, normalize_transition_matrix
using Distributions: Normal, Gamma
using Statist... |
68930e125f58b6e34218b805ecef2a42d10df1c9c6d96e15b7c36d66e5da1521 | Julia | 4,964 | 128 | #= Like the Elife2020 model, but with Gamma turn emissions. =#
mutable struct ZebrafishHMM_Elife2020_Gamma <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
pturn::Float64
pflip::Float64
σforw::Float64
turn::Gamma{Float64}
function ZebrafishHMM_Elife2020_Gamma(
; pinit_turn::Real,... |
2b54a205ffafbb6454c78496d9151a26e4694698845f34b449420ce008c5180b | Julia | 4,976 | 135 | # Here we try to enforce that the 3rd state has the same mean field in the left and right sides.
# Thus resembling a "forward" state.
struct HMM_ARTR_3_SYM <: HiddenMarkovModels.AbstractHMM
transition_matrix::Matrix{Float64} # T[i,j] = P(i -> j)
h::Matrix{Float64} # h[:,i] = fields in hidden state 'i'
pinit... |
a3e063328c3ab4f38eef62e5e9df35d0ad9498f21801052b1477add4a3d512de | Julia | 5,050 | 131 | struct HMM_ARTR_Log <: HiddenMarkovModels.AbstractHMM
transition_matrix::Matrix{LogFloat64} # T[y,z] = P(y -> z)
h::Matrix{Float64} # h[:,z] = fields in hidden state 'z'
pinit::Vector{LogFloat64} # initial state probabilities
pseudocount::Float64 # pseudocount for the inference of 'h'
function HMM_... |
5bae5f8cd18ded148ca0b57fef8d908cb12f1d8eae16db16270419fe1fd7c4b2 | Julia | 5,051 | 132 | struct HMM_ARTR <: HiddenMarkovModels.AbstractHMM
transition_matrix::Matrix{Float64} # T[i,j] = P(i -> j)
h::Matrix{Float64} # h[:,i] = fields in hidden state 'i'
pinit::Vector{Float64} # initial state probabilities
pseudocount::Float64 # pseudocount for the inference of 'h'
function HMM_ARTR(transi... |
f9d735fef7812dd3b329f3373b99e2761588f924f970b7a04434009a33e9ccc9 | Julia | 5,082 | 134 | mutable struct ZebrafishHMM_TN3 <: HiddenMarkovModels.AbstractHMM
#=
Truncated normal (TN) turning angle emissions, with fitted mean.
States are stored in this order:
1. Forward (forward bouts)
2. Left (left turning bouts)
3. Right (right turning bouts)
=#
const initial_probs... |
2d289191535b33c6a4cbce7645c949c0bd6c01e16ef4990dcccc8995be8799e1 | Julia | 5,097 | 193 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ cf46e4a6-0fb2-11f0-3416-d5d2b4b5f546
begin
using Pkg
Pkg.activate(Base.current_project())
Pkg.instantiate()
# loading usefules
using PlutoLinks
using PlutoUI
end
# ╔═╡ e7f1ae5a-e0f1-4052-8b33-99e8ceab7ae9
begin
# loading module... |
3fe0e28c58c636209cdf49eaf7c2b84db26c8225272bfca5a99f8373db554486 | Julia | 5,201 | 151 | @testset "Option defaults" begin
# Test 1: test verbosity
conf = get_empty_config()
@test Hamster.get_verbosity(conf) == 1
set_value!(conf, "verbosity", 0)
@test Hamster.get_verbosity(conf) == 0
set_value!(conf, "verbosity", "none")
@test_throws MethodError Hamster.get_verbosity(conf)
#... |
733a18031b63b59c604397fbff93b5bd3765c46683bee16f3c92609fba8d5ac8 | Julia | 5,215 | 125 | mutable struct ZebrafishHMM_TN04_Sym <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
const transition_matrix::Matrix{Float64}
σforw::Float64
σturn::Float64
function ZebrafishHMM_TN04_Sym(
pinit_turn::Real,
transition_matrix::AbstractMatrix{<:Real},
σforw::Real, σturn::... |
f2d79463b14f71c6f17c07cbd1942efc5ad915ac6c8029ba40f7e37b61b3f436 | Julia | 5,241 | 130 | #= This model should be the Hidden Markov model equivalent of the Markov chain model of
Karpenko et al Elife 2020
The hidden states represent two independent Markov chains, one for Forward/Turn states, and
one for Left/Right states. Left/right orientations are symmetric. Turning angle emissions
are truncated normal wi... |
b120fc5c0a0b8085a456dc01d702f40e17a44914a73f05c793dbc284948088b3 | Julia | 5,298 | 144 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using DelimitedFiles
using Sta... |
8b55ad9f6a25e174c858398392000162d94f9d484a8294cc027b9488f3ee8d13 | Julia | 5,371 | 136 | mutable struct ZebrafishHMM_TN4 <: HiddenMarkovModels.AbstractHMM
#=
Truncated normal (TN) turning angle emissions. States are stored in this order:
1. Forward-Left (forward bouts, but last turn was left)
2. Forward-Right (forward bouts, but last turn was right)
3. Left (left turning bou... |
369a279bf68657f3e445fa2e420de6c8309b03d45308dec64607dceb81f5c8dc | Julia | 5,374 | 137 | """
AdaptiveInterpolator(xmin::Float64, xmax::Float64, Ninit::Int64, Nmax::Int64, tol::Float64)
A struct that defines the settings for adaptive interpolation.
# Fields
- `xmin::Float64`: The minimum value of `x` in the interpolation range.
- `xmax::Float64`: The maximum value of `x` in the interpolation range.
- ... |
3289def14a140acce787de163f1cb2be62a7d3b2e66abca77d20af937ddd454c | Julia | 5,381 | 143 | """
OrbitalConfiguration
Abstract type for defining the configuration of orbitals w.r.t. to the overlap label for a specific TB overlap.
Subtypes:
- `SymOrb`: Symmetry in orbitals allows for interchangeable orbital types in labels.
- `DefOrb`: No symmetry; the order of orbital types in labels must be preserved ex... |
7efce820dd96f17151031d96e42b69eb62adbc8a0ee8a4b7512e5c7cc25327b8 | Julia | 5,505 | 107 | import CairoMakie
import Makie
import MAT
using HiddenMarkovModels: logdensityof, baum_welch, transition_matrix, initial_distribution, viterbi
using Statistics: mean
using Test: @test, @testset
using ZebrafishHMM2023: artr_wolf_2023_distances
using ZebrafishHMM2023: artr_wolf_2023_distances_file
using ZebrafishHMM2023:... |
aa3d069ee1a08cc429ac218a95591a9b760b4503c9d86a148550ad484dca8b21 | Julia | 5,547 | 178 | # test if frac_to_cart is inverse of cart_to_frac
function test_inverse(ε)
Ê = rand(Float64, (3, 3))
r⃗ = rand(Float64, 3)
t1 = norm(r⃗ .- Hamster.frac_to_cart(Hamster.cart_to_frac(r⃗, Ê), Ê)) < ε
t2 = norm(r⃗ .- Hamster.cart_to_frac(Hamster.frac_to_cart(r⃗, Ê), Ê)) < ε
return t1 && t2
end
# t... |
ac8e87db714e5920f64065395e85edbd58fc607dbf738194617f1e629b6fbe51 | Julia | 5,548 | 178 | # test if frac_to_cart is inverse of cart_to_frac
function test_inverse(ε)
Ê = rand(Float64, (3, 3))
r⃗ = rand(Float64, 3)
t1 = norm(r⃗ .- Hamster.frac_to_cart(Hamster.cart_to_frac(r⃗, Ê), Ê)) < ε
t2 = norm(r⃗ .- Hamster.cart_to_frac(Hamster.frac_to_cart(r⃗, Ê), Ê)) < ε
return t1 && t2
end
# t... |
9f88f1464222b548db2ecb525087118bd77898b4fe8cede8f46bf4b0949c426d | Julia | 5,615 | 201 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
5cc026a4dae3889c29cb294cb160ddbeac9bfdd2917b7e2f49f65b0e14b85e0e | Julia | 5,625 | 201 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ ae499992-896f-11f0-2889-d3a6f356213c
begin
using Pkg
Pkg.activate(Base.current_project())
Pkg.instantiate()
# loading usefules
using PlutoLinks
using PlutoUI
end
# ╔═╡ b2c5986b-9944-4430-a1be-c32ec9aedce8
LOAD = @ingredients(joi... |
450c2e2be246b8dc43f7b977e47a2d1b24dc57b786b9f4921d4554c8f7914ca5 | Julia | 5,628 | 164 | @testset "Normal loss" begin
# Test 1: MSE
y = rand(2, 4)
ŷ = rand(2, 4)
mse(y, ŷ) = mean(@. (y - ŷ)^2)
mae(y, ŷ) = mean(@. abs(y - ŷ))
loss_1 = Loss(2)
@test loss_1(y, ŷ) ≈ mse(y, ŷ)
@test Hamster.backward(loss_1, y, ŷ) ≈ FiniteDiff.finite_difference_gradient(y->loss_1(y, ŷ),... |
0a5a7e24ab21b99a157246372f51fa677a3d0c0bf369d7766d0234c17ed3a424 | Julia | 5,634 | 220 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
5f68643ed517a9fe0d989893b906e9216fe3d02e7bff6c72af3ef3e65ea990d1 | Julia | 5,672 | 160 | using Glob
using HDF5
using ProgressMeter
using DataFrames
using MixedModels, StatsModels, Statistics
using StatsPlots
using RCall, JellyMe4 #Get R packages to interpret the LME
R"library(lme4)"
R"library(emmeans)"
R"library(pbkrtest)"
R"library(MuMIn)"
# MAIN PATH
ZENODOPATH = "Your/Path/To/Zenodo/Data"
# FIGURE PA... |
a7a7610267e87e240535cd8760f1da6de6da9065e70705bd2743a7a2fdd2ab89 | Julia | 5,674 | 123 | """
run_calculation(::Val{:optimization}, comm, conf::Config; rank=0, nranks=1)
Performs the optimization using gradient descent of an effective Hamiltonian model using the specified configuration.
The routine iteratively adjusts model parameters to minimize the loss over a training set, while optionally validat... |
f34ab2af62a6348a14a38a5063ebd9dec4d2bfbca7a08f1f7a4043ee9b87d76b | Julia | 5,763 | 224 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ 8696354c-300d-11f0-2524-8dc8a1538c50
begin
using Pkg
Pkg.activate(Base.current_project())
Pkg.instantiate()
# loading usefules
using PlutoLinks
using PlutoUI
end
# ╔═╡ 44d4f416-abec-4694-93bd-9621a65759ba
begin
# loading module... |
01f20406536028bc1e503094b94ec0df482ecc1cae359750099cafbc9be74f51 | Julia | 5,817 | 226 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
361067a7942d7219b8b4424bce9a51276598eca0dcaae02031824d48e21ad3dc | Julia | 5,823 | 144 | @testset "Band index selection" begin
@test Hamster.get_band_indices(17, 5, Int[], 1) ==
[17, 18, 19, 20, 21]
@test Hamster.get_band_indices(17, 5, Int[], 4) ==
[17, 18, 19, 20, 21]
@test Hamster.get_band_indices(17, 5, [13], 1) ==
[13, 17, 18, 19, 20]
@test H... |
f803bef4ed64c400aa2122d09afc89f842d0c3864979a2bd9cfee26293448cad | Julia | 5,823 | 117 | gaas_poscar = string(@__DIR__) * "/../parse/test_files/POSCAR_gaas"
cspbbr_poscar = string(@__DIR__) * "/../strc/test_files/POSCAR_CsPbBr3"
@testset "Parameter label" begin
param_label1 = Hamster.ParameterLabel(1, Hamster.IonLabel("Ga", "As"), SVector{3}([0, 0, 0]))
@test param_label1 == Hamster.string_to_para... |
47cec71402269ec8ab3dbc7af2d857c4851b541156507cfa43f8555942745e2b | Julia | 5,907 | 133 | @testset "greedy farthest-point sampling" begin
ds = rand(3, 100)
cluster_indices = 1:5:100
num_to_take = 5
selected = Hamster.farthest_point_sampling(ds, cluster_indices, num_to_take)
@test length(unique(selected)) == num_to_take
@test all([i ∈ cluster_indices for i in selected])
end
@testset... |
678ea9a3563f1e989a90fcde62ba647bb21242cb9da5dbe311ab9fcb397e41e1 | Julia | 5,937 | 134 | # Unit tests
split_line = Hamster.split_line
@testset "split_line" begin
# Basic tests
@test split_line("This is a test") == ["This", "is", "a", "test"]
@test split_line("Hello World") == ["Hello", "World"]
# Tests with multiple spaces
@test split_line("This is a test") == ["This", "is", "a... |
2233e2f1858836b8c983b8be1b03dc9c157fd71ad3e35d8343af3981b9bb3228 | Julia | 6,084 | 149 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using LinearRNNforFMRIdigitalt... |
32887806b7907041f469519dc02c2bb34a6c74714f1dd772b3ab05252f00eaa9 | Julia | 6,130 | 154 | mutable struct ZebrafishHMM_G4_Sym <: HiddenMarkovModels.AbstractHMM
#=
Imposes Left/Right symmetry
=#
pinit_turn::Float64
const transition_matrix::Matrix{Float64} # T[i,j] = probability of transitions i -> j
σforw::Float64
turn::Gamma{Float64}
min_turn_alpha::Float64
function Zebra... |
e17b2d85f411231d4167b5d914386b59191e20f2903e3b536c704c9655f968d4 | Julia | 6,138 | 122 | """
get_eigenvalue_gradient(vs, Rs, ks, sp_mode, sp_iterator; nthreads_bands, nthreads_kpoints)
Compute the gradient `dE_dHr` of each energy eigenvalue at each k-point w.r.t. the real-space Hamiltonian matrix elements.
# Arguments
-`vs`: Matrix that contains the (sparse) eigenvectors of each eigenvalue `(m, k)`.
... |
4f7cc25e13448dfed9b1a45177107f1ddadf141dbabeb80f03b802e375664344 | Julia | 6,215 | 183 | """
print_hamster(io_stream=stdout)
Prints an ASCII art Hamster logo and description.
# Arguments
- `io_stream::IO`: The output stream to which the text should be printed. Defaults to `stdout`.
"""
function print_hamster(io_stream=stdout)
println(io_stream, """
Welcome to
============================... |
8565d3cfc2f5fe1b1019bbaca0e55a652455df44b30a70a2c5c4500da2062177 | Julia | 6,265 | 135 | """
hyper_optimize(param_values, params, comm, conf; rank=0, nranks=1, verbosity=get_verbosity(conf)) -> Float64
Evaluate a given set of hyperparameters by updating a configuration and running an optimization calculation.
# Arguments
- `param_values::Vector{Float64}`: Numerical values for each parameter to be opt... |
78b831fcd56bfd2064af046e0b02229a8db3c4205783da3b937ed1ce56710056 | Julia | 6,275 | 178 | import CairoMakie
import Dates
import Makie
import MAT
import ZebrafishHMM2023
using HiddenMarkovModels: baum_welch
using HiddenMarkovModels: viterbi
using HiddenMarkovModels: logdensityof
using Statistics: mean
using Distributions: Normal
using ZebrafishHMM2023: ATol
using ZebrafishHMM2023: normalize_transition_matrix... |
401183a5247d46c7044fab3fbdd855f0f7de6e6861f53e49219b86a3e13e2382 | Julia | 6,324 | 163 | const COMMENT_SYMBOLS = ['!', '#', '%']
"""
get_config(; filename="hconf")
Retrieves the configuration from a file if it exists, or returns an empty configuration if the file does not exist.
# Arguments
- `filename` (optional): The name of the configuration file to check for existence. Defaults to `"hconf"`.
# ... |
c96bacd164062e0dbeb8efe2c843239a4015ca062118c1552a0cf51c9376c97e | Julia | 6,364 | 198 | module KernelInterpolation
using NearestNeighbors
using Distances
using LinearAlgebra # dot, mul!
using Statistics # cor
using Random
export gaussian_kernel_interpolate, filtered_correlation
# ---------------------------------------------------------------------
# Internal helpers
# ------------------... |
e6b92ba9845da1c932411ceb938f2304be96497cf9f8a721908ac258bf6cf6eb | Julia | 6,370 | 171 | ### A Pluto.jl notebook ###
# v0.20.13
using Markdown
using InteractiveUtils
# ╔═╡ 7f95a967-426a-465f-bad4-671372ea1092
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 7d355591-dddd-4463-97b1-d53e223bd6b3
using Statistics: mean
# ╔═╡ 8398c332-235b-4f6c-ab1e-8b5fd62d2d5a
using Distributions: Gamma
# ... |
848c700e87c8a6998df8f915f05d5bcbad9204ff9809908330ce3ce0bc349e3d | Julia | 6,407 | 127 | """
Orbital{O<:Angular}(ion_type::Int64, type::O, axis::SVector{3, Float64})
Defines an orbital associated with an ion, characterized by its type, angular momentum properties, and orientation.
# Type Parameters
- `O<:Angular`: Specifies the angular momentum type, such as s, p, or d orbitals.
# Fields
- `ion_type... |
355b0a2bbec82541e07fcde4b9d525ca8fdd4099cc0083d101e487ec198817da | Julia | 6,507 | 183 | ### A Pluto.jl notebook ###
# v0.19.42
using Markdown
using InteractiveUtils
# ╔═╡ 34fc02ca-be22-4200-8dc4-6a0c9d7806bb
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ ec9792cc-1651-46f2-9eb4-216321dde7a7
using Statistics: mean
# ╔═╡ 4f5f45fe-d114-44ca-acad-455afba4c3e3
using Distributions: Normal
#... |
f4653ceaa6df7863b3a5fc86f3655d3b2bcc78bfac92f8ed89e41609352ba6c8 | Julia | 6,521 | 183 | ### A Pluto.jl notebook ###
# v0.19.42
using Markdown
using InteractiveUtils
# ╔═╡ b5731209-833e-400a-bd91-0ca87807f3df
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 5c003b8f-2e2b-498f-af41-033c6b7c691c
using Statistics: mean
# ╔═╡ cf43f299-64fe-4aeb-9a3c-4f963fa72525
using Distributions: Normal
#... |
d851aa8d05f9689fa77be875fb8c01e7d80296ae0d282bb0d73b94be506c47c3 | Julia | 6,524 | 188 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
Pkg.instantiate() # download all the required packages
using LinearRNNforFMRIdigitaltw... |
028e2b01b9af893d08fbaa8efb385bbbb561a5d54e2c1e097eb86131320f9464 | Julia | 6,557 | 193 | file_path = string(@__DIR__) * "/test_files/"
@testset "Phase factor" begin
# Test arrays
R⃗ = rand(3)
k⃗ = rand(3)
result = Hamster.exp_2πi(R⃗, k⃗)
expected = exp(2π * im * dot(k⃗, R⃗))
@test isapprox(result, expected, rtol=1e-10)
@test result isa ComplexF64
# Test matrices
Rs = r... |
21d1e91a613a773eeb31979e42dd0b446791d4f77d18266310319a828a0dbed0 | Julia | 6,618 | 188 | """
EigData
A struct for storing eigenvalue data associated with k-points.
# Fields
- `kp::Matrix{Float64}`: A matrix where each column represents a k-point.
- `Es::Matrix{Float64}`: A matrix where each column represents the eigenvalues corresponding to the respective k-point.
"""
struct EigData
kp :: Matrix... |
6e8a458ba3a7c4e9e53413a74c9f23bfefb91f52f240ef310e18e8eec66234be | Julia | 6,722 | 171 | ### A Pluto.jl notebook ###
# v0.19.42
using Markdown
using InteractiveUtils
# ╔═╡ 167996be-274e-44b7-8cb0-2dc6bebaa57c
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ a36894e5-b139-4d75-8856-f868be1b329a
using Statistics: mean
# ╔═╡ 8e80e780-817d-4486-b74d-f00b7dec33be
using Statistics: cov
# ╔═╡ 8... |
674c0b82235b3e6428642abd4dd90f91fbad3ba7007cf078f9a5a1376451ed59 | Julia | 6,755 | 209 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
Pkg.instantiate() # download all the required packages
using LinearRNNforFMRIdigitaltw... |
4142794bdaaa061eda824d0053581ca9cf6d599732f445efeeb19719c023b8cb | Julia | 6,760 | 181 | using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
##
using MultivariateStats,... |
d4bd725110dc2c3e38625c52ff9c18256b1a36ee39684b9db305a4e704b864fe | Julia | 6,773 | 261 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
81af80bd9c7957e4c1ef74f32bf4872b924accc64da814f9557d884c8df2d8ec | Julia | 6,842 | 175 | """
transform_basis(r⃗::AbstractVector, Ê::AbstractMatrix) -> AbstractVector
Transforms a vector to a new basis using a given transformation matrix.
This function takes a vector `r⃗` and transforms it into a new basis by applying the transformation matrix `Ê`. The transformation is performed by multiplying the ... |
c9280de966ee35a2d38843d671f9d1cfb1550c382607df10cd51ccd2578a946d | Julia | 6,918 | 203 | using MCMCDiagnosticTools, Statistics
using DataFrames, Gadfly
export Sampler, run_diagnostics, plot_diagnostics
"""
Change the number of samples in a sampler
"""
function Sampler(sampler::Sampler, nsamples::Int64)
return Sampler(;
params=sampler.params,
prior_range=sampler.prior_range,
... |
795f4fcc2713ec3170997373fd44da5d5c89e33c1bd0e94ede08997b38b03f59 | Julia | 6,994 | 200 | """
num_mdict::Dict{String, Array{Int}}
A dictionary mapping the orbital type to an array of `m` quantum numbers.
The keys are orbital types as strings ("s", "p", "d") and the values are arrays
containing the possible `m` values for each orbital type.
"""
#TODO: Check whether this is already implemented elsewhere ... |
a0882429ce87899ba732714574411b5e1273f11736c015a0477ce5e5f52ba652 | Julia | 7,145 | 189 | """
transform_basis(r⃗::AbstractVector, Ê::AbstractMatrix) -> AbstractVector
Transforms a vector to a new basis using a given transformation matrix.
This function takes a vector `r⃗` and transforms it into a new basis by applying the transformation matrix `Ê`. The transformation is performed by multiplying the ... |
1f21a33d811f49c787a1fbab17291ed168744caadaeaf104b38f2376c5d28422 | Julia | 7,158 | 156 | @testset "greedy farthest-point sampling" begin
ds = rand(3, 100)
cluster_indices = 1:5:100
num_to_take = 5
selected = Hamster.farthest_point_sampling(ds, cluster_indices, num_to_take)
@test length(unique(selected)) == num_to_take
@test all([i ∈ cluster_indices for i in selected])
end
@testset... |
8ff0d630b9c0485d30fd87ee7310fb2986630731266428380056b59829d894af | Julia | 7,252 | 164 | """
update_tb=haskey(conf, "Optimizer")
The `update_tb` tag determines whether/which parameters of the TB model are updated during the optimization. Defaults to `true` if an `Optimizer` block is provided.
"""
function get_update_tb(conf::Config, NV)::Vector{Bool}
update_tb = Vector{Bool}(undef, NV)
if conf... |
dfa1851fe48cd11487e35c253d3dbbc529c01dbfd27e30a761cd88f090330625 | Julia | 7,318 | 198 | """
clear_hamster_output(; output_files=["hamster_out.h5", "hamster.out", "Es.dat", "vs.dat"])
Delete output files generated by Hamster.
# Keyword Arguments
- `output_files::Vector{String}`: List of filenames to remove. Defaults to
`["hamster_out.h5", "hamster.out", "Es.dat", "vs.dat"]`.
"""
function clear_hams... |
4a26904f40ec824ee38ad0c8601422abd75ce8272c55deb71fc95b33a486bb79 | Julia | 7,452 | 219 | """
update_tb=haskey(conf, "Optimizer")
The `update_tb` tag determines whether/which parameters of the TB model are updated during the optimization. Defaults to `true` if an `Optimizer` block is provided.
"""
function get_update_tb(conf::Config, NV)::Vector{Bool}
update_tb = Vector{Bool}(undef, NV)
if conf... |
25e4d1670928d9b3af4131941c3493338deabf64bb864a26e920aa56fe7a22c9 | Julia | 7,556 | 213 | @testset "Option defaults" begin
# Test 1: test verbosity
conf = get_empty_config()
@test Hamster.get_verbosity(conf) == 1
set_value!(conf, "verbosity", 0)
@test Hamster.get_verbosity(conf) == 0
set_value!(conf, "verbosity", "none")
@test_throws MethodError Hamster.get_verbosity(conf)
#... |
7f8d52a1a3376bf38ed38f3a4c76a2070a92477839d63b645963ebb0235ab1d0 | Julia | 7,589 | 288 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
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