plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | HydroComplexity/MLCan2.0-master | model_forcings.m | .m | MLCan2.0-master/users/model_forcings.m | 83,103 | utf_8 | 2f2c052c89e7d4c9e00a82fed79821a6 | function varargout = model_forcings(varargin)
% MODEL_FORCINGS M-file for model_forcings.fig
% MODEL_FORCINGS, by itself, creates a new MODEL_FORCINGS or raises
% the existing
% singleton*.
%
% H = MODEL_FORCINGS returns the handle to a new MODEL_FORCINGS or the handle to
% the existing singlet... |
github | HydroComplexity/MLCan2.0-master | setup_root_profile4.m | .m | MLCan2.0-master/users/setup_root_profile4.m | 20,220 | utf_8 | d07b82a2e4dcced7a4622757975b792e | function varargout = setup_root_profile4(varargin)
% SETUP_ROOT_PROFILE4 M-file for setup_root_profile4.fig
% SETUP_ROOT_PROFILE4, by itself, creates a new SETUP_ROOT_PROFILE4 or raises the existing
% singleton*.
%
% H = SETUP_ROOT_PROFILE4 returns the handle to a new SETUP_ROOT_PROFILE4 or the handle to... |
github | HydroComplexity/MLCan2.0-master | setup_LAD_profile3.m | .m | MLCan2.0-master/users/setup_LAD_profile3.m | 6,917 | utf_8 | 4bb7d1471fa997bb416d81c24b1f8ce6 | function varargout = setup_LAD_profile3(varargin)
% SETUP_LAD_PROFILE3 M-file for setup_LAD_profile3.fig
% SETUP_LAD_PROFILE3, by itself, creates a new SETUP_LAD_PROFILE3 or raises the existing
% singleton*.
%
% H = SETUP_LAD_PROFILE3 returns the handle to a new SETUP_LAD_PROFILE3 or the handle to
% ... |
github | HydroComplexity/MLCan2.0-master | setup_LAD_profile4.m | .m | MLCan2.0-master/users/setup_LAD_profile4.m | 6,923 | utf_8 | 79b46a9d231d609e721cfe6351a6fbf1 | function varargout = setup_LAD_profile4(varargin)
% SETUP_LAD_PROFILE4 M-file for setup_LAD_profile4.fig
% SETUP_LAD_PROFILE4, by itself, creates a new SETUP_LAD_PROFILE4 or raises the existing
% singleton*.
%
% H = SETUP_LAD_PROFILE4 returns the handle to a new SETUP_LAD_PROFILE4 or the handle to
% ... |
github | HydroComplexity/MLCan2.0-master | ROOTSOIL.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/ROOTSOIL.m | 8,239 | utf_8 | 1627888b9ed1dc0466d11687a5d7f421 | % Dongkook
%function [rpp,rpp_wgt,krad,kax,dwat,smp,kboundary,klayer,...
% qlayer,layeruptake,layeruptake_all,mberrormm, type, hor_drainage,hor_drainage_lay]=...
% ROOTSOIL(SWITCHES, VERTSTRUC, PARAMS, VARIABLES, CONSTANTS, nspecies)
function [rpp,rpp_wgt,krad,kax,dwat,smp,kboundary,klayer,...
qlayer,layerupt... |
github | HydroComplexity/MLCan2.0-master | ROOTS_NOHR.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/ROOTS_NOHR.m | 5,185 | utf_8 | 13100f891c4639132446e58860946559 |
function [rpp, rpp_weight, krad, kax] = ROOTS_NOHR( SWITCHES, VERTSTRUC, PARAMS, VARIABLES )
%=========================================================================
% This code solves the model for water flow in the plant root system.
% The upper boundary condition is set to the transpiration rate while
% the lo... |
github | HydroComplexity/MLCan2.0-master | FLUXES_WATER_SOIL.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/FLUXES_WATER_SOIL.m | 14,146 | utf_8 | e8fbe1857efbabbd019d3a80f4ef6b78 |
function [VARIABLES] = FLUXES_WATER_SOIL (PARAMS, VARIABLES, CONSTANTS,...
FORCING, SWITCHES)
%=========================================================================
% Solve surface energy balance (With snow and No Litter)
%
% Written by Juan Quijano, UIUC, 2013
% All rights reserved!
%
%----------------------... |
github | HydroComplexity/MLCan2.0-master | FLUXES_WATER_SOIL_LITTER.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/FLUXES_WATER_SOIL_LITTER.m | 14,517 | utf_8 | e7cb5a69fd7f7a4230821f288345f56f |
function [VARIABLES] = FLUXES_WATER_SOIL_LITTER (PARAMS, VARIABLES, CONSTANTS,...
FORCING, SWITCHES)
%=========================================================================
% Solve surface energy balance with a snow-litter pack
%
% Written by Juan Quijano, UIUC, 2013
% All rights reserved!
%
%-----------------... |
github | HydroComplexity/MLCan2.0-master | correctheat.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/correctheat.m | 2,908 | utf_8 | 7525f122bd2b4b0f94bf890bdf4bc8fd |
function [Ts_new] = correctheat (Ts_new, Ts_prev, Tf, TKsoil_h, cpv, volliq, volice,...
rho_liq, rho_ice, bsw, grav, psi0, znode, dz, dt, nl_soil, porsl, alph,...
Hg, wice, wliq)
if sum(Ts_new < 0)>0;
stop = 43;
end
% This function corrects the energy balance in the soil for those cases
%... |
github | HydroComplexity/MLCan2.0-master | FLUXES_WATER_SOIL.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/Previous(2016.4.5)/FLUXES_WATER_SOIL.m | 13,946 | utf_8 | 5d25cd4173e4f1bd49af2ff2c0c10431 |
function [VARIABLES] = FLUXES_WATER_SOIL (PARAMS, VARIABLES, CONSTANTS,...
FORCING, SWITCHES)
%=========================================================================
% Solve surface energy balance (With snow and No Litter)
%
% Written by Juan Quijano, UIUC, 2013
% All rights reserved!
%
%----------------------... |
github | HydroComplexity/MLCan2.0-master | FLUXES_WATER_SOIL_LITTER.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/Previous(2016.4.5)/FLUXES_WATER_SOIL_LITTER.m | 14,105 | utf_8 | 92624e0f5bb46e6b6b22443acf4f4813 |
function [VARIABLES] = FLUXES_WATER_SOIL_LITTER (PARAMS, VARIABLES, CONSTANTS,...
FORCING, SWITCHES)
%=========================================================================
% Solve surface energy balance with a snow-litter pack
%
% Written by Juan Quijano, UIUC, 2013
% All rights reserved!
%
%-----------------... |
github | HydroComplexity/MLCan2.0-master | CN_biofluxes.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/CN_biofluxes.m | 1,843 | utf_8 | 34ef036502c6854ba41e3a97be705125 | % This function computes the fluxes of bioturbatino in each
% Horizon
function [Cin_m2, Cout_m2, difbio_m2, Bioflux] = CN_biofluxes (Clnew, dz, deltaz, D, BC)
nlayer = length(Clnew);
% allocate vectors
Bioflux = zeros(nlayer,2);
Cin_m2_m = zeros(nlayer,2);
Cout_m2_m = zeros(nlayer,2);
Cin_m2 = zeros(nlayer,1);
Cout_... |
github | HydroComplexity/MLCan2.0-master | CN_computephi.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/CN_computephi.m | 4,958 | utf_8 | fc9ee85ad7b1c87f2a4711474ddfd1c9 |
% compute PHI
function [phi, PHI, MIN_net, IMM_net, MIN_gross, IMM_gross, Nreg, DECl, DECh] = CN_computephi (VARIABLES, PARAMS, SWITCHES, fSd, fTd, phi, ADD, CNa)
Cl = VARIABLES.Cl;% Cl = carbon concentration in litter pool [gC / m^3]
Ch = VARIABLES.Ch;% Ch = carbon concentration in humus pool [gC / m^3... |
github | HydroComplexity/MLCan2.0-master | core_N.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/core_N.m | 48,535 | utf_8 | 385336efcd61c0da1dda77349bb19e1e | % Dongkook Woo - Comment
% function []= core_N(VARIN)
% % Generate char for root cut type
% % Decode info for root cutting
% if VARIN(4) == 1
% strcut = 'NN';
% elseif VARIN(4) == 2
% strcut = 'OH';
% elseif VARIN(4) == 3
% strcut = 'AH1';
% elseif VARIN(4) == 4
% strcut = 'AH2';
% end
%
%
% % Generate VA... |
github | HydroComplexity/MLCan2.0-master | CN_bioturbation.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/CN_bioturbation.m | 6,977 | utf_8 | 03fe11274036a97fa91f3d28064f8250 |
function [Cl, VARIABLES] = CN_bioturbation (PARAMS, VARIABLES, CONSTANTS, FORCING, VERTSTRUC, SWITCHES, Cl, fTd)
% ALLOCATE MATRICES TO USE
nspecies = PARAMS.CanStruc.nspecies;
% Dongkook Woo - Edit
if SWITCHES.CN.NupRootBiomass == 1
CNveg = nan(1,nspecies);
elseif SWITCHES.CN.NupRootBiomass == 0
CNabove = na... |
github | HydroComplexity/MLCan2.0-master | CN_biofluxes.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/Previously.here.Delete.at.the.end/CN_biofluxes.m | 659 | utf_8 | 26aa74e5833c8ec10c6624cb3f0735ae | % This function computes the fluxes of bioturbatino in each
% Horizon
function [Cin_m3, Cout_m3, Cin_m2, Cout_m2] = CN_biofluxes (Clsim, deltaz_diff, dz_diff, top, bottom,D)
nlayer = length(Clsim);
% allocate vectors
Cin_m2 = nan(nlayer,1);
Cout_m2 = nan(nlayer,1);
Cin_m2(1) = top(1);
Cout_m2(1) = -(Clsim(2)-Clsim... |
github | HydroComplexity/MLCan2.0-master | CN_computephi.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/Previously.here.Delete.at.the.end/CN_computephi.m | 4,494 | utf_8 | db0bb551254649e1789dd5022f524aaa |
% compute PHI
function [phi, PHI, MIN_net, IMM_net, MIN_gross, IMM_gross, Nreg, DECl] = CN_computephi (VARIABLES, PARAMS, SWITCHES, fSd, fTd, phi, ADD, CNa)
Cl = VARIABLES.Cl;% Cl = carbon concentration in litter pool [gC / m^3]
Ch = VARIABLES.Ch;% Ch = carbon concentration in humus pool [gC / m^3]
Cb =... |
github | HydroComplexity/MLCan2.0-master | CN_bioturbation.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/CN_MODEL/Previously.here.Delete.at.the.end/CN_bioturbation.m | 6,109 | utf_8 | 7807bb829d1cb69ca2cc8eb7859d79bc |
function [Cl, VARIABLES] = CN_bioturbation (PARAMS, VARIABLES, CONSTANTS, FORCING, VERTSTRUC, SWITCHES, Cl, fTd)
% ALLOCATE MATRICES TO USE
nspecies = PARAMS.CanStruc.nspecies;
CNveg = nan(1,nspecies);
% INPUTS:
% DE REFERENCE BLOCKS
% VARIABLES structure
timestep = VARIABLES.timestep; % timestep = Curren... |
github | HydroComplexity/MLCan2.0-master | rootmodel.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/rootmodel.m | 2,821 | utf_8 | 8ce67fac40ff8dcb26be4335d12ab6a7 |
function [rpp] = rootmodel(nl_soil,nl_root,z,etr,smp,krad,kax)
%=========================================================================
% This code solves the model for water flow in the plant root system.
% The upper boundary condition is set to the transpiration rate while
% the lower boundary is set to no flux... |
github | HydroComplexity/MLCan2.0-master | soilmodel.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/soilmodel.m | 9,505 | utf_8 | 2fe9dac99848e12cf3d3a4a193c0d62d | % Dongkook
%function [dwat,psicom,kf,kl,fluxt,fluxb,flux_s,flux_sr,flux_sr_all,mberrormm,type, hor_drainage, hor_drainage_lay] ...
function [dwat,psicom,kf,kl,fluxt,fluxb,flux_s,flux_sr,flux_sr_all,mberrormm,type, hor_drainage, hor_drainage_lay,flux_Ss] ...
= soilmodel(nl_soil,dtime,thetas,...
... |
github | HydroComplexity/MLCan2.0-master | tridia.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/tridia.m | 1,388 | utf_8 | ded5bb3c94ddf4beca2eab122a647198 |
function x = tridia(n, a, b, c, r)
%=========================================================================
% TRIDIA solves triadiagonal systems of equations using Thomas algorithm.
% The system of equation to be solved has the form (Ax = d), where A is
% the triadiagonal matrix with [a b c] forming its diagonals.... |
github | HydroComplexity/MLCan2.0-master | matrices.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/matrices.m | 3,513 | utf_8 | 7d486c84290e2bd48e9b43396efb9438 | %function [A,KK,GG,CC,KKr] = matrices(Ne,Ce,Ke,dz,dt,ft,fb,zsoi,krad,nspecies)
function [A,KK,GG,CC,KKr,CC_Ss] = matrices(Ne,Ce,Ke,dz,dt,ft,fb,zsoi,krad,nspecies,thetas,thetaant)
%=========================================================================
% This code computes the matrices that compose the linear system ... |
github | HydroComplexity/MLCan2.0-master | fimplicit.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/FUNCTION_SOILS/fimplicit.m | 7,974 | utf_8 | 77ff732ffb22f152245138ca458d2526 |
function [dwat,psicom,kf,kl,fluxt,fluxb,flux_s,flux_sr,mberrormm,type] ...
= fimplicit(nl_soil,dtime,thetas,...
pentry,bpar,ks,zsoi,dzsoi,zisoi,...
thetai,ki,psii,...
psiroot1,psiroot2,krad1,krad2,pthr)
... |
github | HydroComplexity/MLCan2.0-master | soilmodel_i.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/FUNCTION_SOILS/soilmodel_i.m | 8,471 | utf_8 | f69e67ba8c1847ca44de46828e5ecb94 |
function [dwat,psicom,kf,kl,fluxt,fluxb,flux_s,flux_sr,flux_sr_all,mberrormm,type] ...
= soilmodel(nl_soil,dtime,thetas,...
pentry,bpar,ks,zsoi,dzsoi,zisoi,...
thetai,...
psiroot,krad,pthr,nspecies)
... |
github | HydroComplexity/MLCan2.0-master | fimplicit_original.m | .m | MLCan2.0-master/LOCAL_CODES/ROOT_SOIL/IMPLICIT/FUNCTION_SOILS/fimplicit_original.m | 7,013 | utf_8 | fc8231a50fd83426291b7fe4eb55cc48 |
function [dwat,psicom,kf,kl,fluxt,fluxb,flux_s,flux_sr,mberrormm,type] ...
= fimplicit(nl_soil,dtime,thetas,...
pentry,bpar,ks,zsoi,dzsoi,zisoi,...
thetai,ki,psii,...
psiroot,krad,pthr,type)
%=========================... |
github | HydroComplexity/MLCan2.0-master | Teffentropy.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/Teffentropy.m | 1,091 | utf_8 | 0720d58a1025a93a4a1ed9999c2b8947 | % % This function is used to compute the Effective Temperature
% % from the Canopy Using the Entropy Calculated at each
% % Level
%
% function [remain] = Teffentropy (SSeco_tot, SSsoil_in, SScan_in, SSsoildif_out_tot, SScandif_out_tot, ...
% LWemi_net, LE_net, H_net, SSnewXout, Teffe)
%
% remain ... |
github | HydroComplexity/MLCan2.0-master | Teffentropy2.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/Teffentropy2.m | 469 | utf_8 | c27b01e9f4b5bf6bb5f994d7a7d9aab8 | % This function is used to compute the Effective X
% from the Canopy Using the Entropy Calculated at each
% Level
function [remain] = Teffentropy2(SScanLW_out_tot, SSsoilLW_out_tot, ...
SSnetLW_in, SScanLW_in_tot, SSsoilLW_in_tot,...
LWout_net, Teffent, Xnet)
... |
github | HydroComplexity/MLCan2.0-master | ENTROPY_results.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/ENTROPY_results.m | 9,982 | utf_8 | 67c949f7f5fa568848c0c6a921de4c64 |
function [SSresults] = ENTROPY_results(SSresults, VERTSTRUC, PARAMS, VARIABLES)
% Compute the output of entropy and save in different variables
fLAIz = VERTSTRUC.fLAIz;
nspecies = PARAMS.CanStruc.nspecies;
% SHORTWAVE
SScandir_in = SSresults.SScandir_in;
SScandir_in_tot = SSresults.SScandir_in_tot;
SScandir_out =... |
github | HydroComplexity/MLCan2.0-master | ENTROPY_SW.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/ENTROPY_SW.m | 12,602 | UNKNOWN | 88e4f93380cdb00d4d4d7c917219e288 |
function [SSresults] = ENTROPY_SW (SWcandir_in, SWcandir_out, SWcandif_in, SWcandif_out,...
SWsoildir_in, SWsoildir_out, SWsoildif_in, SWsoildif_out,...
SWout, fdiff, entropymethod, Rg, zicesl, PARAMS)
%===============================... |
github | HydroComplexity/MLCan2.0-master | ENTROPY_PHO.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/ENTROPY_PHO.m | 3,905 | utf_8 | 8d95c95317704f467e4de42f7361e001 |
function [SSresults] = ENTROPY_PHO (VARIABLES, SWITCHES, VERTSTRUC, PARAMS, SSresults)
%=========================================================================
% This code computes the fluxes of entropy due to photosynthesis. Onlyt
% the incoming fluxes are computed. It is assumed that all the energy
% captured ... |
github | HydroComplexity/MLCan2.0-master | ENTROPY_LW.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/ENTROPY_LW.m | 11,718 | utf_8 | 79a72b45cb2b206d2f93c7a3055ac269 |
function [SSresults] = ENTROPY_LW (LWabs_canM, LWabs_soilM, LWemit_soil, LWemit_sun, LWemit_shade,...
LWin, LWout, Tatop, Tsurf, boltz, entropymethod, zicesl, ...
PARAMS, VARIABLES, CONSTANTS, SWITCHES, SSresults)
%=================================... |
github | HydroComplexity/MLCan2.0-master | ENTROPY_net_results.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/ENTROPY_net_results.m | 483 | utf_8 | a3d61590e1c9fff66adac99525e67467 |
function [SSresults] = ENTROPY_net_results(SSresults)
% Compute the output of entropy and save in different variables
% SHORTWAVE
SScandir_net_in = SSresults.SSnetdir_in;
SScandir_net_out = SSresults.SSnetdir_out;
SScandif_net_in = SSresults.SSnetdif_in;
SScandif_net_out = SSresults.SSnetdif_out;
% LONGWAVE
SSca... |
github | HydroComplexity/MLCan2.0-master | COMPUENTROPY.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/COMPUENTROPY.m | 4,945 | utf_8 | e4c0d3d135af16505ea0618146dd4149 |
function [SSresults] = ...
COMPUENTROPY (SWcandir_in, SWcandir_out, SWcandif_in, SWcandif_out,...
SWsoildir_in, SWsoildir_out, SWsoildif_in, SWsoildif_out,...
SWout, fdiff,LWabs_canM, LWabs_soilM, LWemit_soil, LWemit_sun, LWemit_shade,...
LWout, Tsurf, ... |
github | HydroComplexity/MLCan2.0-master | Xeffentropy2.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/Xeffentropy2.m | 946 | utf_8 | 2a0de4ffe13c87cea3523f1d0129440c | % % This function is used to compute the Effective Temperature
% % from the Canopy Using the Entropy Calculated at each
% % Level
%
% function [remain] = Teffentropy (SSeco_tot, SSsoil_in, SScan_in, SSsoildif_out_tot, SScandif_out_tot, ...
% LWemi_net, LE_net, H_net, SSnewXout, Teffe)
%
% remain ... |
github | HydroComplexity/MLCan2.0-master | Xeffentropy.m | .m | MLCan2.0-master/LOCAL_CODES/ENTROPY/Xeffentropy.m | 468 | utf_8 | 0727b9efcde19b53b812e4d08d4da511 | % This function is used to compute the Effective X
% from the Canopy Using the Entropy Calculated at each
% Level
function [remain] = Xeffentropy(SScanLW_out_tot, SSsoilLW_out_tot, ...
SSnetLW_in, SScanLW_in_tot, SSsoilLW_in_tot,...
LWout_net, Teffent, Xnet)
... |
github | HydroComplexity/MLCan2.0-master | TRIDIAG.m | .m | MLCan2.0-master/LOCAL_CODES/NUMERICAL/OTHERS/TRIDIAG.m | 1,389 | utf_8 | 5d14d492daf1ae5e31bdabea1a80d003 |
function x = TRIDIAG(n, a, b, c, r)
%=========================================================================
% TRIDIA solves triadiagonal systems of equations using Thomas algorithm.
% The system of equation to be solved has the form (Ax = d), where A is
% the triadiagonal matrix with [a b c] forming its diagonals... |
github | HydroComplexity/MLCan2.0-master | SW_ATTENUATION.m | .m | MLCan2.0-master/LOCAL_CODES/CANOPY/SW_ATTENUATION.m | 9,129 | utf_8 | 27854e1ea1c5fa7075d6cf3da9f56e8a |
function [sun_abs, shade_abs, candir_in, candir_out, candif_in, candif_out,...
soil_abs, soildir_in, soildir_out, soildif_in, soildif_out, fsun, fshade, diffdn, diffup, ...
radabs_tot, radlost, radremain] = ...
SW_ATTENUATION (beam_top, diff_top, LAIz, ...
trans, refl, ... |
github | HGGM-LIM/Efficient-ART-Split-Bregman-Reconstruction-master | ARTReconstruction_Fast.m | .m | Efficient-ART-Split-Bregman-Reconstruction-master/ARTReconstruction_Fast.m | 3,680 | utf_8 | 7be370e9f58c4115047afef13d0ecc24 | % [x, errors, xNorms] = ARTReconstruction_Fast(A, b, relaxationParameter, nbIterations, x0)
%
% Algebraic reconstruction technique, also known as Kaczmarz method.
%
% Inputs:
%
% A = System matrix or Jacobian matrix, nr x nc
% = d, data, nr x 1
% nbIterations ... |
github | andersonwinkler/HCP-master | hcp2solar.m | .m | HCP-master/share/hcp2solar.m | 5,861 | utf_8 | 7de36f51384a096cfc7781c9e3145a90 | function hcp2solar(restrfile,unrestrfile,pedfile,hhoption)
% Takes a "restricted" and an "unrestricted" CSV files from the HCP
% and generates a pedigree file that can be used in SOLAR.
%
% Usage:
% hcp2solar(restrfile,unrestrfile,pedfile,hhoption)
%
% restrfile : CSV file downloaded from https://db.humanconnectome... |
github | pytaunay/weno-tests-master | uinit.m | .m | weno-tests-master/matlab/burgers_1d/uinit.m | 185 | utf_8 | 2004e879de65b23f729e6b18be70ce30 | %%% Function: uinit
%%% Returns the initial distribution of points to advect
function u0 = uinit( xcell )
%u0 = 0.25 + 0.5*sin(pi*xcell);
u0 = (xcell>=0) .* (xcell <= 0.5);
end
|
github | pytaunay/weno-tests-master | numerical_flux.m | .m | weno-tests-master/matlab/burgers_1d/numerical_flux.m | 2,349 | utf_8 | d85e34be7e80cbf62092132dca19e32c | %%% 09/2016 Pierre-Yves Taunay
%%% Function: numerical_flux
%%% Computers the numerical flux of user's choosing
%%% Inputs:
%%% - un, up: reconstructed values at the boundary of interest (un = u_{-}
%%% or u_{L})
%%% - DT, DX: self-explanatory
%%% - fluxFunc, dfluxFunc: a function handle to the analytical flux
%%% func... |
github | pytaunay/weno-tests-master | WENO5LF1d.m | .m | weno-tests-master/matlab/euler_1d/WENO5LF1d.m | 4,615 | utf_8 | 423a8601b78126d25722fb8fe3d5a792 | function res = WENO5LF1d(a,w,dx)
% *************************************************************************
% Input: u(i) = [u(i-2) u(i-1) u(i) u(i+1) u(i+2)];
% Output: res = df/dx;
%
% Based on:
% C.W. Shu's Lectures notes on: 'ENO and WENO schemes for Hyperbolic
% Conservation Laws'
%
% coded by Manuel Diaz, 02.10... |
github | pytaunay/weno-tests-master | jacobian.m | .m | weno-tests-master/matlab/euler_1d/jacobian.m | 1,164 | utf_8 | 612543b63324ea278f90671334f02530 | %%% 09/2016 Pierre-Yves Taunay
%%% Function: Jacobian
%%% Input: the vector of physical quantities q and the value of gamma
%%% for the gas of interest
%%% The function calculates the Jacobian of the flux function based on the
%%% input vector q.
%%% q fed to the Jacobian function is the result of the Roe averages.
%... |
github | pytaunay/weno-tests-master | speedOfSound.m | .m | weno-tests-master/matlab/euler_1d/speedOfSound.m | 162 | utf_8 | 7c4bc24b41c3445fcd410b9aa5ae7bee | % Calculates the speed of sound
function a = speedOfSound(q,GAM,stateOrPhysical)
rho = q(:,1);
P = pressure(q,GAM,stateOrPhysical);
a = sqrt(GAM.*P./rho);
end |
github | pytaunay/weno-tests-master | flux.m | .m | weno-tests-master/matlab/euler_1d/flux.m | 289 | utf_8 | 2ad5480c8e4e8d5d7dc610585903f9e7 | %%% 09/2016
%%% Euler flux vector
function Fq = flux( q, GAM )
q1 = q(:,1);
q2 = q(:,2);
q3 = q(:,3);
Fq = zeros(size(q,1),3);
Fq(:,1) = q2;
Fq(:,2) = q2.^2./(2*q1)*(3-GAM) + (GAM-1)*q3;
Fq(:,3) = (1-GAM)*q2.^3./(2*q1.^2) + GAM*q3.*q2./q1;
end
|
github | pytaunay/weno-tests-master | eigMat.m | .m | weno-tests-master/matlab/euler_1d/eigMat.m | 889 | utf_8 | 79257c0dafc9cce6363568c05592b4b8 | %%% 09/2016 P-Y Taunay
%%% FUnction eigMat calculates the eigenvalues and eigenvectors of the
%%% Jacobian matrix of the system based on the Roe decomposition
function [D,R,Rinv] = eigMat( q, a, GAM )
% No scaling necessary since we are based on the Roe decomposition
rho = q(:,1); % rho
u = q(:,2); % u
e0 = q(:,3); ... |
github | pytaunay/weno-tests-master | pressure.m | .m | weno-tests-master/matlab/euler_1d/pressure.m | 261 | utf_8 | 99086134256c6f2c84c89dc34c194b5c | % Calculates the pressure
function P = pressure(q,GAM,stateOrPhysical)
rho = q(:,1);
q2 = q(:,2);
q3 = q(:,3);
if( strcmp(stateOrPhysical,'state') )
u = q2./rho;
e0 = q3./rho;
else
u = q2;
e0 = q3;
end
P = rho.*(GAM-1).*(e0 - 1/2*u.^2);
end |
github | pytaunay/weno-tests-master | numerical_flux.m | .m | weno-tests-master/matlab/euler_1d/numerical_flux.m | 2,346 | utf_8 | 2b4f0b57cd36a8ac8048aed08cea7c0b | %%% 09/2016 Pierre-Yves Taunay
%%% Function: numerical_flux
%%% Computers the numerical flux of user's choosing
%%% Inputs:
%%% - un, up: reconstructed values at the boundary of interest (un = u_{-}
%%% or u_{L})
%%% - DT, DX: self-explanatory
%%% - fluxFunc, dfluxFunc: a function handle to the analytical flux
%%% func... |
github | pytaunay/weno-tests-master | uinit.m | .m | weno-tests-master/matlab/advection_1d/uinit.m | 382 | utf_8 | e89e9903291121f3a0ac6c4b6dfd49e4 | %%% Function: uinit
%%% Returns the initial distribution of points to advect
function u0 = uinit( xcell )
u0 = exp(-log(2)*(xcell+0.7).^2/9e-4).*(xcell>=-0.8).*(xcell<=-0.6);
u0 = u0 + 1.*(xcell >= -0.4).*(xcell <= -0.2);
u0 = u0 + (1-abs(10*xcell-1)).*(xcell>=0).*(xcell<=0.2);
u0 = u0 + sqrt(... |
github | pytaunay/weno-tests-master | numerical_flux.m | .m | weno-tests-master/matlab/advection_1d/numerical_flux.m | 2,346 | utf_8 | 2b4f0b57cd36a8ac8048aed08cea7c0b | %%% 09/2016 Pierre-Yves Taunay
%%% Function: numerical_flux
%%% Computers the numerical flux of user's choosing
%%% Inputs:
%%% - un, up: reconstructed values at the boundary of interest (un = u_{-}
%%% or u_{L})
%%% - DT, DX: self-explanatory
%%% - fluxFunc, dfluxFunc: a function handle to the analytical flux
%%% func... |
github | anatoli-ulmer/HoloShow-master | statusbar.m | .m | HoloShow-master/src/gui/statusbar.m | 12,315 | utf_8 | 6176fc5787ed76c11528600131d2d655 | function statusbarHandles = statusbar(varargin)
%statusbar set/get the status-bar of Matlab desktop or a figure
%
% statusbar sets the status-bar text of the Matlab desktop or a figure.
% statusbar accepts arguments in the format accepted by the <a href="matlab:doc sprintf">sprintf</a>
% function and returns the ... |
github | anatoli-ulmer/HoloShow-master | parameter_window.m | .m | HoloShow-master/src/gui/parameter_window.m | 4,868 | utf_8 | ba626d3eb73aa84b95c6014dd75f5f5e | function varargout = parameter_window(app, varargin)
% PARAMETER_WINDOW MATLAB code for parameter_window.fig
% PARAMETER_WINDOW, by itself, creates a new PARAMETER_WINDOW or raises the existing
% singleton*.
%
% H = PARAMETER_WINDOW returns the handle to a new PARAMETER_WINDOW or the handle to
% the... |
github | anatoli-ulmer/HoloShow-master | uipickfiles.m | .m | HoloShow-master/src/gui/uipickfiles/uipickfiles.m | 60,084 | utf_8 | cce528186b62d6264b291028da07ebff | function out = uipickfiles(varargin)
%uipickfiles: GUI program to select files and/or folders.
%
% Syntax:
% files = uipickfiles('PropertyName',PropertyValue,...)
%
% The current folder can be changed by operating in the file navigator:
% double-clicking on a folder in the list or pressing Enter to move further
% dow... |
github | anatoli-ulmer/HoloShow-master | find_CC_testing.m | .m | HoloShow-master/src/analysis/find_CC_testing.m | 4,669 | utf_8 | 9081d27c03bd9ca70d45bd45ace52ad3 | %% modified segmentation algorithm from http://de.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html
function centroids = find_CC_testing(hologram, varargin)
show_img = true;
min_dist = 100;
int_thresh = 5;
r_ignored = 75;
r_dilate = 30;
r_erode = 20;
fudge_factor = 1;
crop = 1;
if exis... |
github | anatoli-ulmer/HoloShow-master | find_CC.m | .m | HoloShow-master/src/analysis/find_CC.m | 4,519 | utf_8 | 6b007ef91b091ac0645afee9e7eac8aa | %% modified segmentation algorithm from http://de.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html
function centroids = findCrossCorrelation(hologram, varargin)
show_img = true;
min_dist = 100;
int_thresh = 5;
r_ignored = 75;
r_dilate = 15;
r_erode = 10;
fudge_factor = 1;
crop_factor =... |
github | anatoli-ulmer/HoloShow-master | findCrossCorrelations.m | .m | HoloShow-master/src/analysis/findCrossCorrelations.m | 6,639 | utf_8 | 6d962993552643c6673ceffffbdef52d | %% modified segmentation algorithm from http://de.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html
function centroids = findCrossCorrelations(app, hologram, parameter)
show_img = true;
show_segmenation = false;
min_dist = 100;
int_thresh = 5;
r_ignored = 75;
r_dilate = 15;
r_erode = 10... |
github | anatoli-ulmer/HoloShow-master | rscan.m | .m | HoloShow-master/src/analysis/rscan.m | 8,646 | utf_8 | 91f5e15191afcfede49df4d5c9e8ed6c | % % % % function [rdat,xcoord,ycoord] = rscan(M0,varargin)
% % % %
% % % % % RDAT = RSCAN(M0,VARARGIN)
% % % % % Get radial scan of a matrix using the following procedure:
% % % % % [1] Get coordinates of a circle around an origin.
% % % % % [2] Average values of points where the circle passes through.
% % % % % [3] Ch... |
github | anatoli-ulmer/HoloShow-master | find_obj.m | .m | HoloShow-master/src/analysis/find_obj.m | 3,665 | utf_8 | b1ec62865918c9652418e0e038705f3e | %% modified segmentation algorithm from http://de.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html
function obj_area = find_obj(recon)
% basically the same function as find_CC but without cutting the
% autocorrelation term in the middle
%% Step 1: Read Image
fudgeFactor = 0.5;
% Iorig... |
github | anatoli-ulmer/HoloShow-master | split_dataset.m | .m | HoloShow-master/src/analysis/FRC/split_dataset.m | 1,908 | utf_8 | bcbc38c44e5084c312cd8ba01dd007c7 | function [imageA,imageB] = split_dataset(input,varargin)
% Split the input dataset into two downsampled sets by following algorithm
% from:
% Hantke, M., Hasse, D., Maia, F. et al. High-throughput imaging of heterogen-
% eous cell organelles with an X-ray laser. Nature Photon 8, 943–949 (2014).
% https://doi.org/10.1... |
github | minsulander/helisharp-master | heliread.m | .m | helisharp-master/scripts/octave/heliread.m | 1,941 | utf_8 | a56cd7297df387a80f21ce5e6d35abd5 | %HELIREAD Read a HeliLib data file
%
% [data,header] = HELIREAD(file)
%
% The file may either be a binary BlackBox log file (.bblog) or CSV file.
% Should work both in Matlab and Octave.
% Returns data as a structure and the file header.
function [data,header]=heliread(filename)
data={};
if (strcmp(filename(e... |
github | minsulander/helisharp-master | trimdataplot.m | .m | helisharp-master/scripts/octave/trimdataplot.m | 1,537 | utf_8 | b3cef243f6847dec71940457b2e57916 | %TRIMDATAPLOT Plot trim data from HeliLib
% [data,header] = TRIMDATAPLOT(file)
% see also HELIREAD for file formats and such
function [data,header] = trimdataplot(file)
disp('Loading...')
[data,header]=heliread(file);
disp('Plotting...')
% Power required curve
figure(1)
plot(data.u,(data.Helicopter.powerreq)/10... |
github | minsulander/helisharp-master | simdataplot.m | .m | helisharp-master/scripts/octave/simdataplot.m | 1,797 | utf_8 | e85be16863df41852c63f4a24453b133 | %SIMDATAPLOT Plot simulation data from HeliLib
% [data,header] = SIMDATAPLOT(file)
% see also HELIREAD for file formats and such
function [data,header] = simdataplot(file)
disp('Loading...')
[data,header]=heliread(file);
disp('Plotting...')
figure(1)
plot(data.t,[data.Helicopter.theta_0 data.Helicopter.theta_si... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | refinegui2.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/refinegui2.m | 15,992 | utf_8 | 72f31930a9ea624ad58ce96b71540da7 | function varargout = refinegui2(varargin)
% REFINEGUI2 MATLAB code for refinegui2.fig
% REFINEGUI2, by itself, creates a new REFINEGUI2 or raises the existing
% singleton*.
%
% H = REFINEGUI2 returns the handle to a new REFINEGUI2 or the handle to
% the existing singleton*.
%
% REFINEGUI2('CALL... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | timeimagegui.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/timeimagegui.m | 4,261 | utf_8 | 4e5ddf913fe5a3a6536ac6a71bdf5adb | function varargout = timeimagegui(varargin)
% TIMEIMAGEGUI MATLAB code for timeimagegui.fig
% TIMEIMAGEGUI, by itself, creates a new TIMEIMAGEGUI or raises the existing
% singleton*.
%
% H = TIMEIMAGEGUI returns the handle to a new TIMEIMAGEGUI or the handle to
% the existing singleton*.
%
% TI... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | averagecurve.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/averagecurve.m | 689 | utf_8 | 8765ca5c9619a83b1745ce89f93a0af5 |
function averagecurve(label,cropI,T,Num,string)
sizecrop=size(cropI{1});
f=find(label~=0);
% for i=1:length(f)
% [a,b,c]=ind2sub([sizecrop(1),sizecrop(2),sizecrop(4)],f(i));
% for j=1:max(T)
% intensity_label(i,j)=cropI(a,b,1,c+(j-1)*Num);
% end
% end
for i=1:length(f)
for ... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | judgegui2.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/judgegui2.m | 22,441 | utf_8 | 70fd230337be349488d69d5b14e51e2d | function varargout = judgegui2(varargin)
% JUDGEGUI2 MATLAB code for judgegui2.fig
% JUDGEGUI2, by itself, creates a new JUDGEGUI2 or raises the existing
% singleton*.
%
% H = JUDGEGUI2 returns the handle to a new JUDGEGUI2 or the handle to
% the existing singleton*.
%
% JUDGEGUI2('CALLBACK',hO... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | ave_curve.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/ave_curve.m | 699 | utf_8 | c44803f70e349fcaa7a0fa031aedc2c2 |
function ave=ave_curve(label,cropI,T,Num,string)
sizecrop=size(cropI{1});
f=find(label~=0);
% for i=1:length(f)
% [a,b,c]=ind2sub([sizecrop(1),sizecrop(2),sizecrop(4)],f(i));
% for j=1:max(T)
% intensity_label(i,j)=cropI(a,b,1,c+(j-1)*Num);
% end
% end
for i=1:length(f)
for... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | labelgui.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/labelgui.m | 12,240 | utf_8 | 4c6726816a829b1e21cac98a1dc29e8b | function varargout = labelgui(varargin)
% LABELGUI MATLAB code for labelgui.fig
% LABELGUI, by itself, creates a new LABELGUI or raises the existing
% singleton*.
%
% H = LABELGUI returns the handle to a new LABELGUI or the handle to
% the existing singleton*.
%
% LABELGUI('CALLBACK',hObject,ev... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | maskgui.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/maskgui.m | 4,720 | utf_8 | ef8c5256cb639d099b1f5dab8fa3051f | function varargout = maskgui(varargin)
% MASKGUI MATLAB code for maskgui.fig
% MASKGUI, by itself, creates a new MASKGUI or raises the existing
% singleton*.
%
% H = MASKGUI returns the handle to a new MASKGUI or the handle to
% the existing singleton*.
%
% MASKGUI('CALLBACK',hObject,eventData,... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | showimagegui.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/showimagegui.m | 7,612 | utf_8 | 3044147d6a2cff5810720a97dabafe4a | function varargout = showimagegui(varargin)
% SHOWIMAGEGUI MATLAB code for showimagegui.fig
% SHOWIMAGEGUI, by itself, creates a new SHOWIMAGEGUI or raises the existing
% singleton*.
%
% H = SHOWIMAGEGUI returns the handle to a new SHOWIMAGEGUI or the handle to
% the existing singleton*.
%
% SH... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | start.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/start.m | 3,171 | utf_8 | 303798394e1fce5bdea0942c825ac2e1 | function varargout = start(varargin)
% START MATLAB code for start.fig
% START, by itself, creates a new START or raises the existing
% singleton*.
%
% H = START returns the handle to a new START or the handle to
% the existing singleton*.
%
% START('CALLBACK',hObject,eventData,handles,...) cal... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | gui.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/gui.m | 6,583 | utf_8 | 2b516ddb0b962a7faa6d95504c3dfc34 | function varargout = gui(varargin)
% GUI MATLAB code for gui.fig
% GUI, by itself, creates a new GUI or raises the existing
% singleton*.
%
% H = GUI returns the handle to a new GUI or the handle to
% the existing singleton*.
%
% GUI('CALLBACK',hObject,eventData,handles,...) calls the local
% ... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | loaddicom.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/loaddicom.m | 554 | utf_8 | 0fe36f179045f24c52899772fdad1e94 |
function [I,Num,T,info]=loaddicom
%This function is for loadding dicom images
dname = uigetdir(pwd);
dicomlist = dir(fullfile(dname,'*.dcm'));
h = waitbar(0,'Loading dicom images...');
parfor cnt = 1 : numel(dicomlist)
I(:,:,1,cnt)=dicomread(fullfile(dname,dicomlist(cnt).name));
info{cnt}=dicominfo(fullfile(dname... |
github | xinyang-hust/kidney-compartment-segmentation-from-MRR-images-master | select_timepoint.m | .m | kidney-compartment-segmentation-from-MRR-images-master/MSTV_KIDNEY_COMPARTMENT_SEGMENTATION/select_timepoint.m | 13,902 | utf_8 | d58ecbd6731afdc23e7da62198f17f1c | function varargout = select_timepoint(varargin)
% SELECT_TIMEPOINT MATLAB code for select_timepoint.fig
% SELECT_TIMEPOINT, by itself, creates a new SELECT_TIMEPOINT or raises the existing
% singleton*.
%
% H = SELECT_TIMEPOINT returns the handle to a new SELECT_TIMEPOINT or the handle to
% the exis... |
github | YunpengZhai/MATCONVNET-master | cnn_mnist_init.m | .m | MATCONVNET-master/cnn_mnist_init.m | 3,112 | utf_8 | a01ae991f71fdfc03c1d0da71c085a26 | function net = cnn_mnist_init(varargin)
% CNN_MNIST_LENET Initialize a CNN similar for MNIST
opts.batchNormalization = true ;
opts.networkType = 'simplenn' ;
opts = vl_argparse(opts, varargin) ;
rng('default');
rng(0) ;
f=1/100 ;
net.layers = {} ;
net.layers{end+1} = struct('type', 'conv', ...
... |
github | josefkoller/ambient_image_processor-master | normalize_image.m | .m | ambient_image_processor-master/scripts/octave/bias_simulator/normalize_image.m | 245 | utf_8 | 43b0b25784a49822d1f012406c4f3e15 | % transforms the intensity values to the range 0..1
function [normalized_image] = normalize_image(image)
min_value = min(min(image));
max_value = max(max(image));
normalized_image = (image - min_value) ./ (max_value - min_value);
end |
github | jte0419/NACA_4_Digit_Airfoil-master | GUI_NACA_4_Digit_Airfoil.m | .m | NACA_4_Digit_Airfoil-master/GUI_NACA_4_Digit_Airfoil.m | 23,700 | utf_8 | b04a9ec0f8917fa4e25701248c678eb6 | % NACA 4-Digit Airfoil GUI
% Written by: JoshTheEngineer
% Started: 03/08/15
% Updated: 03/08/15
% 08/14/16 - Rearranged layout
% - Made code a little more efficient
% 08/22/16 - Added output formatting for Inventor files
% 09/22/16 - Added output formatting for Gmsh files
... |
github | liangzheng06/MARS-evaluation-master | LOMO.m | .m | MARS-evaluation-master/LOMO_XQDA/code/LOMO.m | 11,239 | utf_8 | c01c8801f3f7694fa809cc25b196a270 | function descriptors = LOMO(images, options)
%% function Descriptors = LOMO(images, options)
% Function for the Local Maximal Occurrence (LOMO) feature extraction
%
% Input:
% <images>: a set of n RGB color images. Size: [h, w, 3, n]
% [optioins]: optional parameters. A structure containing any of the
% fo... |
github | liangzheng06/MARS-evaluation-master | evalData.m | .m | MARS-evaluation-master/KISSME/evalData.m | 4,256 | utf_8 | bc9f590680e986310ac885ac335f622e | function [ds,rocPlot] = evalData(pairs, ds, params)
% EVALDATA Evaluate results and plot figures
%
% Input:
% pairs - [1xN] struct. N is the number of pairs. Fields: pairs.fold
% pairs.match, pairs.img1, pairs.img2.
% ds - [1xF] data struct. F is the number of folds.
% ds.method.dist is required ... |
github | liangzheng06/MARS-evaluation-master | LearnAlgoLMNN.m | .m | MARS-evaluation-master/KISSME/learnAlgos/LearnAlgoLMNN.m | 2,936 | utf_8 | 4762d8d225d4144d20b5ff539e819fe6 | %LEARNALGOLMNN Wrapper class to the actual LMNN code
classdef LearnAlgoLMNN < LearnAlgo
properties
p %parameters
s %struct
available
fhanlde
end
properties (Constant)
type = 'lmnn'
end
methods
function obj = LearnAlgoLMNN(p)... |
github | liangzheng06/MARS-evaluation-master | icg_roc.m | .m | MARS-evaluation-master/KISSME/helper/icg_roc.m | 1,425 | utf_8 | 11d04e9c4c3db15aa1c3b9b771eff30e | function [tpr,fpr,thresh] = icg_roc(tp,confs)
% ICG_ROC computes ROC measures (tpr,fpr)
%
% Input:
% tp - [m x n] matrix of zero-one labels. one row per class.
% confs - [m x n] matrix of classifier scores. one row per class.
%
% Output:
% tpr - true positive rate in interval [0,1], [m x n+1] matrix
% ... |
github | liangzheng06/MARS-evaluation-master | draw_confusion_matrix.m | .m | MARS-evaluation-master/utils/draw_confusion_matrix.m | 1,059 | utf_8 | 14e408bfc1fe393a2c36b66ce5e7a4ec | % calculate and draw confusion matrix
function [ap_mat, r1_mat] = draw_confusion_matrix(ap, r1, queryCam)
ap_mat = zeros(6, 6);
r1_mat = zeros(6, 6);
count1 = zeros(6, 6);
count2 = zeros(6, 6);
for n = 1:length(queryCam)
for k = 1:6
ap_mat(queryCam(n), k) = ap_mat(queryCam(n), k) + ap(n, k);
... |
github | mkokshoorn/Genetic-Algorithm-Edge-Detector-master | gen_main.m | .m | Genetic-Algorithm-Edge-Detector-master/Source_Code/gen_main.m | 19,937 | utf_8 | b51e03ef7c282e98b2043fe35d5f1eac | function gen_main ()
global popSize;
global generations;
global breedNum;
global surviveNum;
global noises;
global noiseWeights;
global totCount;
global mutateGains;
% --------------------------------------------------------------------
% Variables / Initialisation
% -... |
github | josephdviviano/qcmon-master | analyze_dti_phantom.m | .m | qcmon-master/assets/matlab/analyze_dti_phantom.m | 13,019 | utf_8 | 4ae958982fac3d44ae0af04b42bcf710 | % analyze_dti_phantom(dwi, fa, bval, output, nyqopt)
%
% 'dwi': 4D diffusion weighted image
% 'fa': FA map from DTIfit
% 'bval': B value files from dcm2nii
% 'output': full path to output prefix
% 'accel': ('y', 'n') 'n' to measure nyquist ghost on non-accelerated data.
function analyze_dti_phantom(dwi,... |
github | josephdviviano/qcmon-master | analyze_fmri_phantom.m | .m | qcmon-master/assets/matlab/analyze_fmri_phantom.m | 7,379 | utf_8 | 595e43fd62b30b30d0ad8bc379cd7bf6 | % A modified version of the fBIRN fMRI QC pipeline.
%
% Performs a quantitation of snr, sfnr, stability and drift
% including a weisskoff plot MRM 36:643 (1996)
%
% rev 0 3/03/00 original from noiseave and imgroi
% rev 1 3/29/02 fix a few header things
% rev 2 9/04/02 add weissnois... |
github | josephdviviano/qcmon-master | wm_seg_afd.m | .m | qcmon-master/assets/matlab/freesurfer/wm_seg_afd.m | 3,956 | utf_8 | c9ad19684ddf34c5ef47d999a496eabc | function [Dice,pval]=wm_seg_adf(subject, th_pval)
% For the subject "subject": computes the Dice coefficient D=2Nab/Na+Nb
% where:
% Na is the volume of the WM obtrained trough the volume-based labeling
% Nb is the volume of the WM segmented in the surface-based stream
% Nab is the volume of the overlap
% Uses... |
github | josephdviviano/qcmon-master | load_dicom_series.m | .m | qcmon-master/assets/matlab/freesurfer/load_dicom_series.m | 3,255 | utf_8 | b60aa048f680fe00980380c850cd4dd3 | function [vol, M, tmpdcminfo, mr_parms] = load_dicom_series(seriesno,dcmdir,dcmfile)
% [vol, M, dcminfo] = load_dicom_series(seriesno,<dcmdir>,<dcmfile>)
%
% Reads in a dicom series given:
% 1. The series number and directory, or
% 2. A dicom file from the desired series
%
% If the series number is given but no dcmdi... |
github | josephdviviano/qcmon-master | write_annotation.m | .m | qcmon-master/assets/matlab/freesurfer/write_annotation.m | 5,161 | utf_8 | 65cffd8c342a5cbc1d5d6f6109db8945 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modific... |
github | josephdviviano/qcmon-master | cc_cut_dir_afd.m | .m | qcmon-master/assets/matlab/freesurfer/cc_cut_dir_afd.m | 8,948 | utf_8 | 0f0f00b54724b5bc6d70ccbae4d0bf2b | function [ddr, ddl, Isubj]=cc_cut_dir_adf(dirname, th_pval)
% For each subject in the directory "dirname":
% Computes the Dice coefficients measuring the overlap
% of the WM volume in right and left hemispheres to check
% if the corpus_callosum is correctly located.
%
% Uses the p values
%
%
% cc_cut_dir_afd.m
%... |
github | josephdviviano/qcmon-master | ribbon_afd.m | .m | qcmon-master/assets/matlab/freesurfer/ribbon_afd.m | 7,593 | utf_8 | 105801cd74c8eed1c807b10f37842421 | function [Dice]=ribbon_adf(subject, th_pval)
% For each subject "subject":
% Computes the Dice coefficients measuring the overlap of the
% Cortical Ribbon volume computed
% 1- from the subcortical labeling
% 2- as the space between the white and the pial surface
%
% Uses the pvalues, tr... |
github | josephdviviano/qcmon-master | subcortical_labeling_afd.m | .m | qcmon-master/assets/matlab/freesurfer/subcortical_labeling_afd.m | 4,804 | utf_8 | 9c621c12c9503b2b135eb577c0a81f59 | function [y]=check_ROI(SubjectDir,th_pval)
%
% For one subject: check if the size of 20 ROIs is within the normal range
% The 20 following ROIs are checked: Left-Lateral-Ventricle Right-Lateral-Ventricle
% Left-Hippocampus Right-Hippocampus Left-Thalamus-Proper Right-Thalamus-Proper
% Left-Caudate Right-Cauda... |
github | josephdviviano/qcmon-master | unwarp_resample.m | .m | qcmon-master/assets/matlab/freesurfer/unwarp_resample.m | 11,180 | utf_8 | 4f62076f2cdf3422888c26deabf1142b | function [imvol_out, M_out] = unwarp_resample(imvol,M,imvol_out_size,M_out,Mdc,unwarpflag,Jacobianflag,plotflag,interp_method,inflag,thruflag,gradfilename)
%
% In this file:
%
% unwarp_resample - from AD's unwarp_and_resample_vol
% proj, jdproj - for projecting out e.g. throughplane component of
% displ... |
github | josephdviviano/qcmon-master | cortical_labeling_afd_txt.m | .m | qcmon-master/assets/matlab/freesurfer/cortical_labeling_afd_txt.m | 7,062 | utf_8 | 1e9fedefb4b79b1cb80f9931181ecff1 | function [A_lh, A_rh]=cortical_label_adf(subject, p_val)
% Computes the area of the different cortical labels
% and compare them to the normal range
% Uses p_value to detect the abnormal areas
% Uses the lh/rh.parc.txt files
%
%
% cortical_labeling_afd_txt.m
%
% Original Author: Laurence Wastiaux
% CVS Revision Info... |
github | josephdviviano/qcmon-master | cc_cut_afd.m | .m | qcmon-master/assets/matlab/freesurfer/cc_cut_afd.m | 7,765 | utf_8 | 353c06ba9788caae3dfc98e3b8e9b9b8 | function [dr,dl]=cc_cut_adf(subject, name,th_pval)
% For each subject "subject":
% Computes the Dice coefficients measuring the overlap
% of the WM volume in right and left hemispheres to check
% if the corpus_callosum is correctly located.
%
% Uses .lta transform and p values
%
%
% cc_cut_afd.m
%
% O... |
github | josephdviviano/qcmon-master | load_dicom_fl.m | .m | qcmon-master/assets/matlab/freesurfer/load_dicom_fl.m | 5,467 | utf_8 | efaa1cd90a63c6f97c1a432ae0784c87 | function [vol, M, dcminfo, mr_parms] = load_dicom_fl(flist)
% [vol, M, dcminfo, mr_parms] = load_dicom_fl(flist)
%
% Loads a volume from the dicom files in flist.
%
% The volume dimensions are arranged such that the
% readout dimension is first, followed by the phase-encode,
% followed by the slices (this is not implem... |
github | josephdviviano/qcmon-master | convert_unwarp_resample.m | .m | qcmon-master/assets/matlab/freesurfer/convert_unwarp_resample.m | 13,982 | utf_8 | a2759cd5b258cb5b88b8a6086835f230 | function convert_unwarp_resample(infile,series,outfile,corfovflag,unwarpflag,jacflag,interp_method,user_gradwarpfile,called_by_script)
%
%% convert_unwarp_resample.m contains:
% convert_unwarp_resample()
% load_dicom_and_stuff()
% mdc()
% header2map(), type2map(), map2manuf() refer to TABLE = GRADWARPPATH/table.mat
%
... |
github | josephdviviano/qcmon-master | talairaching_dir_afd.m | .m | qcmon-master/assets/matlab/freesurfer/talairaching_dir_afd.m | 5,712 | utf_8 | 583571aad74bc6c6e5cf998815a7891a | function [probas, Isubj,nf]=taldir(dirname, th_pval, DirTable)
%
% Computes the probability of the Talairach transform matrices
% of all the subjects found in the directory "dirname".
% Uses the mean vector and covariance matrix obtained with talairachin_table.m from
% the data set (default data set: /space/... |
github | josephdviviano/qcmon-master | wm_seg_dir_afd.m | .m | qcmon-master/assets/matlab/freesurfer/wm_seg_dir_afd.m | 4,655 | utf_8 | a56b19b685866251b51ffedfcb1a08a2 | function [Dice, Pval, Isubj]=wm_seg_dir_adf(dirname, th_pval)
% For all the subjects in the directory "dirname":
% Computes the Dice coefficients D=2Nab/Na+Nb
% where:
% Na is the volume of the WM obtained trough the volume-based labeling
% Nb is the volume of the WM ... |
github | josephdviviano/qcmon-master | talairaching_afd.m | .m | qcmon-master/assets/matlab/freesurfer/talairaching_afd.m | 4,437 | utf_8 | 9c33512f5396ed541ae81d98f7f92488 | function [proba, pinf]=talmat(filename, th_pval, DirTable)
%
% Computes the probability of the Talairach transform matrix
% 'filename/mri/transforms/talairach.xfm'.
% Uses the mean vector and covariance matrix obtained with talairachin_table.m from
% the data set (default data set: /space/neo/2/recon/buck... |
github | josephdviviano/qcmon-master | surf_registration_afd.m | .m | qcmon-master/assets/matlab/freesurfer/surf_registration_afd.m | 4,846 | utf_8 | c243515fe07fa094dc4a23afd21ed444 | function [prv ] = surf_registration_adf(subject, th_pval)
%% Tests the overall surface based registration %%
%
%
% surf_registration_afd.m
%
% Original Author: Laurence Wastiaux
% CVS Revision Info:
% $Author: nicks $
% $Date: 2011/03/02 00:04:13 $
% $Revision: 1.3 $
%
% Copyright © 2011 The General Hospita... |
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