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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 | cocoanlab/humanfmri_preproc_bids-master | nii_tool.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/nii_tool.m | 48,496 | utf_8 | b25318c88e1f9bee05462b06ac0f8cca | function varargout = nii_tool(cmd, varargin)
% Basic function to create, load and save NIfTI file.
%
% rst = nii_tool('cmd', para);
%
% To list all command, type
% nii_tool ?
%
% To get help information for each command, include '?' in cmd, for example:
% nii_tool init?
% nii_tool('init?')
%
% Here i... |
github | cocoanlab/humanfmri_preproc_bids-master | dicm2nii.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/dicm2nii.m | 128,433 | utf_8 | 9017400933423c6f35d9ec43a688b5d3 | function varargout = dicm2nii(src, niiFolder, fmt, varargin)
% Convert dicom and more into nii or img/hdr files.
%
% DICM2NII(dcmSource, niiFolder, outFormat)
%
% The input arguments are all optional:
% 1. source file or folder. It can be a zip or tgz file, a folder containing
% dicom files, or other con... |
github | cocoanlab/humanfmri_preproc_bids-master | dicm_hdr.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/dicm_hdr.m | 62,090 | utf_8 | b5094a6d10aab8edfae3dea1bff32612 | function [s, info, dict] = dicm_hdr(fname, dict, iFrames)
% Return header of a dicom file in a struct.
%
% [s, err] = DICM_HDR(dicomFileName, dict, iFrames);
%
% The mandatory 1st input is the dicom file name.
%
% The optional 2nd input is a dicom dictionary returned by dicm_dict. It may
% have only part of... |
github | cocoanlab/humanfmri_preproc_bids-master | nii_viewer.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/nii_viewer.m | 147,002 | utf_8 | 9704a0e67438819449f6d0f5a1dc4334 | function varargout = nii_viewer(fname, varargin)
% Basic tool to visualize NIfTI images.
%
% NII_VIEWER('/data/subj2/fileName.nii.gz')
% NII_VIEWER('background.nii', 'overlay.nii')
% NII_VIEWER('background.nii', {'overlay1.nii' 'overlay2.nii'})
%
% If no input is provided, the viewer will load included MNI_... |
github | cocoanlab/humanfmri_preproc_bids-master | nii_moco.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/nii_moco.m | 10,422 | utf_8 | 4b02f2199b90d3823468dba1a430723e | function varargout = nii_moco(nii, out, ref)
% Perform motion correction to the input NIfTI data.
%
% Syntax:
% p = NII_MOCO(filename_in); % return correction parameter only
% NII_MOCO(filename_in, filename_out); % save corrected image file
% [p, nii_out] = NII_MOCO(nii_in); % also return correct NIfTI without savin... |
github | cocoanlab/humanfmri_preproc_bids-master | java_dnd.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/java_dnd.m | 2,820 | utf_8 | b72dadc83df5d9f523b72cf084b3e056 | function java_dnd(jObj, dropFcn)
% Set Matlab dropFcn for java object, like JavaFrame or JTextField.
% 170421 Xiangrui Li adapted from dndcontrol class by Maarten van der Seijs:
% https://www.mathworks.com/matlabcentral/fileexchange/53511
% Required: MLDropTarget.class under the same folder
if ~exist('MLDrop... |
github | cocoanlab/humanfmri_preproc_bids-master | nii_xform.m | .m | humanfmri_preproc_bids-master/external/dicm2nii/nii_xform.m | 9,448 | utf_8 | f1220c195ff9723fdad045a1477dbf77 | function varargout = nii_xform(src, target, rst, intrp, missVal)
% Transform a NIfTI into different resolution, or into a template space.
%
% NII_XFORM('source.nii', 'template.nii', 'result.nii')
% NII_XFORM(nii, 'template.nii', 'result.nii')
% NII_XFORM('source.nii', [1 1 1], 'result.nii')
% nii = NII_XFORM... |
github | TREE-Ind/speaker-rec-skill-test-master | estimate_x_and_u.m | .m | speaker-rec-skill-test-master/jfa/estimate_x_and_u.m | 5,477 | utf_8 | 1f30c33b7f0eecda4b7fa1266a4b23ba | function [x u]=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
% ESTIMATE_X_AND_U estimates channel factors and eigenchannels for
% joint factor analysis model
%
%
% [x u]=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% provides new estimates of channel factors, x, and 'eigenchannels', u,
% ... |
github | TREE-Ind/speaker-rec-skill-test-master | estimate_y_and_v.m | .m | speaker-rec-skill-test-master/jfa/estimate_y_and_v.m | 5,502 | utf_8 | 1e4d706f8060302120ad648461d7a943 | function [y v C]=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
% ESTIMATE_Y_AND_V estimates speaker factors and eigenvoices for
% joint factor analysis model
%
%
% [y v]=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% provides new estimates of channel factors, x, and 'eigenchannels', u,
% ... |
github | nathanie/DataHack-2017-master | csv2kml.m | .m | DataHack-2017-master/visualiztion/csv2kml.m | 3,175 | utf_8 | 9c842c1e4597dfe89d1b5b200d7443bf | function csv2kml(mainDir,data2WorkOn,class2show,lines2show,nedOrigin,openFileWhenDone)
%%%%
% mainDir - Dir where train/test data is
% data2WorkOn - Name of the data CSV file
% class2show - Which class in CSV file to draw, or (-1) if using test set or lines2show parameter
% lines2show - Which lines in CSV file to draw
... |
github | risetarnished/VehicleDetection-master | getBWratio.m | .m | VehicleDetection-master/Meng/getBWratio.m | 1,609 | utf_8 | 91fdec4a7183e0a15d6dc1b484eb2cc2 |
function features1 = getBWratio(img)
% foregroundDetector = vision.ForegroundDetector('NumGaussians', 3, ...
% 'NumTrainingFrames', 50);
%foreground = step(foregroundDetector, img);
foreground = rgb2gray(img);
image=imresize(foreground, [256 256]);
imwrite(image, 'temp.jpg');
blockCo... |
github | rajaeipour/spatial-carrier-master | FTP10.m | .m | spatial-carrier-master/FTP10.m | 47,519 | utf_8 | 88ee2a3d9801c3ebcdbab29b2792bc10 | function varargout = FTP10(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @FTP10_OpeningFcn, ...
'gui_OutputFcn', @FTP10_OutputFcn... |
github | rajaeipour/spatial-carrier-master | cunwrap_nodisp.m | .m | spatial-carrier-master/cunwrap_nodisp.m | 16,666 | utf_8 | f64eda6acf71fe85dfd64078206275c3 | function PhiUnwrap = cunwrap_nodisp(Psi, options)
% PhiUnwrap = cunwrap(Psi, options)
%
% Purpose: Costantini's 2D unwrapping based on Minimum Network Flow
%
% INPUTS:
% - Psi: 2D-array wrapped phase (radian)
% - options: optional structure used to modify the behavior of the
% unwrapping algor... |
github | EPFL-LCSB/matTFA-master | solveTFAmodelCplex.m | .m | matTFA-master/matTFA/solveTFAmodelCplex.m | 5,589 | utf_8 | 8ab7d957942db50f3dd288fbaa9e3c70 | function sol = solveTFAmodelCplex(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay,CPXPARAMdisp)
% Solve a model using specific solver settings. More details in
% changeToCPLEX_WithOptions
%
% INPUTS
% tModel: a TFA-ready model (has a .A matrix)
% TimeInSec: timelimit for the solver... |
github | EPFL-LCSB/matTFA-master | solveFBAmodelCplex.m | .m | matTFA-master/matTFA/solveFBAmodelCplex.m | 30,450 | utf_8 | 6e803c4720697333350bcd6e8563f5b5 | function FBAsolution = solveFBAmodelCplex(model, scalPar, feasTol, emphPar, osenseStr)
%optimizeCbModel Solve a flux balance analysis problem
%
% Georgios Fengos 24/05/2016 Created this version of optimizeCbModel
% to be able to control externally the cplex parameters
%% Process a... |
github | EPFL-LCSB/matTFA-master | splitString.m | .m | matTFA-master/matTFA/utilities/splitString.m | 1,729 | utf_8 | d9ebd7e1d412e1d0b9832c5f9c1f89f6 | function fields = splitString(string,delimiter)
%splitString Splits a string Perl style
%
% fields = splitString(string,delimiter)
%
% string Either a single string or a cell array of strings
% delimiter Splitting delimiter
%
% fields Either a single cell array of fields or a cell array of cell
% ... |
github | EPFL-LCSB/matTFA-master | strescape.m | .m | matTFA-master/matTFA/utilities/MatlabBuiltInFunctions/strescape.m | 1,148 | utf_8 | e50bfb2ad948fb14d6732ec00fbd2b6a | function escapedStr = strescape(str)
%STRESCAPE Escape control character sequences in a string.
% STRESCAPE(STR) converts the escape sequences in a string to the values
% they represent.
%
% Example:
%
% strescape('Hello World\n')
%
% See also SPRINTF.
% Copyright 2012 The MathWorks, Inc.
escapeFcn =... |
github | EPFL-LCSB/matTFA-master | strsplit.m | .m | matTFA-master/matTFA/utilities/MatlabBuiltInFunctions/strsplit.m | 4,356 | utf_8 | 27145ac2a6cf2a3d7f3e9c0f300d34e3 | function [c, matches] = strsplit(str, aDelim, varargin)
%STRSPLIT Split string at delimiter
% C = STRSPLIT(S) splits the string S at whitespace into the cell array
% of strings C.
%
% C = STRSPLIT(S, DELIMITER) splits S at DELIMITER into C. DELIMITER can
% be a string or a cell array of strings. If DELIMITER i... |
github | EPFL-LCSB/matTFA-master | generateDoc.m | .m | matTFA-master/ext/Cobra205_vDec2014/generateDoc.m | 3,858 | utf_8 | fdb222d907785762dddb4a82c06b02f7 | function generateDoc(pathname, graph)
%generateDoc uses m2html to create a set of html docs
%in the cba toolbox and place them in a directory called 'docs'.
%
% generateDoc(pathname, graph)
%
%OPTIONAL INPUTS
% pathname Path to folder to generate documents for
% graph Generate function dependcy graph (Default = o... |
github | EPFL-LCSB/matTFA-master | solveFBAmodelCplex.m | .m | matTFA-master/ext/Cobra205_vDec2014/solveFBAmodelCplex.m | 28,006 | utf_8 | 6478764de59239a1782fac0520b6dc20 | function FBAsolution = solveFBAmodelCplex(model, scalPar, feasTol, emphPar, osenseStr)
%optimizeCbModel Solve a flux balance analysis problem
%
% Georgios Fengos 24/05/2016 Created this version of optimizeCbModel
% to be able to control externally the cplex parameters
%% Process a... |
github | EPFL-LCSB/matTFA-master | geometricFBA.m | .m | matTFA-master/ext/Cobra205_vDec2014/geometricFBA.m | 6,629 | utf_8 | 511013ff705cedf3231d79af4e99e023 | function flux = geometricFBA(model,varargin)
%geometricFBA finds a unique optimal FBA solution that is (in some sense)
%central to the range of possible fluxes; as described in
% K Smallbone, E Simeonidis (2009). Flux balance analysis:
% A geometric perspective. J Theor Biol 258: 311-315
% http://dx.doi.org/10.1... |
github | EPFL-LCSB/matTFA-master | changeRxnMets.m | .m | matTFA-master/ext/Cobra205_vDec2014/changeRxnMets.m | 3,484 | utf_8 | a54ed5421c1d7e06d54c21d49c1dd01a | function [model ModifiedRxns] = changeRxnMets(model,Mets2change,NewMets,Rxn,NewStoich)
%changeRxnMets Change metabolites in a specified reaction, or
% randomly chosen reactions.
%
% [model ModifiedRxns] = changeRxnMets(model,Mets2change,NewMets,Rxn,NewStoich)
%
%INPUTS
% model COBRA model structure
% Mets... |
github | EPFL-LCSB/matTFA-master | convertModelToEX.m | .m | matTFA-master/ext/Cobra205_vDec2014/convertModelToEX.m | 2,482 | utf_8 | 262c28a115d8194846f4c7562681fe0e | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% convert Matlab Model to XPA format
% Inputs:
% model Model Structure
% filename Filename of Output File (make sure to include '.txt' or
% '.xpa')
% rxnzero Matrix containing all no flux var rxns (to skip, set=0)
%... |
github | EPFL-LCSB/matTFA-master | pFBA.m | .m | matTFA-master/ext/Cobra205_vDec2014/pFBA.m | 9,274 | utf_8 | ec4edfb9cb08758b017493c5cb612fcd | function [GeneClasses RxnClasses modelIrrevFM] = pFBA(model, varargin)
% Parsimoneous enzyme usage Flux Balance Analysis - method that optimizes
% the user's objective function and then minimizes the flux through the
% model and subsequently classifies each gene by how it contributes to the
% optimal solution. See Lewi... |
github | EPFL-LCSB/matTFA-master | reduceModel.m | .m | matTFA-master/ext/Cobra205_vDec2014/reduceModel.m | 8,348 | utf_8 | 1d56cf233017a4d6aa106e6c8714ab94 | function [modelRed,hasFlux,maxes,mins] = reduceModel(model,tol,irrevFlag,verbFlag,negFluxAllowedFlag,checkConsistencyFlag,changeBoundsFlag)
%reduceModel Removes from the model all of the reactions that are never used (max and
% min are < tol). Finds the minimal bounds for the flux through each reaction.
% Also returns ... |
github | EPFL-LCSB/matTFA-master | drawLine.m | .m | matTFA-master/ext/Cobra205_vDec2014/maps/tools/drawLine.m | 6,310 | utf_8 | 4e8f08121c24f5717852ff9ffa6451d7 | function drawLine(node1,node2,map,edgeColor,edgeArrowColor,edgeWeight,nodeWeight,rxnDir,rxnDirMultiplier)
%drawLine
%
% drawLine(node1,node2,map,edgeColor,edgeArrowColor,edgeWeight,nodeWeight)
%
%INPUTS
% node1 start node
% node2 end node
% map COBRA map structure
% edgeColor ... |
github | EPFL-LCSB/matTFA-master | calcGroupStats.m | .m | matTFA-master/ext/Cobra205_vDec2014/tools/calcGroupStats.m | 3,452 | utf_8 | 06bebf75a99b8cf627b1054f5738961f | function [groupStat,groupList,groupCnt,zScore] = calcGroupStats(data,groups,statName,groupList,randStat,nRand)
%calcGroupStats Calculate statistics such as mean or standard deviation for
%subgroups of a population
%
% [groupStat,groupList,groupCnt,zScore] =
% calcGroupStats(data,groups,statName,groupList,randStat,nRand... |
github | EPFL-LCSB/matTFA-master | solveBooleanRegModel.m | .m | matTFA-master/ext/Cobra205_vDec2014/rFBA/solveBooleanRegModel.m | 3,855 | utf_8 | c3c1af861606efb5eb37d3e177c748a7 | function [finalState,finalInputs1States,finalInputs2States] = solveBooleanRegModel(model,initialState,inputs1States,inputs2States)
% solveBooleanRegModel - determines the next state of the regulatory
% network based on the current state. Called by optimizeRegModel and
% dynamicRFBA
%
% [finalState,finalInputs1States,fi... |
github | EPFL-LCSB/matTFA-master | readCbModel.m | .m | matTFA-master/ext/Cobra205_vDec2014/io/readCbModel.m | 12,794 | utf_8 | 96786224cfdf9e5aa3330142d7524196 | function model = readCbModel(fileName,defaultBound,fileType,modelDescription,compSymbolList,compNameList)
%readCbModel Read in a constraint-based model
%
% model = readCbModel(fileName,defaultBound,fileType,modelDescription)
%
% If no arguments are passed to the function, the user will be prompted for
% a file name.
%
... |
github | EPFL-LCSB/matTFA-master | convertCobraToSBML.m | .m | matTFA-master/ext/Cobra205_vDec2014/io/convertCobraToSBML.m | 10,266 | utf_8 | ff076a85c6b0755e496ccb290d0442e2 | function sbmlModel = convertCobraToSBML(model,sbmlLevel,sbmlVersion,compSymbolList,compNameList,debug_function)
%convertCobraToSBML converts a cobra structure to an sbml
%structure using the structures provided in the SBML toolbox 3.1.0
%
% sbmlModel = convertCobraToSBML(model,sbmlLevel,sbmlVersion,compSymbolList,compN... |
github | EPFL-LCSB/matTFA-master | writeCbModel.m | .m | matTFA-master/ext/Cobra205_vDec2014/io/writeCbModel.m | 10,729 | utf_8 | 0a6994071e50ffd3dc681e8043552a69 | function writeCbModel(model,format,fileName,compSymbolList,compNameList,sbmlLevel,sbmlVersion)
%writeCbModel Write out COBRA models in various formats
%
% writeCbModel(model,format,fileName,compSymbolList,compNameList,sbmlLevel,sbmlVersion)
%
%INPUTS
% model Standard COBRA model structure
% format ... |
github | EPFL-LCSB/matTFA-master | convertSBMLToCobra.m | .m | matTFA-master/ext/Cobra205_vDec2014/io/convertSBMLToCobra.m | 14,410 | utf_8 | ca4c9588a99e906f4a3636188d2c0574 | function model = convertSBMLToCobra(modelSBML,defaultBound,compSymbolList,compNameList)
%convertSBMLToCobra Convert SBML format model (created using SBML Toolbox)
%to Cobra format
%
% model = convertSBMLToCobra(modelSBML,defaultBound)
%
%INPUTS
% modelSBML SBML model structure
%
%OPTIONAL INPUTS
% defaultBound ... |
github | EPFL-LCSB/matTFA-master | lp_solve.m | .m | matTFA-master/ext/Cobra205_vDec2014/solvers/lp_solve.m | 2,708 | utf_8 | 80baa061e65e08df66a4b417047cd713 | %LP_SOLVE Solves mixed integer linear programming problems.
%
% SYNOPSIS: [obj,x,duals,stat] = lp_solve(f,a,b,e,vlb,vub,xint,scalemode,keep)
%
% solves the MILP problem
%
% max v = f'*x
% a*x <> b
% vlb <= x <= vub
% x(int) are integer
%
% ARGUMENTS: The ... |
github | EPFL-LCSB/matTFA-master | cpxcb_INCUMBENT.m | .m | matTFA-master/ext/Cobra205_vDec2014/solvers/cpxcb_INCUMBENT.m | 3,387 | utf_8 | c53a9437062846671fbafd7691e91c80 | % function ret = cpxcb_INCUMBENT(x,f,Prob,cbxCBInfo)
%
% CPLEX MIP Incumbent callback
%
% Called from TOMLAB /CPLEX during mixed integer optimization when a new integer
% solution has been found but before this solution has replaced the current best known integer solution.
%
% This file can be used to perform any desir... |
github | EPFL-LCSB/matTFA-master | solveCobraLP.m | .m | matTFA-master/ext/Cobra205_vDec2014/solvers/solveCobraLP.m | 21,393 | utf_8 | 015fc2b9bee21ee6eb4f30f6e94e39d8 | function solution = solveCobraLP(LPproblem, varargin)
%solveCobraLP Solve constraint-based LP problems
%
% solution = solveCobraLP(LPproblem, parameters)
%
%INPUT
% LPproblem Structure containing the following fields describing the LP
% problem to be solved
% A LHS matrix
% b RHS vector
% c Objective ... |
github | EPFL-LCSB/matTFA-master | optGeneFitnessTilt.m | .m | matTFA-master/ext/Cobra205_vDec2014/design/optGeneFitnessTilt.m | 4,526 | utf_8 | b9d818464262c0403801cde0424f0834 | function [val] = optGeneFitnessTilt(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%optGeneFitnessTilt GeneOptFitness the fitness function
%
% [val] = optGeneFitnessTilt(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%
%INPUTS
% rxn_vector_matrix
% model
% targetRxn... |
github | EPFL-LCSB/matTFA-master | GDLS.m | .m | matTFA-master/ext/Cobra205_vDec2014/design/GDLS.m | 14,440 | utf_8 | 217f0fb80c846b4d2bb8d8b633753282 | function [gdlsSolution, bilevelMILPProblem, gdlsSolutionStructs] = GDLS(model, targetRxns, varargin)
%GDLS (Genetic Design through Local Search) attempts to find genetic
% designs with greater in silico production of desired metabolites.
%
% [gdlsSolution, bilevelMILPProblem, gdlsSolutionStructs] = GDLS(model, varargin... |
github | EPFL-LCSB/matTFA-master | optGene.m | .m | matTFA-master/ext/Cobra205_vDec2014/design/optGene.m | 10,378 | utf_8 | 096047845ee9473fe011e1224eda05b7 | function [x, population, scores, optGeneSol] = optGene(model, targetRxn, substrateRxn, generxnList, MaxKOs, population)
%OPTGENE implements the optgene algorithm.
%
% [x, population, scores, optGeneSol] = optGene(model, targetRxn, substrateRxn, generxnList, MaxKOs, population)
%
%INPTUS
% mode Model of reconst... |
github | EPFL-LCSB/matTFA-master | optGeneFitness.m | .m | matTFA-master/ext/Cobra205_vDec2014/design/optGeneFitness.m | 4,201 | utf_8 | af651aa05b3544eb6d725b9ac5cfa801 | function [val] = optGeneFitness(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%optGeneFitness GeneOptFitness the fitness function
%
% [val] = optGeneFitness(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%
%INPUTS
% rxn_vector_matrix
% model
% targetRxn
% rxnListInput
% isGeneList
%
%OU... |
github | EPFL-LCSB/matTFA-master | compareMultSamp.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/compareMultSamp.m | 3,253 | utf_8 | 2cdd10a7b9419f8d2af32bf86b455456 | function [totalz,zscore,mdvs] = compareMultSamp(xglc,model,samps,measuredMetabolites)
% Compare the multiple sets of samples
% xglc is optional, a random sugar distribution is calculated if empty
% expects samp1 and samp2 to have a field named points containing
% an array of sampled points
% expects model.rxns... |
github | EPFL-LCSB/matTFA-master | C13ConfidenceInterval.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/C13ConfidenceInterval.m | 14,161 | utf_8 | 4b5572a4c36fbfc32729f15f709e7683 | function [vs, output, v0] = C13ConfidenceInterval(v0, expdata, model, max_score, directions, majorIterationLimit)
% v0 - set of flux vectors to be used as initial guesses. They may be
% valid or not.
% expdata - experimental data.
% model - The standard model. Additional field .N (= null(S)) should also
% be provide... |
github | EPFL-LCSB/matTFA-master | runHiLoExp.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/runHiLoExp.m | 10,864 | utf_8 | f754c1508023d127daf3b1f489af2798 | function [experiment] = runHiLoExp(experiment)
% runHiLoExp
% takes an experiment with the following structure
% and splits the sample space at the median of a target flux
% solves the two spaces with a given sugar and compares the
% resulting mdvs to provide a z-score.
%
% experiment -
% ... |
github | EPFL-LCSB/matTFA-master | compareTwoSamp.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/compareTwoSamp.m | 3,031 | utf_8 | 5a0c5086089c00108fbf0be445048674 | function [totalz,zscore,mdv1,mdv2] = compareTwoSamp(xglc,model,samp1,samp2,measuredMetabolites)
% Compare the 2 sets of samples
% xglc is optional, a random sugar distribution is calculated if empty
% expects samp1 and samp2 to have a field named points containing
% an array of sampled points
% expects model.r... |
github | EPFL-LCSB/matTFA-master | computeConfidenceInterval2.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/obsolete/computeConfidenceInterval2.m | 9,292 | utf_8 | 76f328a01a51b8ee184e498657e94f7e | function [vs, output, v0] = computeConfidenceInterval2(v0, expdata, model, max_score)
majorIterationLimit = 2000; %max number of iterations
minorIterationLimit = 1e7; % essentially infinity
diffInterval = 1e-5; %gradient step size.
feasibilityTolerance = max_score/20; % how close you need to be to the max s... |
github | EPFL-LCSB/matTFA-master | computeRatioConfidenceInterval.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/obsolete/computeRatioConfidenceInterval.m | 6,966 | utf_8 | 910c32ca417673f241f14c0350b9c7a3 | function [vs, output, v0] = computeRatioConfidenceInterval(v0, expdata, model, max_score, ratio)
% v0 - set of flux vectors to be used as initial guesses. They may be
% valid or not.
% expdata - experimental data.
% model - The standard model. Additional field .N (= null(S)) should also
% be provided. This is a bas... |
github | EPFL-LCSB/matTFA-master | Combination.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/c13solver/Combination.m | 1,354 | utf_8 | e737cd2414f521a8b1701de9c05cff10 | function [out] = Combination(n,k)
% produces the array of combinations possible picking k from n
% adapted from Combinadics
% http://msdn.microsoft.com/en-us/library/aa289166(VS.71).aspx
if (n < 0 || k < 0) % normally n >= k
disp('Negative parameter in constructor');
return
end
data(k) = 0... |
github | EPFL-LCSB/matTFA-master | idv2mdv.m | .m | matTFA-master/ext/Cobra205_vDec2014/fluxomics/c13solver/idv2mdv.m | 1,629 | utf_8 | 4602db4ffd72989e332f08b0d92cf05f | function [out] = idv2mdv(n, fragment)
% returns transofmation matrix from idv's (either Jennie's or Jan's order).
% MDV = idv2mdv(log2(length(idv)))*idv;
%
% fragment (optional): a vector of carbons to be included. [ 0, 0, 1,1,1]' = last 3 carbons.
global pseudohash1 pseudohash2
if isempty(pseudohash1)
pseudoha... |
github | EPFL-LCSB/matTFA-master | createTissueSpecificModel.m | .m | matTFA-master/ext/Cobra205_vDec2014/reconstruction/createTissueSpecificModel.m | 22,833 | utf_8 | b1e36173def8a0675727e3d42c0bb7e9 | function [tissueModel,Rxns] = createTissueSpecificModel(model, ...
expressionData,proceedExp,orphan,exRxnRemove,solver,options,funcModel)
%createTissueSpecificModel Create draft tissue specific model from mRNA expression data
%
% [tissueModel,Rxns] =
% createTissueSpeci... |
github | EPFL-LCSB/matTFA-master | removeFieldEntriesForType.m | .m | matTFA-master/ext/Cobra205_vDec2014/reconstruction/refinement/removeFieldEntriesForType.m | 7,139 | utf_8 | 702148175917ef57ddf13c5c8740e153 | function model = removeFieldEntriesForType(model, indicesToRemove, type, fieldSize, varargin)
% Remove field entries at the specified indices from all fields associated
% with the given type
% USAGE:
% model = removeFieldEntriesForType(model, indicesToRemove, type, varargin)
%
% INPUTS:
%
% model: th... |
github | EPFL-LCSB/matTFA-master | sparseNull.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/sparseNull.m | 9,145 | utf_8 | a10b073ba5651689e2e10fa7a5e6ca65 | function N = sparseNull(S, tol)
% sparseNull returns computes the sparse Null basis of a matrix
%
% N = sparseNull(S, tol)
%
% Computes a basis of the null space for a sparse matrix. For sparse
% matrixes this is much faster than using null. It does however have lower
% numerical accuracy. N is itself sparse and no... |
github | EPFL-LCSB/matTFA-master | ezimplot3.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/ezimplot3.m | 8,154 | utf_8 | 7bbd5c9f9dba80200fd1fb799e7c8cb3 | function h = ezimplot3(varargin)
% EZIMPLOT3 Easy to use 3D implicit plotter.
% EZIMPLOT3(FUN) plots the function FUN(X,Y,Z) = 0 (vectorized or not)
% over the default domain:
% -2*PI < X < 2*PI, -2*PI < Y < 2*PI, -2*PI < Z < 2*PI.
% FUN can be a string, an anonymous function handle, a .M-file handle, an
% ... |
github | EPFL-LCSB/matTFA-master | m2html.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/m2html/m2html.m | 38,334 | utf_8 | 9e0ccc8f5147c96ff4bde2efa2b4787b | function m2html(varargin)
%M2HTML - Documentation System for Matlab M-files in HTML
% M2HTML by itself generates an HTML documentation of Matlab M-files in the
% current directory. HTML files are also written in the current directory.
% M2HTML('PropertyName1',PropertyValue1,'PropertyName2',PropertyValue2,...)
% set... |
github | EPFL-LCSB/matTFA-master | qpsolng.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/qpsolng.m | 2,447 | utf_8 | 4b2e7f7c92565cb039eed9907693651d | % Core QP Solver. Use qpng.m instead.
%
% This routine solves the following optimization problem:
%
% min_x .5x' H x + q' x
% s.t. Aeq x = beq
% Ain x <= bin
%
% note that x0 is a feasible starting point.
%
% (C) Nicolo Giorgetti, 2006.
function [x, lam, k, status]=qpsolng(H, q, Aeq, beq, Ain, bin, x0)
nmax=2... |
github | EPFL-LCSB/matTFA-master | qpng.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/qpng.m | 8,266 | utf_8 | a76ee167df8e11072eea16b6f9407482 | % Quadratic programming solver using a null-space active-set method.
%
% [x, obj, lambda, info] = qpng (H, q, A, b, ctype, lb, ub, x0)
%
% Solve the general quadratic program
%
% min 0.5 x'*H*x + q'*x
% x
%
% subject to
% A*x [ "=" | "<=" | ">=" ] b
% lb <= x <= ub
%
% and given x0 as initial gues... |
github | EPFL-LCSB/matTFA-master | glpk.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/glpk.m | 20,365 | utf_8 | d8e67c6977ba79760299289ebfca225f | % Matlab MEX interface for the GLPK library
%
% [xopt, fmin, status, extra] = glpk (c, a, b, lb, ub, ctype, vartype,
% sense, param)
%
% Solve an LP/MILP problem using the GNU GLPK library. Given three
% arguments, glpk solves the following standard LP:
%
% min C'*x subject to A*x <= b
%
% but may also solve problems... |
github | EPFL-LCSB/matTFA-master | glpkmex.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/glpkmex.m | 3,052 | utf_8 | 33b5f8ff88c0469e04a4e77cd09ef9da | % ***OBSOLETE*** GLPKMEX interface. Use glpk instead.
%
% [xmin,fmin,status,extra]=glpkmex(sense,c,a,b,ctype,lb,ub,vartype,param,lp,solver,save)
%
% This function is provided for compatibility with the old Matlab
% interface to the GNU GLPK library. You should use the glpk function
% instead.
%
% See also: glpk, qpn... |
github | EPFL-LCSB/matTFA-master | isBindingInstalled.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/isBindingInstalled.m | 3,030 | utf_8 | fd7bfb0254686f102c3dfc6170e65038 | function installed = isBindingInstalled()
% installed = isBindingInstalled()
%
% Returns
%
% 1. installed =
% - 1 if the libSBML executables are installed
% - 0 otherwise
%
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.... |
github | EPFL-LCSB/matTFA-master | install.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/install.m | 9,088 | utf_8 | 881213623382d9ea90f52aa2142f33e7 | function install
% install
%
% 1. reports whether the libsbml binding is installed
% 2. adds the toolbox dirctories to the Path
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the la... |
github | EPFL-LCSB/matTFA-master | isBindingFbcEnabled.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/fbc_package/isBindingFbcEnabled.m | 2,265 | utf_8 | 8cb0fb5729183cd42636bc97918fb7e8 | function fbcEnabled = isBindingFbcEnabled()
% fbcEnabled = isBindingFbcEnabled()
%
% Returns
%
% 1. fbcEnabled =
% - 1 if the executables are enabled with fbc support
% - 0 otherwise
%
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit ... |
github | EPFL-LCSB/matTFA-master | bind_isSBML_Model.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Validate_MATLAB_SBML_Structures/bind_isSBML_Model.m | 139,862 | utf_8 | 6b19c286b430b99baed148584e663c49 | function [valid, message] = isValidSBML_Model(SBMLStructure)
% [valid, message] = isValidSBML_Model(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Model structure of the appropriate
% level and version
% - 0... |
github | EPFL-LCSB/matTFA-master | isSBML_Rule.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Validate_MATLAB_SBML_Structures/isSBML_Rule.m | 4,719 | utf_8 | 82221b39c9f485c76bc0c4cb4425712d | function [valid, message] = isSBML_Rule(varargin)
% [valid, message] = isSBML_Rule(SBMLRule, level, version(optional))
%
% Takes
%
% 1. SBMLRule, an SBML Rule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
%
% Returns
%
% 1. valid =
% - 1,... |
github | EPFL-LCSB/matTFA-master | AnalyseSpecies.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/AnalyseSpecies.m | 14,715 | utf_8 | 8b6973e0bfad96e3ccee4c6adb214328 | function Species = AnalyseSpecies(SBMLModel)
% [analysis] = AnalyseSpecies(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. a structure detailing the species and how they are manipulated
% within the model
%
%
% *EXAMPLE:*
%
% Using the model from toolbox/Test/te... |
github | EPFL-LCSB/matTFA-master | WriteODEFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteODEFunction.m | 29,879 | utf_8 | 9d231760d2c9e73dd506f73078e5a7da | function WriteODEFunction(varargin)
% WriteODEFunction(SBMLModel, name(optional))
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, an optional string representing the name of the ode function to be used
%
% Outputs
%
% 1. a file 'name.m' defining a function that defines the ode equations of
% the mo... |
github | EPFL-LCSB/matTFA-master | WriteEventAssignmentFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteEventAssignmentFunction.m | 9,101 | utf_8 | 0b45ac0f8184fe7240a489b6399337d3 | function WriteEventAssignmentFunction(SBMLModel, Name)
% WriteEventAssignmentFunction(SBMLModel, name)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, a string representing the name of the ode function being used
%
% Outputs
%
% 1. a file 'name_eventAssign.m' defining a function that assigns values fo... |
github | EPFL-LCSB/matTFA-master | AnalyseVaryingParameters.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/AnalyseVaryingParameters.m | 10,969 | utf_8 | eadb1635027fd7b7829377f0df6f9f66 | function VaryingParameters = AnalyseVaryingParameters(SBMLModel)
% [analysis] = AnalyseVaryingParameters(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. a structure detailing any parameters that are not constant and how they are manipulated
% within the model
%
% *EXAMP... |
github | EPFL-LCSB/matTFA-master | WriteEventHandlerFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteEventHandlerFunction.m | 12,176 | utf_8 | f5fbcd1778a9be55b55816f0d6e020a8 | function WriteEventHandlerFunction(SBMLModel, Name)
% WriteEventHandlerFunction(SBMLModel, name)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, a string representing the name of the ode function being used
%
% Outputs
%
% 1. a file 'name_events.m' defining a function that tests whether events
% ha... |
github | EPFL-LCSB/matTFA-master | SolveODEFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/SolveODEFunction.m | 13,085 | utf_8 | f779f53ab96b648094f18c546b0837c7 | function [t, data] = SolveODEFunction(varargin)
% SolveODEFunction(varargin)
%
% Takes
%
% 1. a MATLAB_SBML model structure (required argument)
% 2. time limit (default = 10)
% 3. number of time steps (default lets the solver decide)
% 4. a flag to indicate whether to output species values in amount/concentrat... |
github | EPFL-LCSB/matTFA-master | SubstituteFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/SubstituteFunction.m | 5,155 | utf_8 | 66c788cb09b115ecfad961f50a6ac138 | function Formula = SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)
% newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. SBMLFunctionDefinition, an SBML FunctionDefinition structure
%
% Returns
%
% 1. newEx... |
github | EPFL-LCSB/matTFA-master | RemoveDuplicates.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/RemoveDuplicates.m | 2,898 | utf_8 | 46f7aade9e3235449589d381f0890c24 | function y = RemoveDuplicates(FullArray)
% newArray = RemoveDuplicates(array)
%
% Takes
%
% 1. array, any array
%
% Returns
%
% 1. the array with any duplicate entries removed
%
% *EXAMPLE:*
%
% newArray = RemoveDuplicates([2, 3, 4, 3, 2, 5])
% newArray = [2, 3, 4, 5]
% ... |
github | EPFL-LCSB/matTFA-master | Rearrange.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/Rearrange.m | 11,479 | utf_8 | 6ed57da4458b9e994a775fa3c990b46f | function output = Rearrange(formula, x)
% output = Rearrange(expression, name)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. name, a string representing the name of a variable
%
% Returns
%
% 1. the expression rearranged in terms of the variable
%
% *EXAMPLE:*
%
% output ... |
github | EPFL-LCSB/matTFA-master | propagateLevelVersion.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/structFieldnames/propagateLevelVersion.m | 2,729 | utf_8 | ac0c57fde5be4302fbf3241c14e3787e | function model = propagateLevelVersion(SBMLModel)
% SBMLModel = propagateLevelVersion(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. the SBML Model structure with level and version fields added to all
% sub structures
%
% *NOTE:* This function facilitates keeping track of the level... |
github | EPFL-LCSB/matTFA-master | testObject.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/Test/testObject.m | 10,178 | utf_8 | 7294eab33dbb7ea5880923e3769a8072 | function [fail, num, message] = testObject(obj, attributes, component, fail, num, message)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyr... |
github | EPFL-LCSB/matTFA-master | Model_getListOfByTypecode.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/Model/Model_getListOfByTypecode.m | 3,470 | utf_8 | 3ee51ba7a44c4697be5cce017e9c2346 | function array = Model_getListOfByTypecode(SBMLModel, SBMLTypecode)
% listOf = Model_getListOfByTypecode(SBMLModel, typecode)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. typecode; a string representing the typecode of SBML ListOf structure
%
% Returns
%
% 1. the SBML ListOf structure that has this typecode... |
github | EPFL-LCSB/matTFA-master | GetRateLawsFromReactions.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/AccessModel/GetRateLawsFromReactions.m | 17,010 | utf_8 | e123fc8f39c36d33d5ef39991f08688a | function [Species, RateLaws] = GetRateLawsFromReactions(SBMLModel)
% [species, rateLaws] = GetRateLawsFromReactions(SBMLModel)
%
% Takes
%
% 1. SBMLModel; an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all species
% 2. an array of
%
% - the character representation ... |
github | EPFL-LCSB/matTFA-master | TestFunction.m | .m | matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Test/TestFunction.m | 4,751 | utf_8 | 20ffcfa9c79433da3fc9998246d20dd8 | function y = TestFunction(varargin)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2011 jointly by the following organizatio... |
github | EPFL-LCSB/matTFA-master | sampleScatterMatrix.m | .m | matTFA-master/ext/Cobra205_vDec2014/sampling/sampleScatterMatrix.m | 4,767 | utf_8 | 58deec35b12aa4bb50273bc36cd3f221 | function sampleScatterMatrix(rxnNames,model,sample,nPoints,fontSize,dispRFlag,rxnNames2)
%sampleScatterMatrix Draws a scatterplot matrix with pairwise scatterplots
%for multiple reactions
%
% sampleScatterMatrix(rxnNames,model,sample,nPoints,dispRFlag,rxnNames2)
%
%INPUTS
% rxnNames Cell array of reaction names t... |
github | EPFL-LCSB/matTFA-master | verifyPoints.m | .m | matTFA-master/ext/Cobra205_vDec2014/sampling/verifyPoints.m | 1,925 | utf_8 | 51f9f4c742a6369a2be6b835d274e08f | % function [errorsA, errorsLUB] = verifyPoints(sampleStruct)
function [errorsA, errorsLUB, stuckPoints] = verifyPoints(sampleStruct)
%verifyPoints Verify that a set of points are in the solutoin space of sampleStruct.
% Typically, this method would be called to check a set of warmup points or
% points generated via gpS... |
github | EPFL-LCSB/matTFA-master | gpSampler_tFBAVersiontUsed.m | .m | matTFA-master/ext/Cobra205_vDec2014/sampling/gpSampler_tFBAVersiontUsed.m | 12,932 | utf_8 | e82b2581d217d3925c1a3fa2c4ff003e | function [sampleStructOut, mixedFrac] = gpSampler(sampleStruct, nPoints, bias, maxTime, maxSteps, threads, nPointsCheck)
%gpSampler Samples an arbitrary linearly constrained space using a fixed
%number of points that are moved in parallel
%
% [sampleStructOut, mixedFraction] = gpSampler(sampleStruct, nPoints, bias, max... |
github | EPFL-LCSB/matTFA-master | ACHRSamplerParallelGeneral.m | .m | matTFA-master/ext/Cobra205_vDec2014/sampling/ACHRSamplerParallelGeneral.m | 13,226 | utf_8 | a57266feeacacc3b5068e1cf4d95fc38 | function [sampleStruct] = ACHRSamplerParallelGeneral(sampleStruct,nLoops,stepsPerPoint, maxtime, proc, fdirectory)
% ACHRSamplerParallelGeneral Artificial Centering Hit-and-Run sampler with in place (memory) point
% managmenet
%
% sampleStruct = ACHRSamplerParallelGeneral(sampleStruct,nLoops,stepsPerPoint)
%
%INPUTS
% ... |
github | EPFL-LCSB/matTFA-master | generateSUXMatrix.m | .m | matTFA-master/ext/Cobra205_vDec2014/gapFilling/growthExpMatch/generateSUXMatrix.m | 3,883 | utf_8 | 7765018ced7286373cb6eabb2a70249c | function MatricesSUX =generateSUXMatrix(model,dictionary, KEGGFilename, KEGGBlackList, compartment, addModel)
% generateSUXMatrix creates the matrices for matlab smiley -- > combines S, U
% (KEGG), X (transport)
%
% MatricesSUX =generateSUXMatrix(model,CompAbr, KEGGID,
% KEGGFilename, compartment)
%
% model ... |
github | EPFL-LCSB/matTFA-master | growthExpMatch.m | .m | matTFA-master/ext/Cobra205_vDec2014/gapFilling/growthExpMatch/growthExpMatch.m | 6,053 | utf_8 | 7b4d9288dec14e0b4979d70ba9f64043 | function [solution]=growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold)
%growExpMatch run the growthExpMatch algorythm
%
% [solution]=growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold)
%
%INPUTS
% model COBRA model structure
% ... |
github | CollinGuo/GoDec_plus-master | SpectralClustering.m | .m | GoDec_plus-master/SpectralClustering.m | 1,247 | utf_8 | 21c3ecc5345706307b629c9e01180798 | %--------------------------------------------------------------------------
% This function takes an adjacency matrix of a graph and computes the
% clustering of the nodes using the spectral clustering algorithm of
% Ng, Jordan and Weiss.
% CMat: NxN adjacency matrix
% n: number of groups for clustering
% group... |
github | walid1992/AndroidSpeexDenoise-master | echo_diagnostic.m | .m | AndroidSpeexDenoise-master/app/src/main/jni/libspeexdsp/echo_diagnostic.m | 2,076 | utf_8 | 8d5e7563976fbd9bd2eda26711f7d8dc | % Attempts to diagnose AEC problems from recorded samples
%
% out = echo_diagnostic(rec_file, play_file, out_file, tail_length)
%
% Computes the full matrix inversion to cancel echo from the
% recording 'rec_file' using the far end signal 'play_file' using
% a filter length of 'tail_length'. The output is saved to 'o... |
github | brennankoopman/MTE204_Robot_Arm_Control-master | Jacobian.m | .m | MTE204_Robot_Arm_Control-master/Jacobian.m | 575 | utf_8 | 7231c1c63fd0e284853ed024883d2ea1 | % calculates the jacobian based on the joint angles
function J = Jacobian(q);
len = [0 1 1];
dx1 = -(len(2)*cos(q(2)) + len(3)*cos(q(2)-q(3)))*sin(q(1));
dx2 = (-len(2)*sin(q(2))-len(3)*sin(q(2)-q(3)))*cos(q(1));
dx3 = (len(3)*sin(q(2)-q(3)))*cos(q(1));
dy1 = (len(2)*cos(q(2))+len(3)*cos(q(2)-q(3)))*cos(q... |
github | brennankoopman/MTE204_Robot_Arm_Control-master | timeOutputTest.m | .m | MTE204_Robot_Arm_Control-master/timeOutputTest.m | 2,015 | utf_8 | 4d5da938ce78aadae33aca4b8d618470 |
%{
%this times the numerical method verses n subintervals, the calculations in this function are the major ones a real
%time system would need to operate with our mething method
q - the initial position in angles of deg
t - the target position in cartesian coords, col vesctor
Jerr - the end case error on the Jacobian... |
github | brennankoopman/MTE204_Robot_Arm_Control-master | armFunction_midJoint.m | .m | MTE204_Robot_Arm_Control-master/armFunction_midJoint.m | 387 | utf_8 | ef5a3716f0aca41119ee61b2002b8ec0 |
%this function calculates the postion of the midjoint with the inputs of
%q, which is the joint angles of the arm
%P is the reference point of the arm in 3D space, typically (0,0,0)
function [smid] = armFunction_midJoint (q, P)
len = [0;1;1];
y = (len(2)*cos(q(2)))*sin(q(1)) - P(1);
x = (len(2)*cos(q(2)))*cos(q(1))... |
github | brennankoopman/MTE204_Robot_Arm_Control-master | armFunction.m | .m | MTE204_Robot_Arm_Control-master/armFunction.m | 458 | utf_8 | af0cc0db3ec240f263d95ab51ab4835f | %this function calculates the postion of the end effector with the inputs of
%q, which is the joints angles of the arm
%P is the reference point of the arm in 3D space, typically (0,0,0)
function s = armFunction(q, P)
len = [0 1 1];
x = (len(2)*cos(q(2)) + len(3)*cos(q(2)-q(3)))*cos(q(1)) - P(1); % x
y = (len... |
github | brennankoopman/MTE204_Robot_Arm_Control-master | sectionPath.m | .m | MTE204_Robot_Arm_Control-master/sectionPath.m | 764 | utf_8 | fc563b76c2ae1de650cea01e7498cf4d | %{
Version = Test
this version will be used for the analysis of the time efficiency of the algorithm
this function will take any linear path between s and t, and break it up into an
efficient number of smaller steps in order to make the path as straight as
possible
%}
%t is the target position, q is the i... |
github | zeakey/edgeval-master | checkNumArgs.m | .m | edgeval-master/utils/checkNumArgs.m | 3,796 | utf_8 | 726c125c7dc994c4989c0e53ad4be747 | function [ x, er ] = checkNumArgs( x, siz, intFlag, signFlag )
% Helper utility for checking numeric vector arguments.
%
% Runs a number of tests on the numeric array x. Tests to see if x has all
% integer values, all positive values, and so on, depending on the values
% for intFlag and signFlag. Also tests to see if ... |
github | zeakey/edgeval-master | edgesEvalDir.m | .m | edgeval-master/utils/edgesEvalDir.m | 5,852 | utf_8 | b708b92045eaa75fa68d09e169447bb6 | function varargout = edgesEvalDir( varargin )
% Calculate edge precision/recall results for directory of edge images.
%
% Enhanced replacement for boundaryBench() from BSDS500 code:
% http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/
% Uses same format for results and is fully compatible with boundary... |
github | zeakey/edgeval-master | fevalDistr.m | .m | edgeval-master/utils/fevalDistr.m | 11,227 | utf_8 | 7e4d5077ef3d7a891b2847cb858a2c6c | function [out,res] = fevalDistr( funNm, jobs, varargin )
% Wrapper for embarrassingly parallel function evaluation.
%
% Runs "r=feval(funNm,jobs{i}{:})" for each job in a parallel manner. jobs
% should be a cell array of length nJob and each job should be a cell array
% of parameters to pass to funNm. funNm must be a f... |
github | isamabdullah88/Visual-Inertial-Odometry-master | integrateIMU.m | .m | Visual-Inertial-Odometry-master/SourceCode/Functions/integrateIMU.m | 3,116 | utf_8 | 26979cd3549c449c0e7ca5da743e2957 | function[xUpdate] = integrateIMU(xPrev, a, omega, dt, g_w)
%INTEGRATEIMUSTREAM Integrate IMU stream and return state and covariance
%estimates
%The state is given by :
%x =[p_I_G q_IG v_I_G b_g b_a];
%Set noise to 0
noise_params.sigma_g = 0;
noise_params.sigma_a = 0;
noise_params.sigma_bg = 0;
noise_params.sigma_ba ... |
github | isamabdullah88/Visual-Inertial-Odometry-master | calcGNPosEstTODO.m | .m | Visual-Inertial-Odometry-master/SourceCode/Functions/calcGNPosEstTODO.m | 2,592 | utf_8 | 79942d6dfc17224ece353c06cb16e2a5 | function[p_f_G, cost, RCOND] = calcGNPosEst(camState, observations, noiseParams)
%CALCGNPOSEST Calculate the position estimate of the feature using Gauss
%Newton optimization
% INPUT :
% observations : 2xM matrix of pixel values of the current landmark
% camStates : Cell array of M structs of camera poses
% cam... |
github | isamabdullah88/Visual-Inertial-Odometry-master | match.m | .m | Visual-Inertial-Odometry-master/SourceCode/Functions/match.m | 1,927 | utf_8 | f7d5bf4c2b0a7056954aaa41a7ab575e | % num = match(image1, image2)
%
% This function reads two images, finds their SIFT features, and
% displays lines connecting the matched keypoints. A match is accepted
% only if its distance is less than distRatio times the distance to the
% second closest match.
% It returns the number of matches displayed.
%
%... |
github | isamabdullah88/Visual-Inertial-Odometry-master | loadImuData.m | .m | Visual-Inertial-Odometry-master/SourceCode/Functions/loadImuData.m | 1,522 | utf_8 | 376c7c00df767b65f51449e0d08648eb | function[ imuData, gpsData, velocity ] = loadImuData( imuDir )
%loadImuData loads the imu data from kitti dataset in required format i.e.
%gyro, accelerometer and timestamps
fileDir =[imuDir ' / data /'];
fileNames = dir(fullfile(fileDir, ' * .txt'));
dateStrings = loadTimestamps(imuDir);
len = size(dateStrings, 1);
... |
github | isamabdullah88/Visual-Inertial-Odometry-master | loadCalibrationCamToCam.m | .m | Visual-Inertial-Odometry-master/SourceCode/Utils/loadCalibrationCamToCam.m | 1,837 | utf_8 | ab070dd26d9e2df2f7739d6d203c4547 | function calib = loadCalibrationCamToCam(filename)
% open file
fid = fopen(filename, 'r');
if fid < 0
calib =[];
return;
end
% read corner distance
calib.cornerdist = readVariable(fid, 'corner_dist', 1, 1);
% read all cameras (maximum : 100)
for cam = 1 : 100
% read variables
S_ = readVariable(fid, ['S_' num2str(c... |
github | isamabdullah88/Visual-Inertial-Odometry-master | loadCalibrationRigid.m | .m | Visual-Inertial-Odometry-master/SourceCode/Utils/loadCalibrationRigid.m | 834 | utf_8 | f52ca08e93a8e8441acb81012628dfa4 | function Tr = loadCalibrationRigid(filename)
% open file
fid = fopen(filename, 'r');
if fid < 0
error(['ERROR : Could not load : ' filename]);
end
% read calibration
R = readVariable(fid, 'R', 3, 3);
T = readVariable(fid, 'T', 3, 1);
Tr =[R T;0 0 0 1];
% close file
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
github | isamabdullah88/Visual-Inertial-Odometry-master | simCamera.m | .m | Visual-Inertial-Odometry-master/Gauss Newton Simulation/simCamera.m | 1,700 | utf_8 | 25bcc63217dba70a35b10547d459fb33 | function[ obs, camStates ] = simCamera( C1_p_f, camera, C1_p_C2, thetas, n )
%simCamera simulates a camera of n frames given the parameters and returns 2D feature
%coordinates in each frame
% C1_p_f : 3D position coordinates of feature in C1, which would be
% tracked in sub - sequent camera frames
% cam... |
github | epilepsyecosystem/1stplace_notsorandomanymore-master | spatFilt.m | .m | 1stplace_notsorandomanymore-master/Andriy/code/spatFilt.m | 1,113 | utf_8 | 9e5d17114745661029930c1558855096 | %James Ethridge , Will Weaver
%Spatial filtering function. Returns the filtered signal Y.
%
%Inputs:
%x: the input matrix where M rows are the channels and N columns are the
% time bins
%
%coef: the entire P' matrix of filter coefficients
%
%dimm: the number of dimensions the filter should attemp t... |
github | epilepsyecosystem/1stplace_notsorandomanymore-master | sub_pos.m | .m | 1stplace_notsorandomanymore-master/Andriy/code/sub_pos.m | 496 | utf_8 | 12fb7f8d85bca88f653bf530a3e02f07 | %
% Stephen Faul
% 21st July 2004
%
% SUB_POS: returns the starting positions of each subband of the
% resultant vector from wt
%
% input: data_len -- the length of the original signal
% num_coeffs -- the number of filter coefficients (2*order for Daubechie
%
% outpu... |
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