From: Benjamin Auder Date: Sat, 14 Jan 2017 03:27:48 +0000 (+0100) Subject: remove utils.c, prepare testing 'R-only' X-Git-Url: https://git.auder.net/variants/%24%7Bvname%7D/current/pieces/doc/index.css?a=commitdiff_plain;h=df3ef2db3d9d01161973a67b4f7d25e1da4d502b;p=valse.git remove utils.c, prepare testing 'R-only' --- diff --git a/src/test/generate_test_data/MATLAB_test_helpers/Octave.m b/src/test/generate_test_data/MATLAB_test_helpers/Octave.m deleted file mode 100644 index 8f105d2..0000000 --- a/src/test/generate_test_data/MATLAB_test_helpers/Octave.m +++ /dev/null @@ -1,5 +0,0 @@ -% Run this file if using Octave -if exist('OCTAVE_VERSION', 'builtin') ~= 0 - pkg load statistics %for random() - more off %to prevent bufferizing output -end diff --git a/src/test/generate_test_data/MATLAB_test_helpers/README b/src/test/generate_test_data/MATLAB_test_helpers/README deleted file mode 100644 index e94c0a0..0000000 --- a/src/test/generate_test_data/MATLAB_test_helpers/README +++ /dev/null @@ -1 +0,0 @@ -Subset of select/ project: only files required to generate tests outputs diff --git a/src/test/generate_test_data/MATLAB_test_helpers/covariance.m b/src/test/generate_test_data/MATLAB_test_helpers/covariance.m deleted file mode 100644 index 839c33c..0000000 --- a/src/test/generate_test_data/MATLAB_test_helpers/covariance.m +++ /dev/null @@ -1,9 +0,0 @@ -%covariance matrix for tests on synthetic data: A(i,j) = a^|i-j| -function[A] = covariance(p,a) - - A = a*ones(p,p); - for i=1:p - A(i,:) = A(i,:) .^ abs(i-(1:p)); - end - -end diff --git a/src/test/generate_test_data/R_test_helpers/checkOutput.R b/src/test/generate_test_data/R_test_helpers/checkOutput.R deleted file mode 100644 index 1faddaa..0000000 --- a/src/test/generate_test_data/R_test_helpers/checkOutput.R +++ /dev/null @@ -1,10 +0,0 @@ -checkOutput = function(varName, matrix, refMatrix, tol){ - print('Checking %s\n',varName); - maxError = max(max(max(max(abs(matrix - refMatrix))))); - if(maxError >= tol){ - print('Inaccuracy: max(abs(error)) = %g >= %g\n',maxError,tol) - } - else{ - print('OK\n') - } -} \ No newline at end of file diff --git a/src/test/generate_test_data/R_test_helpers/covariance.R b/src/test/generate_test_data/R_test_helpers/covariance.R deleted file mode 100644 index 2dea7f2..0000000 --- a/src/test/generate_test_data/R_test_helpers/covariance.R +++ /dev/null @@ -1,9 +0,0 @@ -covariance= function(p,a){ - A = matrix(a, p,p) - for{i in 1:p}{ - for{k in 1:p}{ - A[i,]= A[i,]^abs(i-k) - } - } - return(A=A) -} \ No newline at end of file diff --git a/src/test/generate_test_data/R_test_helpers/testEMGLLF.R b/src/test/generate_test_data/R_test_helpers/testEMGLLF.R deleted file mode 100644 index 0eb3483..0000000 --- a/src/test/generate_test_data/R_test_helpers/testEMGLLF.R +++ /dev/null @@ -1,46 +0,0 @@ -testEMGLLF = function(){ - testFolder = 'data/' - - #get dimensions - dimensions = read.table(strcat(testFolder,'dimensions'), header=FALSE) - n = dimensions[1] - p = dimensions[2] - m = dimensions[3] - k = dimensions[4] - - #get all input arrays - phiInit = read.table(strcat(testFolder,'phiInit'), header=FALSE) - rhoInit = read.table(strcat(testFolder,'rhoInit'), header=FALSE) - piInit = t(read.table(strcat(testFolder,'piInit'), header=FALSE)) - gamInit = read.table(strcat(testFolder,'gamInit'), header=FALSE) - mini = read.table(strcat(testFolder,'mini'), header=FALSE) - maxi = read.table(strcat(testFolder,'maxi'), header=FALSE) - gamma = read.table(strcat(testFolder,'gamma'), header=FALSE) - lambda = read.table(strcat(testFolder,'lambda'), header=FALSE) - X = rread.table(strcat(testFolder,'X'), header=FALSE) - Y = read.table(strcat(testFolder,'Y'), header=FALSE) - tau = read.table(strcat(testFolder,'tau'), header=FALSE) - - #run EMGLLF.c - EMG = .Call("EMGLLF_core",phiInit,rhoInit,piInit1,gamInit,mini,maxi,gamma,lambda,X,Y,tau) - phi = EMG$phi - rho = EMG$rho - pi = EMG$pi - LLF = EMG$LLF - S = EMG$S - - #get all stored outputs - ref_phi =read.table(strcat(testFolder,'phi'), header=FALSE) - ref_rho = read.table(strcat(testFolder,'rho'), header=FALSE) - ref_pi = read.table(strcat(testFolder,'pi'), header=FALSE) - ref_LLF = read.table(strcat(testFolder,'LLF'), header=FALSE) - ref_S = read.table(strcat(testFolder,'S'), header=FALSE) - - #check that output correspond to stored output - tol = 1e-5; - checkOutput('phi',phi,ref_phi,tol); - checkOutput('rho',rho,ref_rho,tol); - checkOutput('pi',pi,ref_pi,tol); - checkOutput('LLF',LLF,ref_LLF,tol); - checkOutput('S',S,ref_S,tol); -} diff --git a/src/test/generate_test_data/MATLAB_test_helpers/EMGLLF.m b/src/test/generate_test_data/helpers/EMGLLF.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/EMGLLF.m rename to src/test/generate_test_data/helpers/EMGLLF.m diff --git a/src/test/generate_test_data/MATLAB_test_helpers/EMGrank.m b/src/test/generate_test_data/helpers/EMGrank.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/EMGrank.m rename to src/test/generate_test_data/helpers/EMGrank.m diff --git a/src/test/generate_test_data/MATLAB_test_helpers/basicInitParameters.m b/src/test/generate_test_data/helpers/basicInitParameters.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/basicInitParameters.m rename to src/test/generate_test_data/helpers/basicInitParameters.m diff --git a/src/test/generate_test_data/helpers/checkOutput.R b/src/test/generate_test_data/helpers/checkOutput.R new file mode 100644 index 0000000..187536a --- /dev/null +++ b/src/test/generate_test_data/helpers/checkOutput.R @@ -0,0 +1,12 @@ +checkOutput = function(varName, array, refArray, tol) +{ + print(paste("Checking ",varName,sep="")) + maxError = max(abs(array - refArray)) + if(maxError >= tol) + { + print(paste("Inaccuracy: max(abs(error)) = ",maxError," >= ",tol,sep="")) + } else + { + print("OK") + } +} diff --git a/src/test/generate_test_data/MATLAB_test_helpers/constructionModelesLassoMLE.m b/src/test/generate_test_data/helpers/constructionModelesLassoMLE.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/constructionModelesLassoMLE.m rename to src/test/generate_test_data/helpers/constructionModelesLassoMLE.m diff --git a/src/test/generate_test_data/MATLAB_test_helpers/constructionModelesLassoRank.m b/src/test/generate_test_data/helpers/constructionModelesLassoRank.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/constructionModelesLassoRank.m rename to src/test/generate_test_data/helpers/constructionModelesLassoRank.m diff --git a/src/test/generate_test_data/helpers/covariance.R b/src/test/generate_test_data/helpers/covariance.R new file mode 100644 index 0000000..15cd693 --- /dev/null +++ b/src/test/generate_test_data/helpers/covariance.R @@ -0,0 +1,8 @@ +covariance = function(p,a) +{ + A = matrix(a, p,p) + for (i in 1:p) + A[i,] = A[i,]^abs(i-(1:p)) + + return (A) +} diff --git a/src/test/generate_test_data/MATLAB_test_helpers/generateIO.m b/src/test/generate_test_data/helpers/generateIO.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/generateIO.m rename to src/test/generate_test_data/helpers/generateIO.m diff --git a/src/test/generate_test_data/MATLAB_test_helpers/generateIOdefault.m b/src/test/generate_test_data/helpers/generateIOdefault.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/generateIOdefault.m rename to src/test/generate_test_data/helpers/generateIOdefault.m diff --git a/src/test/generate_test_data/MATLAB_test_helpers/selectiontotale.m b/src/test/generate_test_data/helpers/selectiontotale.m similarity index 100% rename from src/test/generate_test_data/MATLAB_test_helpers/selectiontotale.m rename to src/test/generate_test_data/helpers/selectiontotale.m diff --git a/src/test/testEMGLLF.R b/src/test/testEMGLLF.R new file mode 100644 index 0000000..9ba7058 --- /dev/null +++ b/src/test/testEMGLLF.R @@ -0,0 +1,50 @@ +testEMGLLF = function() +{ + testFolder = "data/" + array_delimiter = " " + + #get dimensions + dimensions = read.table(paste(testFolder,"dimensions",sep=""), header=FALSE, + sep=array_delimiter) + n = dimensions[1] + p = dimensions[2] + m = dimensions[3] + k = dimensions[4] + + #get all input arrays + phiInit = read.table(paste(testFolder,"phiInit",sep=""), header=FALSE, sep=array_delimiter) + rhoInit = read.table(paste(testFolder,"rhoInit",sep=""), header=FALSE, sep=array_delimiter) + piInit = read.table(paste(testFolder,"piInit",sep=""), header=FALSE, sep=array_delimiter) + gamInit = read.table(paste(testFolder,"gamInit",sep=""), header=FALSE, sep=array_delimiter) + mini = read.table(paste(testFolder,"mini",sep=""), header=FALSE, sep=array_delimiter) + maxi = read.table(paste(testFolder,"maxi",sep=""), header=FALSE, sep=array_delimiter) + gamma = read.table(paste(testFolder,"gamma",sep=""), header=FALSE, sep=array_delimiter) + lambda = read.table(paste(testFolder,"lambda",sep=""), header=FALSE, sep=array_delimiter) + X = read.table(paste(testFolder,"X",sep=""), header=FALSE, sep=array_delimiter) + Y = read.table(paste(testFolder,"Y",sep=""), header=FALSE, sep=array_delimiter) + tau = read.table(paste(testFolder,"tau",sep=""), header=FALSE, sep=array_delimiter) + + #run EMGLLF.c + EMG = .Call("EMGLLF_core",phiInit,rhoInit,piInit1,gamInit,mini,maxi,gamma,lambda,X,Y,tau, + PACKAGE="valse") + phi = EMG$phi + rho = EMG$rho + pi = EMG$pi + LLF = EMG$LLF + S = EMG$S + + #get all stored outputs + ref_phi = read.table(paste(testFolder,"phi",sep=""), header=FALSE, sep=array_delimiter) + ref_rho = read.table(paste(testFolder,"rho",sep=""), header=FALSE, sep=array_delimiter) + ref_pi = read.table(paste(testFolder,"pi",sep=""), header=FALSE, sep=array_delimiter) + ref_LLF = read.table(paste(testFolder,"LLF",sep=""), header=FALSE, sep=array_delimiter) + ref_S = read.table(paste(testFolder,"S",sep=""), header=FALSE, sep=array_delimiter) + + #check that output correspond to stored output + tol = 1e-5; + checkOutput("phi",phi,ref_phi,tol); + checkOutput("rho",rho,ref_rho,tol); + checkOutput("pi",pi,ref_pi,tol); + checkOutput("LLF",LLF,ref_LLF,tol); + checkOutput("S",S,ref_S,tol); +} diff --git a/src/test/utils.c b/src/test/utils.c deleted file mode 100644 index a6370b0..0000000 --- a/src/test/utils.c +++ /dev/null @@ -1,111 +0,0 @@ -#include -#include -#include -#include - -// Check if array == refArray -void compareArray(const char* ID, const void* array, const void* refArray, int size, - int isinteger) -{ - float EPS = 1e-5; //precision - printf("Checking %s\n",ID); - float maxError = 0.0; - for (int i=0; i= maxError) - maxError = error; - } - if (maxError >= EPS) - printf(" Inaccuracy: max(abs(error)) = %g >= %g\n",maxError,EPS); - else - printf(" OK\n"); -} - -void compareArray_real(const char* ID, const void* array, const void* refArray, int size) -{ - return compareArray(ID, array, refArray, size, 0); -} - -void compareArray_int(const char* ID, const void* array, const void* refArray, int size) -{ - return compareArray(ID, array, refArray, size, 1); -} - -// Read array by columns (as in MATLAB) and return by-rows encoding -void* readArray(const char* fileName, int isinteger) -{ - // need to prepend '../data/' (not really nice code...) - char* fullFileName = (char*)calloc(5+strlen(fileName)+1, sizeof(char)); - strcat(fullFileName, "data/"); - strcat(fullFileName, fileName); - - // first pass to know how many elements to allocate - char* command = (char*)calloc(12+strlen(fullFileName)+8+1, sizeof(char)); - strcat(command, "grep -o ' ' "); - strcat(command, fullFileName); - strcat(command, " | wc -l"); - FILE *countSpaces = popen(command, "r"); - char* buffer = (char*)calloc(32, sizeof(char)); - fgets(buffer, sizeof(buffer), countSpaces); - int n = atoi(buffer) + 1; - free(buffer); - pclose(countSpaces); - - // open file for reading - FILE* file = fopen(fullFileName, "r"); - free(fullFileName); - - int d = 1; - size_t elementSize = isinteger - ? sizeof(int) - : sizeof(float); - - // read all values, and convert them to by-rows matrices format - void* array = malloc(n*elementSize); - char curChar = ' '; - char bufferNum[64]; - for (int u=0; u