fix generateRunSave_EMGLLF, simplify arrays readings

diff --git a/src/.gitignore b/src/.gitignore
index bdfbcfb..da9ff21 100644 (file)
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1,4 +1,3 @@
 #ignore object files, library and test executables
 *.o
 *.so
-vgcore.*

diff --git a/src/test/.gitignore b/src/test/.gitignore
index 05354ad..1a02474 100644 (file)
--- a/src/test/.gitignore
+++ b/src/test/.gitignore
@@ -1,3 +1,4 @@
 test.*
 !test.*.c
 /data/
+vgcore.*

diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R b/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
index 2c2dc2a..f6059e5 100644 (file)
--- a/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
+++ b/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
@@ -9,26 +9,38 @@ generateRunSaveTest_EMGLLF = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
        require(valse)
        params = valse:::basic_Init_Parameters(n, p, m, k)
        io = generateIOdefault(n, p, m, k)
-       write.table(paste(testFolder,"phiInit",sep=""), params$phiInit, sep=delimiter);
-       write.table(paste(testFolder,"rhoInit",sep=""), params$rhoInit, sep=delimiter);
-       write.table(paste(testFolder,"piInit",sep=""), params$piInit, sep=delimiter);
-       write.table(paste(testFolder,"gamInit",sep=""), params$gamInit, sep=delimiter);
-       write.table(paste(testFolder,"mini",sep=""), mini, sep=delimiter);
-       write.table(paste(testFolder,"maxi",sep=""), maxi, sep=delimiter);
-       write.table(paste(testFolder,"gamma",sep=""), gamma, sep=delimiter);
-       write.table(paste(testFolder,"lambda",sep=""), lambda, sep=delimiter);
-       write.table(paste(testFolder,"X",sep=""), io$X, sep=delimiter);
-       write.table(paste(testFolder,"Y",sep=""), io$Y, sep=delimiter);
-       write.table(paste(testFolder,"tau",sep=""), tau, sep=delimiter);
-       write.table(paste(testFolder,"dimensions",sep=""), c(n,p,m,k), sep=delimiter);
+       write.table(as.double(params$phiInit), paste(testFolder,"phiInit",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(params$rhoInit), paste(testFolder,"rhoInit",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(params$piInit), paste(testFolder,"piInit",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(params$gamInit), paste(testFolder,"gamInit",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.integer(mini), paste(testFolder,"mini",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.integer(maxi), paste(testFolder,"maxi",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(gamma), paste(testFolder,"gamma",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(lambda), paste(testFolder,"lambda",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(io$X), paste(testFolder,"X",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(io$Y), paste(testFolder,"Y",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.double(tau), paste(testFolder,"tau",sep=""),
+               row.names=F, col.names=F)
+       write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
+               row.names=F, col.names=F)
 
        res = EMGLLF(params$phiInit,params$rhoInit,params$piInit,params$gamInit,mini,maxi,
-               gamma,lambda,io$X,io$Y,tau);
+               gamma,lambda,io$X,io$Y,tau)
 
        #save outputs
-       write.table(paste(testFolder,"phi",sep=""), res$phi, sep=delimiter);
-       write.table(paste(testFolder,"rho",sep=""), res$rho, sep=delimiter);
-       write.table(paste(testFolder,"pi",sep=""), res$pi, sep=delimiter);
-       write.table(paste(testFolder,"LLF",sep=""), res$LLF, sep=delimiter);
-       write.table(paste(testFolder,"S",sep=""), res$S, sep=delimiter);
+       write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F, col.names=F)
+       write.table(as.double(res$rho), paste(testFolder,"rho",sep=""), row.names=F, col.names=F)
+       write.table(as.double(res$pi), paste(testFolder,"pi",sep=""), row.names=F, col.names=F)
+       write.table(as.double(res$LLF), paste(testFolder,"LLF",sep=""), row.names=F, col.names=F)
+       write.table(as.double(res$S), paste(testFolder,"S",sep=""), row.names=F, col.names=F)
 }

diff --git a/src/test/generate_test_data/helpers/EMGLLF.R b/src/test/generate_test_data/helpers/EMGLLF.R
index b0d95a3..02fbb47 100644 (file)
--- a/src/test/generate_test_data/helpers/EMGLLF.R
+++ b/src/test/generate_test_data/helpers/EMGLLF.R
@@ -169,5 +169,5 @@ EMGLLF = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau)
   }
     
   Pi = t(Pi)
-  return(list(phi=phi, rho=rho, Pi=Pi, LLF=LLF, S=S))
+  return(list("phi"=phi, "rho"=rho, "pi"=Pi, "LLF"=LLF, "S"=S))
 }

diff --git a/src/test/utils.c b/src/test/utils.c
index a6370b0..2eac0c2 100644 (file)
--- a/src/test/utils.c
+++ b/src/test/utils.c
@@ -37,55 +37,38 @@ void compareArray_int(const char* ID, const void* array, const void* refArray, i
 // 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...)
+       // 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, "wc -l ");
        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);
+       FILE *arraySize = popen(command, "r");
+       char* bufferNum = (char*)calloc(64, sizeof(char));
+       fgets(bufferNum, sizeof(bufferNum), arraySize);
+       int n = atoi(bufferNum);
+       pclose(arraySize);
 
        // open file for reading
-       FILE* file = fopen(fullFileName, "r");
+       FILE* arrayFile = 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
+       size_t elementSize = isinteger ? sizeof(int) : sizeof(float);
        void* array = malloc(n*elementSize);
-       char curChar = ' ';
-       char bufferNum[64];
-       for (int u=0; u<n; u++)
+       for (int i=0; i<n; i++)
        {
-               // read number (as a string)
-               int bufferIndex = 0;
-               while (!feof(file) && curChar!=' ')
-               {
-                       curChar = fgetc(file);
-                       bufferNum[bufferIndex++] = curChar;
-               }
-               bufferNum[bufferIndex] = 0;
-               // transform string into float, and store it at appropriate location
+               // transform buffer content into float or int, and store it at appropriate location
                if (isinteger)
-                       ((int*)array)[u] = atoi(bufferNum);
+                       ((int*)array)[i] = atoi(bufferNum);
                else
-                       ((float*)array)[u] = atof(bufferNum);
-               // position to next non-separator character
-               curChar = fgetc(file);
+                       ((float*)array)[i] = atof(bufferNum);
        }
-       fclose(file);
+       fclose(arrayFile);
+       free(bufferNum);
 
        return array;
 }