add ifndef and GENSVM_ before defines

7 files changed, 48 insertions, 42 deletions

diff --git a/src/GenSVMgrid.c b/src/GenSVMgrid.c
index 14b7457..9e3586d 100644
--- a/src/GenSVMgrid.c
+++ b/src/GenSVMgrid.c
@@ -59,7 +59,7 @@ void read_grid_from_file(char *input_filename, struct GenGrid *grid);
  * @brief Help function
  *
  * @details
- * Print help for this program and exit. Note that VERSION is provided by the 
+ * Print help for this program and exit. Note that VERSION is provided by the
  * Makefile.
  *
  * @param[in] 	argv 	command line arguments
@@ -96,7 +96,7 @@ void exit_with_help(char **argv)
  */
 int main(int argc, char **argv)
 {
-	char input_filename[MAX_LINE_LENGTH];
+	char input_filename[GENSVM_MAX_LINE_LENGTH];
 
 	struct GenGrid *grid = gensvm_init_grid();
 	struct GenData *train_data = gensvm_init_data();
@@ -189,10 +189,10 @@ void parse_command_line(int argc, char **argv, char *input_filename)
  * @brief Parse the kernel string from the training file
  *
  * @details
- * This is a utility function for the read_grid_from_file() function, to keep 
- * the main code a bit shorter. It reads the line from the given buffer and 
+ * This is a utility function for the read_grid_from_file() function, to keep
+ * the main code a bit shorter. It reads the line from the given buffer and
  * returns the corresponding KernelType.
- * 
+ *
  * @param[in] 	kernel_line 	line from the file with the kernel
  * 				specification
  * @return 	the corresponding kerneltype
@@ -233,11 +233,11 @@ void read_grid_from_file(char *input_filename, struct GenGrid *grid)
 {
 	long i, nr = 0;
 	FILE *fid;
-	char buffer[MAX_LINE_LENGTH];
-	char train_filename[MAX_LINE_LENGTH];
-	char test_filename[MAX_LINE_LENGTH];
-	double *params = Calloc(double, MAX_LINE_LENGTH);
-	long *lparams = Calloc(long, MAX_LINE_LENGTH);
+	char buffer[GENSVM_MAX_LINE_LENGTH];
+	char train_filename[GENSVM_MAX_LINE_LENGTH];
+	char test_filename[GENSVM_MAX_LINE_LENGTH];
+	double *params = Calloc(double, GENSVM_MAX_LINE_LENGTH);
+	long *lparams = Calloc(long, GENSVM_MAX_LINE_LENGTH);
 
 	fid = fopen(input_filename, "r");
 	if (fid == NULL) {
@@ -246,18 +246,18 @@ void read_grid_from_file(char *input_filename, struct GenGrid *grid)
 		exit(1);
 	}
 	grid->traintype = CV;
-	while ( fgets(buffer, MAX_LINE_LENGTH, fid) != NULL ) {
-		Memset(params, double,  MAX_LINE_LENGTH);
-		Memset(lparams, long, MAX_LINE_LENGTH);
+	while ( fgets(buffer, GENSVM_MAX_LINE_LENGTH, fid) != NULL ) {
+		Memset(params, double,  GENSVM_MAX_LINE_LENGTH);
+		Memset(lparams, long, GENSVM_MAX_LINE_LENGTH);
 		if (str_startswith(buffer, "train:")) {
 			sscanf(buffer, "train: %s\n", train_filename);
 			grid->train_data_file = Calloc(char,
-					MAX_LINE_LENGTH);
+					GENSVM_MAX_LINE_LENGTH);
 			strcpy(grid->train_data_file, train_filename);
 		} else if (str_startswith(buffer, "test:")) {
 			sscanf(buffer, "test: %s\n", test_filename);
 			grid->test_data_file = Calloc(char,
-				       	MAX_LINE_LENGTH);
+					GENSVM_MAX_LINE_LENGTH);
 			strcpy(grid->test_data_file, test_filename);
 			grid->traintype = TT;
 		} else if (str_startswith(buffer, "p:")) {
diff --git a/src/GenSVMtraintest.c b/src/GenSVMtraintest.c
index 4f4cabb..40c4321 100644
--- a/src/GenSVMtraintest.c
+++ b/src/GenSVMtraintest.c
@@ -132,7 +132,7 @@ int main(int argc, char **argv)
 
 	// read data from files
 	gensvm_read_data(traindata, training_inputfile);
-	model->data_file = Calloc(char, MAX_LINE_LENGTH);
+	model->data_file = Calloc(char, GENSVM_MAX_LINE_LENGTH);
 	strcpy(model->data_file, training_inputfile);
 
 	// seed the random number generator
diff --git a/src/gensvm_gridsearch.c b/src/gensvm_gridsearch.c
index 9c30d3a..d5b1247 100644
--- a/src/gensvm_gridsearch.c
+++ b/src/gensvm_gridsearch.c
@@ -360,7 +360,7 @@ void gensvm_train_queue(struct GenQueue *q)
 void gensvm_gridsearch_progress(struct GenTask *task, long N, double perf, 
 		double duration, double current_max)
 {
-	char buffer[MAX_LINE_LENGTH];
+	char buffer[GENSVM_MAX_LINE_LENGTH];
 	sprintf(buffer, "(%03li/%03li)\t", task->ID+1, N);
 	if (task->kerneltype == K_POLY)
 		sprintf(buffer + strlen(buffer), "d = %2.2f\t",
diff --git a/src/gensvm_io.c b/src/gensvm_io.c
index e77d647..78838b1 100644
--- a/src/gensvm_io.c
+++ b/src/gensvm_io.c
@@ -61,7 +61,7 @@ void gensvm_read_data(struct GenData *dataset, char *data_file)
 	double value;
 	long *uniq_y = NULL;
 
-	char buf[MAX_LINE_LENGTH];
+	char buf[GENSVM_MAX_LINE_LENGTH];
 
 	if ((fid = fopen(data_file, "r")) == NULL) {
 		// LCOV_EXCL_START
@@ -84,7 +84,7 @@ void gensvm_read_data(struct GenData *dataset, char *data_file)
 		matrix_set(dataset->RAW, m+1, 0, j, value);
 	}
 
-	if (fgets(buf, MAX_LINE_LENGTH, fid) == NULL) {
+	if (fgets(buf, GENSVM_MAX_LINE_LENGTH, fid) == NULL) {
 		// LCOV_EXCL_START
 		err("[GenSVM Error]: No label found on first line.\n");
 		exit(EXIT_FAILURE);
@@ -187,8 +187,8 @@ void gensvm_read_model(struct GenModel *model, char *model_filename)
 {
 	long i, j, nr = 0;
 	FILE *fid = NULL;
-	char buffer[MAX_LINE_LENGTH];
-	char data_filename[MAX_LINE_LENGTH];
+	char buffer[GENSVM_MAX_LINE_LENGTH];
+	char data_filename[GENSVM_MAX_LINE_LENGTH];
 	double value = 0;
 
 	fid = fopen(model_filename, "r");
@@ -216,7 +216,7 @@ void gensvm_read_model(struct GenModel *model, char *model_filename)
 		next_line(fid, model_filename);
 
 	// read filename of data file
-	if (fgets(buffer, MAX_LINE_LENGTH, fid) == NULL) {
+	if (fgets(buffer, GENSVM_MAX_LINE_LENGTH, fid) == NULL) {
 		// LCOV_EXCL_START
 		err("[GenSVM Error]: Error reading from model file %s\n",
 				model_filename);
@@ -224,7 +224,7 @@ void gensvm_read_model(struct GenModel *model, char *model_filename)
 		// LCOV_EXCL_STOP
 	}
 	sscanf(buffer, "filename = %s\n", data_filename);
-	model->data_file = Calloc(char, MAX_LINE_LENGTH);
+	model->data_file = Calloc(char, GENSVM_MAX_LINE_LENGTH);
 	strcpy(model->data_file, data_filename);
 
 	// read all data variables
@@ -271,7 +271,7 @@ void gensvm_write_model(struct GenModel *model, char *output_filename)
 {
 	FILE *fid = NULL;
 	long i, j;
-	char timestr[MAX_LINE_LENGTH];
+	char timestr[GENSVM_MAX_LINE_LENGTH];
 
 	// open output file
 	fid = fopen(output_filename, "w");
@@ -372,7 +372,7 @@ void gensvm_write_predictions(struct GenData *data, long *predy,
 void gensvm_time_string(char *buffer)
 {
 	int diff, hours, minutes;
-	char timestr[MAX_LINE_LENGTH];
+	char timestr[GENSVM_MAX_LINE_LENGTH];
 	time_t current_time, lt, gt;
 	struct tm *lclt = NULL;
 
@@ -387,7 +387,7 @@ void gensvm_time_string(char *buffer)
 
 	// convert time to local time and create a string
 	lclt = localtime(&current_time);
-	strftime(timestr, MAX_LINE_LENGTH, "%c", lclt);
+	strftime(timestr, GENSVM_MAX_LINE_LENGTH, "%c", lclt);
 	if (timestr == NULL) {
 		err("[GenSVM Error]: Failed to convert time to string.\n");
 		return;
diff --git a/src/gensvm_optimize.c b/src/gensvm_optimize.c
index a7172be..95f9df2 100644
--- a/src/gensvm_optimize.c
+++ b/src/gensvm_optimize.c
@@ -33,12 +33,16 @@
 /**
  * Maximum number of iterations of the algorithm.
  */
-#define MAX_ITER 1000000000
+#ifndef GENSVM_MAX_ITER
+  #define GENSVM_MAX_ITER 1000000000
+#endif
 
 /**
  * Iteration frequency with which to print to stdout
  */
-#define PRINT_ITER 100
+#ifndef GENSVM_PRINT_ITER
+  #define GENSVM_PRINT_ITER 100
+#endif
 
 /**
  * @brief The main training loop for GenSVM
@@ -90,7 +94,7 @@ void gensvm_optimize(struct GenModel *model, struct GenData *data)
 	Lbar = L + 2.0*model->epsilon*L;
 
 	// run main loop
-	while ((it < MAX_ITER) && (Lbar - L)/L > model->epsilon)
+	while ((it < GENSVM_MAX_ITER) && (Lbar - L)/L > model->epsilon)
 	{
 		// ensures V contains newest V and Vbar contains V from
 		// previous
@@ -101,7 +105,7 @@ void gensvm_optimize(struct GenModel *model, struct GenData *data)
 		Lbar = L;
 		L = gensvm_get_loss(model, data, work);
 
-		if (it%PRINT_ITER == 0)
+		if (it % GENSVM_PRINT_ITER == 0)
 			note("iter = %li, L = %15.16f, Lbar = %15.16f, "
 			     "reldiff = %15.16f\n", it, L, Lbar, (Lbar - L)/L);
 		it++;
@@ -111,7 +115,7 @@ void gensvm_optimize(struct GenModel *model, struct GenData *data)
 	if (L > Lbar)
 		err("[GenSVM Warning]: Negative step occurred in "
 				"majorization.\n");
-	if (it >= MAX_ITER)
+	if (it >= GENSVM_MAX_ITER)
 		err("[GenSVM Warning]: maximum number of iterations "
 				"reached.\n");
 
diff --git a/src/gensvm_strutil.c b/src/gensvm_strutil.c
index c18f2d4..f6bb8f7 100644
--- a/src/gensvm_strutil.c
+++ b/src/gensvm_strutil.c
@@ -70,7 +70,7 @@ bool str_endswith(const char *str, const char *suf)
  */
 void next_line(FILE *fid, char *filename)
 {
-	char buffer[MAX_LINE_LENGTH];
+	char buffer[GENSVM_MAX_LINE_LENGTH];
 	get_line(fid, filename, buffer);
 }
 
@@ -83,7 +83,7 @@ void next_line(FILE *fid, char *filename)
  */
 char *get_line(FILE *fid, char *filename, char *buffer)
 {
-	char *retval = fgets(buffer, MAX_LINE_LENGTH, fid);
+	char *retval = fgets(buffer, GENSVM_MAX_LINE_LENGTH, fid);
 	if (retval == NULL) {
 		err("[GenSVM Error]: Error reading from file %s\n", filename);
 	}
@@ -104,7 +104,7 @@ char *get_line(FILE *fid, char *filename, char *buffer)
  */
 double get_fmt_double(FILE *fid, char *filename, const char *fmt)
 {
-	char buffer[MAX_LINE_LENGTH];
+	char buffer[GENSVM_MAX_LINE_LENGTH];
 	double value = NAN;
 	int retval;
 
@@ -125,7 +125,7 @@ double get_fmt_double(FILE *fid, char *filename, const char *fmt)
  */
 long get_fmt_long(FILE *fid, char *filename, const char *fmt)
 {
-	char buffer[MAX_LINE_LENGTH];
+	char buffer[GENSVM_MAX_LINE_LENGTH];
 	long value = 0;
 	int retval;
 
diff --git a/src/gensvm_update.c b/src/gensvm_update.c
index f81d224..aca586f 100644
--- a/src/gensvm_update.c
+++ b/src/gensvm_update.c
@@ -30,7 +30,9 @@
  * Number of rows in a single block for the ZAZ calculation in 
  * gensvm_get_ZAZ_ZB_sparse().
  */
-#define BLOCK_SIZE 512
+#ifndef GENSVM_BLOCK_SIZE
+  #define GENSVM_BLOCK_SIZE 512
+#endif
 
 /**
  * @brief Calculate the value of omega for a single instance
@@ -461,8 +463,8 @@ void gensvm_get_ZAZ_ZB_dense(struct GenModel *model, struct GenData *data,
  * daxpy call.
  *
  * This function calculates the matrix product Z'*A*Z in separate blocks, 
- * based on the number of rows defined in the BLOCK_SIZE variable. This is 
- * done to improve numerical precision for very large datasets. Due to 
+ * based on the number of rows defined in the GENSVM_BLOCK_SIZE variable. This 
+ * is done to improve numerical precision for very large datasets. Due to 
  * rounding errors, precision can become an issue for these large datasets, 
  * when separate blocks are used and added to the result separately, this can 
  * be alleviated a little bit. See also: http://stackoverflow.com/q/40286989
@@ -495,13 +497,13 @@ void gensvm_get_ZAZ_ZB_sparse(struct GenModel *model, struct GenData *data,
 	// rounding errors, which increases precision, and in turn helps 
 	// convergion of the IM algorithm.
 	// see also: http://stackoverflow.com/q/40286989/
-	n_blocks = floor(n_row / BLOCK_SIZE);
-	rem_size = n_row % BLOCK_SIZE;
+	n_blocks = floor(n_row / GENSVM_BLOCK_SIZE);
+	rem_size = n_row % GENSVM_BLOCK_SIZE;
 
 	for (b=0; b<=n_blocks; b++) {
-		blk_start = b * BLOCK_SIZE;
+		blk_start = b * GENSVM_BLOCK_SIZE;
 		blk_end = blk_start;
-		blk_end += (b == n_blocks) ? rem_size : BLOCK_SIZE;
+		blk_end += (b == n_blocks) ? rem_size : GENSVM_BLOCK_SIZE;
 
 		Memset(work->tmpZAZ, double, n_col*n_col);
 		for (i=blk_start; i<blk_end; i++) {