moved input/output functions to seperate file

12 files changed, 513 insertions, 448 deletions

diff --git a/Makefile b/Makefile
index c618859..1c4ee22 100644
--- a/Makefile
+++ b/Makefile
@@ -11,8 +11,34 @@ all: lib/libmsvmmaj.a $(EXECS)
 
 override LDFLAGS+=-lblas -llapack -lm
 
-lib/libmsvmmaj.a: src/libMSVMMaj.o src/util.o src/msvmmaj_matrix.o src/msvmmaj_lapack.o src/strutil.o src/crossval.o src/msvmmaj_init.o src/msvmmaj_train.o src/msvmmaj_train_dataset.o src/msvmmaj_pred.o src/timer.o src/msvmmaj_kernel.o
-	@ar rcs lib/libmsvmmaj.a src/libMSVMMaj.o src/util.o src/msvmmaj_matrix.o src/msvmmaj_lapack.o src/strutil.o src/crossval.o src/msvmmaj_init.o src/msvmmaj_train.o src/msvmmaj_train_dataset.o src/msvmmaj_pred.o src/timer.o src/msvmmaj_kernel.o
+lib/libmsvmmaj.a: \
+	src/crossval.o \
+	src/libMSVMMaj.o \
+	src/msvmmaj_init.o \
+	src/msvmmaj_io.o \
+	src/msvmmaj_kernel.o \
+	src/msvmmaj_lapack.o \
+	src/msvmmaj_matrix.o \
+	src/msvmmaj_pred.o \
+	src/msvmmaj_train.o \
+	src/msvmmaj_train_dataset.o \
+	src/strutil.o \
+	src/timer.o \
+	src/util.o 
+	@ar rcs lib/libmsvmmaj.a \
+		src/crossval.o \
+		src/libMSVMMaj.o \
+		src/msvmmaj_init.o \
+		src/msvmmaj_io.o \
+		src/msvmmaj_matrix.o \
+		src/msvmmaj_kernel.o \
+		src/msvmmaj_lapack.o \
+		src/msvmmaj_pred.o \
+		src/msvmmaj_train.o \
+		src/msvmmaj_train_dataset.o \
+		src/strutil.o \
+		src/timer.o \
+		src/util.o 
 	@echo libmsvmmaj.a...
 
 trainMSVMMaj: src/trainMSVMMaj.c lib/libmsvmmaj.a
@@ -47,6 +73,9 @@ src/msvmmaj_init.o:
 	@$(CC) -c -o src/msvmmaj_init.o src/msvmmaj_init.c $(CFLAGS) $(INCLUDE)
 	@echo msvmmaj_init.o...
 
+src/msvmmaj_io.o:
+	@$(CC) -c -o $@ src/msvmmaj_io.c $(CFLAGS) $(INCLUDE)
+
 src/msvmmaj_pred.o:
 	@$(CC) -c -o src/msvmmaj_pred.o src/msvmmaj_pred.c $(CFLAGS) $(INCLUDE)
 	@echo msvmmaj_pred.o...
diff --git a/doc/mainpage.c b/doc/mainpage.dox
index e3c4057..e3c4057 100644
--- a/doc/mainpage.c
+++ b/doc/mainpage.dox
diff --git a/doc/specifications.c b/doc/specifications.dox
index 5b5a8ae..5b5a8ae 100644
--- a/doc/specifications.c
+++ b/doc/specifications.dox
diff --git a/include/msvmmaj_init.h b/include/msvmmaj_init.h
index 6e2e36f..febfb4a 100644
--- a/include/msvmmaj_init.h
+++ b/include/msvmmaj_init.h
@@ -20,4 +20,8 @@ struct MajModel *msvmmaj_init_model();
 
 struct MajData *msvmmaj_init_data();
 
+void msvmmaj_allocate_model(struct MajModel *model);
+void msvmmaj_free_model(struct MajModel *model);
+void msvmmaj_free_data(struct MajData *data);
+
 #endif
diff --git a/include/msvmmaj_io.h b/include/msvmmaj_io.h
new file mode 100644
index 0000000..99fb4dc
--- /dev/null
+++ b/include/msvmmaj_io.h
@@ -0,0 +1,30 @@
+/**
+ * @file msvmmaj_io.h
+ * @author Gertjan van den Burg
+ * @date January, 2014
+ * @brief Header files for msvmmaj_io.c
+ *
+ * @details
+ * Function declarations for input/output functions.
+ *
+ */
+
+#ifndef MSVMMAJ_IO_H
+#define MSVMMAJ_IO_H
+
+#include "globals.h"
+
+// forward declarations
+struct MajData;
+struct MajModel;
+
+// function declarations
+void msvmmaj_read_data(struct MajData *dataset, char *data_file);
+
+void msvmmaj_read_model(struct MajModel *model, char *model_filename);
+void msvmmaj_write_model(struct MajModel *model, char *output_filename);
+
+void msvmmaj_write_predictions(struct MajData *data, long *predy, 
+		char *output_filename);
+
+#endif
diff --git a/include/util.h b/include/util.h
index 995a927..375a9c2 100644
--- a/include/util.h
+++ b/include/util.h
@@ -19,21 +19,9 @@ struct MajData;
 struct MajModel;
 
 // function declarations
-void msvmmaj_read_data(struct MajData *dataset, char *data_file);
-
-void msvmmaj_read_model(struct MajModel *model, char *model_filename);
-void msvmmaj_write_model(struct MajModel *model, char *output_filename);
-
-void msvmmaj_write_predictions(struct MajData *data, long *predy, 
-		char *output_filename);
-
 int msvmmaj_check_argv(int argc, char **argv, char *str);
 int msvmmaj_check_argv_eq(int argc, char **argv, char *str);
 
 void note(const char *fmt,...);
 
-void msvmmaj_allocate_model(struct MajModel *model);
-void msvmmaj_free_model(struct MajModel *model);
-void msvmmaj_free_data(struct MajData *data);
-
 #endif
diff --git a/src/msvmmaj_init.c b/src/msvmmaj_init.c
index 14278f9..b4384be 100644
--- a/src/msvmmaj_init.c
+++ b/src/msvmmaj_init.c
@@ -7,7 +7,9 @@
  * @details 
  * This file contains functions for initializing a MajModel instance
  * and a MajData instance. In addition, default values for these 
- * structures are defined here (and only here).
+ * structures are defined here (and only here). Functions for allocating
+ * memory for the model structure and freeing of the model and data structures
+ * are also included.
  *
  */
 
@@ -62,3 +64,122 @@ struct MajData *msvmmaj_init_data()
 	return data;
 }	
 
+/**
+ * @brief Allocate memory for a MajModel
+ *
+ * @details
+ * This function can be used to allocate the memory needed for a MajModel. All
+ * arrays in the model are specified and initialized to 0.
+ *
+ * @param[in] 	model 	MajModel to allocate
+ *
+ */
+void msvmmaj_allocate_model(struct MajModel *model)
+{
+	long n = model->n;
+	long m = model->m;
+	long K = model->K;
+
+	model->W = Calloc(double, m*(K-1));
+	if (model->W == NULL) {
+		fprintf(stderr, "Failed to allocate memory for W.\n");
+		exit(1);
+	}
+
+	model->t = Calloc(double, K-1);
+	if (model->t == NULL) {
+		fprintf(stderr, "Failed to allocate memory for t.\n");
+		exit(1);
+	}
+
+	model->V = Calloc(double, (m+1)*(K-1));
+	if (model->V == NULL) {
+		fprintf(stderr, "Failed to allocate memory for V.\n");
+		exit(1);
+	}
+
+	model->Vbar = Calloc(double, (m+1)*(K-1));
+	if (model->Vbar == NULL) {
+		fprintf(stderr, "Failed to allocate memory for Vbar.\n");
+		exit(1);
+	}
+
+	model->U = Calloc(double, K*(K-1));
+	if (model->U == NULL) {
+		fprintf(stderr, "Failed to allocate memory for U.\n");
+		exit(1);
+	}
+
+	model->UU = Calloc(double, n*K*(K-1));
+	if (model->UU == NULL) {
+		fprintf(stderr, "Failed to allocate memory for UU.\n");
+		exit(1);
+	}
+
+	model->Q = Calloc(double, n*K);
+	if (model->Q == NULL) {
+		fprintf(stderr, "Failed to allocate memory for Q.\n");
+		exit(1);
+	}
+
+	model->H = Calloc(double, n*K);
+	if (model->H == NULL) {
+		fprintf(stderr, "Failed to allocate memory for H.\n");
+		exit(1);
+	}
+
+	model->R = Calloc(double, n*K);
+	if (model->R == NULL) {
+		fprintf(stderr, "Failed to allocate memory for R.\n");
+		exit(1);
+	}
+
+	model->rho = Calloc(double, n);
+	if (model->rho == NULL) {
+		fprintf(stderr, "Failed to allocate memory for rho.\n");
+		exit(1);
+	}
+}
+
+/**
+ * @brief Free allocated MajModel struct
+ *
+ * @details
+ * Simply free a previously allocated MajModel by freeing all its component
+ * arrays. Note that the model struct itself is also freed here.
+ *
+ * @param[in] 	model 	MajModel to free
+ *
+ */
+void msvmmaj_free_model(struct MajModel *model)
+{
+	free(model->W);
+	free(model->t);
+	free(model->V);
+	free(model->Vbar);
+	free(model->U);
+	free(model->UU);
+	free(model->Q);
+	free(model->H);
+	free(model->rho);
+	free(model->R);
+
+	free(model);
+}
+
+/**
+ * @brief Free allocated MajData struct 
+ *
+ * @details
+ * Simply free a previously allocated MajData struct by freeing all its
+ * components. Note that the data struct itself is also freed here.
+ *
+ * @param[in] 	data 	MajData struct to free
+ *
+ */
+void msvmmaj_free_data(struct MajData *data)
+{
+	free(data->Z);
+	free(data->y);
+	free(data);
+}
diff --git a/src/msvmmaj_io.c b/src/msvmmaj_io.c
new file mode 100644
index 0000000..7abb182
--- /dev/null
+++ b/src/msvmmaj_io.c
@@ -0,0 +1,322 @@
+/**
+ * @file msvmmaj_io.c
+ * @author Gertjan van den Burg
+ * @date January, 2014
+ * @brief Functions for input and output of data and model files
+ *
+ * @details
+ * This file contains functions for reading and writing model files, and data
+ * files. 
+ *
+ */
+
+#include <time.h>
+
+#include "msvmmaj.h"
+#include "msvmmaj_io.h"
+#include "msvmmaj_matrix.h"
+#include "strutil.h"
+
+/**
+ * @brief Read data from file
+ * 
+ * @details
+ * Read the data from the data_file. The data matrix X is augmented
+ * with a column of ones, to get the matrix Z. The data is expected
+ * to follow a specific format, which is specified in the @ref spec_data_file.
+ * The class labels are corrected internally to correspond to the interval 
+ * [1 .. K], where K is the total number of classes.
+ *
+ * @todo
+ * Make sure that this function allows datasets without class labels for
+ * testing.
+ *
+ * @param[in,out] 	dataset 	initialized MajData struct
+ * @param[in] 		data_file 	filename of the data file.
+ */
+void msvmmaj_read_data(struct MajData *dataset, char *data_file)
+{
+	FILE *fid;
+	long i, j;
+	long n, m; // dimensions of data
+	long nr = 0; // used to check consistency of data
+	double value;
+	long K = 0;
+	long min_y = 1000000;
+
+	char buf[MAX_LINE_LENGTH];
+
+	if ((fid = fopen(data_file, "r")) == NULL) {
+		fprintf(stderr, "\nERROR: datafile %s could not be opened.\n",
+				data_file);
+		exit(0);
+	}
+
+	// Read data dimensions
+	nr += fscanf(fid, "%ld", &n);
+	nr += fscanf(fid, "%ld", &m);
+
+	// Allocate memory
+	dataset->Z = Malloc(double, n*(m+1));
+
+	// Read first line of data
+	for (j=1; j<m+1; j++) {
+		nr += fscanf(fid, "%lf", &value);
+		matrix_set(dataset->Z, n, 0, j, value);
+	}
+
+	// Check if there is a label at the end of the line
+	if (fgets(buf, MAX_LINE_LENGTH, fid) == NULL) {
+		fprintf(stderr, "ERROR: No label found on first line.\n");
+		exit(1);
+	}
+	if (sscanf(buf, "%lf", &value) > 0) {
+		dataset->y = Malloc(long, n);
+		dataset->y[0] = value;
+	} else if (dataset->y != NULL) {
+		free(dataset->y);
+		dataset->y = NULL;
+	}
+
+	// Read the rest of the file
+	for (i=1; i<n; i++) {
+		for (j=1; j<m+1; j++) {
+			nr += fscanf(fid, "%lf", &value);
+			matrix_set(dataset->Z, m+1, i, j, value);
+		}
+		if (dataset->y != NULL) {
+			nr += fscanf(fid, "%lf", &value);
+			dataset->y[i] = (long) value;
+			K = maximum(K, value);
+			min_y = minimum(min_y, value);
+		}
+	}
+	fclose(fid);
+
+	// Correct labels: must be in [1, K]
+	if (min_y == 0) {
+		for (i=0; i<n; i++)
+			dataset->y[i]++;
+		K++;
+	} else if (min_y < 0 ) {
+		fprintf(stderr, "ERROR: wrong class labels in %s, minimum "
+				"value is: %ld\n",
+				data_file, min_y);
+		exit(0);
+	}
+
+	if (nr < n * m) {
+		fprintf(stderr, "ERROR: not enough data found in %s\n", 
+				data_file);
+		exit(0);
+	}
+	
+	// Set the column of ones
+	for (i=0; i<n; i++)
+		matrix_set(dataset->Z, m+1, i, 0, 1.0);
+
+	dataset->n = n;
+	dataset->m = m;
+	dataset->K = K;
+}
+
+
+/**
+ * @brief Read model from file
+ *
+ * @details
+ * Read a MajModel from a model file. The MajModel struct must have been
+ * initalized elswhere. The model file is expected to follow the @ref
+ * spec_model_file. The easiest way to generate a model file is through
+ * msvmmaj_write_model(), which can for instance be used in trainMSVMMaj.c.
+ *
+ * @param[in,out] 	model 		initialized MajModel
+ * @param[in] 		model_filename 	filename of the model file
+ *
+ */
+void msvmmaj_read_model(struct MajModel *model, char *model_filename)
+{
+	long i, j, nr = 0;
+	FILE *fid;
+	char buffer[MAX_LINE_LENGTH];
+	char data_filename[MAX_LINE_LENGTH];
+	double value = 0;
+
+	fid = fopen(model_filename, "r");
+	if (fid == NULL) {
+		fprintf(stderr, "Error opening model file %s\n", 
+				model_filename);
+		exit(1);
+	}
+	// skip the first four lines
+	for (i=0; i<4; i++)
+		next_line(fid, model_filename);
+
+	// read all model variables
+	model->p = get_fmt_double(fid, model_filename, "p = %lf");
+	model->lambda = get_fmt_double(fid, model_filename, "lambda = %lf");
+	model->kappa = get_fmt_double(fid, model_filename, "kappa = %lf");
+	model->epsilon = get_fmt_double(fid, model_filename, "epsilon = %lf");
+	model->weight_idx = (int) get_fmt_long(fid, model_filename, 
+			"weight_idx = %li");
+
+	// skip to data section
+	for (i=0; i<2; i++)
+		next_line(fid, model_filename);
+
+	// read filename of data file
+	if (fgets(buffer, MAX_LINE_LENGTH, fid) == NULL) {
+		fprintf(stderr, "Error reading model file %s\n", 
+				model_filename);
+		exit(1);
+	}
+	sscanf(buffer, "filename = %s\n", data_filename);
+	model->data_file = data_filename;
+
+	// read all data variables
+	model->n = get_fmt_long(fid, model_filename, "n = %li\n");
+	model->m = get_fmt_long(fid, model_filename, "m = %li\n");
+	model->K = get_fmt_long(fid, model_filename, "K = %li\n");
+
+	// skip to output
+	for (i=0; i<2; i++)
+		next_line(fid, model_filename);
+
+	// read the matrix V and check for consistency
+	model->V = Malloc(double, (model->m+1)*(model->K-1));
+	for (i=0; i<model->m+1; i++) {
+		for (j=0; j<model->K-1; j++) {
+			nr += fscanf(fid, "%lf ", &value);
+			matrix_set(model->V, model->K-1, i, j, value);
+		}
+	}
+	if (nr != (model->m+1)*(model->K-1)) {
+		fprintf(stderr, "Error reading model file %s. "
+				"Not enough elements of V found.\n", 
+				model_filename);
+		exit(1);
+	}
+}
+
+/**
+ * @brief Write model to file
+ *
+ * @details
+ * Write a MajModel to a file. The current time is specified in the file in
+ * UTC + offset. The model file further corresponds to the @ref
+ * spec_model_file.
+ *
+ * @param[in] 	model 		MajModel which contains an estimate for 
+ * 				MajModel::V
+ * @param[in] 	output_filename the output file to write the model to
+ *
+ */
+void msvmmaj_write_model(struct MajModel *model, char *output_filename)
+{
+	FILE *fid;
+	long i, j;
+	int diff, hours, minutes;
+	char timestr[1000];
+	time_t current_time, lt, gt;
+	struct tm *lclt;
+
+	// open output file
+	fid = fopen(output_filename, "w");
+	if (fid == NULL) {
+		fprintf(stderr, "Error opening output file %s", 
+				output_filename);
+		exit(1);
+	}
+
+	// get current time (in epoch)
+	current_time = time(NULL);
+	if (current_time == ((time_t)-1)) {
+		fprintf(stderr, "Failed to compute the current time.\n");
+		exit(1);
+	}
+
+	// convert time to local time and create a string
+	lclt = localtime(&current_time);
+	strftime(timestr, 1000, "%c", lclt);
+	if (timestr == NULL) {
+		fprintf(stderr, "Failed to convert time to string.\n");
+		exit(1);
+	}
+
+	// calculate the difference from UTC including DST
+	lt = mktime(localtime(&current_time));
+	gt = mktime(gmtime(&current_time));
+	diff = -difftime(gt, lt);
+	hours = (diff/3600);
+	minutes = (diff%3600)/60;
+	if (lclt->tm_isdst == 1)
+		hours++;
+
+	// Write output to file
+	fprintf(fid, "Output file for MSVMMaj (version %1.1f)\n", VERSION);
+	fprintf(fid, "Generated on: %s (UTC %+03i:%02i)\n\n", 
+			timestr, hours, minutes);
+	fprintf(fid, "Model:\n");
+	fprintf(fid, "p = %15.16f\n", model->p);
+	fprintf(fid, "lambda = %15.16f\n", model->lambda);
+	fprintf(fid, "kappa = %15.16f\n", model->kappa);
+	fprintf(fid, "epsilon = %g\n", model->epsilon);
+	fprintf(fid, "weight_idx = %i\n", model->weight_idx);
+	fprintf(fid, "\n");
+	fprintf(fid, "Data:\n");
+	fprintf(fid, "filename = %s\n", model->data_file);
+	fprintf(fid, "n = %li\n", model->n);
+	fprintf(fid, "m = %li\n", model->m);
+	fprintf(fid, "K = %li\n", model->K);
+	fprintf(fid, "\n");
+	fprintf(fid, "Output:\n");
+	for (i=0; i<model->m+1; i++) {
+		for (j=0; j<model->K-1; j++) {
+			fprintf(fid, "%+15.16f ", 
+					matrix_get(model->V, 
+						model->K-1, i, j));
+		}
+		fprintf(fid, "\n");
+	}
+
+	fclose(fid);
+}
+
+/**
+ * @brief Write predictions to file
+ *
+ * @details
+ * Write the given predictions to an output file, such that the resulting file
+ * corresponds to the @ref spec_data_file. 
+ *
+ * @param[in] 	data 		MajData with the original instances
+ * @param[in] 	predy 		predictions of the class labels of the 
+ * 				instances in the given MajData. Note that the
+ * 				order of the instances is assumed to be the
+ * 				same.
+ * @param[in] 	output_filename the file to which the predictions are written
+ *
+ */
+void msvmmaj_write_predictions(struct MajData *data, long *predy, 
+		char *output_filename)
+{
+	long i, j;
+	FILE *fid;
+
+	fid = fopen(output_filename, "w");
+	if (fid == NULL) {
+		fprintf(stderr, "Error opening output file %s", 
+				output_filename);
+		exit(1);
+	}
+
+	for (i=0; i<data->n; i++) {
+		for (j=0; j<data->m; j++) 
+			fprintf(fid, "%f ", 
+					matrix_get(data->Z, 
+						data->m+1, i, j+1));
+		fprintf(fid, "%li\n", predy[i]);
+	}
+
+	fclose(fid);
+}
diff --git a/src/predMSVMMaj.c b/src/predMSVMMaj.c
index b41b137..e67e430 100644
--- a/src/predMSVMMaj.c
+++ b/src/predMSVMMaj.c
@@ -20,6 +20,7 @@
 
 #include "msvmmaj.h"
 #include "msvmmaj_init.h"
+#include "msvmmaj_io.h"
 #include "msvmmaj_pred.h"
 #include "util.h"
 
diff --git a/src/trainMSVMMaj.c b/src/trainMSVMMaj.c
index 4bc9fec..9f71325 100644
--- a/src/trainMSVMMaj.c
+++ b/src/trainMSVMMaj.c
@@ -17,6 +17,7 @@
 #include "msvmmaj_kernel.h"
 #include "libMSVMMaj.h"
 #include "msvmmaj.h"
+#include "msvmmaj_io.h"
 #include "msvmmaj_init.h"
 #include "msvmmaj_train.h"
 #include "util.h"
diff --git a/src/trainMSVMMajdataset.c b/src/trainMSVMMajdataset.c
index a34c642..e9f8b8e 100644
--- a/src/trainMSVMMajdataset.c
+++ b/src/trainMSVMMajdataset.c
@@ -23,6 +23,8 @@
 
 #include "crossval.h"
 #include "msvmmaj.h"
+#include "msvmmaj_io.h"
+#include "msvmmaj_init.h"
 #include "msvmmaj_pred.h"
 #include "msvmmaj_train.h"
 #include "msvmmaj_train_dataset.h"
diff --git a/src/util.c b/src/util.c
index 8e4b806..e76a074 100644
--- a/src/util.c
+++ b/src/util.c
@@ -8,17 +8,8 @@
  * This file contains several utility functions for coordinating input and
  * output of data and model files. It also contains string functions.
  *
- * @todo
- * Pull this apart.
- *
  */
-#include <math.h>
 #include <stdarg.h>
-#include <time.h>
-
-#include "msvmmaj.h"
-#include "msvmmaj_matrix.h"
-#include "strutil.h"
 
 #include "util.h"
 
@@ -34,309 +25,6 @@ FILE *MSVMMAJ_OUTPUT_FILE; 	///< The #MSVMMAJ_OUTPUT_FILE specifies the
 				///< (temporarily) setting it to NULL.
 
 /**
- * @brief Read data from file
- * 
- * @details
- * Read the data from the data_file. The data matrix X is augmented
- * with a column of ones, to get the matrix Z. The data is expected
- * to follow a specific format, which is specified in the @ref spec_data_file.
- * The class labels are corrected internally to correspond to the interval 
- * [1 .. K], where K is the total number of classes.
- *
- * @todo
- * Make sure that this function allows datasets without class labels for
- * testing.
- *
- * @param[in,out] 	dataset 	initialized MajData struct
- * @param[in] 		data_file 	filename of the data file.
- */
-void msvmmaj_read_data(struct MajData *dataset, char *data_file)
-{
-	FILE *fid;
-	long i, j;
-	long n, m; // dimensions of data
-	long nr = 0; // used to check consistency of data
-	double value;
-	long K = 0;
-	long min_y = 1000000;
-
-	char buf[MAX_LINE_LENGTH];
-
-	if ((fid = fopen(data_file, "r")) == NULL) {
-		fprintf(stderr, "\nERROR: datafile %s could not be opened.\n",
-				data_file);
-		exit(0);
-	}
-
-	// Read data dimensions
-	nr += fscanf(fid, "%ld", &n);
-	nr += fscanf(fid, "%ld", &m);
-
-	// Allocate memory
-	dataset->Z = Malloc(double, n*(m+1));
-
-	// Read first line of data
-	for (j=1; j<m+1; j++) {
-		nr += fscanf(fid, "%lf", &value);
-		matrix_set(dataset->Z, n, 0, j, value);
-	}
-
-	// Check if there is a label at the end of the line
-	if (fgets(buf, MAX_LINE_LENGTH, fid) == NULL) {
-		fprintf(stderr, "ERROR: No label found on first line.\n");
-		exit(1);
-	}
-	if (sscanf(buf, "%lf", &value) > 0) {
-		dataset->y = Malloc(long, n);
-		dataset->y[0] = value;
-	} else if (dataset->y != NULL) {
-		free(dataset->y);
-		dataset->y = NULL;
-	}
-
-	// Read the rest of the file
-	for (i=1; i<n; i++) {
-		for (j=1; j<m+1; j++) {
-			nr += fscanf(fid, "%lf", &value);
-			matrix_set(dataset->Z, m+1, i, j, value);
-		}
-		if (dataset->y != NULL) {
-			nr += fscanf(fid, "%lf", &value);
-			dataset->y[i] = (long) value;
-			K = maximum(K, value);
-			min_y = minimum(min_y, value);
-		}
-	}
-	fclose(fid);
-
-	// Correct labels: must be in [1, K]
-	if (min_y == 0) {
-		for (i=0; i<n; i++)
-			dataset->y[i]++;
-		K++;
-	} else if (min_y < 0 ) {
-		fprintf(stderr, "ERROR: wrong class labels in %s, minimum "
-				"value is: %ld\n",
-				data_file, min_y);
-		exit(0);
-	}
-
-	if (nr < n * m) {
-		fprintf(stderr, "ERROR: not enough data found in %s\n", 
-				data_file);
-		exit(0);
-	}
-	
-	// Set the column of ones
-	for (i=0; i<n; i++)
-		matrix_set(dataset->Z, m+1, i, 0, 1.0);
-
-	dataset->n = n;
-	dataset->m = m;
-	dataset->K = K;
-}
-
-/**
- * @brief Read model from file
- *
- * @details
- * Read a MajModel from a model file. The MajModel struct must have been
- * initalized elswhere. The model file is expected to follow the @ref
- * spec_model_file. The easiest way to generate a model file is through
- * msvmmaj_write_model(), which can for instance be used in trainMSVMMaj.c.
- *
- * @param[in,out] 	model 		initialized MajModel
- * @param[in] 		model_filename 	filename of the model file
- *
- */
-void msvmmaj_read_model(struct MajModel *model, char *model_filename)
-{
-	long i, j, nr = 0;
-	FILE *fid;
-	char buffer[MAX_LINE_LENGTH];
-	char data_filename[MAX_LINE_LENGTH];
-	double value = 0;
-
-	fid = fopen(model_filename, "r");
-	if (fid == NULL) {
-		fprintf(stderr, "Error opening model file %s\n", 
-				model_filename);
-		exit(1);
-	}
-	// skip the first four lines
-	for (i=0; i<4; i++)
-		next_line(fid, model_filename);
-
-	// read all model variables
-	model->p = get_fmt_double(fid, model_filename, "p = %lf");
-	model->lambda = get_fmt_double(fid, model_filename, "lambda = %lf");
-	model->kappa = get_fmt_double(fid, model_filename, "kappa = %lf");
-	model->epsilon = get_fmt_double(fid, model_filename, "epsilon = %lf");
-	model->weight_idx = (int) get_fmt_long(fid, model_filename, 
-			"weight_idx = %li");
-
-	// skip to data section
-	for (i=0; i<2; i++)
-		next_line(fid, model_filename);
-
-	// read filename of data file
-	if (fgets(buffer, MAX_LINE_LENGTH, fid) == NULL) {
-		fprintf(stderr, "Error reading model file %s\n", 
-				model_filename);
-		exit(1);
-	}
-	sscanf(buffer, "filename = %s\n", data_filename);
-	model->data_file = data_filename;
-
-	// read all data variables
-	model->n = get_fmt_long(fid, model_filename, "n = %li\n");
-	model->m = get_fmt_long(fid, model_filename, "m = %li\n");
-	model->K = get_fmt_long(fid, model_filename, "K = %li\n");
-
-	// skip to output
-	for (i=0; i<2; i++)
-		next_line(fid, model_filename);
-
-	// read the matrix V and check for consistency
-	model->V = Malloc(double, (model->m+1)*(model->K-1));
-	for (i=0; i<model->m+1; i++) {
-		for (j=0; j<model->K-1; j++) {
-			nr += fscanf(fid, "%lf ", &value);
-			matrix_set(model->V, model->K-1, i, j, value);
-		}
-	}
-	if (nr != (model->m+1)*(model->K-1)) {
-		fprintf(stderr, "Error reading model file %s. "
-				"Not enough elements of V found.\n", 
-				model_filename);
-		exit(1);
-	}
-}
-
-/**
- * @brief Write model to file
- *
- * @details
- * Write a MajModel to a file. The current time is specified in the file in
- * UTC + offset. The model file further corresponds to the @ref
- * spec_model_file.
- *
- * @param[in] 	model 		MajModel which contains an estimate for 
- * 				MajModel::V
- * @param[in] 	output_filename the output file to write the model to
- *
- */
-void msvmmaj_write_model(struct MajModel *model, char *output_filename)
-{
-	FILE *fid;
-	long i, j;
-	int diff, hours, minutes;
-	char timestr[1000];
-	time_t current_time, lt, gt;
-	struct tm *lclt;
-
-	// open output file
-	fid = fopen(output_filename, "w");
-	if (fid == NULL) {
-		fprintf(stderr, "Error opening output file %s", 
-				output_filename);
-		exit(1);
-	}
-
-	// get current time (in epoch)
-	current_time = time(NULL);
-	if (current_time == ((time_t)-1)) {
-		fprintf(stderr, "Failed to compute the current time.\n");
-		exit(1);
-	}
-
-	// convert time to local time and create a string
-	lclt = localtime(&current_time);
-	strftime(timestr, 1000, "%c", lclt);
-	if (timestr == NULL) {
-		fprintf(stderr, "Failed to convert time to string.\n");
-		exit(1);
-	}
-
-	// calculate the difference from UTC including DST
-	lt = mktime(localtime(&current_time));
-	gt = mktime(gmtime(&current_time));
-	diff = -difftime(gt, lt);
-	hours = (diff/3600);
-	minutes = (diff%3600)/60;
-	if (lclt->tm_isdst == 1)
-		hours++;
-
-	// Write output to file
-	fprintf(fid, "Output file for MSVMMaj (version %1.1f)\n", VERSION);
-	fprintf(fid, "Generated on: %s (UTC %+03i:%02i)\n\n", 
-			timestr, hours, minutes);
-	fprintf(fid, "Model:\n");
-	fprintf(fid, "p = %15.16f\n", model->p);
-	fprintf(fid, "lambda = %15.16f\n", model->lambda);
-	fprintf(fid, "kappa = %15.16f\n", model->kappa);
-	fprintf(fid, "epsilon = %g\n", model->epsilon);
-	fprintf(fid, "weight_idx = %i\n", model->weight_idx);
-	fprintf(fid, "\n");
-	fprintf(fid, "Data:\n");
-	fprintf(fid, "filename = %s\n", model->data_file);
-	fprintf(fid, "n = %li\n", model->n);
-	fprintf(fid, "m = %li\n", model->m);
-	fprintf(fid, "K = %li\n", model->K);
-	fprintf(fid, "\n");
-	fprintf(fid, "Output:\n");
-	for (i=0; i<model->m+1; i++) {
-		for (j=0; j<model->K-1; j++) {
-			fprintf(fid, "%+15.16f ", 
-					matrix_get(model->V, 
-						model->K-1, i, j));
-		}
-		fprintf(fid, "\n");
-	}
-
-	fclose(fid);
-}
-
-/**
- * @brief Write predictions to file
- *
- * @details
- * Write the given predictions to an output file, such that the resulting file
- * corresponds to the @ref spec_data_file. 
- *
- * @param[in] 	data 		MajData with the original instances
- * @param[in] 	predy 		predictions of the class labels of the 
- * 				instances in the given MajData. Note that the
- * 				order of the instances is assumed to be the
- * 				same.
- * @param[in] 	output_filename the file to which the predictions are written
- *
- */
-void msvmmaj_write_predictions(struct MajData *data, long *predy, 
-		char *output_filename)
-{
-	long i, j;
-	FILE *fid;
-
-	fid = fopen(output_filename, "w");
-	if (fid == NULL) {
-		fprintf(stderr, "Error opening output file %s", 
-				output_filename);
-		exit(1);
-	}
-
-	for (i=0; i<data->n; i++) {
-		for (j=0; j<data->m; j++) 
-			fprintf(fid, "%f ", 
-					matrix_get(data->Z, 
-						data->m+1, i, j+1));
-		fprintf(fid, "%li\n", predy[i]);
-	}
-
-	fclose(fid);
-}
-
-/**
  * @brief Check if any command line arguments contain string
  *
  * @details
@@ -438,124 +126,3 @@ void note(const char *fmt,...)
 	va_end(ap);
 	(*msvmmaj_print_string)(buf);
 }
-
-/**
- * @brief Allocate memory for a MajModel
- *
- * @details
- * This function can be used to allocate the memory needed for a MajModel. All
- * arrays in the model are specified and initialized to 0.
- *
- * @param[in] 	model 	MajModel to allocate
- *
- */
-void msvmmaj_allocate_model(struct MajModel *model)
-{
-	long n = model->n;
-	long m = model->m;
-	long K = model->K;
-
-	model->W = Calloc(double, m*(K-1));
-	if (model->W == NULL) {
-		fprintf(stderr, "Failed to allocate memory for W.\n");
-		exit(1);
-	}
-
-	model->t = Calloc(double, K-1);
-	if (model->t == NULL) {
-		fprintf(stderr, "Failed to allocate memory for t.\n");
-		exit(1);
-	}
-
-	model->V = Calloc(double, (m+1)*(K-1));
-	if (model->V == NULL) {
-		fprintf(stderr, "Failed to allocate memory for V.\n");
-		exit(1);
-	}
-
-	model->Vbar = Calloc(double, (m+1)*(K-1));
-	if (model->Vbar == NULL) {
-		fprintf(stderr, "Failed to allocate memory for Vbar.\n");
-		exit(1);
-	}
-
-	model->U = Calloc(double, K*(K-1));
-	if (model->U == NULL) {
-		fprintf(stderr, "Failed to allocate memory for U.\n");
-		exit(1);
-	}
-
-	model->UU = Calloc(double, n*K*(K-1));
-	if (model->UU == NULL) {
-		fprintf(stderr, "Failed to allocate memory for UU.\n");
-		exit(1);
-	}
-
-	model->Q = Calloc(double, n*K);
-	if (model->Q == NULL) {
-		fprintf(stderr, "Failed to allocate memory for Q.\n");
-		exit(1);
-	}
-
-	model->H = Calloc(double, n*K);
-	if (model->H == NULL) {
-		fprintf(stderr, "Failed to allocate memory for H.\n");
-		exit(1);
-	}
-
-	model->R = Calloc(double, n*K);
-	if (model->R == NULL) {
-		fprintf(stderr, "Failed to allocate memory for R.\n");
-		exit(1);
-	}
-
-	model->rho = Calloc(double, n);
-	if (model->rho == NULL) {
-		fprintf(stderr, "Failed to allocate memory for rho.\n");
-		exit(1);
-	}
-
-}	
-
-/**
- * @brief Free allocated MajModel struct
- *
- * @details
- * Simply free a previously allocated MajModel by freeing all its component
- * arrays. Note that the model struct itself is also freed here.
- *
- * @param[in] 	model 	MajModel to free
- *
- */
-void msvmmaj_free_model(struct MajModel *model)
-{
-	free(model->W);
-	free(model->t);
-	free(model->V);
-	free(model->Vbar);
-	free(model->U);
-	free(model->UU);
-	free(model->Q);
-	free(model->H);
-	free(model->rho);
-	free(model->R);
-
-	free(model);
-}
-
-/**
- * @brief Free allocated MajData struct 
- *
- * @details
- * Simply free a previously allocated MajData struct by freeing all its
- * components. Note that the data struct itself is also freed here.
- *
- * @param[in] 	data 	MajData struct to free
- *
- */
-void msvmmaj_free_data(struct MajData *data)
-{
-	free(data->Z);
-	free(data->y);
-	free(data);
-}