path: root/src/util.c

/**
 * @file util.c
 * @author Gertjan van den Burg
 * @date January, 2014
 * @brief Utility functions
 *
 * @details
 * 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"

FILE *MSVMMAJ_OUTPUT_FILE; 	///< The #MSVMMAJ_OUTPUT_FILE specifies the 
				///< output stream to which all output is 
				///< written. This is done through the
				///< internal (!)
				///< function msvmmaj_print_string(). The
				///< advantage of using a global output 
				///< stream variable is that the output can
				///< temporarily be suppressed by importing
				///< this variable through @c extern and 
				///< (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
 * Check if any of a given array of command line arguments contains a given 
 * string. If the string is found, the index of the string in argv is 
 * returned. If the string is not found, 0 is returned.
 *
 * This function is copied from MSVMpack/libMSVM.c.
 *
 * @param[in] 	argc 	number of command line arguments
 * @param[in] 	argv 	command line arguments
 * @param[in] 	str 	string to find in the arguments
 * @returns 		index of the string in the arguments if found, 0
 * 			otherwise
 */
int msvmmaj_check_argv(int argc, char **argv, char *str)
{
	int i;
	int arg_str = 0;
	for (i=1; i<argc; i++)
		if (strstr(argv[i], str) != NULL) {
			arg_str = i;
			break;
		}

	return arg_str;
}

/**
 * @brief Check if a command line argument equals a string
 *
 * @details
 * Check if any of the command line arguments is exactly equal to a given
 * string. If so, return the index of the corresponding command line argument.
 * If not, return 0.
 *
 * This function is copied from MSVMpack/libMSVM.c
 *
 * @param[in] 	argc 	number of command line arguments
 * @param[in] 	argv 	command line arguments
 * @param[in] 	str 	string to find in the arguments
 * @returns 		index of the command line argument that corresponds to
 * 			the string, 0 if none matches.
 */
int msvmmaj_check_argv_eq(int argc, char **argv, char *str) 
{
	int i;
	int arg_str = 0;
	for (i=1; i<argc; i++)
		if (strcmp(argv[i], str) == 0) {
			arg_str = i;
			break;
		}

	return arg_str;
}


/**
 * @brief Print a given string to the specified output stream
 *
 * @details
 * This function is used to print a given string to the output stream
 * specified by #MSVMMAJ_OUTPUT_FILE. The stream is flushed after the string 
 * is written to the stream. If #MSVMMAJ_OUTPUT_FILE is NULL, nothing is
 * written. Note that this function is only used by note(), it should never be
 * used directly.
 *
 * @param[in] 	s 	string to write to the stream
 *
 */
static void msvmmaj_print_string(const char *s)
{
	if (MSVMMAJ_OUTPUT_FILE != NULL) {
		fputs(s, MSVMMAJ_OUTPUT_FILE);
		fflush(MSVMMAJ_OUTPUT_FILE);
	}
}

/**
 * @brief Parse a formatted string and write to the output stream
 *
 * @details
 * This function is a replacement of fprintf(), such that the output stream
 * does not have to be specified at each function call. The functionality is
 * exactly the same however. Writing the formatted string to the output stream
 * is handled by msvmmaj_print_string().
 *
 * @param[in] 	fmt 	String format
 * @param[in] 	... 	variable argument list for the string format
 *
 */
void note(const char *fmt,...)
{
	char buf[BUFSIZ];
	va_list ap;
	va_start(ap,fmt);
	vsprintf(buf,fmt,ap);
	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);
}