rename msvmmaj to gensvm

1 files changed, 295 insertions, 0 deletions

diff --git a/src/gensvm_io.c b/src/gensvm_io.c
new file mode 100644
index 0000000..546ecd5
--- /dev/null
+++ b/src/gensvm_io.c
@@ -0,0 +1,295 @@
+/**
+ * @file gensvm_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 "gensvm.h"
+#include "gensvm_io.h"
+#include "gensvm_matrix.h"
+#include "strutil.h"
+#include "timer.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 GenData struct
+ * @param[in] 		data_file 	filename of the data file.
+ */
+void gensvm_read_data(struct GenData *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->RAW = 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->RAW, 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->RAW, 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->RAW, m+1, i, 0, 1.0);
+
+	dataset->n = n;
+	dataset->m = m;
+	dataset->K = K;
+	dataset->Z = dataset->RAW;
+}
+
+
+/**
+ * @brief Read model from file
+ *
+ * @details
+ * Read a GenModel from a model file. The GenModel 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
+ * gensvm_write_model(), which can for instance be used in trainGenSVM.c.
+ *
+ * @param[in,out] 	model 		initialized GenModel
+ * @param[in] 		model_filename 	filename of the model file
+ *
+ */
+void gensvm_read_model(struct GenModel *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 GenModel 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 		GenModel which contains an estimate for 
+ * 				GenModel::V
+ * @param[in] 	output_filename the output file to write the model to
+ *
+ */
+void gensvm_write_model(struct GenModel *model, char *output_filename)
+{
+	FILE *fid;
+	long i, j;
+	char timestr[MAX_LINE_LENGTH];
+
+	// open output file
+	fid = fopen(output_filename, "w");
+	if (fid == NULL) {
+		fprintf(stderr, "Error opening output file %s", 
+				output_filename);
+		exit(1);
+	}
+	get_time_string(timestr);
+
+	// Write output to file
+	fprintf(fid, "Output file for GenSVM (version %1.1f)\n", VERSION);
+	fprintf(fid, "Generated on: %s\n\n", timestr);
+	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 		GenData with the original instances
+ * @param[in] 	predy 		predictions of the class labels of the 
+ * 				instances in the given GenData. 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 gensvm_write_predictions(struct GenData *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);
+}