rename execs and fix some unintended renames

1 files changed, 180 insertions, 0 deletions

diff --git a/src/GenSVMpred.c b/src/GenSVMpred.c
new file mode 100644
index 0000000..c874aaf
--- /dev/null
+++ b/src/GenSVMpred.c
@@ -0,0 +1,180 @@
+/*
+ * 20140317:
+ * THIS FUNCTION IS DEPRECATED, SINCE IT DOES NOT WORK WITH KERNELS.
+ *
+ */
+
+/**
+ * @file GenSVM_pred.c
+ * @author Gertjan van den Burg
+ * @date January, 2014
+ * @brief Command line interface for predicting class labels
+ *
+ * @details
+ * This is a command line program for predicting the class labels or
+ * determining the predictive performance of a pre-determined model on a given
+ * test dataset. The predictive performance can be written to the screen or
+ * the predicted class labels can be written to a specified output file. This
+ * is done using gensvm_write_predictions().
+ *
+ * The specified model file must follow the specification given in
+ * gensvm_write_model().
+ *
+ * For usage information, see the program help function.
+ *
+ */
+
+#include "gensvm.h"
+#include "gensvm_init.h"
+#include "gensvm_io.h"
+#include "gensvm_pred.h"
+#include "util.h"
+
+#define MINARGS 3
+
+extern FILE *GENSVM_OUTPUT_FILE;
+
+// function declarations
+void exit_with_help();
+void parse_command_line(int argc, char **argv, 
+		char *input_filename, char *output_filename, 
+		char *model_filename);
+
+/**
+ * @brief Help function
+ */
+void exit_with_help()
+{
+	printf("This is GenSVM, version %1.1f\n\n", VERSION);
+	printf("Usage: predGenSVM [options] test_data_file model_file\n");
+	printf("Options:\n");
+	printf("-o output_file : write output to file\n");
+	printf("-q : quiet mode (no output)\n");
+	exit(0);
+}
+
+/**
+ * @brief Main interface function for predGenSVM
+ *
+ * @details
+ * Main interface for the command line program. A given model file is read and
+ * a test dataset is initialized from the given data. The predictive
+ * performance (hitrate) of the model on the test set is printed to the output
+ * stream (default = stdout). If an output file is specified the predictions
+ * are written to the file.
+ *
+ * @todo
+ * Ensure that the program can read model files without class labels
+ * specified. In that case no prediction accuracy is printed to the screen.
+ *
+ * @param[in] 	argc 	number of command line arguments
+ * @param[in] 	argv 	array of command line arguments
+ *
+ */
+int main(int argc, char **argv)
+{
+	long *predy;
+	double performance;
+
+	char input_filename[MAX_LINE_LENGTH];
+	char model_filename[MAX_LINE_LENGTH];
+	char output_filename[MAX_LINE_LENGTH];;
+
+	if (argc < MINARGS || gensvm_check_argv(argc, argv, "-help") 
+			|| gensvm_check_argv_eq(argc, argv, "-h") )
+		exit_with_help();
+	parse_command_line(argc, argv, input_filename, output_filename,
+			model_filename);
+
+	// read the data and model
+	struct GenModel *model = gensvm_init_model();
+	struct GenData *data = gensvm_init_data();
+	gensvm_read_data(data, input_filename);
+	gensvm_read_model(model, model_filename);
+
+	// check if the number of attributes in data equals that in model
+	if (data->m != model->m) {
+		fprintf(stderr, "Error: number of attributes in data (%li) "
+				"does not equal the number of attributes in "
+				"model (%li)\n", data->m, model->m);
+		exit(1);
+	} else if (data->K != model->K) {
+		fprintf(stderr, "Error: number of classes in data (%li) "
+				"does not equal the number of classes in "
+				"model (%li)\n", data->K, model->K);
+		exit(1);
+	}
+
+	// predict labels and performance if test data has labels
+	predy = Calloc(long, data->n);
+	gensvm_predict_labels(data, model, predy);
+	if (data->y != NULL) {
+		performance = gensvm_prediction_perf(data, predy);
+		note("Predictive performance: %3.2f%%\n", performance);
+	}
+
+	// if output file is specified, write predictions to it
+	if (gensvm_check_argv_eq(argc, argv, "-o")) {
+		gensvm_write_predictions(data, predy, output_filename);
+		note("Predictions written to: %s\n", output_filename);
+	}
+
+	// free the model, data, and predictions
+	gensvm_free_model(model);
+	gensvm_free_data(data);
+	free(predy);
+
+	return 0;
+}
+
+/**
+ * @brief Parse command line arguments
+ *
+ * @details
+ * Read the data filename and model filename from the command line arguments.
+ * If specified, also read the output filename. If the quiet flag is given,
+ * set the global output stream to NULL. On error, exit_with_help().
+ *
+ * @param[in] 	argc 			number of command line arguments
+ * @param[in] 	argv 			array of command line arguments
+ * @param[in] 	input_filename 		pre-allocated array for the input 
+ * 					filename
+ * @param[in] 	output_filename 	pre-allocated array for the output
+ * 					filename
+ * @param[in] 	model_filename 		pre-allocated array for the model
+ * 					filename
+ *
+ */
+void parse_command_line(int argc, char **argv, char *input_filename,
+		char *output_filename, char *model_filename)
+{
+	int i;
+
+	GENSVM_OUTPUT_FILE = stdout;
+
+	for (i=1; i<argc; i++) {
+		if (argv[i][0] != '-') break;
+		if (++i >= argc)
+			exit_with_help();
+		switch (argv[i-1][1]) {
+			case 'o':
+				strcpy(output_filename, argv[i]);
+				break;
+			case 'q':
+				GENSVM_OUTPUT_FILE = NULL;
+				i--;
+				break;
+			default:
+				fprintf(stderr, "Unknown option: -%c\n", 
+						argv[i-1][1]);
+				exit_with_help();
+		}
+	}
+
+	if (i >= argc)
+		exit_with_help();
+
+	strcpy(input_filename, argv[i]);
+	i++;
+	strcpy(model_filename, argv[i]);
+}