moved check for class labels to seperate module

8 files changed, 286 insertions, 44 deletions

diff --git a/include/gensvm_checks.h b/include/gensvm_checks.h
new file mode 100644
index 0000000..08bad02
--- /dev/null
+++ b/include/gensvm_checks.h
@@ -0,0 +1,36 @@
+/**
+ * @file gensvm_checks.h
+ * @author G.J.J. van den Burg
+ * @date 2016-12-07
+ * @brief Header file for gensvm_checks.c
+ *
+ * @copyright
+ Copyright 2016, G.J.J. van den Burg.
+
+ This file is part of GenSVM.
+
+ GenSVM is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ GenSVM is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with GenSVM. If not, see <http://www.gnu.org/licenses/>.
+
+ */
+
+#ifndef GENSVM_CHECKS_H
+#define GENSVM_CHECKS_H
+
+// includes
+#include "gensvm_base.h"
+
+// function declarations
+bool gensvm_check_outcome_contiguous(struct GenData *data);
+
+#endif
diff --git a/include/gensvm_globals.h b/include/gensvm_globals.h
index 8ca3189..1151069 100644
--- a/include/gensvm_globals.h
+++ b/include/gensvm_globals.h
@@ -38,6 +38,7 @@
 
 #include "gensvm_memory.h"
 
+// all system libraries are included here
 #include <stdarg.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -46,6 +47,7 @@
 #include <math.h>
 #include <time.h>
 #include <cblas.h>
+#include <limits.h>
 
 // ########################### Type definitions ########################### //
 
diff --git a/src/GenSVMgrid.c b/src/GenSVMgrid.c
index 1fd7463..3799de3 100644
--- a/src/GenSVMgrid.c
+++ b/src/GenSVMgrid.c
@@ -37,6 +37,7 @@
 
  */
 
+#include "gensvm_checks.h"
 #include "gensvm_cmdarg.h"
 #include "gensvm_io.h"
 #include "gensvm_gridsearch.h"
@@ -114,6 +115,14 @@ int main(int argc, char **argv)
 	note("Reading data from %s\n", grid->train_data_file);
 	gensvm_read_data(train_data, grid->train_data_file);
 
+	// check labels of training data
+	gensvm_check_outcome_contiguous(train_data);
+	if (!gensvm_check_outcome_contiguous(train_data)) {
+		err("[GenSVM Error]: Class labels should start from 1 and "
+				"have no gaps. Please reformat your data.\n");
+		exit(EXIT_FAILURE);
+	}
+
 	// check if we are sparse and want nonlinearity
 	if (train_data->Z == NULL && grid->kerneltype != K_LINEAR) {
 		err("[GenSVM Warning]: Sparse matrices with nonlinear kernels "
diff --git a/src/GenSVMtraintest.c b/src/GenSVMtraintest.c
index ecf455b..8bebf3a 100644
--- a/src/GenSVMtraintest.c
+++ b/src/GenSVMtraintest.c
@@ -28,6 +28,7 @@
 
  */
 
+#include "gensvm_checks.h"
 #include "gensvm_cmdarg.h"
 #include "gensvm_io.h"
 #include "gensvm_train.h"
@@ -130,8 +131,15 @@ int main(int argc, char **argv)
 		       	&training_inputfile, &testing_inputfile,
 		       	&model_outputfile, &prediction_outputfile);
 
-	// read data from files
+	// read data from file and check labels
 	gensvm_read_data(traindata, training_inputfile);
+	if (!gensvm_check_outcome_contiguous(traindata)) {
+		err("[GenSVM Error]: Class labels should start from 1 and "
+				"have no gaps. Please reformat your data.\n");
+		exit(EXIT_FAILURE);
+	}
+
+	// save data filename to model
 	model->data_file = Calloc(char, GENSVM_MAX_LINE_LENGTH);
 	strcpy(model->data_file, training_inputfile);
 
diff --git a/src/gensvm_checks.c b/src/gensvm_checks.c
new file mode 100644
index 0000000..0f7c499
--- /dev/null
+++ b/src/gensvm_checks.c
@@ -0,0 +1,77 @@
+/**
+ * @file gensvm_checks.c
+ * @author G.J.J. van den Burg
+ * @date 2016-12-07
+ * @brief Sanity checks used to ensure inputs are as expected
+ *
+ * @copyright
+ Copyright 2016, G.J.J. van den Burg.
+
+ This file is part of GenSVM.
+
+ GenSVM is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ GenSVM is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with GenSVM. If not, see <http://www.gnu.org/licenses/>.
+
+ */
+
+#include "gensvm_checks.h"
+
+/**
+ * @brief Check if the labels are contiguous on [1 .. K]
+ *
+ * @details
+ * The GenSVM library currently requires that the labels that are supplied in 
+ * a dataset are contigous on the interval [1 .. K] and have no gaps. This is 
+ * required because the dimensionality of the problem is directly related to 
+ * the maximum class label K. This function checks if the labels are indeed in 
+ * the desired range.
+ *
+ * @param[in] 	data 	a GenData struct with the current data
+ *
+ * @return 		whether the labels are contiguous or not
+ */
+bool gensvm_check_outcome_contiguous(struct GenData *data)
+{
+	bool in_uniq, is_contiguous = true;
+	long i, j, K = 1;
+	long max_y = -1,
+	     min_y = LONG_MAX;
+	long *uniq_y = Calloc(long, K);
+	uniq_y[0] = data->y[0];
+
+	for (i=1; i<data->n; i++) {
+		in_uniq = false;
+		for (j=0; j<K; j++) {
+			if (uniq_y[j] == data->y[i]) {
+				in_uniq = true;
+				break;
+			}
+		}
+
+		if (!in_uniq) {
+			uniq_y = Realloc(uniq_y, long, K+1);
+			uniq_y[K++] = data->y[i];
+		}
+
+		max_y = maximum(max_y, data->y[i]);
+		min_y = minimum(min_y, data->y[i]);
+	}
+
+	if (min_y < 1 || max_y > K) {
+		is_contiguous = false;
+	}
+
+	free(uniq_y);
+
+	return is_contiguous;
+}
diff --git a/src/gensvm_io.c b/src/gensvm_io.c
index 78838b1..0d14144 100644
--- a/src/gensvm_io.c
+++ b/src/gensvm_io.c
@@ -29,7 +29,6 @@
 
  */
 
-#include <limits.h>
 #include "gensvm_io.h"
 
 /**
@@ -39,12 +38,8 @@
  * 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 checked to make sure they correspond to the interval
- * [1 .. K], where K is the total number of classes, without any gaps.
- *
- * @todo
- * Make sure that this function allows datasets without class labels for
- * testing.
+ * The class labels are assumed to be in the interval [1 .. K], which can be 
+ * checked using the function gensvm_check_outcome_contiguous().
  *
  * @param[in,out] 	dataset 	initialized GenData struct
  * @param[in] 		data_file 	filename of the data file.
@@ -52,15 +47,10 @@
 void gensvm_read_data(struct GenData *dataset, char *data_file)
 {
 	FILE *fid = NULL;
-	bool in_uniq;
 	long i, j, n, m,
 	     nr = 0,
-	     K = 0,
-	     max_y = -1,
-	     min_y = LONG_MAX;
+	     K = 0;
 	double value;
-	long *uniq_y = NULL;
-
 	char buf[GENSVM_MAX_LINE_LENGTH];
 
 	if ((fid = fopen(data_file, "r")) == NULL) {
@@ -96,8 +86,6 @@ void gensvm_read_data(struct GenData *dataset, char *data_file)
 		dataset->y = Malloc(long, n);
 		dataset->y[0] = value;
 		K = 1;
-		uniq_y = Calloc(long, K);
-		uniq_y[0] = value;
 	} else {
 		free(dataset->y);
 		dataset->y = NULL;
@@ -112,33 +100,11 @@ void gensvm_read_data(struct GenData *dataset, char *data_file)
 		if (dataset->y != NULL) {
 			nr += fscanf(fid, "%lf", &value);
 			dataset->y[i] = (long) value;
-
-			// this is to keep track of the unique values of y, so 
-			// we can warn when they're not encoded correctly
-			in_uniq = false;
-			for (j=0; j<K; j++) {
-				if (uniq_y[j] == dataset->y[i])
-					in_uniq = true;
-			}
-			if (!in_uniq) {
-				uniq_y = Realloc(uniq_y, long, K+1);
-				uniq_y[K++] = value;
-			}
-			max_y = maximum(max_y, value);
-			min_y = minimum(min_y, value);
+			K = maximum(K, dataset->y[i]);
 		}
 	}
 	fclose(fid);
 
-	// Correct labels: must be in [1, K]
-	if (min_y < 1 || max_y > K) {
-		// LCOV_EXCL_START
-		err("[GenSVM Error]: Class labels should start from 1 and "
-				"have no gaps. Please reformat your data.\n");
-		exit(EXIT_FAILURE);
-		// LCOV_EXCL_STOP
-	}
-
 	if (nr < n * m) {
 		// LCOV_EXCL_START
 		err("[GenSVM Error]: not enough data found in %s\n",
@@ -165,8 +131,6 @@ void gensvm_read_data(struct GenData *dataset, char *data_file)
 		dataset->RAW = NULL;
 		dataset->Z = NULL;
 	}
-
-	free(uniq_y);
 }
 
 
diff --git a/tests/src/test_gensvm_checks.c b/tests/src/test_gensvm_checks.c
new file mode 100644
index 0000000..9b163be
--- /dev/null
+++ b/tests/src/test_gensvm_checks.c
@@ -0,0 +1,146 @@
+/**
+ * @file test_gensvm_checks.c
+ * @author G.J.J. van den Burg
+ * @date 2016-12-07
+ * @brief Unit tests for gensvm_checks.c functions
+ *
+ * @copyright
+ Copyright 2016, G.J.J. van den Burg.
+
+ This file is part of GenSVM.
+
+ GenSVM is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ GenSVM is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with GenSVM. If not, see <http://www.gnu.org/licenses/>.
+
+ */
+
+#include "minunit.h"
+#include "gensvm_checks.h"
+
+char *test_check_outcome_contiguous_correct()
+{
+	struct GenData *data = gensvm_init_data();
+	data->n = 10;
+	data->y = Calloc(long, data->n);
+	data->y[0] = 1;
+	data->y[1] = 2;
+	data->y[2] = 3;
+	data->y[3] = 4;
+	data->y[4] = 1;
+	data->y[5] = 1;
+	data->y[6] = 2;
+	data->y[7] = 2;
+	data->y[8] = 4;
+	data->y[9] = 3;
+
+	// start test code //
+	mu_assert(gensvm_check_outcome_contiguous(data) == true, 
+			"Incorrect check outcome for correct");
+	// end test code //
+
+	gensvm_free_data(data);
+
+	return NULL;
+}
+
+char *test_check_outcome_contiguous_gap()
+{
+	struct GenData *data = gensvm_init_data();
+	data->n = 10;
+	data->y = Calloc(long, data->n);
+	data->y[0] = 1;
+	data->y[1] = 2;
+	data->y[2] = 4;
+	data->y[3] = 4;
+	data->y[4] = 1;
+	data->y[5] = 1;
+	data->y[6] = 2;
+	data->y[7] = 2;
+	data->y[8] = 4;
+	data->y[9] = 4;
+
+	// start test code //
+	mu_assert(gensvm_check_outcome_contiguous(data) == false, 
+			"Incorrect check outcome for gap");
+	// end test code //
+
+	gensvm_free_data(data);
+
+	return NULL;
+}
+
+char *test_check_outcome_contiguous_gaps()
+{
+	struct GenData *data = gensvm_init_data();
+	data->n = 10;
+	data->y = Calloc(long, data->n);
+	data->y[0] = 1;
+	data->y[1] = 6;
+	data->y[2] = 4;
+	data->y[3] = 4;
+	data->y[4] = 1;
+	data->y[5] = 1;
+	data->y[6] = 6;
+	data->y[7] = 6;
+	data->y[8] = 4;
+	data->y[9] = 4;
+
+	// start test code //
+	mu_assert(gensvm_check_outcome_contiguous(data) == false, 
+			"Incorrect check outcome for gaps");
+	// end test code //
+
+	gensvm_free_data(data);
+
+	return NULL;
+}
+
+char *test_check_outcome_contiguous_shift()
+{
+	struct GenData *data = gensvm_init_data();
+	data->n = 10;
+	data->y = Calloc(long, data->n);
+	data->y[0] = 2;
+	data->y[1] = 3;
+	data->y[2] = 4;
+	data->y[3] = 5;
+	data->y[4] = 2;
+	data->y[5] = 3;
+	data->y[6] = 3;
+	data->y[7] = 4;
+	data->y[8] = 5;
+	data->y[9] = 5;
+
+	// start test code //
+	mu_assert(gensvm_check_outcome_contiguous(data) == false, 
+			"Incorrect check outcome for shift");
+	// end test code //
+
+	gensvm_free_data(data);
+
+	return NULL;
+}
+
+char *all_tests()
+{
+	mu_suite_start();
+
+	mu_run_test(test_check_outcome_contiguous_correct);
+	mu_run_test(test_check_outcome_contiguous_gap);
+	mu_run_test(test_check_outcome_contiguous_gaps);
+	mu_run_test(test_check_outcome_contiguous_shift);
+
+	return NULL;
+}
+
+RUN_TESTS(all_tests);
diff --git a/tests/src/test_gensvm_train.c b/tests/src/test_gensvm_train.c
index 4e3c0b4..4994eb6 100644
--- a/tests/src/test_gensvm_train.c
+++ b/tests/src/test_gensvm_train.c
@@ -1,8 +1,8 @@
 /**
- * @file test_gensvm_optimize.c
+ * @file test_gensvm_train.c
  * @author G.J.J. van den Burg
- * @date 2016-09-01
- * @brief Unit tests for gensvm_optimize.c functions
+ * @date 2016-12-06
+ * @brief Unit tests for gensvm_train.c functions
  *
  * @copyright
  Copyright 2016, G.J.J. van den Burg.