prepare for gridsearch unit testing

5 files changed, 95 insertions, 11 deletions

diff --git a/include/gensvm_consistency.h b/include/gensvm_consistency.h
new file mode 100644
index 0000000..cc0eeea
--- /dev/null
+++ b/include/gensvm_consistency.h
@@ -0,0 +1,43 @@
+/**
+ * @file gensvm_consistency.h
+ * @author G.J.J. van den Burg
+ * @date 2016-10-24
+ * @brief Header file for gensvm_consistency.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_CONSISTENCY_H
+#define GENSVM_CONSISTENCY_H
+
+// includes
+#include "gensvm_queue.h"
+#include "gensvm_print.h"
+#include "gensvm_cv_util.h"
+#include "gensvm_cross_validation.h"
+#include "gensvm_timer.h"
+
+// function declarations
+struct GenQueue *gensvm_top_queue(struct GenQueue *q, double percentile);
+void gensvm_consistency_repeats(struct GenQueue *q, long repeats,
+		double percentile);
+double gensvm_percentile(double *values, long N, double p);
+
+#endif
diff --git a/include/gensvm_cross_validation.h b/include/gensvm_cross_validation.h
new file mode 100644
index 0000000..16c7223
--- /dev/null
+++ b/include/gensvm_cross_validation.h
@@ -0,0 +1,41 @@
+/**
+ * @file gensvm_cross_validation.h
+ * @author G.J.J. van den Burg
+ * @date 2016-10-24
+ * @brief Header file for gensvm_cross_validation.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_CROSS_VALIDATION_H
+#define GENSVM_CROSS_VALIDATION_H
+
+// includes
+#include "gensvm_base.h"
+#include "gensvm_init.h"
+#include "gensvm_optimize.h"
+#include "gensvm_predict.h"
+
+// function declarations
+double gensvm_cross_validation(struct GenModel *model,
+		struct GenData **train_folds, struct GenData **test_folds,
+		int folds, long n_total);
+
+#endif
diff --git a/include/gensvm_grid.h b/include/gensvm_grid.h
index 5876448..24a6e9a 100644
--- a/include/gensvm_grid.h
+++ b/include/gensvm_grid.h
@@ -67,8 +67,9 @@
 struct GenGrid {
 	TrainType traintype;
 	KernelType kerneltype;
-	long repeats;
 	long folds;
+	long repeats;
+	double percentile;
 	long Np;
 	long Nl;
 	long Nk;
diff --git a/include/gensvm_gridsearch.h b/include/gensvm_gridsearch.h
index c4ddb98..f0be067 100644
--- a/include/gensvm_gridsearch.h
+++ b/include/gensvm_gridsearch.h
@@ -34,22 +34,20 @@
 #define GENSVM_GRIDSEARCH_H
 
 // includes
+#include "gensvm_cross_validation.h"
 #include "gensvm_cv_util.h"
-#include "gensvm_init.h"
 #include "gensvm_grid.h"
-#include "gensvm_optimize.h"
-#include "gensvm_predict.h"
 #include "gensvm_queue.h"
 #include "gensvm_timer.h"
 
 // function declarations
 void gensvm_fill_queue(struct GenGrid *grid, struct GenQueue *queue,
 		struct GenData *train_data, struct GenData *test_data);
-void consistency_repeats(struct GenQueue *q, long repeats, TrainType traintype);
-void make_model_from_task(struct GenTask *task, struct GenModel *model);
-void print_progress_string(struct GenTask *task, long N);
-void start_training(struct GenQueue *q);
-double gensvm_cross_validation(struct GenModel *model,
-	       	struct GenData **train_folds, struct GenData **test_folds,
-		int folds, long n_total);
+bool gensvm_kernel_changed(struct GenTask *newtask, struct GenTask *oldtask);
+void gensvm_kernel_folds(int folds, struct GenModel *model,
+		struct GenData **train_folds, struct GenData **test_folds);
+void gensvm_gridsearch_progress(struct GenTask *task, long N, double perf,
+		double duration, double current_max);
+void gensvm_train_queue(struct GenQueue *q);
+
 #endif
diff --git a/include/gensvm_task.h b/include/gensvm_task.h
index 41aef7a..a9b675a 100644
--- a/include/gensvm_task.h
+++ b/include/gensvm_task.h
@@ -67,5 +67,6 @@ struct GenTask {
 
 struct GenTask *gensvm_init_task();
 void gensvm_free_task(struct GenTask *task);
+void gensvm_task_to_model(struct GenTask *task, struct GenModel *model);
 
 #endif