re-added some essential routines; updated example sceipts to reflect new layout

c_tools/jozov2/jozov2.hpp

@@ -0,0 +1,65 @@
+/*+
+    VIDE -- Void IDentification and Examination -- ./c_tools/zobov2/jozov2/jozov2.hpp
+    Copyright (C) 2010-2014 Guilhem Lavaux
+    Copyright (C) 2011-2014 P. M. Sutter
+
+    This program 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; version 2 of the License.
+
+    This program 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 this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
++*/
+#ifndef __JOZOV2_HPP
+#define __JOZOV2_HPP
+
+#include <string>
+#include <exception>
+#include "zobov.hpp"
+
+#define BIGFLT 1e30 /* Biggest possible floating-point number */
+#define NLINKS 1000 /* Number of possible links with the same rho_sl */
+#define FF cout.flush()
+
+class FileError: virtual std::exception
+{
+};
+
+void readAdjacencyFile(const std::string& adjfile, PARTICLE*& p, pid_t& np)
+  throw(FileError);
+
+void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np, 
+                    pid_t mockIndex)
+  throw(FileError);
+
+void buildInitialZones(PARTICLE *p, pid_t np, pid_t* jumped, 
+                       pid_t *numinh, pid_t& numZones);
+
+void buildZoneAdjacencies(PARTICLE *p, pid_t np,
+                          ZONE *z, ZONET *zt,
+                          int numZones,
+                          pid_t *jumped,
+                          int *zonenum,
+                          int *numinh);
+
+void buildZones(PARTICLE *p, pid_t np, pid_t *&jumped,
+                ZONE*& z, int& nzones,
+                int*& zonenum);
+
+void doWatershed(PARTICLE *p, pid_t np, ZONE *z, int numZones, float maxvol, float voltol);
+
+void writeZoneFile(const std::string& zonfile, PARTICLE* p, pid_t np,
+                   ZONE *z, int numZones, int* zonenum, int *jumped);
+
+void writeVoidFile(const std::string& zonfile2, ZONE *z, int numZones);
+
+
+extern "C" void findrtop(double *a, int na, int *iord, int nb);
+
+#endif