/****************************************************************************
 * Copyright (C) 2009-2015 EPAM Systems
 * 
 * This file is part of Indigo toolkit.
 * 
 * This file may be distributed and/or modified under the terms of the
 * GNU General Public License version 3 as published by the Free Software
 * Foundation and appearing in the file LICENSE.GPL included in the
 * packaging of this file.
 * 
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 ***************************************************************************/

#include "graph/edge_rotation_matcher.h"
#include "graph/graph.h"
#include "graph/spanning_tree.h"
#include "graph/graph_affine_matcher.h"
#include "math/algebra.h"

using namespace indigo;

IMPL_ERROR(EdgeRotationMatcher, "edge rotation matcher");

EdgeRotationMatcher::EdgeRotationMatcher (Graph &subgraph, Graph &supergraph, const int *mapping) :
_subgraph(subgraph),
_supergraph(supergraph),
_mapping(mapping)
{
   cb_get_xyz = 0;
   cb_can_rotate = 0;
   equalize_edges = false;
}

bool EdgeRotationMatcher::match (float rms_threshold, float eps)
{
   if (cb_get_xyz == 0)
      throw Error("cb_get_xyz not specified");

   if (_subgraph.vertexCount() < 2 || _subgraph.edgeCount() < 1)
      return true;

   QS_DEF(Array<int>, in_cycle);
   QS_DEF(Array<_DirEdge>, edge_queue);
   QS_DEF(Array<int>, vertex_queue);
   QS_DEF(Array<int>, states);

   in_cycle.clear_resize(_subgraph.edgeEnd());
   edge_queue.clear();
   states.clear_resize(__max(_subgraph.edgeEnd(), _subgraph.vertexEnd() + 1));
   
   int i, j, k, bottom;

   // Find all subgraph bridges
   SpanningTree spt(_subgraph, 0);

   in_cycle.zerofill();

   spt.markAllEdgesInCycles(in_cycle.ptr(), 1);

   // Find the first bridge, put it to the queue 2 times
   for (i = _subgraph.edgeBegin(); i < _subgraph.edgeEnd(); i = _subgraph.edgeNext(i))
      if (!in_cycle[i] && (cb_can_rotate == 0 || cb_can_rotate(_subgraph, i)))
      {
         const Edge &edge = _subgraph.getEdge(i);

         if (_mapping[edge.beg] < 0 || _mapping[edge.end] < 0)
            continue;

         edge_queue.push();
         edge_queue.top().idx = i;
         edge_queue.top().beg = edge.beg;
         edge_queue.top().end = edge.end;

         edge_queue.push();
         edge_queue.top().idx = i;
         edge_queue.top().beg = edge.end;
         edge_queue.top().end = edge.beg;
         break;
      }

   // If the queue is empty, then we have no bridge
   if (edge_queue.size() == 0)
   {
      GraphAffineMatcher afm(_subgraph, _supergraph, _mapping);

      afm.cb_get_xyz = cb_get_xyz;
      return afm.match(rms_threshold);
   }

   float scale = 1.f;

   // detect scaling factor by average bond length
   if (equalize_edges)
   {
      float sum_sub = 0.f, sum_super = 0.f;
      
      for (i = _subgraph.edgeBegin(); i < _subgraph.edgeEnd(); i = _subgraph.edgeNext(i))
      {
         const Edge &edge = _subgraph.getEdge(i);
         Vec3f beg, end;

         cb_get_xyz(_subgraph, edge.beg, beg);
         cb_get_xyz(_subgraph, edge.end, end);

         sum_sub += Vec3f::dist(beg, end);
      }

      for (i = _supergraph.edgeBegin(); i < _supergraph.edgeEnd(); i = _supergraph.edgeNext(i))
      {
         const Edge &edge = _supergraph.getEdge(i);
         Vec3f beg, end;

         cb_get_xyz(_supergraph, edge.beg, beg);
         cb_get_xyz(_supergraph, edge.end, end);

         sum_super += Vec3f::dist(beg, end);
      }

      if (sum_sub > EPSILON && sum_super > EPSILON)
      {
         sum_sub /= _subgraph.edgeCount();
         sum_super /= _supergraph.edgeCount();
         scale = sum_super / sum_sub;
      }
   }

   // save vertex positions

   QS_DEF(Array<Vec3f>, xyz_sub);
   QS_DEF(Array<Vec3f>, xyz_super);
   QS_DEF(Array<int>, xyzmap);

   xyzmap.clear_resize(_supergraph.vertexEnd());
   xyz_sub.clear();
   xyz_super.clear();

   for (i = _subgraph.vertexBegin(); i != _subgraph.vertexEnd();
        i = _subgraph.vertexNext(i))
   {
      if (_mapping[i] < 0)
         continue;

      Vec3f &pos_sub   = xyz_sub.push();
      Vec3f &pos_super = xyz_super.push();

      cb_get_xyz(_subgraph, i, pos_sub);
      cb_get_xyz(_supergraph, _mapping[i], pos_super);

      pos_sub.scale(scale);

      xyzmap[_mapping[i]] = xyz_sub.size() - 1;
   }

   // Make queue of edges
   states.zerofill();
   bottom = 0;

   while (edge_queue.size() != bottom)
   {
      // extract edge from queue
      int edge_end = edge_queue[bottom].end;
      int edge_idx = edge_queue[bottom].idx;
      bottom++;
      
      // mark it as 'completed'
      states[edge_idx] = 2;

      // look for neighbors
      const Vertex &end_vertex = _subgraph.getVertex(edge_end);

      for (i = end_vertex.neiBegin(); i != end_vertex.neiEnd(); i = end_vertex.neiNext(i))
      {
         int nei_edge_idx = end_vertex.neiEdge(i);

         // check that neighbor have 'untouched' status
         if (states[nei_edge_idx] != 0)
            continue;

         const Edge &nei_edge = _subgraph.getEdge(nei_edge_idx);
         int other_end = nei_edge.findOtherEnd(edge_end);

         if (_mapping[other_end] < 0)
            continue;

         // set status 'in process'
         states[nei_edge_idx] = 1;

         // push the neighbor edge to the queue
         edge_queue.push();
         edge_queue.top().idx = nei_edge_idx;
         edge_queue.top().beg = edge_end;
         edge_queue.top().end = other_end;
      }
   }

   // do initial transform (impose first subgraph edge in the queue on corresponding one in the graph)
   int beg2 = edge_queue[0].beg;
   int end2 = edge_queue[0].end;
   int beg1 = _mapping[beg2];
   int end1 = _mapping[end2];
   Vec3f g1_v1, g1_v2, g2_v1, g2_v2, diff1, diff2;
   Transform3f matr;

   cb_get_xyz(_supergraph, beg1, g1_v1);
   cb_get_xyz(_supergraph, end1, g1_v2);

   cb_get_xyz(_subgraph, beg2, g2_v1);
   cb_get_xyz(_subgraph, end2, g2_v2);

   g2_v1.scale(scale);
   g2_v2.scale(scale);

   diff1.diff(g1_v2, g1_v1);
   diff2.diff(g2_v2, g2_v1);

   matr.identity();
   if (!matr.rotationVecVec(diff2, diff1))
      throw Error("error calling RotationVecVec()");

   matr.translateLocal(-g2_v1.x, -g2_v1.y, -g2_v1.z);
   matr.translate(g1_v1);

   for (k = 0; k < xyz_sub.size(); k++)
      xyz_sub[k].transformPoint(matr);

   // for all edges in queue that are subject to rotate...
   for (i = 0; i < edge_queue.size(); i++)
   {
      int edge_beg = edge_queue[i].beg;
      int edge_end = edge_queue[i].end;
      int edge_idx = edge_queue[i].idx;

      if (in_cycle[edge_idx])
         continue;

      if (cb_can_rotate != 0 && !cb_can_rotate(_subgraph, edge_idx))
         continue;

      // start BFS from the end of the edge
      states.zerofill();
      states[edge_end] = 1;

      vertex_queue.clear();
      vertex_queue.push(edge_end);
      bottom = 0;

      while (vertex_queue.size() != bottom)
      {
         // extract vertex from queue
         const Vertex &vertex = _subgraph.getVertex(vertex_queue[bottom]);

         states[vertex_queue[bottom]] = 2;
         bottom++;

         // look over neighbors
         for (int j = vertex.neiBegin(); j != vertex.neiEnd(); j = vertex.neiNext(j))
         {
            int nei_idx = vertex.neiVertex(j);

            if (nei_idx == edge_beg)
               continue;
            if (states[nei_idx] != 0)
               continue;
            
            states[nei_idx] = 1;
            vertex_queue.push(nei_idx);
         }
      }

      // now states[j] == 0 if j-th vertex shound not be moved

      Vec3f edge_beg_pos, edge_end_pos, rot_axis;

      // get rotation axis
      edge_beg_pos.copy(xyz_sub[xyzmap[_mapping[edge_beg]]]);
      edge_end_pos.copy(xyz_sub[xyzmap[_mapping[edge_end]]]);

      rot_axis.diff(edge_end_pos, edge_beg_pos);
      if (!rot_axis.normalize())
         continue;

      const Vertex &edge_end_vertex = _subgraph.getVertex(edge_end);

      float max_sum_len = -1;

      for (j = edge_end_vertex.neiBegin(); j != edge_end_vertex.neiEnd();
           j = edge_end_vertex.neiNext(j))
      {
         int nei_idx_2 = edge_end_vertex.neiVertex(j);
         int nei_idx_1 = _mapping[nei_idx_2];

         if (nei_idx_2 == edge_beg)
            continue;

         if (nei_idx_1 == -1)
            continue;

         Vec3f nei1_pos;
         Vec3f nei2_pos;

         nei1_pos.copy(xyz_super[xyzmap[nei_idx_1]]);
         nei2_pos.copy(xyz_sub[xyzmap[_mapping[nei_idx_2]]]);

         nei1_pos.sub(edge_end_pos);
         nei2_pos.sub(edge_end_pos);

         float dot1 = Vec3f::dot(nei1_pos, rot_axis);
         float dot2 = Vec3f::dot(nei2_pos, rot_axis);

         nei1_pos.addScaled(rot_axis, -dot1);
         nei2_pos.addScaled(rot_axis, -dot2);

         if (max_sum_len > nei1_pos.length() + nei1_pos.length())
            continue;

         max_sum_len = nei1_pos.length() + nei1_pos.length();

         if (!nei1_pos.normalize() || !nei2_pos.normalize())
            continue;

         double dp = Vec3f::dot(nei1_pos, nei2_pos);

         if (dp > 1 - EPSILON)
            dp = 1 - EPSILON;
         if (dp < -1 + EPSILON)
            dp = -1 + EPSILON;

         double ang = acos(dp);

         Vec3f cross;

         cross.cross(nei1_pos, nei2_pos);

         if (Vec3f::dot(cross, rot_axis) < 0)
            ang = -ang;

         matr.rotation(rot_axis.x, rot_axis.y, rot_axis.z, (float)ang);
         matr.translateLocalInv(edge_end_pos);
         matr.translate(edge_end_pos);
      }

      if (max_sum_len > 0)
      {
         for (j = _subgraph.vertexBegin(); j < _subgraph.vertexEnd(); j = _subgraph.vertexNext(j))
            if (_mapping[j] >= 0 && states[j] != 0)
               xyz_sub[xyzmap[_mapping[j]]].transformPoint(matr);
      }
   }

   float sqsum = 0;

   for (k = 0; k < xyz_sub.size(); k++)
      sqsum += Vec3f::distSqr(xyz_sub[k], xyz_super[k]);

   sqsum = sqrt(sqsum / xyz_sub.size());

   if (sqsum > rms_threshold + eps)
      return false;

   return true;
}