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coreAlan.c

/*
  Teem: Tools to process and visualize scientific data and images              
  Copyright (C) 2008, 2007, 2006, 2005  Gordon Kindlmann
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998  University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public License
  (LGPL) as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
  The terms of redistributing and/or modifying this software also
  include exceptions to the LGPL that facilitate static linking.

  This library 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
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public License
  along with this library; if not, write to Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
*/

/*
** learned: valgrind is sometimes far off when reporting the line
** number for an invalid read- have to comment out various lines in
** order to find the real offending line
*/

#include "alan.h"

int
_alanCheck(alanContext *actx) {
  char me[]="alanCheck", err[BIFF_STRLEN];

  if (!actx) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(ALAN, err); return 1;
  }
  if (0 == actx->dim) {
    sprintf(err, "%s: dimension of texture not set", me);
    biffAdd(ALAN, err); return 1;
  }
  if (alanTextureTypeUnknown == actx->textureType) {
    sprintf(err, "%s: texture type not set", me);
    biffAdd(ALAN, err); return 1;
  }
  if (!( actx->size[0] > 0 && actx->size[1] > 0
         && (2 == actx->dim || actx->size[2] > 0) )) {
    sprintf(err, "%s: texture sizes invalid", me);
    biffAdd(ALAN, err); return 1;
  }
  if (0 == actx->deltaT) {
    sprintf(err, "%s: deltaT == 0", me);
    biffAdd(ALAN, err); return 1;
  }

  return 0;
}

int
alanUpdate(alanContext *actx) {
  char me[]="alanUpdate", err[BIFF_STRLEN];
  int ret;

  if (_alanCheck(actx)) {
    sprintf(err, "%s: ", me);
    biffAdd(ALAN, err); return 1;
  }
  if (actx->_nlev[0] || actx->_nlev[0]) {
    sprintf(err, "%s: confusion: _nlev[0,1] already allocated?", me);
    biffAdd(ALAN, err); return 1;
  }
  actx->_nlev[0] = nrrdNew();
  actx->_nlev[1] = nrrdNew();
  actx->nparm = nrrdNew();
  if (2 == actx->dim) {
    ret = (nrrdMaybeAlloc_va(actx->_nlev[0], alan_nt, 3,
                             AIR_CAST(size_t, 2),
                             AIR_CAST(size_t, actx->size[0]),
                             AIR_CAST(size_t, actx->size[1]))
           || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
           || nrrdMaybeAlloc_va(actx->nparm, alan_nt, 3,
                                AIR_CAST(size_t, 3),
                                AIR_CAST(size_t, actx->size[0]),
                                AIR_CAST(size_t, actx->size[1])));
  } else {
    ret = (nrrdMaybeAlloc_va(actx->_nlev[0], alan_nt, 4,
                             AIR_CAST(size_t, 2),
                             AIR_CAST(size_t, actx->size[0]),
                             AIR_CAST(size_t, actx->size[1]),
                             AIR_CAST(size_t, actx->size[2]))
           || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
           || nrrdMaybeAlloc_va(actx->nparm, alan_nt, 4,
                                AIR_CAST(size_t, 3),
                                AIR_CAST(size_t, actx->size[0]),
                                AIR_CAST(size_t, actx->size[1]),
                                AIR_CAST(size_t, actx->size[2])));
  }
  if (ret) {
    sprintf(err, "%s: trouble allocating buffers", me);
    biffMove(ALAN, err, NRRD); return 1;
  }
  
  return 0;
}

int 
alanInit(alanContext *actx, const Nrrd *nlevInit, const Nrrd *nparmInit) {
  char me[]="alanInit", err[BIFF_STRLEN];
  alan_t *levInit=NULL, *lev0, *parmInit=NULL, *parm;
  size_t I, N;

  if (_alanCheck(actx)) {
    sprintf(err, "%s: ", me);
    biffAdd(ALAN, err); return 1;
  }
  if (!( actx->_nlev[0] && actx->_nlev[0] && actx->nparm )) {
    sprintf(err, "%s: _nlev[0,1] not allocated: call alanUpdate", me);
    biffAdd(ALAN, err); return 1;
  }
  
  if (nlevInit) {
    if (nrrdCheck(nlevInit)) {
      sprintf(err, "%s: given nlevInit has problems", me);
      biffMove(ALAN, err, NRRD); return 1;
    }
    if (!( alan_nt == nlevInit->type 
           && nlevInit->dim == 1 + actx->dim
           && actx->_nlev[0]->axis[0].size == nlevInit->axis[0].size
           && actx->size[0] == nlevInit->axis[1].size
           && actx->size[1] == nlevInit->axis[2].size 
           && (2 == actx->dim || actx->size[2] == nlevInit->axis[3].size) )) {
      sprintf(err, "%s: type/size mismatch with given nlevInit", me);
      biffAdd(ALAN, err); return 1;
    }
    levInit = (alan_t*)(nlevInit->data);
  }
  if (nparmInit) {
    if (nrrdCheck(nparmInit)) {
      sprintf(err, "%s: given nparmInit has problems", me);
      biffMove(ALAN, err, NRRD); return 1;
    }
    if (!( alan_nt == nparmInit->type 
           && nparmInit->dim == 1 + actx->dim
           && 3 == nparmInit->axis[0].size
           && actx->size[0] == nparmInit->axis[1].size
           && actx->size[1] == nparmInit->axis[2].size 
           && (2 == actx->dim || actx->size[2] == nparmInit->axis[3].size) )) {
      sprintf(err, "%s: type/size mismatch with given nparmInit", me);
      biffAdd(ALAN, err); return 1;
    }
    parmInit = (alan_t*)(nparmInit->data);
  }

#define RAND AIR_AFFINE(0, airDrandMT(), 1, -actx->randRange, actx->randRange)

  N = nrrdElementNumber(actx->_nlev[0])/actx->_nlev[0]->axis[0].size;
  lev0 = (alan_t*)(actx->_nlev[0]->data);
  parm = (alan_t*)(actx->nparm->data);
  for (I=0; I<N; I++) {
    if (levInit) {
      lev0[0 + 2*I] = levInit[0 + 2*I];
      lev0[1 + 2*I] = levInit[1 + 2*I];
    } else {
      /* NOTE: the random number stuff here is OUTSIDE the multi-threaded
         segment of the program- only the init thread does this */
      lev0[0 + 2*I] = AIR_CAST(alan_t, actx->initA + RAND);
      lev0[1 + 2*I] = AIR_CAST(alan_t, actx->initB + RAND);
    }
    if (parmInit) {
      parm[0 + 3*I] = parmInit[0 + 3*I];
      parm[1 + 3*I] = parmInit[1 + 3*I];
      parm[2 + 3*I] = parmInit[2 + 3*I];
    } else {
      parm[0 + 3*I] = actx->deltaT;
      parm[1 + 3*I] = actx->alpha;
      parm[2 + 3*I] = actx->beta;
    }
  }
  return 0;
}

int
_alanPerIteration(alanContext *actx, int iter) {
  char me[]="_alanPerIteration", fname[AIR_STRLEN_MED];
  Nrrd *nslc, *nimg;
  
  if (!(actx->saveInterval || actx->frameInterval)) {
    if (actx->verbose && !(iter % 100)) {
      fprintf(stderr, "%s: iter = %d, averageChange = %g\n",
              me, iter, actx->averageChange);
    }
  }
  if (actx->saveInterval && !(iter % actx->saveInterval)) {
    sprintf(fname, "%06d.nrrd", actx->constFilename ? 0 : iter);
    nrrdSave(fname, actx->_nlev[(iter+1) % 2], NULL);
    fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
            me, iter, actx->averageChange, fname);
  }
  if (actx->frameInterval && !(iter % actx->frameInterval)) {
    nrrdSlice(nslc=nrrdNew(), actx->_nlev[(iter+1) % 2], 0, 0);
    nrrdQuantize(nimg=nrrdNew(), nslc, NULL, 8);
    sprintf(fname, (2 == actx->dim ? "%06d.png" : "%06d.nrrd"),
            actx->constFilename ? 0 : iter);
    nrrdSave(fname, nimg, NULL);
    fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
            me, iter, actx->averageChange, fname);
    nrrdNuke(nslc);
    nrrdNuke(nimg);
  }
  return 0;
}


typedef struct {
  /* these two are genuine input to each worker thread */
  alanContext *actx;  
  int idx;
  /* this is just a convenient place to put airThread (so that alanRun()
     doesn't have to make multiple arrays of per-thread items) */
  airThread *thread;
  /* pointless: a pointer to this is passed to airThreadJoin for its
     return, and currently that will just end up pointing back to this
     struct */
  void *me;
} alanTask;

void *
_alanTuringWorker(void *_task) {
  alan_t *tendata, *ten, react,
    conf, Dxx, Dxy, Dyy, /* Dxz, Dyz, */
    *tpx, *tmx, *tpy, *tmy, /* *tpz, *tmz, */
    *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
    *v[27], lapA, lapB, corrA, corrB, 
    deltaA, deltaB, diffA, diffB, change;
  int dim, iter, stop, startW, endW, idx,
    px, mx, py, my, pz, mz,
    startY, endY, startZ, endZ, sx, sy, sz, x, y, z;
  alanTask *task;

  task = (alanTask *)_task;
  dim = task->actx->dim;
  sx = task->actx->size[0];
  sy = task->actx->size[1];
  sz = (2 == dim ? 1 : task->actx->size[2]);
  parm = (alan_t*)(task->actx->nparm->data);
  diffA = AIR_CAST(alan_t, task->actx->diffA/pow(task->actx->deltaX, dim));
  diffB = AIR_CAST(alan_t, task->actx->diffB/pow(task->actx->deltaX, dim));
  startW = task->idx*sy/task->actx->numThreads;
  endW = (task->idx+1)*sy/task->actx->numThreads;
  tendata = task->actx->nten ? (alan_t *)task->actx->nten->data : NULL;
  react = task->actx->react;

  if (2 == dim) {
    startZ = 0;
    endZ = 1;
    startY = startW;
    endY = endW;
  } else {
    startZ = startW;
    endZ = endW;
    startY = 0;
    endY = sy;
  }

  for (iter = 0; 
       (alanStopNot == task->actx->stop 
        && (0 == task->actx->maxIteration
            || iter < task->actx->maxIteration)); 
       iter++) {

    if (0 == task->idx) {
      task->actx->iter = iter;
      task->actx->nlev = task->actx->_nlev[(iter+1) % 2];
    }
    lev0 = (alan_t*)(task->actx->_nlev[iter % 2]->data);
    lev1 = (alan_t*)(task->actx->_nlev[(iter+1) % 2]->data);
    stop = alanStopNot;
    change = 0;
    conf = 1;  /* if you have no data; this will stay 1 */
    for (z = startZ; z < endZ; z++) {
      if (task->actx->wrap) {
        pz = AIR_MOD(z+1, sz);
        mz = AIR_MOD(z-1, sz);
      } else {
        pz = AIR_MIN(z+1, sz-1);
        mz = AIR_MAX(z-1, 0);
      }
      for (y = startY; y < endY; y++) {
        if (task->actx->wrap) {
          py = AIR_MOD(y+1, sy);
          my = AIR_MOD(y-1, sy);
        } else {
          py = AIR_MIN(y+1, sy-1);
          my = AIR_MAX(y-1, 0);
        }
        for (x = 0; x < sx; x++) {
          if (task->actx->wrap) {
            px = AIR_MOD(x+1, sx);
            mx = AIR_MOD(x-1, sx);
          } else {
            px = AIR_MIN(x+1, sx-1);
            mx = AIR_MAX(x-1, 0);
          }
          idx = x + sx*(y + sy*z);
          A = lev0[0 + 2*idx];
          B = lev0[1 + 2*idx];
          deltaT = parm[0 + 3*idx];
          alpha = parm[1 + 3*idx];
          beta = parm[2 + 3*idx];
          lapA = lapB = corrA = corrB = 0;
          if (2 == dim) {
            /*
            **  0 1 2 ----> X
            **  3 4 5
            **  6 7 8
            **  |
            **  v Y
            */
            v[1] = lev0 + 2*( x + sx*(my));
            v[3] = lev0 + 2*(mx + sx*( y));
            v[5] = lev0 + 2*(px + sx*( y));
            v[7] = lev0 + 2*( x + sx*(py));
            if (tendata) {
              /*
              **  0 1 2    Dxy/2          Dyy        -Dxy/2
              **  3 4 5     Dxx     -2*(Dxx + Dyy)     Dxx
              **  6 7 8   -Dxy/2          Dyy         Dxy/2
              */
              v[0] = lev0 + 2*(mx + sx*(my));
              v[2] = lev0 + 2*(px + sx*(my));
              v[6] = lev0 + 2*(mx + sx*(py));
              v[8] = lev0 + 2*(px + sx*(py));
              ten = tendata + 4*idx;
              conf = AIR_CAST(alan_t, (AIR_CLAMP(0.3, ten[0], 1) - 0.3)/0.7);
              if (conf) {
                Dxx = ten[1];
                Dxy = ten[2];
                Dyy = ten[3];
                lapA = (Dxy*(v[0][0] + v[8][0] - v[2][0] - v[6][0])/2
                        + Dxx*(v[3][0] + v[5][0]) + Dyy*(v[1][0] + v[7][0])
                        - 2*(Dxx + Dyy)*A);
                lapB = (Dxy*(v[0][1] + v[8][1] - v[2][1] - v[6][1])/2
                        + Dxx*(v[3][1] + v[5][1]) + Dyy*(v[1][1] + v[7][1])
                        - 2*(Dxx + Dyy)*B);
                if (!(task->actx->homogAniso)) {
                  tpx = tendata + 4*(px + sx*( y + sy*( z)));
                  tmx = tendata + 4*(mx + sx*( y + sy*( z)));
                  tpy = tendata + 4*( x + sx*(py + sy*( z)));
                  tmy = tendata + 4*( x + sx*(my + sy*( z)));
                  corrA = ((tpx[1]-tmx[1])*(v[5][0]-v[3][0])/4+ /* Dxx,x*A,x */
                           (tpx[2]-tmx[2])*(v[7][0]-v[1][0])/4+ /* Dxy,x*A,y */
                           (tpy[2]-tmy[2])*(v[5][0]-v[3][0])/4+ /* Dxy,y*A,x */
                           (tpy[3]-tmy[3])*(v[7][0]-v[1][0]));  /* Dyy,y*A,y */
                  corrB = ((tpx[1]-tmx[1])*(v[5][1]-v[3][1])/4+ /* Dxx,x*B,x */
                           (tpx[2]-tmx[2])*(v[7][1]-v[1][1])/4+ /* Dxy,x*B,y */
                           (tpy[2]-tmy[2])*(v[5][1]-v[3][1])/4+ /* Dxy,y*B,x */
                           (tpy[3]-tmy[3])*(v[7][1]-v[1][1]));  /* Dyy,y*B,y */
                }
              } else {
                /* no confidence; you diffuse */
                lapA = v[1][0] + v[3][0] + v[5][0] + v[7][0] - 4*A;
                lapB = v[1][1] + v[3][1] + v[5][1] + v[7][1] - 4*B;
              }
            } else {
              /* no data; you diffuse */
              lapA = v[1][0] + v[3][0] + v[5][0] + v[7][0] - 4*A;
              lapB = v[1][1] + v[3][1] + v[5][1] + v[7][1] - 4*B;
            }
          } else {
            /* 3 == dim */
            /*
            **          0   1   2   ---- X
            **        3   4   5
            **      6   7   8
            **    /
            **  /       9  10  11
            ** Y     12  13  14
            **     15  16  17
            **
            **         18  19  20
            **       21  22  23
            **     24  25  26
            **         |
            **         |
            **         Z
            */
            v[ 4] = lev0 + 2*( x + sx*( y + sy*(mz)));
            v[10] = lev0 + 2*( x + sx*(my + sy*( z)));
            v[12] = lev0 + 2*(mx + sx*( y + sy*( z)));
            v[14] = lev0 + 2*(px + sx*( y + sy*( z)));
            v[16] = lev0 + 2*( x + sx*(py + sy*( z)));
            v[22] = lev0 + 2*( x + sx*( y + sy*(pz)));
            if (tendata) {

              if (!(task->actx->homogAniso)) {
                
              }
            } else {
              lapA = (v[ 4][0] + v[10][0] + v[12][0]
                      + v[14][0] + v[16][0] + v[22][0] - 6*A);
              lapB = (v[ 4][1] + v[10][1] + v[12][1]
                      + v[14][1] + v[16][1] + v[22][1] - 6*B);
            }
          }
          
          deltaA = deltaT*(react*conf*task->actx->K*(alpha - A*B) 
                           + diffA*(lapA + corrA));
          if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {
            stop = alanStopDiverged;
          }
          change += AIR_ABS(deltaA);
          deltaB = deltaT*(react*conf*task->actx->K*(A*B - B - beta)
                           + diffB*(lapB + corrB));
          if (!( AIR_EXISTS(deltaA) && AIR_EXISTS(deltaB) )) {
            stop = alanStopNonExist;
          }
          
          A += deltaA;
          B = AIR_MAX(0, B + deltaB);
          lev1[0 + 2*idx] = A;
          lev1[1 + 2*idx] = B; 
        }
      }
    }
    
    /* add change to global sum in a threadsafe way */
    airThreadMutexLock(task->actx->changeMutex);
    task->actx->averageChange += change/(sx*sy*sz);
    task->actx->changeCount += 1;
    if (task->actx->changeCount == task->actx->numThreads) {
      /* I must be the last thread to reach this point; all 
         others must have passed the mutex unlock, and are
         sitting at the barrier */
      if (alanStopNot != stop) {
        /* there was some problem in going from lev0 to lev1, which
           we deal with now by setting actx->stop */
        task->actx->stop = stop;
      } else if (task->actx->averageChange < task->actx->minAverageChange) {
        /* we converged */
        task->actx->stop = alanStopConverged;
      } else {
        /* we keep going */
        _alanPerIteration(task->actx, iter);
        if (task->actx->perIteration) {
          task->actx->perIteration(task->actx, iter);
        }
      }
      task->actx->averageChange = 0;
      task->actx->changeCount = 0;
    }
    airThreadMutexUnlock(task->actx->changeMutex);

    /* force all threads to line up here, once per iteration */
    airThreadBarrierWait(task->actx->iterBarrier);
  }
  
  if (iter == task->actx->maxIteration) {
    /* HEY: all threads will agree on this, right? */
    task->actx->stop = alanStopMaxIteration;
  }
  /* else: the non-alanStopNot value of task->actx->stop made us stop */
  return _task;
}

int
alanRun(alanContext *actx) {
  char me[]="alanRun", err[BIFF_STRLEN];
  int tid, hack=AIR_FALSE;
  alanTask task[ALAN_THREAD_MAX];

  if (_alanCheck(actx)) {
    sprintf(err, "%s: ", me);
    biffAdd(ALAN, err); return 1;
  }
  if (!( actx->_nlev[0] && actx->_nlev[0] )) {
    sprintf(err, "%s: _nlev[0,1] not allocated: "
            "call alanUpdate + alanInit", me);
    biffAdd(ALAN, err); return 1;
  }

  if (!airThreadCapable && 1 == actx->numThreads) {
    hack = airThreadNoopWarning;
    airThreadNoopWarning = AIR_FALSE;
  }
  actx->changeMutex = airThreadMutexNew();
  actx->iterBarrier = airThreadBarrierNew(actx->numThreads);
  actx->averageChange = 0;
  actx->changeCount = 0;
  actx->stop = alanStopNot;
  for (tid=0; tid<actx->numThreads; tid++) {
    task[tid].actx = actx;
    task[tid].idx = tid;
    task[tid].thread = airThreadNew();
    airThreadStart(task[tid].thread, _alanTuringWorker,
                   (void *)&(task[tid]));
  }
  for (tid=0; tid<actx->numThreads; tid++) {
    airThreadJoin(task[tid].thread, &(task[tid].me));
    task[tid].thread = airThreadNix(task[tid].thread);
  }
  actx->iterBarrier = airThreadBarrierNix(actx->iterBarrier);
  actx->changeMutex = airThreadMutexNix(actx->changeMutex);

  if (!airThreadCapable && 1 == actx->numThreads) {
    airThreadNoopWarning = hack;
  }

  /* we assume that someone set actx->stop */
  return 0;
}

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