/*

  Teem: Tools to process and visualize scientific data and images             .

  Copyright (C) 2013, 2012, 2011, 2010, 2009  University of Chicago

  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

*/

#include "gage.h"

#include "privateGage.h"

typedef union {

  void **vd;

  gagePerVolume ***pvl;

} perVolumeUnion;

/*

******** gageContextNew()

**

** doesn't use biff

*/

gageContext *

gageContextNew() {

  gageContext *ctx;

  perVolumeUnion pvu;

  int ii;

    }

                              sizeof(gagePerVolume*),

                              GAGE_PERVOLUME_ARR_INCR);

    }

    }

    }

}

/*

******** gageContextCopy()

**

** gives you a new context, which behaves the same as the given context,

** with newly allocated pervolumes attached.  With the avoidance of

** padding to create a private copy of the volume, the gageContext is

** light-weight enough that there is no reason that this function can't

** return an independent and fully functioning copy of the context (whereas

** before you weren't allowed to do anything but gageProbe() on the

** copied context).

*/

gageContext * /*Teem: biff if (!ret) */

gageContextCopy(gageContext *ctx) {

  static const char me[]="gageContextCopy";

  gageContext *ntx;

  unsigned int fd, pvlIdx;

  perVolumeUnion pvu;

  int ki;

  }

  /* we should probably restrict ourselves to gage API calls, but given the

     constant state of gage construction, this seems much simpler.

     Pointers are fixed below */

  }

                            sizeof(gagePerVolume*),

                            GAGE_PERVOLUME_ARR_INCR);

  }

    }

  }

    }

    }

  } else {

  }

             me, fd);

  }

  /* the content of the offset array needs to be copied because

     it won't be refilled simply by calls to gageProbe() */

  /* make sure gageProbe() has to refill caches */

/*

******** gageContextNix()

**

** responsible for freeing and clearing up everything hanging off a

** context so that things can be returned to the way they were prior

** to gageContextNew().

**

** does not use biff

*/

gageContext *

gageContextNix(gageContext *ctx) {

  /* static const char me[]="gageContextNix"; */

  unsigned int pvlIdx;

      /* no point in doing a detach, the whole context is going bye-bye */

    }

}

/*

******** gageKernelSet()

**

** sets one kernel in a gageContext; but the value of this function

** is all the error checking it does.

**

** Refers to ctx->checkIntegrals and acts appropriately.

**

** Does use biff.

*/

int

gageKernelSet(gageContext *ctx,

              int which, const NrrdKernel *k, const double *kparm) {

  static const char me[]="gageKernelSet";

  int numParm;

  double support, integral;

  }

             which, gageKernelUnknown+1, gageKernelLast-1);

  }

  }

             me, numParm, 0, NRRD_KERNEL_PARMS_NUM);

  }

  }

                 me, integral);

      }

    } else {

      /* its a derivative, so integral must be near zero */

        return 1;

      }

    }

  }

  /* okay, enough enough, go set the kernel */

/*

******** gageKernelReset()

**

** reset kernels (including the stack ksp) and parameters.

*/

void

gageKernelReset(gageContext *ctx) {

  /* static const char me[]="gageKernelReset"; */

  int i;

    }

  return;

/*

******** gageParmSet()

**

** for setting the boolean-ish flags in the context in a safe and

** intelligent manner, since changing some of them can have many

** consequences

*/

void

gageParmSet(gageContext *ctx, int which, double val) {

  static const char me[]="gageParmSet";

  unsigned int pvlIdx;

  case gageParmVerbose:

    }

                ctx->pvl[pvlIdx]->verbose);

      }

    }

    break;

  case gageParmRenormalize:

    /* we have to make sure that any existing filter weights

       are not re-used; because gageUpdage() is not called mid-probing,

       we don't use the flag machinery.  Instead we just invalidate

       the last known fractional probe locations */

  case gageParmCheckIntegrals:

    /* no flags to set, simply affects future calls to gageKernelSet() */

  case gageParmK3Pack:

  case gageParmGradMagCurvMin:

    /* no flag to set, simply affects future calls to gageProbe() */

  case gageParmCurvNormalSide:

    /* no flag to set, simply affects future calls to gageProbe() */

  case gageParmKernelIntegralNearZero:

    /* no flag to set, simply affects future calls to gageKernelSet() */

  case gageParmDefaultCenter:

    /* no flag to set, I guess, although the value here effects the

       action of _gageShapeSet when called by gagePerVolumeAttach . . . */

  case gageParmStackUse:

    /* no flag to set, right? simply affects future calls to gageProbe()? */

    /* HEY: no? because if you're turning on the stack behavior, you now

       should be doing the error checking to make sure that all the pvls

       have the same kind!  This should be caught by gageUpdate(), which is

       supposed to be called after changing anything, prior to gageProbe() */

  case gageParmStackNormalizeRecon:

  case gageParmStackNormalizeDeriv:

  case gageParmStackNormalizeDerivBias:

  case gageParmOrientationFromSpacing:

    /* affects future calls to _gageShapeSet */

  case gageParmGenerateErrStr:

  case gageParmTwoDimZeroZ:

  default:

  }

  return;

/*

******** gagePerVolumeIsAttached()

**

*/

int

gagePerVolumeIsAttached(const gageContext *ctx, const gagePerVolume *pvl) {

  int ret;

  unsigned int pvlIdx;

  ret = AIR_FALSE;

      ret = AIR_TRUE;

    }

  }

}

/*

******** gagePerVolumeAttach()

**

** attaches a pervolume to a context, which actually involves

** very little work

*/

int

gagePerVolumeAttach(gageContext *ctx, gagePerVolume *pvl) {

  static const char me[]="gagePerVolumeAttach";

  gageShape *shape;

  unsigned int newidx;

  }

  }

    /* the volume "shape" is context state that we set now, because unlike

       everything else (handled by gageUpdate()), it does not effect

       the kind or amount of padding done */

    }

    /* have to check to that new pvl matches first one.  Since all

       attached pvls were at some point the "new" one, they all

       should match each other */

    }

    }

  }

  /* here we go */

  }

/*

******** gagePerVolumeDetach()

**

** detaches a pervolume from a context, but does nothing else

** with the pervolume; caller may want to call gagePerVolumeNix

** if this pervolume will no longer be used

*/

int

gagePerVolumeDetach(gageContext *ctx, gagePerVolume *pvl) {

  static const char me[]="gagePerVolumeDetach";

  unsigned int pvlIdx, foundIdx=0;

  }

  }

      foundIdx = pvlIdx;

    }

  }

  }

    /* leave things the way that they started */

  }

}

/*

** gageIv3Fill()

**

** based on ctx's shape and radius, and the (xi,yi,zi) determined from

** the probe location, fills the iv3 cache in the given pervolume

**

** This function is a bottleneck for so many things, so forcing off

** the verbose comments seems like one way of trying to speed it up.

** However, temporarily if-def'ing out unused branches of the

** "switch(pvl->kind->valLen)", and #define'ing fddd to 64 (for 4x4x4

** neighborhoods) did not noticeably speed anything up.

**

*/

void

gageIv3Fill(gageContext *ctx, gagePerVolume *pvl) {

  static const char me[]="gageIv3Fill";

  int lx, ly, lz, hx, hy, hz, _xx, _yy, _zz;

  unsigned int xx, yy, zz,

    fr, cacheIdx, dataIdx, fddd;

  unsigned int sx, sy, sz;

  char *data, *here;

  unsigned int tup;

  /* idx[0]-1: see Thu Jan 14 comment in filter.c */

            sx, sy, sz, fr);

            lx, ly, lz, hx, hy, hz, fddd);

  }

    /* all the samples we need are inside the existing volume */

    }

              "%s:     fd = %d; coord = (%u,%u,%u) --> dataIdx = %d\n",

              me, sx, sy, sz, me, 2*fr,

              dataIdx);

              "%d,%d,%d,%d,%d,%d,%d,%d\n",

    }

    case 1:

      }

      break;

      /* NOTE: the tuple axis is being shifted from the fastest to

         the slowest axis, to anticipate component-wise filtering

         operations */

    case 3:

      }

      break;

    case 7:

      /* this might come in handy for tenGage . . . */

      }

      break;

    default:

        }

      }

      break;

    }

    unsigned int edgeNum, dataStride, valLen;

    /* the query requires samples which don't actually lie

       within the volume- more care has to be taken */

    double *iv3;

    cacheIdx = 0;

    edgeNum = 0;

      /* working with 2D images is now common enough that we try to make

         simplifications for that (HEY copy and paste). We first do the

         needed lup()s to fill first slice of iv3 ... */

          }

        }

      }

      /* ... and then copy from first slice into rest of iv3 */

        unsigned int z0ci;

        z0ci = 0;

            }

          }

        }

      }

      /* we would have been outside for all the other z slices besides

         z=0, but don't report this if the whole point is to pretend

         that we're working with 2D data */

      }

    } else {

      /* sz > 1 */

                      _xx, _yy, _zz, xx, yy, zz);

                      dataIdx, data, here);

            }

                        cacheIdx, fddd, tup, cacheIdx + fddd*tup,

                        iv3[cacheIdx + fddd*tup]);

              }

            }

          }

        }

      }

    }

  }

  }

  return;

/*

** _gageProbe

**

** how to do probing.  (x,y,z) position is *index space* position.

** Note, however, that derivatives (gradients and hessians) will

** effectively be computed in *world space*.

**

** doesn't actually do much more than call callbacks in the gageKind

** structs of the attached pervolumes

**

** NOTE: the stack filter weights are (like the spatial filter weights)

** computed inside _gageLocationSet()

*/

int

_gageProbe(gageContext *ctx, double _xi, double _yi, double _zi, double _si) {

  static const char me[]="_gageProbe";

  unsigned int oldIdx[4], oldNnz=0, pvlIdx;

  int idxChanged;

  }

            _xi, _yi, _zi, _si);

  }

    /* we're outside the volume; leave ctx->errNum and ctx->errStr set;

       as they have just been set by _gageLocationSet() */

    /* GLK had added but not checked in the following line;

       the logic of this has to be studied further */

    /* ctx->edgeFrac = 0.666; */

  }

  /* if necessary, refill the iv3 cache */

    /* this is subtle (and the source of a difficult bug): even if

       point.idx[3] has not changed, you can still have a change in

       which of the stackFw[] are non-zero, which in turn determines

       which iv3s have to be refilled.  For example, changing _si

       from 0.0 to 0.1, using tent or hermite reconstruction, will

       newly require pvl[1]'s iv3 to be refilled.  To catch this kind

       of situation, we could keep a list of which iv3s are active and

       look for changes in that, or, we could just look for changes in

       point.idx[3] AND changes in stackFwNonZeroNum */

  }

            me, oldIdx[0], oldIdx[1], oldIdx[2], oldIdx[3],

  }

        }

      }

    } else {

        /* note that we only fill the cache for the stack samples that

           have a non-zero weight. HEY, however, it would be nice to

           only refill the iv3 that we have to, based on the change in

           scale, instead of refilling all of them in the support of

           the stack recon */

                    pvlIdx, ctx->stackFw[pvlIdx]);

          }

                    pvlIdx, ctx->stackFw[pvlIdx]);

          }

        }

      }

    }

  }

    unsigned int baseIdx, vi;

                "coords = %u,%u,%u:\n", me, vi,

      }

    }

              "coords = %u,%u,%u:\n", me,

    }

                "coords = %u,%u,%u:\n", me, pvlIdx, ctx->pvlNum,

      }

    }

  }

  }

/*

******** gageProbe()

**

** bummer: the non-stack gageProbe function is now just a wrapper

** around the stack-based gageProbe

*/

int

gageProbe(gageContext *ctx, double xi, double yi, double zi) {

}

int

_gageProbeSpace(gageContext *ctx, double xx, double yy, double zz, double ss,

               int indexSpace, int clamp) {

  static const char me[]="_gageProbeSpace";

  unsigned int *size;

  double xi, yi, zi, si;

  }

    xi = xx;

    yi = yy;

    zi = zz;

      si = ss;

      si = 0;

    }

              xi, yi, zi);

    }

  } else {

    /* have to convert from world to index.  NOTE: the [4]s here are

       for homogeneous coordinates, not for anything stack-related */

    double icoord[4]; double wcoord[4];

    ELL_4V_SET(wcoord, xx, yy, zz, 1);

    xi = icoord[0];

    yi = icoord[1];

    zi = icoord[2];

      unsigned int sidx;

      /* HEY: this is a stupid linear search! */

        /* we'll extrapolate from stackPos[0] and [1]. um, actually the

         extrapolation is overkill because we're either going to clamp

         out-of-range scale index positions, or they'll cause a

         gageErrStackBounds error downstream */

        sidx = 0;

        /* extrapolate from stackPos[ctx->pvlNum-3] and [ctx->pvlNum-2];

           gageStackPerVolumeAttach ensures that we there are at least

           two blurrings pvls and one base pvl */

            break;

          }

        }

          }

        }

      }

                      sidx, sidx+1);

                ctx->stackPos[sidx], ss, ctx->stackPos[sidx+1],

                sidx, sidx+1, si);

      }

      si = 0;

    }

              xx, yy, zz, xi, yi, zi);

    }

    }

    }

              xi, yi, zi);

    }

  }

int

gageProbeSpace(gageContext *ctx, double xx, double yy, double zz,

               int indexSpace, int clamp) {

}