/*

  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 "nrrd.h"

#include "privateNrrd.h"

/*

  (this was written before airMopSub ... )

learned: if you start using airMop stuff, and you register a free, but

then you free the memory yourself, YOU HAVE GOT TO register a NULL in

place of the original free.  The next malloc may end up at the same

address as what you just freed, and if you want this memory to NOT be

mopped up, then you'll be confused with the original registered free

goes into effect and mops it up for you, even though YOU NEVER

REGISTERED a free for the second malloc.  If you want simple stupid

tools, you have to treat them accordingly (be extremely careful with

fire).

learned: well, duh.  The reason to use:

    for (I=0; I<numOut; I++) {

instead of

    for (I=0; I<=numOut-1; I++) {

is that if numOut is of an unsigned type and has value 0, then these

two will have very different results!

*/

int

nrrdSimpleResample(Nrrd *nout, const Nrrd *nin,

                   const NrrdKernel *kernel, const double *parm,

                   const size_t *samples, const double *scalings) {

  static const char me[]="nrrdSimpleResample";

  NrrdResampleInfo *info;

  int p, np, center;

  unsigned ai;

  }

  }

    double axmin, axmax;

      }

    }

    /* set the min/max for this axis if not already set to something */

      /* HEY: started as copy/paste of body of nrrdAxisInfoMinMaxSet,

         because we wanted to enable const-correctness, and this

         function had previously been setting per-axis min/max in

         *input* when it hasn't been already set */

      double spacing;

        axmin = 0;

        axmin = 0;

      }

      axmin = nin->axis[ai].min;

      axmax = nin->axis[ai].max;

    }

  }

  /* we go with the defaults (enstated by _nrrdResampleInfoInit())

     for all the remaining fields */

  }

}

/*

** _nrrdResampleCheckInfo()

**

** checks validity of given NrrdResampleInfo *info:

** - all required parameters exist

** - both min[d] and max[d] for all axes d

*/

int

_nrrdResampleCheckInfo(const Nrrd *nin, const NrrdResampleInfo *info) {

  static const char me[] = "_nrrdResampleCheckInfo";

  const NrrdKernel *k;

  int center, p, np;

  unsigned int ai, minsmp;

  }

  }

             "%s: asked for boundary padding, but no pad value set\n", me);

  }

    /* we only care about the axes being resampled */

      continue;

    }

               "both been set", me, ai);

    }

    }

                 me, p, np, ai);

      }

    }

               " invalid for %s centering", me, ai,

    }

  }

}

/*

** _nrrdResampleComputePermute()

**

** figures out information related to how the axes in a nrrd are

** permuted during resampling: permute, topRax, botRax, passes, ax[][], sz[][]

*/

void

_nrrdResampleComputePermute(unsigned int permute[],

                            unsigned int ax[NRRD_DIM_MAX][NRRD_DIM_MAX],

                            size_t sz[NRRD_DIM_MAX][NRRD_DIM_MAX],

                            int *topRax,

                            int *botRax,

                            unsigned int *passes,

                            const Nrrd *nin,

                            const NrrdResampleInfo *info) {

  /* char me[]="_nrrdResampleComputePermute"; */

  unsigned int bi, ai, pi;

  /* what are the first (top) and last (bottom) axes being resampled? */

      }

    }

  }

  /* figure out total number of passes needed, and construct the

     permute[] array.  permute[i] = j means that the axis in position

     i of the old array will be in position j of the new one

     (permute[] answers "where do I put this", not "what do I put here").

  */

      do {

    }

  }

    /* none of the kernels was non-NULL */

  }

  /*

  fprintf(stderr, "%s: permute:\n", me);

  for (d=0; d<nin->dim; d++) {

    fprintf(stderr, "   permute[%d] = %d\n", d, permute[ai]);

  }

  */

  /* create array of how the axes will be arranged in each pass ("ax"),

     and create array of how big each axes is in each pass ("sz").

     The input to pass i will have axis layout described in ax[i] and

     axis sizes described in sz[i] */

  }

        /* this is the axis which is getting resampled,

           so the number of samples is potentially changing */

        /* this axis is just a shuffled version of the

           previous axis; no resampling this pass.

           Note: this case also includes axes which aren't

           getting resampled whatsoever */

      }

    }

  }

}

/*

** _nrrdResampleMakeWeightIndex()

**

** _allocate_ and fill the arrays of indices and weights that are

** needed to process all the scanlines along a given axis; also

** be so kind as to set the sampling ratio (<1: downsampling,

** new sample spacing larger, >1: upsampling, new sample spacing smaller)

**

** returns "dotLen", the number of input samples which are required

** for resampling this axis, or 0 if there was an error.  Uses biff.

*/

int

_nrrdResampleMakeWeightIndex(nrrdResample_t **weightP,

                             int **indexP, double *ratioP,

                             const Nrrd *nin, const NrrdResampleInfo *info,

                             unsigned int ai) {

  static const char me[]="_nrrdResampleMakeWeightIndex";

  int sizeIn, sizeOut, center, dotLen, halfLen, *indx, base, idx;

  nrrdResample_t minIn, maxIn, minOut, maxOut, spcIn, spcOut,

    ratio, support, integral, pos, idxD, wght;

  nrrdResample_t *weight;

  int e, i;

  }

                     info->kernel[ai]->support(info->parm[ai]));

                      info->kernel[ai]->integral(info->parm[ai]));

  /*

  fprintf(stderr,

          "!%s(%d): size{In,Out} = %d, %d, support = %f; ratio = %f\n",

          me, d, sizeIn, sizeOut, support, ratio);

  */

    /* if upsampling, we need only as many samples as needed for

       interpolation with the given kernel */

    /* if downsampling, we need to use all the samples covered by

       the stretched out version of the kernel */

    }

  }

  /*

  fprintf(stderr, "!%s(%d): dotLen = %d\n", me, d, dotLen);

  */

  }

  }

  /* calculate sample locations and do first pass on indices */

                   NRRD_POS(center, minOut, maxOut, sizeOut, i));

                    NRRD_IDX(center, minIn, maxIn, sizeIn, pos));

    }

    /* ********

    if (!i) {

      fprintf(stderr, "%s: sample locations:\n", me);

    }

    fprintf(stderr, "%s: %d (sample locations)\n        ", me, i);

    for (e=0; e<dotLen; e++) {

      fprintf(stderr, "%d/%g ", indx[e + dotLen*i], weight[e + dotLen*i]);

    }

    fprintf(stderr, "\n");

    ******** */

  }

  /* figure out what to do with the out-of-range indices */

      case nrrdBoundaryPad:

      case nrrdBoundaryWeight:  /* this will be further handled later */

        idx = sizeIn;

      case nrrdBoundaryBleed:

      case nrrdBoundaryWrap:

      case nrrdBoundaryMirror:

      default:

                 me, info->boundary);

      }

    }

  }

  /* run the sample locations through the chosen kernel.  We play a

     sneaky trick on the kernel parameter 0 in case of downsampling

     to create the blurring of the old index space, but only if !cheap */

  }

  /* ********

  for (i=0; i<sizeOut; i++) {

    fprintf(stderr, "%s: %d (sample weights)\n        ", me, i);

    for (e=0; e<dotLen; e++) {

      fprintf(stderr, "%d/%g ", indx[e + dotLen*i], weight[e + dotLen*i]);

    }

    fprintf(stderr, "\n");

  }

  ******** */

      /* above, we set to sizeIn all the indices that were out of

         range.  We now use that to determine the sum of the weights

         for the indices that were in-range */

        wght = 0;

          }

        }

          }

        }

      }

    }

  } else {

    /* try to remove ripple/grating on downsampling */

    /* if (ratio < 1 && info->renormalize && integral) { */

        wght = 0;

        }

            /* this used to normalize the weights so that they summed

               to integral ("*= integral/wght"), which meant that if

               you use a very truncated Gaussian, then your over-all

               image brightness goes down.  This seems very contrary

               to the whole point of renormalization. */

          }

        }

      }

    }

  }

  /* ********

  fprintf(stderr, "%s: sample weights:\n", me);

  for (i=0; i<sizeOut; i++) {

    fprintf(stderr, "%s: %d\n        ", me, i);

    wght = 0;

    for (e=0; e<dotLen; e++) {

      fprintf(stderr, "%d/%g ", indx[e + dotLen*i], weight[e + dotLen*i]);

      wght += weight[e + dotLen*i];

    }

    fprintf(stderr, " (sum = %g)\n", wght);

  }

  ******** */

  /*

  fprintf(stderr, "!%s: dotLen = %d\n", me, dotLen);

  */

}

/*

******** nrrdSpatialResample()

**

** general-purpose array-resampler: resamples a nrrd of any type

** (except block) and any dimension along any or all of its axes, with

** any combination of up- or down-sampling along the axes, with any

** kernel (specified by callback), with potentially a different kernel

** for each axis.  Whether or not to resample along axis d is

** controlled by the non-NULL-ity of info->kernel[ai].  Where to sample

** on the axis is controlled by info->min[ai] and info->max[ai]; these

** specify a range of "positions" aka "world space" positions, as

** determined by the per-axis min and max of the input nrrd, which must

** be set for every resampled axis.

**

** we cyclically permute those axes being resampled, and never touch

** the position (in axis ordering) of axes along which we are not

** resampling.  This strategy is certainly not the most intelligent

** one possible, but it does mean that the axis along which we're

** currently resampling-- the one along which we'll have to look at

** multiple adjecent samples-- is that resampling axis which is

** currently most contiguous in memory.  It may make sense to precede

** the resampling with an axis permutation which bubbles all the

** resampled axes to the front (most contiguous) end of the axis list,

** and then puts them back in place afterwards, depending on the cost

** of such axis permutation overhead.

*/

int

nrrdSpatialResample(Nrrd *nout, const Nrrd *nin,

                    const NrrdResampleInfo *info) {

  static const char me[]="nrrdSpatialResample", func[]="resample";

    *array[NRRD_DIM_MAX],      /* intermediate copies of the input data

                                  undergoing resampling; we don't need a full-

                                  fledged nrrd for these.  Only about two of

                                  these arrays will be allocated at a time;

                                  intermediate results will be free()d when not

                                  needed */

    *_inVec,                   /* current input vector being resampled;

                                  not necessarily contiguous in memory

                                  (if strideIn != 1) */

    *inVec,                    /* buffer for input vector; contiguous */

    *_outVec;                  /* output vector in context of volume;

                                  never contiguous */

  double tmpF;

    ratios[NRRD_DIM_MAX];      /* record of "ratio" for all resampled axes,

                                  used to compute new spacing in output */

  Nrrd *floatNin;              /* if the input nrrd type is not nrrdResample_t,

                                  then we convert it and keep it here */

    pi,                        /* current pass */

    topLax,

    permute[NRRD_DIM_MAX],     /* how to permute axes of last pass to get

                                  axes for current pass */

    ax[NRRD_DIM_MAX+1][NRRD_DIM_MAX],  /* axis ordering on each pass */

    passes;                    /* # of passes needed to resample all axes */

    topRax,                    /* the lowest index of an axis which is

                                  resampled.  If all axes are being resampled,

                                  then this is 0.  If for some reason the

                                  "x" axis (fastest stride) is not being

                                  resampled, but "y" is, then topRax is 1 */

    botRax,                    /* index of highest axis being resampled */

    typeIn, typeOut;           /* types of input and output of resampling */

                               /* how many samples along each

                                  axis, changing on each pass */

  /* all these variables have to do with the spacing of elements in

     memory for the current pass of resampling, and they (except

     strideIn) are re-set at the beginning of each pass */

    *weight;                  /* sample weights */

    co[NRRD_DIM_MAX+1];

    sizeIn, sizeOut,          /* lengths of input and output vectors */

    dotLen,                   /* # input samples to dot with weights to get

                                 one output sample */

    doRound,                  /* actually do rounding on output: we DO NOT

                                 round when info->round but the output

                                 type is not integral */

    *indx;                    /* dotLen*sizeOut 2D array of input indices */

  size_t

    I,                        /* swiss-army int */

    strideIn,                 /* the stride between samples in the input

                                 "scanline" being resampled */

    strideOut,                /* stride between samples in output

                                 "scanline" from resampling */

    L, LI, LO, numLines,      /* top secret */

    numOut;                   /* # of _samples_, total, in output volume;

                                 this is for allocating the output */

  airArray *mop;              /* for cleaning up */

  }

  }

  }

                              &topRax, &botRax, &passes,

                              nin, info);

  /* not sure where else to put this:

     (want to put it before 0 == passes branch)

     We have to assume some centering when doing resampling, and it would

     be stupid to not record it in the outgoing nrrd, since the value of

     nrrdDefaultCenter could always change. */

    }

  }

    /* actually, no resampling was desired.  Copy input to output,

       but with the clamping that we normally do at the end of resampling */

    }

    }

    /* HEY: need to create textual representation of resampling parameters */

    }

                          NRRD_BASIC_INFO_DATA_BIT

                          | NRRD_BASIC_INFO_TYPE_BIT

                          | NRRD_BASIC_INFO_BLOCKSIZE_BIT

                          | NRRD_BASIC_INFO_DIMENSION_BIT

                          | NRRD_BASIC_INFO_CONTENT_BIT

                          | NRRD_BASIC_INFO_COMMENTS_BIT

                             ? 0

                             : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {

    }

  }

  /* convert input nrrd to nrrdResample_t if necessary */

    }

    floatNin = NULL;

  }

  /* compute strideIn; this is actually the same for every pass

     because (strictly speaking) in every pass we are resampling

     the same axis, and axes with lower indices are constant length */

  strideIn = 1;

  }

  /* printf("%s: strideIn = " _AIR_SIZE_T_CNV "\n", me, strideIn); */

  /* go! */

    /*

    printf("%s: --- pass %d --- \n", me, pi);

    */

    numLines = strideOut = 1;

      }

      }

    }

    /* for the rest of the loop body, d is the original "dimension"

       for the axis being resampled */

    /* printf("%s(%d): numOut = " _AIR_SIZE_T_CNV "\n", me, pi, numOut); */

    /* printf("%s(%d): numLines = " _AIR_SIZE_T_CNV "\n", me, pi, numLines); */

    /* printf("%s(%d): stride: In=%d, Out=%d\n", me, pi,  */

    /*        (int)strideIn, (int)strideOut); */

    /* printf("%s(%d): sizeIn = %d\n", me, pi, sizeIn); */

    /* printf("%s(%d): sizeOut = %d\n", me, pi, sizeOut); */

    /* we can free the input to the previous pass

       (if its not the given data) */

          /*

          printf("%s: pi %d: freeing array[0]\n", me, pi);

          */

        }

      } else {

        /*

        printf("%s: pi %d: freeing array[%d]\n", me, pi, pi-1);

        */

      }

    }

    /* allocate output volume */

    }

    /*

    printf("%s: allocated array[%d]\n", me, pi+1);

    */

    /* allocate contiguous input scanline buffer, we alloc one more

       than needed to provide a place for the pad value.  That is, in

       fact, the over-riding reason to copy a scanline to a local

       array: so that there is a simple consistent (non-branchy) way

       to incorporate the pad values */

                                          nin, info, ai);

               me);

    }

    /* the skinny: resample all the scanlines */

    _outVec = array[pi+1];

      /* calculate the index to get to input and output scanlines,

         according the coordinates of the start of the scanline */

      /* read input scanline into contiguous array */

      }

      /* do the weighting */

        tmpF = 0.0;

        /*

        fprintf(stderr, "%s: i = %d (tmpF=0)\n", me, (int)i);

        */

          /*

          fprintf(stderr, "  tmpF += %g*%g == %g\n",

                  inVec[indx[s + dotLen*i]], weight[s + dotLen*i], tmpF);

          */

        }

        /*

        fprintf(stderr, "--> out[%d] = %g\n",

                i*strideOut, _outVec[i*strideOut]);

        */

      }

      /* update the coordinates for the scanline starts.  We don't

         use the usual NRRD_COORD macros because we're subject to

         the unusual constraint that ci[topRax] and co[permute[topRax]]

         must stay exactly zero */

      e = topLax;

      }

    }

    /* pass-specific clean up */

  }

  /* clean up second-to-last array and scanline buffers */

    /*

    printf("%s: now freeing array[%d]\n", me, passes-1);

    */

  }

  /* create output nrrd and set axis info */

  }

                   (NRRD_AXIS_INFO_SIZE_BIT

                    | NRRD_AXIS_INFO_MIN_BIT

                    | NRRD_AXIS_INFO_MAX_BIT

                    | NRRD_AXIS_INFO_SPACING_BIT

                    | NRRD_AXIS_INFO_SPACEDIRECTION_BIT  /* see below */

                    | NRRD_AXIS_INFO_THICKNESS_BIT

                    | NRRD_AXIS_INFO_KIND_BIT));

      /* we do resample this axis */

      /* no way to usefully update thickness: we could be doing blurring

         but maintaining the number of samples: thickness increases, or

         we could be downsampling, in which the relationship between the

         sampled and the skipped regions of space becomes complicated:

         no single scalar can represent it, or we could be upsampling,

         in which the notion of "skip" could be rendered meaningless */

      /*

        HEY: this is currently a bug: all this code was written long

        before there were space directions, so min/max are always

        set, regardless of whethere there are incoming space directions

        which then disallows output space directions on the same axes

      _nrrdSpaceVecScale(nout->axis[ai].spaceDirection,

                         1.0/ratios[ai], nin->axis[ai].spaceDirection);

      */

      /* this axis remains untouched */

    }

  }

  /* HEY: need to create textual representation of resampling parameters */

  }

  /* copy the resampling final result into the output nrrd, maybe

     rounding as we go to make sure that 254.9999 is saved as 255

     in uchar output, and maybe clamping as we go to insure that

     integral results don't have unexpected wrap-around. */

              "rounding of %s output type due to int-based implementation "

    }

    doRound = AIR_FALSE;

  }

    }

    }

  }

                        NRRD_BASIC_INFO_DATA_BIT

                        | NRRD_BASIC_INFO_TYPE_BIT

                        | NRRD_BASIC_INFO_BLOCKSIZE_BIT

                        | NRRD_BASIC_INFO_DIMENSION_BIT

                        | NRRD_BASIC_INFO_CONTENT_BIT

                        | NRRD_BASIC_INFO_COMMENTS_BIT

                           ? 0

                           : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {

  }

  /* enough already */

}