/*=============================================================================
                                 pbmclean
===============================================================================
  Pixel cleaner:   Remove pixel if less than N connected identical neighbors

=============================================================================*/
#include <assert.h>
#include <stdio.h>
#include <stdbool.h>

#include "pm_c_util.h"
#include "mallocvar.h"
#include "shhopt.h"
#include "pbm.h"

struct CmdlineInfo {
    /* All the information the user supplied in the command line,
       in a form easy for the program to use.
    */
    const char * inputFileName;  /* File name of input file */
    bool flipWhite;
    bool flipBlack;
    unsigned int minneighbors;
    unsigned int verbose;
    unsigned int extended;
};



static void
parseCommandLine(int argc, const char ** argv,
                 struct CmdlineInfo *cmdlineP) {
/*----------------------------------------------------------------------------
   Note that the file spec array we return is stored in the storage that
   was passed to us as the argv array.
-----------------------------------------------------------------------------*/
    optStruct3 opt;  /* set by OPTENT3 */
    optEntry * option_def;
    unsigned int option_def_index;

    unsigned int black, white;
    unsigned int minneighborsSpec;

    MALLOCARRAY(option_def, 100);

    option_def_index = 0;   /* incremented by OPTENT3 */
    OPTENT3(0,   "verbose",          OPT_FLAG, NULL, &cmdlineP->verbose, 0);
    OPTENT3(0,   "black",            OPT_FLAG, NULL, &black, 0);
    OPTENT3(0,   "white",            OPT_FLAG, NULL, &white, 0);
    OPTENT3(0,   "minneighbors",     OPT_UINT, &cmdlineP->minneighbors,
            &minneighborsSpec, 0);
    OPTENT3(0,   "extended",         OPT_FLAG, NULL, &cmdlineP->extended, 0);

    opt.opt_table = option_def;
    opt.short_allowed = false;  /* We have no short (old-fashioned) options */
    opt.allowNegNum = true;  /* We sort of allow negative numbers as parms */

    pm_optParseOptions3(&argc, (char **)argv, opt, sizeof(opt), 0);
        /* Uses and sets argc, argv, and some of *cmdlineP and others. */

    free(option_def);

    if (cmdlineP->extended) {
        if (black && white)
            pm_error("With -extended, you cannot specify both "
                     "-black and -white");
        else if (!black & !white) {
            cmdlineP->flipBlack = true;
            cmdlineP->flipWhite = false;
        } else {
            cmdlineP->flipBlack = !!black;
            cmdlineP->flipWhite = !!white;
        }
    } else {
        if (!black && !white) {
            cmdlineP->flipBlack = TRUE;
            cmdlineP->flipWhite = TRUE;
        } else {
            cmdlineP->flipBlack = !!black;
            cmdlineP->flipWhite = !!white;
        }
    }
    if (!minneighborsSpec) {
        /* Now we do a sleazy tour through the parameters to see if
           one is -N where N is a positive integer.  That's for
           backward compatibility, since Pbmclean used to have
           unconventional syntax where a -N option was used instead of
           the current -minneighbors option.  The only reason -N didn't
           get processed by pm_pm_optParseOptions3() is that it looked
           like a negative number parameter instead of an option.
           If we find a -N, we make like it was a -minneighbors=N option.
        */
        int i;
        bool foundNegative;

        cmdlineP->minneighbors = 1;  /* default */
        foundNegative = FALSE;

        for (i = 1; i < argc; ++i) {
            if (foundNegative)
                argv[i-1] = argv[i];
            else {
                if (atoi(argv[i]) < 0) {
                    cmdlineP->minneighbors = - atoi(argv[i]);
                    foundNegative = TRUE;
                }
            }
        }
        if (foundNegative)
            --argc;
    }

    if (argc-1 < 1)
        cmdlineP->inputFileName = "-";
    else if (argc-1 == 1)
        cmdlineP->inputFileName = argv[1];
    else
        pm_error("You specified too many arguments (%d).  The only "
                 "argument is the optional input file specification.",
                 argc-1);
}



static unsigned int
bitpop8(unsigned char const x) {
/*----------------------------------------------------------------------------
   Return the number of 1 bits in 'x'
-----------------------------------------------------------------------------*/
static unsigned int const p[256] = {
    0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4,
    1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
    1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
    1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
    2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
    3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
    3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
    4, 5, 5, 6, 5, 6, 6, 7, 5, 6, 6, 7, 6, 7, 7, 8 };

    return p[x];
}



static unsigned int
bitpop24(uint32_t const w){
/*----------------------------------------------------------------------------
   Return the number of 1 bits in the lower 24 bits of 'w'
   A GCC builtin, __builtin_popcountl(), is available, but it
   emits a call to an external function instead of inlining (GCC 4.4.3).

   This table lookup method is faster.
-----------------------------------------------------------------------------*/
    return (bitpop8((w >> 16) & 0xff) +
            bitpop8((w >>  8) & 0xff) +
            bitpop8((w >>  0) & 0xff));
}



/*----------------------------------------------------------------------------
Fast algorithm for counting friendly neighbor pixels

In this program both input and output rows are in raw (packed) PBM format.

We handle input rows in groups of three, named "prevrow", "thisrow",
"nextrow" and scan from left to right.  At every byte boundary, 10 bits
are read from each of the three rows and placed into a temporary storage
we call "sample".

prevrow: ... ... _______M NNNNNNNN O_______ ...
thisrow: ... ... _______W cCCCCCCC E_______ ...
nextrow: ... ... _______R SSSSSSSS T_______ ...

sample : xxMNNNNNNNNOWcCCCCCCCERSSSSSSST

We count bits by taking the logical and of "sample" and a bit-mask called
"selection", and feeding the result to a table-based bit-population counter.

For example, the bits around the leftmost bit of the byte ("c") are selected
like this:

sample :       xxMNNNNNNNNOWcCCCCCCCERSSSSSSST
selection: & | __111_______1_1_______111______

(In the actual process, "sample" is shifted right and anded against a
 constant "selection" mask.)

The above reports one bits.  For the zero (white) bits we replace "sample"
with its inverse.

If the friendly neighbor count is below a threshold (default 1), we record
that as a one bit in "flipmask".  Bits are flipped in units of eight
and written to outrow at the byte boundary.
-----------------------------------------------------------------------------*/



static unsigned int
likeNeighbors(uint32_t     const blackSample,
              unsigned int const offset) {

    bool const thispoint = ( blackSample >> (18-offset) ) & 0x01;
    uint32_t const sample = (thispoint == PBM_BLACK )
                          ?   blackSample
                          : ~ blackSample ;
    uint32_t const selection = 0x701407;

    return (bitpop24((sample >> (7-offset)) & selection));
}



static uint32_t
setSample(const bit *  const prevrow,
          const bit *  const thisrow,
          const bit *  const nextrow,
          unsigned int const col){

    int const col8 = col/8;

    uint32_t sample;

    sample =
        ((prevrow[col8 - 1]       )  << 29) |
        ((prevrow[col8]           )  << 21) |
        ((prevrow[col8 + 1] & 0x80)  << 13) |
        ((thisrow[col8 - 1] & 0x01)  << 19) |
        ((thisrow[col8]           )  << 11) |
        ((thisrow[col8 + 1] & 0x80)  <<  3) |
        ((nextrow[col8 - 1] & 0x01)  <<  9) |
        ((nextrow[col8]           )  <<  1) |
        ((nextrow[col8 + 1] & 0x80)  >>  7);

    return sample;
}



static unsigned char
setTestmask(unsigned char const whiteTestmask,
            bool          const testWhite,
            bool          const testBlack) {
/* -----------------------------------------------------------------------
  Make a byte pattern of what bits should be tested within a given "thisrow"
  (current inrow) byte.  0 means test, 1 means skip.
-------------------------------------------------------------------------- */
    if (testWhite == testBlack) {
        assert(testWhite); assert(testBlack);
        return 0x00;
    } else if (testWhite == TRUE) {
        assert(!testBlack);
        return whiteTestmask;
    } else
        return ~whiteTestmask;
}



static void
cleanrow(const bit *    const prevrow,
         const bit *    const thisrow,
         const bit *    const nextrow,
         bit *          const outrow,
         unsigned int   const cols,
         unsigned int   const threshold,
         bool           const flipWhite,
         bool           const flipBlack,
         unsigned int * const nFlippedP) {
/* ----------------------------------------------------------------------
  Work through row, scanning for bits that require flipping, and write
  the results to 'outrow'.

  Returns the number of bits flipped within this one row as *nFlippedP.
-------------------------------------------------------------------------*/
    uint32_t sample;
    unsigned char testmask;
    unsigned char flipmask;
    unsigned int col;
    unsigned int nFlipped;

    flipmask = 0x00;  /* initial value */
    nFlipped = 0;     /* initial value */

    for (col=0 ; col < cols ; ++col) {
        unsigned int const col8 = col / 8;
        unsigned int const offset = col % 8;

        if (offset == 0) {
            if (flipmask != 0x00) {
                /* Some bits have to be flipped */
                outrow[col8 -1] = thisrow [col8 -1] ^ flipmask;
                nFlipped += bitpop8(flipmask);
                flipmask = 0x00;
            } else if (col8 > 0)
                outrow[col8 -1] = thisrow [col8 -1];

            sample = setSample(prevrow, thisrow, nextrow, col);
            testmask = setTestmask(thisrow[col8], flipWhite, flipBlack);
        }

        if (((testmask << offset) & 0x80 ) ==0) {
            if (likeNeighbors(sample, offset ) < threshold)
                flipmask |= (0x80 >> offset);
        }
    }

    {
        /* Write out last byte */
        unsigned int const col8Last = pbm_packed_bytes(cols) -1;

        if (flipmask != 0x00) {
            outrow[col8Last] = thisrow[col8Last] ^ flipmask;
            nFlipped += bitpop8(flipmask);
        } else
            outrow[col8Last] = thisrow[col8Last];
    }
    *nFlippedP = nFlipped;
}



static void
setupInputBuffers(FILE *       const ifP,
                  unsigned int const cols,
                  int          const format,
                  bit ***      const bufferP,
                  bit **       const edgeRowP,
                  bit **       const thisRowP,
                  bit **       const nextRowP) {
/*----------------------------------------------------------------------------
  Initialize input buffers.
  We add a margin of 8 bits each on the left and right of the rows.

  On the top and bottom of the image we place an imaginary blank row
  ("edgerow") to facilitate the process.
-----------------------------------------------------------------------------*/
    bit ** const buffer  = pbm_allocarray_packed(cols+16, 3);
    bit *  const edgeRow = pbm_allocrow_packed(cols+16);

    bit * nextRow;
    unsigned int i;

    for (i = 0; i < pbm_packed_bytes(cols+16); ++i)
        edgeRow[i] = 0x00;

    for (i = 0; i < 3; ++i) {
        /* Add blank (all white) bytes beside the edges */
        buffer[i][0] = buffer[i][ pbm_packed_bytes( cols +16 ) - 1] = 0x00;
    }
    nextRow = &buffer[0][1];

    /* Read the top line into nextrow and clean the right end. */

    pbm_readpbmrow_packed(ifP, nextRow, cols, format);

    pbm_cleanrowend_packed(nextRow, cols);

    *bufferP  = buffer;
    *edgeRowP = edgeRow;
    *thisRowP = &edgeRow[1];
    *nextRowP = nextRow;
}



static void
cleanSimple(FILE *             const ifP,
            FILE *             const ofP,
            struct CmdlineInfo const cmdline,
            double *           const nFlippedP) {
/*----------------------------------------------------------------------------
   Do the traditional clean where you look only at the immediate neighboring
   pixels of a subject pixel to determine whether to erase that pixel.
-----------------------------------------------------------------------------*/
    bit ** buffer;
        /* The rows of the input relevant to our current processing:
           the current row and the one above and below it.
        */
    bit * edgeRow;
        /* A blank (all white) row.  Constant */
    bit * prevRow;
    bit * thisRow;
    bit * nextRow;
    bit * outRow;
    int cols, rows, format;
    unsigned int row;

    pbm_readpbminit(ifP, &cols, &rows, &format);

    setupInputBuffers(ifP, cols, format, &buffer, &edgeRow,
                      &thisRow, &nextRow);

    outRow = pbm_allocrow(cols);

    pbm_writepbminit(ofP, cols, rows, 0) ;

    *nFlippedP = 0;  /* none flipped yet */

    for (row = 0; row < rows; ++row) {
        unsigned int nFlipped;

        prevRow = thisRow;  /* Slide up the input row window */
        thisRow = nextRow;
        if (row < rows -1){
            nextRow = &buffer[(row+1)%3][1];
            /* We take the address directly instead of shuffling the rows
               with the help of a temporary.  This provision is for proper
               handling of the initial edgerow.
            */
            pbm_readpbmrow_packed(ifP, nextRow, cols, format);
            pbm_cleanrowend_packed(nextRow, cols);

        } else  /* Bottom of image.  */
            nextRow = &edgeRow[1];

        cleanrow(prevRow, thisRow, nextRow, outRow, cols, cmdline.minneighbors,
                 cmdline.flipWhite, cmdline.flipBlack, &nFlipped);

        *nFlippedP += nFlipped;

        pbm_writepbmrow_packed(ofP, outRow, cols, 0) ;
    }

    pbm_freearray(buffer, 3);
    pbm_freerow(edgeRow);
    pbm_freerow(outRow);
}



struct PixQueueElt {
    struct PixQueueElt * nextP;
    pm_pixelcoord        coord;
};

typedef struct {
/*----------------------------------------------------------------------------
   A queue of pixel locations.
-----------------------------------------------------------------------------*/
    unsigned int size;

    struct PixQueueElt * headP;
    struct PixQueueElt * tailP;
} PixQueue;



static void
pixQueue_init(PixQueue * const queueP) {

    queueP->size = 0;
    queueP->headP = NULL;
    queueP->tailP = NULL;
}



static unsigned int
pixQueue_size(PixQueue * const queueP) {

    return queueP->size;
}



static bool
pixQueue_isEmpty(PixQueue * const queueP) {

    return !queueP->headP;
}



static void
pixQueue_push(PixQueue *    const queueP,
              pm_pixelcoord const newValue) {

    struct PixQueueElt * newEltP;

    MALLOCVAR(newEltP);

    if (!newEltP)
        pm_error("Out of memory putting a pixel on a queue");

    newEltP->coord = newValue;

    newEltP->nextP = NULL;
    if (queueP->tailP)
        queueP->tailP->nextP = newEltP;

    queueP->tailP = newEltP;

    if (!queueP->headP)
        queueP->headP = newEltP;

    ++queueP->size;
}



static pm_pixelcoord
pixQueue_pop(PixQueue * const queueP) {
/*----------------------------------------------------------------------------
   Pop and return the pixel location at the head of queue *queueP.
-----------------------------------------------------------------------------*/
    struct PixQueueElt * const newHeadP = queueP->headP->nextP;

    pm_pixelcoord retval;

    assert(queueP->headP);

    retval = queueP->headP->coord;

    if (queueP->tailP == queueP->headP)
        queueP->tailP = NULL;

    free(queueP->headP);

    queueP->headP = newHeadP;

    --queueP->size;

    return retval;
}



static void
pixQueue_term(PixQueue * const queueP) {

    struct PixQueueElt * p;
    struct PixQueueElt * nextP;

    for (p = queueP->headP; p; p = nextP) {
        nextP = p->nextP;
        free(p);
    }
}



static void
queueNeighbors(pm_pixelcoord const center,
               bit **        const pixels,
               unsigned int  const cols,
               unsigned int  const rows,
               bool **       const visited,
               PixQueue *    const queueP) {
/*----------------------------------------------------------------------------
   Add to queue *queueP all the pixels in 'pixels' that touch 'center' and are
   the same color as 'center'.

   But ignore pixels that 'visited' says have already been queued and
   mark everything we queue as visited.
-----------------------------------------------------------------------------*/
    bit const blobColor = pixels[center.row][center.col];

    int row;
        /* Row number of a neighbor; might be off the canvas; even negative */

    /* Note that we consider the center pixel here, but it has necessarily
       already been visited, so we don't queue it.
    */

    for (row = (int)center.row - 1; row <= (int)center.row + 1; ++row) {
        int col;  /* Analogous to 'row' */

        for (col = (int)center.col - 1; col <= (int)center.col + 1; ++col) {
            if (row < 0 || row >= rows || col < 0 || col >= cols) {
                /* It's off the canvas; nothing to queue */
            } else {
                if (pixels[row][col] == blobColor) {
                    if (visited[row][col]) {
                        /* We've already explored this one */
                    } else {
                        /* Queue it! */
                        pm_pixelcoord neighbor;
                        neighbor.row = row;
                        neighbor.col = col;
                        pixQueue_push(queueP, neighbor);
                        visited[row][col] = true;
                    }
                }
            }
        }
    }
}



static void
setColor(PixQueue * const blobP,
         bit **     const pixels,
         bit        const newColor) {
/*----------------------------------------------------------------------------
   Change all the pixels in (blobP) to 'newColor'.  More precisely, change
   the pixels in 'pixels' that are listed in *blobP.
-----------------------------------------------------------------------------*/
    while (!pixQueue_isEmpty(blobP)) {
        pm_pixelcoord const thisPix = pixQueue_pop(blobP);

        pixels[thisPix.row][thisPix.col] = newColor;
    }
}



static void
processBlob(pm_pixelcoord const start,
            bit **        const pixels,
            unsigned int  const cols,
            unsigned int  const rows,
            unsigned int  const trivialSize,
            bool **       const visited,
            double *      const nFlippedP) {
/*----------------------------------------------------------------------------
   Process the blob that contains the pixel at 'start'.

   That pixel is part of a blob.  A blob is a maximal set of contiguous
   pixels of the same color.

   None of the blob is marked visited in visited[][].

   If the blob has fewer than 'trivialSize' pixels, erase it (flip its color).

   Update visited[][] to flag all pixels of the blob as visited.

   Return as *nFlippedP how many pixels we flipped (i.e. either zero or the
   size of the blob).
-----------------------------------------------------------------------------*/
    /* In addition to putting output in it, we use visited[][] for working
       memory.  It indicates pixels of the blob that we've queued for
       processing so far.
    */
    PixQueue toExplore;
    PixQueue blob;

    pixQueue_init(&toExplore);
    pixQueue_init(&blob);

    pixQueue_push(&toExplore, start);
    visited[start.row][start.col] = true;

    while (!pixQueue_isEmpty(&toExplore)) {
        pm_pixelcoord const thisPix = pixQueue_pop(&toExplore);

        pixQueue_push(&blob, thisPix);

        queueNeighbors(thisPix, pixels, cols, rows, visited, &toExplore);
    }

    if (pixQueue_size(&blob) <= trivialSize) {
        bit const blobColor = pixels[start.row][start.col];

        *nFlippedP = pixQueue_size(&blob);

        setColor(&blob, pixels,
                 blobColor == PBM_WHITE ? PBM_BLACK : PBM_WHITE);
    } else
        *nFlippedP = 0;

    pixQueue_term(&blob);
    pixQueue_term(&toExplore);
}



static void
setAllNotVisited(bool **      const visited,
                 unsigned int const cols,
                 unsigned int const rows)  {

    unsigned int row;
    for (row = 0; row < rows; ++row) {
        unsigned int col;
        for (col = 0; col < cols; ++col)
            visited[row][col] = false;
    }
}



static void
cleanPixels(bit **       const pixels,
            unsigned int const cols,
            unsigned int const rows,
            bit          const foregroundColor,
            unsigned int const trivialSize,
            double *     const nFlippedP) {
/*----------------------------------------------------------------------------
   Same as cleanExtended(), except we work on the pixels 'pixels' instead
   of input and output files.
-----------------------------------------------------------------------------*/
    pm_pixelcoord thisPix;

    bool ** visited;  /* malloced */
        /* visited[row][col] means we have processed the pixel at (row, col)
           and flipped it if it needed to be flipped.
        */

    MALLOCARRAY2(visited, rows, cols);

    if (!visited)
        pm_error("Could not allocate a %u x %u array for visited flags",
                 rows, cols);

    setAllNotVisited(visited, cols, rows);

    *nFlippedP = 0;  /* initial value */

    for (thisPix.row = 0; thisPix.row < rows; ++thisPix.row) {
        for (thisPix.col = 0; thisPix.col < cols; ++thisPix.col) {
            if (pixels[thisPix.row][thisPix.col] == foregroundColor
                && !visited[thisPix.row][thisPix.col]) {

                double nFlipped;

                processBlob(thisPix, pixels, cols, rows, trivialSize,
                            visited, &nFlipped);

                *nFlippedP += nFlipped;
            } else
                visited[thisPix.row][thisPix.col] = true;
        }
    }

    pm_freearray2((void **)visited);
}



static void
cleanExtended(FILE *             const ifP,
              FILE *             const ofP,
              bit                const foregroundColor,
              unsigned int       const trivialSize,
              double *           const nFlippedP) {
/*----------------------------------------------------------------------------
   Clean the image on *ifP and write the result to *ofP.

   Look at arbitrarily shaped and sized blobs to determine what to erase.

   A blob is a contiguous set of pixels of the foreground color
   ('foregroundColor') which is not contiguous with any other pixels of that
   color.

   We erase (flip) every pixel in every trivial blob.  A trivial blob is
   one with 'trivialSize' pixels or fewer.
-----------------------------------------------------------------------------*/
    bit ** pixels;
    int cols, rows;

    pixels = pbm_readpbm(ifP, &cols, &rows);

	cleanPixels(pixels, cols, rows, foregroundColor, trivialSize, nFlippedP);

    pbm_writepbm(ofP, pixels, cols, rows, 0);

    pbm_freearray(pixels, rows);
}



static void
pbmclean(FILE *             const ifP,
         FILE *             const ofP,
         struct CmdlineInfo const cmdline,
         double *           const nFlippedP) {

    if (cmdline.extended) {
        bit const foregroundColor = cmdline.flipWhite ? PBM_WHITE : PBM_BLACK;

        assert(cmdline.flipWhite + cmdline.flipBlack == 1);

        cleanExtended(ifP, ofP, foregroundColor, cmdline.minneighbors,
                      nFlippedP);
    } else
        cleanSimple(ifP, ofP, cmdline, nFlippedP);
}



int
main(int argc, const char *argv[]) {

    struct CmdlineInfo cmdline;
    FILE * ifP;
    double nFlipped;
        /* Number of pixels we have flipped so far.  Use type double to
           prevent overflow.
        */

    pm_proginit(&argc, argv);

    parseCommandLine(argc, argv, &cmdline);

    ifP = pm_openr(cmdline.inputFileName);

    pbmclean(ifP, stdout, cmdline, &nFlipped);

    if (cmdline.verbose)
        pm_message("%f pixels flipped", nFlipped);

    pm_close(ifP);

    return 0;
}



