#include	<stdio.h>

#ifdef NO_POPEN_PROTOTYPE
	/*
	 *	This is supposed to be found in stdio.h.
	 */

	FILE	*popen(char *popen_command, const char *type);
	int		pclose(FILE *stream);
#endif

#include	<stdlib.h>
#include	<string.h>
#include	"cbf.h"
#include        "cbf_string.h"

/****************************************************************/

static void gethd ( char* field, char* value, char* header )
{
  char *hp, *lhp, *fp, *vp;
  int l, j;
  char *newfield;

  /*
   * Find the last occurance of "field" in "header"
   */
  l = strlen (field);
  newfield = (char*) malloc ( l + 3 );
  *newfield = 10;
  memcpy (newfield+1, field, l);
  *(newfield+l+1) = '=';
  *(newfield+l+2) = (char) 0;
  l += 2;

  lhp = 0;
  for (hp=header; *hp != '}'; hp++)
    {
      for (fp=newfield, j=0; j<l && *(hp+j) == *fp; fp++, j++);
      if ( j == l ) lhp=hp;
    }

  if ( lhp == 0 )
    value[0] = 0;
  else
    {
      /*
       * Find the '='.  hp will now point to the '='
       */
      for (hp=lhp; *hp!='='; hp++);
      
      /*
       * Copy into the returned value until the ';'
       */
      for (lhp=hp+1, vp=value; *lhp!=';' && *lhp!=0; lhp++, vp++) *vp = *lhp;
      *(vp++)=0;
    }
  free (newfield);
}

static int	endswith(char *haystack, char *needle)
{
	char	*cp;

	if(NULL == (cp = (char *) strstr(haystack, needle)))
		return(0);
	if('\0' == *(cp + strlen(needle)))
		return(1);
	return(0);
}

static void usage( void )
{
    fprintf(stderr,"Usage: adscimg2cbf [--flag[,modifier]] file1.img ... filen.img     (creates file1.cbf ... filen.cbf)\n");
    fprintf(stderr,"       Image files may also be compressed (.gz, .bz2, .Z)\n");
    fprintf(stderr,"Flags:\n");
    fprintf(stderr,"\t--input ifile         Input image of name ifile.  The extension is stripped and replaced\n");
    fprintf(stderr,"\t                        .cbf to form the desired output file name.  Only flags given\n");
    fprintf(stderr,"\t                        priot to this flag apply to processing this file.\n");
    fprintf(stderr,"\t--output ofile        Output cbf name ofile.  All images will be concatenated into this cbf\n");
    fprintf(stderr,"\t--cbf_byte_offset		Use BYTE_OFFSET compression (DEFAULT).\n");
    fprintf(stderr,"\t--cbf_packed			Use CCP4 packing (JPA) compression.\n");
    fprintf(stderr,"\t--cbf_packed_v2		Use CCP4 packing version 2 (JPA) compression.\n");
    fprintf(stderr,"\t--no_compression		No compression.\n\n");
    fprintf(stderr,"The following two modifiers can be appended to the flags (syntax: --flag,modifier):\n");
    fprintf(stderr,"\t,flat				    Flat (linear) images.\n");
    fprintf(stderr,"\t,uncorrelated			Uncorrelated sections.\n\n");
    fprintf(stderr,"The following describe how to interpret the beam center in the ADSC header:\n");
    fprintf(stderr,"\t--beam_center_from_header	Figure out beam center from ADSC header information (default)\n");
    fprintf(stderr,"\t--beam_center_mosflm		Beam center in ADSC header: MOSFLM coordinates.\n");
    fprintf(stderr,"\t--beam_center_ulhc		Beam center in ADSC header: origin: upper left hand corner of image.(HKL mm)\n");
    fprintf(stderr,"\t--beam_center_llhc		Beam center in ADSC header: origin: lower left hand corner of image.(adxv mm)\n");
    fprintf(stderr,"\t--region-of-interest=fastlow,fasthigh,slowlow,slowhigh\n");
    fprintf(stderr,"\t                          Region of interest to map to CBF\n");
    fprintf(stderr,"\t--sensor-thickness=0.00000000\n");
    fprintf(stderr,"\t                          Sensor layer thickness in mm\n");
    fprintf(stderr,"\t--add-minicbf-header      Add a minicbf header for fast_dp\n");
    fprintf(stderr,"\t--polarization-source-ratio=ratio\n");
    fprintf(stderr,"\t                          Polarization source ratio (Ip-In)/(Ip+In)\n");
    fprintf(stderr,"\t--scale=1.0              Scale the data\n");
    fprintf(stderr,"\t--offset=0.0             Offset the data\n");
    fprintf(stderr,"\t--cliplow=0.0            Clip the scaled and offset data below\n");
    fprintf(stderr,"\t--cliphigh=16384.0       Clip the scaled and offset deata above\n");
    fprintf(stderr,"\t--radial-smooth=nn       Radially smooth over nn pixels\n");

    
    
}

/*
 *	Jiffy to take one or more adsc .img files, convert each in turn to
 *	.cbf files, and output the files.  The input file is preserved; the
 *	output file has the same name as the input file with the suffix .img
 *	replaced by .cbf.
 */

char	popen_command[1080];

#define BEAM_CENTER_FROM_HEADER 0
#define BEAM_CENTER_MOSFLM      1
#define BEAM_CENTER_ULHC        2
#define BEAM_CENTER_LLHC        3

int adscimg2cbf_sub2(char *header,
                     unsigned short *data,
                     int * old_int_data,
                     size_t old_int_data_size,
                     int * * new_int_data,
                     size_t * new_int_data_size,
                     char *cbf_filename,
                     int pack_flags,
                     int beam_center_convention,
                     int pad_flag,
                     const char *roi,
                     const char *thickstr,
                     int add_mini_cbf_header,
                     const char *polarstr,
                     int bin,
                     const char *scalestr,
                     const char *offsetstr,
                     const char *cliplowstr,
                     const char *cliphighstr,
                     const char *rad_smoothstr,
                     int transpose,
                     int interleave);


int	main(int argc, char *argv[])
{
	FILE		*fp;
	char		in_filename[1024], out_filename[1024];
	char		field[128];
	char		*hptr;
	unsigned short	*uptr;
	char		header_bytes[6];
    int     numargs = argc;
    int     iarg;
    int     argtype_array[argc];
    int     *argtype=argtype_array;
    int     filec;
    int		file_size, header_size_char, actread;
    int		cbf_status;
    int		i, j, k=0;
    int		size1, size2;
    int		file_type;
    int		pack_flags;
    int     pad_flag;
    int		status_pclose;
    int		beam_center_convention;
    int     add_minicbf_header=0;
    int     bin=0;
    int     transpose=0;
    int     interleave=0;
    int     *new_int_data, *old_int_data;
    size_t  new_int_data_size, old_int_data_size;
    double  thickness=0.;
    const char *    argval_array[argc];
    const char * *  argval=argval_array;
    const char *    roi=NULL;
    const char *    thickstr=NULL;
    const char *    polarstr=NULL;
    const char *    scalestr=NULL;
    const char *    offsetstr=NULL;
    const char *    cliplowstr=NULL;
    const char *    cliphighstr=NULL;
    const char *    rad_smoothstr=NULL;
    const char *    ifile=NULL;
    const char *    ofile=NULL;
    char *     strstrhit;
    static char	*endings[] = {
					".img",
					".img.gz",
					".img.bz2",
					".img.Z",
					NULL
				     };
    static char	*flags[32] = {
					"--cbf_byte_offset",            /* 0 */
					"--cbf_packed_v2",              /* 1 */
					"--cbf_packed",                 /* 2 */
					"--no_compression",             /* 3 */
					"--beam_center_from_header",    /* 4 */
					"--beam_center_mosflm",         /* 5 */
					"--beam_center_ulhc",           /* 6 */
					"--beam_center_llhc",           /* 7 */
                    "--pad_1K",                     /* 8 */
                    "--pad_2K",                     /* 9 */
                    "--pad_4K",                     /*10 */
                    "--no_pad",                     /*11 */
                    "--cbf_nibble_offset",          /*12 */
                    "--region-of-interest",         /*13 */
                    "--region_of_interest",         /*14 */
                    "--sensor-thickness",           /*15 */
                    "--sensor_thickness",           /*16 */
                    "--add-minicbf-header",         /*17 */
                    "--add_minicbf_header",         /*18 */
                    "--polarization-source-ratio",  /*19 */
                    "--polarization_source_ratio",  /*20 */
                    "--bin",                        /*21 */
                    "--scale",                      /*22 */
                    "--offset",                     /*23 */
                    "--cliplow",                    /*24 */
                    "--cliphigh",                   /*25 */
                    "--radial-smooth",              /*26 */
                    "--input",                      /*27 */
                    "--output",                     /*28 */
                    "--transpose",                  /*29 */
                    "--interleave",                 /*30 */
					NULL
				   };

        CBF_UNUSED( cbf_status );
        CBF_UNUSED( thickness );

	if(argc < 2)
	{
		usage();
		exit(0);
	}
    
    argval[0] = argv[0];
    argtype[0] = -1;
    for (iarg = 1; iarg < numargs; iarg ++) {
        char modc;
        if ( argv[iarg][0] == '-' && argv[iarg][1] == '-' ) {
            for(j = 0; flags[j] != NULL; j++) {
                strstrhit = (char *)cbf_cistrnstr(argv[iarg], flags[j], strlen(flags[j]));
                if(NULL != strstrhit && strstrhit==argv[iarg] )
                    break;
            }
            if(NULL == flags[j])
            {
                fprintf(stderr,"adscimg2cbf: %s is an unknown flag\n\n", argv[iarg]);
                usage();
                exit(0);
            }
            argtype[iarg] = j;
            argval[iarg] = argv[iarg]+strlen(flags[j]);
            modc = '\0';
            if (j > 12) modc = '=';
            if(j < 3 || j==12) modc = ',';
            if (argval[iarg][0] != '\0'
                && argval[iarg][0] != modc ) {
                fprintf(stderr,"adscimg2cbf: %s is an unknown flag\n\n", argv[iarg]);
                usage();
                exit(0);
            }
            if (modc != '\0' && argval[iarg][0] == modc) argval[iarg]++;
        } else {
            argval[iarg]=argv[iarg];
            argtype[iarg] = -1;
        }
    }

	pack_flags = CBF_BYTE_OFFSET;
	beam_center_convention = BEAM_CENTER_FROM_HEADER;
	pad_flag = PAD_4K;

	while(argc > 1)
    {
        if ( (j =  argtype[1]) >= 0 ) {
            ifile = NULL;
            switch(j)
            {
                case 0:
                    pack_flags = CBF_BYTE_OFFSET;
                    break;
                case 1:
                    pack_flags = CBF_PACKED_V2;
                    break;
                case 2:
                    pack_flags = CBF_PACKED;
                    break;
                case 3:
                    pack_flags = CBF_NONE;
                    break;
                case 4:
                    beam_center_convention = BEAM_CENTER_FROM_HEADER;
                    break;
                case 5:
                    beam_center_convention = BEAM_CENTER_MOSFLM;
                    break;
                case 6:
                    beam_center_convention = BEAM_CENTER_ULHC;
                    break;
                case 7:
                    beam_center_convention = BEAM_CENTER_LLHC;
                    break;
                case 8:
                    pad_flag = PAD_1K;
                    break;
                case 9:
                    pad_flag = PAD_2K;
                    break;
                case 10:
                    pad_flag = PAD_4K;
                    break;
                case 11:
                    pad_flag = 0;
                    break;
                case 12:
                    pack_flags = CBF_NIBBLE_OFFSET;
                    break;
                case 13:
                case 14:
                    roi = argval[1];
                    break;
                case 15:
                case 16:
                    thickstr = argval[1];
                    break;
                case 17:
                case 18:
                    add_minicbf_header=1;
                    break;
                case 19:
                case 20:
                    polarstr = argval[1];
                    break;
                case 21:
                    bin = 1;
                    break;
                case 22:
                    scalestr = argval[1];
                    break;
                case 23:
                    offsetstr = argval[1];
                    break;
                case 24:
                    cliplowstr = argval[1];
                    break;
                case 25:
                    cliphighstr = argval[1];
                    break;
                case 26:
                    rad_smoothstr = argval[1];
                    break;
                case 27:
                    ifile = argval[1];
                    break;
                case 28:
                    ofile = argval[1];
                    break;
                case 29:
                    if (argval[1][0] == '\0') {
                        transpose = 1;
                    } else {
                        transpose = atoi(argval[1]);
                    }
                    break;
                case 30:
                    if (argval[1][0] == '\0') {
                        interleave = 1;
                    } else {
                        interleave = atoi(argval[1]);
                    }
                    break;

            }
            if(j < 3 || j==12)
            {
                if (cbf_cistrcmp(argval[1],"flat")==0) {
                    pack_flags |= CBF_FLAT_IMAGE;
                } else {
                    if(cbf_cistrcmp(argval[1],"uncorrelated")==0) {
                        pack_flags |= CBF_UNCORRELATED_SECTIONS;
                    } else {
                        fprintf(stderr,"adscimg2cbf: %s is an unknown flag modifier\n\n", argval[1]);
                        usage();
                        exit(0);
                    }
                }
            }
            if (!ifile) {
                argc--;
                argv++;
                argval++;
                argtype++;
            continue;
            }
            
        }
        
        filec = 0;
        for (j = 1; j < argc; j++) {
            if (argtype[j] < 0) filec++;
            if (!ofile || (argtype[j] >= 0 && argtype[j] != 13 && argtype[j] != 14)) break;
        }
        
        old_int_data = NULL;
        old_int_data_size = 0;
        
        while (filec > 0 && argc > 1) {
            
            if (argtype[1]==13 || argtype[1]==14) {
                roi = argval[1];
                argv++;
                argc--;
                argtype++;
                argval++;
                continue;
            }
            
            file_type = 0;
            strcpy(in_filename, argval[1]);
            i = strlen(in_filename);
            for(j = 0; endings[j] != NULL; j++)
            {
                k = strlen(endings[j]);
                if(endswith(in_filename, endings[j]))
                {
                    file_type = j;
                    break;
                }
            }
            if(NULL == endings[j])
            {
                fprintf(stderr,"adscimg2cbf: Input file name %s does not end in .img, .img.gz, or .img.bz2, or .img.Z\n", in_filename);
                exit(0);
            }
            if (!ofile) {
                strcpy(out_filename, in_filename);
                out_filename[i - k] = '\0';
                strcat(out_filename, ".cbf");
            } else {
                strcpy(out_filename,ofile);
            }
            
            if(0 == file_type)
            {
                if(NULL == (fp = fopen(in_filename, "rb")))
                {
                    fprintf(stderr, "adscimg2cbf: Cannot open %s as input .img file\n", in_filename);
                    exit(0);
                }
            }
            else
            {
                if(2 == file_type)
                    sprintf(popen_command, "bzcat %s", in_filename);
                else
                    sprintf(popen_command, "zcat %s", in_filename);
                if(NULL == (fp = popen(popen_command, "rb")))
                {
                    fprintf(stderr, "adscimg2cbf: Cannot exec %s command to uncompress input file\n", popen_command);
                    exit(0);
                }
            }
            
            /*
             *	Get the first header block.  Can't use seeks on input file.
             */
            
            if(NULL == (hptr = malloc(512 * sizeof (char))))
            {
                fprintf(stderr,"adscimg2cbf: cannot allocate memory for first 512 bytes of header of input file %s\n", in_filename);
                exit(0);
            }
            if(512 != (actread=fread(hptr, sizeof (char), 512, fp)))
            {
                fprintf(stderr, "adscimg2cbf: Cannot read first header block of file %s, actual read %d.\n",
                        in_filename,actread);
                if(0 == file_type)
                    fclose(fp);
                else
                {
                    status_pclose = pclose(fp);
                    if(0 != status_pclose)
                    {
                        fprintf(stderr, "Status returned from uncompress command via popen NON-ZERO: %d\n", status_pclose);
                        perror("popen command (maybe this will be useful)");
                        fprintf(stderr, "Program exiting.  This may be evidence of a corrupt compressed file!\n");
                        fprintf(stderr, "Filename being uncompressed: %s with command: %s\n", in_filename, popen_command);
                        exit(0);
                    }
                }
                exit(0);
            }
            for(i = 0; i < 5; i++)
                header_bytes[0 + i] = hptr[15 + i];
            
            header_bytes[5] = '\0';
            header_size_char = atoi(header_bytes);
            
            if(NULL == (hptr = realloc(hptr, header_size_char)))
            {
                fprintf(stderr,"adscimg2cbf: cannot reallocate memory for %d bytes of header of input file %s\n",
                        header_size_char, in_filename);
                exit(0);
            }
            
            if(header_size_char > 512)
            {
                if((header_size_char - 512) != (actread=fread(hptr + 512, sizeof (char),
                                                              (header_size_char - 512), fp)))
                {
                    fprintf(stderr, "adscimg2cbf: Cannot read next %d bytes of header of file %s,"
                            " actual read %d.\n",
                            header_size_char - 512, in_filename, actread);
                    if(0 == file_type)
                        fclose(fp);
                    else
                    {
                        status_pclose = pclose(fp);
                        if(0 != status_pclose)
                        {
                            fprintf(stderr, "Status returned from uncompress command via popen NON-ZERO: %d\n", status_pclose);
                            perror("popen command (maybe this will be useful)");
                            fprintf(stderr, "Program exiting.  This may be evidence of a corrupt compressed file!\n");
                            fprintf(stderr, "Filename being uncompressed: %s with command: %s\n", in_filename, popen_command);
                            exit(0);
                        }
                    }
                    exit(0);
                }
            }
            field[0] = '\0';
            gethd("SIZE1", field, hptr);
            if('\0' == field[0])
            {
                fprintf(stderr,"adscimg2cbf: keyword SIZE1 not found in header.  Cannot convert file %s\n", in_filename);
                exit(0);
            }
            size1 = atoi(field);
            
            field[0] = '\0';
            gethd("SIZE2", field, hptr);
            if('\0' == field[0])
            {
                fprintf(stderr,"adscimg2cbf: keyword SIZE2 not found in header.  Cannot convert file %s\n", in_filename);
                exit(0);
            }
            size2 = atoi(field);
            
            field[0] = '\0';
            gethd("TYPE", field, hptr);
            if (cbf_cistrcmp(field,"unsigned_short") != 0) {
                fprintf(stderr,"adscimg2cbf: TYPE '%s' not processed at this time.  Cannot convert file %s\n", field, in_filename);
                exit(0);
            }
            
            
            file_size = header_size_char + size1 * size2 * sizeof(unsigned short);
            
            if(NULL == (hptr = realloc(hptr, file_size)))
            {
                fprintf(stderr,"adscimg2cbf: cannot reallocate memory (size %d) for input file %s\n",
                        file_size, in_filename);
                exit(0);
            }
            if((file_size - header_size_char) != (actread=fread(hptr + header_size_char, sizeof (char),
                                                                (file_size - header_size_char), fp)))
            {
                fprintf(stderr, "adscimg2cbf: Cannot read data (size %d bytes) from input file %s."
                        " actual read %d\n",
                        file_size - header_size_char, in_filename, actread);
                if(0 == file_type)
                    fclose(fp);
                else
                {
                    status_pclose = pclose(fp);
                    if(0 != status_pclose)
                    {
                        fprintf(stderr, "Status returned from uncompress command via popen NON-ZERO: %d\n", status_pclose);
                        perror("popen command (maybe this will be useful)");
                        fprintf(stderr, "Program exiting.  This may be evidence of a corrupt compressed file!\n");
                        fprintf(stderr, "Filename being uncompressed: %s with command: %s\n", in_filename, popen_command);
                        exit(0);
                    }
                }
                exit(0);
            }
            if(0 == file_type)
                fclose(fp);
            else
            {
                status_pclose = pclose(fp);
                if(0 != status_pclose)
                {
                    fprintf(stderr, "Status returned from uncompress command via popen NON-ZERO: %d\n", status_pclose);
                    perror("popen command (maybe this will be useful)");
                    fprintf(stderr, "Program exiting.  This may be evidence of a corrupt compressed file!\n");
                    fprintf(stderr, "Filename being uncompressed: %s with command: %s\n", in_filename, popen_command);
                    exit(0);
                }
            }
            
            uptr = ((unsigned short *) (hptr + header_size_char));
            
            cbf_status = adscimg2cbf_sub2(hptr,
                                          uptr,
                                          old_int_data,
                                          old_int_data_size,
                                          &new_int_data,
                                          &new_int_data_size,
                                          (ofile && filec > 1)?NULL:out_filename,
                                          pack_flags,
                                          beam_center_convention,
                                          pad_flag,
                                          roi,
                                          thickstr,
                                          add_minicbf_header,
                                          polarstr,
                                          bin,
                                          scalestr,
                                          offsetstr,
                                          cliplowstr,
                                          cliphighstr,
                                          rad_smoothstr,
                                          transpose,
                                          interleave);
            free(hptr);
            if (old_int_data && old_int_data_size) free(old_int_data);
            old_int_data = new_int_data;
            old_int_data_size = new_int_data_size;
            
            argv++;
            argc--;
            argtype++;
            argval++;
            filec--;
        }
    }
	exit(0);
}