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|
#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);
}
|
