int main(int argc, char *argv[])
{
FILE *fp;
char in_filename[1024], out_filename[1024];
char field[128];
char header_bytes[6];
int data_size, header_size_char;
int cbf_status;
int i, j, k;
int size1, size2;
int output_packing;
int status_pclose;
char *header;
unsigned short *data;
char * lbo; /* local byte order */
static char *endings[] = {
".img",
".img.gz",
".img.bz2",
NULL
};
static char *flags[] = {
"--gz",
"--bz2",
NULL
};
int cbf2adscimg_sub(char *filename, char **header, unsigned short **data);
if(argc < 2)
{
usage();
exit(0);
}
output_packing = -1;
while(argc > 1 && argv[1][0] == '-' && argv[1][1] == '-')
{
for(j = 0; flags[j] != NULL; j++)
if(NULL != strstr(argv[1], flags[j]))
break;
if(NULL == flags[j])
{
fprintf(stderr,"cbf2adscimg: %s is an unknown flag\n\n", argv[1]);
usage();
exit(0);
}
output_packing = j;
argc--;
argv++;
}
output_packing++;
while(argc > 1)
{
strcpy(in_filename, argv[1]);
i = strlen(in_filename);
k = strlen(".cbf");
if(0 == endswith(in_filename, ".cbf"))
{
fprintf(stderr,"cbf2adscimg: Input file name %s does not end in .cbf\n", in_filename);
exit(0);
}
strcpy(out_filename, in_filename);
out_filename[i - k] = '\0';
strcat(out_filename, endings[output_packing]);
cbf_status = cbf2adscimg_sub(in_filename, &header, &data);
if(0 != cbf_status)
{
fprintf(stderr, "cbf2adscimg: Error converting cbf file %s to .img format\n", in_filename);
exit(0);
}
if(NULL == header)
{
fprintf(stderr, "cbf2adscimg: Error: cbf2adscimg_sub returned NULL for header on file %s\n", in_filename);
exit(0);
}
if(0 == output_packing)
{
if(NULL == (fp = fopen(out_filename, "wb")))
{
fprintf(stderr, "cbf2adscimg: Cannot create %s as output .img file\n", out_filename);
exit(0);
}
}
else
{
if(0 == output_packing)
sprintf(popen_command, "gzip > %s", out_filename);
else
sprintf(popen_command, "bzip2 > %s", out_filename);
if(NULL == (fp = popen(popen_command, "w")))
{
fprintf(stderr, "cbf2adscimg: Cannot exec %s command to compress output image file.\n", popen_command);
exit(0);
}
}
/*
* Output the header block(s).
*/
for(i = 0; i < 5; i++)
header_bytes[0 + i] = header[15 + i];
header_bytes[5] = '\0';
header_size_char = atoi(header_bytes);
if(header_size_char != fwrite(header, sizeof (char), header_size_char, fp))
{
fprintf(stderr, "cbf2adscimg: Cannot write header, size %d bytes, of file %s.\n", header_size_char, in_filename);
if(0 == output_packing)
fclose(fp);
else
{
status_pclose = pclose(fp);
if(0 != status_pclose)
{
fprintf(stderr, "Status returned from compress command via popen NON-ZERO: %d\n", status_pclose);
perror("popen command (maybe this will be useful)");
fprintf(stderr, "Filename being compressed: %s with command: %s\n", out_filename, popen_command);
fprintf(stderr, "Program exiting.\n");
exit(0);
}
}
exit(0);
}
field[0] = '\0';
gethd("SIZE1", field, header);
if('\0' == field[0])
{
fprintf(stderr,"cbf2adscimg: keyword SIZE1 not found in header. Cannot convert file %s\n", in_filename);
exit(0);
}
size1 = atoi(field);
field[0] = '\0';
gethd("SIZE2", field, header);
if('\0' == field[0])
{
fprintf(stderr,"cbf2adscimg: keyword SIZE2 not found in header. Cannot convert file %s\n", in_filename);
exit(0);
}
size2 = atoi(field);
data_size = size1 * size2 * sizeof(unsigned short);
gethd("BYTE_ORDER", field, header);
cbf_get_local_integer_byte_order(&lbo);
if (cbf_cistrcmp(field,lbo)) {
unsigned char *p;
unsigned char temp;
size_t ii;
p = (unsigned char *)data;
for (ii=0; ii<data_size; ii+=2) {
temp = p[ii];
p[ii] = p[ii+1];
p[ii+1] = temp;
}
}
if(data_size != fwrite(data, sizeof (char), data_size, fp))
{
fprintf(stderr, "cbf2adscimg: Cannot write data (size %d bytes) from input file %s.\n",
data_size, in_filename);
if(0 == output_packing)
fclose(fp);
else
{
status_pclose = pclose(fp);
if(0 != status_pclose)
{
fprintf(stderr, "Status returned from compress command via popen NON-ZERO: %d\n", status_pclose);
perror("popen command (maybe this will be useful)");
fprintf(stderr, "Filename being compressed: %s with command: %s\n", out_filename, popen_command);
fprintf(stderr, "Program exiting.\n");
exit(0);
}
}
exit(0);
}
if(0 == output_packing)
fclose(fp);
else
{
status_pclose = pclose(fp);
if(0 != status_pclose)
{
fprintf(stderr, "Status returned from compress command via popen NON-ZERO: %d\n", status_pclose);
perror("popen command (maybe this will be useful)");
fprintf(stderr, "Filename being compressed: %s with command: %s\n", out_filename, popen_command);
fprintf(stderr, "Program exiting.\n");
exit(0);
}
}
free(header);
free(data);
argv++;
argc--;
}
exit(0);
}
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
};
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 = 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);
}
int main (int argc, char *argv [])
{
int error = CBF_SUCCESS;
FILE *file = NULL;
clock_t a,b;
cbf_handle cif;
cbf_getopt_handle opts;
int c = 0;
int errflg = 0;
size_t cifid = 0;
size_t f = 0;
int h5_write_flags = 0;
cbf_h5handle h5out = NULL;
const char ** const cifin = memset(malloc(argc*sizeof(char*)),0,argc*sizeof(char*));
const char *hdf5out = NULL;
const char *group = NULL;
char *ciftmp=NULL;
#ifndef NOMKSTEMP
int ciftmpfd;
#endif
int ciftmpused = 0;
int nbytes;
char buf[C2CBUFSIZ];
int digest = 0;
const char * optarg = NULL;
cbf_onfailnez(cbf_make_getopt_handle(&opts),free(cifin));
cbf_onfailnez(cbf_getopt_parse(opts, argc, argv, "c(compression):g(group):o(output):Z(register):" ),free(cifin));
if (!cbf_rewind_getopt_option(opts)) {
for(; !cbf_get_getopt_data(opts,&c,NULL,NULL,&optarg); cbf_next_getopt_option(opts)) {
switch (c) {
case 'c': { /* compression */
if (!cbf_cistrcmp("zlib",optarg?optarg:"")) {
h5_write_flags |= CBF_H5COMPRESSION_ZLIB;
h5_write_flags &= ~CBF_H5COMPRESSION_CBF;
} else if (!cbf_cistrcmp("cbf",optarg?optarg:"")) {
h5_write_flags &= ~CBF_H5COMPRESSION_ZLIB;
h5_write_flags |= CBF_H5COMPRESSION_CBF;
}else if (!cbf_cistrcmp("none",optarg?optarg:"")) {
/* remove any previously set (system default?) compressions */
h5_write_flags &= ~CBF_H5COMPRESSION_ZLIB;
h5_write_flags &= ~CBF_H5COMPRESSION_CBF;
}
else ++errflg;
break;
}
case 'g': { /* group within output file where data should be stored */
if (group) errflg++;
else group = optarg;
break;
}
case 'o': { /* output file */
if (hdf5out) errflg++;
else hdf5out = optarg;
break;
}
case 'Z': { /* automatic or manual filter registration? */
if (cbf_cistrcmp(optarg?optarg:"","manual") == 0) {
h5_write_flags |= CBF_H5_REGISTER_COMPRESSIONS;
} else if (cbf_cistrcmp(optarg?optarg:"","plugin") == 0) {
h5_write_flags &= ~CBF_H5_REGISTER_COMPRESSIONS;
} else {
errflg++;
}
break;
}
case 0: { /* input file */
if (NULL != optarg) cifin[cifid++] = optarg;
break;
}
default: {
errflg++;
break;
}
}
}
}
if (!hdf5out) {
fprintf(stderr,"No output file given.\n");
++errflg;
}
if (!cifid) {
fprintf(stderr,"No input files given.\n");
++errflg;
}
if (errflg) {
fprintf(stderr, "Usage:\n\t%s -o|--output output_nexus input_minicbf_files...\n"
"Options:\n"
"\t-c|--compression cbf|none|zlib (default: none)\n"
"\t-g|--group output_group (default: 'entry')\n"
"\t-Z|--register manual|plugin (default: plugin)\n"
"These options are NOT case-sensitive.\n",
argv[0]);
exit(2);
}
// prepare the output file
if(cbf_create_h5handle2(&h5out,hdf5out)) printf ("Couldn't open the HDF5 file '%s'.\n", hdf5out);
cbf_h5handle_require_entry(h5out,0,group);
h5out->flags = h5_write_flags;
#ifdef CBF_USE_ULP
// set up some parameters for comparing floating point numbers
h5out->cmp_double_as_float = 0;
h5out->float_ulp = 4;
#ifndef NO_UINT64_TYPE
h5out->double_ulp = 4;
#endif
#endif
for (f = 0; CBF_SUCCESS == error && f != cifid; ++f) {
/* Read the minicbf */
if (!(cifin[f]) || strcmp(cifin[f]?cifin[f]:"","-") == 0) {
ciftmp = (char *)malloc(strlen("/tmp/cif2cbfXXXXXX")+1);
#ifdef NOTMPDIR
strcpy(ciftmp, "cif2cbfXXXXXX");
#else
strcpy(ciftmp, "/tmp/cif2cbfXXXXXX");
#endif
#ifdef NOMKSTEMP
if ((ciftmp = mktemp(ciftmp)) == NULL ) {
fprintf(stderr,"%s: Can't create temporary file name %s.\n%s\n", argv[0], ciftmp,strerror(errno));
exit(1);
}
if ( (file = fopen(ciftmp,"wb+")) == NULL) {
fprintf(stderr,"Can't open temporary file %s.\n%s\n", ciftmp,strerror(errno));
exit(1);
}
#else
if ((ciftmpfd = mkstemp(ciftmp)) == -1 ) {
fprintf(stderr,"%s: Can't create temporary file %s.\n%s\n", argv[0], ciftmp,strerror(errno));
exit(1);
}
if ( (file = fdopen(ciftmpfd, "w+")) == NULL) {
fprintf(stderr,"Can't open temporary file %s.\n%s\n", ciftmp,strerror(errno));
exit(1);
}
#endif
while ((nbytes = fread(buf, 1, C2CBUFSIZ, stdin))) {
if(nbytes != fwrite(buf, 1, nbytes, file)) {
fprintf(stderr,"Failed to write %s.\n", ciftmp);
exit(1);
}
}
fclose(file);
cifin[f] = ciftmp;
ciftmpused = 1;
}
// start timing
a = clock ();
{ // do the work
// prepare the file
FILE * const in = fopen (cifin[f], "rb");
if (NULL == in) {
fprintf (stderr,"Couldn't open the input CIF file '%s': %s\n", cifin[f], strerror(errno));
exit (1);
}
// ensure temporary file is removed when the program closes
if (ciftmpused) {
if (unlink(ciftmp)) {
fprintf(stderr,"Can't unlink temporary file '%s': %s\n", ciftmp,strerror(errno));
exit(1);
}
}
// make the handle
if ( cbf_make_handle (&cif) ) {
fprintf(stderr,"Failed to create handle for input_cif\n");
exit(1);
}
// read the file
cbf_onfailnez(cbf_read_file(cif, in, MSG_DIGEST|(digest&MSG_DIGESTWARN)),free(cifin));
}
// stop timing
b = clock ();
printf("Time to read '%s': %.3fs\n", cifin[f], ((float)(b - a))/CLOCKS_PER_SEC);
// start timing
a = clock ();
{ // do the work
// convert to nexus format
error |= cbf_write_cbf_h5file(cif, h5out);
}
cbf_free_handle(cif);
// stop timing
b = clock ();
printf("Time to convert the data: %.3fs\n", ((float)(b - a))/CLOCKS_PER_SEC);
}
{ // write the file
// start timing
a = clock ();
// clean up cbf handles
cbf_free_h5handle(h5out);
// stop timing
b = clock ();
printf("Time to write '%s': %.3fs\n", hdf5out, ((float)(b - a))/CLOCKS_PER_SEC);
}
// cleanup
free(cifin);
cbf_failnez(cbf_free_getopt_handle(opts));
return CBF_SUCCESS==error ? 0 : 1;
}
int main (int argc, char *argv [])
{
int error = CBF_SUCCESS;
cbf_getopt_handle opts = NULL;
int h5_write_flags = 0;
int list = 0;
int noCBFnames = 0;
unsigned int frame = 0;
const char * cifout = NULL;
const char * hdf5in = NULL;
const char * group = NULL;
/* Attempt to read the arguments */
if (CBF_SUCCESS != (error |= cbf_make_getopt_handle(&opts))) {
fprintf(stderr,"Could not create a 'cbf_getopt' handle.\n");
} else if (CBF_SUCCESS != (error |= cbf_getopt_parse(opts, argc, argv, "c(compression):g(group):o(output):Z(register):f(frame):\1(list)\2(no-list)\3(CBFnames)\4(noCBFnames)" ))) {
fprintf(stderr,"Could not parse arguments.\n");
} else {
int errflg = 0;
/* successful so far, try to make sense of the options */
if (!cbf_rewind_getopt_option(opts)) {
int c = 0;
const char * optarg = NULL;
for(; !cbf_get_getopt_data(opts,&c,NULL,NULL,&optarg); cbf_next_getopt_option(opts)) {
switch (c) {
case 'f': { /* the index of the frame to be converted */
if (!optarg) {
++errflg;
} else {
char * end = NULL;
const unsigned int _frame = strtoul(optarg,&end,0);
if (end==optarg) {
fprintf(stderr,"error: Expected a number for the frame index, got '%s'.\n",optarg);
++errflg;
} else {
frame = _frame;
}
}
break;
}
case 'g': { /* group within input file where data should be found */
if (group) ++errflg;
else group = optarg;
break;
}
case 'o': { /* output file */
if (cifout) ++errflg;
else cifout = optarg;
break;
}
case 'Z': { /* automatic or manual filter registration? */
if (cbf_cistrcmp(optarg?optarg:"","manual") == 0) {
h5_write_flags |= CBF_H5_REGISTER_COMPRESSIONS;
} else if (cbf_cistrcmp(optarg?optarg:"","plugin") == 0) {
h5_write_flags &= ~CBF_H5_REGISTER_COMPRESSIONS;
} else {
++errflg;
}
break;
}
case 0: { /* input file */
if (hdf5in) ++errflg;
else hdf5in = optarg;
break;
}
case '\1': {
if (list) ++errflg;
list = 1;
break;
}
case '\2': {
if (list) ++errflg;
list = -1;
break;
}
case '\3': {
if (noCBFnames) ++errflg;
noCBFnames = -1;
break;
}
case '\4': {
if (noCBFnames) ++errflg;
noCBFnames = 1;
break;
}
default: {
++errflg;
break;
}
}
}
}
/* check for missing data */
if (!cifout) {
fprintf(stderr,"No output files given.\n");
++errflg;
}
if (!hdf5in) {
fprintf(stderr,"No input file given.\n");
++errflg;
}
if (errflg) {
fprintf(stderr, "Usage:\n\t%s [options] -o|--output output_cbf input_nexus\n"
"Options:\n"
"\t-g|--group output_group (default: 'entry')\n"
"\t-Z|--register manual|plugin (default: plugin)\n"
"\t-f|--frame <unsigned int> (default: 0)\n",
argv[0]);
error |= CBF_ARGUMENT;
}
}
/* If I could read the arguments then attempt to use them */
if (CBF_SUCCESS == error) {
cbf_h5handle h5in = NULL;
cbf_handle cif = NULL;
/* prepare the input file */
{
hid_t hdf_file = CBF_H5FAIL, fapl = CBF_H5FAIL;
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
fprintf(stderr,"Couldn't create file access property list.\n");
error |= CBF_H5ERROR;
} else if ((H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG)) < 0) {
fprintf(stderr,"Couldn't set a file access property.\n");
error |= CBF_H5ERROR;
} else if ((hdf_file = H5Fopen(hdf5in,H5F_ACC_RDONLY,fapl)) < 0) {
fprintf(stderr,"Couldn't open a HDF5 file.\n");
error |= CBF_H5ERROR;
} else if(CBF_SUCCESS != (error |= cbf_create_h5handle3(&h5in,hdf_file))) {
fprintf(stderr,"Couldn't open the HDF5 file '%s'.\n", hdf5in);
} else if (CBF_SUCCESS != (error |= cbf_h5handle_require_entry(h5in,0,group))) {
fprintf(stderr,"Couldn't create an NXentry group in the HDF5 file '%s'.\n", hdf5in);
} else {
h5in->flags = h5_write_flags;
h5in->slice = frame;
#ifdef CBF_USE_ULP
// set up some parameters for comparing floating point numbers
h5in->cmp_double_as_float = 0;
h5in->float_ulp = 4;
#ifndef NO_UINT64_TYPE
h5in->double_ulp = 4;
#endif
#endif
}
H5Pclose(fapl);
}
/* make the handle for the output file */
if (CBF_SUCCESS != (error |= cbf_make_handle(&cif))) {
fprintf(stderr,"Failed to create handle for input_cif\n");
error |= CBF_ALLOC;
}
/* Time the conversion */
if (CBF_SUCCESS == error) {
clock_t a = clock(), b;
h5in->slice = 0;
if (list > 0) h5in->logfile = stdout;
if (noCBFnames >= 0) h5in->flags |= CBF_H5_CBFNONAMES;
error |= cbf_write_nx2cbf(h5in, cif);
b = clock();
printf("Time to convert '%s': %.3fs\n", cifout, ((float)(b - a))/CLOCKS_PER_SEC);
} else {
fprintf(stderr,"An error occured, will not try to convert the file '%s'\n",hdf5in);
}
/* Write the file */
if (CBF_SUCCESS == error) {
/* start timing */
clock_t a = clock(), b;
FILE * const out = fopen(cifout,"wb");
if (NULL == out) {
fprintf(stderr,"Couldn't open the output CIF file '%s': %s\n", cifout, strerror(errno));
error |= CBF_FILEOPEN;
} else if (CBF_SUCCESS != (error |= cbf_write_file(cif,out,0,CBF,0,0))) {
fprintf(stderr,"Couldn't write the output CIF file '%s': %s\n", cifout, cbf_strerror(error));
error |= CBF_FILEWRITE;
}
if (NULL!=out) fclose(out);
/* stop timing */
b = clock();
printf("Time to write '%s': %.3fs\n", cifout, ((float)(b - a))/CLOCKS_PER_SEC);
} else {
fprintf(stderr,"An error occured, will not try to write the file '%s'\n",cifout);
}
/* Clean up */
if (cif) cbf_free_handle(cif);
if (h5in) cbf_free_h5handle(h5in);
}
/*******************************************************************************************************************/
/* Cleanup */
error |= cbf_free_getopt_handle(opts);
return CBF_SUCCESS==error ? 0 : 1;
}
