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;
}
