void QtestceplibCombinedMainWindow::doTestCBFLibrary()
{
QString theFile = QFileDialog::getOpenFileName(
this, "Read CBF File...", defCBFPath);
if (theFile.length()) {
FILE *f;
cbf_handle ch;
int status;
unsigned int m;
char *array_id;
int i, index, dimension[2], precedence[2];
const char *direction[2];
printMessage(tr("cbf test on file %1").arg(theFile));
f = fopen(qPrintable(theFile), "rb");
cbf_make_handle(&ch);
status = CBF_CHECK(cbf_read_widefile(ch, f, MSG_DIGEST));
printMessage(tr("read_widefile (%1)").arg(status));
status = CBF_CHECK(cbf_count_datablocks(ch, &m));
printMessage(tr("count_dbs (%1) = %2").arg(status).arg(m));
status = CBF_CHECK(cbf_rewind_datablock(ch));
if (cbf_find_category(ch, "diffrn_frame_data") !=0 ) {
status = CBF_CHECK(cbf_find_category(ch, "diffrn_data_frame"));
}
status = CBF_CHECK(cbf_find_column(ch, "array_id"));
status = CBF_CHECK(cbf_rewind_row(ch));
status = CBF_CHECK(cbf_get_value(ch, (const char **) &array_id));
status = CBF_CHECK(cbf_find_category(ch, "array_structure_list"));
status = CBF_CHECK(cbf_rewind_row(ch));
status = CBF_CHECK(cbf_find_column(ch, "array_id"));
dimension[0] = dimension[1] = 0;
while (cbf_find_nextrow(ch, array_id) == 0) {
status = CBF_CHECK(cbf_find_column(ch, "index"));
status = CBF_CHECK(cbf_get_integervalue(ch, &index));
i = index;
status = CBF_CHECK(cbf_find_column(ch, "precedence"));
status = CBF_CHECK(cbf_get_integervalue(ch, &index));
if (index >= 1 && index <= 2) {
precedence[i-1] = index;
status = CBF_CHECK(cbf_find_column(ch, "dimension"));
status = CBF_CHECK(cbf_get_integervalue(ch, &dimension[i-1]));
status = CBF_CHECK(cbf_find_column(ch, "direction"));
status = CBF_CHECK(cbf_get_value(ch, &direction[i-1]));
status = CBF_CHECK(cbf_find_column(ch, "array_id"));
}
}
printMessage(tr("Image Dimensions [%1,%2]").arg(dimension[0]).arg(dimension[1]));
status = CBF_CHECK(cbf_rewind_datablock(ch));
if (CBF_CHECK(cbf_find_tag(ch, "_array_data.data")) == 0) {
qint32 *array;
int binary_id, elsigned, elunsigned;
size_t elements,elements_read, elsize;
int minelement, maxelement;
unsigned int cifcompression;
// int realarray;
const char *byteorder;
size_t dim1, dim2, dim3, padding;
status = CBF_CHECK(cbf_get_integerarrayparameters_wdims_fs(
ch, &cifcompression,
&binary_id, &elsize, &elsigned, &elunsigned,
&elements, &minelement, &maxelement,
&byteorder, &dim1, &dim2, &dim3, &padding));
printMessage(tr("elsize %1, dim1 %2, dim2 %3, dim3 %4").arg(elsize).arg(dim1).arg(dim2).arg(dim3));
array = new qint32[dim1*dim2];
if (status == 0) {
status = CBF_CHECK(cbf_get_integerarray(ch, &binary_id,
array,
sizeof(qint32), 1, elements, &elements_read));
if (status == 0) {
printMessage(tr("%1 elements read").arg(elements_read));
for (int y=0; y<10; y++) {
QString msg="[";
for (int x=0; x<9; x++) {
msg += tr("%1, ").arg(array[y*dim1+x]);
}
msg += tr("%1]").arg(array[y*dim1+9]);
printMessage(msg);
}
}
}
delete [] array;
}
// fclose(f);
defCBFPath=theFile;
}
}
int main (int argc, char *argv [])
{
FILE *in, *out;
clock_t a,b;
img_handle img, cbf_img;
cbf_handle cbf;
int id, index;
unsigned int column, row;
size_t nelem_read;
double pixel_size, gain, wavelength, distance;
int overload, dimension [2], precedence [2];
const char *detector;
char *detector_char;
char detector_id [64];
const char *direction [2], *array_id;
/* Usage */
if (argc < 3)
{
fprintf (stderr, "\n Usage: %s imagefile cbffile\n", argv [0]);
exit (2);
}
/* Read the image */
img = img_make_handle ();
a = clock ();
cbf_failnez (img_read (img, argv [1]))
b = clock ();
fprintf (stderr, " Time to read the image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Get some detector parameters */
/* Detector identifier */
detector = img_get_field (img, "DETECTOR");
if (!detector)
detector = "unknown";
strncpy (detector_id, detector, 63);
detector_id [63] = 0;
detector_char = detector_id;
while (*detector_char)
if (isspace (*detector_char))
memmove (detector_char, detector_char + 1, strlen (detector_char));
else
{
*detector_char = tolower (*detector_char);
detector_char++;
}
/* Pixel size */
pixel_size = img_get_number (img, "PIXEL SIZE") * 0.001;
/* Wavelength */
wavelength = img_get_number (img, "WAVELENGTH");
/* Distance */
distance = img_get_number (img, "DISTANCE") * 0.001;
/* Image size and orientation & gain and overload */
if (strcmp (detector_id, "mar180") == 0 ||
strcmp (detector_id, "mar300") == 0)
{
gain = 1.08;
overload = 120000;
dimension [0] = img_rows (img);
dimension [1] = img_columns (img);
precedence [0] = 1;
precedence [1] = 2;
direction [0] = "decreasing";
direction [1] = "increasing";
}
else
if (strcmp (detector_id, "mar345") == 0)
{
gain = 1.55;
overload = 240000;
dimension [0] = img_columns (img);
dimension [1] = img_rows (img);
precedence [0] = 2;
precedence [1] = 1;
direction [0] = "increasing";
direction [1] = "increasing";
}
else
if (strncmp (detector_id, "adscquantum", 11) == 0)
{
gain = 0.20;
overload = 65000;
dimension [0] = img_columns (img);
dimension [1] = img_rows (img);
precedence [0] = 2;
precedence [1] = 1;
direction [0] = "increasing";
direction [1] = "increasing";
}
else
{
gain = 0.0;
overload = 0;
dimension [0] = img_rows (img);
dimension [1] = img_columns (img);
precedence [0] = 1;
precedence [1] = 2;
direction [0] = NULL;
direction [1] = NULL;
}
/* Make a cbf version of the image */
a = clock ();
/* Create the cbf */
cbf_failnez (cbf_make_handle (&cbf))
/* Make a new data block */
cbf_failnez (cbf_new_datablock (cbf, "image_1"))
/* Make the _diffrn category */
cbf_failnez (cbf_new_category (cbf, "diffrn"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
/* Make the _diffrn_source category */
cbf_failnez (cbf_new_category (cbf, "diffrn_source"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "source"))
cbf_failnez (cbf_set_value (cbf, "synchrotron"))
cbf_failnez (cbf_new_column (cbf, "type"))
cbf_failnez (cbf_set_value (cbf, "ssrl crystallography"))
/* Make the _diffrn_radiation category */
cbf_failnez (cbf_new_category (cbf, "diffrn_radiation"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "wavelength_id"))
cbf_failnez (cbf_set_value (cbf, "L1"))
/* Make the _diffrn_radiation_wavelength category */
cbf_failnez (cbf_new_category (cbf, "diffrn_radiation_wavelength"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "L1"))
cbf_failnez (cbf_new_column (cbf, "wavelength"))
if (wavelength)
cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", wavelength))
cbf_failnez (cbf_new_column (cbf, "wt"))
cbf_failnez (cbf_set_value (cbf, "1.0"))
/* Make the _diffrn_measurement category */
cbf_failnez (cbf_new_category (cbf, "diffrn_measurement"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "method"))
cbf_failnez (cbf_set_value (cbf, "oscillation"))
cbf_failnez (cbf_new_column (cbf, "sample_detector_distance"))
if (distance)
cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", distance))
/* Make the _diffrn_detector category */
cbf_failnez (cbf_new_category (cbf, "diffrn_detector"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "type"))
cbf_failnez (cbf_set_value (cbf, detector))
/* Make the _diffrn_detector_element category */
cbf_failnez (cbf_new_category (cbf, "diffrn_detector_element"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "detector_id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
/* Make the _diffrn_frame_data category */
cbf_failnez (cbf_new_category (cbf, "diffrn_frame_data"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "frame_1"))
cbf_failnez (cbf_new_column (cbf, "detector_element_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "detector_id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
/* Make the _array_structure_list category */
cbf_failnez (cbf_new_category (cbf, "array_structure_list"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_row (cbf))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "index"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 2))
cbf_failnez (cbf_new_column (cbf, "dimension"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, dimension [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, dimension [1]))
cbf_failnez (cbf_new_column (cbf, "precedence"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, precedence [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, precedence [1]))
cbf_failnez (cbf_new_column (cbf, "direction"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_value (cbf, direction [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_value (cbf, direction [1]))
/* Make the _array_element_size category */
cbf_failnez (cbf_new_category (cbf, "array_element_size"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_row (cbf))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "index"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 2))
cbf_failnez (cbf_new_column (cbf, "size"))
if (pixel_size > 0)
{
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_doublevalue (cbf, "%.1fe-6", pixel_size * 1e6))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_doublevalue (cbf, "%.1fe-6", pixel_size * 1e6))
}
/* Make the _array_intensities category */
cbf_failnez (cbf_new_category (cbf, "array_intensities"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "linearity"))
cbf_failnez (cbf_set_value (cbf, "linear"))
cbf_failnez (cbf_new_column (cbf, "gain"))
if (gain)
cbf_failnez (cbf_set_doublevalue (cbf, "%.3g", gain))
cbf_failnez (cbf_new_column (cbf, "overload"))
if (overload)
cbf_failnez (cbf_set_integervalue (cbf, overload))
cbf_failnez (cbf_new_column (cbf, "undefined"))
cbf_failnez (cbf_set_integervalue (cbf, 0))
/* Make the _array_data category */
cbf_failnez (cbf_new_category (cbf, "array_data"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "data"))
/* Save the binary data */
cbf_failnez (cbf_set_integerarray_wdims_fs (cbf, CBF_PACKED|CBF_FLAT_IMAGE, 1,
img_pixelptr (img, 0, 0), sizeof (int), 1,
img_rows (img) * img_columns (img),
"little_endian",img_rows (img),img_columns (img),0,0 ))
/* Write the new file */
out = fopen (argv [2], "w+b");
if (!out)
{
fprintf (stderr, " Couldn't open the CBF file %s\n", argv [2]);
exit (1);
}
cbf_failnez (cbf_write_file (cbf, out, 1, CBF, MSG_DIGEST | MIME_HEADERS , 0))
/* Free the cbf */
cbf_failnez (cbf_free_handle (cbf))
b = clock ();
fprintf (stderr, " Time to write the CBF image: %.3fs\n",
((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Read the CBF file and compare the image to the original */
a = clock ();
/* Create the cbf */
cbf_failnez (cbf_make_handle (&cbf))
/* Read the file */
in = fopen (argv [2], "rb");
if (!in)
{
fprintf (stderr, " Couldn't reopen the CBF file %s\n", argv [2]);
exit (1);
}
cbf_failnez (cbf_read_file (cbf, in, MSG_DIGEST))
/* Get the image identifier */
cbf_failnez (cbf_rewind_datablock (cbf))
cbf_failnez (cbf_find_category (cbf, "diffrn_frame_data"))
cbf_failnez (cbf_find_column (cbf, "array_id"))
cbf_failnez (cbf_get_value (cbf, &array_id))
/* Get the image dimensions (second dimension = fast, first = slow) */
cbf_failnez (cbf_find_category (cbf, "array_structure_list"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_find_column (cbf, "array_id"))
dimension [0] = dimension [1] = 0;
while (cbf_find_nextrow (cbf, array_id) == 0)
{
cbf_failnez (cbf_find_column (cbf, "precedence"))
cbf_failnez (cbf_get_integervalue (cbf, &index))
if (index >= 1 && index <= 2)
{
cbf_failnez (cbf_find_column (cbf, "dimension"))
cbf_failnez (cbf_get_integervalue (cbf, &dimension [2 - index]))
}
else
exit (1);
cbf_failnez (cbf_find_column (cbf, "array_id"))
}
if (dimension [0] == 0 || dimension [1] == 0)
exit (1);
/* Create the new image */
cbf_img = img_make_handle ();
img_set_dimensions (cbf_img, dimension [0], dimension [1]);
/* Find the binary data */
cbf_failnez (cbf_find_category (cbf, "array_data"))
cbf_failnez (cbf_find_column (cbf, "array_id"))
cbf_failnez (cbf_find_row (cbf, array_id))
cbf_failnez (cbf_find_column (cbf, "data"))
/* Read the binary data */
cbf_failnez (cbf_get_integerarray (cbf,
&id, img_pixelptr (cbf_img, 0, 0), sizeof (int), 1,
img_rows (cbf_img) * img_columns (cbf_img), &nelem_read))
/* Free the cbf */
cbf_failnez (cbf_free_handle (cbf))
b = clock ();
fprintf (stderr, " Time to read the CBF image: %.3fs\n",
((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Compare the images */
if (img_rows (img) != img_rows (cbf_img) || img_columns (img) != img_columns (cbf_img))
{
fprintf (stderr, " The dimensions of the CBF image don't match the original\n");
exit (1);
}
for (column = 0; column < (unsigned int) img_columns (cbf_img); column++)
for (row = 0; row < (unsigned int) img_rows (cbf_img); row++)
if (img_pixel (cbf_img, column, row) != img_pixel (img, column, row))
{
fprintf (stderr, " The CBF image differs from the original at (%d, %d)\n", column, row);
exit (1);
}
fprintf (stderr, " The CBF image matches the original\n");
/* Free the images */
img_free_handle (img);
img_free_handle (cbf_img);
/* Success */
return 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;
}
