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; 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; }