diff options
author | Thomas White <taw@physics.org> | 2017-06-21 14:13:23 +0200 |
---|---|---|
committer | Thomas White <taw@physics.org> | 2017-06-21 14:13:23 +0200 |
commit | 5e9137947df9330308e1f66fa4a0701481ba6e06 (patch) | |
tree | 660556fc92663b17b76b7a9d12d6e95bbb928fbb /libcrystfel/src | |
parent | bd2d440d4e0db3040ae3a747dcfa55e638e33d42 (diff) | |
parent | 5617c8273e26469689c66fb46d5f7eb34dbf2bf4 (diff) |
Merge branch 'tom/cbf'
Diffstat (limited to 'libcrystfel/src')
-rw-r--r-- | libcrystfel/src/detector.c | 47 | ||||
-rw-r--r-- | libcrystfel/src/detector.h | 3 | ||||
-rw-r--r-- | libcrystfel/src/hdf5-file.c | 57 | ||||
-rw-r--r-- | libcrystfel/src/hdf5-file.h | 4 | ||||
-rw-r--r-- | libcrystfel/src/image.c | 668 | ||||
-rw-r--r-- | libcrystfel/src/image.h | 43 | ||||
-rw-r--r-- | libcrystfel/src/stream.c | 6 | ||||
-rw-r--r-- | libcrystfel/src/stream.h | 12 |
8 files changed, 776 insertions, 64 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c index e160d1e1..e3b351ff 100644 --- a/libcrystfel/src/detector.c +++ b/libcrystfel/src/detector.c @@ -528,37 +528,15 @@ int panel_number(struct detector *det, struct panel *p) } -void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev) +void adjust_centering_for_rail(struct panel *p) { - int i; - - for ( i=0; i<det->n_panels; i++ ) { - - double offs; - struct panel *p = &det->panels[i]; + double offs; - if ( p->clen_from != NULL ) { - - double val; - int r; - - r = hdfile_get_value(f, p->clen_from, ev, &val, - H5T_NATIVE_DOUBLE); - if ( r ) { - ERROR("Failed to read '%s'\n", p->clen_from); - } else { - p->clen = val * 1.0e-3; - } - - } - - /* Offset in +z direction from calibrated clen to actual */ - offs = p->clen - p->clen_for_centering; - p->cnx += p->rail_x * offs; - p->cny += p->rail_y * offs; - p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs; - - } + /* Offset in +z direction from calibrated clen to actual */ + offs = p->clen - p->clen_for_centering; + p->cnx += p->rail_x * offs; + p->cny += p->rail_y * offs; + p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs; } @@ -1076,12 +1054,15 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam, } else if ( strcmp(key, "photon_energy") == 0 ) { if ( beam != NULL ) { - if ( strncmp(val, "/", 1) == 0 ) { + double v; + char *end; + v = strtod(val, &end); + if ( (val[0] != '\0') && (end[0] == '\0') ) { + beam->photon_energy = v; + beam->photon_energy_from = NULL; + } else { beam->photon_energy = 0.0; beam->photon_energy_from = strdup(val); - } else { - beam->photon_energy = atof(val); - beam->photon_energy_from = NULL; } } diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h index 04e3c1ec..e9dd1154 100644 --- a/libcrystfel/src/detector.h +++ b/libcrystfel/src/detector.h @@ -224,9 +224,8 @@ extern void get_pixel_extents(struct detector *det, double *min_x, double *min_y, double *max_x, double *max_y); -extern void fill_in_values(struct detector *det, struct hdfile *f, - struct event* ev); extern void fill_in_adu(struct image *image); +extern void adjust_centering_for_rail(struct panel *p); extern int panel_is_in_rigid_group(const struct rigid_group *rg, struct panel *p); diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index c36a58b3..dc86d641 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -134,8 +134,7 @@ struct hdfile *hdfile_open(const char *filename) } -int hdfile_set_image(struct hdfile *f, const char *path, - struct panel *p) +int hdfile_set_image(struct hdfile *f, const char *path) { f->dh = H5Dopen2(f->fh, path, H5P_DEFAULT); if ( f->dh < 0 ) { @@ -1391,8 +1390,10 @@ int hdfile_get_value(struct hdfile *f, const char *name, } -void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f, - struct event *ev, struct image *image) +static void hdfile_fill_in_beam_parameters(struct beam_params *beam, + struct hdfile *f, + struct event *ev, + struct image *image) { double eV; @@ -1405,8 +1406,8 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f, int r; - r = hdfile_get_value(f, beam->photon_energy_from, ev, &eV, - H5T_NATIVE_DOUBLE); + r = hdfile_get_value(f, beam->photon_energy_from, + ev, &eV, H5T_NATIVE_DOUBLE); if ( r ) { ERROR("Failed to read '%s'\n", beam->photon_energy_from); @@ -1418,6 +1419,36 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f, } +static void hdfile_fill_in_clen(struct detector *det, struct hdfile *f, + struct event *ev) +{ + int i; + + for ( i=0; i<det->n_panels; i++ ) { + + struct panel *p = &det->panels[i]; + + if ( p->clen_from != NULL ) { + + double val; + int r; + + r = hdfile_get_value(f, p->clen_from, ev, &val, + H5T_NATIVE_DOUBLE); + if ( r ) { + ERROR("Failed to read '%s'\n", p->clen_from); + } else { + p->clen = val * 1.0e-3; + } + + } + + adjust_centering_for_rail(p); + + } +} + + int hdf5_read(struct hdfile *f, struct image *image, const char *element, int satcorr) { @@ -1433,7 +1464,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, if ( element == NULL ) { fail = hdfile_set_first_image(f, "/"); } else { - fail = hdfile_set_image(f, element, NULL); + fail = hdfile_set_image(f, element); } if ( fail ) { @@ -1482,7 +1513,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, if ( image->beam != NULL ) { - fill_in_beam_parameters(image->beam, f, NULL, image); + hdfile_fill_in_beam_parameters(image->beam, f, NULL, image); if ( image->lambda > 1000 ) { /* Error message covers a silly value in the beam file @@ -1747,7 +1778,7 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, return 1; } - fail = hdfile_set_image(f, panel_full_path, p); + fail = hdfile_set_image(f, panel_full_path); free(panel_full_path); @@ -1769,7 +1800,7 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, free(image->sat); return 1; } - fail = hdfile_set_image(f, p->data, p); + fail = hdfile_set_image(f, p->data); } @@ -1886,13 +1917,13 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, H5Dclose(f->dh); f->data_open = 0; - fill_in_values(image->det, f, ev); + hdfile_fill_in_clen(image->det, f, ev); if ( satcorr ) debodge_saturation(f, image); if ( image->beam != NULL ) { - fill_in_beam_parameters(image->beam, f, ev, image); + hdfile_fill_in_beam_parameters(image->beam, f, ev, image); if ( (image->lambda > 1.0) || (image->lambda < 1e-20) ) { @@ -2299,7 +2330,7 @@ int hdfile_set_first_image(struct hdfile *f, const char *group) for ( i=0; i<n; i++ ) { if ( is_image[i] ) { - hdfile_set_image(f, names[i], NULL); + hdfile_set_image(f, names[i]); for ( j=0; j<n; j++ ) free(names[j]); free(is_image); free(is_group); diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h index f22d4d54..ab53dd2e 100644 --- a/libcrystfel/src/hdf5-file.h +++ b/libcrystfel/src/hdf5-file.h @@ -67,8 +67,8 @@ extern int hdf5_read2(struct hdfile *f, struct image *image, extern int check_path_existence(hid_t fh, const char *path); extern struct hdfile *hdfile_open(const char *filename); -int hdfile_set_image(struct hdfile *f, const char *path, - struct panel *p); +int hdfile_set_image(struct hdfile *f, const char *path); + extern int16_t *hdfile_get_image_binned(struct hdfile *hdfile, int binning, int16_t *maxp); extern char **hdfile_read_group(struct hdfile *f, int *n, const char *parent, diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 09f4958d..4e1a8b86 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -3,12 +3,12 @@ * * Handle images and image features * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de> - * 2011-2016 Thomas White <taw@physics.org> + * 2011-2017 Thomas White <taw@physics.org> * * This file is part of CrystFEL. * @@ -31,9 +31,14 @@ #include <assert.h> #include <math.h> #include <stdio.h> +#include <hdf5.h> +#include <cbflib/cbf.h> #include "image.h" #include "utils.h" +#include "events.h" +#include "hdf5-file.h" +#include "detector.h" /** * SECTION:image @@ -50,6 +55,14 @@ */ +struct imagefile +{ + enum imagefile_type type; + char *filename; + struct hdfile *hdfile; +}; + + struct _imagefeaturelist { struct imagefeature *features; @@ -299,3 +312,654 @@ void free_all_crystals(struct image *image) free(image->crystals); image->n_crystals = 0; } + + +/**************************** Image field lists *******************************/ + +struct imagefile_field_list +{ + char **fields; + int n_fields; + int max_fields; +}; + + +struct imagefile_field_list *new_imagefile_field_list() +{ + struct imagefile_field_list *n; + + n = calloc(1, sizeof(struct imagefile_field_list)); + if ( n == NULL ) return NULL; + + n->max_fields = 32; + n->fields = malloc(n->max_fields*sizeof(char *)); + if ( n->fields == NULL ) { + free(n); + return NULL; + } + + return n; +} + + +void free_imagefile_field_list(struct imagefile_field_list *n) +{ + int i; + for ( i=0; i<n->n_fields; i++ ) { + free(n->fields[i]); + } + free(n->fields); + free(n); +} + + +void add_imagefile_field(struct imagefile_field_list *copyme, const char *name) +{ + int i; + + /* Already on the list? Don't re-add if so. */ + for ( i=0; i<copyme->n_fields; i++ ) { + if ( strcmp(copyme->fields[i], name) == 0 ) return; + } + + /* Need more space? */ + if ( copyme->n_fields == copyme->max_fields ) { + + char **nfields; + int nmax = copyme->max_fields + 32; + + nfields = realloc(copyme->fields, nmax*sizeof(char *)); + if ( nfields == NULL ) { + ERROR("Failed to allocate space for new HDF5 field.\n"); + return; + } + + copyme->max_fields = nmax; + copyme->fields = nfields; + + } + + copyme->fields[copyme->n_fields] = strdup(name); + if ( copyme->fields[copyme->n_fields] == NULL ) { + ERROR("Failed to add field for copying '%s'\n", name); + return; + } + + copyme->n_fields++; +} + + +/******************************* CBF files ************************************/ + + +static char *cbf_strerr(int e) +{ + char *err; + + err = malloc(1024); + if ( err == NULL ) return NULL; + + err[0] = '\0'; + + /* NB Sum of lengths of all strings must be less than 1024 */ + if ( e & CBF_FORMAT ) strcat(err, "Invalid format"); + if ( e & CBF_ALLOC ) strcat(err, "Memory allocation failed"); + if ( e & CBF_ARGUMENT ) strcat(err, "Invalid argument"); + if ( e & CBF_ASCII ) strcat(err, "Value is ASCII"); + if ( e & CBF_BINARY ) strcat(err, "Value is binary"); + if ( e & CBF_BITCOUNT ) strcat(err, "Wrong number of bits"); + if ( e & CBF_ENDOFDATA ) strcat(err, "End of data"); + if ( e & CBF_FILECLOSE ) strcat(err, "File close error"); + if ( e & CBF_FILEOPEN ) strcat(err, "File open error"); + if ( e & CBF_FILEREAD ) strcat(err, "File read error"); + if ( e & CBF_FILETELL ) strcat(err, "File tell error"); + if ( e & CBF_FILEWRITE ) strcat(err, "File write error"); + if ( e & CBF_IDENTICAL ) strcat(err, "Name already exists"); + if ( e & CBF_NOTFOUND ) strcat(err, "Not found"); + if ( e & CBF_OVERFLOW ) strcat(err, "Overflow"); + if ( e & CBF_UNDEFINED ) strcat(err, "Number undefined"); + if ( e & CBF_NOTIMPLEMENTED ) strcat(err, "Not implemented"); + + return err; +} + + +static int unpack_panels(struct image *image, signed int *data, int data_width, + int data_height) +{ + int pi; + + /* FIXME: Load these masks from an HDF5 file, if filenames are + * given in the geometry file */ + uint16_t *flags = NULL; + float *sat = NULL; + + image->dp = malloc(image->det->n_panels * sizeof(float *)); + image->bad = malloc(image->det->n_panels * sizeof(int *)); + image->sat = malloc(image->det->n_panels * sizeof(float *)); + if ( (image->dp == NULL) || (image->bad == NULL) + || (image->sat == NULL) ) + { + ERROR("Failed to allocate panels.\n"); + return 1; + } + + for ( pi=0; pi<image->det->n_panels; pi++ ) { + + struct panel *p; + int fs, ss; + + p = &image->det->panels[pi]; + image->dp[pi] = malloc(p->w*p->h*sizeof(float)); + image->bad[pi] = calloc(p->w*p->h, sizeof(int)); + image->sat[pi] = malloc(p->w*p->h*sizeof(float)); + if ( (image->dp[pi] == NULL) || (image->bad[pi] == NULL) + || (image->sat[pi] == NULL) ) + { + ERROR("Failed to allocate panel\n"); + return 1; + } + + if ( p->mask != NULL ) { + ERROR("WARNING: Bad pixel masks do not currently work " + "with CBF files\n"); + ERROR(" (bad pixel regions specified in the geometry " + "file will be used, however)\n"); + } + + if ( p->satmap != NULL ) { + ERROR("WARNING: Saturation maps do not currently work " + "with CBF files\n"); + } + + if ( (p->orig_min_fs + p->w > data_width) + || (p->orig_min_ss + p->h > data_height) ) + { + ERROR("Panel %s is outside range of data in CBF file\n", + p->name); + return 1; + } + + for ( ss=0; ss<p->h; ss++ ) { + for ( fs=0; fs<p->w; fs++ ) { + + int idx; + int cfs, css; + int bad = 0; + + cfs = fs+p->orig_min_fs; + css = ss+p->orig_min_ss; + idx = cfs + css*data_width; + + image->dp[pi][fs+p->w*ss] = data[idx]; + + if ( sat != NULL ) { + image->sat[pi][fs+p->w*ss] = sat[idx]; + } else { + image->sat[pi][fs+p->w*ss] = INFINITY; + } + + if ( p->no_index ) bad = 1; + + if ( in_bad_region(image->det, p, cfs, css) ) { + bad = 1; + } + + if ( flags != NULL ) { + + int f; + + f = flags[idx]; + + /* Bad if it's missing any of the "good" bits */ + if ( (f & image->det->mask_good) + != image->det->mask_good ) bad = 1; + + /* Bad if it has any of the "bad" bits. */ + if ( f & image->det->mask_bad ) bad = 1; + + } + image->bad[pi][fs+p->w*ss] = bad; + + } + } + + } + + return 0; +} + + +static void cbf_fill_in_beam_parameters(struct beam_params *beam, + struct imagefile *f, + struct image *image) +{ + double eV; + + if ( beam->photon_energy_from == NULL ) { + + /* Explicit value given */ + eV = beam->photon_energy; + + } else { + + ERROR("Can't get photon energy from CBF yet.\n"); + eV = 0.0; + + } + + image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale; +} + + +static void cbf_fill_in_clen(struct detector *det, struct imagefile *f) +{ + int i; + + for ( i=0; i<det->n_panels; i++ ) { + + struct panel *p = &det->panels[i]; + + if ( p->clen_from != NULL ) { + + ERROR("Can't get clen from CBF yet.\n"); + + } + + adjust_centering_for_rail(p); + + } +} + + +static int read_cbf(struct imagefile *f, struct image *image) +{ + cbf_handle cbfh; + FILE *fh; + int r; + unsigned int compression; + int binary_id, minelement, maxelement, elsigned, elunsigned; + size_t elsize, elements, elread, dimfast, dimmid, dimslow, padding; + const char *byteorder; + signed int *data; + + if ( image->det == NULL ) { + ERROR("read_cbf() needs a geometry\n"); + return 1; + } + + if ( cbf_make_handle(&cbfh) ) { + ERROR("Failed to allocate CBF handle\n"); + return 1; + } + + fh = fopen(f->filename, "rb"); + if ( fh == NULL ) { + ERROR("Failed to open '%s'\n", f->filename); + return 1; + } + /* CBFlib calls fclose(fh) when it's ready */ + + if ( cbf_read_widefile(cbfh, fh, 0) ) { + ERROR("Failed to read CBF file '%s'\n", f->filename); + cbf_free_handle(cbfh); + return 1; + } + + /* Select row 0 in data column inside array_data */ + cbf_find_category(cbfh, "array_data"); + cbf_find_column(cbfh, "data"); + cbf_select_row(cbfh, 0); + + /* Get parameters for array read */ + r = cbf_get_integerarrayparameters_wdims(cbfh, &compression, &binary_id, + &elsize, &elsigned, &elunsigned, + &elements, + &minelement, &maxelement, + &byteorder, + &dimfast, &dimmid, &dimslow, + &padding); + if ( r ) { + char *err = cbf_strerr(r); + ERROR("Failed to read CBF array parameters: %s\n", err); + free(err); + cbf_free_handle(cbfh); + return 1; + } + + if ( dimslow != 0 ) { + ERROR("CBF data array is 3D - don't know what to do with it\n"); + cbf_free_handle(cbfh); + return 1; + } + + if ( dimfast*dimmid*elsize > 10e9 ) { + ERROR("CBF data is far too big (%i x %i x %i bytes).\n", + (int)dimfast, (int)dimmid, (int)elsize); + cbf_free_handle(cbfh); + return 1; + } + + if ( elsize != 4 ) { + STATUS("Don't know what to do with element size %i\n", + (int)elsize); + cbf_free_handle(cbfh); + return 1; + } + + if ( strcmp(byteorder, "little_endian") != 0 ) { + STATUS("Don't know what to do with non-little-endian datan\n"); + cbf_free_handle(cbfh); + return 1; + } + + data = malloc(elsize*dimfast*dimmid); + if ( data == NULL ) { + ERROR("Failed to allocate memory for CBF data\n"); + cbf_free_handle(cbfh); + return 1; + } + + r = cbf_get_integerarray(cbfh, &binary_id, data, elsize, 1, + elsize*dimfast*dimmid, &elread); + if ( r ) { + char *err = cbf_strerr(r); + ERROR("Failed to read CBF array: %s\n", err); + free(err); + cbf_free_handle(cbfh); + return 1; + } + + unpack_panels(image, data, dimfast, dimmid); + free(data); + + if ( image->beam != NULL ) { + cbf_fill_in_beam_parameters(image->beam, f, image); + if ( image->lambda > 1000 ) { + ERROR("WARNING: Missing or nonsensical wavelength " + "(%e m) for %s.\n", + image->lambda, image->filename); + } + } + cbf_fill_in_clen(image->det, f); + fill_in_adu(image); + + cbf_free_handle(cbfh); + return 0; +} + + +static float *convert_float(signed int *data, int w, int h) +{ + float *df; + long int i; + + df = malloc(sizeof(float)*w*h); + if ( df == NULL ) return NULL; + + for ( i=0; i<w*h; i++ ) { + df[i] = data[i]; + } + + return df; +} + + +static int read_cbf_simple(struct imagefile *f, struct image *image) +{ + cbf_handle cbfh; + FILE *fh; + int r; + unsigned int compression; + int binary_id, minelement, maxelement, elsigned, elunsigned; + size_t elsize, elements, elread, dimfast, dimmid, dimslow, padding; + const char *byteorder; + signed int *data; + + if ( cbf_make_handle(&cbfh) ) { + ERROR("Failed to allocate CBF handle\n"); + return 1; + } + + fh = fopen(f->filename, "rb"); + if ( fh == NULL ) { + ERROR("Failed to open '%s'\n", f->filename); + return 1; + } + /* CBFlib calls fclose(fh) when it's ready */ + + if ( cbf_read_widefile(cbfh, fh, 0) ) { + ERROR("Failed to read CBF file '%s'\n", f->filename); + cbf_free_handle(cbfh); + return 1; + } + + /* Select row 0 in data column inside array_data */ + cbf_find_category(cbfh, "array_data"); + cbf_find_column(cbfh, "data"); + cbf_select_row(cbfh, 0); + + /* Get parameters for array read */ + r = cbf_get_integerarrayparameters_wdims(cbfh, &compression, &binary_id, + &elsize, &elsigned, &elunsigned, + &elements, + &minelement, &maxelement, + &byteorder, + &dimfast, &dimmid, &dimslow, + &padding); + if ( r ) { + char *err = cbf_strerr(r); + ERROR("Failed to read CBF array parameters: %s\n", err); + free(err); + cbf_free_handle(cbfh); + return 1; + } + + if ( dimslow != 0 ) { + ERROR("CBF data array is 3D - don't know what to do with it\n"); + cbf_free_handle(cbfh); + return 1; + } + + if ( dimfast*dimmid*elsize > 10e9 ) { + ERROR("CBF data is far too big (%i x %i x %i bytes).\n", + (int)dimfast, (int)dimmid, (int)elsize); + cbf_free_handle(cbfh); + return 1; + } + + if ( elsize != 4 ) { + STATUS("Don't know what to do with element size %i\n", + (int)elsize); + cbf_free_handle(cbfh); + return 1; + } + + if ( strcmp(byteorder, "little_endian") != 0 ) { + STATUS("Don't know what to do with non-little-endian datan\n"); + cbf_free_handle(cbfh); + return 1; + } + + data = malloc(elsize*dimfast*dimmid); + if ( data == NULL ) { + ERROR("Failed to allocate memory for CBF data\n"); + cbf_free_handle(cbfh); + return 1; + } + + r = cbf_get_integerarray(cbfh, &binary_id, data, elsize, 1, + elsize*dimfast*dimmid, &elread); + if ( r ) { + char *err = cbf_strerr(r); + ERROR("Failed to read CBF array: %s\n", err); + free(err); + cbf_free_handle(cbfh); + return 1; + } + + image->det = simple_geometry(image, dimfast, dimmid); + image->dp = malloc(sizeof(float *)); + if ( image->dp == NULL ) { + ERROR("Failed to allocate dp array\n"); + return 1; + } + image->dp[0] = convert_float(data, dimfast, dimmid); + if ( image->dp[0] == NULL ) { + ERROR("Failed to allocate dp array\n"); + return 1; + } + + if ( image->beam != NULL ) { + cbf_fill_in_beam_parameters(image->beam, f, image); + if ( image->lambda > 1000 ) { + ERROR("WARNING: Missing or nonsensical wavelength " + "(%e m) for %s.\n", + image->lambda, image->filename); + } + } + cbf_fill_in_clen(image->det, f); + fill_in_adu(image); + + cbf_free_handle(cbfh); + return 0; +} + + +/****************************** Image files ***********************************/ + + +static signed int is_cbf_file(const char *filename) +{ + FILE *fh; + char line[1024]; + + fh = fopen(filename, "r"); + if ( fh == NULL ) return -1; + + if ( fgets(line, 1024, fh) == NULL ) return -1; + fclose(fh); + + if ( strstr(line, "CBF") == NULL ) { + return 0; + } + + return 1; +} + + +struct imagefile *imagefile_open(const char *filename) +{ + struct imagefile *f; + + f = malloc(sizeof(struct imagefile)); + if ( f == NULL ) return NULL; + + if ( H5Fis_hdf5(filename) > 0 ) { + + /* This is an HDF5, pass through to HDF5 layer */ + f->type = IMAGEFILE_HDF5; + f->hdfile = hdfile_open(filename); + + if ( f->hdfile == NULL ) { + free(f); + return NULL; + } + + } else if ( is_cbf_file(filename) > 0 ) { + + f->type = IMAGEFILE_CBF; + + } + + f->filename = strdup(filename); + return f; +} + + +int imagefile_read(struct imagefile *f, struct image *image, + struct event *event) +{ + if ( f->type == IMAGEFILE_HDF5 ) { + return hdf5_read2(f->hdfile, image, event, 0); + } else if ( f->type == IMAGEFILE_CBF ) { + return read_cbf(f, image); + } else { + ERROR("Unknown file type %i\n", f->type); + return 1; + } +} + + +/* Read a simple file, no multi-event, no prior geometry etc, and + * generate a geometry for it */ +int imagefile_read_simple(struct imagefile *f, struct image *image) +{ + if ( f->type == IMAGEFILE_HDF5 ) { + return hdf5_read(f->hdfile, image, NULL, 0); + } else { + return read_cbf_simple(f, image); + } +} + + +enum imagefile_type imagefile_get_type(struct imagefile *f) +{ + assert(f != NULL); + return f->type; +} + + +struct hdfile *imagefile_get_hdfile(struct imagefile *f) +{ + if ( f->type != IMAGEFILE_HDF5 ) { + ERROR("Not an HDF5 file!\n"); + return NULL; + } + + return f->hdfile; +} + + +void imagefile_copy_fields(struct imagefile *f, + const struct imagefile_field_list *copyme, + FILE *fh, struct event *ev) +{ + int i; + + if ( copyme == NULL ) return; + + for ( i=0; i<copyme->n_fields; i++ ) { + + char *val; + char *field; + + field = copyme->fields[i]; + + if ( f->type == IMAGEFILE_HDF5 ) { + val = hdfile_get_string_value(f->hdfile, field, ev); + if ( field[0] == '/' ) { + fprintf(fh, "hdf5%s = %s\n", field, val); + } else { + fprintf(fh, "hdf5/%s = %s\n", field, val); + } + free(val); + + } else { + STATUS("Mock CBF variable\n"); + fprintf(fh, "cbf/%s = %s\n", field, "(FIXME)"); + } + + + } +} + + +void imagefile_close(struct imagefile *f) +{ + if ( f->type == IMAGEFILE_HDF5 ) { + hdfile_close(f->hdfile); + } + free(f->filename); + free(f); +} diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 9fd9b495..ead5cd4d 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -3,11 +3,11 @@ * * Handle images and image features * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2009-2016 Thomas White <taw@physics.org> + * 2009-2017 Thomas White <taw@physics.org> * 2014 Valerio Mariani * * @@ -44,6 +44,8 @@ struct detector; struct imagefeature; struct sample; struct image; +struct imagefile; +struct imagefile_field_list; #include "utils.h" #include "cell.h" @@ -51,6 +53,7 @@ struct image; #include "reflist.h" #include "crystal.h" #include "index.h" +#include "events.h" /** * SpectrumType: @@ -87,6 +90,15 @@ struct imagefeature { const char *name; }; + +/* An enum representing the image file formats we can handle */ +enum imagefile_type +{ + IMAGEFILE_HDF5, + IMAGEFILE_CBF +}; + + /* An opaque type representing a list of image features */ typedef struct _imagefeaturelist ImageFeatureList; @@ -120,7 +132,7 @@ struct beam_params * struct detector *det; * struct beam_params *beam; * char *filename; - * const struct copy_hdf5_field *copyme; + * const struct imagefile_field_list *copyme; * * int id; * @@ -152,8 +164,8 @@ struct beam_params * returned by the low-level indexing system. <structfield>n_crystals</structfield> * is the number of crystals which were found in the image. * - * <structfield>copyme</structfield> represents a list of HDF5 fields to copy - * to the output stream. + * <structfield>copyme</structfield> represents a list of fields in the image + * file (e.g. HDF5 fields or CBF headers) to copy to the output stream. **/ struct image; @@ -171,7 +183,7 @@ struct image { struct beam_params *beam; /* The nominal beam parameters */ char *filename; struct event *event; - const struct copy_hdf5_field *copyme; + const struct imagefile_field_list *copyme; struct stuff_from_stream *stuff_from_stream; double avg_clen; /* Average camera length extracted @@ -233,6 +245,25 @@ extern void image_add_crystal(struct image *image, Crystal *cryst); extern void remove_flagged_crystals(struct image *image); extern void free_all_crystals(struct image *image); +/* Image files */ +extern struct imagefile *imagefile_open(const char *filename); +extern int imagefile_read(struct imagefile *f, struct image *image, + struct event *event); +extern int imagefile_read_simple(struct imagefile *f, struct image *image); +extern struct hdfile *imagefile_get_hdfile(struct imagefile *f); +extern enum imagefile_type imagefile_get_type(struct imagefile *f); +extern void imagefile_copy_fields(struct imagefile *f, + const struct imagefile_field_list *copyme, + FILE *fh, struct event *ev); +extern void imagefile_close(struct imagefile *f); + +/* Field lists */ +extern struct imagefile_field_list *new_imagefile_field_list(void); +extern void free_imagefile_field_list(struct imagefile_field_list *f); + +extern void add_imagefile_field(struct imagefile_field_list *copyme, + const char *name); + #ifdef __cplusplus } #endif diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index 17da74b2..fb4b0c70 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -806,8 +806,8 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections) } -int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile, - int include_peaks, int include_reflections, struct event* ev) +int write_chunk(Stream *st, struct image *i, struct imagefile *imfile, + int include_peaks, int include_reflections, struct event *ev) { int j; char *indexer; @@ -832,7 +832,7 @@ int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile, fprintf(st->fh, "beam_divergence = %.2e rad\n", i->div); fprintf(st->fh, "beam_bandwidth = %.2e (fraction)\n", i->bw); - copy_hdf5_fields(hdfile, i->copyme, st->fh, ev); + imagefile_copy_fields(imfile, i->copyme, st->fh, ev); if ( i->det != NULL ) { diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h index ff8628c0..764e3e36 100644 --- a/libcrystfel/src/stream.h +++ b/libcrystfel/src/stream.h @@ -3,11 +3,11 @@ * * Stream tools * - * Copyright © 2013-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2013-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2014 Thomas White <taw@physics.org> + * 2010-2017 Thomas White <taw@physics.org> * 2014 Valerio Mariani * 2011 Andrew Aquila * @@ -39,6 +39,7 @@ struct image; struct hdfile; struct event; +struct imagefile; #include "cell.h" #define GEOM_START_MARKER "----- Begin geometry file -----" @@ -106,10 +107,15 @@ extern int read_chunk(Stream *st, struct image *image); extern int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf); -extern int write_chunk(Stream *st, struct image *image, struct hdfile *hdfile, +extern int write_chunk(Stream *st, struct image *image, struct imagefile *imfile, int include_peaks, int include_reflections, struct event *ev); +extern int write_chunk_2(Stream *st, struct image *image, + struct imagefile *imfile, + int include_peaks, int include_reflections, + struct event *ev); + extern void write_command(Stream *st, int argc, char *argv[]); extern void write_geometry_file(Stream *st, const char *geom_filename); extern int rewind_stream(Stream *st); |