diff options
| -rw-r--r-- | libcrystfel/src/image-cbf.c | 10 | ||||
| -rw-r--r-- | libcrystfel/src/image-cbf.h | 3 | ||||
| -rw-r--r-- | libcrystfel/src/image-hdf5.c | 109 | ||||
| -rw-r--r-- | libcrystfel/src/image-hdf5.h | 6 | ||||
| -rw-r--r-- | libcrystfel/src/image-msgpack.c | 67 | ||||
| -rw-r--r-- | libcrystfel/src/image-msgpack.h | 6 | ||||
| -rw-r--r-- | libcrystfel/src/image.c | 153 | ||||
| -rw-r--r-- | libcrystfel/src/image.h | 24 | ||||
| -rw-r--r-- | libcrystfel/src/stream.c | 64 |
9 files changed, 278 insertions, 164 deletions
diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c index 2ea5f0a5..19b38607 100644 --- a/libcrystfel/src/image-cbf.c +++ b/libcrystfel/src/image-cbf.c @@ -630,3 +630,13 @@ int image_cbf_read(struct image *image, return 0; } + + +int image_cbf_read_header_to_cache(struct image *image, + const char *from) +{ + /* FIXME: Implementation + * https://gitlab.desy.de/thomas.white/crystfel/-/issues/10 */ + ERROR("Reading headers from CBF files is not currently supported.\n"); + return 1; +} diff --git a/libcrystfel/src/image-cbf.h b/libcrystfel/src/image-cbf.h index ca79a1a3..f6936981 100644 --- a/libcrystfel/src/image-cbf.h +++ b/libcrystfel/src/image-cbf.h @@ -53,4 +53,7 @@ extern int image_cbf_read_mask(struct panel_template *p, int gz, int *bad, int mask_good, int mask_bad); +extern int image_cbf_read_header_to_cache(struct image *image, + const char *from); + #endif /* IMAGE_CBF_H */ diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c index c939e136..2995654d 100644 --- a/libcrystfel/src/image-hdf5.c +++ b/libcrystfel/src/image-hdf5.c @@ -633,8 +633,7 @@ int image_hdf5_read_mask(struct panel_template *p, } -double image_hdf5_get_value(const char *name, const char *filename, - const char *event, char *ptype) +int image_hdf5_read_header_to_cache(struct image *image, const char *name) { hid_t dh; hid_t type; @@ -653,47 +652,44 @@ double image_hdf5_get_value(const char *name, const char *filename, int i; char *subst_name = NULL; hid_t fh; - double val; int *dim_vals; int n_dim_vals; int dim_val_pos; - if ( access(filename, R_OK) == -1 ) { - ERROR("File does not exist or cannot be read: %s\n", filename); - return NAN; + if ( access(image->filename, R_OK) == -1 ) { + ERROR("File does not exist or cannot be read: %s\n", + image->filename); + return 1; } - fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT); + fh = H5Fopen(image->filename, H5F_ACC_RDONLY, H5P_DEFAULT); if ( fh < 0 ) { - ERROR("Couldn't open file: %s\n", filename); - return NAN; + ERROR("Couldn't open file: %s\n", image->filename); + return 1; } - subst_name = substitute_path(event, name, 1); + subst_name = substitute_path(image->ev, name, 1); if ( subst_name == NULL ) { - ERROR("Invalid event ID '%s'\n", event); + ERROR("Invalid event ID '%s'\n", image->ev); close_hdf5(fh); - return NAN; + return 1; } dh = H5Dopen2(fh, subst_name, H5P_DEFAULT); if ( dh < 0 ) { ERROR("No such numeric field '%s'\n", subst_name); close_hdf5(fh); - return NAN; + return 1; } type = H5Dget_type(dh); class = H5Tget_class(type); - if ( class == H5T_FLOAT ) { - *ptype = 'f'; - } else if ( class == H5T_INTEGER ) { - *ptype = 'i'; - } else { + /* FIXME: Handle strings as well */ + if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) { ERROR("Not a floating point or integer value.\n"); close_hdf5(fh); - return NAN; + return 1; } /* Get the dimensionality. We have to cope with scalars expressed as @@ -703,7 +699,7 @@ double image_hdf5_get_value(const char *name, const char *filename, if ( ndims > 64 ) { ERROR("Too many dimensions for numeric value\n"); close_hdf5(fh); - return NAN; + return 1; } H5Sget_simple_extent_dims(sh, size, NULL); @@ -719,37 +715,42 @@ double image_hdf5_get_value(const char *name, const char *filename, if ( class == H5T_FLOAT ) { - r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, &val); + double val; + r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, + &val); if ( r < 0 ) { ERROR("Couldn't read scalar value from %s.\n", subst_name); free(subst_name); close_hdf5(fh); - return NAN; + return 1; } - return val; + image_cache_header_float(image, name, val); + return 0; } else { - int vali; - r = H5Dread(dh, H5T_NATIVE_INT, ms, sh, H5P_DEFAULT, &vali); + int val; + r = H5Dread(dh, H5T_NATIVE_INT, ms, sh, H5P_DEFAULT, + &val); if ( r < 0 ) { ERROR("Couldn't read scalar value from %s.\n", subst_name); free(subst_name); close_hdf5(fh); - return NAN; + return 1; } - return vali; + image_cache_header_int(image, name, val); + return 0; } } - dim_vals = read_dim_parts(event, &n_dim_vals); + dim_vals = read_dim_parts(image->ev, &n_dim_vals); if ( dim_vals == NULL ) { ERROR("Couldn't parse event '%s'\n"); close_hdf5(fh); - return NAN; + return 1; } f_offset = malloc(ndims*sizeof(hsize_t)); @@ -757,7 +758,7 @@ double image_hdf5_get_value(const char *name, const char *filename, if ( (f_offset == NULL) || (f_count == NULL) ) { ERROR("Couldn't allocate dimension arrays\n"); close_hdf5(fh); - return NAN; + return 1; } /* Every dimension of the dataset must either be size 1 or @@ -774,7 +775,7 @@ double image_hdf5_get_value(const char *name, const char *filename, subst_name, i, dim_vals[dim_val_pos], size[i]); close_hdf5(fh); - return NAN; + return 1; } f_offset[i] = dim_vals[dim_val_pos]; @@ -790,6 +791,8 @@ double image_hdf5_get_value(const char *name, const char *filename, } + free(subst_name); + check = H5Sselect_hyperslab(sh, H5S_SELECT_SET, f_offset, NULL, f_count, NULL); if ( check <0 ) { @@ -797,33 +800,49 @@ double image_hdf5_get_value(const char *name, const char *filename, free(f_offset); free(f_count); close_hdf5(fh); - return NAN; + return 1; } + free(f_offset); + free(f_count); + ms = H5Screate_simple(1,msdims,NULL); check = H5Sselect_hyperslab(ms, H5S_SELECT_SET, m_offset, NULL, m_count, NULL); if ( check < 0 ) { ERROR("Error selecting memory dataspace for float value\n"); - free(f_offset); - free(f_count); close_hdf5(fh); - return NAN; + return 1; } - r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, &val); - if ( r < 0 ) { - ERROR("Couldn't read value.\n"); + if ( class == H5T_FLOAT ) { + + double val; + r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, &val); + if ( r < 0 ) { + ERROR("Couldn't read value.\n"); + close_hdf5(fh); + return 1; + } + + image_cache_header_float(image, name, val); close_hdf5(fh); - return NAN; - } + return 0; - free(f_offset); - free(f_count); - free(subst_name); - close_hdf5(fh); + } else { - return val; + int val; + r = H5Dread(dh, H5T_NATIVE_INT, ms, sh, H5P_DEFAULT, &val); + if ( r < 0 ) { + ERROR("Couldn't read value.\n"); + close_hdf5(fh); + return 1; + } + + image_cache_header_int(image, name, val); + close_hdf5(fh); + return 0; + } } diff --git a/libcrystfel/src/image-hdf5.h b/libcrystfel/src/image-hdf5.h index 4c36cf89..239bb20d 100644 --- a/libcrystfel/src/image-hdf5.h +++ b/libcrystfel/src/image-hdf5.h @@ -34,10 +34,8 @@ #include "datatemplate_priv.h" -extern double image_hdf5_get_value(const char *from, - const char *filename, - const char *ev, - char *type); +extern int image_hdf5_read_header_to_cache(struct image *image, + const char *name); extern int image_hdf5_read(struct image *image, const DataTemplate *dtempl, diff --git a/libcrystfel/src/image-msgpack.c b/libcrystfel/src/image-msgpack.c index 0f5ab746..6785fd5f 100644 --- a/libcrystfel/src/image-msgpack.c +++ b/libcrystfel/src/image-msgpack.c @@ -242,93 +242,76 @@ static char *terminate_str(const char *ptr, size_t len) } -double image_msgpack_get_value(const char *name, - void *data_block, - size_t data_block_size, - char *ptype) +int image_msgpack_read_header_to_cache(struct image *image, + const char *name) { msgpack_unpacked unpacked; msgpack_object *value_obj; msgpack_object *obj; int r; - float val = NAN; char *str; - *ptype = 'x'; - - if ( data_block == NULL ) { + if ( image->data_block == NULL ) { ERROR("No MsgPack data!\n"); - goto out; + return 1; } msgpack_unpacked_init(&unpacked); - r = msgpack_unpack_next(&unpacked, data_block, data_block_size, NULL); + r = msgpack_unpack_next(&unpacked, image->data_block, + image->data_block_size, NULL); if ( r != MSGPACK_UNPACK_SUCCESS ) { ERROR("MessagePack unpack failed: %i\n", r); - goto out; + return 1; } obj = find_main_object(&unpacked); if ( obj == NULL ) { ERROR("Failed to find main MsgPack object.\n"); msgpack_unpacked_destroy(&unpacked); - goto out; + return 1; } value_obj = find_msgpack_kv(obj, name); if ( value_obj == NULL ) { ERROR("Couldn't find '%s' in MessagePack object\n", name); msgpack_unpacked_destroy(&unpacked); - goto out; + return 1; } switch ( value_obj->type ) { case MSGPACK_OBJECT_FLOAT64: case MSGPACK_OBJECT_FLOAT32: - //case MSGPACK_OBJECT_FLOAT: - *ptype = 'f'; - val = value_obj->via.f64; - break; + image_cache_header_float(image, name, value_obj->via.f64); + msgpack_unpacked_destroy(&unpacked); + return 0; case MSGPACK_OBJECT_POSITIVE_INTEGER: case MSGPACK_OBJECT_NEGATIVE_INTEGER: - *ptype = 'i'; - val = value_obj->via.i64; - break; + image_cache_header_int(image, name, value_obj->via.i64); + msgpack_unpacked_destroy(&unpacked); + return 0; case MSGPACK_OBJECT_STR: str = terminate_str(value_obj->via.str.ptr, value_obj->via.str.size); - if ( str != NULL ) { - int ival; - if ( convert_int(str, &ival) == 0 ) { - *ptype = 'i'; - val = ival; - } else { - ERROR("MsgPack header %s has a string type (%s)" - "(need a number, and can't convert).\n", - name, str); - val = NAN; - } - free(str); - } else { - ERROR("Failed to read MsgPack string (%s)\n", name); - val = NAN; + if ( str == NULL ) { + msgpack_unpacked_destroy(&unpacked); + return 1; } - break; + + image_cache_header_str(image, name, str); + free(str); + msgpack_unpacked_destroy(&unpacked); + return 0; default: ERROR("Unrecognised MsgPack type %i (%s)\n", value_obj->type, name); - break; + msgpack_unpacked_destroy(&unpacked); + return 1; } - - msgpack_unpacked_destroy(&unpacked); - -out: - return val; } diff --git a/libcrystfel/src/image-msgpack.h b/libcrystfel/src/image-msgpack.h index 26cf6b4e..738adc91 100644 --- a/libcrystfel/src/image-msgpack.h +++ b/libcrystfel/src/image-msgpack.h @@ -42,9 +42,7 @@ extern ImageFeatureList *image_msgpack_read_peaks(const DataTemplate *dtempl, size_t data_size, int half_pixel_shift); -extern double image_msgpack_get_value(const char *name, - void *data_block, - size_t data_block_size, - char *ptype); +extern int image_msgpack_read_header_to_cache(struct image *image, + const char *name); #endif /* IMAGE_MSGPACK_H */ diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 1e2b7a3c..97112fa3 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -307,7 +307,7 @@ void image_cache_header_int(struct image *image, if ( ce != NULL ) { ce->header_name = strdup(header_name); ce->val_int = header_val; - ce->type = 'i'; + ce->type = HEADER_INT; image->header_cache[image->n_cached_headers++] = ce; } else { ERROR("Failed to add header cache entry.\n"); @@ -318,7 +318,7 @@ void image_cache_header_int(struct image *image, void image_cache_header_float(struct image *image, const char *header_name, - float header_val) + double header_val) { if ( image->n_cached_headers >= HEADER_CACHE_SIZE ) { ERROR("Too many headers to copy.\n"); @@ -330,7 +330,7 @@ void image_cache_header_float(struct image *image, if ( ce != NULL ) { ce->header_name = strdup(header_name); ce->val_float = header_val; - ce->type = 'f'; + ce->type = HEADER_FLOAT; image->header_cache[image->n_cached_headers++] = ce; } else { ERROR("Failed to add header cache entry.\n"); @@ -339,77 +339,130 @@ void image_cache_header_float(struct image *image, } -static double get_value(struct image *image, const char *from, - int *is_literal_number) +void image_cache_header_str(struct image *image, + const char *header_name, + const char *header_val) { - double val; - char *rval; - struct header_cache_entry *ce; - char type; + if ( image->n_cached_headers >= HEADER_CACHE_SIZE ) { + ERROR("Too many headers to copy.\n"); + } else { - if ( from == NULL ) return NAN; + struct header_cache_entry *ce; + ce = malloc(sizeof(struct header_cache_entry)); - val = strtod(from, &rval); - if ( (*rval == '\0') && (rval != from) ) { - if ( is_literal_number != NULL ) { - *is_literal_number = 1; + if ( ce != NULL ) { + ce->header_name = strdup(header_name); + ce->val_str = strdup(header_val); + ce->type = HEADER_STR; + image->header_cache[image->n_cached_headers++] = ce; + } else { + ERROR("Failed to add header cache entry.\n"); } - return val; } +} + + +static int read_header_to_cache(struct image *image, const char *from) +{ + switch ( image->data_source_type ) { + + case DST_HDF5: + return image_hdf5_read_header_to_cache(image, from); + + case DST_CBF: + case DST_CBFGZ: + return image_cbf_read_header_to_cache(image, from); + + case DST_MSGPACK: + return image_msgpack_read_header_to_cache(image, from); + + default: + ERROR("Unrecognised file type %i (read_header_to_cache)\n", + image->data_source_type); + return 1; + + } +} + + +static struct header_cache_entry *cached_header(struct image *image, const char *from) +{ + struct header_cache_entry *ce; if ( image == NULL ) { ERROR("Attempt to retrieve a header value without an image\n"); - return NAN; + return NULL; } ce = find_cache_entry(image, from); - if ( ce != NULL ) { - if ( ce->type == 'f' ) { - return ce->val_float; - } else if ( ce->type == 'i' ) { - return ce->val_int; - } else { - ERROR("Unrecognised header cache type '%c'\n", - ce->type); - return NAN; - } + if ( ce != NULL ) return ce; + /* Try to get the value from the file */ + if ( read_header_to_cache(image, from) == 0 ) { + return find_cache_entry(image, from); } else { + ERROR("Couldn't find header value '%s'\n", from); + return NULL; + } +} - switch ( image->data_source_type ) { - case DST_HDF5: - val = image_hdf5_get_value(from, image->filename, - image->ev, &type); - break; +int image_read_header_float(struct image *image, const char *from, double *val) +{ + struct header_cache_entry *ce; - case DST_CBF: - case DST_CBFGZ: - /* FIXME: Implementation */ - val = NAN; - break; + ce = cached_header(image, from); + if ( ce == NULL ) return 1; - case DST_MSGPACK: - val = image_msgpack_get_value(from, image->data_block, - image->data_block_size, - &type); - break; + switch ( ce->type ) { - default: - ERROR("Unrecognised file type %i (get_value)\n", - image->data_source_type); - return 1; + case HEADER_FLOAT: + *val = ce->val_float; + return 0; + + case HEADER_INT: + *val = ce->val_int; + return 0; + case HEADER_STR: + if ( convert_float(ce->val_str, val) == 0 ) { + return 0; + } else { + ERROR("Value '%s' (%s) can't be converted to float\n", + ce->val_str, from); + return 1; } + default: + ERROR("Unrecognised header cache type %i\n", ce->type); + return 1; + } +} + +static double get_value(struct image *image, const char *from, + int *is_literal_number) +{ + double val; + char *rval; + + if ( from == NULL ) return NAN; + + val = strtod(from, &rval); + if ( (*rval == '\0') && (rval != from) ) { + if ( is_literal_number != NULL ) { + *is_literal_number = 1; + } + return val; } - if ( type == 'f' ) { - image_cache_header_float(image, from, val); - } else if ( type == 'i' ) { - image_cache_header_int(image, from, val); + if ( is_literal_number != NULL ) { + *is_literal_number = 0; + } + if ( image_read_header_float(image, from, &val) == 0 ) { + return val; + } else { + return NAN; /* FIXME: Use out-of-band flag */ } - return val; } diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 045f3e77..0d8e7166 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -78,12 +78,20 @@ typedef struct _imagefeaturelist ImageFeatureList; #define HEADER_CACHE_SIZE (128) +typedef enum +{ + HEADER_FLOAT, + HEADER_INT, + HEADER_STR +} HeaderCacheType; + struct header_cache_entry { char *header_name; - char type; + HeaderCacheType type; union { int val_int; - float val_float; + double val_float; + char *val_str; }; }; @@ -221,14 +229,24 @@ extern struct image *image_read_data_block(const DataTemplate *dtempl, int no_mask_data); extern void image_free(struct image *image); +extern int image_read_header_float(struct image *image, const char *from, + double *val); + +/* NB image_read_header_int and image_read_header_str should exist, but there + * is currently no use for them. Get in touch if you disagree! */ + extern void image_cache_header_float(struct image *image, const char *header_name, - float header_val); + double header_val); extern void image_cache_header_int(struct image *image, const char *header_name, int header_val); +extern void image_cache_header_str(struct image *image, + const char *header_name, + const char *header_val); + extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl, const char *filename, const char *event, diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index 89f59ddc..47438614 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -638,15 +638,27 @@ int stream_write_chunk(Stream *st, const struct image *i, for ( j=0; j<i->n_cached_headers; j++ ) { struct header_cache_entry *ce = i->header_cache[j]; - if ( ce->type == 'f' ) { + switch ( ce->type ) { + + case HEADER_FLOAT: fprintf(st->fh, "header/float/%s = %f\n", ce->header_name, ce->val_float); - } else if ( ce->type == 'i' ) { + break; + + case HEADER_INT: fprintf(st->fh, "header/int/%s = %i\n", ce->header_name, ce->val_int); - } else { - ERROR("Unrecognised header cache type '%c'\n", - ce->type); + break; + + case HEADER_STR: + fprintf(st->fh, "header/str/%s = %s\n", + ce->header_name, ce->val_str); + break; + + default: + ERROR("Unrecognised header cache type %i\n", ce->type); + break; + } } @@ -899,12 +911,14 @@ static void read_crystal(Stream *st, struct image *image, } -static void parse_header(const char *line_in, struct image *image, char type) +static void parse_header(const char *line_in, struct image *image, + HeaderCacheType type) { char *line; char *pos; line = strdup(line_in); + chomp(line); pos = strchr(line, ' '); if ( pos == NULL ) { @@ -923,20 +937,34 @@ static void parse_header(const char *line_in, struct image *image, char type) return; } - if ( type == 'f' ) { - float v; - if ( sscanf(pos+3, "%f", &v) != 1 ) { + switch ( type ) { + + double vf; + int vi; + + case HEADER_FLOAT: + if ( convert_float(pos+3, &vf) != 0 ) { ERROR("Invalid header line '%s' (invalid value)\n", line); return; } - image_cache_header_float(image, line, v); - } else { - int v; - if ( sscanf(pos+3, "%i", &v) != 1 ) { + image_cache_header_float(image, line, vf); + break; + + case HEADER_INT: + if ( convert_int(pos+3, &vi) != 0 ) { ERROR("Invalid header line '%s' (invalid value)\n", line); return; } - image_cache_header_int(image, line, v); + image_cache_header_int(image, line, vi); + break; + + case HEADER_STR: + image_cache_header_str(image, line, pos+3); + break; + + default: + ERROR("Unrecognised header cache type %i (from stream)\n", type); + break; } } @@ -983,11 +1011,15 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf) } if ( strncmp(line, "header/int/", 11) == 0 ) { - parse_header(line+11, image, 'i'); + parse_header(line+11, image, HEADER_INT); } if ( strncmp(line, "header/float/", 13) == 0 ) { - parse_header(line+13, image, 'f'); + parse_header(line+13, image, HEADER_FLOAT); + } + + if ( strncmp(line, "header/str/", 13) == 0 ) { + parse_header(line+11, image, HEADER_STR); } if ( strncmp(line, "indexed_by = ", 13) == 0 ) { |