From f18ac239e4f3489282d54b5bff3232f9e24acda6 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 15 Apr 2019 18:28:54 +0200 Subject: Basic CBF reader with byte offset decompression --- libcrystfel/src/image.c | 197 ++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 159 insertions(+), 38 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 2306d6e7..d2d68a62 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -547,50 +547,85 @@ static void cbf_fill_in_clen(struct detector *det, struct imagefile *f) } -static float *convert_sint32_float(int32_t *data, int w, int h) +static void add_out(float val, float *data_out, int nmemb_out, + int *outpos, int *nrej) { - float *df; - long int i; - - df = malloc(sizeof(float)*w*h); - if ( df == NULL ) return NULL; - - for ( i=0; i= -127) && (delta <= 127) ) { + val += delta; + add_out(val, data_out, nmemb_out, &outpos, &nrej); + continue; + } + + delta = *(int16_t *)(data_in+inpos); + inpos += 2; + + if ( (delta >= -32767) && (delta <= 32767) ) { + val += delta; + add_out(val, data_out, nmemb_out, &outpos, &nrej); + continue; + } + + delta = *(int32_t *)(data_in+inpos); + inpos += 4; + + if ( (delta >= -2147483647) && (delta <= 2147483647) ) { + val += delta; + add_out(val, data_out, nmemb_out, &outpos, &nrej); + continue; + } + + delta = *(int64_t *)(data_in+inpos); + inpos += 8; + val += delta; + add_out(val, data_out, nmemb_out, &outpos, &nrej); - df = malloc(sizeof(float)*w*h); - if ( df == NULL ) return NULL; + } - for ( i=0; i 0 ) { + STATUS("%i elements rejected\n", nrej); } +} - return df; + +static int binary_start(char *data) +{ + char *datac = data; + if ( (datac[0] == (char)0x0c) && (datac[1] == (char)0x1a) + && (datac[2] == (char)0x04) && (datac[3] == (char)0xd5) ) return 1; + return 0; } -static float *read_cbf_data(struct imagefile *f, int *w, int *h, cbf_handle *pcbfh) +static float *read_cbf_data(struct imagefile *f, int *w, int *h) { - 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; - void *data; - float *dataf; void *buf = NULL; + char *rval; + size_t data_compressed_len = 0; + float *data_out = NULL; + + *w = 0; + *h = 0; if ( f->type == IMAGEFILE_CBF ) { @@ -641,11 +676,101 @@ static float *read_cbf_data(struct imagefile *f, int *w, int *h, cbf_handle *pcb return NULL; } + /* .... read data .... */ + do { + + char line[1024]; + long line_start; + + line_start = ftell(fh); + rval = fgets(line, 1023, fh); + if ( rval == NULL ) break; + chomp(line); + + if ( strncmp(line, "X-Binary-Size: ", 15) == 0 ) { + data_compressed_len = atoi(line+15); + } + + if ( strncmp(line, "X-Binary-Size-Fastest-Dimension: ", 33) == 0 ) { + *w = atoi(line+33); + } + + if ( strncmp(line, "X-Binary-Size-Second-Dimension: ", 32) == 0 ) { + *h = atoi(line+32); + } + + if ( strncmp(line, "X-Binary-Element-Type: ", 23) == 0 ) { + STATUS("binary type: %s\n", line+23); + } + + if ( binary_start(line) ) { + + size_t len_read; + int nmemb_exp; + int8_t *data_compressed; + + if ( data_compressed_len == 0 ) { + ERROR("Found CBF data before X-Binary-Size!\n"); + free(buf); + fclose(fh); + return NULL; + } + + if ( (*w == 0) || (*h == 0) ) { + ERROR("Found CBF data before dimensions!\n"); + free(buf); + fclose(fh); + return NULL; + } + + if ( data_compressed_len > 100*1024*1024 ) { + ERROR("Stated CBF data size too big\n"); + free(buf); + fclose(fh); + return NULL; + } + + data_compressed = malloc(data_compressed_len); + if ( data_compressed == NULL ) { + ERROR("Failed to allocate memory for CBF data\n"); + free(buf); + fclose(fh); + return NULL; + } + + fseek(fh, line_start+4, SEEK_SET); + len_read = fread(data_compressed, 1, data_compressed_len, fh); + if ( len_read < data_compressed_len ) { + ERROR("Couldn't read entire CBF data\n"); + free(buf); + free(data_compressed); + fclose(fh); + return NULL; + } + + nmemb_exp = (*w) * (*h); + data_out = malloc(nmemb_exp*sizeof(float)); + if ( data_out == NULL ) { + ERROR("Failed to allocate memory for CBF data\n"); + free(buf); + free(data_compressed); + fclose(fh); + return NULL; + } + + decode_cbf_byte_offset(data_out, nmemb_exp, + data_compressed, + data_compressed_len); + + free(data_compressed); + + } + + } while ( rval != NULL ); + + free(buf); /* might be NULL */ - *w = dimfast; - *h = dimmid; - *pcbfh = cbfh; - return dataf; + return data_out; } @@ -653,9 +778,8 @@ static int read_cbf(struct imagefile *f, struct image *image) { float *data; int w, h; - cbf_handle cbfh; - data = read_cbf_data(f, &w, &h, &cbfh); + data = read_cbf_data(f, &w, &h); if ( data == NULL ) { ERROR("Failed to read CBF data\n"); return 1; @@ -675,7 +799,6 @@ static int read_cbf(struct imagefile *f, struct image *image) cbf_fill_in_clen(image->det, f); fill_in_adu(image); - cbf_free_handle(cbfh); return 0; } @@ -684,9 +807,8 @@ static int read_cbf_simple(struct imagefile *f, struct image *image) { float *data; int w, h; - cbf_handle cbfh; - data = read_cbf_data(f, &w, &h, &cbfh); + data = read_cbf_data(f, &w, &h); if ( data == NULL ) { ERROR("Failed to read CBF data\n"); return 1; @@ -712,7 +834,6 @@ static int read_cbf_simple(struct imagefile *f, struct image *image) cbf_fill_in_clen(image->det, f); fill_in_adu(image); - cbf_free_handle(cbfh); return 0; } -- cgit v1.2.3