diff options
| -rw-r--r-- | libcrystfel/CMakeLists.txt | 6 | ||||
| -rw-r--r-- | libcrystfel/src/image.c | 76 | ||||
| -rw-r--r-- | libcrystfel/src/image.h | 3 |
3 files changed, 76 insertions, 9 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt index 4651aeb1..3d7bec38 100644 --- a/libcrystfel/CMakeLists.txt +++ b/libcrystfel/CMakeLists.txt @@ -6,6 +6,7 @@ find_package(XGANDALF) find_package(PINKINDEXER) find_package(NBP) find_package(FDIP) +find_package(ZLIB REQUIRED) pkg_search_module(FFTW fftw3) set(HAVE_CURSES ${CURSES_FOUND}) @@ -125,8 +126,9 @@ target_include_directories(${PROJECT_NAME} INTERFACE ${PROJECT_SOURCE_DIR}/src) include_directories(${CMAKE_CURRENT_BINARY_DIR}) add_definitions(-DHAVE_CONFIG_H) -target_include_directories(${PROJECT_NAME} PRIVATE ${HDF5_INCLUDE_DIRS}) -target_link_libraries(${PROJECT_NAME} PRIVATE util ${HDF5_C_LIBRARIES} Threads::Threads GSL::gsl m) +target_include_directories(${PROJECT_NAME} PRIVATE ${HDF5_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS}) +target_link_libraries(${PROJECT_NAME} PRIVATE util ${HDF5_C_LIBRARIES} ${ZLIB_LIBRARIES} + Threads::Threads GSL::gsl m) if (XGANDALF_FOUND) target_include_directories(${PROJECT_NAME} PRIVATE ${XGANDALF_INCLUDES}) diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index d62e7ad5..a51f415a 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -34,6 +34,7 @@ #include <math.h> #include <stdio.h> #include <hdf5.h> +#include <zlib.h> #ifdef HAVE_CBFLIB #ifdef HAVE_CBFLIB_CBF_H @@ -50,6 +51,9 @@ #include "hdf5-file.h" #include "detector.h" +/* Maximum size of uncompressed CBF file in gzip format */ +#define GZIP_BUFFER_SIZE (16*1024*1024) + /** * SECTION:image * @short_description: Data structure representing an image @@ -630,18 +634,49 @@ static float *read_cbf_data(struct imagefile *f, int *w, int *h, cbf_handle *pcb const char *byteorder; void *data; float *dataf; + void *buf = NULL; - if ( cbf_make_handle(&cbfh) ) { - ERROR("Failed to allocate CBF handle\n"); + if ( f->type == IMAGEFILE_CBF ) { + + fh = fopen(f->filename, "rb"); + if ( fh == NULL ) { + ERROR("Failed to open '%s'\n", f->filename); + return NULL; + } + + } else if ( f->type == IMAGEFILE_CBFGZ ) { + + gzFile gzfh; + size_t len; + + gzfh = gzopen(f->filename, "rb"); + if ( gzfh == NULL ) return NULL; + + /* Set larger buffer size for hopefully faster uncompression */ + gzbuffer(gzfh, 128*1024); + + buf = malloc(GZIP_BUFFER_SIZE); + if ( buf == NULL ) return NULL; + + len = gzread(gzfh, buf, GZIP_BUFFER_SIZE); + if ( len == -1 ) return NULL; + + fh = fmemopen(buf, len, "rb"); + if ( fh == NULL ) return NULL; + + gzclose_r(gzfh); + + } else { + /* Don't know how we ended up here */ return NULL; } - fh = fopen(f->filename, "rb"); - if ( fh == NULL ) { - ERROR("Failed to open '%s'\n", f->filename); + if ( cbf_make_handle(&cbfh) ) { + ERROR("Failed to allocate CBF handle\n"); return NULL; } - /* CBFlib calls fclose(fh) when it's ready */ + + /* CBFlib will call fclose(fh) when it's ready */ if ( cbf_read_widefile(cbfh, fh, 0) ) { ERROR("Failed to read CBF file '%s'\n", f->filename); @@ -727,6 +762,8 @@ static float *read_cbf_data(struct imagefile *f, int *w, int *h, cbf_handle *pcb } free(data); + free(buf); /* Might be NULL */ + *w = dimfast; *h = dimmid; *pcbfh = cbfh; @@ -801,6 +838,7 @@ static int read_cbf_simple(struct imagefile *f, struct image *image) return 0; } + #else /* HAVE_CBFLIB */ static int read_cbf_simple(struct imagefile *f, struct image *image) @@ -842,6 +880,24 @@ signed int is_cbf_file(const char *filename) } +signed int is_cbfgz_file(const char *filename) +{ + gzFile gzfh; + char line[1024]; + + gzfh = gzopen(filename, "rb"); + if ( gzfh == NULL ) return -1; + if ( gzgets(gzfh, line, 1024) == NULL ) return -1; + gzclose_r(gzfh); + + if ( strstr(line, "CBF") == NULL ) { + return 0; + } + + return 1; +} + + struct imagefile *imagefile_open(const char *filename) { struct imagefile *f; @@ -864,6 +920,10 @@ struct imagefile *imagefile_open(const char *filename) f->type = IMAGEFILE_CBF; + } else if ( is_cbfgz_file(filename) ) { + + f->type = IMAGEFILE_CBFGZ; + } else { ERROR("Unrecognised file type: %s\n", filename); @@ -883,6 +943,8 @@ int imagefile_read(struct imagefile *f, struct image *image, return hdf5_read2(f->hdfile, image, event, 0); } else if ( f->type == IMAGEFILE_CBF ) { return read_cbf(f, image); + } else if ( f->type == IMAGEFILE_CBFGZ ) { + return read_cbf(f, image); } else { ERROR("Unknown file type %i\n", f->type); return 1; @@ -898,6 +960,8 @@ int imagefile_read_simple(struct imagefile *f, struct image *image) return hdf5_read(f->hdfile, image, NULL, 0); } else if ( f->type == IMAGEFILE_CBF ) { return read_cbf_simple(f, image); + } else if ( f->type == IMAGEFILE_CBFGZ ) { + return read_cbf_simple(f, image); } else { ERROR("Unknown file type %i\n", f->type); return 1; diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 3e46575e..2909e401 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -116,7 +116,8 @@ struct imagefeature { enum imagefile_type { IMAGEFILE_HDF5, - IMAGEFILE_CBF + IMAGEFILE_CBF, + IMAGEFILE_CBFGZ }; |