diff options
Diffstat (limited to 'libcrystfel')
| -rw-r--r-- | libcrystfel/src/hdf5-file.c | 123 | ||||
| -rw-r--r-- | libcrystfel/src/hdf5-file.h | 11 |
2 files changed, 124 insertions, 10 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index 9bcdb1b7..76617ee4 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -44,6 +44,19 @@ #include "utils.h" +/** + * SECTION:hdf5-file + * @short_description: HDF5 file handling + * @title: HDF5 file handling + * @section_id: + * @see_also: + * @include: "hdf5-file.h" + * @Image: + * + * Routines for accessing HDF5 files. + **/ + + struct hdf5_write_location { const char *location; @@ -320,9 +333,34 @@ static float *read_hdf5_data(struct hdfile *f, char *path, int line) } -/* Get peaks from HDF5, in "CXI format" (as in "CXIDB") */ -int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, - struct filename_plus_event *fpe) +/** + * get_peaks_cxi_2: + * @image: An %image structure + * @f: An %hdfile structure + * @p: The HDF5 path to the peak data + * @fpe: A %filename_plus_event structure specifying the event + * @half_pixel_shift: Non-zero if 0.5 should be added to all peak coordinates + * + * Get peaks from HDF5, in "CXI format" (as in "CXIDB"). The data should be in + * a set of arrays under @p. The number of peaks should be in a 1D array at + * @p/nPeaks. The fast-scan and slow-scan coordinates should be in 2D arrays at + * @p/peakXPosRaw and @p/peakYPosRaw respectively (sorry about the naming). The + * first dimension of these arrays should be the event number (as given by + * @fpe). The intensities are expected to be at @p/peakTotalIntensity in a + * similar 2D array. + * + * CrystFEL considers all peak locations to be distances from the corner of the + * detector panel, in pixel units, consistent with its description of detector + * geometry (see 'man crystfel_geometry'). The software which generates the + * CXI files, including Cheetah, may instead consider the peak locations to be + * pixel indices in the data array. In this case, the peak coordinates should + * have 0.5 added to them. This will be done if @half_pixel_shift is non-zero. + * + * Returns: non-zero on error, zero otherwise. + * + */ +int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p, + struct filename_plus_event *fpe, int half_pixel_shift) { char path_n[1024]; char path_x[1024]; @@ -338,6 +376,8 @@ int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, float *buf_y; float *buf_i; + double peak_offset = half_pixel_shift ? 0.5 : 0.0; + if ( (fpe != NULL) && (fpe->ev != NULL) && (fpe->ev->dim_entries != NULL) ) { @@ -375,8 +415,8 @@ int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, float fs, ss, val; struct panel *p; - fs = buf_x[pk]; - ss = buf_y[pk]; + fs = buf_x[pk] + peak_offset; + ss = buf_y[pk] + peak_offset; val = buf_i[pk]; p = find_orig_panel(image->det, fs, ss); @@ -395,7 +435,53 @@ int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, } -int get_peaks(struct image *image, struct hdfile *f, const char *p) +/** + * get_peaks_cxi: + * @image: An %image structure + * @f: An %hdfile structure + * @p: The HDF5 path to the peak data + * @fpe: A %filename_plus_event structure specifying the event + * + * This is a wrapper function to preserve API compatibility with older CrystFEL + * versions. Use get_peaks_cxi_2() instead. + * + * This function is equivalent to get_peaks_cxi_2(@image, @f, @p, @fpe, 1). + * + * Returns: non-zero on error, zero otherwise. + * + */ +int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, + struct filename_plus_event *fpe) +{ + return get_peaks_cxi_2(image, f, p, fpe, 1); +} + + +/** + * get_peaks_2: + * @image: An %image structure + * @f: An %hdfile structure + * @p: The HDF5 path to the peak data + * @half_pixel_shift: Non-zero if 0.5 should be added to all peak coordinates + * + * Get peaks from HDF5. The peak list should be located at @p in the HDF5 file, + * a 2D array where the first dimension equals the number of peaks and second + * dimension is three. The first two columns contain the fast scan and slow + * scan coordinates, respectively, of the peaks. The third column contains the + * intensities. + * + * CrystFEL considers all peak locations to be distances from the corner of the + * detector panel, in pixel units, consistent with its description of detector + * geometry (see 'man crystfel_geometry'). The software which generates the + * CXI files, including Cheetah, may instead consider the peak locations to be + * pixel indices in the data array. In this case, the peak coordinates should + * have 0.5 added to them. This will be done if @half_pixel_shift is non-zero. + * + * Returns: non-zero on error, zero otherwise. + * + */ +int get_peaks_2(struct image *image, struct hdfile *f, const char *p, + int half_pixel_shift) { hid_t dh, sh; hsize_t size[2]; @@ -405,6 +491,7 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p) herr_t r; int tw; char *np; + double peak_offset = half_pixel_shift ? 0.5 : 0.0; if ( image->event != NULL ) { np = retrieve_full_path(image->event, p); @@ -473,8 +560,8 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p) float fs, ss, val; struct panel *p; - fs = buf[tw*i+0]; - ss = buf[tw*i+1]; + fs = buf[tw*i+0] + peak_offset; + ss = buf[tw*i+1] + peak_offset; val = buf[tw*i+2]; p = find_orig_panel(image->det, fs, ss); @@ -499,6 +586,26 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p) } +/** + * get_peaks: + * @image: An %image structure + * @f: An %hdfile structure + * @p: The HDF5 path to the peak data + * + * This is a wrapper function to preserve API compatibility with older CrystFEL + * versions. Use get_peaks_2() instead. + * + * This function is equivalent to get_peaks_2(@image, @f, @p, 1). + * + * Returns: non-zero on error, zero otherwise. + * + */ +int get_peaks(struct image *image, struct hdfile *f, const char *p) +{ + return get_peaks_2(image, f, p, 1); +} + + static void cleanup(hid_t fh) { int n_ids, i; diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h index 8c89eb93..f22d4d54 100644 --- a/libcrystfel/src/hdf5-file.h +++ b/libcrystfel/src/hdf5-file.h @@ -3,11 +3,11 @@ * * Read/write HDF5 data files * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2009-2015 Thomas White <taw@physics.org> + * 2009-2017 Thomas White <taw@physics.org> * 2014 Valerio Mariani * @@ -78,9 +78,16 @@ extern void hdfile_close(struct hdfile *f); extern int get_peaks(struct image *image, struct hdfile *f, const char *p); +extern int get_peaks_2(struct image *image, struct hdfile *f, const char *p, + int half_pixel_shift); + extern int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, struct filename_plus_event *fpe); +extern int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p, + struct filename_plus_event *fpe, + int half_pixel_shift); + extern struct copy_hdf5_field *new_copy_hdf5_field_list(void); extern void free_copy_hdf5_field_list(struct copy_hdf5_field *f); |