From 32aa9fdf2cd23cd2d7f9fc6574ffec59b629a7f3 Mon Sep 17 00:00:00 2001 From: Valerio Mariani Date: Mon, 26 Jan 2015 16:34:46 +0100 Subject: Formatting --- libcrystfel/src/detector.c | 29 +++++++++++++++++++---------- libcrystfel/src/hdf5-file.c | 40 +++++++++++++++++++++++++--------------- libcrystfel/src/image.c | 3 ++- libcrystfel/src/stream.c | 25 ++++++++++++++++--------- src/dw-hdfsee.c | 10 ++++++---- src/hdfsee.c | 1 - 6 files changed, 68 insertions(+), 40 deletions(-) diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c index 1e160f7d..f5f6bb57 100644 --- a/libcrystfel/src/detector.c +++ b/libcrystfel/src/detector.c @@ -496,7 +496,8 @@ void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev) if (det->path_dim !=0 || det->dim_dim !=0 ){ - p->clen = get_ev_based_value(f, p->clen_from, ev) * 1.0e-3; + p->clen = get_ev_based_value(f, p->clen_from, + ev) * 1.0e-3; } else { p->clen = get_value(f, p->clen_from) * 1.0e-3; } @@ -1031,6 +1032,7 @@ struct detector *get_detector_geometry(const char *filename, n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE); if ( n2 < 2 ) { + /* This was a top-level option, not handled above. */ parse_toplevel(det, beam, bits[0], bits[2]); for ( i=0; ipanels[i].dim_structure->num_dims; di++ ) { - if ( det->panels[i].dim_structure->dims[di] == HYSL_UNDEFINED ) { + if ( det->panels[i].dim_structure->dims[di] == + HYSL_UNDEFINED ) { dim_dim_reject = 1; } - if ( det->panels[i].dim_structure->dims[di] == HYSL_PLACEHOLDER ) { + if ( det->panels[i].dim_structure->dims[di] == + HYSL_PLACEHOLDER ) { panel_dim_dim += 1; } - if ( det->panels[i].dim_structure->dims[di] == HYSL_SS ) { + if ( det->panels[i].dim_structure->dims[di] == + HYSL_SS ) { found_ss += 1; } - if ( det->panels[i].dim_structure->dims[di] == HYSL_FS ) { + if ( det->panels[i].dim_structure->dims[di] == + HYSL_FS ) { found_fs += 1; } @@ -1183,7 +1189,8 @@ struct detector *get_detector_geometry(const char *filename, } if ( panel_dim_dim > 1 ) { - ERROR("Maximum one placeholder dim coordinate is allowed\n"); + ERROR("Maximum one placeholder dim coordinate is " + "allowed\n"); dim_dim_reject = 1; } @@ -1269,8 +1276,10 @@ struct detector *get_detector_geometry(const char *filename, det->panels[i].orig_max_ss = det->panels[i].max_ss; det->panels[i].orig_min_ss = det->panels[i].min_ss; - det->panels[i].w = det->panels[i].max_fs-det->panels[i].min_fs+1; - det->panels[i].h = det->panels[i].max_ss-det->panels[i].min_ss+1; + det->panels[i].w = + det->panels[i].max_fs-det->panels[i].min_fs+1; + det->panels[i].h = + det->panels[i].max_ss-det->panels[i].min_ss+1; det->panels[i].min_fs = 0; det->panels[i].max_fs = det->panels[i].w-1; diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index 41fbc17c..e38ae67b 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -530,7 +530,8 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p, fs = fs - p->orig_min_fs + p->min_fs; ss = ss - p->orig_min_ss + p->min_ss; - image_add_feature(image->features, fs, ss, image, val, NULL); + image_add_feature(image->features, fs, ss, image, val, + NULL); } @@ -807,12 +808,13 @@ static void write_location(hid_t fh, struct image *image, m_offset[1] = p.min_fs; m_count[0] = p.max_ss - p.min_ss +1; m_count[1] = p.max_fs - p.min_fs +1; + dimsm[0] = image->height; dimsm[1] = image->width; memspace = H5Screate_simple(2, dimsm, NULL); + r = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, m_offset, NULL, m_count, NULL); - r = H5Dwrite(dh, H5T_NATIVE_FLOAT, memspace, dh_dataspace, H5P_DEFAULT, image->data); if ( r < 0 ) { @@ -978,15 +980,18 @@ int hdf5_write_image(const char *filename, struct image *image, char *element) write_location(fh, image, &locations[li]); } - if ( image->beam->photon_energy_from == NULL ) { + if ( image->beam == NULL || image->beam->photon_energy_from == NULL ) { ph_en_loc = "photon_energy_eV"; } else { ph_en_loc = image->beam->photon_energy_from; } + write_photon_energy(fh, ph_lambda_to_eV(image->lambda), ph_en_loc); - if ( image->spectrum_size > 0 ) { + + if ( image->spectrum != NULL && image->spectrum_size > 0 ) { + write_spectrum(fh, image->spectrum, image->spectrum_size, - image->nsamples); + image->nsamples); } H5Fclose(fh); @@ -994,8 +999,8 @@ int hdf5_write_image(const char *filename, struct image *image, char *element) for ( li=0; lievents[ei]); if ( fail_add ) { @@ -2380,19 +2386,23 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det) int hsdi; int panel_path_dim = 0; - full_panel_path = retrieve_full_path(master_el->events[evi], - det->panels[pai].data); + full_panel_path = retrieve_full_path( + master_el->events[evi], + det->panels[pai].data); - dh = H5Dopen2(hdfile->fh, full_panel_path, H5P_DEFAULT); + dh = H5Dopen2(hdfile->fh, full_panel_path, + H5P_DEFAULT); sh = H5Dget_space(dh); dims = H5Sget_simple_extent_ndims(sh); size = malloc(dims*sizeof(hsize_t)); max_size = malloc(dims*sizeof(hsize_t)); - dims = H5Sget_simple_extent_dims(sh, size, max_size); + dims = H5Sget_simple_extent_dims(sh, size, + max_size); - for ( hsdi=0; hsdipanels[pai].dim_structure->num_dims; + for ( hsdi=0; + hsdipanels[pai].dim_structure->num_dims; hsdi++ ) { if (det->panels[pai].dim_structure->dims[hsdi] == HYSL_PLACEHOLDER ) { @@ -2408,8 +2418,8 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det) } else if ( panel_path_dim != global_path_dim ) { - ERROR("Data blocks paths for panels must have the same " - "number of placeholders"); + ERROR("Data blocks paths for panels must " + "have the same number of placeholders"); free(size); free(max_size); return NULL; @@ -2424,7 +2434,7 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det) mlwd_ev = copy_event(master_el->events[evi]); push_dim_entry_to_event(mlwd_ev, mlwd); append_event_to_event_list(master_el_with_dims, - mlwd_ev); + mlwd_ev); free(mlwd_ev); } diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 3cabef96..3dfccea3 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -121,7 +121,8 @@ struct imagefeature *image_feature_closest(ImageFeatureList *flist, double ds; struct panel *p2; - p2 = find_panel(det, flist->features[i].fs, flist->features[i].ss); + p2 = find_panel(det, flist->features[i].fs, + flist->features[i].ss); if ( p1 != p2 ) { continue; diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index 6d741d9d..17c0619a 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -59,7 +59,6 @@ #define AT_LEAST_VERSION(st, a, b) ((st->major_version>=(a)) \ && (st->minor_version>=(b))) - struct _stream { FILE *fh; @@ -211,8 +210,8 @@ static int write_peaks(struct image *image, FILE *ofh) return 1; } - /* Convert coordinates to match arrangement of panels in HDF5 - * file */ + /* Convert coordinates to match arrangement of panels in + * HDF5 file */ write_fs = f->fs - p->min_fs + p->orig_min_fs; write_ss = f->ss - p->min_ss + p->orig_min_ss; @@ -588,7 +587,8 @@ static int write_stream_reflections_2_2(FILE *fh, RefList *list, fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f" " %6.1f %6.1f\n", - h, k, l, intensity, esd_i, pk, bg, write_fs, write_ss); + h, k, l, intensity, esd_i, pk, bg, write_fs, + write_ss); } else { @@ -735,14 +735,19 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections) fprintf(st->fh, REFLECTION_START_MARKER"\n"); if ( AT_LEAST_VERSION(st, 2, 3) ) { - ret = write_stream_reflections_2_3(st->fh, reflist, + ret = write_stream_reflections_2_3(st->fh, + reflist, image); } else if ( AT_LEAST_VERSION(st, 2, 2) ) { - ret = write_stream_reflections_2_2(st->fh, reflist, image); + ret = write_stream_reflections_2_2(st->fh, + reflist, + image); } else { /* This function writes like a normal reflection * list was written in stream 2.1 */ - ret = write_stream_reflections_2_1(st->fh, reflist, image); + ret = write_stream_reflections_2_1(st->fh, + reflist, + image); } fprintf(st->fh, REFLECTION_END_MARKER"\n"); @@ -983,9 +988,11 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf) reflist = read_stream_reflections_2_3(st->fh, image->det); } else if ( AT_LEAST_VERSION(st, 2, 2) ) { - reflist = read_stream_reflections_2_2(st->fh, image->det); + reflist = read_stream_reflections_2_2(st->fh, + image->det); } else { - reflist = read_stream_reflections_2_1(st->fh, image->det); + reflist = read_stream_reflections_2_1(st->fh, + image->det); } if ( reflist == NULL ) { ERROR("Failed while reading reflections\n"); diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c index d86d70cc..ea15077f 100644 --- a/src/dw-hdfsee.c +++ b/src/dw-hdfsee.c @@ -329,7 +329,8 @@ static void maybe_draw_focus(DisplayWindow *dw, cairo_t *cr, int i, break; case CALIBMODE_GROUPS: - if ( dw->image->det->panels[i].rigid_group == dw->calib_mode_curr_rg ) + if ( dw->image->det->panels[i].rigid_group == + dw->calib_mode_curr_rg ) { draw_calib_focus_rectangle(cr, basic_m, dw, i); cairo_stroke(cr); @@ -1096,8 +1097,8 @@ static void load_features_from_file(struct image *image, const char *filename) "(no geometry file given?)\n", pn); } else { - /* Convert coordinates to match rearranged panels in - * memory */ + /* Convert coordinates to match rearranged panels + * in memory */ fs = fs - p->orig_min_fs + p->min_fs; ss = ss - p->orig_min_ss + p->min_ss; @@ -1847,7 +1848,8 @@ static GtkWidget *displaywindow_addhdfgroup(struct hdfile *hdfile, item = gtk_menu_item_new_with_label(names[i]); if ( hdfile_is_scalar(hdfile, names[i], 0) ) { - tmp = hdfile_get_string_value(hdfile, names[i], NULL); + tmp = hdfile_get_string_value(hdfile, names[i], + NULL); } else { tmp = NULL; } diff --git a/src/hdfsee.c b/src/hdfsee.c index 56f1e6f1..b9394d33 100644 --- a/src/hdfsee.c +++ b/src/hdfsee.c @@ -219,7 +219,6 @@ int main(int argc, char *argv[]) case 'g' : geom_filename = strdup(optarg); det_geom = get_detector_geometry(geom_filename, &cbeam); - if ( det_geom == NULL ) { ERROR("Failed to read detector geometry " "from '%s'\n", optarg); -- cgit v1.2.3