From 43b71428b68e94d22c2c5f9e8a25b1b46bc04a4c Mon Sep 17 00:00:00 2001 From: Thomas White Date: Tue, 4 Aug 2020 15:25:19 +0200 Subject: Add image_create_for_simulation() ...and factorise common code --- libcrystfel/src/datatemplate.c | 101 ---------------------- libcrystfel/src/datatemplate.h | 2 - libcrystfel/src/image.c | 184 +++++++++++++++++++++++++++++------------ libcrystfel/src/image.h | 8 +- 4 files changed, 136 insertions(+), 159 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c index 5941109e..43313441 100644 --- a/libcrystfel/src/datatemplate.c +++ b/libcrystfel/src/datatemplate.c @@ -1383,107 +1383,6 @@ void data_template_add_copy_header(DataTemplate *dt, } -static double unit_string_to_unit(const char *str) -{ - if ( strcmp(str, "mm") == 0 ) return 1e-3; - if ( strcmp(str, "m") == 0 ) return 1.0; - ERROR("Invalid length unit '%s'\n", str); - return NAN; -} - - -static double dt_get_length(const char *from) -{ - double units; - char *sp; - char *fromcpy; - double val; - char *rval; - - if ( from == NULL ) return NAN; - - fromcpy = strdup(from); - if ( fromcpy == NULL ) return NAN; - - sp = strchr(fromcpy, ' '); - if ( sp == NULL ) { - units = 1.0e-3; - } else { - units = unit_string_to_unit(sp+1); - } - - sp[0] = '\0'; - val = strtod(fromcpy, &rval); - if ( !( (*rval == '\0') && (rval != fromcpy)) ) { - ERROR("Invalid length value: %s\n", fromcpy); - free(fromcpy); - return NAN; - } - - return val * units; -} - - -/* If possible, i.e. if there are no references to image headers in - * 'dt', generate a detgeom structure from it. - * - * NB This is probably not the function you're looking for! - * The detgeom structure should normally come from loading an image, - * reading a stream or similar. This function should only be used - * when there is really no data involved, e.g. in make_pixelmap. - */ -struct detgeom *data_template_to_detgeom(const DataTemplate *dt) -{ - struct detgeom *detgeom; - int i; - - if ( dt == NULL ) return NULL; - - detgeom = malloc(sizeof(struct detgeom)); - if ( detgeom == NULL ) return NULL; - - detgeom->panels = malloc(dt->n_panels*sizeof(struct detgeom_panel)); - if ( detgeom->panels == NULL ) return NULL; - - detgeom->n_panels = dt->n_panels; - - for ( i=0; in_panels; i++ ) { - - detgeom->panels[i].name = safe_strdup(dt->panels[i].name); - - detgeom->panels[i].pixel_pitch = dt->panels[i].pixel_pitch; - - /* NB cnx,cny are in pixels, cnz is in m */ - detgeom->panels[i].cnx = dt->panels[i].cnx; - detgeom->panels[i].cny = dt->panels[i].cny; - detgeom->panels[i].cnz = dt_get_length(dt->panels[i].cnz_from); - - /* Apply offset (in m) and then convert cnz from - * m to pixels */ - detgeom->panels[i].cnz += dt->panels[i].cnz_offset; - detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch; - - detgeom->panels[i].max_adu = dt->panels[i].max_adu; - detgeom->panels[i].adu_per_photon = 1.0; /* FIXME ! */ - - detgeom->panels[i].w = dt->panels[i].orig_max_fs - - dt->panels[i].orig_min_fs + 1; - detgeom->panels[i].h = dt->panels[i].orig_max_ss - - dt->panels[i].orig_min_ss + 1; - - detgeom->panels[i].fsx = dt->panels[i].fsx; - detgeom->panels[i].fsy = dt->panels[i].fsy; - detgeom->panels[i].fsz = dt->panels[i].fsz; - detgeom->panels[i].ssx = dt->panels[i].ssx; - detgeom->panels[i].ssy = dt->panels[i].ssy; - detgeom->panels[i].ssz = dt->panels[i].ssz; - - } - - return detgeom; -} - - static int dt_num_placeholders(const struct panel_template *p) { int i; diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h index c6054409..88a002f0 100644 --- a/libcrystfel/src/datatemplate.h +++ b/libcrystfel/src/datatemplate.h @@ -69,8 +69,6 @@ extern int data_template_panel_to_file_coords(const DataTemplate *dt, extern void data_template_add_copy_header(DataTemplate *dt, const char *header); -extern struct detgeom *data_template_to_detgeom(const DataTemplate *dt); - extern int data_template_get_slab_extents(const DataTemplate *dt, int *pw, int *ph); extern int data_template_in_bad_region(const DataTemplate *dtempl, diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 2e9249e8..d2fb30ba 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -397,21 +397,21 @@ static double convert_to_m(double val, int units) } -void create_detgeom(struct image *image, const DataTemplate *dtempl) +int create_detgeom(struct image *image, const DataTemplate *dtempl) { struct detgeom *detgeom; int i; if ( dtempl == NULL ) { ERROR("NULL data template!\n"); - return; + return 1; } detgeom = malloc(sizeof(struct detgeom)); - if ( detgeom == NULL ) return; + if ( detgeom == NULL ) return 1; detgeom->panels = malloc(dtempl->n_panels*sizeof(struct detgeom_panel)); - if ( detgeom->panels == NULL ) return; + if ( detgeom->panels == NULL ) return 1; detgeom->n_panels = dtempl->n_panels; @@ -483,7 +483,7 @@ void create_detgeom(struct image *image, const DataTemplate *dtempl) image->detgeom = detgeom; - /* FIXME: spectrum */ + return 0; } @@ -572,43 +572,9 @@ int image_read_image_data(struct image *image, } -struct image *image_read(DataTemplate *dtempl, - const char *filename, - const char *event, - int no_image_data, - int no_mask_data) +static void set_image_parameters(struct image *image, + const DataTemplate *dtempl) { - struct image *image; - int i; - int r; - - if ( dtempl == NULL ) { - ERROR("NULL data template!\n"); - return NULL; - } - - image = image_new(); - if ( image == NULL ) { - ERROR("Couldn't allocate image structure.\n"); - return NULL; - } - - if ( !no_image_data ) { - - r = image_read_image_data(image, dtempl, - filename, event); - - } else { - - r = image_set_zero_data(image, dtempl); - - } - - if ( r ) { - image_free(image); - return NULL; - } - /* Wavelength might be needed to create detgeom (adu_per_eV) */ image->lambda = convert_to_m(get_value(image, dtempl->wavelength_from), @@ -620,12 +586,19 @@ struct image *image_read(DataTemplate *dtempl, image->spectrum = spectrum_generate_gaussian(image->lambda, image->bw); - create_detgeom(image, dtempl); +} + + +static int create_badmap(struct image *image, + const DataTemplate *dtempl, + int no_mask_data) +{ + int i; image->bad = malloc(dtempl->n_panels * sizeof(int *)); if ( image->bad == NULL ) { ERROR("Failed to allocate bad pixel mask\n"); - return NULL; + return 1; } for ( i=0; in_panels; i++ ) { @@ -640,7 +613,7 @@ struct image *image_read(DataTemplate *dtempl, image->bad[i] = calloc(p_w*p_h, sizeof(int)); if ( image->bad[i] == NULL ) { ERROR("Failed to allocate bad pixel mask\n"); - return NULL; + return 1; } /* Panel marked as bad? */ @@ -669,37 +642,142 @@ struct image *image_read(DataTemplate *dtempl, if ( (!no_mask_data) && (!p->bad) && (p->mask != NULL) ) { if ( p->mask_file == NULL ) { - mask_fn = filename; + mask_fn = image->filename; } else { mask_fn = p->mask_file; } if ( is_hdf5_file(mask_fn) ) { - image_hdf5_read_mask(p, mask_fn, event, + image_hdf5_read_mask(p, mask_fn, + image->ev, image->bad[i], dtempl->mask_good, dtempl->mask_bad); - } else if ( is_cbf_file(filename) ) { - image_cbf_read_mask(p, mask_fn, event, + } else if ( is_cbf_file(mask_fn) ) { + image_cbf_read_mask(p, mask_fn, + image->ev, 0, image->bad[i], dtempl->mask_good, dtempl->mask_bad); - } else if ( is_cbfgz_file(filename) ) { - image_cbf_read_mask(p, mask_fn, event, + } else if ( is_cbfgz_file(mask_fn) ) { + image_cbf_read_mask(p, mask_fn, + image->ev, 1, image->bad[i], dtempl->mask_good, dtempl->mask_bad); } else { ERROR("Unrecognised mask file type" - " (%s)\n", filename); - return NULL; + " (%s)\n", mask_fn); + return 1; } } } + return 0; +} + + +static int create_satmap(struct image *image, + const DataTemplate *dtempl) +{ + /* FIXME: Implementation */ + return 0; +} + + +struct image *image_create_for_simulation(const DataTemplate *dtempl) +{ + struct image *image; + + if ( dtempl == NULL ) { + ERROR("NULL data template!\n"); + return NULL; + } + + image = image_new(); + if ( image == NULL ) { + ERROR("Couldn't allocate image structure.\n"); + return NULL; + } + + if ( image_set_zero_data(image, dtempl) ) { + image_free(image); + return NULL; + } - /* FIXME: Load saturation map */ + set_image_parameters(image, dtempl); + + if ( create_detgeom(image, dtempl) ) { + image_free(image); + return NULL; + } + + if ( create_badmap(image, dtempl, 1) ) { + image_free(image); + return NULL; + } + + if ( create_satmap(image, dtempl) ) { + image_free(image); + return NULL; + } + + return image; +} + + +struct image *image_read(const DataTemplate *dtempl, + const char *filename, + const char *event, + int no_image_data, + int no_mask_data) +{ + struct image *image; + int r; + + if ( dtempl == NULL ) { + ERROR("NULL data template!\n"); + return NULL; + } + + image = image_new(); + if ( image == NULL ) { + ERROR("Couldn't allocate image structure.\n"); + return NULL; + } + + image->filename = strdup(filename); + image->ev = strdup(event); + + /* Load the image data */ + if ( !no_image_data ) { + r = image_read_image_data(image, dtempl, + filename, event); + } else { + r = image_set_zero_data(image, dtempl); + } + if ( r ) { + image_free(image); + return NULL; + } + + set_image_parameters(image, dtempl); + + if ( create_detgeom(image, dtempl) ) { + image_free(image); + return NULL; + } + + if ( create_badmap(image, dtempl, no_mask_data) ) { + image_free(image); + return NULL; + } + + if ( create_satmap(image, dtempl) ) { + image_free(image); + return NULL; + } return image; } diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 9f88d0e7..a2f160af 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -186,11 +186,12 @@ extern void mark_resolution_range_as_bad(struct image *image, double min, double max); extern struct image *image_new(void); -extern struct image *image_read(DataTemplate *dtempl, +extern struct image *image_read(const DataTemplate *dtempl, const char *filename, const char *event, int no_image_data, int no_mask_data); +extern struct image *image_create_for_simulation(const DataTemplate *dtempl); extern void image_free(struct image *image); extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl, @@ -208,9 +209,10 @@ extern int image_set_zero_mask(struct image *image, const DataTemplate *dtempl); /* Use within libcrystfel only */ -extern void create_detgeom(struct image *image, - const DataTemplate *dtempl); +extern int create_detgeom(struct image *image, + const DataTemplate *dtempl); +/* Use within libcrystfel only */ extern int image_read_image_data(struct image *image, const DataTemplate *dtempl, const char *filename, -- cgit v1.2.3