Port indexamajig to new API, part II

This also removes a large chunk of legacy code

1 files changed, 0 insertions, 439 deletions

diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 3ba71118..c7d46978 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -48,14 +48,6 @@
 
 /** \file image.h */
 
-struct imagefile
-{
-	enum imagefile_type type;
-	char *filename;
-	struct hdfile *hdfile;
-};
-
-
 struct _imagefeaturelist
 {
 	struct imagefeature *features;
@@ -331,233 +323,6 @@ void free_all_crystals(struct image *image)
 }
 
 
-/**************************** Image field lists *******************************/
-
-struct imagefile_field_list
-{
-	char **fields;
-	int n_fields;
-	int max_fields;
-};
-
-
-struct imagefile_field_list *new_imagefile_field_list()
-{
-	struct imagefile_field_list *n;
-
-	n = calloc(1, sizeof(struct imagefile_field_list));
-	if ( n == NULL ) return NULL;
-
-	n->max_fields = 32;
-	n->fields = malloc(n->max_fields*sizeof(char *));
-	if ( n->fields == NULL ) {
-		free(n);
-		return NULL;
-	}
-
-	return n;
-}
-
-
-void free_imagefile_field_list(struct imagefile_field_list *n)
-{
-	int i;
-	for ( i=0; i<n->n_fields; i++ ) {
-		free(n->fields[i]);
-	}
-	free(n->fields);
-	free(n);
-}
-
-
-void add_imagefile_field(struct imagefile_field_list *copyme, const char *name)
-{
-	int i;
-
-	/* Already on the list?   Don't re-add if so. */
-	for ( i=0; i<copyme->n_fields; i++ ) {
-		if ( strcmp(copyme->fields[i], name) == 0 ) return;
-	}
-
-	/* Need more space? */
-	if ( copyme->n_fields == copyme->max_fields ) {
-
-		char **nfields;
-		int nmax = copyme->max_fields + 32;
-
-		nfields = realloc(copyme->fields, nmax*sizeof(char *));
-		if ( nfields == NULL ) {
-			ERROR("Failed to allocate space for new HDF5 field.\n");
-			return;
-		}
-
-		copyme->max_fields = nmax;
-		copyme->fields = nfields;
-
-	}
-
-	copyme->fields[copyme->n_fields] = strdup(name);
-	if ( copyme->fields[copyme->n_fields] == NULL ) {
-		ERROR("Failed to add field for copying '%s'\n", name);
-		return;
-	}
-
-	copyme->n_fields++;
-}
-
-
-/******************************* CBF files ************************************/
-
-static int unpack_panels(struct image *image, float *data, int data_width,
-                         int data_height)
-{
-	int pi;
-
-	/* FIXME: Load these masks from an HDF5 file, if filenames are
-	 * given in the geometry file */
-	uint16_t *flags = NULL;
-	float *sat = NULL;
-
-	image->dp = malloc(image->det->n_panels * sizeof(float *));
-	image->bad = malloc(image->det->n_panels * sizeof(int *));
-	image->sat = malloc(image->det->n_panels * sizeof(float *));
-	if ( (image->dp == NULL) || (image->bad == NULL)
-	  || (image->sat == NULL) )
-	{
-		ERROR("Failed to allocate panels.\n");
-		return 1;
-	}
-
-	for ( pi=0; pi<image->det->n_panels; pi++ ) {
-
-		struct panel *p;
-		int fs, ss;
-
-		p = &image->det->panels[pi];
-		image->dp[pi] = malloc(p->w*p->h*sizeof(float));
-		image->bad[pi] = calloc(p->w*p->h, sizeof(int));
-		image->sat[pi] = malloc(p->w*p->h*sizeof(float));
-		if ( (image->dp[pi] == NULL) || (image->bad[pi] == NULL)
-		  || (image->sat[pi] == NULL) )
-		{
-			ERROR("Failed to allocate panel\n");
-			return 1;
-		}
-
-		if ( p->mask != NULL ) {
-			ERROR("WARNING: Bad pixel masks do not currently work "
-			      "with CBF files\n");
-			ERROR(" (bad pixel regions specified in the geometry "
-			      "file will be used, however)\n");
-		}
-
-		if ( p->satmap != NULL ) {
-			ERROR("WARNING: Saturation maps do not currently work "
-			      "with CBF files\n");
-		}
-
-		if ( (p->orig_min_fs + p->w > data_width)
-		  || (p->orig_min_ss + p->h > data_height) )
-		{
-			ERROR("Panel %s is outside range of data in CBF file\n",
-			      p->name);
-			return 1;
-		}
-
-		for ( ss=0; ss<p->h; ss++ ) {
-		for ( fs=0; fs<p->w; fs++ ) {
-
-			int idx;
-			int cfs, css;
-			int bad = 0;
-
-			cfs = fs+p->orig_min_fs;
-			css = ss+p->orig_min_ss;
-			idx = cfs + css*data_width;
-
-			image->dp[pi][fs+p->w*ss] = data[idx];
-
-			if ( sat != NULL ) {
-				image->sat[pi][fs+p->w*ss] = sat[idx];
-			} else {
-				image->sat[pi][fs+p->w*ss] = INFINITY;
-			}
-
-			if ( p->no_index ) bad = 1;
-
-			if ( in_bad_region(image->det, p, cfs, css) ) {
-				bad = 1;
-			}
-
-			if ( isnan(data[idx]) || isinf(data[idx]) ) bad = 1;
-
-			if ( flags != NULL ) {
-
-				int f;
-
-				f = flags[idx];
-
-				/* Bad if it's missing any of the "good" bits */
-				if ( (f & image->det->mask_good)
-				       != image->det->mask_good ) bad = 1;
-
-				/* Bad if it has any of the "bad" bits. */
-				if ( f & image->det->mask_bad ) bad = 1;
-
-			}
-			image->bad[pi][fs+p->w*ss] = bad;
-
-		}
-		}
-
-	}
-
-	return 0;
-}
-
-
-static void cbf_fill_in_beam_parameters(struct beam_params *beam,
-                                        struct imagefile *f,
-                                        struct image *image)
-{
-	double eV;
-
-	if ( beam->photon_energy_from == NULL ) {
-
-		/* Explicit value given */
-		eV = beam->photon_energy;
-
-	} else {
-
-		ERROR("Can't get photon energy from CBF yet.\n");
-		eV = 0.0;
-
-	}
-
-	image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale;
-}
-
-
-static void cbf_fill_in_clen(struct detector *det, struct imagefile *f)
-{
-	int i;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		struct panel *p = &det->panels[i];
-
-		if ( p->clen_from != NULL ) {
-
-			ERROR("Can't get clen from CBF yet.\n");
-
-		}
-
-		adjust_centering_for_rail(p);
-
-	}
-}
-
-
 static void add_out(float val, float *data_out, int nmemb_out,
                     int *outpos, int *nrej)
 {
@@ -1017,75 +782,6 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)
 }
 
 
-static int read_cbf(struct imagefile *f, struct image *image)
-{
-	float *data;
-	int w, h;
-
-	data = read_cbf_data(f->filename, f->type == IMAGEFILE_CBF,
-	                     &w, &h);
-	if ( data == NULL ) {
-		ERROR("Failed to read CBF data\n");
-		return 1;
-	}
-
-	unpack_panels(image, data, w, h);
-	free(data);
-
-	if ( image->beam != NULL ) {
-		cbf_fill_in_beam_parameters(image->beam, f, image);
-		if ( image->lambda > 1000 ) {
-			ERROR("WARNING: Missing or nonsensical wavelength "
-			      "(%e m) for %s.\n",
-			      image->lambda, image->filename);
-		}
-	}
-	cbf_fill_in_clen(image->det, f);
-	fill_in_adu(image);
-
-	return 0;
-}
-
-
-static int read_cbf_simple(struct imagefile *f, struct image *image)
-{
-	float *data;
-	int w, h;
-
-	data = read_cbf_data(f->filename, f->type == IMAGEFILE_CBF,
-	                     &w, &h);
-	if ( data == NULL ) {
-		ERROR("Failed to read CBF data\n");
-		return 1;
-	}
-
-	image->det = simple_geometry(image, w, h);
-	image->dp = malloc(sizeof(float *));
-	if ( image->dp == NULL ) {
-		ERROR("Failed to allocate dp array\n");
-		return 1;
-	}
-
-	image->dp[0] = data;
-
-	if ( image->beam != NULL ) {
-		cbf_fill_in_beam_parameters(image->beam, f, image);
-		if ( image->lambda > 1000 ) {
-			ERROR("WARNING: Missing or nonsensical wavelength "
-			      "(%e m) for %s.\n",
-			      image->lambda, image->filename);
-		}
-	}
-	cbf_fill_in_clen(image->det, f);
-	fill_in_adu(image);
-
-	return 0;
-}
-
-
-/****************************** Image files ***********************************/
-
-
 signed int is_cbf_file(const char *filename)
 {
 	FILE *fh;
@@ -1123,141 +819,6 @@ signed int is_cbfgz_file(const char *filename)
 }
 
 
-struct imagefile *imagefile_open(const char *filename)
-{
-	struct imagefile *f;
-
-	f = malloc(sizeof(struct imagefile));
-	if ( f == NULL ) return NULL;
-
-	if ( H5Fis_hdf5(filename) > 0 ) {
-
-		/* This is an HDF5, pass through to HDF5 layer */
-		f->type = IMAGEFILE_HDF5;
-		f->hdfile = hdfile_open(filename);
-
-		if ( f->hdfile == NULL ) {
-			free(f);
-			return NULL;
-		}
-
-	} else if ( is_cbf_file(filename) > 0 ) {
-
-		f->type = IMAGEFILE_CBF;
-
-	} else if ( is_cbfgz_file(filename) ) {
-
-		f->type = IMAGEFILE_CBFGZ;
-
-	} else {
-
-		ERROR("Unrecognised file type: %s\n", filename);
-		return NULL;
-
-	}
-
-	f->filename = strdup(filename);
-	return f;
-}
-
-
-int imagefile_read(struct imagefile *f, struct image *image,
-                   struct event *event)
-{
-	if ( f->type == IMAGEFILE_HDF5 ) {
-		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;
-	}
-}
-
-
-/* Read a simple file, no multi-event, no prior geometry etc, and
- * generate a geometry for it */
-int imagefile_read_simple(struct imagefile *f, struct image *image)
-{
-	if ( f->type == IMAGEFILE_HDF5 ) {
-		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;
-	}
-}
-
-
-enum imagefile_type imagefile_get_type(struct imagefile *f)
-{
-	assert(f != NULL);
-	return f->type;
-}
-
-
-struct hdfile *imagefile_get_hdfile(struct imagefile *f)
-{
-	if ( f == NULL ) return NULL;
-
-	if ( f->type != IMAGEFILE_HDF5 ) {
-		ERROR("Not an HDF5 file!\n");
-		return NULL;
-	}
-
-	return f->hdfile;
-}
-
-
-void imagefile_copy_fields(struct imagefile *f,
-                           const struct imagefile_field_list *copyme,
-                           FILE *fh, struct event *ev)
-{
-	int i;
-
-	if ( copyme == NULL ) return;
-
-	for ( i=0; i<copyme->n_fields; i++ ) {
-
-		char *val;
-		char *field;
-
-		field = copyme->fields[i];
-
-		if ( f->type == IMAGEFILE_HDF5 ) {
-			val = hdfile_get_string_value(f->hdfile, field, ev);
-			if ( field[0] == '/' ) {
-				fprintf(fh, "hdf5%s = %s\n", field, val);
-			} else {
-				fprintf(fh, "hdf5/%s = %s\n", field, val);
-			}
-			free(val);
-
-		} else {
-			STATUS("Mock CBF variable\n");
-			fprintf(fh, "cbf/%s = %s\n", field, "(FIXME)");
-		}
-
-
-	}
-}
-
-
-void imagefile_close(struct imagefile *f)
-{
-	if ( f->type == IMAGEFILE_HDF5 ) {
-		hdfile_close(f->hdfile);
-	}
-	free(f->filename);
-	free(f);
-}
-
-
 /************************** New API (DataTemplate) ****************************/
 
 struct image *image_new()