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-rw-r--r--libcrystfel/src/indexers/fromfile.c436
1 files changed, 198 insertions, 238 deletions
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index 400683ae..aa2c8999 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -38,336 +38,296 @@
/** \file fromfile.h */
-/* There are 9 vector components,
- * 2 detector shifts, 1 profile radius,
- * 1 resolution limit */
-#define NPARAMS_PER_LINE 11
-/* The keys read from file
- * are the filename, event */
-#define NKEYS_PER_LINE 2
-
-
struct fromfile_options
{
char *filename;
};
+#define MAX_KEY_LEN (256)
+#define MAX_CRYSTALS (16)
-struct fromfile_keys
+struct fromfile_key
{
- char filename[100];
- char event[100];
- int crystal_number;
+ char filename[MAX_KEY_LEN];
+ char event[MAX_KEY_LEN];
};
-struct fromfile_entries
+struct fromfile_entry
{
- struct fromfile_keys key;
- float solution[NPARAMS_PER_LINE];
+ struct fromfile_key key_field;
+ Crystal *crystals[MAX_CRYSTALS];
+ int n_crystals;
UT_hash_handle hh;
};
struct fromfile_private
{
- UnitCell *cellTemplate;
- struct fromfile_entries *sol_hash;
+ struct fromfile_entry *sol_hash;
};
-void print_struct(struct fromfile_entries *sol_hash)
+static int make_key(struct fromfile_key *key,
+ const char *filename, const char *ev)
{
- struct fromfile_entries *s;
+ if ( (strlen(filename) > MAX_KEY_LEN) || (strlen(ev) > MAX_KEY_LEN) ) {
+ ERROR("Filename/event too long: %s %s\n", filename, ev);
+ return 1;
+ }
- s = calloc(1, sizeof(struct fromfile_entries));
- if ( s == NULL ) return;
+ /* The entire structure is used as a key, not just the pre-terminator
+ * parts of the strings. Therefore it must be initialised to zero */
+ memset(key, 0, sizeof(struct fromfile_key));
- for( s=sol_hash; s != NULL; s=s->hh.next ) {
- printf("File %s, event %s, and crystal_number %d \n",
- s->key.filename, s->key.event, s->key.crystal_number);
- }
+ strcpy(key->filename, filename);
+ strcpy(key->event, ev);
+
+ return 0;
}
-void full_print_struct(struct fromfile_entries *sol_hash)
+struct fromfile_entry *add_unique(struct fromfile_entry **phead,
+ struct fromfile_key key)
{
- struct fromfile_entries *s;
- s = calloc(1, sizeof(struct fromfile_entries));
- if ( s == NULL ) return;
-
- for( s=sol_hash; s != NULL; s=s->hh.next ) {
- printf("File %s, event %s, and crystal_number %d \n",
- s->key.filename, s->key.event,
- s->key.crystal_number);
-
- printf("Solution parameters:\n");
- for( int i = 0; i < NPARAMS_PER_LINE; i++ ){
- printf("%e", s->solution[i]);
- }
- printf("\n");
+ struct fromfile_entry *p;
+ struct fromfile_entry *head = *phead;
+
+ HASH_FIND(hh, head, &key, sizeof(struct fromfile_key), p);
+ if ( p == NULL ) {
+
+ struct fromfile_entry *item;
+
+ item = malloc(sizeof(struct fromfile_entry));
+ if ( item == NULL ) return NULL;
+
+ item->n_crystals = 0;
+ item->key_field = key;
+
+ HASH_ADD(hh, head, key_field, sizeof(struct fromfile_key), item);
+ *phead = head;
+ return item;
+
+ } else {
+ return p;
}
}
-int ncrystals_in_sol(char *path)
+static int set_ua(UnitCell *cell, const char *ltsym)
{
- FILE *fh;
- int count = 0; /* Line counter (result) */
- char c; /* To store a character read from file */
+ if ( strlen(ltsym) != 3 ) return 1;
+ cell_set_unique_axis(cell, ltsym[2]);
+ return 0;
+}
- fh = fopen(path, "r");
- if ( fh == NULL ) {
- ERROR("%s not found by ncrystals_in_sol\n", path);
- return 0;
- }
+static int set_lattice(UnitCell *cell, const char *ltsym)
+{
+ if ( (strlen(ltsym) != 2) && (strlen(ltsym) != 3) ) return 1;
+
+ switch ( ltsym[1] ) {
+ case 'P':
+ case 'A':
+ case 'B':
+ case 'C':
+ case 'I':
+ case 'F':
+ case 'R':
+ case 'H':
+ break;
- for ( c = getc(fh); c != EOF; c = getc(fh) ) {
- if ( c == '\n' ) {
- count = count + 1;
- }
+ default:
+ return 1;
}
+ cell_set_centering(cell, ltsym[1]);
- /* For the last line, which has no \n at the end*/
- count = count + 1;
+ switch ( ltsym[0] ) {
- fclose(fh);
+ case 'a' :
+ cell_set_lattice_type(cell, L_TRICLINIC);
+ break;
- return count;
-}
+ case 'm' :
+ cell_set_lattice_type(cell, L_MONOCLINIC);
+ return set_ua(cell, ltsym);
+ case 'o' :
+ cell_set_lattice_type(cell, L_ORTHORHOMBIC);
+ break;
-char *read_unknown_string(FILE *fh)
-{
- /* Source: "https://stackoverflow.com/questions/16870485/
- * how-can-i-read-an-input-string-of-unknown-length" */
+ case 't' :
+ cell_set_lattice_type(cell, L_TETRAGONAL);
+ return set_ua(cell, ltsym);
- char *str = NULL;
- int ch;
- size_t len = 0;
- size_t size = 1;
+ case 'c' :
+ cell_set_lattice_type(cell, L_CUBIC);
+ break;
- str = realloc(NULL, sizeof(char)*size); //size is start size
- if ( !str ) {
- ERROR("Can't reallocate string size");
- }
+ case 'r' :
+ cell_set_lattice_type(cell, L_RHOMBOHEDRAL);
+ break;
- while( ( ch = fgetc(fh) ) != ' ' && ch != EOF ){
- if (ch != '\n'){
- str[len++]=ch;
- }
- if(len==size){
- size+=64;
- str = realloc(str, sizeof(char)*(size));
- if ( !str ) {
- ERROR("Can't reallocate string size");
- }
- }
+ case 'h' :
+ cell_set_lattice_type(cell, L_HEXAGONAL);
+ return set_ua(cell, ltsym);
+
+ default :
+ return 1;
}
- return realloc(str, sizeof(char)*len);
+ return 0;
}
void *fromfile_prepare(IndexingMethod *indm, struct fromfile_options *opts)
{
FILE *fh;
- int nlines;
- int nparams_in_solution;
- int nentries;
- char *filename;
- char *event;
- int crystal_number;
- int current_line;
- int position_in_current_line;
- struct fromfile_entries *sol_hash = NULL;
- struct fromfile_entries *item = NULL;
- float params[NPARAMS_PER_LINE];
+ struct fromfile_private *dp;
- fh = fopen(opts->filename, "r");
- if ( fh == NULL ) {
- ERROR("%s not found by fromfile_prepare\n", opts->filename);
+ if ( opts->filename == NULL ) {
+ ERROR("Please try again with --fromfile-input-file\n");
return NULL;
- } else {
- STATUS("Found solution file %s\n", opts->filename);
}
- nlines = ncrystals_in_sol(opts->filename);
- /* Total crystal parameters in solution file */
- nparams_in_solution = nlines*NPARAMS_PER_LINE;
- /* Total entries in solution file */
- nentries = nlines*(NPARAMS_PER_LINE+NKEYS_PER_LINE);
-
- STATUS("Parsing solution file containing %d lines...\n", nlines);
-
- /* Reads indexing solutions */
- int j = 0; /* follows the solution parameter [0,NPARAMS_PER_LINE] */
- for(int i = 0; i < nentries; i++) {
-
- crystal_number = 0;
-
- current_line = i/(NPARAMS_PER_LINE+NKEYS_PER_LINE);
-
- position_in_current_line = (i)%(NPARAMS_PER_LINE+NKEYS_PER_LINE);
-
- if ( position_in_current_line == 0 ) {
+ dp = malloc(sizeof(struct fromfile_private));
+ if ( dp == NULL ) return NULL;
- filename = read_unknown_string(fh);
-
- if ( !filename ){
- if ( current_line == nlines-1 ) break;
- printf("Failed to read a filename\n");
- return 0;
- }
+ fh = fopen(opts->filename, "r");
+ if ( fh == NULL ) {
+ ERROR("Couldn't find solution file '%s'\n", opts->filename);
+ return NULL;
+ }
+ dp->sol_hash = NULL;
+
+ /* Read indexing solutions */
+ do {
+
+ char *rval;
+ char line[1024];
+ int i, n;
+ char **bits;
+ float vals[11];
+ struct fromfile_key key;
+ Crystal *cr;
+ UnitCell *cell;
+ struct fromfile_entry *item = NULL;
+
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) break;
+
+ /* FIXME: Replace this with something that can handle quoted
+ * filenames with possible spaces */
+ chomp(line);
+ notrail(line);
+ n = assplode(line, " \t,", &bits, ASSPLODE_NONE);
+ if ( n < 14 ) {
+ ERROR("Badly formatted line '%s'\n", line);
+ return NULL;
}
- if ( position_in_current_line == 1 ) {
- event = read_unknown_string(fh);
- if ( !event ){
- printf("Failed to read a event\n");
- return 0;
+ /* filename, event, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz,
+ * det_shift_x, det_shift_y, latticetype+centering */
+ for ( i=2; i<13; i++ ) {
+ if (sscanf(bits[i], "%f", &vals[i-2]) != 1)
+ {
+ ERROR("Invalid value for number %i\n", i);
+ return NULL;
}
+ }
+ if ( make_key(&key, bits[0], bits[1]) ) {
+ ERROR("Failed to make key for %s %s\n",
+ bits[0], bits[1]);
+ continue;
}
- if ( position_in_current_line > 1 ) {
- if ( fscanf(fh, "%e", &params[j]) != 1 ) {
- printf("Failed to read a parameter\n");
- return 0;
- }
- j+=1;
+ item = add_unique(&dp->sol_hash, key);
+ if ( item == NULL ) {
+ ERROR("Failed to add/find entry for %s %s\n",
+ bits[0], bits[1]);
+ continue;
}
- if ( j == (NPARAMS_PER_LINE) ) {
+ if ( item->n_crystals == MAX_CRYSTALS ) {
- /* Prepare to add to the hash table */
- item = (struct fromfile_entries *)malloc(sizeof *item);
- memset(item, 0, sizeof *item);
- strcpy(item->key.filename, filename);
- strcpy(item->key.event, event);
- item->key.crystal_number = crystal_number;
- for ( int k = 0; k < NPARAMS_PER_LINE; k++){
- item->solution[k] = params[k];
- }
+ ERROR("Too many crystals for %s %s\n", bits[0], bits[1]);
- /* Verify the uniqueness of the key */
- struct fromfile_entries *uniqueness_test;
- HASH_FIND(hh, sol_hash, &item->key,
- sizeof(struct fromfile_keys), uniqueness_test);
+ } else {
- if ( uniqueness_test == NULL ) {
- HASH_ADD(hh, sol_hash, key,
- sizeof(struct fromfile_keys), item);
+ cr = crystal_new();
+
+ /* mm -> m */
+ crystal_set_det_shift(cr, vals[9]*1e-3, vals[10]*1e-3);
+
+ cell = cell_new();
+ cell_set_reciprocal(cell, vals[0]*1e9, vals[1]*1e9, vals[2]*1e9,
+ vals[3]*1e9, vals[4]*1e9, vals[5]*1e9,
+ vals[6]*1e9, vals[7]*1e9, vals[8]*1e9);
+ if ( set_lattice(cell, bits[13]) ) {
+ ERROR("Invalid lattice type '%s'\n", bits[13]);
} else {
- /* Look for the next available set of keys */
- do {
- uniqueness_test = NULL;
- crystal_number += 1;
- item->key.crystal_number = crystal_number;
- HASH_FIND(hh, sol_hash, &item->key,
- sizeof(struct fromfile_keys),
- uniqueness_test);
- } while ( uniqueness_test != NULL );
-
- HASH_ADD(hh, sol_hash, key,
- sizeof(struct fromfile_keys), item);
+ crystal_set_cell(cr, cell);
+ item->crystals[item->n_crystals++] = cr;
}
- j=0;
-
}
- }
- fclose(fh);
+ for ( i=0; i<n; i++ ) free(bits[i]);
+ free(bits);
- STATUS("Solution parsing done. Have %d parameters and %d total entries.\n",
- nparams_in_solution, nentries);
-
- struct fromfile_private *dp;
- dp = (struct fromfile_private *) malloc( sizeof(struct fromfile_private));
-
- if ( dp == NULL ){
- return NULL;
- }
+ } while ( 1 );
- dp->cellTemplate = cell;
- dp->sol_hash = sol_hash;
+ fclose(fh);
- STATUS("Solution lookup table initialized!\n");
+ STATUS("Read %i crystals from %s\n",
+ HASH_CNT(hh, dp->sol_hash), opts->filename);
- return (void *)dp;
+ return dp;
}
-int fromfile_index(struct image *image, void *mpriv, int crystal_number)
+int fromfile_index(struct image *image, void *mpriv)
{
- Crystal *cr;
- UnitCell *cell;
- float asx, asy, asz, bsx, bsy, bsz, csx, csy, csz;
- float xshift, yshift;
- struct fromfile_entries *item, *p, *pprime;
- int ncryst = 0;
- float *sol;
+ struct fromfile_entry *p;
struct fromfile_private *dp = mpriv;
+ struct fromfile_key key;
+ int i;
+
+ make_key(&key, image->filename, image->ev);
- /* Look up the hash table */
- item = calloc(1, sizeof(struct fromfile_entries));
- strcpy(item->key.filename, image->filename);
- strcpy(item->key.event, image->ev);
- item->key.crystal_number = crystal_number;
-
- /* key already in the hash? */
- HASH_FIND(hh, dp->sol_hash, &item->key, sizeof(struct fromfile_keys), p);
- if ( p == NULL ) return 0;
-
- sol = &(p->solution)[0];
-
- asx = sol[0] * 1e9;
- asy = sol[1] * 1e9;
- asz = sol[2] * 1e9;
- bsx = sol[3] * 1e9;
- bsy = sol[4] * 1e9;
- bsz = sol[5] * 1e9;
- csx = sol[6] * 1e9;
- csy = sol[7] * 1e9;
- csz = sol[8] * 1e9;
- xshift = sol[9] * 1e-3;
- yshift = sol[10] * 1e-3;
-
- cell = cell_new();
- cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
- cell_set_lattice_type(cell, cell_get_lattice_type(dp->cellTemplate));
- cell_set_centering(cell, cell_get_centering(dp->cellTemplate));
- cell_set_unique_axis(cell, cell_get_unique_axis(dp->cellTemplate));
-
- cr = crystal_new();
- ncryst += 1;
- crystal_set_cell(cr, cell);
- crystal_set_det_shift(cr, xshift , yshift);
- image_add_crystal(image, cr);
-
- /* Look for additional crystals */
- item->key.crystal_number = crystal_number+1;
- HASH_FIND(hh, dp->sol_hash, &item->key,
- sizeof(struct fromfile_keys), pprime);
-
- /* If a similar tag exist,
- * recursive call increasing the crystal_number by 1 */
- if ( pprime != NULL ) {
- ncryst += fromfile_index(image, mpriv, crystal_number+1);
+ HASH_FIND(hh, dp->sol_hash, &key, sizeof(struct fromfile_key), p);
+ if ( p == NULL ) {
+ STATUS("WARNING: No solution for %s %s\n",
+ image->filename, image->ev);
+ return 0;
}
- return ncryst;
+ for ( i=0; i<p->n_crystals; i++ ) {
+ Crystal *cr;
+ cr = crystal_copy_deep(p->crystals[i]);
+ image_add_crystal(image, cr);
+ }
+
+ return p->n_crystals;
}
void fromfile_cleanup(void *mpriv)
{
struct fromfile_private *dp = mpriv;
-
- /* FIXME: Implementation */
+ struct fromfile_entry *item, *tmp;
+
+ HASH_ITER(hh, dp->sol_hash, item, tmp) {
+ int i;
+ HASH_DEL(dp->sol_hash, item);
+ for ( i=0; i<item->n_crystals; i++ ) {
+ Crystal *cr = item->crystals[i];
+ cell_free(crystal_get_cell(cr));
+ crystal_free(cr);
+ }
+ }
free(dp);
}
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