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-rw-r--r--libcrystfel/src/dirax.c123
1 files changed, 104 insertions, 19 deletions
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 160df719..0b2debda 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -53,6 +53,7 @@
#include "dirax.h"
#include "utils.h"
#include "peaks.h"
+#include "cell-utils.h"
#define DIRAX_VERBOSE 0
@@ -68,6 +69,13 @@ typedef enum {
} DirAxInputType;
+struct dirax_private {
+ IndexingMethod indm;
+ float *ltl;
+ UnitCell *template;
+};
+
+
struct dirax_data {
/* DirAx auto-indexing low-level stuff */
@@ -85,10 +93,56 @@ struct dirax_data {
int best_acl_nh;
int acls_tried[MAX_CELL_CANDIDATES];
int n_acls_tried;
+ UnitCell *cur_cell;
+ int done;
+ int success;
+
+ struct dirax_private *dp;
};
+static int check_cell(struct dirax_private *dp, struct image *image,
+ UnitCell *cell)
+{
+ UnitCell *out;
+ Crystal *cr;
+
+ if ( dp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
+
+ out = match_cell(cell, dp->template, 0, dp->ltl, 1);
+ if ( out == NULL ) return 0;
+
+ } else if ( dp->indm & INDEXING_CHECK_CELL_AXES ) {
+
+ out = match_cell(cell, dp->template, 0, dp->ltl, 0);
+ if ( out == NULL ) return 0;
+
+ } else {
+ out = cell_new_from_cell(cell);
+ }
+
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 0;
+ }
+
+ crystal_set_cell(cr, cell);
+
+ if ( dp->indm & INDEXING_CHECK_PEAKS ) {
+ if ( !peak_sanity_check(image, &cr, 1) ) {
+ crystal_free(cr); /* Frees the cell as well */
+ return 0;
+ }
+ }
+
+ image_add_crystal(image, cr);
+
+ return 1;
+}
+
+
static void dirax_parseline(const char *line, struct image *image,
struct dirax_data *dirax)
{
@@ -119,7 +173,7 @@ static void dirax_parseline(const char *line, struct image *image,
if ( line[i] == 'R' ) rf = 1;
if ( (line[i] == 'D') && rf ) {
dirax->read_cell = 1;
- image->candidate_cells[image->ncells] = cell_new();
+ dirax->cur_cell = cell_new();
return;
}
i++;
@@ -127,6 +181,7 @@ static void dirax_parseline(const char *line, struct image *image,
/* Parse unit cell vectors as appropriate */
if ( dirax->read_cell == 1 ) {
+
/* First row of unit cell values */
float ax, ay, az;
int r;
@@ -136,14 +191,16 @@ static void dirax_parseline(const char *line, struct image *image,
ERROR("Couldn't understand cell line:\n");
ERROR("'%s'\n", line);
dirax->read_cell = 0;
- cell_free(image->candidate_cells[image->ncells]);
+ cell_free(dirax->cur_cell);
return;
}
- cell_set_cartesian_a(image->candidate_cells[image->ncells],
+ cell_set_cartesian_a(dirax->cur_cell,
ax*1e-10, ay*1e-10, az*1e-10);
dirax->read_cell++;
return;
+
} else if ( dirax->read_cell == 2 ) {
+
/* Second row of unit cell values */
float bx, by, bz;
int r;
@@ -153,14 +210,16 @@ static void dirax_parseline(const char *line, struct image *image,
ERROR("Couldn't understand cell line:\n");
ERROR("'%s'\n", line);
dirax->read_cell = 0;
- cell_free(image->candidate_cells[image->ncells]);
+ cell_free(dirax->cur_cell);
return;
}
- cell_set_cartesian_b(image->candidate_cells[image->ncells],
+ cell_set_cartesian_b(dirax->cur_cell,
bx*1e-10, by*1e-10, bz*1e-10);
dirax->read_cell++;
return;
+
} else if ( dirax->read_cell == 3 ) {
+
/* Third row of unit cell values */
float cx, cy, cz;
int r;
@@ -170,13 +229,21 @@ static void dirax_parseline(const char *line, struct image *image,
ERROR("Couldn't understand cell line:\n");
ERROR("'%s'\n", line);
dirax->read_cell = 0;
- cell_free(image->candidate_cells[image->ncells]);
+ cell_free(dirax->cur_cell);
return;
}
- cell_set_cartesian_c(image->candidate_cells[image->ncells++],
+ cell_set_cartesian_c(dirax->cur_cell,
cx*1e-10, cy*1e-10, cz*1e-10);
dirax->read_cell = 0;
+
+ /* Finished reading a cell. Time to check it... */
+ if ( check_cell(dirax->dp, image, dirax->cur_cell) ) {
+ dirax->done = 1;
+ dirax->success = 1;
+ }
+
return;
+
}
dirax->read_cell = 0;
@@ -351,8 +418,7 @@ static int dirax_readable(struct image *image, struct dirax_data *dirax)
switch ( type ) {
- case DIRAX_INPUT_LINE :
-
+ case DIRAX_INPUT_LINE :
block_buffer = malloc(i+1);
memcpy(block_buffer, dirax->rbuffer, i);
block_buffer[i] = '\0';
@@ -366,20 +432,17 @@ static int dirax_readable(struct image *image, struct dirax_data *dirax)
endbit_length = i+2;
break;
- case DIRAX_INPUT_PROMPT :
-
+ case DIRAX_INPUT_PROMPT :
dirax_send_next(image, dirax);
endbit_length = i+7;
break;
- case DIRAX_INPUT_ACL :
-
+ case DIRAX_INPUT_ACL :
dirax_send_next(image,dirax );
endbit_length = i+10;
break;
- default :
-
+ default :
/* Obviously, this never happens :) */
ERROR("Unrecognised DirAx input mode! "
"I don't know how to understand DirAx\n");
@@ -456,7 +519,7 @@ static void write_drx(struct image *image)
}
-void run_dirax(struct image *image)
+int run_dirax(struct image *image, IndexingPrivate *ipriv)
{
unsigned int opts;
int status;
@@ -468,13 +531,13 @@ void run_dirax(struct image *image)
dirax = malloc(sizeof(struct dirax_data));
if ( dirax == NULL ) {
ERROR("Couldn't allocate memory for DirAx data.\n");
- return;
+ return 0;
}
dirax->pid = forkpty(&dirax->pty, NULL, NULL, NULL);
if ( dirax->pid == -1 ) {
ERROR("Failed to fork for DirAx: %s\n", strerror(errno));
- return;
+ return 0;
}
if ( dirax->pid == 0 ) {
@@ -505,6 +568,9 @@ void run_dirax(struct image *image)
dirax->read_cell = 0;
dirax->n_acls_tried = 0;
dirax->best_acl_nh = 0;
+ dirax->done = 0;
+ dirax->success = 0;
+ dirax->dp = (struct dirax_private *)ipriv;
do {
@@ -543,7 +609,7 @@ void run_dirax(struct image *image)
rval = 1;
}
- } while ( !rval );
+ } while ( !rval && !dirax->success );
close(dirax->pty);
free(dirax->rbuffer);
@@ -553,5 +619,24 @@ void run_dirax(struct image *image)
ERROR("DirAx doesn't seem to be working properly.\n");
}
+ rval = dirax->success;
free(dirax);
+ return rval;
+}
+
+
+IndexingPrivate *dirax_prepare(IndexingMethod indm, UnitCell *cell,
+ const char *filename, struct detector *det,
+ struct beam_params *beam, float *ltl)
+{
+ struct dirax_private *dp;
+
+ dp = malloc(sizeof(struct dirax_private));
+ if ( dp == NULL ) return NULL;
+
+ dp->ltl = ltl;
+ dp->template = cell;
+ dp->indm = indm;
+
+ return (IndexingPrivate *)dp;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 18:31:55 +0000