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-rw-r--r--libcrystfel/src/grainspotter.c242
-rw-r--r--libcrystfel/src/grainspotter.h10
-rw-r--r--libcrystfel/src/image.c10
-rw-r--r--libcrystfel/src/image.h1
-rw-r--r--libcrystfel/src/index.c37
-rw-r--r--libcrystfel/src/index.h6
6 files changed, 245 insertions, 61 deletions
diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
index 7d0f74ce..bfb61df7 100644
--- a/libcrystfel/src/grainspotter.c
+++ b/libcrystfel/src/grainspotter.c
@@ -54,13 +54,25 @@
#include "peaks.h"
#include "cell.h"
#include "cell-utils.h"
+#include "grainspotter.h"
#define GRAINSPOTTER_VERBOSE 0
+/* Global private data, prepared once */
+struct grainspotter_private
+{
+ IndexingMethod indm;
+ UnitCell *cell;
+};
+
+
+/* Data needed during the run of Grainspotter */
struct grainspotter_data {
+ struct grainspotter_private *gp;
+
/* Low-level stuff */
int pty;
pid_t pid;
@@ -71,7 +83,8 @@ struct grainspotter_data {
};
-static int read_matrix(struct image *image, char *filename)
+static int read_matrix(struct grainspotter_private *gp, struct image *image,
+ char *filename)
{
FILE *fh;
int d1;
@@ -94,68 +107,157 @@ static int read_matrix(struct image *image, char *filename)
return 1;
}
- /* One line per grain */
- if ( fgets(line, 1024, fh) == NULL ) {
- ERROR("Failed to read GFF file.\n");
- return 1;
- }
+ do {
- STATUS("'%s'\n", line);
+ Crystal *cr;
+ UnitCell *cell;
- r = sscanf(line,
- "%i %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",
- &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
- &ubi11, &ubi12, &ubi13, &ubi21, &ubi22, &ubi23, &ubi31, &ubi32, &ubi33);
+ /* One line per grain */
+ if ( fgets(line, 1024, fh) == NULL ) {
+ ERROR("Failed to read GFF file.\n");
+ return 1;
+ }
- if ( r != 24 ) {
- ERROR("Only %i parameters in GFF file\n", r);
- return 1;
- }
+ STATUS("'%s'\n", line);
- fclose(fh);
+ r = sscanf(line, "%i %f %f %f %f %f %f %f %f %f %f %f %f"
+ "%f %f %f %f %f %f %f %f %f %f %f",
+ &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
+ &d2, &d2, &d2, &d2, &d2, &d2,
+ &ubi11, &ubi12, &ubi13,
+ &ubi21, &ubi22, &ubi23,
+ &ubi31, &ubi32, &ubi33);
- image->candidate_cells[0] = cell_new();
+ if ( r != 24 ) {
+ ERROR("Only %i parameters in GFF file\n", r);
+ return 1;
+ }
+
+ cell = cell_new();
+
+ cell_set_cartesian(cell, ubi12/1e10, ubi13/1e10, ubi11/1e10,
+ ubi22/1e10, ubi23/1e10, ubi21/1e10,
+ ubi32/1e10, ubi33/1e10, ubi31/1e10);
+
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 0;
+ }
-// cell_set_cartesian(image->candidate_cells[0],
-// ubi11/1e10, ubi12/1e10, ubi13/1e10,
-// ubi21/1e10, ubi22/1e10, ubi23/1e10,
-// ubi31/1e10, ubi32/1e10, ubi33/1e10);
+ crystal_set_cell(cr, cell);
+ image_add_crystal(image, cr);
- cell_set_cartesian(image->candidate_cells[0],
- ubi12/1e10, ubi13/1e10, ubi11/1e10,
- ubi22/1e10, ubi23/1e10, ubi21/1e10,
- ubi32/1e10, ubi33/1e10, ubi31/1e10);
+ } while ( !feof(fh) );
+ fclose(fh);
- image->ncells = 1;
- cell_print(image->candidate_cells[0]);
+ if ( gp->indm & INDEXING_CHECK_PEAKS ) {
+ if ( !peak_sanity_check(image, image->crystals,
+ image->n_crystals) )
+ {
+ free_all_crystals(image);
+ return 0;
+ }
+ }
return 0;
}
+static void gs_parseline(char *line, struct image *image,
+ struct grainspotter_data *gs)
+{
+ #if GRAINSPOTTER_VERBOSE
+ STATUS("%s\n", line);
+ #endif
+}
+
+
static int grainspotter_readable(struct image *image,
- struct grainspotter_data *grainspotter)
+ struct grainspotter_data *gs)
{
int rval;
+ int no_string = 0;
- rval = read(grainspotter->pty,
- grainspotter->rbuffer, grainspotter->rbuflen);
+ rval = read(gs->pty, gs->rbuffer+gs->rbufpos, gs->rbuflen-gs->rbufpos);
- if ( rval == -1 ) {
- ERROR("Read failed: %s\n", strerror(errno));
- return 1;
- }
+ if ( (rval == -1) || (rval == 0) ) return 1;
+
+ gs->rbufpos += rval;
+ assert(gs->rbufpos <= gs->rbuflen);
+
+ while ( (!no_string) && (gs->rbufpos > 0) ) {
+
+ int i;
+ int block_ready = 0;
+
+ /* See if there's a full line in the buffer yet */
+ for ( i=0; i<gs->rbufpos-1; i++ ) {
+ /* Means the last value looked at is rbufpos-2 */
+
+ if ( (gs->rbuffer[i] == '\r')
+ && (gs->rbuffer[i+1] == '\n') ) {
+ block_ready = 1;
+ break;
+ }
+
+ }
+
+ if ( block_ready ) {
- grainspotter->rbuffer[rval] = '\0';
+ unsigned int new_rbuflen;
+ unsigned int endbit_length;
+ char *block_buffer = NULL;
- printf("GrainSpotter: '%s'\n", grainspotter->rbuffer);
+ block_buffer = malloc(i+1);
+ memcpy(block_buffer, gs->rbuffer, i);
+ block_buffer[i] = '\0';
+
+ if ( block_buffer[0] == '\r' ) {
+ memmove(block_buffer, block_buffer+1, i);
+ }
+
+ gs_parseline(block_buffer, image, gs);
+ free(block_buffer);
+ endbit_length = i+2;
+
+ /* Now the block's been parsed, it should be
+ * forgotten about */
+ memmove(gs->rbuffer,
+ gs->rbuffer + endbit_length,
+ gs->rbuflen - endbit_length);
+
+ /* Subtract the number of bytes removed */
+ gs->rbufpos = gs->rbufpos - endbit_length;
+ new_rbuflen = gs->rbuflen - endbit_length;
+ if ( new_rbuflen == 0 ) new_rbuflen = 256;
+ gs->rbuffer = realloc(gs->rbuffer, new_rbuflen);
+ gs->rbuflen = new_rbuflen;
+
+ } else {
+
+ if ( gs->rbufpos==gs->rbuflen ) {
+
+ /* More buffer space is needed */
+ gs->rbuffer = realloc(gs->rbuffer,
+ gs->rbuflen + 256);
+ gs->rbuflen = gs->rbuflen + 256;
+ /* The new space gets used at the next
+ * read, shortly... */
+
+ }
+ no_string = 1;
+
+ }
+
+ }
return 0;
}
-static void write_gve(struct image *image, UnitCell *cell)
+static void write_gve(struct image *image, struct grainspotter_private *gp)
{
FILE *fh;
int i;
@@ -170,7 +272,7 @@ static void write_gve(struct image *image, UnitCell *cell)
return;
}
- cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
+ cell_get_parameters(gp->cell, &a, &b, &c, &al, &be, &ga);
fprintf(fh, "%.6f %.6f %.6f %.6f %.6f %.6f P\n", a*1e10, b*1e10, c*1e10,
rad2deg(al), rad2deg(be), rad2deg(ga));
fprintf(fh, "# wavelength = %.6f\n", image->lambda*1e10);
@@ -242,36 +344,39 @@ static char *write_ini(struct image *image)
}
-void run_grainspotter(struct image *image, UnitCell *cell)
+int grainspotter_index(struct image *image, IndexingPrivate *ipriv)
{
unsigned int opts;
int status;
int rval;
struct grainspotter_data *grainspotter;
+ struct grainspotter_private *gp = (struct grainspotter_private *)ipriv;
char *ini_filename;
char gff_filename[1024];
- write_gve(image, cell);
+ write_gve(image, gp);
ini_filename = write_ini(image);
if ( ini_filename == NULL ) {
ERROR("Failed to write ini file for GrainSpotter.\n");
- return;
+ return 0;
}
grainspotter = malloc(sizeof(struct grainspotter_data));
if ( grainspotter == NULL ) {
ERROR("Couldn't allocate memory for GrainSpotter data.\n");
- return;
+ return 0;
}
+ grainspotter->gp = gp;
+
snprintf(gff_filename, 1023, "xfel-%i.gff", image->id);
remove(gff_filename);
grainspotter->pid = forkpty(&grainspotter->pty, NULL, NULL, NULL);
if ( grainspotter->pid == -1 ) {
ERROR("Failed to fork for GrainSpotter: %s\n", strerror(errno));
- return;
+ return 0;
}
if ( grainspotter->pid == 0 ) {
@@ -283,8 +388,8 @@ void run_grainspotter(struct image *image, UnitCell *cell)
t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
tcsetattr(STDIN_FILENO, TCSANOW, &t);
- STATUS("Running GrainSpotter.0.90 '%s'\n", ini_filename);
- execlp("GrainSpotter.0.90", "", ini_filename, (char *)NULL);
+ STATUS("Running GrainSpotter.0.93 '%s'\n", ini_filename);
+ execlp("GrainSpotter.0.93", "", ini_filename, (char *)NULL);
ERROR("Failed to invoke GrainSpotter.\n");
_exit(0);
@@ -344,11 +449,54 @@ void run_grainspotter(struct image *image, UnitCell *cell)
if ( status != 0 ) {
ERROR("GrainSpotter doesn't seem to be working properly.\n");
+ free(grainspotter);
+ return 0;
}
- if ( read_matrix(image, gff_filename) != 0 ) {
- ERROR("Failed to read matrix\n");
+ if ( read_matrix(gp, image, gff_filename) != 0 ) {
+ free(grainspotter);
+ return 0;
}
+ /* Success! */
free(grainspotter);
+ return 1;
+}
+
+
+
+IndexingPrivate *grainspotter_prepare(IndexingMethod *indm, UnitCell *cell,
+ const char *filename,
+ struct detector *det,
+ struct beam_params *beam, float *ltl)
+{
+ struct grainspotter_private *gp;
+
+ if ( cell == NULL ) {
+ ERROR("GrainSpotter needs a unit cell.\n");
+ return NULL;
+ }
+
+ gp = calloc(1, sizeof(*gp));
+ if ( gp == NULL ) return NULL;
+
+ /* Flags that GrainSpotter knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS;
+
+ /* Flags that GrainSpotter requires */
+ *indm |= INDEXING_USE_LATTICE_TYPE;
+
+ gp->cell = cell;
+ gp->indm = *indm;
+
+ return (IndexingPrivate *)gp;
+}
+
+
+void grainspotter_cleanup(IndexingPrivate *pp)
+{
+ struct grainspotter_private *p;
+
+ p = (struct grainspotter_private *)pp;
+ free(p);
}
diff --git a/libcrystfel/src/grainspotter.h b/libcrystfel/src/grainspotter.h
index 1aedf57f..720fc486 100644
--- a/libcrystfel/src/grainspotter.h
+++ b/libcrystfel/src/grainspotter.h
@@ -35,8 +35,16 @@
#include "cell.h"
+extern IndexingPrivate *grainspotter_prepare(IndexingMethod *indm,
+ UnitCell *cell,
+ const char *filename,
+ struct detector *det,
+ struct beam_params *beam,
+ float *ltl);
-extern void run_grainspotter(struct image *image, UnitCell *cell);
+extern void grainspotter_cleanup(IndexingPrivate *pp);
+
+extern int grainspotter_index(struct image *image, IndexingPrivate *p);
#endif /* GRAINSPOTTER_H */
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 6e4fd40a..8fe3d69c 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -177,3 +177,13 @@ void image_add_crystal(struct image *image, Crystal *cryst)
image->crystals = crs;
image->n_crystals = n+1;
}
+
+
+void free_all_crystals(struct image *image)
+{
+ int i;
+
+ for ( i=0; i<image->n_crystals; i++ ) {
+ crystal_free(image->crystals[i]);
+ }
+}
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 3739c01f..0d131451 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -175,5 +175,6 @@ extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
extern void image_add_crystal(struct image *image, Crystal *cryst);
+extern void free_all_crystals(struct image *image);
#endif /* IMAGE_H */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 89fdec4f..eee2e814 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -51,6 +51,7 @@
#include "grainspotter.h"
#include "geometry.h"
#include "cell-utils.h"
+#include "grainspotter.h"
IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
@@ -68,6 +69,7 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
int i;
IndexingMethod in;
+ char *str;
in = indm[n];
@@ -82,16 +84,17 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
iprivs[n] = mosflm_prepare(&indm[n], cell, filename,
det, beam, ltl);
break;
-
- case INDEXING_GRAINSPOTTER :
- iprivs[n] = indexing_private(indm[n]);
- break;
-
case INDEXING_REAX :
iprivs[n] = reax_prepare(&indm[n], cell, filename,
det, beam, ltl);
break;
+ case INDEXING_GRAINSPOTTER :
+ iprivs[n] = grainspotter_prepare(&indm[n], cell,
+ filename, det, beam,
+ ltl);
+ break;
+
default :
ERROR("Don't know how to prepare indexing method %i\n",
indm[n]);
@@ -101,8 +104,9 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
if ( iprivs[n] == NULL ) return NULL;
- STATUS("Prepared indexing method %i: %s\n",
- n, indexer_str(indm[n]));
+ str = indexer_str(indm[n]);
+ STATUS("Prepared indexing method %i: %s\n", n, str);
+ free(str);
if ( in != indm[n] ) {
ERROR("Note: flags were altered to take into account "
@@ -149,14 +153,14 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
mosflm_cleanup(privs[n]);
break;
- case INDEXING_GRAINSPOTTER :
- free(priv[n]);
- break;
-
case INDEXING_REAX :
reax_cleanup(privs[n]);
break;
+ case INDEXING_GRAINSPOTTER :
+ grainspotter_cleanup(privs[n]);
+ break;
+
default :
ERROR("Don't know how to clean up indexing method %i\n",
indms[n]);
@@ -213,6 +217,10 @@ static int try_indexer(struct image *image, IndexingMethod indm,
return reax_index(image, ipriv);
break;
+ case INDEXING_GRAINSPOTTER :
+ return grainspotter_index(image, ipriv);
+ break;
+
default :
ERROR("Unrecognised indexing method: %i\n", indm);
break;
@@ -321,8 +329,13 @@ char *indexer_str(IndexingMethod indm)
strcpy(str, "reax");
break;
+ case INDEXING_GRAINSPOTTER :
+ strcpy(str, "grainspotter");
+ break;
+
default :
- ERROR("Unrecognised indexing method %i\n", indm);
+ ERROR("Unrecognised indexing method %i\n",
+ indm & INDEXING_METHOD_MASK);
strcpy(str, "(unknown)");
break;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index a47ee9a0..3c91486b 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -54,6 +54,10 @@
#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE \
| INDEXING_CHECK_PEAKS)
+#define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER \
+ | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_CHECK_PEAKS)
+
/**
* IndexingMethod:
* @INDEXING_NONE: No indexing to be performed
@@ -75,7 +79,7 @@ typedef enum {
INDEXING_GRAINSPOTTER = 4,
/* Bits at the top of the IndexingMethod are flags which modify the
- * behaviour of the indexer, at the moment just by adding checks. */
+ * behaviour of the indexer. */
INDEXING_CHECK_CELL_COMBINATIONS = 256,
INDEXING_CHECK_CELL_AXES = 512,
INDEXING_CHECK_PEAKS = 1024,
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 12:48:07 +0000