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-rw-r--r--libcrystfel/src/crystal.c77
-rw-r--r--libcrystfel/src/crystal.h3
-rw-r--r--libcrystfel/src/dirax.c5
-rw-r--r--libcrystfel/src/image.c18
-rw-r--r--libcrystfel/src/mosflm.c2
-rw-r--r--libcrystfel/src/reax.c66
-rw-r--r--libcrystfel/src/stream.c64
-rw-r--r--libcrystfel/src/stream.h5
8 files changed, 165 insertions, 75 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index 3c0649cc..8ba955f6 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -55,7 +55,7 @@ struct _crystal
double osf;
double profile_radius;
int pr_dud;
- double diffracting_resolution;
+ double resolution_limit;
/* Integrated (or about-to-be-integrated) reflections */
RefList *reflections;
@@ -63,7 +63,7 @@ struct _crystal
};
-/************************** Setters and Constructors **************************/
+/************************** Constructor / Destructor **************************/
/**
@@ -83,7 +83,7 @@ Crystal *crystal_new()
cryst->cell = NULL;
cryst->reflections = NULL;
- cryst->diffracting_resolution = 0.0;
+ cryst->resolution_limit = 0.0;
cryst->n_saturated = 0;
return cryst;
@@ -97,11 +97,78 @@ Crystal *crystal_new()
* Frees a %Crystal, and all internal resources concerning that crystal.
*
*/
-void crystal_free(UnitCell *cryst)
+void crystal_free(Crystal *cryst)
{
if ( cryst == NULL ) return;
- free(crysta);
+ if ( cryst->cell != NULL ) cell_free(cryst->cell);
+ if ( cryst->reflections != NULL ) reflist_free(cryst->reflections);
+ free(cryst);
}
/********************************** Getters ***********************************/
+
+
+UnitCell *crystal_get_cell(Crystal *cryst)
+{
+ return cryst->cell;
+}
+
+
+double crystal_get_profile_radius(Crystal *cryst)
+{
+ return cryst->profile_radius;
+}
+
+
+RefList *crystal_get_reflections(Crystal *cryst)
+{
+ return cryst->reflections;
+}
+
+
+double crystal_get_resolution_limit(Crystal *cryst)
+{
+ return cryst->resolution_limit;
+}
+
+
+long long int crystal_get_num_saturated_reflections(Crystal *cryst)
+{
+ return cryst->n_saturated;
+}
+
+
+/********************************** Setters ***********************************/
+
+
+void crystal_set_cell(Crystal *cryst, UnitCell *cell)
+{
+ if ( cryst->cell != NULL ) cell_free(cryst->cell);
+ cryst->cell = cell_new_from_cell(cell);
+}
+
+
+void crystal_set_profile_radius(Crystal *cryst, double r)
+{
+ cryst->profile_radius = r;
+}
+
+
+void crystal_set_reflections(Crystal *cryst, RefList *reflist)
+{
+ if ( cryst->reflections != NULL ) reflist_free(reflist);
+ cryst->reflections = reflist;
+}
+
+
+void crystal_set_resolution_limit(Crystal *cryst, double res)
+{
+ cryst->resolution_limit = res;
+}
+
+
+void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n)
+{
+ cryst->n_saturated = n;
+}
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index e5e40589..ca215399 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -60,7 +60,8 @@ extern void crystal_set_cell(Crystal *cryst, UnitCell *cell);
extern void crystal_set_profile_radius(Crystal *cryst, double r);
extern void crystal_set_reflections(Crystal *cryst, RefList *reflist);
extern void crystal_set_resolution_limit(Crystal *cryst, double res);
-extern void crystal_set_num_saturated_reflections(Crystal *cryst, int n);
+extern void crystal_set_num_saturated_reflections(Crystal *cryst,
+ long long int n);
#endif /* CRYSTAL_H */
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 0b2debda..6fbb9663 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -128,17 +128,20 @@ static int check_cell(struct dirax_private *dp, struct image *image,
return 0;
}
- crystal_set_cell(cr, cell);
+ crystal_set_cell(cr, out);
if ( dp->indm & INDEXING_CHECK_PEAKS ) {
if ( !peak_sanity_check(image, &cr, 1) ) {
crystal_free(cr); /* Frees the cell as well */
+ cell_free(out);
return 0;
}
}
image_add_crystal(image, cr);
+ cell_free(out); /* Crystal makes its own copy */
+
return 1;
}
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 093e20f2..6e4fd40a 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -159,3 +159,21 @@ void image_remove_feature(ImageFeatureList *flist, int idx)
{
flist->features[idx].valid = 0;
}
+
+
+void image_add_crystal(struct image *image, Crystal *cryst)
+{
+ Crystal **crs;
+ int n;
+
+ n = image->n_crystals;
+ crs = realloc(image->crystals, (n+1)*sizeof(Crystal *));
+ if ( crs == NULL ) {
+ ERROR("Failed to allocate memory for crystals.\n");
+ return;
+ }
+
+ crs[n] = cryst;
+ image->crystals = crs;
+ image->n_crystals = n+1;
+}
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 8b300012..d1d3c134 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -149,7 +149,7 @@ static int check_cell(struct mosflm_private *mp, struct image *image,
return 0;
}
- crystal_set_cell(cr, cell);
+ crystal_set_cell(cr, out);
if ( mp->indm & INDEXING_CHECK_PEAKS ) {
if ( !peak_sanity_check(image, &cr, 1) ) {
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 7529d12f..b144e266 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -103,7 +103,7 @@ struct reax_search
struct reax_private
{
- IndexingPrivate base;
+ IndexingMethod indm;
struct dvec *directions;
int n_dir;
double angular_inc;
@@ -915,9 +915,39 @@ static void add_cell_candidate(struct cell_candidate_list *cl, UnitCell *cnew,
}
+static int check_cell(struct reax_private *dp, struct image *image,
+ UnitCell *cell)
+{
+ UnitCell *out;
+ Crystal *cr;
+
+ out = cell_new_from_cell(cell);
+
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 0;
+ }
+
+ crystal_set_cell(cr, out);
+
+ 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 assemble_cells_from_candidates(struct image *image,
struct reax_search *s,
- UnitCell *cell)
+ UnitCell *cell,
+ struct reax_private *p)
{
int i, j, k;
signed int ti, tj, tk;
@@ -967,7 +997,9 @@ static void assemble_cells_from_candidates(struct image *image,
continue;
}
- peak_lattice_agreement(image, cnew, &fom);
+ /* FIXME! */
+ //peak_lattice_agreement(image, cnew, &fom);
+ fom = 1.0;
add_cell_candidate(&cl, cnew, fom);
}
@@ -985,22 +1017,20 @@ static void assemble_cells_from_candidates(struct image *image,
cell_get_parameters(cl.cand[i].cell, &a, &b, &c, &al, &be, &ga);
cell_get_parameters(cl.cand[i].cell, &aA, &bA, &cA,
&alA, &beA, &gaA);
- if ( (a - aA) > aA/10.0 ) w = 1;
- if ( (b - bA) > bA/10.0 ) w = 1;
- if ( (c - cA) > cA/10.0 ) w = 1;
- if ( (al - alA) > deg2rad(5.0) ) w = 1;
- if ( (be - beA) > deg2rad(5.0) ) w = 1;
- if ( (ga - gaA) > deg2rad(5.0) ) w = 1;
+ if ( fabs(a - aA) > aA/10.0 ) w = 1;
+ if ( fabs(b - bA) > bA/10.0 ) w = 1;
+ if ( fabs(c - cA) > cA/10.0 ) w = 1;
+ if ( fabs(al - alA) > deg2rad(5.0) ) w = 1;
+ if ( fabs(be - beA) > deg2rad(5.0) ) w = 1;
+ if ( fabs(ga - gaA) > deg2rad(5.0) ) w = 1;
if ( w ) {
STATUS("This cell is a long way from that sought:\n");
cell_print(cl.cand[i].cell);
}
}
- image->ncells = cl.n_cand;
- assert(image->ncells <= MAX_CELL_CANDIDATES);
for ( i=0; i<cl.n_cand; i++ ) {
- image->candidate_cells[i] = cl.cand[i].cell;
+ if ( check_cell(p, image, cl.cand[i].cell) ) break;
}
free(cl.cand);
@@ -1016,7 +1046,6 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
struct reax_search *s;
int i;
- assert(pp->indm == INDEXING_REAX);
p = (struct reax_private *)pp;
fft_in = fftw_malloc(p->nel*sizeof(double));
@@ -1039,7 +1068,7 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
// fft_in, fft_out, p->plan, smin, smax,
// image->det, p);
- assemble_cells_from_candidates(image, s, cell);
+ assemble_cells_from_candidates(image, s, cell, p);
for ( i=0; i<s->n_search; i++ ) {
free(s->search[i].cand);
@@ -1051,7 +1080,9 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
}
-IndexingPrivate *reax_prepare()
+IndexingPrivate *reax_prepare(IndexingMethod indm, UnitCell *cell,
+ const char *filename, struct detector *det,
+ struct beam_params *beam, float *ltl)
{
struct reax_private *p;
int samp;
@@ -1060,8 +1091,6 @@ IndexingPrivate *reax_prepare()
p = calloc(1, sizeof(*p));
if ( p == NULL ) return NULL;
- p->base.indm = INDEXING_REAX;
-
p->angular_inc = deg2rad(1.0);
/* Reserve memory, over-estimating the number of directions */
@@ -1122,6 +1151,8 @@ IndexingPrivate *reax_prepare()
p->r_plan = fftw_plan_dft_2d(p->cw, p->ch, p->r_fft_in, p->r_fft_out,
1, FFTW_MEASURE);
+ p->indm = indm;
+
return (IndexingPrivate *)p;
}
@@ -1130,7 +1161,6 @@ void reax_cleanup(IndexingPrivate *pp)
{
struct reax_private *p;
- assert(pp->indm == INDEXING_REAX);
p = (struct reax_private *)pp;
free(p->directions);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 943ee656..31fb8527 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -69,30 +69,6 @@ struct _stream
};
-int count_patterns(FILE *fh)
-{
- char *rval;
-
- int n_total_patterns = 0;
- do {
- char line[1024];
-
- rval = fgets(line, 1023, fh);
- if ( rval == NULL ) continue;
- chomp(line);
- if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_total_patterns++;
-
- } while ( rval != NULL );
-
- if ( ferror(fh) ) {
- ERROR("Read error while counting patterns.\n");
- return 0;
- }
-
- return n_total_patterns;
-}
-
-
static int read_peaks(FILE *fh, struct image *image)
{
char *rval = NULL;
@@ -482,28 +458,6 @@ void write_stream_header(FILE *ofh, int argc, char *argv[])
}
-int skip_some_files(FILE *fh, int n)
-{
- char *rval = NULL;
- int n_patterns = 0;
-
- do {
-
- char line[1024];
-
- if ( n_patterns == n ) return 0;
-
- rval = fgets(line, 1023, fh);
- if ( rval == NULL ) continue;
- chomp(line);
- if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_patterns++;
-
- } while ( rval != NULL );
-
- return 1;
-}
-
-
Stream *open_stream_for_read(const char *filename)
{
Stream *st;
@@ -591,3 +545,21 @@ int is_stream(const char *filename)
return 0;
}
+
+
+/**
+ * rewind_stream:
+ * @st: A %Stream
+ *
+ * Attempts to set the file pointer for @st to the start of the stream, so that
+ * later calls to read_chunk() will repeat the sequence of chunks from the
+ * start.
+ *
+ * Programs must not assume that this operation always succeeds!
+ *
+ * Returns: non-zero if the stream could not be rewound.
+ */
+int rewind_stream(Stream *st)
+{
+ return fseek(st->fh, 0, SEEK_SET);
+}
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index db74583d..9340ca0d 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -49,9 +49,8 @@ extern void write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
extern int read_chunk(Stream *st, struct image *image);
-/* Nasty functions that should be avoided */
-extern int count_patterns(FILE *fh);
-extern int skip_some_files(FILE *fh, int n);
+extern int rewind_stream(Stream *st);
+
extern int is_stream(const char *filename);
#endif /* STREAM_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 08:31:55 +0000