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-rw-r--r--src/basis.c30
-rw-r--r--src/cache.c18
-rw-r--r--src/cache.h4
-rw-r--r--src/control.h4
-rw-r--r--src/displaywindow.c14
-rw-r--r--src/ipr.c8
-rw-r--r--src/main.c10
-rw-r--r--src/mapping.c14
-rw-r--r--src/mapping.h2
-rw-r--r--src/qdrp.c2
-rw-r--r--src/reflections.c100
-rw-r--r--src/reflections.h24
-rw-r--r--src/reproject.c18
-rw-r--r--src/reproject.h2
14 files changed, 125 insertions, 125 deletions
diff --git a/src/basis.c b/src/basis.c
index a7ff978..939dc93 100644
--- a/src/basis.c
+++ b/src/basis.c
@@ -21,12 +21,12 @@
#include "reflections.h"
#include "basis.h"
-static double basis_efom(ReflectionContext *rctx, Basis *basis) {
+static double basis_efom(ReflectionList *reflectionlist, Basis *basis) {
int n_indexed, n_counted;
Reflection *cur;
- cur = rctx->reflections;
+ cur = reflectionlist->reflections;
n_indexed = 0;
n_counted = 0;
while ( cur ) {
@@ -80,14 +80,14 @@ static int basis_lfom(ControlContext *ctx, double vx, double vy, double vz) {
lfom = 0;
tol = modulus(vx, vy, vz)/10.0;
- tcentre = ctx->reflectionctx->reflections;
+ tcentre = ctx->reflectionlist->reflections;
do {
for ( j=-20; j<=20; j++ ) {
Reflection *check;
- check = reflection_find_nearest(ctx->reflectionctx, tcentre->x+vx*j, tcentre->y+vy*j, tcentre->z+vz*j);
+ check = reflection_find_nearest(ctx->reflectionlist, tcentre->x+vx*j, tcentre->y+vy*j, tcentre->z+vz*j);
if ( check && (distance3d(check->x, check->y, check->z, tcentre->x+vx*j, tcentre->y+vy*j, tcentre->z+vz*j) < tol) ) {
lfom++;
}
@@ -102,7 +102,7 @@ static int basis_lfom(ControlContext *ctx, double vx, double vy, double vz) {
}
-static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
+static ReflectionList *basis_find_seeds(ControlContext *ctx) {
double tilt_min;
double tilt_max;
@@ -113,7 +113,7 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
double x, y, z;
Reflection *centre;
int i;
- ReflectionContext *seeds;
+ ReflectionList *seeds;
seeds = reflection_init();
@@ -134,17 +134,17 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
z = z_temp;
/* Find the point in the middle of the "wedge" */
- scale = reflection_largest_g(ctx->reflectionctx)/4;
+ scale = reflection_largest_g(ctx->reflectionlist)/4;
x *= scale;
y *= scale;
z *= scale;
- reflection_add(ctx->reflectionctx, x, y, z, 1.0, REFLECTION_VECTOR_MARKER_2);
+ reflection_add(ctx->reflectionlist, x, y, z, 1.0, REFLECTION_VECTOR_MARKER_2);
/* Find an "origin" reflection */
- centre = reflection_find_nearest(ctx->reflectionctx, x, y, z);
+ centre = reflection_find_nearest(ctx->reflectionlist, x, y, z);
if ( !centre ) return NULL;
centre->found = 1;
- reflection_add(ctx->reflectionctx, centre->x, centre->y, centre->z, 1.0, REFLECTION_GENERATED);
+ reflection_add(ctx->reflectionlist, centre->x, centre->y, centre->z, 1.0, REFLECTION_GENERATED);
for ( i=1; i<=10; i++ ) {
@@ -160,7 +160,7 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
accept = 1;
/* Find a "candidate vector" reflection */
- vector = reflection_find_nearest_longer(ctx->reflectionctx, centre->x, centre->y, centre->z, 1e9); /* 0.5 A^-1 */
+ vector = reflection_find_nearest_longer(ctx->reflectionlist, centre->x, centre->y, centre->z, 1e9); /* 0.5 A^-1 */
if ( !vector ) {
printf("BS: Couldn't find enough seeds\n");
return NULL;
@@ -173,7 +173,7 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
vz = vector->z - centre->z;
/* Proximity test */
- check = reflection_find_nearest_type(ctx->reflectionctx, vx, vy, vz, REFLECTION_NORMAL);
+ check = reflection_find_nearest_type(ctx->reflectionlist, vx, vy, vz, REFLECTION_NORMAL);
if ( check ) {
if ( distance3d(vx, vy, vz, check->x, check->y, check->z) < 1e9 ) {
/* Too close to another seed */
@@ -193,7 +193,7 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
} while ( !accept );
reflection_add(seeds, vx, vy, vz, 1.0, REFLECTION_NORMAL);
- reflection_add(ctx->reflectionctx, vx, vy, vz, 1.0, REFLECTION_MARKER);
+ reflection_add(ctx->reflectionlist, vx, vy, vz, 1.0, REFLECTION_MARKER);
}
@@ -204,7 +204,7 @@ static ReflectionContext *basis_find_seeds(ControlContext *ctx) {
Basis *basis_find(ControlContext *ctx) {
Basis *basis;
- ReflectionContext *seeds;
+ ReflectionList *seeds;
Reflection *ref;
int i;
@@ -244,7 +244,7 @@ Basis *basis_find(ControlContext *ctx) {
}
- printf("BS: eFOM = %7.3f %%\n", basis_efom(ctx->reflectionctx, basis)*100);
+ printf("BS: eFOM = %7.3f %%\n", basis_efom(ctx->reflectionlist, basis)*100);
return basis;
diff --git a/src/cache.c b/src/cache.c
index f3b85af..eb164aa 100644
--- a/src/cache.c
+++ b/src/cache.c
@@ -28,17 +28,17 @@ typedef struct struct_cacheheader {
double scale;
} CacheHeader;
-ReflectionContext *cache_load(const char *filename) {
+ReflectionList *cache_load(const char *filename) {
FILE *f;
CacheHeader ch;
- ReflectionContext *rctx;
+ ReflectionList *reflectionlist;
size_t cachedreflection_size;
int i;
cachedreflection_size = sizeof(Reflection) - sizeof(Reflection *);
- rctx = reflection_init();
+ reflectionlist = reflection_init();
f = fopen(filename, "rb");
if ( !f ) {
fprintf(stderr, "Couldn't read reflections from cache\n");
@@ -58,22 +58,22 @@ ReflectionContext *cache_load(const char *filename) {
fprintf(stderr, "Couldn't read reflections from cache\n");
fclose(f);
free(cr);
- reflection_clear(rctx);
+ reflection_clear(reflectionlist);
return NULL;
}
cr->next = NULL; /* Guarantee swift failure in the event of a screw-up */
//printf("reading (%f,%f,%f) i=%f (%d,%d,%d) %d\n",cr->x,cr->y,cr->z,cr->intensity,cr->h,cr->k,cr->l,cr->type);
- reflection_add_from_reflection(rctx, cr);
+ reflection_add_from_reflection(reflectionlist, cr);
}
fclose(f);
- return rctx;
+ return reflectionlist;
}
-int cache_save(const char *input_filename, ReflectionContext *rctx) {
+int cache_save(const char *input_filename, ReflectionList *reflectionlist) {
FILE *f;
CacheHeader ch;
@@ -91,7 +91,7 @@ int cache_save(const char *input_filename, ReflectionContext *rctx) {
cachedreflection_size = sizeof(Reflection) - sizeof(Reflection *);
count = 0;
- r = rctx->reflections;
+ r = reflectionlist->reflections;
while ( r != NULL ) {
count++;
r = r->next;
@@ -108,7 +108,7 @@ int cache_save(const char *input_filename, ReflectionContext *rctx) {
ch.scale = 0.; //temp, currently doesn't do anything
fwrite(&ch, sizeof(CacheHeader), 1, f);
- r = rctx->reflections;
+ r = reflectionlist->reflections;
while ( r != NULL ) {
fwrite(r, cachedreflection_size, 1, f); /* Write the reflection block, stopping just short of the "next" pointer */
diff --git a/src/cache.h b/src/cache.h
index 716f0ee..a52edfe 100644
--- a/src/cache.h
+++ b/src/cache.h
@@ -17,8 +17,8 @@
#include <config.h>
#endif
-extern ReflectionContext *cache_load(const char *filename);
-extern int cache_save(const char *filename, ReflectionContext *rctx);
+extern ReflectionList *cache_load(const char *filename);
+extern int cache_save(const char *filename, ReflectionList *reflectionlist);
extern unsigned int cache_is_cachefile(const char *filename);
#endif /*CACHE_H_*/
diff --git a/src/control.h b/src/control.h
index 50c7230..5b0d187 100644
--- a/src/control.h
+++ b/src/control.h
@@ -111,7 +111,7 @@ typedef struct cctx_struct {
ImageRecord images[MAX_IMAGES];
/* Output */
- struct rctx_struct *reflectionctx;
+ struct reflectionlist_struct *reflectionlist;
struct dw_struct *dw;
/* GTK bits */
@@ -123,7 +123,7 @@ typedef struct cctx_struct {
/* IPR stuff */
int ipr_cur_image;
struct imagedisplay_struct *ipr_id;
- struct rctx_struct *ipr_lat;
+ struct reflectionlist_struct *ipr_lat;
struct basis_struct *ipr_basis;
} ControlContext;
diff --git a/src/displaywindow.c b/src/displaywindow.c
index 867b2cb..b38007d 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -358,7 +358,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
if ( dw->gl_use_buffers ) {
glGenBuffersARB(1, &dw->gl_ref_vertex_buffer);
}
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
i = 0;
do {
if ( reflection->type == REFLECTION_NORMAL ) i++;
@@ -366,7 +366,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
} while ( reflection != NULL );
dw->gl_ref_num_vertices = i;
i = 0;
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
vertices = malloc(3*dw->gl_ref_num_vertices*sizeof(GLfloat));
do {
if ( reflection->type == REFLECTION_NORMAL ) {
@@ -390,7 +390,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
glGenBuffersARB(1, &dw->gl_marker_vertex_buffer);
glGenBuffersARB(1, &dw->gl_marker_normal_buffer);
}
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
i = 0;
do {
if ( reflection->type == REFLECTION_MARKER ) i++;
@@ -398,7 +398,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
} while ( reflection != NULL );
dw->gl_marker_num_vertices = i*VERTICES_IN_A_BLOB;
i = 0;
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
vertices = malloc(3*dw->gl_marker_num_vertices*sizeof(GLfloat));
normals = malloc(3*dw->gl_marker_num_vertices*sizeof(GLfloat));
do {
@@ -424,7 +424,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
glGenBuffersARB(1, &dw->gl_gen_vertex_buffer);
glGenBuffersARB(1, &dw->gl_gen_normal_buffer);
}
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
i = 0;
do {
if ( reflection->type == REFLECTION_GENERATED ) i++;
@@ -432,7 +432,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
} while ( reflection != NULL );
dw->gl_gen_num_vertices = i*VERTICES_IN_A_BLOB;
i = 0;
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
vertices = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
normals = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
do {
@@ -517,7 +517,7 @@ static void displaywindow_gl_create_list(DisplayWindow *dw) {
glPopMatrix();
/* Plot the other reflections */
- reflection = ctx->reflectionctx->reflections;
+ reflection = ctx->reflectionlist->reflections;
quadric = gluNewQuadric();
do {
diff --git a/src/ipr.c b/src/ipr.c
index 56f871c..a5845b0 100644
--- a/src/ipr.c
+++ b/src/ipr.c
@@ -29,9 +29,9 @@
#include "basis.h"
/* Generate list of reflections to analyse */
-static ReflectionContext *ipr_generate(ControlContext *ctx, Basis *basis) {
+static ReflectionList *ipr_generate(ControlContext *ctx, Basis *basis) {
- ReflectionContext *ordered;
+ ReflectionList *ordered;
double max_res;
signed int h, k, l;
int max_order_a, max_order_b, max_order_c;
@@ -73,7 +73,7 @@ static ReflectionContext *ipr_generate(ControlContext *ctx, Basis *basis) {
ref->h = h; ref->k = k; ref->l = l;
}
if ( (h!=0) || (k!=0) || (l!=0) ) {
- // reflection_add(ctx->reflectionctx, x, y, z, 1, REFLECTION_GENERATED);
+ // reflection_add(ctx->reflectionlist, x, y, z, 1, REFLECTION_GENERATED);
reflection_add(ordered, x, y, z, 1, REFLECTION_GENERATED);
}
}
@@ -95,7 +95,7 @@ static gint ipr_clicked(GtkWidget *widget, GdkEventButton *event, ControlContext
if ( ctx->ipr_cur_image == ctx->n_images ) ctx->ipr_cur_image = 0;
imagedisplay_clear_circles(ctx->ipr_id);
- reflection_clear_markers(ctx->reflectionctx);
+ reflection_clear_markers(ctx->reflectionlist);
refl = reproject_get_reflections(ctx->images[ctx->ipr_cur_image], &n, ctx->ipr_lat, ctx);
for ( j=0; j<n; j++ ) {
diff --git a/src/main.c b/src/main.c
index 3be412b..578c2fe 100644
--- a/src/main.c
+++ b/src/main.c
@@ -43,15 +43,15 @@ void main_do_reconstruction(ControlContext *ctx) {
mapping_create(ctx);
}
- if ( (ctx->inputfiletype != INPUT_CACHE) && !val && ctx->reflectionctx && ctx->savecache ) {
- cache_save(ctx->filename, ctx->reflectionctx);
+ if ( (ctx->inputfiletype != INPUT_CACHE) && !val && ctx->reflectionlist && ctx->savecache ) {
+ cache_save(ctx->filename, ctx->reflectionlist);
}
- if ( (ctx->rmode == RECONSTRUCTION_PREDICTION) && (ctx->reflectionctx) ) {
+ if ( (ctx->rmode == RECONSTRUCTION_PREDICTION) && (ctx->reflectionlist) ) {
val = ipr_refine(ctx);
}
- if ( !val && (ctx->reflectionctx) ) {
+ if ( !val && (ctx->reflectionlist) ) {
ctx->dw = displaywindow_open(ctx);
} else {
fprintf(stderr, "Reconstruction failed.\n");
@@ -102,7 +102,7 @@ static gint main_method_window_response(GtkWidget *method_window, gint response,
} else if ( ctx->inputfiletype == INPUT_MRC ) {
val = mrc_read(ctx);
} else if ( ctx->inputfiletype == INPUT_CACHE ) {
- ctx->reflectionctx = cache_load(ctx->filename);
+ ctx->reflectionlist = cache_load(ctx->filename);
val=0;
}
diff --git a/src/mapping.c b/src/mapping.c
index fdce9ea..8570966 100644
--- a/src/mapping.c
+++ b/src/mapping.c
@@ -17,24 +17,24 @@
#include "control.h"
#include "itrans.h"
-ReflectionContext *mapping_create(ControlContext *ctx) {
+ReflectionList *mapping_create(ControlContext *ctx) {
- ReflectionContext *rctx;
+ ReflectionList *reflectionlist;
int i;
/* Create reflection context */
- rctx = reflection_init();
+ reflectionlist = reflection_init();
/* Pass all images through itrans
- * (let itrans add the reflections to rctx for now) */
+ * (let itrans add the reflections to reflectionlist for now) */
printf("MP: Processing images..."); fflush(stdout);
- ctx->reflectionctx = rctx;
+ ctx->reflectionlist = reflectionlist;
for ( i=0; i<ctx->n_images; i++ ) {
itrans_process_image(&ctx->images[i], ctx);
}
- printf("done: %i 'measured' reflections\n", ctx->reflectionctx->n_reflections);
+ printf("done: %i 'measured' reflections\n", ctx->reflectionlist->n_reflections);
- return rctx;
+ return reflectionlist;
}
diff --git a/src/mapping.h b/src/mapping.h
index f40d8f1..601ad46 100644
--- a/src/mapping.h
+++ b/src/mapping.h
@@ -19,7 +19,7 @@
#include "reflections.h"
#include "control.h"
-extern ReflectionContext *mapping_create(ControlContext *ctx);
+extern ReflectionList *mapping_create(ControlContext *ctx);
#endif /* MAPPING_H */
diff --git a/src/qdrp.c b/src/qdrp.c
index 86384bd..5fe0c50 100644
--- a/src/qdrp.c
+++ b/src/qdrp.c
@@ -107,7 +107,7 @@ static int qdrp_parseline(ControlContext *ctx, const char *line) {
}
ctx->started = 1;
- ctx->reflectionctx = reflection_init();
+ ctx->reflectionlist = reflection_init();
}
diff --git a/src/reflections.c b/src/reflections.c
index 3fa1b6d..a0ff76d 100644
--- a/src/reflections.c
+++ b/src/reflections.c
@@ -22,34 +22,34 @@
#include "reflections.h"
#include "utils.h"
-static void reflection_addfirst(ReflectionContext *reflectionctx) {
+static void reflection_addfirst(ReflectionList *reflectionlist) {
/* Create first items on lists - saves faffing later. Corresponds to a central marker.
Reflections are only stored if they have non-zero value. */
- reflectionctx->reflections = malloc(sizeof(Reflection));
- reflectionctx->reflections->next = NULL;
- reflectionctx->reflections->x = 0;
- reflectionctx->reflections->y = 0;
- reflectionctx->reflections->z = 0;
- reflectionctx->reflections->type = REFLECTION_CENTRAL;
- reflectionctx->last_reflection = reflectionctx->reflections;
- reflectionctx->n_reflections = 1;
- reflectionctx->list_capped = 0;
+ reflectionlist->reflections = malloc(sizeof(Reflection));
+ reflectionlist->reflections->next = NULL;
+ reflectionlist->reflections->x = 0;
+ reflectionlist->reflections->y = 0;
+ reflectionlist->reflections->z = 0;
+ reflectionlist->reflections->type = REFLECTION_CENTRAL;
+ reflectionlist->last_reflection = reflectionlist->reflections;
+ reflectionlist->n_reflections = 1;
+ reflectionlist->list_capped = 0;
}
-ReflectionContext *reflection_init() {
+ReflectionList *reflection_init() {
- ReflectionContext *reflectionctx = malloc(sizeof(ReflectionContext));
- reflectionctx->n_reflections = 0;
- reflection_addfirst(reflectionctx);
- reflectionctx->list_capped = 0;
+ ReflectionList *reflectionlist = malloc(sizeof(ReflectionList));
+ reflectionlist->n_reflections = 0;
+ reflection_addfirst(reflectionlist);
+ reflectionlist->list_capped = 0;
- return reflectionctx;
+ return reflectionlist;
}
-void reflection_clear_markers(ReflectionContext *reflectionctx) {
+void reflection_clear_markers(ReflectionList *reflectionlist) {
- Reflection *reflection = reflectionctx->reflections;
+ Reflection *reflection = reflectionlist->reflections;
Reflection *prev = NULL;
int del = 0;
@@ -64,7 +64,7 @@ void reflection_clear_markers(ReflectionContext *reflectionctx) {
if ( prev ) {
prev->next = next;
} else {
- reflectionctx->reflections = next;
+ reflectionlist->reflections = next;
}
} else {
prev = reflection;
@@ -74,48 +74,48 @@ void reflection_clear_markers(ReflectionContext *reflectionctx) {
} while ( reflection );
- reflectionctx->n_reflections -= del;
- reflectionctx->last_reflection = prev;
+ reflectionlist->n_reflections -= del;
+ reflectionlist->last_reflection = prev;
}
-void reflection_clear(ReflectionContext *reflectionctx) {
+void reflection_clear(ReflectionList *reflectionlist) {
- Reflection *reflection = reflectionctx->reflections;
+ Reflection *reflection = reflectionlist->reflections;
do {
Reflection *next = reflection->next;
free(reflection);
reflection = next;
} while ( reflection );
- reflectionctx->n_reflections = 0;
- reflectionctx->list_capped = 0;
- reflection_addfirst(reflectionctx);
+ reflectionlist->n_reflections = 0;
+ reflectionlist->list_capped = 0;
+ reflection_addfirst(reflectionlist);
}
-void reflection_free(ReflectionContext *reflectionctx) {
- reflection_clear(reflectionctx);
- free(reflectionctx->reflections);
- free(reflectionctx);
+void reflection_free(ReflectionList *reflectionlist) {
+ reflection_clear(reflectionlist);
+ free(reflectionlist->reflections);
+ free(reflectionlist);
}
-Reflection *reflection_add(ReflectionContext *reflectionctx, double x, double y, double z, double intensity, ReflectionType type) {
+Reflection *reflection_add(ReflectionList *reflectionlist, double x, double y, double z, double intensity, ReflectionType type) {
Reflection *new_reflection;
Reflection *nearest;
- if ( reflectionctx->list_capped ) return NULL;
+ if ( reflectionlist->list_capped ) return NULL;
- if ( reflectionctx->n_reflections > 1e7 ) {
+ if ( reflectionlist->n_reflections > 1e7 ) {
fprintf(stderr, "More than 10 million reflections on list. I think this is silly.\n");
fprintf(stderr, "No further reflections will be stored. Go and fix the peak detection.\n");
- reflectionctx->list_capped = 1;
+ reflectionlist->list_capped = 1;
}
- nearest = reflection_find_nearest_type(reflectionctx, x, y, z, type);
+ nearest = reflection_find_nearest_type(reflectionlist, x, y, z, type);
if ( nearest && distance3d(x, y, z, nearest->x, nearest->y, nearest->z) < 0.1e9 ) return NULL;
- reflectionctx->n_reflections++;
+ reflectionlist->n_reflections++;
new_reflection = malloc(sizeof(Reflection));
new_reflection->next = NULL;
@@ -126,8 +126,8 @@ Reflection *reflection_add(ReflectionContext *reflectionctx, double x, double y,
new_reflection->type = type;
new_reflection->found = 0;
- reflectionctx->last_reflection->next = new_reflection;
- reflectionctx->last_reflection = new_reflection;
+ reflectionlist->last_reflection->next = new_reflection;
+ reflectionlist->last_reflection = new_reflection;
return new_reflection;
@@ -216,23 +216,23 @@ void reflection_add_from_dp(ControlContext *ctx, double x, double y, ImageRecord
refl.intensity = intensity;
if ( !reflection_map_to_space(&refl, &nx, &ny, &nz, &twotheta) ) {
- reflection_add(ctx->reflectionctx, nx, ny, nz, intensity, REFLECTION_NORMAL);
+ reflection_add(ctx->reflectionlist, nx, ny, nz, intensity, REFLECTION_NORMAL);
}
}
-void reflection_add_from_reflection(ReflectionContext *rctx, Reflection *r) {
+void reflection_add_from_reflection(ReflectionList *reflectionlist, Reflection *r) {
r->next = NULL;
- rctx->last_reflection->next = r;
- rctx->last_reflection = r;
+ reflectionlist->last_reflection->next = r;
+ reflectionlist->last_reflection = r;
}
-double reflection_largest_g(ReflectionContext *reflectionctx) {
+double reflection_largest_g(ReflectionList *reflectionlist) {
double max = 0.0;
Reflection *reflection;
- reflection = reflectionctx->reflections;
+ reflection = reflectionlist->reflections;
while ( reflection ) {
if ( reflection->type == REFLECTION_NORMAL ) {
double mod;
@@ -246,13 +246,13 @@ double reflection_largest_g(ReflectionContext *reflectionctx) {
}
-Reflection *reflection_find_nearest(ReflectionContext *reflectionctx, double x, double y, double z) {
+Reflection *reflection_find_nearest(ReflectionList *reflectionlist, double x, double y, double z) {
double max = +INFINITY;
Reflection *reflection;
Reflection *best = NULL;
- reflection = reflectionctx->reflections;
+ reflection = reflectionlist->reflections;
while ( reflection ) {
if ( reflection->type == REFLECTION_NORMAL ) {
double mod;
@@ -269,13 +269,13 @@ Reflection *reflection_find_nearest(ReflectionContext *reflectionctx, double x,
}
-Reflection *reflection_find_nearest_longer(ReflectionContext *reflectionctx, double x, double y, double z, double min_distance) {
+Reflection *reflection_find_nearest_longer(ReflectionList *reflectionlist, double x, double y, double z, double min_distance) {
double max = +INFINITY;
Reflection *reflection;
Reflection *best = NULL;
- reflection = reflectionctx->reflections;
+ reflection = reflectionlist->reflections;
while ( reflection ) {
if ( (reflection->type == REFLECTION_NORMAL) && (!reflection->found) ) {
double mod;
@@ -292,13 +292,13 @@ Reflection *reflection_find_nearest_longer(ReflectionContext *reflectionctx, dou
}
-Reflection *reflection_find_nearest_type(ReflectionContext *reflectionctx, double x, double y, double z, ReflectionType type) {
+Reflection *reflection_find_nearest_type(ReflectionList *reflectionlist, double x, double y, double z, ReflectionType type) {
double max = +INFINITY;
Reflection *reflection;
Reflection *best = NULL;
- reflection = reflectionctx->reflections;
+ reflection = reflectionlist->reflections;
while ( reflection ) {
if ( reflection->type == type ) {
double mod;
diff --git a/src/reflections.h b/src/reflections.h
index 9dd281a..9ac0cec 100644
--- a/src/reflections.h
+++ b/src/reflections.h
@@ -45,7 +45,7 @@ typedef struct reflection_struct {
} Reflection;
-typedef struct rctx_struct {
+typedef struct reflectionlist_struct {
Reflection *reflections;
Reflection *last_reflection;
@@ -53,24 +53,24 @@ typedef struct rctx_struct {
unsigned int n_reflections;
unsigned int list_capped;
-} ReflectionContext;
+} ReflectionList;
-extern ReflectionContext *reflection_init(void);
-extern void reflection_clear(ReflectionContext *reflectionctx);
-extern void reflection_clear_markers(ReflectionContext *reflectionctx);
-extern void reflection_free(ReflectionContext *reflectionctx);
+extern ReflectionList *reflection_init(void);
+extern void reflection_clear(ReflectionList *reflectionlist);
+extern void reflection_clear_markers(ReflectionList *reflectionlist);
+extern void reflection_free(ReflectionList *reflectionlist);
-extern Reflection *reflection_add(ReflectionContext *reflectionctx, double x, double y, double z, double intensity, ReflectionType type);
+extern Reflection *reflection_add(ReflectionList *reflectionlist, double x, double y, double z, double intensity, ReflectionType type);
#include "control.h"
extern void reflection_add_from_dp(ControlContext *ctx, double x, double y, ImageRecord *imagerecord, double intensity);
-extern void reflection_add_from_reflection(ReflectionContext *rctx, Reflection *r);
-extern double reflection_largest_g(ReflectionContext *reflectionctx);
+extern void reflection_add_from_reflection(ReflectionList *reflectionlist, Reflection *r);
+extern double reflection_largest_g(ReflectionList *reflectionlist);
extern int reflection_map_to_space(ImageReflection *refl, double *ddx, double *ddy, double *ddz, double *twotheta);
-extern Reflection *reflection_find_nearest(ReflectionContext *reflectionctx, double x, double y, double z);
-extern Reflection *reflection_find_nearest_longer(ReflectionContext *reflectionctx, double x, double y, double z, double min_distance);
-extern Reflection *reflection_find_nearest_type(ReflectionContext *reflectionctx, double x, double y, double z, ReflectionType type);
+extern Reflection *reflection_find_nearest(ReflectionList *reflectionlist, double x, double y, double z);
+extern Reflection *reflection_find_nearest_longer(ReflectionList *reflectionlist, double x, double y, double z, double min_distance);
+extern Reflection *reflection_find_nearest_type(ReflectionList *reflectionlist, double x, double y, double z, ReflectionType type);
#endif /* REFLECTION_H */
diff --git a/src/reproject.c b/src/reproject.c
index ed359fc..38f15ff 100644
--- a/src/reproject.c
+++ b/src/reproject.c
@@ -18,7 +18,7 @@
#define MAX_IMAGE_REFLECTIONS 8*1024
-ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, ReflectionContext *rctx, ControlContext *ctx) {
+ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, ReflectionList *reflectionlist, ControlContext *ctx) {
ImageReflection *refl;
Reflection *reflection;
@@ -42,7 +42,7 @@ ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, Reflect
kx = nx / image.lambda;
ky = ny / image.lambda;
kz = nz / image.lambda; /* This is the centre of the Ewald sphere */
- //reflection_add(ctx->reflectionctx, kx, ky, kz, 1, REFLECTION_VECTOR_MARKER_1);
+ //reflection_add(ctx->reflectionlist, kx, ky, kz, 1, REFLECTION_VECTOR_MARKER_1);
/* Determine where "up" is
* See above. */
@@ -50,10 +50,10 @@ ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, Reflect
ux = uxt; uy = cos(tilt)*uyt + sin(tilt)*uzt; uz = -sin(tilt)*uyt + cos(tilt)*uzt;
uxt = ux; uyt = uy; uzt = uz;
ux = uxt*cos(-omega) + uyt*-sin(omega); uy = -uxt*sin(omega) + uyt*cos(omega); uz = uzt;
- //reflection_add(ctx->reflectionctx, ux*50e9, uy*50e9, uz*50e9, 1, REFLECTION_VECTOR_MARKER_2);
+ //reflection_add(ctx->reflectionlist, ux*50e9, uy*50e9, uz*50e9, 1, REFLECTION_VECTOR_MARKER_2);
refl = malloc(MAX_IMAGE_REFLECTIONS*sizeof(ImageReflection));
- reflection = rctx->reflections;
+ reflection = reflectionlist->reflections;
i = 0;
do {
@@ -99,8 +99,8 @@ ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, Reflect
double psi, disc;
- //reflection_add(ctx->reflectionctx, xl, yl, zl, 1, REFLECTION_GENERATED);
- //reflection_add(ctx->reflectionctx, xi, yi, zi, 1, REFLECTION_MARKER);
+ //reflection_add(ctx->reflectionlist, xl, yl, zl, 1, REFLECTION_GENERATED);
+ //reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_MARKER);
/* Calculate azimuth of point in image (clockwise from "up", will be changed later) */
cx = yi*nz-zi*ny; cy = nx*zi-nz*xi; cz = ny*xi-nx*yi; /* c = i x n */
@@ -110,9 +110,9 @@ ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, Reflect
rx = cy*nz-cz*ny; ry = nx*cz-nz*cx; rz = ny*cx-nx*cy; /* r = [i x n] x n */
disc = angle_between(rx, ry, rz, ux, uy, uz);
// if ( (i==20) && !done_debug ) {
- // reflection_add(ctx->reflectionctx, xi, yi, zi, 1, REFLECTION_VECTOR_MARKER_3);
- // reflection_add(ctx->reflectionctx, cx, cy, cz, 1, REFLECTION_VECTOR_MARKER_4);
- // reflection_add(ctx->reflectionctx, rx, ry, rz, 1, REFLECTION_VECTOR_MARKER_4);
+ // reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_VECTOR_MARKER_3);
+ // reflection_add(ctx->reflectionlist, cx, cy, cz, 1, REFLECTION_VECTOR_MARKER_4);
+ // reflection_add(ctx->reflectionlist, rx, ry, rz, 1, REFLECTION_VECTOR_MARKER_4);
// printf("psi=%f deg, disc=%f deg\n", rad2deg(psi), rad2deg(disc));
// }
if ( (psi >= M_PI_2) && (disc >= M_PI_2) ) {
diff --git a/src/reproject.h b/src/reproject.h
index 790f43d..95a2b77 100644
--- a/src/reproject.h
+++ b/src/reproject.h
@@ -19,7 +19,7 @@
#include "control.h"
#include "reflections.h"
-extern ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, ReflectionContext *rctx, ControlContext *ctx);
+extern ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, ReflectionList *reflectionlist, ControlContext *ctx);
#endif /* REPROJECT_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 20:28:18 +0000