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-rw-r--r--src/intensities.c154
1 files changed, 73 insertions, 81 deletions
diff --git a/src/intensities.c b/src/intensities.c
index a2e19c3..86f3de1 100644
--- a/src/intensities.c
+++ b/src/intensities.c
@@ -3,7 +3,7 @@
*
* Extract integrated intensities by relrod estimation
*
- * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
@@ -24,8 +24,8 @@
/* Extract integrated reflection intensities by estimating the spike function
* based on the observed intensity and the calculated excitation error from
* the lattice refinement. Easy. */
-void intensities_extract(ControlContext *ctx) {
-
+void intensities_extract(ControlContext *ctx)
+{
int i, j;
int n_meas, n_dupl, n_notf;
double max;
@@ -36,123 +36,111 @@ void intensities_extract(ControlContext *ctx) {
reflectionlist_free(ctx->integrated);
}
ctx->integrated = reflectionlist_new();
-
+
n_meas = 0;
n_dupl = 0;
n_notf = 0;
max = 0;
for ( i=0; i<ctx->images->n_images; i++ ) {
-
+
ImageRecord *image;
-
+
image = &ctx->images->images[i];
- if ( image->rflist == NULL ) image->rflist = reproject_get_reflections(image, ctx->cell_lattice);
-
+ if ( image->rflist == NULL )
+ image->rflist = reproject_get_reflections(image,
+ ctx->cell_lattice);
+
for ( j=0; j<image->rflist->n_features; j++ ) {
-
+
ImageFeature *feature;
signed int h, k, l;
-
+
feature = &image->rflist->features[j];
-
+
h = feature->reflection->h;
k = feature->reflection->k;
l = feature->reflection->l;
-
+
if ( feature->partner != NULL ) {
-
+
if ( (h!=0) || (k!=0) || (l!=0) ) {
-
+
double intensity;
Reflection *ref;
-
- /* Perform relrod calculation of doom here.
- * TODO: Figure out if this is even possible. */
+
intensity = feature->partner->intensity;
-
- ref = reflectionlist_find(ctx->integrated, h, k, l);
-
+
+ ref = reflectionlist_find(
+ ctx->integrated, h, k, l);
+
if ( ref == NULL ) {
-
+
Reflection *new;
-
- printf("IN: Adding %3i %3i %3i, intensity=%f\n", h, k, l, intensity);
-
- new = reflection_add(ctx->integrated,
- feature->reflection->x, feature->reflection->y, feature->reflection->z,
- intensity, REFLECTION_GENERATED);
-
+
+ new = reflection_add(
+ ctx->integrated,
+ feature->reflection->x,
+ feature->reflection->y,
+ feature->reflection->z,
+ intensity,
+ REFLECTION_GENERATED);
+
new->h = h;
new->k = k;
new->l = l;
-
- if ( intensity > max ) max = intensity;
-
+
+ if ( intensity > max )
+ max = intensity;
+
n_meas++;
-
+
} else {
-
- printf("IN: Duplicate measurement for %3i %3i %3i - ", h, k, l);
-
+
if ( intensity > ref->intensity ) {
-
- printf("stronger.\n");
-
+
ref->x = feature->reflection->x;
ref->y = feature->reflection->y;
ref->z = feature->reflection->z;
ref->intensity = intensity;
-
- } else {
- printf("weaker.\n");
+
}
-
+
n_dupl++;
-
+
}
-
+
}
-
+
} else {
//printf("IN: %3i %3i %3i not found\n", h, k, l);
n_notf++;
}
-
+
}
-
+
}
-
+
/* Normalise all reflections to the most intense reflection */
reflection = ctx->integrated->reflections;
while ( reflection ) {
-
reflection->intensity /= max;
-
- /* Test mode */
- // if ( (reflection->h == 0) && (reflection->k == -1) && (reflection->l == 0) ) {
- // reflection->intensity = 1.0;
- // } else {
- // reflection->intensity /= 10;
- // }
-
reflection = reflection->next;
-
}
-
+
printf("IN: %5i intensities measured\n", n_meas);
printf("IN: %5i duplicated measurements\n", n_dupl);
printf("IN: %5i predicted reflections not found\n", n_notf);
-
}
-static int intensities_do_save(ReflectionList *integrated, Basis *cell, const char *filename) {
-
+static int intensities_do_save(ReflectionList *integrated, Basis *cell,
+ const char *filename)
+{
FILE *fh;
Reflection *reflection;
UnitCell rcell;
-
+
fh = fopen(filename, "w");
-
+
rcell = basis_get_cell(cell);
fprintf(fh, "a %12.8f\n", rcell.a*1e9);
fprintf(fh, "b %12.8f\n", rcell.b*1e9);
@@ -160,46 +148,50 @@ static int intensities_do_save(ReflectionList *integrated, Basis *cell, const ch
fprintf(fh, "alpha %12.8f\n", rad2deg(rcell.alpha));
fprintf(fh, "beta %12.8f\n", rad2deg(rcell.beta));
fprintf(fh, "gamma %12.8f\n", rad2deg(rcell.gamma));
-
+
reflection = integrated->reflections;
while ( reflection ) {
- fprintf(fh, "%3i %3i %3i %12.8f\n", reflection->h, reflection->k, reflection->l, reflection->intensity);
+ fprintf(fh, "%3i %3i %3i %12.8f\n",
+ reflection->h, reflection->k, reflection->l,
+ reflection->intensity);
reflection = reflection->next;
}
fclose(fh);
-
- return 0;
+ return 0;
}
-static gint intensities_save_response(GtkWidget *widget, gint response, ControlContext *ctx) {
-
+static gint intensities_save_response(GtkWidget *widget, gint response,
+ ControlContext *ctx)
+{
if ( response == GTK_RESPONSE_ACCEPT ) {
char *filename;
- filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER(widget));
- if ( intensities_do_save(ctx->integrated, ctx->cell, filename) ) {
- displaywindow_error("Failed to save cache file.", ctx->dw);
+ filename = gtk_file_chooser_get_filename(
+ GTK_FILE_CHOOSER(widget));
+ if ( intensities_do_save(ctx->integrated,
+ ctx->cell, filename) ) {
+ displaywindow_error("Failed to save cache file.",
+ ctx->dw);
}
g_free(filename);
}
-
+
gtk_widget_destroy(widget);
return 0;
-
}
-void intensities_save(ControlContext *ctx) {
-
+void intensities_save(ControlContext *ctx)
+{
GtkWidget *save;
- save = gtk_file_chooser_dialog_new("Save Reflections to File", GTK_WINDOW(ctx->dw->window),
+ save = gtk_file_chooser_dialog_new("Save Reflections to File",
+ GTK_WINDOW(ctx->dw->window),
GTK_FILE_CHOOSER_ACTION_SAVE,
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
NULL);
- g_signal_connect(G_OBJECT(save), "response", G_CALLBACK(intensities_save_response), ctx);
+ g_signal_connect(G_OBJECT(save), "response",
+ G_CALLBACK(intensities_save_response), ctx);
gtk_widget_show_all(save);
-
}
-
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 09:32:19 +0000