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-rw-r--r--src/control.c1
-rw-r--r--src/control.h9
-rw-r--r--src/displaywindow.c2
-rw-r--r--src/gtk-valuegraph.c2
-rw-r--r--src/image.c10
-rw-r--r--src/image.h6
-rw-r--r--src/mapping.c2
-rw-r--r--src/mapping.h1
-rw-r--r--src/refine.c137
-rw-r--r--src/refine.h4
-rw-r--r--src/reproject.c5
11 files changed, 152 insertions, 27 deletions
diff --git a/src/control.c b/src/control.c
index 6efae0f..f5b5b12 100644
--- a/src/control.c
+++ b/src/control.c
@@ -29,6 +29,7 @@ ControlContext *control_ctx_new() {
ctx->dirax = NULL;
ctx->images = image_list_new();
ctx->reflectionlist = NULL;
+ ctx->refine_window = NULL;
return ctx;
diff --git a/src/control.h b/src/control.h
index 7de8025..df6eb02 100644
--- a/src/control.h
+++ b/src/control.h
@@ -88,12 +88,6 @@ typedef struct cctx_struct {
GtkWidget *checkbox_finecentering;
GtkWidget *cache_file_selector;
- /* IPR stuff */
- int ipr_cur_image;
- struct imagedisplay_struct *ipr_id;
- struct reflectionlist_struct *ipr_lat;
- struct basis_struct *ipr_basis;
-
/* DirAx low-level stuff */
GIOChannel *dirax;
int dirax_pty;
@@ -110,6 +104,9 @@ typedef struct cctx_struct {
int reproject_cur_image;
struct imagedisplay_struct *reproject_id;
+ /* Refinement stuff */
+ GtkWidget *refine_window;
+
} ControlContext;
extern ControlContext *control_ctx_new(void);
diff --git a/src/displaywindow.c b/src/displaywindow.c
index 1ef4aab..324b921 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -1088,7 +1088,7 @@ static gint displaywindow_setaxis(GtkWidget *widget, DisplayWindow *dw) {
}
static gint displaywindow_refine(GtkWidget *widget, DisplayWindow *dw) {
- refine_open(dw);
+ refine_open(dw->ctx);
return 0;
}
diff --git a/src/gtk-valuegraph.c b/src/gtk-valuegraph.c
index 47c6060..b5d2bf1 100644
--- a/src/gtk-valuegraph.c
+++ b/src/gtk-valuegraph.c
@@ -164,7 +164,7 @@ static gint gtk_value_graph_draw(GtkWidget *graph, GdkEventExpose *event, gpoint
cairo_line_to(cr, bw_left+((double)i/vg->xmax)*(width-bw_left-bw_right), height-bw_bottom-1-scale*(vg->data[i]-vg->ymin));
}
- cairo_set_line_width(cr, 1.0);
+ cairo_set_line_width(cr, 0.5);
cairo_set_source_rgb(cr, 0.0, 0.0, 1.0);
cairo_stroke(cr);
diff --git a/src/image.c b/src/image.c
index 00848cf..96afe3c 100644
--- a/src/image.c
+++ b/src/image.c
@@ -65,7 +65,8 @@ ImageList *image_list_new() {
}
-void image_add_feature(ImageFeatureList *flist, double x, double y, ImageRecord *parent, double intensity) {
+void image_add_feature_index(ImageFeatureList *flist, double x, double y, ImageRecord *parent, double intensity,
+ signed int h, signed int k, signed int l) {
if ( flist->features ) {
flist->features = realloc(flist->features, (flist->n_features+1)*sizeof(ImageFeature));
@@ -80,11 +81,18 @@ void image_add_feature(ImageFeatureList *flist, double x, double y, ImageRecord
flist->features[flist->n_features].parent = parent;
flist->features[flist->n_features].partner = NULL;
flist->features[flist->n_features].partner_d = 0.0;
+ flist->features[flist->n_features].h = h;
+ flist->features[flist->n_features].k = k;
+ flist->features[flist->n_features].l = l;
flist->n_features++;
}
+void image_add_feature(ImageFeatureList *flist, double x, double y, ImageRecord *parent, double intensity) {
+ image_add_feature_index(flist, x, y, parent, intensity, 0, 0, 0);
+}
+
ImageFeatureList *image_feature_list_new() {
ImageFeatureList *flist;
diff --git a/src/image.h b/src/image.h
index c87498c..87f330e 100644
--- a/src/image.h
+++ b/src/image.h
@@ -25,6 +25,10 @@ typedef struct imagefeature_struct {
double y;
double intensity;
+ signed int h;
+ signed int k;
+ signed int l;
+
struct imagefeature_struct *partner; /* Partner for this feature (in another feature list) or NULL */
double partner_d; /* Distance between this feature and its partner, if any. */
@@ -71,6 +75,8 @@ extern int image_add(ImageList *list, uint16_t *image, int width, int height, do
extern ImageFeatureList *image_feature_list_new(void);
extern void image_feature_list_free(ImageFeatureList *flist);
extern void image_add_feature(ImageFeatureList *flist, double x, double y, ImageRecord *parent, double intensity);
+extern void image_add_feature_index(ImageFeatureList *flist, double x, double y, ImageRecord *parent, double intensity,
+ signed int h, signed int k, signed int l);
#endif /* IMAGE_H */
diff --git a/src/mapping.c b/src/mapping.c
index def29c4..668bfc4 100644
--- a/src/mapping.c
+++ b/src/mapping.c
@@ -21,7 +21,7 @@
#include "displaywindow.h"
#include "cache.h"
-static int mapping_map_to_space(ImageFeature *refl, double *ddx, double *ddy, double *ddz, double *twotheta) {
+int mapping_map_to_space(ImageFeature *refl, double *ddx, double *ddy, double *ddz, double *twotheta) {
/* "Input" space */
double d, x, y;
diff --git a/src/mapping.h b/src/mapping.h
index ca4a087..380e876 100644
--- a/src/mapping.h
+++ b/src/mapping.h
@@ -21,6 +21,7 @@
extern ReflectionList *mapping_create(ControlContext *ctx);
extern void mapping_adjust_axis(ControlContext *ctx, double offset);
+extern int mapping_map_to_space(ImageFeature *refl, double *ddx, double *ddy, double *ddz, double *twotheta);
#endif /* MAPPING_H */
diff --git a/src/refine.c b/src/refine.c
index ede96cb..aaefdf9 100644
--- a/src/refine.c
+++ b/src/refine.c
@@ -24,17 +24,17 @@
#include "reflections.h"
#include "image.h"
#include "reproject.h"
+#include "control.h"
+#include "mapping.h"
+/* Return the root sum squared deviation distance for all the "reprojectable" features in an image */
static double refine_image_deviation(ImageRecord *image, ReflectionList *cell_lattice) {
ImageFeatureList *rflist;
ImageFeatureList *flist;
- double xc, yc;
int i;
double total;
- xc = image->x_centre;
- yc = image->y_centre;
rflist = reproject_get_reflections(image, cell_lattice);
flist = image->features;
@@ -56,12 +56,59 @@ static double refine_image_deviation(ImageRecord *image, ReflectionList *cell_la
}
-void refine_open(DisplayWindow *dw) {
+/* Use the IPR algorithm to make "cell" fit the given image */
+static void refine_fit_image(Basis *cell, ImageRecord *image) {
+
+ ImageFeatureList *rflist;
+ ImageFeatureList *flist;
+ int i;
+ ReflectionList *cell_lattice;
+
+ cell_lattice = reflection_list_from_cell(cell);
+ rflist = reproject_get_reflections(image, cell_lattice);
+ flist = image->features;
+ reproject_partner_features(rflist, image);
+
+ for ( i=0; i<rflist->n_features; i++ ) {
+
+ double dx, dy;
+ double x, y, z, twotheta;
+ double old_x, old_y;
+
+ /* Skip if no partner */
+ if ( !rflist->features[i].partner ) continue;
+
+ /* Determine the difference vector */
+ dx = rflist->features[i].partner->x - rflist->features[i].x;
+ dy = rflist->features[i].partner->y - rflist->features[i].y;
+
+ /* Map the difference vector to the relevant tilted plane */
+ old_x = rflist->features[i].partner->x;
+ old_y = rflist->features[i].partner->y;
+ rflist->features[i].partner->x = dx;
+ rflist->features[i].partner->y = dy;
+ mapping_map_to_space(rflist->features[i].partner, &x, &y, &z, &twotheta);
+ rflist->features[i].partner->x = old_x;
+ rflist->features[i].partner->y = old_y;
+
+ printf("Feature %3i: %3i %3i %3i dev=%8e %8e %8e (%5f mrad)\n",
+ i, rflist->features[i].h, rflist->features[i].k, rflist->features[i].l, x, y, z, twotheta*1e3);
+
+ /* Work out weightings for a, b and c */
+
+
+ }
+
+ image_feature_list_free(rflist);
+
+}
+
+/* Display a graph of root sum squared deviation distance against some other parameter */
+static void refine_show_graph(ControlContext *ctx, int n) {
GtkWidget *window;
GtkWidget *graph;
double old_tilt;
- int n;
double *values;
size_t idx;
double tilt;
@@ -71,16 +118,16 @@ void refine_open(DisplayWindow *dw) {
gtk_window_set_title(GTK_WINDOW(window), "Refinement Graph");
graph = gtk_value_graph_new();
- dw->ctx->cell_lattice = reflection_list_from_cell(dw->ctx->cell);
- n = 0;
- idx = 0;
- old_tilt = dw->ctx->images->images[n].tilt;
+ ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
+ old_tilt = ctx->images->images[n].tilt;
values = malloc(401*sizeof(double));
- for ( tilt=old_tilt-0.2; tilt<=old_tilt+0.2; tilt+=0.001 ) {
- dw->ctx->images->images[n].tilt = tilt;
- values[idx++] = refine_image_deviation(&dw->ctx->images->images[n], dw->ctx->cell_lattice);
+ tilt = old_tilt-0.2;
+ for ( idx=0; idx<401; idx++ ) {
+ ctx->images->images[n].tilt = tilt;
+ values[idx] = refine_image_deviation(&ctx->images->images[n], ctx->cell_lattice);
+ tilt += 0.001;
}
- dw->ctx->images->images[n].tilt = old_tilt;
+ ctx->images->images[n].tilt = old_tilt;
gtk_value_graph_set_data(GTK_VALUE_GRAPH(graph), values, idx);
gtk_container_add(GTK_CONTAINER(window), graph);
@@ -88,3 +135,67 @@ void refine_open(DisplayWindow *dw) {
}
+static gint refine_graph(GtkWidget *step_button, ControlContext *ctx) {
+ refine_show_graph(ctx, ctx->reproject_cur_image);
+ return 0;
+}
+
+static gint refine_step(GtkWidget *step_button, ControlContext *ctx) {
+
+ if ( ctx->reproject_id ) {
+ refine_fit_image(ctx->cell, &ctx->images->images[ctx->reproject_cur_image]);
+ } else {
+ displaywindow_error("Please first open the reprojection window and select the image to fit", ctx->dw);
+ }
+
+ return 0;
+
+}
+
+static gint refine_response(GtkWidget *refine_window, gint response, ControlContext *ctx) {
+
+ ctx->refine_window = NULL;
+ gtk_widget_destroy(refine_window);
+
+ return 0;
+
+}
+
+void refine_open(ControlContext *ctx) {
+
+ GtkWidget *vbox;
+ GtkWidget *hbox;
+ GtkWidget *table;
+ GtkWidget *step_button;
+ GtkWidget *graph_button;
+
+ if ( ctx->refine_window ) return;
+
+ ctx->refine_window = gtk_dialog_new_with_buttons("Refine Reconstruction", GTK_WINDOW(ctx->dw->window),
+ GTK_DIALOG_DESTROY_WITH_PARENT, GTK_STOCK_CLOSE, GTK_RESPONSE_CLOSE, NULL);
+ gtk_window_set_default_size(GTK_WINDOW(ctx->refine_window), 256, -1);
+
+ vbox = gtk_vbox_new(FALSE, 0);
+ hbox = gtk_hbox_new(TRUE, 0);
+ gtk_box_pack_start(GTK_BOX(GTK_DIALOG(ctx->refine_window)->vbox), GTK_WIDGET(hbox), FALSE, FALSE, 7);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, FALSE, 5);
+
+ table = gtk_table_new(2, 1, FALSE);
+ gtk_table_set_row_spacings(GTK_TABLE(table), 5);
+ gtk_table_set_col_spacings(GTK_TABLE(table), 5);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(table), FALSE, FALSE, 0);
+
+ step_button = gtk_button_new_with_label("Refine Lattice to Fit Current Pattern");
+ gtk_table_attach_defaults(GTK_TABLE(table), step_button, 1, 2, 1, 2);
+ g_signal_connect(G_OBJECT(step_button), "clicked", G_CALLBACK(refine_step), ctx);
+
+ graph_button = gtk_button_new_with_label("Show Graph of Deviation Against Parameter");
+ gtk_table_attach_defaults(GTK_TABLE(table), graph_button, 1, 2, 2, 3);
+ g_signal_connect(G_OBJECT(graph_button), "clicked", G_CALLBACK(refine_graph), ctx);
+
+ g_signal_connect(G_OBJECT(ctx->refine_window), "response", G_CALLBACK(refine_response), ctx);
+ gtk_widget_show_all(ctx->refine_window);
+
+
+}
+
diff --git a/src/refine.h b/src/refine.h
index 679c47f..f52d130 100644
--- a/src/refine.h
+++ b/src/refine.h
@@ -16,9 +16,9 @@
#include <config.h>
#endif
-#include "displaywindow.h"
+#include "control.h"
-extern void refine_open(DisplayWindow *dw);
+extern void refine_open(ControlContext *ctx);
#endif /* REFINE_H */
diff --git a/src/reproject.c b/src/reproject.c
index e919523..c41f173 100644
--- a/src/reproject.c
+++ b/src/reproject.c
@@ -160,7 +160,8 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
if ( (xtest>=0) && (xtest<image->width) && (ytest>=0) && (ytest<image->height) ) {
/* Record the reflection */
- image_add_feature(flist, x, y, image, reflection->intensity);
+ image_add_feature_index(flist, x, y, image, reflection->intensity,
+ reflection->h, reflection->k, reflection->l);
//printf("Reflection at %f, %f\n", x, y);
} /* else it's outside the picture somewhere */
@@ -198,7 +199,7 @@ static ImageFeature *reproject_find_partner(ImageFeature *feature, ImageRecord *
}
- if ( dmin <= 70.0 ) {
+ if ( dmin <= 20.0 ) {
*d = dmin;
return &image->features->features[closest];
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 19:59:46 +0000