Quantification stuff

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@223 bf6ca9ba-c028-0410-8290-897cf20841d1

1 files changed, 155 insertions, 116 deletions

diff --git a/src/displaywindow.c b/src/displaywindow.c
index 9769a07..4eef09e 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -36,6 +36,7 @@
 #include "mapping.h"
 #include "refine.h"
 #include "imagedisplay.h"
+#include "intensities.h"
 
 static void displaywindow_gl_set_ortho(DisplayWindow *dw, GLfloat w, GLfloat h) {
 
@@ -73,6 +74,14 @@ static gint displaywindow_changeview(GtkWidget *widget, GtkRadioAction *action,
 	
 }
 
+static gint displaywindow_changemode(GtkWidget *widget, GtkRadioAction *action, DisplayWindow *dw) {
+
+	dw->mode = gtk_radio_action_get_current_value(action);	
+	displaywindow_update(dw);
+	
+	return 0;
+	
+}
 static gboolean displaywindow_gl_button_press(GtkWidget *widget, GdkEventButton *event, DisplayWindow *dw) {
 	dw->x_start = event->x;
 	dw->y_start = event->y;
@@ -134,7 +143,6 @@ static gint displaywindow_gl_motion_notify(GtkWidget *widget, GdkEventMotion *ev
 	
 #define DRAW_BLOB							\
 	double step = M_PI/(double)BLOB_BITS;				\
-	double size = 0.15;						\
 	int is, js;							\
 	for ( is=0; is<BLOB_BITS; is++ ) {				\
 		for ( js=0; js<BLOB_BITS*2; js++ ) {			\
@@ -264,6 +272,7 @@ static void displaywindow_gl_prepare(DisplayWindow *dw) {
 		normals = malloc(3*dw->gl_marker_num_vertices*sizeof(GLfloat));
 		while ( reflection != NULL ) {
 			if ( reflection->type == REFLECTION_MARKER ) {
+				double size = 0.15;
 				DRAW_BLOB
 			}
 			reflection = reflection->next;
@@ -286,36 +295,39 @@ static void displaywindow_gl_prepare(DisplayWindow *dw) {
 		glGenBuffersARB(1, &dw->gl_gen_vertex_buffer);
 		glGenBuffersARB(1, &dw->gl_gen_normal_buffer);
 	}
-	reflection = ctx->reflectionlist->reflections;
-	i = 0;
-	while ( reflection != NULL ) {
-		if ( reflection->type == REFLECTION_GENERATED ) i++;
-		reflection = reflection->next;
-	};
-	dw->gl_gen_num_vertices = i*VERTICES_IN_A_BLOB;
-	if ( dw->gl_gen_num_vertices ) {
+	if ( ctx->integrated != NULL ) {
+		reflection = ctx->integrated->reflections;
 		i = 0;
-		reflection = ctx->reflectionlist->reflections;
-		vertices = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
-		normals = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
 		while ( reflection != NULL ) {
-			if ( reflection->type == REFLECTION_GENERATED ) {
+			if ( reflection->type == REFLECTION_GENERATED ) i++;
+			reflection = reflection->next;
+		};
+		dw->gl_gen_num_vertices = i*VERTICES_IN_A_BLOB;
+		if ( dw->gl_gen_num_vertices ) {
+			i = 0;
+			reflection = ctx->integrated->reflections;
+			vertices = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
+			normals = malloc(3*dw->gl_gen_num_vertices*sizeof(GLfloat));
+			while ( reflection != NULL ) {
+				double size = 5.0 * log(1+0.1*reflection->intensity);
 				DRAW_BLOB
+				reflection = reflection->next;
+			};	
+			if ( dw->gl_use_buffers ) {
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_vertex_buffer);
+				glBufferDataARB(GL_ARRAY_BUFFER, 3*dw->gl_gen_num_vertices*sizeof(GLfloat), vertices, GL_STATIC_DRAW);
+				free(vertices);
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_normal_buffer);
+				glBufferDataARB(GL_ARRAY_BUFFER, 3*dw->gl_gen_num_vertices*sizeof(GLfloat), normals, GL_STATIC_DRAW);
+				free(normals);
+				glBindBufferARB(GL_ARRAY_BUFFER, 0);	/* ************* */
+			} else {
+				dw->gl_gen_vertex_array = vertices;
+				dw->gl_gen_normal_array = normals;
 			}
-			reflection = reflection->next;
-		};	
-		if ( dw->gl_use_buffers ) {
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_vertex_buffer);
-			glBufferDataARB(GL_ARRAY_BUFFER, 3*dw->gl_gen_num_vertices*sizeof(GLfloat), vertices, GL_STATIC_DRAW);
-			free(vertices);
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_normal_buffer);
-			glBufferDataARB(GL_ARRAY_BUFFER, 3*dw->gl_gen_num_vertices*sizeof(GLfloat), normals, GL_STATIC_DRAW);
-			free(normals);
-			glBindBufferARB(GL_ARRAY_BUFFER, 0);	/* ************* */
-		} else {
-			dw->gl_gen_vertex_array = vertices;
-			dw->gl_gen_normal_array = normals;
 		}
+	} else {
+		dw->gl_gen_num_vertices = 0;
 	}
 	
 	/* Indexing lines */
@@ -709,98 +721,104 @@ static gint displaywindow_gl_expose(GtkWidget *widget, GdkEventExpose *event, Di
 	build_rotmatrix(m, dw->view_quat);
 	glMultMatrixf(&m[0][0]);
 	
-	/* Draw the "measured" reflections */
-	if ( dw->gl_ref_num_vertices ) {
-		glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
-		glEnableClientState(GL_VERTEX_ARRAY);
-		glEnableClientState(GL_NORMAL_ARRAY);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, green);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, black);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, black);
-		glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 0.0);
-		if ( dw->gl_use_buffers ) {
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_ref_vertex_buffer);
-			glVertexPointer(3, GL_FLOAT, 0, NULL);
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_ref_normal_buffer);
-			glNormalPointer(GL_FLOAT, 0, NULL);
-			glDrawArrays(GL_POINTS, 0, dw->gl_ref_num_vertices);
-			glBindBufferARB(GL_ARRAY_BUFFER, 0);
-		} else {
-			glVertexPointer(3, GL_FLOAT, 0, dw->gl_ref_vertex_array);
-			glNormalPointer(GL_FLOAT, 0, dw->gl_ref_normal_array);
-			glDrawArrays(GL_POINTS, 0, dw->gl_ref_num_vertices);
+	if ( dw->mode == DW_MAPPED ) {
+		
+		/* Draw the "measured" reflections */
+		if ( dw->gl_ref_num_vertices ) {
+			glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
+			glEnableClientState(GL_VERTEX_ARRAY);
+			glEnableClientState(GL_NORMAL_ARRAY);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, green);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, black);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, black);
+			glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 0.0);
+			if ( dw->gl_use_buffers ) {
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_ref_vertex_buffer);
+				glVertexPointer(3, GL_FLOAT, 0, NULL);
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_ref_normal_buffer);
+				glNormalPointer(GL_FLOAT, 0, NULL);
+				glDrawArrays(GL_POINTS, 0, dw->gl_ref_num_vertices);
+				glBindBufferARB(GL_ARRAY_BUFFER, 0);
+			} else {
+				glVertexPointer(3, GL_FLOAT, 0, dw->gl_ref_vertex_array);
+				glNormalPointer(GL_FLOAT, 0, dw->gl_ref_normal_array);
+				glDrawArrays(GL_POINTS, 0, dw->gl_ref_num_vertices);
+			}
+			glDisableClientState(GL_NORMAL_ARRAY);
+			glPopClientAttrib();
 		}
-		glDisableClientState(GL_NORMAL_ARRAY);
-		glPopClientAttrib();
-	}
-	
-	/* Draw marker points */
-	if ( dw->gl_marker_num_vertices ) {
-		glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
-		glEnableClientState(GL_VERTEX_ARRAY);
-		glEnableClientState(GL_NORMAL_ARRAY);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, blue);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, black);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, blue_spec);
-		glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 50.0);
-		if ( dw->gl_use_buffers ) {
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_marker_vertex_buffer);
-			glVertexPointer(3, GL_FLOAT, 0, NULL);
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_marker_normal_buffer);
-			glNormalPointer(GL_FLOAT, 0, NULL);
-			glDrawArrays(GL_QUADS, 0, dw->gl_marker_num_vertices);
-			glBindBufferARB(GL_ARRAY_BUFFER, 0);
-		} else {
-			glVertexPointer(3, GL_FLOAT, 0, dw->gl_marker_vertex_array);
-			glNormalPointer(GL_FLOAT, 0, dw->gl_marker_normal_array);
-			glDrawArrays(GL_QUADS, 0, dw->gl_marker_num_vertices);
+		
+		/* Draw marker points */
+		if ( dw->gl_marker_num_vertices ) {
+			glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
+			glEnableClientState(GL_VERTEX_ARRAY);
+			glEnableClientState(GL_NORMAL_ARRAY);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, blue);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, black);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, blue_spec);
+			glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 50.0);
+			if ( dw->gl_use_buffers ) {
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_marker_vertex_buffer);
+				glVertexPointer(3, GL_FLOAT, 0, NULL);
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_marker_normal_buffer);
+				glNormalPointer(GL_FLOAT, 0, NULL);
+				glDrawArrays(GL_QUADS, 0, dw->gl_marker_num_vertices);
+				glBindBufferARB(GL_ARRAY_BUFFER, 0);
+			} else {
+				glVertexPointer(3, GL_FLOAT, 0, dw->gl_marker_vertex_array);
+				glNormalPointer(GL_FLOAT, 0, dw->gl_marker_normal_array);
+				glDrawArrays(GL_QUADS, 0, dw->gl_marker_num_vertices);
+			}
+			glDisableClientState(GL_NORMAL_ARRAY);
+			glPopClientAttrib();
 		}
-		glDisableClientState(GL_NORMAL_ARRAY);
-		glPopClientAttrib();
-	}
-	
-	/* Draw generated reflections */
-	if ( dw->gl_gen_num_vertices ) {
-		glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
-		glEnableClientState(GL_VERTEX_ARRAY);
-		glEnableClientState(GL_NORMAL_ARRAY);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, black);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, gold);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, gold_spec);
-		glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 70.0);
-		if ( dw->gl_use_buffers ) {
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_vertex_buffer);
-			glVertexPointer(3, GL_FLOAT, 0, NULL);
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_normal_buffer);
-			glNormalPointer(GL_FLOAT, 0, NULL);
-			glDrawArrays(GL_QUADS, 0, dw->gl_gen_num_vertices);
-			glBindBufferARB(GL_ARRAY_BUFFER, 0);
-		} else {
-			glVertexPointer(3, GL_FLOAT, 0, dw->gl_gen_vertex_array);
-			glNormalPointer(GL_FLOAT, 0, dw->gl_gen_normal_array);
-			glDrawArrays(GL_QUADS, 0, dw->gl_gen_num_vertices);
+		
+		/* Draw indexing lines */
+		if ( dw->lines && dw->gl_line_num_vertices ) {
+			glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
+			glEnableClientState(GL_VERTEX_ARRAY);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, grey);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, black);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, black);
+			if ( dw->gl_use_buffers ) {
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_line_vertex_buffer);
+				glVertexPointer(3, GL_FLOAT, 0, NULL);
+				glDrawArrays(GL_LINES, 0, dw->gl_line_num_vertices);
+				glBindBufferARB(GL_ARRAY_BUFFER, 0);
+			} else {
+				glVertexPointer(3, GL_FLOAT, 0, dw->gl_line_vertex_array);
+				glDrawArrays(GL_LINES, 0, dw->gl_line_num_vertices);
+			}
+			glPopClientAttrib();
 		}
-		glDisableClientState(GL_NORMAL_ARRAY);
-		glPopClientAttrib();
-	}
 	
-	/* Draw indexing lines */
-	if ( dw->lines && dw->gl_line_num_vertices ) {
-		glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
-		glEnableClientState(GL_VERTEX_ARRAY);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, grey);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, black);
-		glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, black);
-		if ( dw->gl_use_buffers ) {
-			glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_line_vertex_buffer);
-			glVertexPointer(3, GL_FLOAT, 0, NULL);
-			glDrawArrays(GL_LINES, 0, dw->gl_line_num_vertices);
-			glBindBufferARB(GL_ARRAY_BUFFER, 0);
-		} else {
-			glVertexPointer(3, GL_FLOAT, 0, dw->gl_line_vertex_array);
-			glDrawArrays(GL_LINES, 0, dw->gl_line_num_vertices);
+	} else {
+
+		/* Draw generated reflections */
+		if ( dw->gl_gen_num_vertices ) {
+			glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
+			glEnableClientState(GL_VERTEX_ARRAY);
+			glEnableClientState(GL_NORMAL_ARRAY);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_EMISSION, black);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_AMBIENT_AND_DIFFUSE, gold);
+			glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, gold_spec);
+			glMaterialf(GL_FRONT_AND_BACK, GL_SHININESS, 70.0);
+			if ( dw->gl_use_buffers ) {
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_vertex_buffer);
+				glVertexPointer(3, GL_FLOAT, 0, NULL);
+				glBindBufferARB(GL_ARRAY_BUFFER, dw->gl_gen_normal_buffer);
+				glNormalPointer(GL_FLOAT, 0, NULL);
+				glDrawArrays(GL_QUADS, 0, dw->gl_gen_num_vertices);
+				glBindBufferARB(GL_ARRAY_BUFFER, 0);
+			} else {
+				glVertexPointer(3, GL_FLOAT, 0, dw->gl_gen_vertex_array);
+				glNormalPointer(GL_FLOAT, 0, dw->gl_gen_normal_array);
+				glDrawArrays(GL_QUADS, 0, dw->gl_gen_num_vertices);
+			}
+			glDisableClientState(GL_NORMAL_ARRAY);
+			glPopClientAttrib();
 		}
-		glPopClientAttrib();
+	
 	}
 	
 	/* Draw everything else */
@@ -1130,6 +1148,12 @@ static gint displaywindow_refinestack(GtkWidget *widget, DisplayWindow *dw) {
 	return 0;
 }
 
+static gint displaywindow_extract(GtkWidget *widget, DisplayWindow *dw) {
+	intensities_extract(dw->ctx);
+	displaywindow_update(dw);
+	return 0;
+}
+
 static void displaywindow_addmenubar(DisplayWindow *dw) {
 
 	GtkActionEntry entries[] = {
@@ -1146,9 +1170,10 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 		{ "StopDirAxAction", NULL, "Stop DirAx", NULL, NULL, G_CALLBACK(displaywindow_dirax_stop) },
 		{ "RefineStepAction", GTK_STOCK_EXECUTE, "Refine Current Image", NULL, NULL, G_CALLBACK(displaywindow_refinestep) },
 		{ "RefineSeqAction", GTK_STOCK_EXECUTE, "Refine Entire Stack", NULL, NULL, G_CALLBACK(displaywindow_refinestack) },
-		{ "SetAxisAction", NULL, "Set Tilt Axis Position", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
+		{ "SetAxisAction", NULL, "Set Tilt Axis Position...", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
 		{ "IncrAxisAction", NULL, "Increase Tilt Axis Position", "<Ctrl>Up", NULL, G_CALLBACK(displaywindow_incraxis) },
 		{ "DecrAxisAction", NULL, "Decrease Tilt Axis Position", "<Ctrl>Down", NULL, G_CALLBACK(displaywindow_decraxis) },
+		{ "ExtractIntensitiesAction", GTK_STOCK_EXECUTE, "Extract Reflection Intensities", NULL, NULL, G_CALLBACK(displaywindow_extract) },
 		
 		{ "HelpAction", NULL, "_Help", NULL, NULL, NULL },
 		{ "AboutAction", GTK_STOCK_ABOUT, "_About DTR...", NULL, NULL, G_CALLBACK(displaywindow_about) },
@@ -1164,11 +1189,19 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 	
 	};
 	guint n_entries = G_N_ELEMENTS(entries);
+	
 	GtkRadioActionEntry radios[] = {
-		{ "OrthoAction", NULL, "_Orthographic", NULL, NULL, DW_ORTHO },
-		{ "PerspectiveAction", NULL, "_Perspective", NULL, NULL, DW_PERSPECTIVE },
+		{ "OrthoAction", NULL, "_Orthographic Projection", NULL, NULL, DW_ORTHO },
+		{ "PerspectiveAction", NULL, "_Perspective Projection", NULL, NULL, DW_PERSPECTIVE },
 	};
 	guint n_radios = G_N_ELEMENTS(radios);
+	
+	GtkRadioActionEntry radios2[] = {
+		{ "MappedAction", NULL, "Show Mapped Features", NULL, NULL, DW_MAPPED },
+		{ "MeasuredAction", NULL, "Show Measured Intensities", NULL, NULL, DW_MEASURED },
+	};
+	guint n_radios2 = G_N_ELEMENTS(radios2);
+	
 	GtkToggleActionEntry toggles[] = {
 		{ "CubeAction", NULL, "Show 100 nm^-1 _Cube", NULL, NULL, G_CALLBACK(displaywindow_changecube), dw->cube },
 		{ "LinesAction", NULL, "Show Indexing Lines", NULL, NULL, G_CALLBACK(displaywindow_changelines), dw->lines },
@@ -1181,6 +1214,7 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 	dw->action_group = gtk_action_group_new("dtrdisplaywindow");
 	gtk_action_group_add_actions(dw->action_group, entries, n_entries, dw);
 	gtk_action_group_add_radio_actions(dw->action_group, radios, n_radios, -1, G_CALLBACK(displaywindow_changeview), dw);
+	gtk_action_group_add_radio_actions(dw->action_group, radios2, n_radios2, -1, G_CALLBACK(displaywindow_changemode), dw);
 	gtk_action_group_add_toggle_actions(dw->action_group, toggles, n_toggles, dw);
 	
 	dw->ui = gtk_ui_manager_new();
@@ -1296,6 +1330,7 @@ DisplayWindow *displaywindow_open(ControlContext *ctx) {
 	
 	dw->gl_use_buffers = 1;
 	dw->view = DW_ORTHO;
+	dw->mode = DW_MAPPED;
 	dw->distance = 150;
 	dw->x_pos = 0;
 	dw->y_pos = 0;
@@ -1409,6 +1444,10 @@ void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) {
 	gtk_widget_set_sensitive(d, g);
 	d = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindowtoolbar/refinestep");
 	gtk_widget_set_sensitive(d, g);
+	d = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindow/tools/extractintensities");
+	gtk_widget_set_sensitive(d, g);
+	d = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindowtoolbar/extractintensities");
+	gtk_widget_set_sensitive(d, g);
 
 }