Merge branch 'millepede-gui'

29 files changed, 608 insertions, 50 deletions

diff --git a/data/crystfel-geometry.png b/data/crystfel-geometry.png
new file mode 100644
index 00000000..df5ee8b2
--- /dev/null
+++ b/data/crystfel-geometry.png
diff --git a/data/crystfel-geometry.svg b/data/crystfel-geometry.svg
new file mode 100644
index 00000000..7cac81a1
--- /dev/null
+++ b/data/crystfel-geometry.svg
@@ -0,0 +1,132 @@
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diff --git a/data/crystfel.gresource.xml b/data/crystfel.gresource.xml
index c000973a..fa7a1752 100644
--- a/data/crystfel.gresource.xml
+++ b/data/crystfel.gresource.xml
@@ -21,5 +21,6 @@
     <file>crystfel-merge.png</file>
     <file>crystfel-peak-detection.png</file>
     <file>crystfel-unitcell.png</file>
+    <file>crystfel-geometry.png</file>
   </gresource>
 </gresources>
diff --git a/doc/man/align_detector.1.md b/doc/man/align_detector.1.md
index aa5f5061..f5991641 100644
--- a/doc/man/align_detector.1.md
+++ b/doc/man/align_detector.1.md
@@ -45,6 +45,10 @@ panel "dominoes", and level **3** would refine the individual (roughly square)
 ASICs.  Higher refinement levels will generally require more and
 higher-resolution diffraction data.
 
+You can use **indexamajig** option **--max-mille-level** to reduce the size of
+the calibration data files, at the cost of limiting the maximum refinement
+level.
+
 The default behaviour is to refine only the position components in the x-y
 plane, perpendicular to the beam.  In favourable circumstances, you can add
 option **--out-of-plane** to refine the panel tilts and shifts out of this
diff --git a/doc/man/indexamajig.1.md b/doc/man/indexamajig.1.md
index 85566240..1955ef76 100644
--- a/doc/man/indexamajig.1.md
+++ b/doc/man/indexamajig.1.md
@@ -594,6 +594,13 @@ INDEXING OPTIONS
 **--mille-dir=dirname**
 : Write the Millepede-II data into _dirname_.
 
+**--max-mille-level=n**
+: Write the Millepede-II data up to a maximum hierarchy depth _n_.  If _n_ is
+: 0, only the overall detector position can be refined.  Larger numbers allow
+: finer-grained refinement.  Set this to a large number (9 is high enough!)
+: to disable the limit, although this can make the Millepede-II files quite
+: large.
+
 **--wavelength-estimate=m** **--camera-length-estimate=m**
 : Some indexing algorithms need to know the camera length or the wavelength of
 : the incident radiation in advance, e.g. to prepare an internal look-up table.
diff --git a/libcrystfel/src/crystfel-mille.c b/libcrystfel/src/crystfel-mille.c
index 0fca6f30..8eacaa60 100644
--- a/libcrystfel/src/crystfel-mille.c
+++ b/libcrystfel/src/crystfel-mille.c
@@ -145,11 +145,28 @@ static void mille_add_measurement(Mille *m,
 }
 
 
+/* group must not be NULL
+ * count_depth() = 0 means this is the top group */
+static int count_depth(const struct detgeom_panel_group *group)
+{
+	int depth = 0;
+	assert(group != NULL);
+	do {
+		depth++;
+		group = group->parent;
+	} while ( group != NULL );
+	return depth-1;
+}
+
+
 void write_mille(Mille *mille, int n, UnitCell *cell,
                  struct reflpeak *rps, struct image *image,
-                 gsl_matrix **Minvs)
+                 int max_level, gsl_matrix **Minvs)
 {
 	int i;
+	int depth;
+
+	assert(max_level >= 0);
 
 	/* No groups -> no refinement */
 	if ( image->detgeom->top_group == NULL ) {
@@ -212,8 +229,13 @@ void write_mille(Mille *mille, int n, UnitCell *cell,
 		/* Global gradients for each hierarchy level, starting at the
 		 * individual panel and working up to the top level */
 		j = 0;
-		levels = 0;
 		group = image->detgeom->panels[rps[i].peak->pn].group;
+		depth = count_depth(group);
+		while ( depth > max_level ) {
+			depth--;
+			group = group->parent;
+		}
+		levels = 0;
 		while ( group != NULL ) {
 
 			double cx, cy, cz;
diff --git a/libcrystfel/src/crystfel-mille.h b/libcrystfel/src/crystfel-mille.h
index a4b83815..d6602ef0 100644
--- a/libcrystfel/src/crystfel-mille.h
+++ b/libcrystfel/src/crystfel-mille.h
@@ -51,7 +51,7 @@ extern enum gparam mille_unlabel(int n);
 
 extern void write_mille(Mille *mille, int n, UnitCell *cell,
                         struct reflpeak *rps, struct image *image,
-                        gsl_matrix **Minvs);
+                        int max_level, gsl_matrix **Minvs);
 
 extern void crystfel_mille_delete_last_record(Mille *m);
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index f519c3b9..d93664b1 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -592,7 +592,7 @@ static float real_time()
 /* Return non-zero for "success" */
 static int try_indexer(struct image *image, IndexingMethod indm,
                        IndexingPrivate *ipriv, void *mpriv, char *last_task,
-                       Mille *mille)
+                       Mille *mille, int max_mille_level)
 {
 	int i, r;
 	int n_bad = 0;
@@ -720,7 +720,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		{
 			int r;
 			profile_start("refine");
-			r = refine_prediction(image, cr, mille);
+			r = refine_prediction(image, cr, mille, max_mille_level);
 			profile_end("refine");
 			if ( r ) {
 				crystal_set_user_flag(cr, 1);
@@ -921,25 +921,25 @@ static int finished_retry(IndexingMethod indm, IndexingFlags flags,
 
 void index_pattern(struct image *image, IndexingPrivate *ipriv)
 {
-	index_pattern_4(image, ipriv, NULL, NULL, NULL);
+	index_pattern_4(image, ipriv, NULL, NULL, NULL, 0);
 }
 
 
 void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
 {
-	index_pattern_4(image, ipriv, ping, NULL, NULL);
+	index_pattern_4(image, ipriv, ping, NULL, NULL, 0);
 }
 
 
 void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
                      char *last_task)
 {
-	index_pattern_4(image, ipriv, ping, last_task, NULL);
+	index_pattern_4(image, ipriv, ping, last_task, NULL, 0);
 }
 
 
 void index_pattern_4(struct image *image, IndexingPrivate *ipriv, int *ping,
-                     char *last_task, Mille *mille)
+                     char *last_task, Mille *mille, int max_mille_level)
 {
 	int n = 0;
 	ImageFeatureList *orig;
@@ -994,7 +994,7 @@ void index_pattern_4(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 			r = try_indexer(image, ipriv->methods[n],
 			                ipriv, ipriv->engine_private[n],
-			                last_task, mille);
+			                last_task, mille, max_mille_level);
 			success += r;
 			ntry++;
 			done = finished_retry(ipriv->methods[n], ipriv->flags,
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index fa371276..10d07f08 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -253,7 +253,8 @@ extern void index_pattern_3(struct image *image, IndexingPrivate *ipriv,
                             int *ping, char *last_task);
 
 extern void index_pattern_4(struct image *image, IndexingPrivate *ipriv,
-                            int *ping, char *last_task, Mille *mille);
+                            int *ping, char *last_task, Mille *mille,
+                            int max_mille_level);
 
 extern void cleanup_indexing(IndexingPrivate *ipriv);
 
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 32d0f77b..d5a3b403 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -796,7 +796,8 @@ static void free_rps_noreflist(struct reflpeak *rps, int n)
 }
 
 
-int refine_prediction(struct image *image, Crystal *cr, Mille *mille)
+int refine_prediction(struct image *image, Crystal *cr,
+                      Mille *mille, int max_mille_level)
 {
 	int n;
 	int i;
@@ -879,7 +880,8 @@ int refine_prediction(struct image *image, Crystal *cr, Mille *mille)
 
 	if ( mille != NULL ) {
 		profile_start("mille-calc");
-		write_mille(mille, n, crystal_get_cell(cr), rps, image, Minvs);
+		write_mille(mille, n, crystal_get_cell(cr), rps, image,
+		            max_mille_level, Minvs);
 		profile_end("mille-calc");
 	}
 
diff --git a/libcrystfel/src/predict-refine.h b/libcrystfel/src/predict-refine.h
index 604799c0..080e5923 100644
--- a/libcrystfel/src/predict-refine.h
+++ b/libcrystfel/src/predict-refine.h
@@ -67,7 +67,8 @@ struct reflpeak {
  * Prediction refinement: refinement of indexing solutions before integration.
  */
 
-extern int refine_prediction(struct image *image, Crystal *cr, Mille *mille);
+extern int refine_prediction(struct image *image, Crystal *cr,
+                             Mille *mille, int max_mille_level);
 
 extern int refine_radius(Crystal *cr, struct image *image);
 
diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c
index 10e4c38e..44faa7ee 100644
--- a/libcrystfel/src/utils.c
+++ b/libcrystfel/src/utils.c
@@ -933,6 +933,20 @@ int file_exists(const char *filename)
 }
 
 
+int is_dir(const char *filename)
+{
+	struct stat statbuf;
+	int r;
+
+	r = stat(filename, &statbuf);
+	if ( r != 0 ) {
+		return 0;
+	}
+
+	return S_ISDIR(statbuf.st_mode);
+}
+
+
 int compare_double(const void *av, const void *bv)
 {
 	double a = *(double *)av;
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index 3a228b22..cb68069e 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -247,6 +247,7 @@ extern char *safe_strdup(const char *in);
 extern void strip_extension(char *bfn);
 extern char *load_entire_file(const char *filename);
 extern int file_exists(const char *filename);
+extern int is_dir(const char *filename);
 extern const char *filename_extension(const char *fn, const char **ext2);
 
 
diff --git a/meson.build b/meson.build
index 248a75fa..d0cb0081 100644
--- a/meson.build
+++ b/meson.build
@@ -218,6 +218,7 @@ if gtkdep.found()
                  'src/gui_fom.c',
                  'src/gui_export.c',
                  'src/gui_ambi.c',
+                 'src/gui_align.c',
                  'src/gui_backend_local.c',
                  'src/gui_backend_slurm.c',
                  'src/gui_project.c',
diff --git a/src/align_detector.c b/src/align_detector.c
index bdad7039..bb2eb029 100644
--- a/src/align_detector.c
+++ b/src/align_detector.c
@@ -34,6 +34,7 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 #include <unistd.h>
+#include <dirent.h>
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
@@ -255,6 +256,22 @@ static int run_pede()
 }
 
 
+static void write_children(FILE *fh, const char *dir)
+{
+	DIR *d = opendir(dir);
+	struct dirent *dent = readdir(d);
+
+	while ( dent != NULL ) {
+		if ( dent->d_name[0] == 'm' ) {
+			fprintf(fh, "%s/%s\n", dir, dent->d_name);
+		}
+		dent = readdir(d);
+	}
+
+	closedir(d);
+}
+
+
 int main(int argc, char *argv[])
 {
 	int c;
@@ -352,7 +369,7 @@ int main(int argc, char *argv[])
 
 		r = stat(argv[i], &statbuf);
 		if ( r != 0 ) {
-			ERROR("File '%s' not found\n", argv[i]);
+			ERROR("File/directory '%s' not found\n", argv[i]);
 			return 1;
 		}
 
@@ -364,7 +381,11 @@ int main(int argc, char *argv[])
 			}
 		}
 
-		fprintf(fh, "%s\n", argv[i]);
+		if ( is_dir(argv[i]) ) {
+			write_children(fh, argv[i]);
+		} else {
+			fprintf(fh, "%s\n", argv[i]);
+		}
 	}
 
 	if ( warn_times ) print_time_warning();
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index d0fab3b1..b3d3bc3f 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -56,6 +56,7 @@
 #include "gui_merge.h"
 #include "gui_fom.h"
 #include "gui_export.h"
+#include "gui_align.h"
 #include "gui_ambi.h"
 #include "gui_project.h"
 #include "version.h"
@@ -467,34 +468,6 @@ static gint rescan_sig(GtkWidget *widget, struct crystfelproject *proj)
 }
 
 
-static gint detector_shift_sig(GtkWidget *widget, struct crystfelproject *proj)
-{
-	struct gui_indexing_result *res = current_result(proj);
-	if ( res != NULL ) {
-		GError *error = NULL;
-		const gchar *args[64];
-		GSubprocess *sp;
-		int i;
-		args[0] = "detector-shift";
-		args[1] = "--";
-		for ( i=0; i<MIN(res->n_streams, 60); i++ ) {
-			args[2+i] = res->streams[i];
-		}
-		args[2+res->n_streams] = NULL;
-
-		sp = g_subprocess_newv(args, G_SUBPROCESS_FLAGS_NONE, &error);
-		if ( sp == NULL ) {
-			ERROR("Failed to invoke detector-shift: %s\n",
-			      error->message);
-			g_error_free(error);
-		}
-	} else {
-		ERROR("Select indexing result first!\n");
-	}
-	return FALSE;
-}
-
-
 static gint peakogram_sig(GtkWidget *widget, struct crystfelproject *proj)
 {
 	struct gui_indexing_result *res = current_result(proj);
@@ -825,7 +798,6 @@ static void add_menu_bar(struct crystfelproject *proj, GtkWidget *vbox)
 		"	<menuitem name=\"rescan\" action=\"RescanAction\" />"
 		"	<menuitem name=\"jumpframe\" action=\"JumpFrameAction\" />"
 		"       <separator />"
-		"	<menuitem name=\"detectorshift\" action=\"DetectorShiftAction\" />"
 		"	<menuitem name=\"peakogram\" action=\"PeakogramAction\" />"
 		"</menu>"
 		"<menu name=\"help\" action=\"HelpAction\">"
@@ -852,8 +824,6 @@ static void add_menu_bar(struct crystfelproject *proj, GtkWidget *vbox)
 			G_CALLBACK(rescan_sig) },
 		{ "JumpFrameAction", NULL, "Jump to frame", NULL, NULL,
 			G_CALLBACK(goto_frame_sig) },
-		{ "DetectorShiftAction", NULL, "Check detector shift", NULL, NULL,
-			G_CALLBACK(detector_shift_sig) },
 		{ "PeakogramAction", NULL, "Check detector saturation (peakogram)", NULL, NULL,
 			G_CALLBACK(peakogram_sig) },
 
@@ -933,6 +903,8 @@ static void add_task_buttons(GtkWidget *vbox, struct crystfelproject *proj)
 	           G_CALLBACK(index_all_sig), proj);
 	add_button(vbox, "Determine unit cell", "crystfel-unitcell",
 	           G_CALLBACK(cell_explorer_sig), proj);
+	add_button(vbox, "Refine detector geometry", "crystfel-geometry",
+	           G_CALLBACK(align_sig), proj);
 	add_button(vbox, "Indexing ambiguity", "crystfel-ambiguity",
 	           G_CALLBACK(ambi_sig), proj);
 	add_button(vbox, "Merge", "crystfel-merge",
diff --git a/src/crystfelindexingopts.c b/src/crystfelindexingopts.c
index d1cf515f..50a36748 100644
--- a/src/crystfelindexingopts.c
+++ b/src/crystfelindexingopts.c
@@ -734,6 +734,7 @@ static GtkWidget *stream_parameters(CrystFELIndexingOpts *io)
 	GtkCellRenderer *renderer;
 	GtkWidget *button;
 	GtkWidget *hbox;
+	GtkWidget *label;
 
 	box = gtk_box_new(GTK_ORIENTATION_VERTICAL, 8);
 	gtk_container_set_border_width(GTK_CONTAINER(box), 8);
@@ -759,6 +760,24 @@ static GtkWidget *stream_parameters(CrystFELIndexingOpts *io)
 	gtk_widget_set_tooltip_text(io->no_refls_in_stream,
 	                            "--no-refls-in-stream");
 
+	io->millepede = gtk_check_button_new_with_label("Write calibration data for detector alignment");
+	gtk_box_pack_start(GTK_BOX(box), GTK_WIDGET(io->millepede),
+	                   FALSE, FALSE, 4.0);
+	gtk_widget_set_tooltip_text(io->millepede, "--mille");
+
+	hbox = gtk_box_new(GTK_ORIENTATION_HORIZONTAL, 8);
+	gtk_box_pack_start(GTK_BOX(box), GTK_WIDGET(hbox),
+	                   FALSE, FALSE, 0.0);
+	label = gtk_label_new("Maximum refinement level:");
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+	                   FALSE, FALSE, 16.0);
+	io->max_mille = gtk_spin_button_new_with_range(0.0, 9.0, 1.0);
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(io->max_mille),
+	                   FALSE, FALSE, 4.0);
+	gtk_widget_set_tooltip_text(io->max_mille, "--max-mille-level");
+	i_disable_if_not(io->millepede, io->max_mille);
+	i_disable_if_not(io->millepede, label);
+
 	io->copy_metadata_store = gtk_list_store_new(1, G_TYPE_STRING);
 
 	treeview = gtk_tree_view_new_with_model(GTK_TREE_MODEL(io->copy_metadata_store));
@@ -1055,6 +1074,14 @@ int crystfel_indexing_opts_get_exclude_reflections(CrystFELIndexingOpts *opts)
 }
 
 
+int crystfel_indexing_opts_get_millepede(CrystFELIndexingOpts *opts,
+                                         int *pmax_level)
+{
+	*pmax_level = gtk_spin_button_get_value_as_int(GTK_SPIN_BUTTON(opts->max_mille));
+	return gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(opts->millepede));
+}
+
+
 char **crystfel_indexing_opts_get_metadata_to_copy(CrystFELIndexingOpts *opts,
                                                    int *pn)
 {
@@ -1381,6 +1408,14 @@ void crystfel_indexing_opts_set_integration_radii(CrystFELIndexingOpts *opts,
 }
 
 
+void crystfel_indexing_opts_set_millepede(CrystFELIndexingOpts *opts,
+                                          int enable, int max_level)
+{
+	gtk_spin_button_set_value(GTK_SPIN_BUTTON(opts->max_mille), max_level);
+	gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(opts->millepede), enable);
+}
+
+
 void crystfel_indexing_opts_set_metadata_to_copy(CrystFELIndexingOpts *opts,
                                                  char *const *headers,
                                                  int n)
diff --git a/src/crystfelindexingopts.h b/src/crystfelindexingopts.h
index 567bdb8e..e87d2dac 100644
--- a/src/crystfelindexingopts.h
+++ b/src/crystfelindexingopts.h
@@ -96,6 +96,8 @@ struct _crystfelindexingopts
 	GtkWidget *exclude_nonhits;
 	GtkWidget *no_peaks_in_stream;
 	GtkWidget *no_refls_in_stream;
+	GtkWidget *millepede;
+	GtkWidget *max_mille;
 	GtkListStore *copy_metadata_store;
 };
 
@@ -133,6 +135,8 @@ extern int crystfel_indexing_opts_get_exclude_peaks(CrystFELIndexingOpts *opts);
 extern int crystfel_indexing_opts_get_exclude_reflections(CrystFELIndexingOpts *opts);
 extern char **crystfel_indexing_opts_get_metadata_to_copy(CrystFELIndexingOpts *opts,
                                                           int *n);
+extern int crystfel_indexing_opts_get_millepede(CrystFELIndexingOpts *opts,
+                                                int *pmax_level);
 extern double crystfel_indexing_opts_get_fixed_profile_radius(CrystFELIndexingOpts *opts,
                                                               int *active);
 extern double crystfel_indexing_opts_get_fixed_divergence(CrystFELIndexingOpts *opts);
@@ -191,6 +195,10 @@ extern void crystfel_indexing_opts_set_exclude_peaks(CrystFELIndexingOpts *opts,
                                                      int flag);
 extern void crystfel_indexing_opts_set_exclude_reflections(CrystFELIndexingOpts *opts,
                                                            int flag);
+
+extern void crystfel_indexing_opts_set_millepede(CrystFELIndexingOpts *opts,
+                                                 int enable, int max_level);
+
 extern void crystfel_indexing_opts_set_fixed_profile_radius(CrystFELIndexingOpts *opts,
                                                             int active,
                                                             double val);
diff --git a/src/gui_align.c b/src/gui_align.c
new file mode 100644
index 00000000..b712681b
--- /dev/null
+++ b/src/gui_align.c
@@ -0,0 +1,235 @@
+/*
+ * gui_align.c
+ *
+ * Align detector via CrystFEL GUI
+ *
+ * Copyright © 2024 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2024 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdarg.h>
+#include <stdio.h>
+#include <string.h>
+#include <gtk/gtk.h>
+#include <assert.h>
+
+#include "version.h"
+#include "gui_project.h"
+#include "crystfel_gui.h"
+#include "gtk-util-routines.h"
+
+
+struct align_window
+{
+	struct crystfelproject *proj;
+	GtkWidget *window;
+	GtkWidget *input_combo;
+	GtkWidget *out_of_plane;
+	GtkWidget *level;
+};
+
+
+
+static int run_align(const char *input_name, int level, int out_of_plane,
+                     const char *out_geom, struct crystfelproject *proj)
+{
+	GSubprocess *sp;
+	struct gui_indexing_result *res;
+	GError *error;
+	const char *cmdline[16];
+	char level_str[64];
+	GFile *gstream;
+	GFile *gworkdir;
+	GFile *ggeom;
+	GFile *gmilledir;
+	char *input_geom;
+	int i;
+	char *mille_dir;
+
+	res = find_indexing_result_by_name(proj, input_name);
+	if ( res == NULL ) {
+		ERROR("Results for '%s' not found!\n", input_name);
+		return 1;
+	}
+
+	/* Figure out working directory for indexing job */
+	if ( res->n_streams < 1 ) {
+		ERROR("No streams?\n");
+		return 1;
+	}
+	gstream = g_file_new_for_path(res->streams[0]);
+	gworkdir = g_file_get_parent(gstream);
+	g_object_unref(gstream);
+
+	/* Look for Millepede files */
+	gmilledir = g_file_get_child(gworkdir, "mille-data");
+	if ( !g_file_query_exists(gmilledir, NULL) ) {
+		ERROR("No detector alignment data found for indexing run '%s'\n", input_name);
+		return 1;
+	}
+	mille_dir = g_file_get_path(gmilledir);
+	g_object_unref(gmilledir);
+
+	/* Input geometry file */
+	ggeom = g_file_get_child(gworkdir, "detector.geom");
+	input_geom = g_file_get_path(ggeom);
+	g_object_unref(ggeom);
+
+	/* Build command line */
+	snprintf(level_str, 63, "%i", level);
+	cmdline[0] = "align_detector";
+	cmdline[1] = "-g";
+	cmdline[2] = input_geom;
+	cmdline[3] = "--level";
+	cmdline[4] = level_str;
+	cmdline[5] = "-o";
+	cmdline[6] = out_geom;
+	if ( out_of_plane ) {
+		cmdline[7] = "--out-of-plane";
+		cmdline[8] = mille_dir;
+		cmdline[9] = NULL;
+	} else {
+		cmdline[7] = mille_dir;
+		cmdline[8] = NULL;
+	}
+
+	STATUS("Running program: ");
+	i = 0;
+	while ( cmdline[i] != NULL ) {
+		STATUS("%s ", cmdline[i++]);
+	}
+	STATUS("\n");
+
+	error = NULL;
+	sp = g_subprocess_newv(cmdline, G_SUBPROCESS_FLAGS_NONE, &error);
+	if ( sp == NULL ) {
+		ERROR("Failed to run align_detector: %s\n", error->message);
+		g_error_free(error);
+		return 1;
+	}
+
+	g_object_unref(gworkdir);
+	g_free(mille_dir);
+	g_free(input_geom);
+
+	return 0;
+}
+
+
+static void align_response_sig(GtkWidget *dialog, gint resp,
+                               struct align_window *win)
+{
+	int r = 0;
+
+	if ( resp == GTK_RESPONSE_ACCEPT ) {
+
+		int level;
+		const char *input_name;
+		int out_of_plane;
+		gchar *filename;
+
+		level = gtk_spin_button_get_value_as_int(GTK_SPIN_BUTTON(win->level));
+
+		input_name = get_combo_id(win->input_combo);
+		if ( input_name == NULL ) {
+			ERROR("Please select the input\n");
+			r = 1;
+		}
+
+		out_of_plane = get_bool(win->out_of_plane);
+		filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER(dialog));
+
+		r = run_align(input_name, level, out_of_plane, filename, win->proj);
+
+		g_free(filename);
+	}
+
+	if ( !r ) gtk_widget_destroy(dialog);
+}
+
+
+gint align_sig(GtkWidget *widget, struct crystfelproject *proj)
+{
+	GtkWidget *hbox;
+	GtkWidget *label;
+	struct align_window *win;
+	int i;
+
+	win = malloc(sizeof(struct align_window));
+	if ( win == NULL ) return 0;
+
+	win->proj = proj;
+
+	win->window = gtk_file_chooser_dialog_new("Align detector",
+	                                          GTK_WINDOW(proj->window),
+	                                          GTK_FILE_CHOOSER_ACTION_SAVE,
+	                                          GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
+	                                          GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
+	                                          NULL);
+	gtk_file_chooser_set_do_overwrite_confirmation(GTK_FILE_CHOOSER(win->window),
+	                                               TRUE);
+
+	hbox = gtk_hbox_new(FALSE, 0.0);
+	gtk_file_chooser_set_extra_widget(GTK_FILE_CHOOSER(win->window),
+	                                  GTK_WIDGET(hbox));
+	gtk_container_set_border_width(GTK_CONTAINER(hbox), 4);
+
+	label = gtk_label_new("Refine using indexing result:");
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+	                   FALSE, FALSE, 4.0);
+	win->input_combo = gtk_combo_box_text_new();
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->input_combo),
+	                   FALSE, FALSE, 4.0);
+	for ( i=0; i<proj->n_results; i++ ) {
+		gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(win->input_combo),
+		                          proj->results[i].name,
+		                          proj->results[i].name);
+	}
+	gtk_combo_box_set_active_id(GTK_COMBO_BOX(win->input_combo),
+	                            selected_result(proj));
+
+	label = gtk_label_new("Hierarchy level:");
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+	                   FALSE, FALSE, 16.0);
+	win->level = gtk_spin_button_new_with_range(0.0, 9.0, 1.0);
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->level),
+	                   FALSE, FALSE, 4.0);
+	gtk_widget_set_tooltip_text(win->level, "--level");
+
+	win->out_of_plane = gtk_check_button_new_with_label("Include out-of-plane positions and tilts");
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->out_of_plane),
+	                   FALSE, FALSE, 4.0);
+	gtk_widget_set_tooltip_text(win->out_of_plane, "--out-of-plane");
+
+	g_signal_connect(G_OBJECT(win->window), "response",
+	                 G_CALLBACK(align_response_sig), win);
+
+	gtk_dialog_set_default_response(GTK_DIALOG(win->window),
+	                                GTK_RESPONSE_CLOSE);
+	gtk_widget_show_all(win->window);
+
+	return FALSE;
+}
diff --git a/src/gui_align.h b/src/gui_align.h
new file mode 100644
index 00000000..50250e6a
--- /dev/null
+++ b/src/gui_align.h
@@ -0,0 +1,38 @@
+/*
+ * gui_align.h
+ *
+ * Align detector via CrystFEL GUI
+ *
+ * Copyright © 2024 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2024 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef GUI_ALIGN_H
+#define GUI_ALIGN_H
+
+#include <gtk/gtk.h>
+
+#include "gui_project.h"
+
+extern gint align_sig(GtkWidget *widget, struct crystfelproject *proj);
+
+#endif
diff --git a/src/gui_backend_local.c b/src/gui_backend_local.c
index 03761474..71c94871 100644
--- a/src/gui_backend_local.c
+++ b/src/gui_backend_local.c
@@ -534,6 +534,10 @@ static void *run_indexing(const char *job_title,
 	gchar *files_rel_filename;
 	gchar *stream_rel_filename;
 	gchar *harvest_rel_filename;
+	gchar *mille_rel_filename;
+	GFile *ggeom;
+	GFile *ggeomcopy;
+	GError *error;
 
 	workdir = make_job_folder(job_title, job_notes);
 	if ( workdir == NULL ) return NULL;
@@ -555,6 +559,17 @@ static void *run_indexing(const char *job_title,
 	files_rel_filename = relative_to_cwd(workdir, "files.lst");
 	stream_rel_filename = relative_to_cwd(workdir, "crystfel.stream");
 	harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+	mille_rel_filename = relative_to_cwd(workdir, "mille-data");
+
+	/* Copy geometry file into working directory
+	 * Used for geometry refinement, not indexing! */
+	ggeom = g_file_new_for_path(proj->geom_filename);
+	ggeomcopy = g_file_get_child(workdir, "detector.geom");
+	error = NULL;
+	g_file_copy(ggeom, ggeomcopy, G_FILE_COPY_BACKUP | G_FILE_COPY_ALL_METADATA,
+	            NULL, NULL, NULL, &error);
+	g_object_unref(ggeom);
+	g_object_unref(ggeomcopy);
 
 	if ( !write_indexamajig_script(sc_rel_filename,
 	                               proj->geom_filename,
@@ -564,6 +579,7 @@ static void *run_indexing(const char *job_title,
 	                               stdout_rel_filename,
 	                               stderr_rel_filename,
 	                               harvest_rel_filename,
+	                               mille_rel_filename,
 	                               NULL,
 	                               &proj->peak_search_params,
 	                               &proj->indexing_params,
@@ -598,6 +614,7 @@ static void *run_indexing(const char *job_title,
 	free(stdout_rel_filename);
 	free(stderr_rel_filename);
 	free(harvest_rel_filename);
+	free(mille_rel_filename);
 
 	return job;
 }
diff --git a/src/gui_backend_slurm.c b/src/gui_backend_slurm.c
index 3961a92d..f5ad31c5 100644
--- a/src/gui_backend_slurm.c
+++ b/src/gui_backend_slurm.c
@@ -797,6 +797,7 @@ static void *run_indexing(const char *job_title,
 	gchar *files_rel_filename;
 	gchar *stream_rel_filename;
 	gchar *harvest_rel_filename;
+	gchar *mille_rel_filename;
 	char *slurm_prologue;
 
 	workdir = make_job_folder(job_title, job_notes);
@@ -842,6 +843,7 @@ static void *run_indexing(const char *job_title,
 	stdout_rel_filename = relative_to_cwd(workdir, "stdout-%a.log");
 	stderr_rel_filename = relative_to_cwd(workdir, "stderr-%a.log");
 	harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+	mille_rel_filename = relative_to_cwd(workdir, "mille-data");
 
 	slurm_prologue = sbatch_bits(&opts->common, job_title, array_inx,
 	                             stdout_rel_filename, stderr_rel_filename);
@@ -853,6 +855,7 @@ static void *run_indexing(const char *job_title,
 	                               stream_rel_filename,
 	                               NULL, NULL,
 	                               harvest_rel_filename,
+	                               mille_rel_filename,
 	                               serial_offs,
 	                               &proj->peak_search_params,
 	                               &proj->indexing_params,
@@ -888,6 +891,7 @@ static void *run_indexing(const char *job_title,
 	free(stdout_rel_filename);
 	free(stderr_rel_filename);
 	free(harvest_rel_filename);
+	free(mille_rel_filename);
 	g_object_unref(workdir);
 
 	return job;
diff --git a/src/gui_index.c b/src/gui_index.c
index aa2301ef..2cc8e8db 100644
--- a/src/gui_index.c
+++ b/src/gui_index.c
@@ -140,6 +140,8 @@ static void get_indexing_opts(struct crystfelproject *proj,
 	proj->indexing_params.exclude_nonhits = crystfel_indexing_opts_get_exclude_blanks(opts);
 	proj->indexing_params.exclude_peaks = crystfel_indexing_opts_get_exclude_peaks(opts);
 	proj->indexing_params.exclude_refls = crystfel_indexing_opts_get_exclude_reflections(opts);
+	proj->indexing_params.millepede = crystfel_indexing_opts_get_millepede(opts,
+	                       &proj->indexing_params.max_mille_level);
 	proj->indexing_params.metadata_to_copy = crystfel_indexing_opts_get_metadata_to_copy(opts,
 		               &proj->indexing_params.n_metadata);
 }
@@ -383,6 +385,9 @@ static void set_indexing_opts(struct crystfelproject *proj,
 	                                         proj->indexing_params.exclude_peaks);
 	crystfel_indexing_opts_set_exclude_reflections(opts,
 	                                               proj->indexing_params.exclude_refls);
+	crystfel_indexing_opts_set_millepede(opts,
+	                                     proj->indexing_params.millepede,
+	                                     proj->indexing_params.max_mille_level);
 	crystfel_indexing_opts_set_metadata_to_copy(opts,
 	                                            proj->indexing_params.metadata_to_copy,
 	                                            proj->indexing_params.n_metadata);
@@ -846,6 +851,7 @@ static char **indexamajig_command_line(const char *geom_filename,
                                        const char *files_list,
                                        const char *stream_filename,
                                        const char *harvest_filename,
+                                       const char *mille_filename,
                                        const char *serial_start,
                                        struct peak_params *peak_search_params,
                                        struct index_params *indexing_params,
@@ -997,6 +1003,11 @@ static char **indexamajig_command_line(const char *geom_filename,
 	if ( indexing_params->exclude_nonhits ) add_arg(args, n_args++, "--no-non-hits-in-stream");
 	if ( indexing_params->exclude_peaks ) add_arg(args, n_args++, "--no-peaks-in-stream");
 	if ( indexing_params->exclude_refls ) add_arg(args, n_args++, "--no-refls-in-stream");
+	if ( indexing_params->millepede ) {
+		add_arg(args, n_args++, "--mille");
+		add_arg_string(args, n_args++, "mille-dir", mille_filename);
+		add_arg_int(args, n_args++, "max-mille-level", indexing_params->max_mille_level);
+	}
 	for ( i=0; i<indexing_params->n_metadata; i++ ) {
 		add_arg_string(args, n_args++, "copy-header",
 		               indexing_params->metadata_to_copy[i]);
@@ -1079,6 +1090,7 @@ int write_indexamajig_script(const char *script_filename,
                              const char *stdout_filename,
                              const char *stderr_filename,
                              const char *harvest_filename,
+                             const char *mille_filename,
                              const char *serial_start,
                              struct peak_params *peak_search_params,
                              struct index_params *indexing_params,
@@ -1095,6 +1107,7 @@ int write_indexamajig_script(const char *script_filename,
 	                                   files_list,
 	                                   stream_filename,
 	                                   harvest_filename,
+	                                   mille_filename,
 	                                   serial_start,
 	                                   peak_search_params,
 	                                   indexing_params,
diff --git a/src/gui_index.h b/src/gui_index.h
index 2f5c1a56..33594e8e 100644
--- a/src/gui_index.h
+++ b/src/gui_index.h
@@ -51,6 +51,7 @@ extern int write_indexamajig_script(const char *script_filename,
                                     const char *stdout_filename,
                                     const char *stderr_filename,
                                     const char *harvest_filename,
+                                    const char *mille_filename,
                                     const char *serial_start,
                                     struct peak_params *peak_search_params,
                                     struct index_params *indexing_params,
diff --git a/src/gui_project.c b/src/gui_project.c
index 32d6473c..c77e2704 100644
--- a/src/gui_project.c
+++ b/src/gui_project.c
@@ -429,6 +429,12 @@ static void parse_stream_opt(const char *key, const char *val,
 	if ( strcmp(key, "stream.exclude_refls") == 0 ) {
 		ip->exclude_refls = parse_int(val);
 	}
+	if ( strcmp(key, "stream.millepede") == 0 ) {
+		ip->millepede = parse_int(val);
+	}
+	if ( strcmp(key, "stream.max_mille_level") == 0 ) {
+		ip->max_mille_level = parse_int(val);
+	}
 	if ( strcmp(key, "stream.metadata") == 0 ) {
 		add_metadata_to_copy(ip, val);
 	}
@@ -1048,6 +1054,10 @@ int save_project(struct crystfelproject *proj)
 	        proj->indexing_params.exclude_peaks);
 	fprintf(fh, "stream.exclude_refls %i\n",
 	        proj->indexing_params.exclude_refls);
+	fprintf(fh, "stream.millepede %i\n",
+	        proj->indexing_params.millepede);
+	fprintf(fh, "stream.max_mille_level %i\n",
+	        proj->indexing_params.max_mille_level);
 	if ( proj->indexing_params.metadata_to_copy != NULL ) {
 		int i;
 		for ( i=0; i<proj->indexing_params.n_metadata; i++ ) {
@@ -1287,6 +1297,8 @@ int default_project(struct crystfelproject *proj)
 	proj->indexing_params.exclude_nonhits = 0;
 	proj->indexing_params.exclude_peaks = 0;
 	proj->indexing_params.exclude_refls = 0;
+	proj->indexing_params.millepede = 1;
+	proj->indexing_params.max_mille_level = 1;
 	proj->indexing_params.metadata_to_copy = NULL;
 	proj->indexing_params.n_metadata = 0;
 	proj->indexing_params.fix_profile_radius = 0.01e9;
diff --git a/src/gui_project.h b/src/gui_project.h
index 318f9453..6d704b81 100644
--- a/src/gui_project.h
+++ b/src/gui_project.h
@@ -87,6 +87,8 @@ struct index_params {
 	int exclude_refls;
 	char **metadata_to_copy;
 	int n_metadata;
+	int millepede;
+	int max_mille_level;
 };
 
 struct merging_params {
diff --git a/src/indexamajig.c b/src/indexamajig.c
index cca7dbba..ce8b2cbf 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -748,6 +748,18 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		args->iargs.milledir = strdup(arg);
 		break;
 
+		case 418 :
+		if (sscanf(arg, "%d", &args->iargs.max_mille_level) != 1)
+		{
+			ERROR("Invalid value for --max-mille-level\n");
+			return EINVAL;
+		}
+		if ( args->iargs.max_mille_level < 0 ) {
+			ERROR("Invalid value for --max-mille-level\n");
+			return EINVAL;
+		}
+		break;
+
 		/* ---------- Integration ---------- */
 
 		case 501 :
@@ -996,6 +1008,7 @@ int main(int argc, char *argv[])
 	args.iargs.data_format = DATA_SOURCE_TYPE_UNKNOWN;
 	args.iargs.mille = 0;
 	args.iargs.milledir = strdup(".");
+	args.iargs.max_mille_level = 99;
 
 	argp_program_version_hook = show_version;
 
@@ -1122,8 +1135,8 @@ int main(int argc, char *argv[])
 		        "Estimate of the camera length, in metres."},
 		{"mille", 416, NULL, 0,
 		        "Generate data for detector geometry refinement using Millepede"},
-		{"mille-dir", 417, "dirname", 0,
-		        "Save Millepede data in folder"},
+		{"mille-dir", 417, "dirname", 0, "Save Millepede data in folder"},
+		{"max-mille-level", 418, "n", 0, "Maximum geometry refinement level"},
 
 		{NULL, 0, 0, OPTION_DOC, "Integration options:", 5},
 		{"integration", 501, "method", OPTION_NO_USAGE, "Integration method"},
diff --git a/src/process_image.c b/src/process_image.c
index 57a994ac..2f856594 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -420,7 +420,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	set_last_task(last_task, "indexing");
 	profile_start("index");
 	index_pattern_4(image, iargs->ipriv, &sb_shared->pings[cookie],
-	                last_task, mille);
+	                last_task, mille, iargs->max_mille_level);
 	profile_end("index");
 
 	r = chdir(rn);
diff --git a/src/process_image.h b/src/process_image.h
index f5e27631..10c9ec31 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -76,6 +76,7 @@ struct index_args
 	int n_threads;
 	int mille;
 	char *milledir;
+	int max_mille_level;
 
 	/* Integration */
 	IntegrationMethod int_meth;