partialator/process_hkl: Use geometry

9 files changed, 129 insertions, 6 deletions

diff --git a/src/partialator.c b/src/partialator.c
index a9930d9e..1f87e6b8 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -945,6 +945,8 @@ int main(int argc, char *argv[])
 	PartialityModel pmodel = PMODEL_XSPHERE;
 	int min_measurements = 2;
 	char *rval;
+	const char *geom_str;
+	DataTemplate *dtempl;
 	struct polarisation polarisation = {.fraction = 1.0,
 	                                    .angle = 0.0,
 	                                    .disable = 0};
@@ -1217,6 +1219,19 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	geom_str = stream_geometry_file(st);
+	if ( geom_str == NULL ) {
+		ERROR("No geometry file\n");
+		stream_close(st);
+		return 1;
+	}
+
+	dtempl = data_template_new_from_string(geom_str);
+	if ( dtempl == NULL ) {
+		stream_close(st);
+		return 1;
+	}
+
 	if ( outfile == NULL ) {
 		outfile = strdup("partialator.hkl");
 	}
@@ -1375,8 +1390,8 @@ int main(int argc, char *argv[])
 		RefList *as;
 		int i;
 
-		image = stream_read_chunk(st, NULL, STREAM_REFLECTIONS
-		                                  | STREAM_UNITCELL);
+		image = stream_read_chunk(st, dtempl, STREAM_REFLECTIONS
+		                                    | STREAM_UNITCELL);
 		if ( image == NULL ) break;
 
 		if ( isnan(image->div) || isnan(image->bw) ) {
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 4fe1dbeb..b840f4ce 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -395,7 +395,8 @@ static void display_progress(int n_images, int n_crystals, int n_crystals_used)
 }
 
 
-static int merge_all(Stream *st, RefList *model, RefList *reference,
+static int merge_all(Stream *st, DataTemplate *dtempl,
+                     RefList *model, RefList *reference,
                      const SymOpList *sym,
                      double **hist_vals, signed int hist_h,
                      signed int hist_k, signed int hist_l,
@@ -428,7 +429,7 @@ static int merge_all(Stream *st, RefList *model, RefList *reference,
 		int i;
 
 		/* Get data from next chunk */
-		image = stream_read_chunk(st, NULL,
+		image = stream_read_chunk(st, dtempl,
 		                          STREAM_REFLECTIONS
 		                        | STREAM_UNITCELL);
 		if ( image == NULL ) break;
@@ -514,6 +515,8 @@ int main(int argc, char *argv[])
 	int hist_i;
 	int space_for_hist = 0;
 	char *histo_params = NULL;
+	const char *geom_str;
+	DataTemplate *dtempl;
 	struct polarisation polarisation = {.fraction = 1.0,
 	                                    .angle = 0.0,
 	                                    .disable = 0};
@@ -723,6 +726,19 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	geom_str = stream_geometry_file(st);
+	if ( geom_str == NULL ) {
+		ERROR("No geometry file found in stream\n");
+		stream_close(st);
+		return 1;
+	}
+
+	dtempl = data_template_new_from_string(geom_str);
+	if ( dtempl == NULL ) {
+		stream_close(st);
+		return 1;
+	}
+
 	model = reflist_new();
 
 	if ( histo != NULL ) {
@@ -779,7 +795,8 @@ int main(int argc, char *argv[])
 	if ( config_scale ) twopass = 1;
 
 	hist_i = 0;
-	r = merge_all(st, model, NULL, sym, &hist_vals, hist_h, hist_k, hist_l,
+	r = merge_all(st, dtempl, model, NULL, sym,
+	              &hist_vals, hist_h, hist_k, hist_l,
 	              &hist_i, polarisation, min_measurements, min_snr,
 	              max_adu, start_after, stop_after, min_res, push_res,
 	              min_cc, config_scale, flag_even_odd, stat_output);
@@ -813,7 +830,7 @@ int main(int argc, char *argv[])
 				hist_i = 0;
 			}
 
-			r = merge_all(st, model, reference, sym, &hist_vals,
+			r = merge_all(st, dtempl, model, reference, sym, &hist_vals,
 			              hist_h, hist_k, hist_l, &hist_i,
 				      polarisation, min_measurements, min_snr,
 				      max_adu, start_after, stop_after, min_res,
diff --git a/tests/partialator_merge_check_1 b/tests/partialator_merge_check_1
index 616ccf31..2d4391ef 100755
--- a/tests/partialator_merge_check_1
+++ b/tests/partialator_merge_check_1
@@ -5,6 +5,19 @@ PARTIALATOR=$1
 cat > partialator_merge_check_1.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 6000.0
diff --git a/tests/partialator_merge_check_2 b/tests/partialator_merge_check_2
index 9938f64f..73c5873e 100755
--- a/tests/partialator_merge_check_2
+++ b/tests/partialator_merge_check_2
@@ -5,6 +5,19 @@ PARTIALATOR=$1
 cat > partialator_merge_check_2.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 6000.0
diff --git a/tests/partialator_merge_check_3 b/tests/partialator_merge_check_3
index 2d237b02..6cb50980 100755
--- a/tests/partialator_merge_check_3
+++ b/tests/partialator_merge_check_3
@@ -5,6 +5,19 @@ PARTIALATOR=$1
 cat > partialator_merge_check_3.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 6000.0
diff --git a/tests/process_hkl_check_1 b/tests/process_hkl_check_1
index 2d65c0a9..8496041d 100755
--- a/tests/process_hkl_check_1
+++ b/tests/process_hkl_check_1
@@ -5,6 +5,19 @@ PROCESS_HKL=$1
 cat > process_hkl_check_1.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 2000.0
diff --git a/tests/process_hkl_check_2 b/tests/process_hkl_check_2
index b4d85fb4..2dec8840 100755
--- a/tests/process_hkl_check_2
+++ b/tests/process_hkl_check_2
@@ -5,6 +5,19 @@ PROCESS_HKL=$1
 cat > process_hkl_check_2.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 2000.0
diff --git a/tests/process_hkl_check_3 b/tests/process_hkl_check_3
index cef7996c..763f6e87 100755
--- a/tests/process_hkl_check_3
+++ b/tests/process_hkl_check_3
@@ -5,6 +5,19 @@ PROCESS_HKL=$1
 cat > process_hkl_check_3.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 2000.0
diff --git a/tests/process_hkl_check_4 b/tests/process_hkl_check_4
index aa36f112..1b267cf9 100755
--- a/tests/process_hkl_check_4
+++ b/tests/process_hkl_check_4
@@ -5,6 +5,19 @@ PROCESS_HKL=$1
 cat > process_hkl_check_4.stream << EOF
 CrystFEL stream format 2.1
 Command line: indexamajig -i dummy.lst -o dummy.stream --kraken=prawn
+----- Begin geometry file -----
+photon_energy = 9000 eV
+panel/min_fs = 0
+panel/min_ss = 0
+panel/max_fs = 1023
+panel/max_ss = 1023
+panel/corner_x = -100
+panel/corner_y = -100
+panel/clen = 50 mm
+panel/res = 1000000
+panel/adu_per_photon = 1
+panel/data = /data/data_array
+----- End geometry file -----
 ----- Begin chunk -----
 Image filename: dummy.h5
 photon_energy_eV = 2000.0