From 6ee21aaa02a5c11bd1269bff0bc7d23b0d402c1e Mon Sep 17 00:00:00 2001
From: Chun Hong Yoon <chun.hong.yoon@desy.de>
Date: Mon, 27 Jan 2014 14:02:34 +0100
Subject: Add two colour spectrum

---
 libcrystfel/src/image.h | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 0c189cad..6b49ad91 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -46,7 +46,8 @@
 
 typedef enum {
 	SPECTRUM_TOPHAT,
-	SPECTRUM_SASE
+	SPECTRUM_SASE,
+	SPECTRUM_TWOCOLOUR
 } SpectrumType;
 
 /* Structure describing a feature in an image */
-- 
cgit v1.2.3


From cae96eaf563f6698b69e142cbf19da0f2888b2bb Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 12 Feb 2014 15:18:36 +0100
Subject: partial_sim: Add --images

---
 libcrystfel/src/hdf5-file.c | 89 +++++++++++++++++++++++----------------------
 1 file changed, 46 insertions(+), 43 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index ad9495b5..ed3b1e29 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -384,57 +384,60 @@ int hdf5_write_image(const char *filename, struct image *image)
 
 	H5Dclose(dh);
 
-	arr = malloc(image->spectrum_size*sizeof(double));
-	if ( arr == NULL ) {
-		H5Fclose(fh);
-		return 1;
-	}
-	for ( i=0; i<image->spectrum_size; i++ ) {
-		arr[i] = 1.0e10/image->spectrum[i].k;
-	}
+	if ( image->spectrum_size > 0 ) {
 
-	size[0] = image->spectrum_size;
-	sh = H5Screate_simple(1, size, NULL);
+		arr = malloc(image->spectrum_size*sizeof(double));
+		if ( arr == NULL ) {
+			H5Fclose(fh);
+			return 1;
+		}
+		for ( i=0; i<image->spectrum_size; i++ ) {
+			arr[i] = 1.0e10/image->spectrum[i].k;
+		}
 
-	dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE, sh,
-	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		H5Fclose(fh);
-		return 1;
-	}
-	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
-	             H5S_ALL, H5P_DEFAULT, arr);
-	H5Dclose(dh);
+		size[0] = image->spectrum_size;
+		sh = H5Screate_simple(1, size, NULL);
 
-	for ( i=0; i<image->spectrum_size; i++ ) {
-		arr[i] = image->spectrum[i].weight;
-	}
-	dh = H5Dcreate2(gh, "spectrum_weights", H5T_NATIVE_DOUBLE, sh,
-	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		H5Fclose(fh);
-		return 1;
-	}
-	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
-	             H5S_ALL, H5P_DEFAULT, arr);
+		dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE,
+		                sh, H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+		if ( dh < 0 ) {
+			H5Fclose(fh);
+			return 1;
+		}
+		r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+			     H5S_ALL, H5P_DEFAULT, arr);
+		H5Dclose(dh);
 
-	H5Dclose(dh);
-	free(arr);
+		for ( i=0; i<image->spectrum_size; i++ ) {
+			arr[i] = image->spectrum[i].weight;
+		}
+		dh = H5Dcreate2(gh, "spectrum_weights", H5T_NATIVE_DOUBLE, sh,
+			        H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+		if ( dh < 0 ) {
+			H5Fclose(fh);
+			return 1;
+		}
+		r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+			     H5S_ALL, H5P_DEFAULT, arr);
 
-	size[0] = 1;
-	sh = H5Screate_simple(1, size, NULL);
+		H5Dclose(dh);
+		free(arr);
 
-	dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
-	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		H5Fclose(fh);
-		return 1;
-	}
+		size[0] = 1;
+		sh = H5Screate_simple(1, size, NULL);
+
+		dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
+			        H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+		if ( dh < 0 ) {
+			H5Fclose(fh);
+			return 1;
+		}
 
-	r = H5Dwrite(dh, H5T_NATIVE_INT, H5S_ALL,
-	             H5S_ALL, H5P_DEFAULT, &image->nsamples);
+		r = H5Dwrite(dh, H5T_NATIVE_INT, H5S_ALL,
+			     H5S_ALL, H5P_DEFAULT, &image->nsamples);
 
-	H5Dclose(dh);
+		H5Dclose(dh);
+	}
 
 	H5Gclose(gh);
 
-- 
cgit v1.2.3


From 2cb4c47dc477761fb621a4df6683c3f27fc7d5a1 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 13 Feb 2014 11:58:34 +0100
Subject: Don't proceed with integration if no suitable reference reflections
 were found

---
 libcrystfel/src/integration.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 1b2193fa..b14d0f1c 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -3,11 +3,11 @@
  *
  * Integration of intensities
  *
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
  *                  a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2013 Thomas White <taw@physics.org>
+ *   2010-2014 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -1483,6 +1483,14 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
 	setup_profile_boxes(&ic, list);
 	calculate_reference_profiles(&ic);
 
+	for ( i=0; i<ic.n_reference_profiles; i++ ) {
+		if ( ic.n_profiles_in_reference[i] == 0 ) {
+			ERROR("Reference profile 0 has no contributions.\n");
+			free_intcontext(&ic);
+			return;
+		}
+	}
+
 	for ( i=0; i<ic.n_boxes; i++ ) {
 		struct peak_box *bx;
 		bx = &ic.boxes[i];
-- 
cgit v1.2.3


From 7551e70603982392c2b7d9f4287fd431ecccc7c9 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 13 Feb 2014 13:46:47 +0100
Subject: Fix previous commit

---
 libcrystfel/src/integration.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index b14d0f1c..b86399e9 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1485,7 +1485,8 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
 
 	for ( i=0; i<ic.n_reference_profiles; i++ ) {
 		if ( ic.n_profiles_in_reference[i] == 0 ) {
-			ERROR("Reference profile 0 has no contributions.\n");
+			ERROR("Reference profile %i has no contributions.\n",
+			      i);
 			free_intcontext(&ic);
 			return;
 		}
-- 
cgit v1.2.3