1 files changed, 224 insertions, 0 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
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+/*
+ * crystal.c
+ *
+ * A class representing a single crystal
+ *
+ * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2013 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 "crystal.h"
+#include "utils.h"
+
+
+/**
+ * SECTION:crystal
+ * @short_description: Crystal
+ * @title: Crystal
+ * @section_id:
+ * @see_also:
+ * @include: "crystal.h"
+ * @Image:
+ *
+ * This structure represents a single crystal.
+ */
+
+
+struct _crystal
+{
+	/* The image containing the crystal */
+	struct image            *image;
+
+	/* Information about the crystal */
+	UnitCell                *cell;
+	double                  m;     /* Mosaicity in radians */
+	double                  osf;
+	double                  profile_radius;
+	int                     pr_dud;
+	double                  resolution_limit;
+
+	/* Integrated (or about-to-be-integrated) reflections */
+	RefList                 *reflections;
+	long long int           n_saturated;  /* Number of overloads */
+
+	/* User flag, e.g. for "this is a bad crystal". */
+	int                     user_flag;
+};
+
+
+/************************** Constructor / Destructor **************************/
+
+
+/**
+ * crystal_new:
+ *
+ * Create a new %Crystal.
+ *
+ * Returns: the new unit cell, or NULL on failure.
+ *
+ */
+Crystal *crystal_new()
+{
+	Crystal *cryst;
+
+	cryst = malloc(sizeof(Crystal));
+	if ( cryst == NULL ) return NULL;
+
+	cryst->cell = NULL;
+	cryst->reflections = NULL;
+	cryst->resolution_limit = 0.0;
+	cryst->n_saturated = 0;
+
+	return cryst;
+}
+
+
+/**
+ * crystal_free:
+ * @cryst: A %Crystal to free.
+ *
+ * Frees a %Crystal, and all internal resources concerning that crystal.
+ *
+ */
+void crystal_free(Crystal *cryst)
+{
+	if ( cryst == NULL ) return;
+	free(cryst);
+}
+
+
+/********************************** Getters ***********************************/
+
+
+UnitCell *crystal_get_cell(Crystal *cryst)
+{
+	return cryst->cell;
+}
+
+
+double crystal_get_profile_radius(Crystal *cryst)
+{
+	return cryst->profile_radius;
+}
+
+
+RefList *crystal_get_reflections(Crystal *cryst)
+{
+	return cryst->reflections;
+}
+
+
+double crystal_get_resolution_limit(Crystal *cryst)
+{
+	return cryst->resolution_limit;
+}
+
+
+long long int crystal_get_num_saturated_reflections(Crystal *cryst)
+{
+	return cryst->n_saturated;
+}
+
+
+struct image *crystal_get_image(Crystal *cryst)
+{
+	return cryst->image;
+}
+
+
+double crystal_get_osf(Crystal *cryst)
+{
+	return cryst->osf;
+}
+
+
+int crystal_get_user_flag(Crystal *cryst)
+{
+	return cryst->user_flag;
+}
+
+
+double crystal_get_mosaicity(Crystal *cryst)
+{
+	return cryst->m;
+}
+
+
+/********************************** Setters ***********************************/
+
+
+void crystal_set_cell(Crystal *cryst, UnitCell *cell)
+{
+	cryst->cell = cell;
+}
+
+
+void crystal_set_profile_radius(Crystal *cryst, double r)
+{
+	cryst->profile_radius = r;
+}
+
+
+void crystal_set_reflections(Crystal *cryst, RefList *reflist)
+{
+	cryst->reflections = reflist;
+}
+
+
+void crystal_set_resolution_limit(Crystal *cryst, double res)
+{
+	cryst->resolution_limit = res;
+}
+
+
+void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n)
+{
+	cryst->n_saturated = n;
+}
+
+
+void crystal_set_image(Crystal *cryst, struct image *image)
+{
+	cryst->image = image;
+}
+
+
+void crystal_set_osf(Crystal *cryst, double osf)
+{
+	cryst->osf = osf;
+}
+
+
+void crystal_set_user_flag(Crystal *cryst, int user_flag)
+{
+	cryst->user_flag = user_flag;
+}
+
+
+void crystal_set_mosaicity(Crystal *cryst, double m)
+{
+	cryst->m = m;
+}