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-rw-r--r--libcrystfel/src/crystal.c130
1 files changed, 34 insertions, 96 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index 71d707d6..0cf246ae 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -3,11 +3,11 @@
*
* A class representing a single crystal
*
- * Copyright © 2013-2021 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2013-2024 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2013-2020 Thomas White <taw@physics.org>
+ * 2013-2024 Thomas White <taw@physics.org>
* 2016 Valerio Mariani
*
* This file is part of CrystFEL.
@@ -31,7 +31,6 @@
#include "crystal.h"
#include "utils.h"
-#include "reflist-utils.h"
/**
@@ -41,33 +40,19 @@
struct _crystal
{
- /* The image containing the crystal */
- struct image *image;
-
- /* Information about the crystal */
- UnitCell *cell;
+ UnitCell *cell;
+ int owns_cell;
double m; /* Mosaicity in radians */
double osf;
double Bfac;
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 */
- long long int n_implausible; /* Number of implausibly
- * negative reflectionss */
-
- /* User flag, e.g. for "this is a bad crystal". */
+ long long int n_saturated; /* Number of overloads */
+ long long int n_implausible; /* Number of implausibly negative reflectionss */
int user_flag;
-
- /* Text notes, which go in the stream */
- char *notes;
-
- /* Detector shift in metres */
- double det_shift_x;
- double det_shift_y;
+ char *notes; /* Text notes, which go in the stream */
+ double det_shift_x; /* Detector x-shift in metres */
+ double det_shift_y; /* Detector y-shift in metres */
};
@@ -84,16 +69,20 @@ Crystal *crystal_new()
{
Crystal *cryst;
- cryst = malloc(sizeof(Crystal));
+ cryst = cfmalloc(sizeof(Crystal));
if ( cryst == NULL ) return NULL;
cryst->cell = NULL;
- cryst->reflections = NULL;
+ cryst->owns_cell = 1;
+ cryst->m = 0.0;
+ cryst->osf = 1.0;
+ cryst->Bfac = 0.0;
+ cryst->profile_radius = 0.0;
cryst->resolution_limit = INFINITY;
cryst->n_saturated = 0;
cryst->n_implausible = 0;
- cryst->notes = NULL;
cryst->user_flag = 0;
+ cryst->notes = NULL;
cryst->det_shift_x = 0;
cryst->det_shift_y = 0;
@@ -104,38 +93,14 @@ Crystal *crystal_new()
/**
* \param cryst: A \ref Crystal to copy.
*
- * Creates a new \ref Crystal which is a copy of \p cryst. The copy is a "shallow
- * copy", which means that copies are NOT made of the data structures which
- * \p cryst contains references to, for example its \ref RefList.
- *
- * \returns A (shallow) copy of \p cryst, or NULL on failure.
- *
- */
-Crystal *crystal_copy(const Crystal *cryst)
-{
- Crystal *c;
-
- c = crystal_new();
- if ( c == NULL ) return NULL;
-
- memcpy(c, cryst, sizeof(Crystal));
- if ( c->notes != NULL ) c->notes = strdup(c->notes);
-
- return c;
-}
-
-
-/**
- * \param cryst: A \ref Crystal to copy.
- *
* Creates a new \ref Crystal which is a copy of \p cryst. The copy is a "deep
* copy", which means that copies ARE made of the data structures which
- * \p cryst contains references to, for example its \ref RefList.
+ * \p cryst contains references to, for example its \ref UnitCell.
*
* \returns A (deep) copy of \p cryst, or NULL on failure.
*
*/
-Crystal *crystal_copy_deep(const Crystal *cryst)
+Crystal *crystal_copy(const Crystal *cryst)
{
Crystal *c;
@@ -143,7 +108,7 @@ Crystal *crystal_copy_deep(const Crystal *cryst)
if ( c == NULL ) return NULL;
memcpy(c, cryst, sizeof(Crystal));
- if ( c->notes != NULL ) c->notes = strdup(c->notes);
+ if ( c->notes != NULL ) c->notes = cfstrdup(c->notes);
if ( cryst->cell != NULL ) {
UnitCell *cell;
@@ -152,13 +117,6 @@ Crystal *crystal_copy_deep(const Crystal *cryst)
c->cell = cell;
}
- if ( cryst->reflections != NULL ) {
- RefList *refls;
- refls = copy_reflist(cryst->reflections);
- if ( refls == NULL ) return NULL;
- c->reflections = refls;
- }
-
return c;
}
@@ -172,8 +130,9 @@ Crystal *crystal_copy_deep(const Crystal *cryst)
void crystal_free(Crystal *cryst)
{
if ( cryst == NULL ) return;
- free(cryst->notes);
- free(cryst);
+ if ( cryst->owns_cell ) cell_free(cryst->cell);
+ cffree(cryst->notes);
+ cffree(cryst);
}
@@ -186,21 +145,22 @@ UnitCell *crystal_get_cell(Crystal *cryst)
}
-const UnitCell *crystal_get_cell_const(const Crystal *cryst)
+UnitCell *crystal_relinquish_cell(Crystal *cryst)
{
+ cryst->owns_cell = 0;
return cryst->cell;
}
-double crystal_get_profile_radius(const Crystal *cryst)
+const UnitCell *crystal_get_cell_const(const Crystal *cryst)
{
- return cryst->profile_radius;
+ return cryst->cell;
}
-RefList *crystal_get_reflections(Crystal *cryst)
+double crystal_get_profile_radius(const Crystal *cryst)
{
- return cryst->reflections;
+ return cryst->profile_radius;
}
@@ -222,18 +182,6 @@ long long int crystal_get_num_implausible_reflections(Crystal *cryst)
}
-struct image *crystal_get_image(Crystal *cryst)
-{
- return cryst->image;
-}
-
-
-const struct image *crystal_get_image_const(const Crystal *cryst)
-{
- return cryst->image;
-}
-
-
double crystal_get_osf(Crystal *cryst)
{
return cryst->osf;
@@ -277,7 +225,9 @@ void crystal_get_det_shift(Crystal *cryst, double* shift_x, double *shift_y)
void crystal_set_cell(Crystal *cryst, UnitCell *cell)
{
+ if ( cryst->owns_cell ) cell_free(cryst->cell);
cryst->cell = cell;
+ cryst->owns_cell = 1;
}
@@ -287,12 +237,6 @@ void crystal_set_profile_radius(Crystal *cryst, double 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;
@@ -311,12 +255,6 @@ void crystal_set_num_implausible_reflections(Crystal *cryst, long long int n)
}
-void crystal_set_image(Crystal *cryst, struct image *image)
-{
- cryst->image = image;
-}
-
-
void crystal_set_osf(Crystal *cryst, double osf)
{
cryst->osf = osf;
@@ -343,8 +281,8 @@ void crystal_set_mosaicity(Crystal *cryst, double m)
void crystal_set_notes(Crystal *cryst, const char *notes)
{
- free(cryst->notes); /* free(NULL) is OK */
- cryst->notes = strdup(notes);
+ cffree(cryst->notes); /* free(NULL) is OK */
+ cryst->notes = cfstrdup(notes);
}
@@ -359,7 +297,7 @@ void crystal_add_notes(Crystal *cryst, const char *notes_add)
}
len = strlen(notes_add) + strlen(cryst->notes) + 2;
- nnotes = malloc(len);
+ nnotes = cfmalloc(len);
if ( nnotes == NULL ) {
ERROR("Failed to add notes to crystal.\n");
return;
@@ -368,7 +306,7 @@ void crystal_add_notes(Crystal *cryst, const char *notes_add)
strcpy(nnotes, cryst->notes);
strcat(nnotes, "\n");
strcat(nnotes, notes_add);
- free(cryst->notes);
+ cffree(cryst->notes);
cryst->notes = nnotes;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 05:27:24 +0000