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-rw-r--r--libcrystfel/src/crystal.c55
-rw-r--r--libcrystfel/src/crystal.h25
-rw-r--r--libcrystfel/src/image.c1
3 files changed, 21 insertions, 60 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index e5978795..a21283f9 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"
/**
@@ -41,30 +40,18 @@
struct _crystal
{
- /* Information about the crystal */
- UnitCell *cell;
+ UnitCell *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 */
};
@@ -85,12 +72,15 @@ Crystal *crystal_new()
if ( cryst == NULL ) return NULL;
cryst->cell = NULL;
- cryst->reflections = NULL;
+ 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;
@@ -149,13 +139,6 @@ 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;
}
@@ -195,12 +178,6 @@ double crystal_get_profile_radius(const Crystal *cryst)
}
-RefList *crystal_get_reflections(Crystal *cryst)
-{
- return cryst->reflections;
-}
-
-
double crystal_get_resolution_limit(Crystal *cryst)
{
return cryst->resolution_limit;
@@ -272,12 +249,6 @@ 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;
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index 33764bc0..3f19386c 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -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.
@@ -43,8 +43,6 @@
**/
typedef struct _crystal Crystal;
-#include "reflist.h"
-
#ifdef __cplusplus
extern "C" {
#endif
@@ -55,36 +53,29 @@ extern Crystal *crystal_copy_deep(const Crystal *cryst);
extern void crystal_free(Crystal *cryst);
extern UnitCell *crystal_get_cell(Crystal *cryst);
-extern const UnitCell *crystal_get_cell_const(const Crystal *cryst);
extern double crystal_get_profile_radius(const Crystal *cryst);
-extern RefList *crystal_get_reflections(Crystal *cryst);
extern double crystal_get_resolution_limit(Crystal *cryst);
-extern long long int crystal_get_num_saturated_reflections(Crystal *cryst);
-extern long long int crystal_get_num_implausible_reflections(Crystal *cryst);
extern int crystal_get_user_flag(Crystal *cryst);
extern double crystal_get_osf(Crystal *cryst);
extern double crystal_get_Bfac(Crystal *cryst);
extern double crystal_get_mosaicity(Crystal *cryst);
extern const char *crystal_get_notes(Crystal *cryst);
-extern void crystal_get_det_shift(Crystal *cryst,
- double *shift_x, double* shift_y);
+extern void crystal_get_det_shift(Crystal *cryst, double *shift_x, double *shift_y);
+extern long long int crystal_get_num_saturated_reflections(Crystal *cryst);
+extern long long int crystal_get_num_implausible_reflections(Crystal *cryst);
extern void crystal_set_cell(Crystal *cryst, UnitCell *cell);
extern void crystal_set_profile_radius(Crystal *cryst, double r);
-extern void crystal_set_reflections(Crystal *cryst, RefList *reflist);
extern void crystal_set_resolution_limit(Crystal *cryst, double res);
-extern void crystal_set_num_saturated_reflections(Crystal *cryst,
- long long int n);
-extern void crystal_set_num_implausible_reflections(Crystal *cryst,
- long long int n);
extern void crystal_set_user_flag(Crystal *cryst, int flag);
extern void crystal_set_osf(Crystal *cryst, double osf);
extern void crystal_set_Bfac(Crystal *cryst, double B);
extern void crystal_set_mosaicity(Crystal *cryst, double m);
extern void crystal_set_notes(Crystal *cryst, const char *notes);
-extern void crystal_set_det_shift(Crystal *cryst,
- double shift_x, double shift_y);
extern void crystal_add_notes(Crystal *cryst, const char *notes_add);
+extern void crystal_set_det_shift(Crystal *cryst, double shift_x, double shift_y);
+extern void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n);
+extern void crystal_set_num_implausible_reflections(Crystal *cryst, long long int n);
#ifdef __cplusplus
}
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 0789c6a3..9e9af85c 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -366,7 +366,6 @@ void free_all_crystals(struct image *image)
if ( image->crystals == NULL ) return;
for ( i=0; i<image->n_crystals; i++ ) {
Crystal *cr = image->crystals[i];
- reflist_free(crystal_get_reflections(cr));
cell_free(crystal_get_cell(cr));
crystal_free(image->crystals[i]);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 17:27:31 +0000