fom.h File Reference

Data Structures
struct	fom_rejections
struct	fom_shells

Enumerations
enum	fom_type {   FOM_R1I ,   FOM_R1F ,   FOM_R2 ,   FOM_RSPLIT ,   FOM_CC ,   FOM_CCSTAR ,   FOM_CCANO ,   FOM_CRDANO ,   FOM_RANO ,   FOM_RANORSPLIT ,   FOM_D1SIG ,   FOM_D2SIG ,   FOM_NUM_MEASUREMENTS ,   FOM_REDUNDANCY ,   FOM_SNR ,   FOM_MEAN_INTENSITY ,   FOM_COMPLETENESS }

Functions
struct fom_rejections	fom_select_reflection_pairs (RefList *list1, RefList *list2, RefList **plist1_acc, RefList **plist2_acc, UnitCell *cell, SymOpList *sym, int anom, double rmin_fix, double rmax_fix, double sigma_cutoff, int ignore_negs, int zero_negs, int mul_cutoff)
struct fom_rejections	fom_select_reflections (RefList *list, RefList **plist_acc, UnitCell *cell, SymOpList *sym, double rmin_fix, double rmax_fix, double sigma_cutoff, int ignore_negs, int zero_negs, int mul_cutoff)
struct fom_context *	fom_calculate (RefList *list1, RefList *list2, UnitCell *cell, struct fom_shells *shells, enum fom_type fom, int noscale, const SymOpList *sym)
struct fom_shells *	fom_make_resolution_shells (double rmin, double rmax, int nshells)
double	fom_shell_centre (struct fom_shells *s, int i)
double	fom_overall_value (struct fom_context *fctx)
double	fom_shell_value (struct fom_context *fctx, int i)
int	fom_overall_num_reflections (struct fom_context *fctx)
int	fom_shell_num_reflections (struct fom_context *fctx, int i)
int	fom_overall_num_possible (struct fom_context *fctx)
int	fom_shell_num_possible (struct fom_context *fctx, int i)
int	fom_is_anomalous (enum fom_type f)
int	fom_is_comparison (enum fom_type f)
const char *	fom_name (enum fom_type f)

Detailed Description

Figure of merit calculation

Enumeration Type Documentation

fom_type

enum fom_type

An enumeration of possible figures of merit to calculate

Function Documentation

fom_calculate()

struct fom_context * fom_calculate	(	RefList *	list1,
		RefList *	list2,
		UnitCell *	cell,
		struct fom_shells *	shells,
		enum fom_type	fom,
		int	noscale,
		const SymOpList *	sym
	)

Parameters

list1	A RefList
list2	A RefList
cell	A UnitCell
shells	A fom_shells structure
fom	The figure of merit to calculate
noscale	Non-zero to disable scaline of reflection lists
sym	The symmetry of list1 and list2.

Calculates the specified figure of merit, comparing the two reflection lists.

The cell and sym must match both reflection lists. You should also have called fom_select_reflection_pairs() to pre-process the lists.

If the figure of merit does not involve comparison (e.g. FOM_SNR), then list1 will be used. In this case, list2 and noscale will be ignored. Use fom_select_reflections() instead of fom_select_reflection_pairs() in this case.

Returns

a fom_context structure. Use fom_shell_value() et al., to extract the actual figure of merit values.

fom_make_resolution_shells()

struct fom_shells * fom_make_resolution_shells	(	double	rmin,
		double	rmax,
		int	nshells
	)

Parameters

rmin	The minimum value of 1/d, in m^-1
rmax	The maximum value of 1/d, in m^-1
nshells	The number of shells to use

Create a fom_shells structure for the specified minimum and maximum resolution limits

Returns the fom_shells structure, or NULL on error.

fom_overall_num_possible()

int fom_overall_num_possible

(

struct fom_context *

fctx

)

Parameters

fctx	A fom_context structure

This must only be called on a fom_context for FOM_COMPLETENESS.

Returns

the total number of reflections possible in all shells, taking into account symmetry and lattice absences, but not screw axis/glide place absences.

fom_overall_num_reflections()

int fom_overall_num_reflections

(

struct fom_context *

fctx

)

Parameters

fctx	A fom_context structure

Returns

the total number of unique reflections

fom_overall_value()

double fom_overall_value

(

struct fom_context *

fctx

)

Calculates the overall value for the fom_context

You must have previously called fom_calculate()

fom_select_reflection_pairs()

struct fom_rejections fom_select_reflection_pairs	(	RefList *	list1,
		RefList *	list2,
		RefList **	plist1_acc,
		RefList **	plist2_acc,
		UnitCell *	cell,
		SymOpList *	sym,
		int	anom,
		double	rmin_fix,
		double	rmax_fix,
		double	sigma_cutoff,
		int	ignore_negs,
		int	zero_negs,
		int	mul_cutoff
	)

Parameters

list1	The first input RefList
list2	The second input RefList
plist1_acc	Pointer to location for accepted list
plist2_acc	Pointer to location for accepted list
cell	A UnitCell
sym	The symmetry of raw_list
anom	Non-zero if you will calculate a FoM for anomalous signal
rmin_fix	If positive, minimum resolution to use
rmax_fix	If positive, maximum resolution to use
sigma_cutoff	Minimum I/sigI value
ignore_negs	Non-zero to filter out negative intensities
zero_negs	Non-zero to set negative intensities to zero
mul_cutoff	Minimum number of measurements per reflection

Selects reflections suitable for use with fom_calculate().

Use -INFINITY for sigma_cutoff to disable the check. Set mul_cutoff to zero to disable the check.

Returns

a fom_rejections structure with the counts of reflections.

fom_select_reflections()

struct fom_rejections fom_select_reflections	(	RefList *	raw_list,
		RefList **	plist_acc,
		UnitCell *	cell,
		SymOpList *	sym,
		double	rmin_fix,
		double	rmax_fix,
		double	sigma_cutoff,
		int	ignore_negs,
		int	zero_negs,
		int	mul_cutoff
	)

Parameters

raw_list	The input RefList
plist_acc	Pointer to location for accepted list
cell	A UnitCell
sym	The symmetry of raw_list
rmin_fix	If positive, minimum resolution to use
rmax_fix	If positive, maximum resolution to use
sigma_cutoff	Minimum I/sigI value
ignore_negs	Non-zero to filter out negative intensities
zero_negs	Non-zero to set negative intensities to zero
mul_cutoff	Minimum number of measurements per reflection

Use -INFINITY for sigma_cutoff to disable the check. Set mul_cutoff to zero to disable the check.

Returns

a fom_rejections structure with the counts of reflections.

fom_shell_centre()

double fom_shell_centre	(	struct fom_shells *	s,
		int	i
	)

Parameters

s	A fom_shells structure
i	The shell number

Returns the value of 1/d at the middle of the shell, i.e. the mean of the minimum and maximum 1/d values for the shell

fom_shell_num_possible()

int fom_shell_num_possible	(	struct fom_context *	fctx,
		int	i
	)

Parameters

fctx	A fom_context structure
i	Shell number

This must only be called on a fom_context for FOM_COMPLETENESS.

Returns

the number of reflections possible in the shell, taking into account symmetry and lattice absences, but not screw axis/glide place absences.

fom_shell_num_reflections()

int fom_shell_num_reflections	(	struct fom_context *	fctx,
		int	i
	)

Parameters

fctx	A fom_context structure
i	Shell number

Returns

the number of unique reflections in the shell

fom_shell_value()

double fom_shell_value	(	struct fom_context *	fctx,
		int	i
	)

Calculates the figure of merit for the specified shell number. You must have previously called fom_calculate()