Gwyddion – Free SPM (AFM, SNOM/NSOM, STM, MFM, …) data analysis software

GwyShapeFitPreset

GwyShapeFitPreset — 3D geometrical shape fitting functions

Functions

gboolean gwy_shape_fit_preset_needs_same_units ()
guint gwy_shape_fit_preset_get_nparams ()
const gchar * gwy_shape_fit_preset_get_param_name ()
GwyNLFitParamFlags gwy_shape_fit_preset_get_param_flags ()
GwySIUnit * gwy_shape_fit_preset_get_param_units ()
gint gwy_shape_fit_preset_get_param_power_xy ()
gint gwy_shape_fit_preset_get_param_power_z ()
guint gwy_shape_fit_preset_get_nsecondary ()
const gchar * gwy_shape_fit_preset_get_secondary_name ()
GwyNLFitParamFlags gwy_shape_fit_preset_get_secondary_flags ()
gdouble gwy_shape_fit_preset_get_secondary_value ()
gdouble gwy_shape_fit_preset_get_secondary_error ()
GwySIUnit * gwy_shape_fit_preset_get_secondary_units ()
gint gwy_shape_fit_preset_get_secondary_power_xy ()
gint gwy_shape_fit_preset_get_secondary_power_z ()
void gwy_shape_fit_preset_setup ()
gboolean gwy_shape_fit_preset_guess ()
gdouble gwy_shape_fit_preset_get_value ()
void gwy_shape_fit_preset_calculate_z ()
void gwy_shape_fit_preset_calculate_xyz ()
GwyNLFitter * gwy_shape_fit_preset_create_fitter ()
GwyNLFitter * gwy_shape_fit_preset_fit ()
GwyNLFitter * gwy_shape_fit_preset_quick_fit ()
GwyInventory * gwy_shape_fit_presets ()

Types and Values

struct GwyShapeFitPreset
struct GwyShapeFitPresetClass

Object Hierarchy

    GObject
    ╰── GwyResource
        ╰── GwyShapeFitPreset

Includes

#include <libprocess/gwyprocess.h>

Description

Non-linear fitter 3D geometrical shape

presets are predefined fitting functions that can be used to determine the parameters of various features in images and XYZ data.

As of version 2.47 the defined functions include:

"Grating (simple)"
"Grating (3-level)"
"Holes"
"Sphere"
"Cylinder (lying)"
"Gaussian"
"Lorentzian"
"Pyramid (diamond)"
"Parabolic bump"
"Ring"

Functions

gwy_shape_fit_preset_needs_same_units ()

gboolean
gwy_shape_fit_preset_needs_same_units (GwyShapeFitPreset *preset);

Reports if a 3D geometrical shape fitter preset requires the same lateral and value units.

For instance, fitting a sphere is meaningless if the horizontal and vertical radii would be different physical quantities.

Parameters

preset

A 3D geometrical shape fitting function.

 

Returns

TRUE if the function requires the same lateral and value units.

Since: 2.47

gwy_shape_fit_preset_get_nparams ()

guint
gwy_shape_fit_preset_get_nparams (GwyShapeFitPreset *preset);

Reports the number of parameters of a 3D geometrical shape fitter preset.

Parameters

preset

A 3D geometrical shape fitting function.

 

Returns

The number of function parameters.

Since: 2.47

gwy_shape_fit_preset_get_param_name ()

const gchar *
gwy_shape_fit_preset_get_param_name (GwyShapeFitPreset *preset,
                                     guint i);

Gets the name of a fitting parameter of a 3D geometrical shape fitter preset.

The name may contain Pango markup.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Parameter number.

 

Returns

The name of the i -th parameter.

Since: 2.47

gwy_shape_fit_preset_get_param_flags ()

GwyNLFitParamFlags
gwy_shape_fit_preset_get_param_flags (GwyShapeFitPreset *preset,
                                      guint i);

Gets the properties of a fitting parameter of a 3D geometrical shape fitter preset.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Parameter number.

 

Returns

The flags of the i -th parameter.

Since: 2.47

gwy_shape_fit_preset_get_param_units ()

GwySIUnit *
gwy_shape_fit_preset_get_param_units (GwyShapeFitPreset *preset,
                                      guint i,
                                      GwySIUnit *siunit_xy,
                                      GwySIUnit *siunit_z);

Derives the SI unit of a fitting parameter from the units of abscissa and ordinate.

Note that angle parameters are by default in radians and thus unitless. If you want to convert them to degrees for presentation to the user you must do it explicitly.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Parameter number.

 

siunit_xy

SI unit of lateral coordinates.

 

siunit_z

SI unit of values.

 

Returns

A newly created GwySIUnit with the units of the i -th parameter.

Since: 2.47

gwy_shape_fit_preset_get_param_power_xy ()

gint
gwy_shape_fit_preset_get_param_power_xy
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the power of abscissa units in a shape fitting parameter.

Usually it is easier to let gwy_shape_fit_preset_get_param_units() derive the parameter units.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Parameter number.

 

Returns

The power of abscissa in the parameter.

Since: 2.50

gwy_shape_fit_preset_get_param_power_z ()

gint
gwy_shape_fit_preset_get_param_power_z
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the power of ordinate units in a shape fitting parameter.

Usually it is easier to let gwy_shape_fit_preset_get_param_units() derive the parameter units.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Parameter number.

 

Returns

The power of ordinate in the parameter.

Since: 2.50

gwy_shape_fit_preset_get_nsecondary ()

guint
gwy_shape_fit_preset_get_nsecondary (GwyShapeFitPreset *preset);

Reports the number of secondary (derived) quantities of a 3D geometrical shape fitter preset.

Parameters

preset

A 3D geometrical shape fitting function.

 

Returns

The number of secondary quantities.

Since: 2.47

gwy_shape_fit_preset_get_secondary_name ()

const gchar *
gwy_shape_fit_preset_get_secondary_name
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the name of a secondary (derived) quantity of a 3D geometrical shape fitter preset.

The name may contain Pango markup.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

Returns

The name of the i -th secondary quantity.

Since: 2.47

gwy_shape_fit_preset_get_secondary_flags ()

GwyNLFitParamFlags
gwy_shape_fit_preset_get_secondary_flags
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the properties of a secondary (derived) quantity of a 3D geometrical shape fitter preset.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

Returns

The flags of the i -th secondary quantity.

Since: 2.47

gwy_shape_fit_preset_get_secondary_value ()

gdouble
gwy_shape_fit_preset_get_secondary_value
                               (GwyShapeFitPreset *preset,
                                guint i,
                                const gdouble *param);

Calculates the value of a secondary (derived) quantity of a 3D geometrical shape fitter preset.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

param

Values of fitting parameters for function preset .

 

Returns

The value of the i -th secondary quantity.

Since: 2.47

gwy_shape_fit_preset_get_secondary_error ()

gdouble
gwy_shape_fit_preset_get_secondary_error
                               (GwyShapeFitPreset *preset,
                                guint i,
                                const gdouble *param,
                                const gdouble *error,
                                const gdouble *correl);

Calculates the error of a secondary (derived) quantity of a 3D geometrical shape fitter preset.

The error is calculated by numerical differentiation of the function and applying the law of error propagation.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

param

Values of fitting parameters for function preset .

 

error

Values of errors of fitting parameters for function preset .

 

correl

Parameter correlation matrix for function preset (passed as lower triangular matrix).

 

Returns

The error of the i -th secondary quantity.

Since: 2.47

gwy_shape_fit_preset_get_secondary_units ()

GwySIUnit *
gwy_shape_fit_preset_get_secondary_units
                               (GwyShapeFitPreset *preset,
                                guint i,
                                GwySIUnit *siunit_xy,
                                GwySIUnit *siunit_z);

Derives the SI unit of a secondary (derived) quantity from the units of abscissa and ordinate.

Note that angle parameters are by default in radians and thus unitless. If you want to convert them to degrees for presentation to the user you must do it explicitly.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

siunit_xy

SI unit of lateral coordinates.

 

siunit_z

SI unit of values.

 

Returns

A newly created GwySIUnit with the units of the i -th secondary quantity.

Since: 2.47

gwy_shape_fit_preset_get_secondary_power_xy ()

gint
gwy_shape_fit_preset_get_secondary_power_xy
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the power of abscissa units in a shape fitting secondary (derived) quantity.

Usually it is easier to let gwy_shape_fit_preset_get_secondary_units() derive the quantity units.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

Returns

The power of abscissa in the secondary quantity.

Since: 2.50

gwy_shape_fit_preset_get_secondary_power_z ()

gint
gwy_shape_fit_preset_get_secondary_power_z
                               (GwyShapeFitPreset *preset,
                                guint i);

Gets the power of ordinate units in a shape fitting secondary (derived) quantity.

Usually it is easier to let gwy_shape_fit_preset_get_secondary_units() derive the quantity units.

Parameters

preset

A 3D geometrical shape fitting function.

 

i

Secondary quantity number.

 

Returns

The power of ordinate in the secondary quantity.

Since: 2.50

gwy_shape_fit_preset_setup ()

void
gwy_shape_fit_preset_setup (GwyShapeFitPreset *preset,
                            const GwyXYZ *points,
                            guint n,
                            gdouble *params);

Initialises parameter values of a 3D geometrical shape fitter preset.

The parameters are quickly set to reasonable values that roughly correspond to the ranges of the data points. They may serve as starting values for manual experimentation but often will not be good enough as initial parameter estimates for the fit. See also gwy_shape_fit_preset_guess().

Parameters

preset

A 3D geometrical shape fitting function.

 

points

Array of XYZ data to fit.

 

n

Number of data points.

 

params

The array to fill with initialised parameter values.

 

Since: 2.47

gwy_shape_fit_preset_guess ()

gboolean
gwy_shape_fit_preset_guess (GwyShapeFitPreset *preset,
                            const GwyXYZ *points,
                            guint n,
                            gdouble *params);

Estimates parameter values of a 3D geometrical shape fitter preset.

This function tries to find initial parameter estimates that are good enough for the fit the converge. Of course, it is not guaranteed it always succeeds. For some shapes it can be noticeably slower than gwy_shape_fit_preset_setup().

The estimate may not be deterministic. For large point sets some estimates are carried out using a randomly selected subset of points.

If the function cannot find how the data points could correspond to the preset geometrical shape it return FALSE. Parameter values are still set. However, in this case they may be no better than from gwy_shape_fit_preset_setup().

Parameters

preset

A 3D geometrical shape fitting function.

 

points

Array of XYZ data to fit.

 

n

Number of data points.

 

params

The array to fill with initialised parameter values.

 

Returns

TRUE if the estimation succeeded, FALSE if it failed.

Since: 2.47

gwy_shape_fit_preset_get_value ()

gdouble
gwy_shape_fit_preset_get_value (GwyShapeFitPreset *preset,
                                gdouble x,
                                gdouble y,
                                const gdouble *params);

Calculates the value of a 3D geometrical shape fitter preset in a single point.

If you want multiple values you should use either gwy_shape_fit_preset_calculate_z() or gwy_shape_fit_preset_calculate_xyz() instead of calling this function in a cycle.

Parameters

preset

A 3D geometrical shape fitting function.

 

x

X-coordinate.

 

y

Y-coordinate.

 

params

Fitting parameter values.

 

Returns

The calculated function value in (x ,y ).

Since: 2.47

gwy_shape_fit_preset_calculate_z ()

void
gwy_shape_fit_preset_calculate_z (GwyShapeFitPreset *preset,
                                  const GwyXYZ *points,
                                  gdouble *z,
                                  guint n,
                                  const gdouble *params);

Calculates values of a 3D geometrical shape fitter preset in an array of points.

The z-coordinates in points are ignored. Only the lateral coordinates are used.

See also gwy_shape_fit_preset_calculate_xyz().

Parameters

preset

A 3D geometrical shape fitting function.

 

points

Array of n XYZ data defining the lateral coordinates.

 

z

Array length n to fill with calculated values.

 

n

Number of items in points and z .

 

params

Fitting parameter values.

 

Since: 2.47

gwy_shape_fit_preset_calculate_xyz ()

void
gwy_shape_fit_preset_calculate_xyz (GwyShapeFitPreset *preset,
                                    GwyXYZ *points,
                                    guint n,
                                    const gdouble *params);

Calculates values of a 3D geometrical shape fitter preset in an array of points.

See also gwy_shape_fit_preset_calculate_z().

Parameters

preset

A 3D geometrical shape fitting function.

 

points

Array of n XYZ data defining the lateral coordinates. The z-coordinates will be filled with the calculated values.

 

n

Number of items in points .

 

params

Fitting parameter values.

 

Since: 2.47

gwy_shape_fit_preset_create_fitter ()

GwyNLFitter *
gwy_shape_fit_preset_create_fitter (GwyShapeFitPreset *preset);

Creates a non-linear least-squares fitter for a 3D geometrical shape.

The created fitter will be of the opaque indexed data type, as created with gwy_math_nlfit_new_idx().

If you do not need to modify the fitter settings you can use gwy_shape_fit_preset_fit() directly with NULL fitter.

Parameters

preset

A 3D geometrical shape fitting function.

 

Returns

A newly created fitter for preset .

Since: 2.47

gwy_shape_fit_preset_fit ()

GwyNLFitter *
gwy_shape_fit_preset_fit (GwyShapeFitPreset *preset,
                          GwyNLFitter *fitter,
                          const GwyXYZ *points,
                          guint n,
                          gdouble *params,
                          const gboolean *fixed_param,
                          gdouble *rss);

Performs a non-linear least-squares fit with a 3D geometrical shape fitter.

If you pass NULL fitter the function creates one for you and immediately performs the fit. If you want to modify the fitter settings beforehand or set callback functions create it using gwy_shape_fit_preset_create_fitter() and pass to this function. The fitter must be created for the same preset.

Additional quantities such as parameter errors or the correlation matrix can be obtained from the fitter. See gwy_math_nlfit_fit_full() for details.

Parameters

preset

A 3D geometrical shape fitting function.

 

fitter

A Marquardt-Levenberg nonlinear fitter already initialized for preset 's function, or NULL.

 

points

Array of n XYZ data defining the lateral coordinates and values to fit.

 

n

Number of items in points .

 

params

Fitting parameters filled with initial estimates (the fitting starts from the provided values).

 

fixed_param

Which parameters should be treated as fixed (set corresponding element to TRUE for them). May be NULL if all parameters are free.

 

rss

Location to store the residual sum of squares, as returned by gwy_math_nlfit_fit_idx(), may be NULL.

 

Returns

Either fitter itself, or a newly created fitter if it was NULL.

Since: 2.47

gwy_shape_fit_preset_quick_fit ()

GwyNLFitter *
gwy_shape_fit_preset_quick_fit (GwyShapeFitPreset *preset,
                                GwyNLFitter *fitter,
                                const GwyXYZ *points,
                                guint n,
                                gdouble *params,
                                const gboolean *fixed_param,
                                gdouble *rss);

Performs a rough non-linear least-squares fit with a 3D geometrical shape fitter.

See gwy_shape_fit_preset_fit() for discussion. This functions differs by using a reduced number of points to perform the fit (unless the input set is small) and may also set fitter parameters to make the least squares method terminate faster. The input points are reduced the same way as in gwy_surface_reduce_points().

Parameters

preset

A 3D geometrical shape fitting function.

 

fitter

A Marquardt-Levenberg nonlinear fitter already initialized for preset 's function, or NULL.

 

points

Array of n XYZ data defining the lateral coordinates and values to fit.

 

n

Number of items in points .

 

params

Fitting parameters filled with initial estimates (the fitting starts from the provided values).

 

fixed_param

Which parameters should be treated as fixed (set corresponding element to TRUE for them). May be NULL if all parameters are free.

 

rss

Location to store the residual sum of squares, as returned by gwy_math_nlfit_fit_idx(), may be NULL.

 

Returns

Either fitter itself, or a newly created fitter if it was NULL.

Since: 2.48

gwy_shape_fit_presets ()

GwyInventory *
gwy_shape_fit_presets (void);

Gets inventory with all the 3D geometric shape fitting presets.

Returns

3D geometric shape fitting preset inventory.

Since: 2.47

Types and Values

struct GwyShapeFitPreset

struct GwyShapeFitPreset;

struct GwyShapeFitPresetClass

struct GwyShapeFitPresetClass {
    GwyResourceClass parent_class;
};

See Also

GwyNLFitter

© David Nečas and Petr Klapetek

Home Download News Features Screenshots Documentation Communicate Participate Resources Publications Applications Site Map

Valid XHTML 1.0 Valid CSS