correct: Gwyddion Data Processing Library Reference Manual

## correct correct — Data correction |

## Functions

void | (*GwyCoordTransform2DFunc) ()
void | gwy_data_field_laplace_solve ()
void | gwy_data_field_correct_laplace_iteration ()
void | gwy_data_field_correct_average ()
void | gwy_data_field_correct_average_unmasked ()
void | gwy_data_field_mask_outliers ()
void | gwy_data_field_mask_outliers2 ()
void | gwy_data_field_distort ()
void | gwy_data_field_sample_distorted ()
void | gwy_data_field_affine ()
void | gwy_data_field_affine_prepare ()
gboolean | gwy_data_field_measure_lattice_acf ()
gboolean | gwy_data_field_measure_lattice_psdf ()
gboolean | gwy_data_line_correct_laplace ()
void | gwy_data_field_mark_scars ()
void | gwy_data_field_subtract_row_shifts ()
GwyDataLine * | gwy_data_field_find_row_shifts_trimmed_mean ()
GwyDataLine * | gwy_data_field_find_row_shifts_trimmed_diff ()
void | gwy_data_field_row_level_poly ()
GwyPlaneSymmetry | gwy_data_field_unrotate_find_corrections ()

## Includes

    #include <libprocess/gwyprocess.h>

## Description

## Functions

### GwyCoordTransform2DFunc ()

    void
    (*GwyCoordTransform2DFunc) (gdouble x,
                                gdouble y,
                                gdouble *px,
                                gdouble *py,
                                gpointer user_data);

The type of two-dimensional coordinate transform function.

#### Parameters

x | Old x coordinate. |
y | Old y coordinate. |
px | Location to store new x coordinate. |
py | Location to store new y coordinate. |
user_data | User data passed to the caller function. |

Since: 2.5

### gwy_data_field_laplace_solve ()

    void
    gwy_data_field_laplace_solve (GwyDataField *field,
                                  GwyDataField *mask,
                                  gint grain_id,
                                  gdouble qprec);

Replaces masked areas by the solution of Laplace equation.

The boundary conditions on mask boundaries are Dirichlet with values given by pixels on the outer boundary of the masked area. Boundary conditions at field edges are Neumann conditions ∂z/∂n=0 where n denotes the normal to the edge. If entire area of `field` is to be replaced the problem is underspecified; `field` will be filled with zeros.

For the default value of `qprec` the the result should be good enough for any image processing purposes with the typical local error of order 10⁻⁵ for very large grains and possibly much smaller for small grains. You can lower `qprec` down to about 0.3 or even 0.2 if speed is crucial and some precision can be sacrificed. Below that the result just starts becoming somewhat worse for not much speed increase. Conversely, you may wish to increase `qprec` up to 3 or even 5 if accuracy is important and you can afford the increased computation time.

#### Parameters

field | A two-dimensional data field. |
mask | A two-dimensional data field containing mask defining the areas to interpolate. |
grain_id | The id number of the grain to replace with the solution of Laplace equation, from 1 to `ngrains` (see `gwy_data_field_grain_numbers()`). Passing 0 means to replace the entire empty space outside grains while passing a negative value means to replace the entire masked area. |
qprec | Speed-accuracy tuning parameter. Pass 1.0 for the default that is fast and sufficiently precise. |

Since: 2.47

### gwy_data_field_correct_laplace_iteration ()

    void
    gwy_data_field_correct_laplace_iteration
                                   (GwyDataField *data_field,
                                    GwyDataField *mask_field,
                                    GwyDataField *buffer_field,
                                    gdouble corrfactor,
                                    gdouble *error);

Performs one interation of Laplace data correction.

Tries to remove all the points in mask off the data by using iterative method similar to solving heat flux equation.

Use this function repeatedly until reasonable `error` is reached.

For almost all purposes this function was superseded by non-iterative `gwy_data_field_laplace_solve()` which is simultaneously much faster and more accurate.

#### Parameters

data_field | Data field to be corrected. |
mask_field | Mask of places to be corrected. |
buffer_field | Initialized to same size as mask and data. |
error | Maximum change within last step. |
corrfactor | Correction factor within step. |

### gwy_data_field_correct_average ()

    void
    gwy_data_field_correct_average (GwyDataField *data_field,
                                    GwyDataField *mask_field);

Fills data under mask with the average value.

This function simply puts average value of all the `data_field` values (both masked and unmasked) into points in `data_field` lying under points where `mask_field` values are nonzero.

In most cases you probably want to use `gwy_data_field_correct_average_unmasked()` instead.

#### Parameters

data_field | A data field. |
mask_field | Mask of places to be corrected. |

### gwy_data_field_correct_average_unmasked ()

    void
    gwy_data_field_correct_average_unmasked
                                   (GwyDataField *data_field,
                                    GwyDataField *mask_field);

Fills data under mask with the average value of unmasked data.

This function calculates the average value of all unmasked pixels in `data_field` and then fills all the masked pixels with this average value. It is useful as the first rough step of correction of data under the mask.

If all data are masked the field is filled with zeroes.

#### Parameters

data_field | A data field. |
mask_field | Mask of places to be corrected. |

Since: 2.44

### gwy_data_field_mask_outliers ()

    void
    gwy_data_field_mask_outliers (GwyDataField *data_field,
                                  GwyDataField *mask_field,
                                  gdouble thresh);

Creates mask of data that are above or below `thresh` *sigma from average height.

Sigma denotes root-mean square deviation of heights. This criterium corresponds to the usual Gaussian distribution outliers detection if `thresh` is 3.

#### Parameters

data_field | A data field. |
mask_field | A data field to be filled with mask. |
thresh | Threshold value. |

### gwy_data_field_mask_outliers2 ()

    void
    gwy_data_field_mask_outliers2 (GwyDataField *data_field,
                                   GwyDataField *mask_field,
                                   gdouble thresh_low,
                                   gdouble thresh_high);

Creates mask of data that are above or below multiples of rms from average height.

Data that are below `mean` -`thresh_low` *`sigma` or above `mean` +`thresh_high` *`sigma` are marked as outliers, where `sigma` denotes the root-mean square deviation of heights.

#### Parameters

data_field | A data field. |
mask_field | A data field to be filled with mask. |
thresh_low | Lower threshold value. |
thresh_high | Upper threshold value. |

Since: 2.26

### gwy_data_field_distort ()

    void
    gwy_data_field_distort (GwyDataField *source,
                            GwyDataField *dest,
                            GwyCoordTransform2DFunc invtrans,
                            gpointer user_data,
                            GwyInterpolationType interp,
                            GwyExteriorType exterior,
                            gdouble fill_value);

Distorts a data field in the horizontal plane.

Note the transform function `invtrans` is the inverse transform, in other words it calculates the old coordinates from the new coordinates (the transform would not be uniquely defined the other way round).

The `GWY_EXTERIOR_LAPLACE` exterior type cannot be used with this function.

#### Parameters

source | Source data field. |
dest | Destination data field. |
invtrans | Inverse transform function, that is the transformation from new coordinates to old coordinates. It gets (`j` +0.5, `i` +0.5), where `i` and `j` are the new row and column indices, passed as the input coordinates. The output coordinates should follow the same convention. Unless a special exterior handling is required, the transform function does not need to concern itself with coordinates being outside of the data. |
user_data | Pointer passed as `user_data` to `invtrans` . |
interp | Interpolation type to use. |
exterior | Exterior pixels handling. |
fill_value | The value to use with `GWY_EXTERIOR_FIXED_VALUE` . |

Since: 2.5

### gwy_data_field_sample_distorted ()

    void
    gwy_data_field_sample_distorted (GwyDataField *source,
                                     GwyDataField *dest,
                                     const GwyXY *coords,
                                     GwyInterpolationType interp,
                                     GwyExteriorType exterior,
                                     gdouble fill_value);

Resamples a data field in an arbitrarily distorted manner.

Each item in `coords` corresponds to one pixel in `dest` and gives the coordinates in `source` defining the value to set in this pixel.

The `GWY_EXTERIOR_LAPLACE` exterior type cannot be used with this function.

#### Parameters

source | Source data field. |
dest | Destination data field. |
coords | Array of `source` coordinates with the same number of items as `dest` , ordered as data field data. See `gwy_data_field_distort()` for coordinate convention discussion. |
interp | Interpolation type to use. |
exterior | Exterior pixels handling. |
fill_value | The value to use with `GWY_EXTERIOR_FIXED_VALUE` . |

Since: 2.45

### gwy_data_field_affine ()

    void
    gwy_data_field_affine (GwyDataField *source,
                           GwyDataField *dest,
                           const gdouble *invtrans,
                           GwyInterpolationType interp,
                           GwyExteriorType exterior,
                           gdouble fill_value);

Performs an affine transformation of a data field in the horizontal plane.

Note the transform `invtrans` is the inverse transform, in other words it calculates the old coordinates from the new coordinates. This way even degenerate (non-invertible) transforms can be meaningfully used. Also note that the (column, row) coordinate system is left-handed.

The `GWY_EXTERIOR_LAPLACE` exterior type cannot be used with this function.

#### Parameters

source | Source data field. |
dest | Destination data field. |
invtrans | Inverse transform, that is the transformation from new pixel coordinates to old pixel coordinates, represented as (`j` +0.5, `i` +0.5), where `i` and `j` are the row and column indices. It is represented as a six-element array [`axx` , `axy` , `ayx` , `ayy` , `bx` , `by` ] where `axy` is the coefficient from `x` to `y` . |
interp | Interpolation type to use. |
exterior | Exterior pixels handling. |
fill_value | The value to use with `GWY_EXTERIOR_FIXED_VALUE` . |

Since: 2.34

### gwy_data_field_affine_prepare ()

    void
    gwy_data_field_affine_prepare (GwyDataField *source,
                                   GwyDataField *dest,
                                   const gdouble *a1a2,
                                   gdouble *a1a2_corr,
                                   gdouble *invtrans,
                                   GwyAffineScalingType scaling,
                                   gboolean prevent_rotation,
                                   gdouble oversampling);

Resolves an affine transformation of a data field in the horizontal plane.

This function calculates suitable arguments for `gwy_data_field_affine()` from given images and lattice vectors (in real coordinates).

Data field `dest` will be resized and its real dimensions and units set in anticipation of `gwy_data_field_affine()`. Its contents will be destroyed.

Note that `a1a2_corr` is an input-output parameter. In general, the vectors will be modified according to `scaling` and `prevent_rotation` to the actual vectors in `dest` after the transformation. Only if `prevent_rotation` is `FALSE` and `scaling` is `GWY_AFFINE_SCALING_AS_GIVEN` the vectors are preserved.

#### Parameters

source | Source data field. |
dest | Destination data field. |
a1a2 | Lattice vectors (or generally base vectors) in `source` , as an array of four components: `x1` , `y1` , `x2` and `y2` . |
a1a2_corr | Correct lattice vectors (or generally base vectors) `dest` should have after the affine transform, in the same form as `a1a2` . |
invtrans | Inverse transform as an array of six values to be filled according to `gwy_data_field_affine()` specification. |
scaling | How (or if) to scale the correct lattice vectors. |
prevent_rotation | `TRUE` to prevent rotation of the data by rotating `a1a2_corr` as a whole to a direction preserving the data orientation. `FALSE` to take `a1a2_corr` as given. |
oversampling | Oversampling factor. Values larger than 1 mean smaller pixels (and more of them) in `dest` , values smaller than 1 the opposite. Pass 1.0 for the default pixel size choice. |

Since: 2.49

### gwy_data_field_measure_lattice_acf ()

    gboolean
    gwy_data_field_measure_lattice_acf (GwyDataField *acf2d,
                                        gdouble *a1a2);

Estimates or improves estimate of lattice vectors from a 2D ACF field.

Note that the 2D ACF of a data field has to be passed, not the data field itself. The correlation function can be for instance calculated by `gwy_data_field_2dacf()`. However, you can calculate and/or process the correlation function in any way you see fit.

When the vectors in `a1a2` are zero the function attempts to estimate the lattice from scratch. But if `a1a2` contains two non-zero vectors it takes them as approximate lattice vectors to improve.

If the function return `FALSE` the array `a1a2` is filled with useless values and must be ignored.

#### Parameters

acf2d | Data field containing two-dimensional autocorrelation function. |
a1a2 | Lattice vectors as an array of four components: `x1` , `y1` , `x2` and `y2` (in real coordinates). |

#### Returns

`TRUE` if good lattice vectors were found, `FALSE` on failure.

Since: 2.49

### gwy_data_field_measure_lattice_psdf ()

    gboolean
    gwy_data_field_measure_lattice_psdf (GwyDataField *psdf2d,
                                         gdouble *a1a2);

Estimates or improves estimate of lattice vectors from a 2D PSDF field.

Note that the 2D PSDF of a data field has to be passed, not the data field itself. The spectral density can be for instance calculated by `gwy_data_field_2dfft()` and summing the squares of real and imaginary parts However, you can calculate and/or process the spectral density in any way you see fit.

When the vectors in `a1a2` are zero the function attempts to estimate the lattice from scratch. But if `a1a2` contains two non-zero vectors it takes them as approximate lattice vectors to improve.

If the function return `FALSE` the array `a1a2` is filled with useless values and must be ignored.

#### Parameters

psdf2d | Data field containing two-dimensional power spectrum density function (or alternatively Fourier coefficient modulus). |
a1a2 | Lattice vectors as an array of four components: `x1` , `y1` , `x2` and `y2` (in real coordinates). |

#### Returns

`TRUE` if good lattice vectors were found, `FALSE` on failure.

Since: 2.49

### gwy_data_line_correct_laplace ()

    gboolean
    gwy_data_line_correct_laplace (GwyDataLine *data_line,
                                   GwyDataLine *mask_line);

Fills missing values in a data line using Laplace data correction.

Both data lines must have the same number of values.

For one-dimensional data the missing data interpolation is explicit. Interior missing segments are filled with linear dependence between the edge points. Missing segments with one end open are filled with the edge value.

#### Parameters

data_line | A data line. |
mask_line | Mask of places to be corrected. |

#### Returns

`TRUE` if the line contained any data at all. If there are no data the `FALSE` is returned and `data_line` is filled with zeros.

Since: 2.45

### gwy_data_field_mark_scars ()

    void
    gwy_data_field_mark_scars (GwyDataField *data_field,
                               GwyDataField *result,
                               gdouble threshold_high,
                               gdouble threshold_low,
                               gdouble min_scar_len,
                               gdouble max_scar_width,
                               gboolean negative);

Find and marks scars in a data field.

Scars are linear horizontal defects, consisting of shifted values. Zero or negative values in `result` siginify normal data, positive values siginify samples that are part of a scar.

#### Parameters

data_field | A data field to find scars in. |
result | A data field to store the result to (it is resized to match `data_field` ). |
threshold_high | Miminum relative step for scar marking, must be positive. |
threshold_low | Definite relative step for scar marking, must be at least equal to `threshold_high` . |
min_scar_len | Minimum length of a scar, shorter ones are discarded (must be at least one). |
max_scar_width | Maximum width of a scar, must be at least one. |
negative | `TRUE` to detect negative scars, `FALSE` to positive. |

Since: 2.46

### gwy_data_field_subtract_row_shifts ()

    void
    gwy_data_field_subtract_row_shifts (GwyDataField *data_field,
                                        GwyDataLine *shifts);

Shifts entire data field rows as specified by given data line.

Data line `shifts` must have resolution corresponding to the number of `data_field` rows. Its values are subtracted from individual field rows.

#### Parameters

data_field | A data field. |
shifts | Data line containing the row shifts. |

Since: 2.52

### gwy_data_field_find_row_shifts_trimmed_mean ()

    GwyDataLine *
    gwy_data_field_find_row_shifts_trimmed_mean
                                   (GwyDataField *data_field,
                                    GwyDataField *mask,
                                    GwyMaskingType masking,
                                    gdouble trimfrac,
                                    gint mincount);

Finds row shifts to misaligned row correction using trimmed row means.

For zero `trimfrac` the function calculates row means. For `trimfrac` of 1/2 or larger it calculates row medians. Values between correspond to trimmed means.

#### Parameters

data_field | A data field. |
mask | Mask of values to take values into account/exclude, or `NULL` for full `data_field` . |
masking | Masking mode to use. See the introduction for description of masking modes. |
trimfrac | Fraction of lowest values and highest values to discard when trimming. |
mincount | Minimum number of values in a row necessary for per-row calculation. Rows which are essentially completely masked are not shifted with respect to a global value. Pass a non-positive number to use an automatic minimum count. |

#### Returns

A newly created data line containing the row shifts, for instance row means, medians or trimmed means.

Since: 2.52

### gwy_data_field_find_row_shifts_trimmed_diff ()

    GwyDataLine *
    gwy_data_field_find_row_shifts_trimmed_diff
                                   (GwyDataField *data_field,
                                    GwyDataField *mask,
                                    GwyMaskingType masking,
                                    gdouble trimfrac,
                                    gint mincount);

Finds row shifts to misaligned row correction using trimmed means of row differences.

For zero `trimfrac` the function calculates row means. For `trimfrac` of 1/2 or larger it calculates row medians. Values between correspond to trimmed means.

#### Parameters

data_field | A data field. |
mask | Mask of values to take values into account/exclude, or `NULL` for full `data_field` . |
masking | Masking mode to use. See the introduction for description of masking modes. |
trimfrac | Fraction of lowest values and highest values to discard when trimming. |
mincount | Minimum number of values in a row necessary for per-row calculation. Rows which are essentially completely masked are not shifted with respect to a global value. Pass a non-positive number to use an automatic minimum count. |

#### Returns

A newly created data line containing the row shifts, for instance row means, medians or trimmed means.

Since: 2.52

### gwy_data_field_row_level_poly ()

    void
    gwy_data_field_row_level_poly (GwyDataField *field,
                                   GwyDataField *mask,
                                   GwyMaskingType masking,
                                   gint degree,
                                   GwyDataLine *shifts);

Levels misaligned rows of a data field by fitting and subtracting polynomials.

This function does both the fitting and subtraction in one step.

#### Parameters

field | A data field. |
mask | Mask of values to take values into account/exclude, or `NULL` for full `data_field` . |
masking | Masking mode to use. See the introduction for description of masking modes. |
degree | Polynomial degree (0 is mean value, 1 is tilt, 2 is bow, etc.). |
shifts | Data line where to store the subtracted mean values (constant terms of the polynomials), or `NULL`. It will be resized to match the field vertical dimension. |

Since: 2.67

### gwy_data_field_unrotate_find_corrections ()

    GwyPlaneSymmetry
    gwy_data_field_unrotate_find_corrections
                                   (GwyDataLine *derdist,
                                    gdouble *correction);

Finds rotation corrections.

Rotation correction is computed for for all symmetry types. In addition an estimate is made about the prevalent one.

#### Parameters

derdist | Angular derivation distribution (normally obrained from `gwy_data_field_slope_distribution()`). |
correction | Corrections for particular symmetry types will be stored here (indexed by GwyPlaneSymmetry). `correction` [0] contains the most probable correction. All angles are in radians. |

#### Returns

The estimate type of prevalent symmetry.