Procedures

ProcedureLocationProcedure TypeDescription
abbott_param abbott Subroutine

Function that returns the Abbott’s curve in a svg file as well as smrk1, smrk2, spk, svk, sk

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acv anisotropy Subroutine

Function that returns the acf of an array.

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calc_median stat_mom Subroutine

Function to calculate the median value of a series.

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calc_moments stat_mom Subroutine

Function to calculate the statistical moments of an array with mask, of shape dim. 1 or 2

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calc_moments_1D stat_mom Subroutine

Function to calculate the statistical moments of a 1D array with mask, see calc_moments

calcul_aire asfc Subroutine

Return the area of a surface

calcul_asfc asfc Subroutine

Return the asfc of a surface regarding the default parameter method_asfc

calcul_asfc_hermite asfc Subroutine

Return the asfc of a surface. The different grids are obtained by Hermite interpolation

calcul_asfc_lin_all asfc Subroutine

Return the asfc of a surface. The different grids are obtained by linear interpolation

calcul_asfc_spl_all asfc Subroutine

Return the asfc of a surface. The different grids are obtained by spline of degree 3

calcul_normales morpho Subroutine

Function that returns the fraction of surface nearly horizontal (normal less than 5 degrees from a vertical line)

correlation_parameters anisotropy Subroutine

Function that returns ellipse_acf parameters calculated on the autocorrelation function. But prior to the acf calculation, the mean plane is subtracted.

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count_cell morpho Subroutine

Calculate the number of cells in a mask, as well as the cell median size

curv2 grad_curv Subroutine

Function to calculate the double derivatives of a 2D array

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curvature grad_curv Subroutine

Function to calculate the gaussian curvature of a 2D array, its mean quadratic value and the gradient mean quadratic value

def_masque morpho Subroutine

Height mask without deepest pits and highest peaks

deriv_N grad_curv Subroutine

Function to provide the interpolation functions of a QU9 element, as well as its derivatives

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df_boltz asfc Function

Fitting function partial derivatives.

dn_i asfc Function

1D shape function derivative, quadratic case.

dnq_et_i asfc Function

2D shape function derivative, quadratic case.

dnq_xi_et_i asfc Function

2D shape function , derivative, quadratic case.

dnq_xi_i asfc Function

2D shape function derivative, quadratic case.

ellipse_acf anisotropy Subroutine

Function that returns p_acv which contains parameters on anisotropy.

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erode_dilate morpho Subroutine

Perform erosion or dilation on a binary mask depending on the value of act. The operations utilize a defined kernel to affect neighboring pixels based on the specified val

f_boltz asfc Function

Fitting function.

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fake_acv test_anisotropy Subroutine
fft_filter filter Subroutine

Classical Gaussian filter

flood morpho Subroutine

Perform some kind of flood fill or connected component labeling on a grid (masque), starting from an initial ‘1’ element found and spreading out to adjacent ‘1’ elements, updating them to a specified value or zero if no value (niv) is specified.

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gauss_curv grad_curv Subroutine

Function to calculate the double derivatives of a 2D array

gaussian_filter filter Subroutine

Gaussian kernel

gradient grad_curv Subroutine

Function to calculate the gradient of a 2D array

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gradient_corner grad_curv Subroutine

Function that gives the nodal height gradients

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indice_fractal asfc Subroutine

Function that returns the fractal dimension with the box counting method

init_beta_boltz asfc Subroutine

Function that initializes the fitting tanh function f_boltz parameters.

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label_surf_summits grad_curv Subroutine

Function to output the extrema of a 2D array, as peaks, valleys or saddles.

labelize_point grad_curv Subroutine

Function to label a point as: peak, valley, saddle or nothing particular

locate asfc Function

Function that returns the location of an element in a vector.

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locate2 asfc Function

Function that returns the location of an element in a vector.

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make_composite_mask morpho Subroutine

The subroutine generates a composite mask based on specified parameters. The mask is filled with a number of shapes (in this case, ellipses) placed randomly within a defined area, while ensuring that the shapes do not overlap.

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make_mask morpho Subroutine

Mask a region within a given shape (for the moment an ellipsis)

median_filter filter Subroutine

A bit more complex filter: the overall height standard deviation is taken into account

median_smooth filter Subroutine

Very classical smoothing

morpho_filter filter Subroutine

Morphological filter: uses combinations of roll_smooth to provide all kind of transformation :

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multiple_anisotropy anisotropy Subroutine

Function that returns simple_anisotropy min, max and max/min for different Gaussian filter cutoff

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n_i asfc Function

1D shape function, quadratic case.

nq_i asfc Function

2D shape function, quadratic case.

peaks_and_pits_curvatures grad_curv Subroutine

Function to calculate and output the peaks and pits curvatures as well as then mean quadratic gradient value and the mean quadratic curvature value.

plane test_morpho Function
random_normal stat_mom Function
rnorm stat_mom Function

Generate a random normal deviate using the polar method.

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rnorm_vec stat_mom Function

Vector of reals that follow a normal law

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roll_smooth filter Subroutine

A ball of radius “ray” rolls on / below the surface, hence defining a closing or an opening enveloppe.

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scramble stat_mom Subroutine

scramble a vector of reals

simple_anisotropy anisotropy Subroutine

Function that returns some anisotropy parameters calculated on a polar representation, for each angle from 0 to 179

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soften filter Subroutine

Function to smooth out a 2D array: each point is replaced by a weighted mean of its neighbors.

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surf_area morpho Subroutine

Function that returns the relative area of a surface minus 1.

test_label_surf_summits grad_curv Subroutine

Function to test the capicity in detecting peaks, pits and saddles in a simple double sinus surface.

test_labelize_point grad_curv Subroutine

Function to test the function “labelize_point” on a QU9 domain with a 2nd order polynomial along x and y

test_peaks_and_pits_curvatures grad_curv Subroutine

Function to test the function “peaks_and_pits_curvatures” on a real rough surface. Outputs surface gradients and curvatures as 2D arrays or single values.

topology morpho Subroutine

The function performs the following operations on a surface:

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call~~graph~~CallGraph proc~abbott_param abbott_param proc~calc_moments calc_moments proc~abbott_param->proc~calc_moments get_unit get_unit proc~abbott_param->get_unit init pikaia_class%init proc~abbott_param->init moindres_carres_lineaire moindres_carres_lineaire proc~abbott_param->moindres_carres_lineaire run_gnuplot run_gnuplot proc~abbott_param->run_gnuplot solve pikaia_class%solve proc~abbott_param->solve sort_array2 sort_array2 proc~abbott_param->sort_array2 proc~acv acv proc~acv->proc~calc_moments apod apod proc~acv->apod calc_fftw3_real_bwd calc_fftw3_real_bwd proc~acv->calc_fftw3_real_bwd calc_fftw3_real_fwd calc_fftw3_real_fwd proc~acv->calc_fftw3_real_fwd init_scal init_scal proc~acv->init_scal tab_calc_fftw3_real_bwd tab_calc_fftw3_real_bwd proc~acv->tab_calc_fftw3_real_bwd tab_calc_fftw3_real_fwd tab_calc_fftw3_real_fwd proc~acv->tab_calc_fftw3_real_fwd trans_corner2center trans_corner2center proc~acv->trans_corner2center write_surf write_surf proc~acv->write_surf proc~calc_median calc_median proc~calc_median->sort_array2 proc~calc_moments_1d calc_moments_1D proc~calc_moments->proc~calc_moments_1d proc~calcul_aire calcul_aire proc~calcul_asfc calcul_asfc proc~calcul_asfc_hermite calcul_asfc_hermite proc~calcul_asfc->proc~calcul_asfc_hermite proc~calcul_asfc_lin_all calcul_asfc_lin_all proc~calcul_asfc->proc~calcul_asfc_lin_all proc~calcul_asfc_spl_all calcul_asfc_spl_all proc~calcul_asfc->proc~calcul_asfc_spl_all proc~calcul_asfc->get_unit proc~df_boltz df_boltz proc~calcul_asfc_hermite->proc~df_boltz proc~dnq_et_i dnq_et_i proc~calcul_asfc_hermite->proc~dnq_et_i proc~dnq_xi_i dnq_xi_i proc~calcul_asfc_hermite->proc~dnq_xi_i proc~f_boltz f_boltz proc~calcul_asfc_hermite->proc~f_boltz proc~init_beta_boltz init_beta_boltz proc~calcul_asfc_hermite->proc~init_beta_boltz proc~locate locate proc~calcul_asfc_hermite->proc~locate proc~locate2 locate2 proc~calcul_asfc_hermite->proc~locate2 proc~nq_i nq_i proc~calcul_asfc_hermite->proc~nq_i proc~calcul_asfc_hermite->get_unit lmder1 lmder1 proc~calcul_asfc_hermite->lmder1 omp_get_num_procs omp_get_num_procs proc~calcul_asfc_hermite->omp_get_num_procs proc~calcul_asfc_lin_all->proc~calcul_aire proc~calcul_asfc_lin_all->proc~df_boltz proc~calcul_asfc_lin_all->proc~f_boltz proc~calcul_asfc_lin_all->proc~init_beta_boltz proc~calcul_asfc_lin_all->proc~locate proc~calcul_asfc_lin_all->lmder1 proc~calcul_asfc_spl_all->proc~calcul_aire proc~calcul_asfc_spl_all->proc~df_boltz proc~calcul_asfc_spl_all->proc~f_boltz proc~calcul_asfc_spl_all->proc~init_beta_boltz proc~calcul_asfc_spl_all->proc~locate db2ink db2ink proc~calcul_asfc_spl_all->db2ink db2val db2val proc~calcul_asfc_spl_all->db2val proc~calcul_asfc_spl_all->lmder1 proc~calcul_normales calcul_normales proc~calcul_normales->get_unit proc~correlation_parameters correlation_parameters proc~correlation_parameters->proc~acv proc~ellipse_acf ellipse_acf proc~correlation_parameters->proc~ellipse_acf least_squares_tcheby least_squares_tcheby proc~correlation_parameters->least_squares_tcheby proc~count_cell count_cell proc~count_cell->proc~calc_median proc~flood flood proc~count_cell->proc~flood proc~curv2 curv2 proc~curvature curvature proc~gauss_curv gauss_curv proc~curvature->proc~gauss_curv proc~gradient gradient proc~curvature->proc~gradient proc~def_masque def_masque proc~deriv_n deriv_N proc~dn_i dn_i proc~dnq_et_i->proc~dn_i proc~n_i n_i proc~dnq_et_i->proc~n_i proc~dnq_xi_et_i dnq_xi_et_i proc~dnq_xi_et_i->proc~dn_i proc~dnq_xi_i->proc~dn_i proc~dnq_xi_i->proc~n_i proc~ellipse_acf->get_unit proc~ellipse_acf->omp_get_num_procs proc~ellipse_acf->sort_array2 proc~erode_dilate erode_dilate proc~fake_acv fake_acv proc~fft_filter fft_filter proc~gaussian_filter gaussian_filter proc~fft_filter->proc~gaussian_filter proc~fft_filter->calc_fftw3_real_bwd proc~fft_filter->calc_fftw3_real_fwd extend extend proc~fft_filter->extend proc~fft_filter->tab_calc_fftw3_real_bwd proc~fft_filter->tab_calc_fftw3_real_fwd proc~gauss_curv->proc~gradient proc~gradient_corner gradient_corner proc~indice_fractal indice_fractal proc~indice_fractal->proc~calc_moments proc~indice_fractal->moindres_carres_lineaire proc~label_surf_summits label_surf_summits proc~label_surf_summits->proc~gradient_corner proc~labelize_point labelize_point proc~label_surf_summits->proc~labelize_point selectcase selectcase proc~label_surf_summits->selectcase proc~labelize_point->proc~deriv_n proc~make_composite_mask make_composite_mask proc~make_mask make_mask proc~make_composite_mask->proc~make_mask proc~median_filter median_filter proc~median_filter->proc~calc_median proc~median_filter->proc~calc_moments proc~median_smooth median_smooth proc~median_filter->proc~median_smooth proc~median_smooth->proc~calc_median proc~median_smooth->omp_get_num_procs proc~median_smooth->sort_array2 proc~morpho_filter morpho_filter proc~roll_smooth roll_smooth proc~morpho_filter->proc~roll_smooth proc~multiple_anisotropy multiple_anisotropy proc~multiple_anisotropy->proc~fft_filter proc~simple_anisotropy simple_anisotropy proc~multiple_anisotropy->proc~simple_anisotropy proc~multiple_anisotropy->init_scal proc~multiple_anisotropy->write_surf proc~nq_i->proc~n_i proc~peaks_and_pits_curvatures peaks_and_pits_curvatures proc~peaks_and_pits_curvatures->proc~curvature proc~peaks_and_pits_curvatures->proc~label_surf_summits proc~peaks_and_pits_curvatures->sort_array2 proc~plane plane proc~random_normal random_normal proc~rnorm rnorm proc~rnorm_vec rnorm_vec proc~rnorm_vec->proc~rnorm proc~roll_smooth->omp_get_num_procs proc~scramble scramble proc~scramble->sort_array2 proc~soften soften proc~surf_area surf_area proc~test_label_surf_summits test_label_surf_summits proc~test_label_surf_summits->proc~label_surf_summits proc~test_label_surf_summits->init_scal proc~test_label_surf_summits->write_surf proc~test_labelize_point test_labelize_point proc~test_labelize_point->proc~deriv_n proc~test_labelize_point->proc~labelize_point proc~test_labelize_point->selectcase proc~test_peaks_and_pits_curvatures test_peaks_and_pits_curvatures proc~test_peaks_and_pits_curvatures->proc~curv2 proc~test_peaks_and_pits_curvatures->proc~curvature proc~test_peaks_and_pits_curvatures->proc~fft_filter proc~test_peaks_and_pits_curvatures->proc~gauss_curv proc~test_peaks_and_pits_curvatures->proc~gradient proc~test_peaks_and_pits_curvatures->proc~peaks_and_pits_curvatures end_fftw3 end_fftw3 proc~test_peaks_and_pits_curvatures->end_fftw3 fftw_plan_with_nthreads fftw_plan_with_nthreads proc~test_peaks_and_pits_curvatures->fftw_plan_with_nthreads init_fftw3 init_fftw3 proc~test_peaks_and_pits_curvatures->init_fftw3 omp_get_max_threads omp_get_max_threads proc~test_peaks_and_pits_curvatures->omp_get_max_threads read_surf read_surf proc~test_peaks_and_pits_curvatures->read_surf unit2IUf unit2IUf proc~test_peaks_and_pits_curvatures->unit2IUf proc~test_peaks_and_pits_curvatures->write_surf proc~topology topology proc~topology->proc~count_cell proc~topology->proc~def_masque proc~topology->proc~erode_dilate program~test_abbott test_abbott program~test_abbott->proc~abbott_param program~test_abbott->read_surf program~test_anisotropy test_anisotropy program~test_anisotropy->proc~correlation_parameters program~test_anisotropy->proc~ellipse_acf program~test_anisotropy->proc~fake_acv program~test_anisotropy->proc~multiple_anisotropy program~test_anisotropy->apod program~test_anisotropy->end_fftw3 program~test_anisotropy->fftw_plan_with_nthreads program~test_anisotropy->init_fftw3 program~test_anisotropy->init_scal program~test_anisotropy->omp_get_max_threads program~test_anisotropy->read_surf program~test_anisotropy->unit2IUf program~test_anisotropy->write_surf program~test_asfc test_asfc program~test_asfc->proc~calcul_asfc_hermite program~test_asfc->proc~indice_fractal clean_scratch clean_scratch program~test_asfc->clean_scratch list_files list_files program~test_asfc->list_files program~test_asfc->read_surf program~test_grad_curv test_grad_curv program~test_grad_curv->proc~test_label_surf_summits program~test_grad_curv->proc~test_labelize_point program~test_grad_curv->proc~test_peaks_and_pits_curvatures program~test_morpho test_morpho program~test_morpho->proc~calc_moments program~test_morpho->proc~calcul_normales program~test_morpho->proc~count_cell program~test_morpho->proc~def_masque program~test_morpho->proc~erode_dilate program~test_morpho->proc~plane program~test_morpho->proc~surf_area program~test_morpho->get_unit program~test_morpho->init_scal program~test_morpho->read_surf program~test_morpho->sort_array2 program~test_morpho->write_surf program~test_smooth test_smooth program~test_smooth->proc~fft_filter program~test_smooth->proc~median_filter program~test_smooth->proc~median_smooth program~test_smooth->proc~morpho_filter program~test_smooth->proc~soften program~test_smooth->end_fftw3 program~test_smooth->extend program~test_smooth->fftw_plan_with_nthreads program~test_smooth->init_fftw3 program~test_smooth->omp_get_max_threads program~test_smooth->read_surf program~test_smooth->unit2IUf program~test_smooth->write_surf program~test_stat test_stat program~test_stat->proc~calc_median program~test_stat->proc~calc_moments program~test_stat->proc~rnorm_vec
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