| Bsoft 2.0.5 Bernard's software package

Bimage Member List

This is the complete list of members for Bimage, including all inherited members.

add(long j, double v) | Bimage | inline
add(long j, Complex< double > cv) | Bimage | inline
add(double xx, double yy, double zz, long nn, double v) | Bimage |
add(double v) | Bimage |
add(Bimage *p) | Bimage |
add(long nn, Bimage *p) | Bimage |
add(Bimage *p, double scale, double shift) | Bimage |
add(long nn, Bimage *p, double scale, double shift) | Bimage |
align(long ref_num, Bimage *pmask, double hi_res, double lo_res, double shift_limit, double edge_width, double gauss_width, Vector3< long > bin) | Bimage |
align2D(Bimage *pref, double res_polar, int ann_min, int ann_max, Bimage *prs_mask, double shift_limit, double angle_limit, fft_plan planf_1D, fft_plan planb_1D, fft_plan planf_2D, fft_plan planb_2D) | Bimage |
align2D(Bimage *pref, int ann_min, int ann_max, double res_lo, double res_hi, double shift_limit, double angle_limit) | Bimage |
align2D_pps(Bimage *pref, double res_hi, double res_lo, double shift_limit, double angle_limit, fft_plan planf, fft_plan planb) | Bimage |
align_fast(long ref_num, Bimage *pmask, double hi_res, double lo_res, double shift_limit, double edge_width, double gauss_width) | Bimage |
align_progressive(long nref, Bimage *pmask, double hi_res, double lo_res, double shift_limit, fft_plan planf, fft_plan planb) | Bimage |
align_progressive_fast(long nref, double shift_limit) | Bimage |
alloc_size() const | Bimage | inline
apply_soft_mask(long nn, Bimage *pmask, int fill_type, double fill) | Bimage |
assemble_tiles(Bimage *pt, int flag=0) | Bimage |
auto_correlate(double hires, double lores) | Bimage |
average(long cc, double xf, double yf, double zf, long nn, double iscale) | Bimage |
average() | Bimage | inline
average(double d) | Bimage | inline
average2D(long cc, double xf, double yf, double zf, long nn, double iscale) | Bimage |
average_images() | Bimage | inline
average_images(bool sd) | Bimage |
average_phase_difference(Bimage *p, double res_hi, double res_lo, int weighting=1) | Bimage |
back_project(Bimage *p, double resolution, double axis, fft_plan planf, fft_plan planb) | Bimage |
background(long nn) | Bimage | inline
background(long nn, double bkg) | Bimage | inline
background(double bkg) | Bimage | inline
bar(Vector3< double > start, Vector3< double > end, double width, double edge_width, int fill_type=0, double fill=0) | Bimage |
bar(long nn, Vector3< double > start, Vector3< double > end, double width, double edge_width, int fill_type=0, double fill=0) | Bimage |
Bimage() | Bimage |
Bimage(const Bimage &p) | Bimage |
Bimage(Bstring &fn, int readdata, int img_select) | Bimage |
Bimage(DataType type, CompoundType ctype, long nx, long ny, long nz, long nn) | Bimage |
Bimage(DataType type, CompoundType ctype, Vector3< long > size, long nn) | Bimage |
Bimage(DataType type, CompoundType ctype, vector< long > size, long nn) | Bimage |
Bimage(DataType type, long nc, long nx, long ny, long nz, long nn) | Bimage |
Bimage(DataType type, long nc, Vector3< long > size, long nn) | Bimage |
bin(long b) | Bimage | inline
bin(Vector3< long > bk) | Bimage |
bin_around_origin(int bin) | Bimage |
bin_copy(long b) | Bimage | inline
bin_copy(Vector3< long > bk) | Bimage |
blend(Bimage *p, long number) | Bimage |
blobs(double threshold, double min_size, double max_size, double setvalue, int sign) | Bimage |
calculate_background(long nn, int flag) | Bimage |
calculate_background(int flag=0) | Bimage |
calculate_background(Bimage *pmask, long nn, int flag=0) | Bimage |
calculate_background(Bimage *pmask, int flag=0) | Bimage |
cartesian_to_cylindrical(long nannuli, long nphi, int flag=0) | Bimage |
cartesian_to_spherical(long nannuli, long nphi, long ntheta) | Bimage |
catenate(long m, Bimage **p) | Bimage |
ccmap_confidence(long nn) | Bimage |
center(int fill_type=0, double fill=0) | Bimage |
center_wrap() | Bimage |
central_section(Matrix3 mat, double resolution, FSI_Kernel *kernel) | Bimage |
change_symmetry(Bsymmetry *symold, Bsymmetry *symnu, double radius, double z_slope) | Bimage |
change_transform_size(Vector3< long > nusize) | Bimage |
change_type(char letter) | Bimage |
change_type(char *string) | Bimage |
change_type(DataType newtype) | Bimage |
channels() | Bimage | inline
channels(long cc) | Bimage | inline
check() | Bimage |
check_if_same_image_size(Bimage *p) | Bimage |
check_if_same_size(Bimage *p) | Bimage |
check_neighbors(long idx) | Bimage |
check_point_group(Bstring &check_string) | Bimage |
check_resolution(double &resolution) | Bimage |
check_sampling() | Bimage |
clear() | Bimage | inline
cmyk(long j) | Bimage |
cmyk_to_rgb() | Bimage |
color_blue(double cmin, double cmax, int gray_extremes=0) | Bimage |
color_combine(Bimage *p) | Bimage |
color_green(double cmin, double cmax, int gray_extremes=0) | Bimage |
color_red(double cmin, double cmax, int gray_extremes=0) | Bimage |
color_spectrum(double cmin, double cmax) | Bimage |
color_to_simple() | Bimage |
combine_channels(long nc) | Bimage |
combined_complex_product() | Bimage |
combined_complex_product(Bimage *pmask) | Bimage |
combined_complex_product(double hires, double lores) | Bimage |
combined_complex_product(double hires, double lores, Bimage *pmask) | Bimage |
combined_complex_product_implicit_mask(double hires, double lores) | Bimage |
compatible(Bimage *p) | Bimage |
complex(long j) | Bimage |
complex_apply_dual_mask(Bimage *pmask) | Bimage |
complex_apply_mask(Bimage *pmask) | Bimage |
complex_apply_negative_mask(Bimage *pmask) | Bimage |
complex_bandpass(double hires, double lores) | Bimage |
complex_conjugate() | Bimage |
complex_conjugate_product(Bimage *p) | Bimage |
complex_conjugate_product_one2many(Bimage *p) | Bimage |
complex_multiply(Bimage *p) | Bimage |
complex_normalize() | Bimage |
complex_power() | Bimage |
complex_product(Bimage *p) | Bimage |
complex_to_amplitudes() | Bimage |
complex_to_imaginary() | Bimage |
complex_to_intensities() | Bimage |
complex_to_phases() | Bimage |
complex_to_real() | Bimage |
complex_to_signed_amplitudes() | Bimage |
compound_type() | Bimage | inline
compound_type(CompoundType ct) | Bimage | inline
compound_type_size() | Bimage | inline
compound_type_string() | Bimage |
convert_to_helix(double helix_rise, double helix_angle, Vector3< double > offset) | Bimage |
convolve(Bimage *pkernel) | Bimage |
convolve_chunk(Bimage *pkernel, float *nudata, long i, long len) | Bimage |
coordinates(long i, long &nx, long &ny, long &nz) | Bimage | inline
coordinates(long i, long &nx, long &ny, long &nz, long &nn) | Bimage | inline
coordinates(long i, long &nc, long &nx, long &ny, long &nz, long &nn) | Bimage | inline
coordinates(long i) | Bimage | inline
copy() | Bimage |
copy(long nu_nimg) | Bimage |
copy_header() | Bimage | inline
copy_header(long nu_nimg) | Bimage |
correct_background(long nn, int flag) | Bimage |
correct_background(int flag=0) | Bimage |
correct_background(Bimage *pmask, int flag=0) | Bimage |
correlate(Bimage *p) | Bimage |
correlate(Bimage *p, double rmin, double rmax, Bimage *pmask=NULL, int flag=0) | Bimage |
correlate_annuli(Bimage *polref, int ann_min, int ann_max, double ang_min, double ang_max, fft_plan planf, fft_plan planb, double &cc_max) | Bimage |
correlation_coefficient(Vector3< double > shift) | Bimage |
cross_correlate(Bimage *p, double hires, double lores, fft_plan planf, fft_plan planb) | Bimage |
cross_correlate(Bimage *p, Bimage *pmask=NULL) | Bimage | inline
cross_correlate(Bimage *p, double hires, double lores, Bimage *pmask=NULL) | Bimage |
cross_correlate(Bimage *p, double hires, double lores, Bimage *pmask, fft_plan planf, fft_plan planb) | Bimage |
cross_correlate_fspace(Bimage *p, double hires, double lores, double shift_limit) | Bimage |
cross_correlate_two_way(Bimage *p, double hires, double lores, fft_plan planf, fft_plan planb) | Bimage |
cross_correlate_validate(Bimage *p, Bimage *pmask) | Bimage |
cylinder(Vector3< double > center, double radius, double height, double width, int fill_type=0, double fill=0) | Bimage |
cylindrical_shells() | Bimage |
data_alloc() | Bimage | inline
data_alloc(long nbytes) | Bimage |
data_alloc(DataType type, CompoundType ctype, long nx, long ny, long nz, long nn) | Bimage |
data_assign(unsigned char *nudata) | Bimage |
data_delete() | Bimage |
data_offset() | Bimage | inline
data_offset(long doff) | Bimage | inline
data_pointer() | Bimage | inline
data_pointer(long offset) | Bimage | inline
data_pointer(unsigned char *ptr) | Bimage | inline
data_size() | Bimage | inline
data_type() | Bimage | inline
data_type(DataType dt) | Bimage | inline
data_type_bits() const | Bimage |
data_type_max() | Bimage |
data_type_min() | Bimage |
data_type_size() const | Bimage |
data_type_string() | Bimage |
default_origin() | Bimage | inline
defocus_scale(long nn, double df, double df2, double iCL2, int fill_type) | Bimage |
delete_images(Bstring list, int retain=0) | Bimage |
density(long nn, Vector3< double > coord, double radius, double &sigma) | Bimage |
density(long nn, Vector3< double > coord, double radius) | Bimage | inline
distort_elliptically(double angle, double shift) | Bimage |
divide(Bimage *p, double scale=1, double shift=0) | Bimage |
divide_one(Bimage *p, double scale=1, double shift=0) | Bimage |
dyad_interpolate(long i, int norm_flag=1) | Bimage |
edge(int type, Vector3< long > rect, Vector3< double > start, double width, int fill_type=0, double fill=0) | Bimage |
edge(long nn, int type, Vector3< long > rect, Vector3< double > start, double width, int fill_type=0, double fill=0) | Bimage |
edge_mask(int type, Vector3< long > rect, Vector3< double > start, double width) | Bimage |
enlarge(Vector3< long > scale) | Bimage |
erase(string tag) | Bimage | inline
extract(long nn) | Bimage |
extract(long n1, long n2) | Bimage |
extract(long nn, Vector3< long > coords, Vector3< long > size, int fill_type=0, double fill=0) | Bimage |
extract(long nn, Vector3< double > loc, Vector3< long > size, Vector3< double > origin) | Bimage | inline
extract(long nn, Vector3< double > loc, Vector3< long > size, Vector3< double > origin, Matrix3 mat) | Bimage |
extract(long nn, Vector3< double > loc, Vector3< long > size, Vector3< double > origin, View view) | Bimage | inline
extract_filament(long img_num, double width, int axis, long nspline, Vector3< double > *spline) | Bimage |
extract_line(long nn, Vector3< double > start, Vector3< double > end, long width) | Bimage |
extract_magnify(long nn, Vector3< long > center, Vector3< long > ext_size, double scale) | Bimage |
extract_shell(long nn, double minrad, double maxrad) | Bimage |
extract_show(int aflag) | Bimage |
extract_show_chunk(Bimage *pshow, int aflag, long i, long len) | Bimage |
extract_slice(long nz) | Bimage |
extract_tetrahedron(Vector3< double > *tet, int fill_type=0, double fill=0) | Bimage |
extract_tiles(long nn, vector< Vector3< long >> &coords, Vector3< long > tile_size) | Bimage |
extract_tiles(long nn, Vector3< long > start, Vector3< long > region, Vector3< long > tile_size, Vector3< long > step_size, int exceed) | Bimage |
extract_tiles(long nn, Vector3< long > tile_size, double fraction=0.2) | Bimage |
extract_wrap(long nn, Vector3< double > loc, Vector3< long > size, Vector3< double > origin, Matrix3 mat) | Bimage |
extract_wrap(long nn, Vector3< long > size, Matrix3 mat) | Bimage | inline
extrude_cross_section(long length, double helix_rise, double helix_angle, int fill_type, double fill) | Bimage |
fft() | Bimage | inline
fft(fft_direction dir) | Bimage |
fft(fft_direction dir, bool norm_flag) | Bimage |
fft(fft_plan plan, bool norm_flag=1) | Bimage |
fft_back() | Bimage | inline
fft_back(fft_plan plan, bool norm_flag=1) | Bimage | inline
fft_setup(fft_direction dir, int opt=0) | Bimage |
filament_density(double width) | Bimage |
filament_width(long width, long lim_lo, long lim_hi) | Bimage |
file_name(string s) | Bimage | inline
file_name() | Bimage | inline
fill(double v) | Bimage | inline
fill_gaps(long step) | Bimage |
fill_value(double v) | Bimage |
filter_average(long kernel_size) | Bimage |
filter_average(Vector3< long > k) | Bimage |
filter_bilateral(double sigma1, double sigma2, int kernel_type, long kernel_radius) | Bimage |
filter_bilateral_chunk(Bimage *pkernel, double sigma2, int kernel_type, float *nudata, long i, long len, int first) | Bimage |
filter_dog(double sigma1, double sigma2) | Bimage |
filter_extremes() | Bimage |
filter_extremes(int mod_flag) | Bimage |
filter_gaussian(long kernel_size, double sigma) | Bimage |
filter_ortho(int type) | Bimage |
filter_peak(long kernel_size) | Bimage |
filter_rank(long kernel_size, double rank) | Bimage |
filter_rank_chunk(long kernel_size, double rank, float *nudata, long i, long len) | Bimage |
filter_rolling_ball(long radius, double scale) | Bimage |
filter_sinc() | Bimage |
find_center(Bimage *pmask, double hires, double lores, double radius, double sigma, int refine_flag) | Bimage |
find_cyclic_point_group(Bsymmetry *sym, int binfac, double hires, double lores) | Bimage |
find_helix_parameters(double angle_start, double angle_end, double angle_step, int bin, double hires, double lores, double radius) | Bimage |
find_helix_parameters(double rise_start, double rise_end, double rise_step, double angle_start, double angle_end, double angle_step, int bin, double radius) | Bimage |
find_peak(double radius=1e30, double sigma=0) | Bimage |
find_peaks(long kernelsize) | Bimage |
find_peaks(double excl_dist, long &ncoor, double &threshold_min, double &threshold_max, double pix_min=2, double pix_max=10) | Bimage |
find_point_group(Bsymmetry *sym, double angle_step, int binfac, double hires, double lores, int flags) | Bimage |
find_shift(Bimage *pref, Bimage *pmask, double hires, double lores, double radius, double sigma, int refine_flag) | Bimage |
find_shift(Bimage *pref, Bimage *pmask, double hires, double lores, double radius, double sigma, int refine_flag, double &cc) | Bimage |
find_shift(Bimage *pref, double hires, double lores, double radius, double sigma, int refine_flag, fft_plan planf, fft_plan planb) | Bimage |
find_shift(Bimage *pref, Bimage *pmask, double hires, double lores, double radius, double sigma, int refine_flag, fft_plan planf, fft_plan planb, double &cc) | Bimage |
find_shift(long nn, Bimage *pref, Bimage *pmask, double hi_res, double lo_res, double shift_limit, fft_plan planf, fft_plan planb) | Bimage |
find_shift_in_transform(double shift_limit) | Bimage |
find_shift_in_transform(long nn, Bimage *pref, double shift_limit) | Bimage |
find_symmetric_view(Bimage *ptemp, Bsymmetry *sym, double phi_step, double theta_step, double alpha_step, Vector3< double > shift) | Bimage |
find_template(Bimage *ptemp, Bimage *pmask, double hires, double lores, int bin, fft_plan planf, fft_plan planb) | Bimage |
fit_peak() | Bimage |
fix_type() | Bimage |
fourier_type() | Bimage | inline
fourier_type(FourierType tf) | Bimage | inline
friedel_apply() | Bimage |
friedel_check() | Bimage |
fsc(double hi_res, double sampling_ratio=1) | Bimage |
fsc(Bimage *p, double hi_res, double sampling_ratio=1) | Bimage |
fsc_dpr(double hi_res, double sampling_ratio=1, int flag=0) | Bimage |
fsc_local(Bimage *p, Bimage *pmask, double resolution, double *cutoff, int mask_level, int size, int pad, Vector3< long > vedge, int step=1, int taper=1, double fill=0) | Bimage |
fsc_shell(Bimage *p, double hi_res, double *cutoff, int thickness, int step, int minrad, int maxrad, int pad=1, int smooth=0, double fill=0) | Bimage |
fspace_2D_interpolate(Complex< float > cv, Vector3< double > m, double part_weight, int interp_type, Vector3< double > vscale) | Bimage |
fspace_amp_one() | Bimage |
fspace_amp_threshold(double threshold) | Bimage |
fspace_background() | Bimage |
fspace_bandpass(double res_hi, double res_lo=0, double width=0) | Bimage |
fspace_bandpass(double res_hi, double res_lo, double width, fft_plan planf, fft_plan planb) | Bimage |
fspace_default_bands(double res_lo, double res_hi) | Bimage |
fspace_fit_B_factor(double res_hi=0) | Bimage |
fspace_interpolate(long img_num, Vector3< double > m, FSI_Kernel *kernel) | Bimage |
fspace_maximum_radius(double resolution) | Bimage |
fspace_normalize() | Bimage |
fspace_normalize_radial(Bimage *pmask, double resolution=0, int flag=0) | Bimage |
fspace_pack_2D(Bimage *p, Matrix3 mat, double hi_res=0, double lo_res=0, double scale=1, double part_weight=1, int interp_type=0) | Bimage |
fspace_pack_2D(Bimage *p, View asu_view, Bsymmetry *sym, double hi_res=0, double lo_res=0, double scale=1, double part_weight=1, int interp_type=0) | Bimage |
fspace_pack_2D_into_central_section(Bimage *p, long ft_size, double scale, double hi_res, double lo_res, Matrix3 matr, Matrix3 mat) | Bimage |
fspace_pack_3D(Bimage *p, double hi_res=0, double threshold=0) | Bimage |
fspace_positive() | Bimage |
fspace_radial(long nn, long maxrad, int flag=0) | Bimage |
fspace_radial_power(double resolution) | Bimage |
fspace_reconstruction_add(Bimage *p) | Bimage |
fspace_reconstruction_snr() | Bimage |
fspace_reconstruction_stats(double resolution) | Bimage |
fspace_reconstruction_stats2(double resolution) | Bimage |
fspace_reconstruction_weigh() | Bimage |
fspace_resize(double scale, double res_hi, double res_lo) | Bimage |
fspace_resize(Bimage *pref) | Bimage |
fspace_scale(long maxrad, double *scale, Bimage *pmask=NULL) | Bimage |
fspace_scale(long nn, long maxrad, double *scale, Bimage *pmask=NULL) | Bimage |
fspace_scale(vector< double > &scale, Bimage *pmask=NULL) | Bimage |
fspace_scale(long nn, vector< double > &scale, Bimage *pmask=NULL) | Bimage |
fspace_sqrt_amp() | Bimage |
fspace_square_amp() | Bimage |
fspace_translate(Vector3< double > shift) | Bimage |
fspace_translate(long nn, Vector3< double > shift) | Bimage |
fspace_weigh(long maxrad, double *curve, int flag=0) | Bimage |
fspace_weigh(vector< double > &curve, int flag=0) | Bimage |
fspace_weigh(Bimage *pref, Bimage *pmask, double resolution=0) | Bimage |
fspace_weigh_B_factor(double B, double resolution=0) | Bimage |
fspace_weigh_C_curve(double resolution=0) | Bimage |
fspace_weigh_dose(long nn, double dose_per_frame, vector< double > critdose) | Bimage |
fspace_weigh_dose(double dose_per_frame) | Bimage |
fspace_weigh_FSC_curve(Bplot *plot, double resolution=0) | Bimage |
fspace_weigh_LoG(double resolution, double sigma) | Bimage |
fspace_weigh_ramp(double resolution, fft_plan planf, fft_plan planb) | Bimage |
fspace_weigh_ramp(double resolution, double axis, fft_plan planf, fft_plan planb) | Bimage |
fspace_weigh_RPS_curve(Bplot *plot, double resolution=0) | Bimage |
gaussian_sphere(long nn, Vector3< double > center, double sigma, double amp) | Bimage |
get(long nn, long xx, long yy, long zz, long cc=0) | Bimage |
get(long nn, Vector3< double > vox, long cc=0) | Bimage |
get(Bstring tag) | Bimage |
get_localtime() | Bimage | inline
get_time() | Bimage | inline
gradient_correction() | Bimage |
graph_segment(int type=1, Bimage *pmask=NULL, int connect_type=0, double complexity=0, long min_size=0, int return_type=0) | Bimage |
hanning_taper(double fill=0) | Bimage |
height(View *views, double threshold=0) | Bimage |
helical_cross_section(double helix_rise, double helix_angle, double scale, double hires) | Bimage |
helix_interpolate(long i, double helix_rise, double helix_angle, int zmin, int zmax, double radius, int norm_flag=1) | Bimage |
helix_segment_correlation(int thickness, double angle_start, double angle_end, double angle_step, int bin, double hires, double lores, double radius) | Bimage |
helix_segment_correlation_one(long i, double angle_start, double angle_end, double angle_step, int bin, double hires, double lores, double radius, fft_plan planf, fft_plan planb, double *cc) | Bimage |
helix_symmetrize(double helix_rise, double helix_angle, int dyad_axis, int zmin, int zmax, double radius, int norm_flag=1) | Bimage |
histogram(long bins, double &scale, double &offset) | Bimage |
histogram(long bins) | Bimage |
histogram_counts(int flags=0) | Bimage |
histogram_gauss_fit(long bins, long ngauss=1) | Bimage |
histogram_gauss_plot(long bins, long ngauss=1) | Bimage |
histogram_poisson_fit(long bins, int flag=0) | Bimage |
histogram_thresholds(double &tmin, double &tmax) | Bimage |
histomatch(Bimage *p, long bins) | Bimage |
identifier(Bstring s) | Bimage | inline
identifier() | Bimage | inline
image | Bimage |
image_size() | Bimage | inline
images() | Bimage | inline
images(long nn) | Bimage |
images_to_slices() | Bimage |
impose_superpixels(Bimage *pmask, vector< Bsuperpixel > &seg, int impose) | Bimage |
index(long nx, long ny) const | Bimage | inline
index(long nx, long ny, long nz) const | Bimage | inline
index(long nx, long ny, long nz, long nn) const | Bimage | inline
index(long nc, long nx, long ny, long nz, long nn) const | Bimage | inline
index(Vector3< long > vox, long nn) const | Bimage | inline
index(vector< long > vox, long nn) const | Bimage | inline
index_wrap(long nx, long ny, long nz) const | Bimage | inline
index_wrap(Vector3< long > coor) const | Bimage | inline
index_wrap(vector< long > coor) const | Bimage | inline
information() | Bimage |
integer_interpolation(int integer_factor) | Bimage |
integer_interpolation(int integer_factor, int odd) | Bimage |
intensities_phase_colored(double scale) | Bimage |
internal_volume(double threshold, int mask_out_freq) | Bimage |
interpolate(long cc, double xx, double yy=0, double zz=0, long nn=0, double fill=0) const | Bimage |
interpolate(double xx, double yy=0, double zz=0, long nn=0, double fill=0) const | Bimage | inline
interpolate(long cc, Vector3< double > vec, long nn=0, double fill=0) const | Bimage | inline
interpolate(Vector3< double > vec, long nn=0, double fill=0) const | Bimage | inline
interpolate(vector< double > vec, long nn=0, double fill=0) const | Bimage | inline
interpolate_gaps(long step) | Bimage |
interpolate_wrap(long cc, double xx, double yy=0, double zz=0, long nn=0) const | Bimage |
interpolate_wrap(double xx, double yy=0, double zz=0, long nn=0) const | Bimage | inline
interpolate_wrap(long cc, Vector3< double > vec, long nn=0) const | Bimage | inline
interpolate_wrap(Vector3< double > vec, long nn=0) const | Bimage | inline
inverse(double minval=0) | Bimage |
invert() | Bimage |
kernel_gaussian(double sigma, double max) | Bimage |
kernel_high(long i, long k=1) | Bimage | inline
kernel_high(long i, Vector3< long > k) | Bimage | inline
kernel_laplacian_of_gaussian(double sigma, double max) | Bimage |
kernel_low(long i, long k=1) | Bimage | inline
kernel_low(long i, Vector3< long > k) | Bimage | inline
kernel_max(long idx, long ksize) | Bimage |
kernel_max_neigbor(long idx, long ksize) | Bimage |
kernel_max_wrap(long idx, long ksize) | Bimage |
kmeans_segment(long nregion=2, double ratio=1) | Bimage |
label(string s) | Bimage | inline
label() | Bimage | inline
largest(Bimage *p) | Bimage |
level_mask_extract(Bimage *pmask) | Bimage |
levelmask_add(Bimage *pmask, int add_level=1) | Bimage |
levelmask_asymmetric_units(Bsymmetry *sym, int index) | Bimage |
levelmask_average_region_size() | Bimage |
levelmask_clean() | Bimage |
levelmask_collapse() | Bimage |
levelmask_color_by_size() | Bimage |
levelmask_colorize() | Bimage |
levelmask_dilate(int times) | Bimage |
levelmask_dilate() | Bimage |
levelmask_region_size() | Bimage |
levelmask_select(Bstring &select_list) | Bimage |
levelmask_select(long nn, Vector3< long > voxel) | Bimage |
levelmask_select(Bimage *pmask) | Bimage |
levelmask_size_histogram() | Bimage |
limit_levels(int nlevels) | Bimage |
line_powerspectra(fft_plan plan) | Bimage |
linear_fit(Bimage *p, Bimage *pmask, double max_exclude) | Bimage |
local_filter(Bimage *pmask, int mask_level, Bimage *resmap, int size, Vector3< long > vedge) | Bimage |
logarithm() | Bimage |
mask(Bimage *pmask, double fill) | Bimage |
mask_by_threshold(double threshold) | Bimage |
mask_by_thresholds(vector< double > threshold) | Bimage |
mask_close(int times=1) | Bimage |
mask_combine(Bimage *p, int operation) | Bimage |
mask_dilate(long times=1) | Bimage |
mask_dilate_erode(unsigned char dir) | Bimage |
mask_erode(long times=1) | Bimage |
mask_extract(Bimage *pmask) | Bimage |
mask_fill(Vector3< long > voxel) | Bimage |
mask_fspace_banded(vector< double > &band) | Bimage |
mask_fspace_resize(Vector3< long > nusize) | Bimage |
mask_interface_matrix(int img_num) | Bimage |
mask_invert() | Bimage |
mask_merge_delete(long min_size, long min_if) | Bimage |
mask_missing_cone(Vector3< double > origin, double mis_ang, double resolution) | Bimage |
mask_missing_find(Vector3< double > ori, double resolution, Bstring &mis_type) | Bimage |
mask_missing_pyramid(Vector3< double > origin, double tilt_axis1, double tilt_axis2, double tilt_neg1, double tilt_pos1, double tilt_neg2, double tilt_pos2, double resolution) | Bimage |
mask_missing_wedge(Vector3< double > origin, double tilt_axis, double tilt_neg, double tilt_pos, double resolution) | Bimage |
mask_open(int times=1) | Bimage |
mask_pack_plane(Matrix3 mat, double hi_res, double scale) | Bimage |
mask_plane(Vector3< double > origin, Vector3< double > normal) | Bimage |
mask_rectangle(double length, double width, double rect_angle, int wrap) | Bimage |
mask_region_interfaces(int reg_num) | Bimage |
mask_shell(Vector3< double > origin, double rad_min, double rad_max) | Bimage | inline
mask_split(long voxels_per_level) | Bimage |
mask_stats() | Bimage |
mask_symmetrize(Bsymmetry *sym) | Bimage |
mass_at_threshold(long img_num, double threshold, double rho) | Bimage |
mass_threshold(long img_num, double mol_weight, double rho) | Bimage |
max_in_kernel(long ksize) | Bimage |
maximum() | Bimage | inline
maximum(double d) | Bimage | inline
maximum_included_radius() | Bimage |
median_bin(int binning) | Bimage |
merge_amplitudes_and_phases(Bimage *pamp) | Bimage |
merge_amplitudes_and_phases(Bimage *pref, double res_hi, double res_lo) | Bimage |
meta_data() | Bimage | inline
meta_data_retain_one_image(long img_num) | Bimage |
meta_data_update() | Bimage |
minimum() | Bimage | inline
minimum(double d) | Bimage | inline
mirror() | Bimage |
moments(long max_order) | Bimage |
moments(long max_order, long nn) | Bimage |
montage(int first, int cols, int rows, int skip=0, int flipy=0) | Bimage |
multiply(long j, Complex< double > cv) | Bimage | inline
multiply(double v) | Bimage |
multiply(long nn, double v) | Bimage |
multiply(Bimage *p, double scale, double shift=0) | Bimage |
multiply(long nn, Bimage *p) | Bimage |
multiply(Bimage *p) | Bimage |
nad(double ht, long zw, double lambda, double C, double alpha) | Bimage |
nad_2D(double ht, double lambda, double C, double alpha) | Bimage |
next | Bimage |
noise_gaussian(double ravg=0, double rstd=1) | Bimage |
noise_logistical(double ravg, double rstd) | Bimage |
noise_poisson(double ravg) | Bimage |
noise_spectral(double alpha) | Bimage |
noise_uniform(double rmin, double rmax) | Bimage |
normalize(long imgnum, double average, double stdev, int norm_type, long bins) | Bimage |
normalize(double average, double stdev, int norm_type) | Bimage |
normalize_local(long kernel_size) | Bimage |
normalize_local(Vector3< long > kernel) | Bimage |
one_color(int color, double cmin, double cmax, int gray_extremes=0) | Bimage |
operator+(Bimage &p) | Bimage |
operator=(const Bimage &p) | Bimage |
operator[](string tag) | Bimage | inline
operator[](long j) const | Bimage |
orient(View *views) | Bimage |
origin(double ox, double oy, double oz) | Bimage | inline
origin(vector< double > vec) | Bimage | inline
origin(Vector3< double > vec) | Bimage | inline
origin(long nn, Vector3< double > vec) | Bimage | inline
origin(long nn, vector< double > ori) | Bimage | inline
origin(long nn, double ox, double oy, double oz) | Bimage | inline
orthogonal_slices(long nn, Vector3< long > voxel, Vector3< long > ext_size) | Bimage |
otsu_threshold(long bins) | Bimage |
pack_transform(unsigned char *data, FourierType tf) | Bimage |
pack_transform(int img_select, unsigned char *data, FourierType tf) | Bimage |
pack_two_in_complex(Bimage *p) | Bimage |
pad(long sz, int fill_type=0, double fill=0) | Bimage |
pad(Vector3< long > sz, int fill_type=0, double fill=0) | Bimage |
pad_copy(long sz, int fill_type=0, double fill=0) | Bimage |
pad_copy(Vector3< long > sz, int fill_type=0, double fill=0) | Bimage |
page_size() | Bimage | inline
page_size(long nx, long ny, long nz) | Bimage | inline
page_size(Vector3< long > vec) | Bimage | inline
page_size(vector< long > vec) | Bimage | inline
peak_sigma(long nn, Vector3< long > coor, long kernel_size) | Bimage |
percentiles() | Bimage |
periodic_averaging(Vector3< double > period) | Bimage |
phase_colour_wheel() | Bimage |
phase_difference(Bimage *p, int type=0, double res_hi=0, double res_lo=0) | Bimage |
phase_flip(Bimage *pd) | Bimage |
phase_shift(Vector3< double > shift) | Bimage |
phase_shift(long nn, Vector3< double > shift) | Bimage |
phase_shift_to_center() | Bimage |
phase_shift_to_origin() | Bimage |
place(long nn, Bimage *p, Vector3< double > loc, double radius=0, double scale=1, double shift=0, int operation=0) | Bimage |
place_central_part(Bimage *p, long nn) | Bimage |
place_with_addition(Bimage *p, long nn) | Bimage |
place_with_overlap(Bimage *p, long nn) | Bimage |
plot() | Bimage |
polar_power_spectrum(double resolution, long num_angle) | Bimage |
polar_transform(long nangles, long ann_min, long ann_max, long dann, long zmin, long zmax, long zinc) | Bimage |
power(double v) | Bimage |
power_spectrum(int flags=0) | Bimage |
powerspectrum_tiled(long img_num, Vector3< long > tile_size, int flags=0) | Bimage |
powerspectrum_tiled_and_tilted(Vector3< long > tile_size, double tilt_axis, double tilt_angle, double tilt_offset, double defocus, double iCL2, int flags=0) | Bimage |
powerspectrum_tilt_axis(long img_num, Vector3< long > tile_size, double tilt_axis, double tilt_offset, int flags=0) | Bimage |
powerspectrum_tilted(long img_num, Vector3< long > tile_size, double tilt_axis, double tilt_angle, double defocus, double iCL2, int flags=0) | Bimage |
pps_angular_correlation(Bimage *pref, double res_hi, double res_lo, long nang, fft_plan planf) | Bimage |
project(char axis, int flags=1) | Bimage |
project(View *view, int norm_flag=1) | Bimage |
project(View *view, double resolution, FSI_Kernel *kernel) | Bimage |
pure_color() | Bimage |
quadric(double *param) | Bimage |
quadric_correct(vector< double > param) | Bimage |
quadric_fit() | Bimage |
query(string &path) | Bimage | inline
R_factor(Bimage *p) | Bimage |
radial(long minrad, long maxrad, double rad_step=1, int wrap=0) | Bimage |
radial(long minrad, long maxrad, double rad_step, Bimage *pmask, int wrap=0) | Bimage |
radial(long minrad, long maxrad, double rad_step, double ellipticity, double angle, Bimage *pmask, int wrap=0) | Bimage |
radial_coverage(double threshold, double rad_step=1) | Bimage |
radial_fit(Bimage *pref) | Bimage |
radial_sections(double rad_start, double rad_end, double rad_step, double spherical_fraction, Bsymmetry *sym) | Bimage |
radial_shells() | Bimage |
radial_to_full(Vector3< long > nusize, Vector3< double > origin) | Bimage |
read_data(ifstream *fimg, int img_select, int sb, int vax, long pad) | Bimage |
real_size() | Bimage | inline
red_white_blue(double red_min, double white_min, double white_max, double blue_max) | Bimage |
refine_peak() | Bimage |
region_assign(Bimage *pmask, long idx, long region_number, double threshold, int sign) | Bimage |
region_flood(Bimage *pmask, double threshold_hi, double threshold_lo, double threshold_step, int fill_borders) | Bimage |
region_peaks(long kernel_size, double threshold, int flood=0, int wrap=0) | Bimage |
region_threshold_series(double threshold_first, double threshold_last, double threshold_step) | Bimage |
regions(double threshold, int sign) | Bimage |
relative_density(Bimage *pmask) | Bimage |
replace(Bimage *img) | Bimage |
replace(long nn, Bimage *img, long nr=0) | Bimage |
replace(long nn, Bimage *img, long nr, double fill) | Bimage |
replace_maxima(double threshold) | Bimage |
replicate_asymmetric_unit(Bsymmetry *sym) | Bimage |
rescale(double scale, double shift) | Bimage |
rescale(long nn, double scale, double shift) | Bimage |
rescale_to_avg_std(double nuavg, double nustd) | Bimage |
rescale_to_avg_std(long nn, double nuavg, double nustd) | Bimage |
rescale_to_avg_std(double nuavg, double nustd, Bimage *pmask) | Bimage |
rescale_to_min_max(double numin, double numax) | Bimage |
rescale_to_min_max(long nn, double numin, double numax) | Bimage |
resize(Vector3< long > nusize, Vector3< long > translate, int fill_type=0, double fill=0) | Bimage |
resize_copy(Vector3< long > nusize, Vector3< long > translate, int fill_type=0, double fill=0) | Bimage |
resize_wrap(Vector3< long > nusize, Vector3< long > translate) | Bimage |
resize_wrap_copy(Vector3< long > nusize, Vector3< long > translate) | Bimage |
reslice(const char *order) | Bimage | inline
reslice(Bstring order) | Bimage |
resolution_prepare(Bimage *p) | Bimage |
resolution_prepare(Bimage *p, fft_plan plan) | Bimage |
rgb(long j) | Bimage |
rgb_to_cmyk() | Bimage |
rgb_to_rgba() | Bimage |
rgba(long j) | Bimage |
rgba_to_rgb() | Bimage |
rotate() | Bimage |
rotate(double angle) | Bimage |
rotate(Vector3< double > axis, double angle) | Bimage |
rotate(View view) | Bimage |
rotate(Vector3< double > translate, View view) | Bimage |
rotate(Matrix3 mat) | Bimage |
rotate(Vector3< double > translate, Matrix3 mat) | Bimage |
rotate(Vector3< long > nusize) | Bimage |
rotate(Vector3< long > nusize, double angle) | Bimage |
rotate(Vector3< long > nusize, Vector3< double > axis, double angle) | Bimage |
rotate(Vector3< long > nusize, View view) | Bimage |
rotate(Vector3< long > nusize, Vector3< double > translate, View view) | Bimage |
rotate(Vector3< long > nusize, Matrix3 mat) | Bimage |
rotate_and_add(Bimage *p, Vector3< double > origin, View view) | Bimage |
rotate_correlate(Vector3< double > axis, double angle) | Bimage |
rotate_cross_correlate(Bimage *pref, View view, double hires, double lores, double search_radius, Bimage *pmask, double &cc, fft_plan planf, fft_plan planb) | Bimage |
rotate_cross_correlate_two_way(Bimage *pref, double angle, double res_hi, double res_lo, double shift_limit, fft_plan planf, fft_plan planb) | Bimage |
rotate_find_shift(Matrix3 mat, double hires, double lores, double radius, double sigma, int refine_flag, fft_plan planf, fft_plan planb, double &cc) | Bimage |
rotate_height(Matrix3 mat, Vector3< double > translate, double threshold=0) | Bimage |
rotate_project(Matrix3 mat, Vector3< double > translate, double radial_cutoff, int norm_flag=1) | Bimage |
rotate_to_axis(Bsymmetry *sym, long axis, long axis_flag) | Bimage |
sampling() | Bimage | inline
sampling(long nn, Vector3< double > u) | Bimage | inline
sampling(long nn, double ux, double uy, double uz) | Bimage | inline
sampling(Vector3< double > u) | Bimage | inline
sampling(double ux, double uy, double uz) | Bimage | inline
sampling(long nn) | Bimage | inline
scale_to_reference(Bimage *pref, Bimage *pmask, double scalemin, double scalemax, double step) | Bimage |
scale_to_reference(Bimage *pref, Bimage *pmask=NULL) | Bimage |
scale_to_same_size(Bimage *pref) | Bimage |
seamed_helix_symmetrize(double helix_rise, double helix_angle, double seam_shift, int dyad_axis, int zmin, int zmax, double radius, int norm_flag) | Bimage |
search_views(Bimage *ptemp, View *view, double hires, double lores, double search_radius, Bimage *pmask, View &currview, Vector3< double > &currshift) | Bimage |
search_volume(Bimage *ptemp, View *view, double alpha, double alpha_step, double hires, double lores, Bimage *pmask, double threshold) | Bimage |
search_volume_view(Bimage *ptemp, View view, double hires, double lores, Bimage *pmask, double threshold, Bimage *pfit) | Bimage |
select_images(Bstring list) | Bimage |
set(long j, double v) | Bimage |
set(long j, Complex< double > cv) | Bimage |
set(long j, RGB< double > color) | Bimage |
set(long j, RGBA< double > color) | Bimage |
set(long j, CMYK< double > color) | Bimage |
set(long j, Vector3< double > vec) | Bimage |
set(long j, View view) | Bimage |
set_max(double xx, double yy, double zz, long nn, double v) | Bimage |
set_time(time_t t) | Bimage | inline
set_time(tm *t) | Bimage | inline
shape(int type, Vector3< long > rect, Vector3< double > start, double width, int fill_type=0, double fill=0) | Bimage |
shape(long nn, int type, Vector3< long > rect, Vector3< double > start, double width, int fill_type=0, double fill=0) | Bimage |
shell(Vector3< double > center, double minrad, double maxrad, double width, int fill_type=0, double fill=0) | Bimage |
shell(long nn, Vector3< double > center, double minrad, double maxrad, double width, int fill_type=0, double fill=0) | Bimage |
shell_wrap(long nn, Vector3< double > center, double minrad, double maxrad, double width, int fill_type=0, double fill=0) | Bimage |
shift(Vector3< double > vec, int fill_type=0, double fill=0) | Bimage |
shift(long nn, Vector3< double > vec, int fill_type=0, double fill=0) | Bimage |
shift_background(double bkg) | Bimage |
shift_wrap(Vector3< double > vec) | Bimage |
shift_wrap(long nn, Vector3< double > vec) | Bimage |
show_image() | Bimage | inline
show_image(long nn) | Bimage | inline
show_maximum() | Bimage | inline
show_maximum(double v) | Bimage | inline
show_minimum() | Bimage | inline
show_minimum(double v) | Bimage | inline
show_scale() | Bimage | inline
show_scale(double scale) | Bimage | inline
show_slice() | Bimage | inline
show_slice(long nz) | Bimage | inline
shrink_wrap(Vector3< long > nusize, Vector3< long > translate) | Bimage |
simple_to_complex() | Bimage |
simple_to_rgb() | Bimage |
simple_to_rgba() | Bimage |
size() const | Bimage | inline
size(long nx, long ny, long nz) | Bimage | inline
size(Vector3< long > vec) | Bimage | inline
size(vector< long > vec) | Bimage | inline
sizeX(long nx) | Bimage | inline
sizeX() const | Bimage | inline
sizeY(long ny) | Bimage | inline
sizeY() const | Bimage | inline
sizeZ(long nz) | Bimage | inline
sizeZ() const | Bimage | inline
slices_to_images() | Bimage |
smallest(Bimage *p) | Bimage |
snvariance(double snradius) | Bimage |
space_group() | Bimage | inline
space_group(unsigned int grp) | Bimage | inline
sphere(Vector3< double > center, double radius, double width=0, int fill_type=0, double fill=0) | Bimage |
split_channels() | Bimage |
square() | Bimage |
square_root() | Bimage |
standard_deviation() | Bimage | inline
standard_deviation(double d) | Bimage | inline
statistics() | Bimage |
statistics(long img_num) | Bimage |
statistics(Bimage *pmask, double &regavg, double &regstd) | Bimage |
stats_in_mask(long nn, Bimage *pmask) | Bimage |
stats_in_poly(long nn, int nvert, Vector3< double > *poly, double &vavg, double &vstd) | Bimage |
stats_in_shape(long nn, int type, Vector3< long > start, Vector3< long > end, double &vavg, double &vstd) | Bimage |
stats_within_radii(long nn, Vector3< double > loc, double rad_min, double rad_max, double &vavg, double &vstd) | Bimage |
subimage_information() | Bimage |
subtract(Bimage *p) | Bimage |
subtract_background() | Bimage |
sum(long m, Bimage **p) | Bimage |
sum_images() | Bimage |
superpixels(long step, double colorweight=0.2, long iterations=10, double stop=1) | Bimage |
superpixels_from_mask(long cc, long step) | Bimage |
superpixels_update(Bimage *pmask, vector< long > vstep, double colorweight, vector< Bsuperpixel > &seg) | Bimage |
surface_to_topograph(double threshold, int dir=0) | Bimage |
symmetrize(Bstring &symmetry_string, int flag) | Bimage | inline
symmetrize(Bsymmetry *sym, int flag) | Bimage | inline
symmetrize(Bstring &symmetry_string, View ref_view, int flag) | Bimage | inline
symmetrize(Bsymmetry *sym, View ref_view, int flag) | Bimage |
symmetrize_cylinder(int flag) | Bimage |
symmetrize_cylinder() | Bimage |
symmetry() | Bimage | inline
symmetry(string grp) | Bimage | inline
symmetry_equivalent(Bimage *ptemp, Bimage *pmask, Bsymmetry *sym) | Bimage |
symmetry_equivalent_cyclic(Bimage *pref, Bimage *pmask, Bsymmetry *sym) | Bimage |
tile_coordinates(Vector3< long > &start, Vector3< long > &region, Vector3< long > &tile_size, Vector3< long > &step_size, int exceed) | Bimage |
tile_mask(long step) | Bimage |
to_mask() | Bimage | inline
to_mask(double threshold) | Bimage |
topograph_to_surface(Bimage *psd, long nz, double density, double resolution) | Bimage |
transform(Vector3< double > scale, Vector3< double > origin, Vector3< double > translate, Matrix3 mat, int fill_type=0, double fill=0) | Bimage |
transform(Vector3< long > nusize, Vector3< double > scale, Vector3< double > origin, Vector3< double > translate, Matrix3 mat, int fill_type=0, double fill=0) | Bimage |
transform(long nn, Vector3< long > nusize, Vector3< double > scale, Vector3< double > origin, Vector3< double > translate, Matrix3 mat, int fill_type=0, double fill=0) | Bimage |
transform_lines() | Bimage |
transform_voxel(long i, Bimage *pt, long nn, Vector3< double > oldorigin, Vector3< double > nuorigin, Matrix3 affmat, double fill) | Bimage |
truncate(double minim, double maxim, double setmin, double setmax) | Bimage |
truncate_to_avg(double minim, double maxim) | Bimage |
truncate_to_background(double minim, double maxim) | Bimage |
truncate_to_min_max(double minim, double maxim) | Bimage |
tube_interpolate(long i, int h, int k, double latconst, int zmin, int zmax, double radius, int norm_flag=1) | Bimage |
tube_symmetrize(int h, int k, double latconst, int zmin, int zmax, double radius, int norm_flag=1) | Bimage |
unit_cell(UnitCell uc) | Bimage | inline
unit_cell() | Bimage | inline
unpack_combined_transform() | Bimage |
unpack_transform(unsigned char *data, FourierType tf) | Bimage |
unpack_transform(int img_select, unsigned char *data, FourierType tf) | Bimage |
update_from_meta_data() | Bimage |
values(long i) | Bimage | inline
values(long i, vector< double > val) | Bimage | inline
values(long nn, Vector3< double > vox) | Bimage |
variance(long kernel_size) | Bimage |
variance(Bimage *pweight) | Bimage |
variance_mask(long kernel_size, double lowvar=1e-6, int bkg_flag=0) | Bimage |
variance_threshold(double lowvar) | Bimage |
vector3(long j) | Bimage |
view(double vx, double vy, double vz, double va) | Bimage | inline
view(View vw) | Bimage | inline
voxel_size() | Bimage | inline
within_boundaries(Vector3< double > loc) | Bimage | inline
within_boundaries(long xx, long yy, long zz) | Bimage | inline
write(Bstring &fn) | Bimage |
zero_fourier_origin() | Bimage |
zero_origin() | Bimage |
~Bimage() | Bimage |