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Add average of power spectra for helical samples. #1185

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4eb1257
Add average of power spectra similar to that of cryosparc job-average…
estrozi Sep 26, 2024
e281012
Merge branch '3dem:ver5.0' into ver5.0
estrozi Apr 2, 2025
3273ebe
PR fixes according https://github.com/3dem/relion/pull/1185#discussio…
estrozi Apr 2, 2025
718c708
PR fixes according https://github.com/3dem/relion/pull/1185#issuecomm…
estrozi Apr 2, 2025
8f5e39c
PR fixes according https://github.com/3dem/relion/pull/1185#issuecomm…
estrozi Apr 2, 2025
bc5b69a
log-norm of PS
estrozi May 12, 2025
6f299b6
Merge branch '3dem:ver5.0' into ver5.0
estrozi Nov 2, 2025
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60 changes: 55 additions & 5 deletions src/displayer.cpp
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -301,7 +301,7 @@ int DisplayBox::unSelect()
int basisViewerWindow::fillCanvas(int viewer_type, MetaDataTable &MDin, ObservationModel *obsModel, EMDLabel display_label, EMDLabel text_label, bool _do_read_whole_stacks, bool _do_apply_orient,
RFLOAT _minval, RFLOAT _maxval, RFLOAT _sigma_contrast, RFLOAT _scale, RFLOAT _ori_scale, int _ncol, long int max_nr_images, RFLOAT lowpass, RFLOAT highpass, bool _do_class,
MetaDataTable *_MDdata, int _nr_regroup, bool _do_recenter, bool _is_data, MetaDataTable *_MDgroups,
bool do_allow_save, FileName fn_selected_imgs, FileName fn_selected_parts, int max_nr_parts_per_class)
bool do_allow_save, FileName fn_selected_imgs, FileName fn_selected_parts, int max_nr_parts_per_class, bool _show_fourier_amplitudes, bool _show_fourier_phase_angles)
{
// Scroll bars
Fl_Scroll scroll(0, 0, w(), h());
Expand Down Expand Up @@ -332,6 +332,8 @@ int basisViewerWindow::fillCanvas(int viewer_type, MetaDataTable &MDin, Observat
canvas.fn_selected_imgs= fn_selected_imgs;
canvas.fn_selected_parts = fn_selected_parts;
canvas.max_nr_parts_per_class = max_nr_parts_per_class;
canvas.show_fourier_amplitudes = _show_fourier_amplitudes;
canvas.show_fourier_phase_angles = _show_fourier_phase_angles;
canvas.fill(MDin, obsModel, display_label, text_label, _do_apply_orient, _minval, _maxval, _sigma_contrast, _scale, _ncol, _do_recenter, max_nr_images, lowpass, highpass);
canvas.nr_regroups = _nr_regroup;
canvas.do_recenter = _do_recenter;
Expand Down Expand Up @@ -579,6 +581,12 @@ void basisViewerCanvas::fill(MetaDataTable &MDin, ObservationModel *obsModel, EM
if (highpass > 0. && have_optics_group)
highPassFilterMap(img(), highpass, angpix);

if(this->show_fourier_amplitudes)
{
amplitudeOrPhaseMap(img(), img(), AMPLITUDE_MAP);
} else {
if(this->show_fourier_phase_angles) amplitudeOrPhaseMap(img(), img(), PHASE_MAP);
}
// Dont change the user-provided _minval and _maxval in the getImageContrast routine!
RFLOAT myminval = _minval;
RFLOAT mymaxval = _maxval;
Expand All @@ -604,6 +612,11 @@ void basisViewerCanvas::fill(MetaDataTable &MDin, ObservationModel *obsModel, EM
int xcoor = icol * xsize_box;

DisplayBox* my_box = new DisplayBox(xcoor, ycoor, xsize_box, ysize_box, "");
if(this->show_fourier_phase_angles)
{
myminval = -180.0;
mymaxval = 180.0;
}
my_box->setData(img(), MDin.getObject(my_ipos), my_ipos, myminval, mymaxval, _scale, false);
if (MDin.containsLabel(text_label))
{
Expand Down Expand Up @@ -717,15 +730,17 @@ int multiViewerCanvas::handle(int ev)
{ "Show Fourier phase angles (2x)" },
{ "Show helical layer line profile" },
{ "Show particles from selected classes" },
{ "Show Fourier amplitudes (2x) from selected classes" },
{ "Show Fourier phase angles (2x) from selected classes" },
{ "Set selection type" },
{ "Save selected classes" }, // idx = 14; change below when re-ordered!!
{ "Save selected classes" }, // idx = 16; change below when re-ordered!!
{ "Quit" },
{ 0 }
};

if (!do_allow_save)
{
rclick_menu[14].deactivate();
rclick_menu[16].deactivate();
}

const Fl_Menu_Item *m = rclick_menu->popup(Fl::event_x(), Fl::event_y(), 0, 0, 0);
Expand Down Expand Up @@ -759,6 +774,10 @@ int multiViewerCanvas::handle(int ev)
setSelectionType();
else if ( strcmp(m->label(), "Show particles from selected classes") == 0 )
showSelectedParticles(current_selection_type);
else if ( strcmp(m->label(), "Show Fourier amplitudes (2x) from selected classes") == 0 )
showSelectedFourierAmplitudes(current_selection_type);
else if ( strcmp(m->label(), "Show Fourier phase angles (2x) from selected classes") == 0 )
showSelectedFourierPhaseAngles(current_selection_type);
else if ( strcmp(m->label(), "Save selected classes") == 0 )
{
saveBackupSelection();
Expand Down Expand Up @@ -1432,6 +1451,38 @@ void multiViewerCanvas::showSelectedParticles(int save_selected)
std::cout <<" No classes selected. First select one or more classes..." << std::endl;
}

void multiViewerCanvas::showSelectedFourierAmplitudes(int save_selected)
{
MetaDataTable MDpart;
makeStarFileSelectedParticles(save_selected, MDpart);
int nparts = MDpart.numberOfObjects();
if (nparts > 0)
{
basisViewerWindow win(MULTIVIEW_WINDOW_WIDTH, MULTIVIEW_WINDOW_HEIGHT, "Amplitudes in the selected classes");
win.fillCanvas(MULTIVIEWER, MDpart, obsModel, EMDL_IMAGE_NAME, text_label, do_read_whole_stacks, do_apply_orient, 0., 0., 0., boxes[0]->scale, ori_scale, ncol,
multi_max_nr_images, 0, 0, false, MDdata, nr_regroups, do_recenter, false, MDgroups,
do_allow_save, fn_selected_imgs, fn_selected_parts, max_nr_parts_per_class, true);
}
else
std::cout <<" No classes selected. First select one or more classes..." << std::endl;
}

void multiViewerCanvas::showSelectedFourierPhaseAngles(int save_selected)
{
MetaDataTable MDpart;
makeStarFileSelectedParticles(save_selected, MDpart);
int nparts = MDpart.numberOfObjects();
if (nparts > 0)
{
basisViewerWindow win(MULTIVIEW_WINDOW_WIDTH, MULTIVIEW_WINDOW_HEIGHT, "Phase angles in the selected classes");
win.fillCanvas(MULTIVIEWER, MDpart, obsModel, EMDL_IMAGE_NAME, text_label, do_read_whole_stacks, do_apply_orient, 0., 0., 0., boxes[0]->scale, ori_scale, ncol,
multi_max_nr_images, 0, 0, false, MDdata, nr_regroups, do_recenter, false, MDgroups,
do_allow_save, fn_selected_imgs, fn_selected_parts, max_nr_parts_per_class, false, true);
}
else
std::cout <<" No classes selected. First select one or more classes..." << std::endl;
}

void multiViewerCanvas::saveTrainingSet()
{
FileName fn_rootdir = "/net/dstore1/teraraid3/scheres/trainingset/";
Expand Down Expand Up @@ -2778,7 +2829,6 @@ void Displayer::initialise()
if ( (ZSIZE(img()) > 1) || (NSIZE(img()) > 1) )
REPORT_ERROR("Displayer::initialise ERROR: cannot display Fourier maps for 3D images or stacks!");
}

}

int Displayer::runGui()
Expand Down Expand Up @@ -2994,7 +3044,7 @@ void Displayer::run()
basisViewerWindow win(MULTIVIEW_WINDOW_WIDTH, MULTIVIEW_WINDOW_HEIGHT, fn_in.c_str());
win.fillCanvas(MULTIVIEWER, MDin, &obsModel, display_label, text_label, do_read_whole_stacks, do_apply_orient, minval, maxval, sigma_contrast, scale, ori_scale, ncol,
max_nr_images, lowpass, highpass, do_class, &MDdata, nr_regroups, do_recenter, fn_in.contains("_data.star"), &MDgroups,
do_allow_save, fn_selected_imgs, fn_selected_parts, max_nr_parts_per_class);
do_allow_save, fn_selected_imgs, fn_selected_parts, max_nr_parts_per_class, show_fourier_amplitudes, show_fourier_phase_angles);
}
else
{
Expand Down
9 changes: 8 additions & 1 deletion src/displayer.h
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ class basisViewerWindow : public Fl_Window
RFLOAT _scale, RFLOAT _ori_scale, int _ncol, long int max_nr_images = -1, RFLOAT lowpass = -1.0 , RFLOAT highpass = -1.0,
bool do_class = false, MetaDataTable *MDdata = NULL,
int _nr_regroup = -1, bool do_recenter = false, bool _is_data = false, MetaDataTable *MDgroups = NULL,
bool do_allow_save = false, FileName fn_selected_imgs="", FileName fn_selected_parts="", int max_nr_parts_per_class = -1);
bool do_allow_save = false, FileName fn_selected_imgs="", FileName fn_selected_parts="", int max_nr_parts_per_class = -1, bool _show_fourier_amplitudes = false, bool _show_fourier_phase_angles = false);
int fillSingleViewerCanvas(MultidimArray<RFLOAT> image, RFLOAT _minval, RFLOAT _maxval, RFLOAT _sigma_contrast, RFLOAT _scale);
int fillPickerViewerCanvas(MultidimArray<RFLOAT> image, RFLOAT _minval, RFLOAT _maxval, RFLOAT _sigma_contrast, RFLOAT _scale, RFLOAT _coord_scale,
int _particle_radius, bool do_startend = false, FileName _fn_coords = "",
Expand All @@ -168,6 +168,11 @@ class basisViewerCanvas : public Fl_Widget
int ysize_box;
int xoff;
int yoff;
// Show Fourier amplitudes?
bool show_fourier_amplitudes;

// Show Fourier phase angles?
bool show_fourier_phase_angles;

// To get positions in scrolled canvas...
Fl_Scroll *scroll;
Expand Down Expand Up @@ -277,6 +282,8 @@ class multiViewerCanvas : public basisViewerCanvas
void makeStarFileSelectedParticles(int save_selected, MetaDataTable &MDpart);
void saveSelectedParticles(int save_selected);
void showSelectedParticles(int save_selected);
void showSelectedFourierAmplitudes(int save_selected);
void showSelectedFourierPhaseAngles(int save_selected);
void saveTrainingSet();
void saveSelected(int save_selected);
void saveBackupSelection();
Expand Down
15 changes: 14 additions & 1 deletion src/fftw.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1700,14 +1700,27 @@ void amplitudeOrPhaseMap(const MultidimArray<RFLOAT > &v, MultidimArray<RFLOAT >
out.setXmippOrigin();
out.initZeros(XYdim, XYdim);
maxr2 = (XYdim - 1) * (XYdim - 1) / 4;
//Get maximum value for PS log-normalization. The normalisation of the transform is undone.
RFLOAT val_max = -99999;
unsigned long int size = MULTIDIM_SIZE(out);
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM2D(Faux)
{
if ( (ip > STARTINGY(out)) && (ip < FINISHINGY(out))
&& (jp > STARTINGX(out)) && (jp < FINISHINGX(out))
&& ((ip * ip + jp * jp) < maxr2) )
{
if(FFTW2D_ELEM(Faux, ip, jp).abs()*size > val_max) val_max = FFTW2D_ELEM(Faux, ip, jp).abs()*size;
}
}
RFLOAT logOfMax = log10f(val_max+1.0f);
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM2D(Faux)
{
if ( (ip > STARTINGY(out)) && (ip < FINISHINGY(out))
&& (jp > STARTINGX(out)) && (jp < FINISHINGX(out))
&& ((ip * ip + jp * jp) < maxr2) )
{
if (output_map_type == AMPLITUDE_MAP)
val = FFTW2D_ELEM(Faux, ip, jp).abs();
val = log10f(FFTW2D_ELEM(Faux, ip, jp).abs()*size+1.0f)/logOfMax;
else if (output_map_type == PHASE_MAP)
val = (180.) * (FFTW2D_ELEM(Faux, ip, jp).arg()) / PI;
else
Expand Down