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Merge pull request #3 from 3dem/master
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debugged subtract option for Sami
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@scheres
scheres authored Oct 15, 2020
2 parents 3405ccc + 97a38e2 commit 4f6daec
Showing 1 changed file with 41 additions and 12 deletions.
53 changes: 41 additions & 12 deletions src/apps/particle_reposition.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ class particle_reposition_parameters
int general_section = parser.addSection("Options");

fn_in = parser.getOption("--i", "Input STAR file with rlnMicrographName's ");
fn_out = parser.getOption("--o", "Output rootname, to be added to input micrograph names", "reposition");
fn_out = parser.getOption("--o", "Output rootname, to be added to input micrograph names", "");
fn_odir = parser.getOption("--odir", "Output directory (default is same as input micrographs directory", "");
fn_opt = parser.getOption("--opt", "Optimiser STAR file with the 2D classes or 3D maps to be repositioned");
fn_dat = parser.getOption("--data", "Data STAR file with selected particles (default is to use all particles)", "");
Expand All @@ -67,22 +67,26 @@ class particle_reposition_parameters

void run()
{

if (fn_out == "" && fn_odir == "")
REPORT_ERROR("ERROR: You need to provide either --o or --odir");

if (fn_odir.length() > 0 && fn_odir[fn_odir.length()-1] != '/') fn_odir += "/";

int xdim, ydim, radius;
MetaDataTable DFi, DFopt;
MetaDataTable DFi, DFopt, MDmics_out;
ObservationModel::loadSafely(fn_in, obsModelMics, DFi, "micrographs");

MlOptimiser optimiser;
optimiser.do_preread_images = false;

std::cerr << "Reading optimiser ..." << std::endl;
optimiser.read(fn_opt);
optimiser.mymodel.setFourierTransformMaps(false);
radius = optimiser.particle_diameter / (2. * optimiser.mymodel.pixel_size);

// Use a user-provided subset of particles instead of all of them?
if (fn_dat != "")
{
std::cerr <<"Reading data ..." << std::endl;
std::cout <<" Reading data ..." << std::endl;
MetaDataTable MDdata;
MDdata.read(fn_dat);
optimiser.mydata.MDimg = MDdata;
Expand All @@ -97,16 +101,17 @@ class particle_reposition_parameters
FOR_ALL_OBJECTS_IN_METADATA_TABLE(DFi)
{

FileName fn_mic, fn_mic_out, fn_coord_out;
FileName fn_mic, fn_mic_out;
DFi.getValue(EMDL_MICROGRAPH_NAME, fn_mic);
fn_mic_out = fn_mic.insertBeforeExtension("_" + fn_out);
if (fn_out != "") fn_mic_out = fn_mic.insertBeforeExtension("_" + fn_out);
else fn_mic_out = fn_mic;
if (fn_odir != "")
{
FileName fn_pre, fn_jobnr, fn_post;
if (decomposePipelineFileName(fn_mic_out, fn_pre, fn_jobnr, fn_post))
fn_mic_out = fn_odir + "/" + fn_post;
fn_mic_out = fn_odir + fn_post;
else
fn_mic_out = fn_odir + "/" + fn_mic_out;
fn_mic_out = fn_odir + fn_mic_out;
FileName fn_onlydir = fn_mic_out.beforeLastOf("/");
if (fn_onlydir != fn_prevdir)
{
Expand All @@ -115,7 +120,6 @@ class particle_reposition_parameters
fn_prevdir = fn_onlydir;
}
}
fn_coord_out = fn_mic_out.withoutExtension()+ "_coord.star";

FourierTransformer transformer;
MetaDataTable MDcoord;
Expand Down Expand Up @@ -147,6 +151,9 @@ class particle_reposition_parameters
if (mic_pixel_size<0.)
REPORT_ERROR("ERROR: could not find correct optics group in micrograph star file...");

FileName fn_mic_pre, fn_mic_jobnr, fn_mic_post;
decomposePipelineFileName(fn_mic, fn_mic_pre, fn_mic_jobnr, fn_mic_post);

// Loop over all particles
bool found_one = false;
for (long int part_id = 0; part_id < optimiser.mydata.numberOfParticles(); part_id++)
Expand All @@ -156,10 +163,15 @@ class particle_reposition_parameters
RFLOAT my_pixel_size = optimiser.mydata.getImagePixelSize(part_id, 0);
int my_image_size = optimiser.mydata.getOpticsImageSize(optics_group);

if (do_subtract && fabs(my_pixel_size - mic_pixel_size) > 1e-6)
REPORT_ERROR("ERROR: subtract code has only been validated with same pixel size for particles and micrographs... Sorry!");

FileName fn_mic2;
optimiser.mydata.MDimg.getValue(EMDL_MICROGRAPH_NAME, fn_mic2, ori_img_id);
FileName fn_mic2_pre, fn_mic2_jobnr, fn_mic2_post;
decomposePipelineFileName(fn_mic2, fn_mic2_pre, fn_mic2_jobnr, fn_mic2_post);

if (fn_mic2 == fn_mic)
if (fn_mic2_post == fn_mic_post)
{

found_one = true;
Expand Down Expand Up @@ -369,6 +381,7 @@ class particle_reposition_parameters
Imic_sum.xinit = -ROUND(xcoord);
Imic_sum.yinit = -ROUND(ycoord);
Imic_sum.zinit = -ROUND(zcoord);
radius = optimiser.particle_diameter / (2. * mic_pixel_size);
FOR_ALL_ELEMENTS_IN_ARRAY3D(Mpart_mic)
{
long int idx = ROUND(sqrt(k*k + i*i + j*j));
Expand All @@ -381,7 +394,7 @@ class particle_reposition_parameters
if (kp >= 0 && kp < ZSIZE(Imic_sum) && ip >= 0 && ip < YSIZE(Imic_sum) && jp >= 0 && jp < XSIZE(Imic_sum) )
{
A3D_ELEM(Imic_out(), k, i, j) += norm_factor * A3D_ELEM(Mpart_mic, k, i, j);
A3D_ELEM(Imic_sum, k, i, j) += norm_factor;
A3D_ELEM(Imic_sum, k, i, j) += 1.;
}
}
}
Expand Down Expand Up @@ -416,17 +429,33 @@ class particle_reposition_parameters
// Write out the new micrograph
Imic_out.write(fn_mic_out);

MDmics_out.addObject();
MDmics_out.setObject(DFi.getObject());
MDmics_out.setValue(EMDL_MICROGRAPH_NAME, fn_mic_out);

// Also write out a STAR file with the particles used
FileName fn_coord_out = fn_mic_out.withoutExtension()+ "_coord.star";
MDcoord.write(fn_coord_out);
MDcoord.clear();
}
else
{
MDmics_out.addObject();
MDmics_out.setObject(DFi.getObject());
}

if (imgno%barstep==0) progress_bar(imgno);
imgno++;

} // end loop over input MetadataTable
progress_bar(DFi.numberOfObjects());


FileName fn_star_out = fn_odir + "micrographs_reposition.star";
if (fn_out != "") fn_star_out = fn_star_out.insertBeforeExtension("_" + fn_out);
std::cout << "Writing out star file with the new micrographs: " << fn_star_out << std::endl;
obsModelMics.save(MDmics_out, fn_star_out, "micrographs");

std::cout << " Done!" << std::endl;
}// end run function
};
Expand Down

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