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tomo: respect _rlnTomoVisibleFrames in particle reconstruction #1344

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tomo: respect _rlnTomoVisibleFrames in particle reconstruction #1344

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35 changes: 34 additions & 1 deletion src/jaz/tomography/programs/reconstruct_particle.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -198,6 +198,8 @@ void ReconstructParticleProgram::processTomograms(
const int s = dataImgFS[0].ydim;
const int sh = s/2 + 1;
const int tc = tomoIndices.size();
const bool has_explicit_visible_frames =
particleSet.partTable.containsLabel(EMDL_TOMO_VISIBLE_FRAMES);

if (verbosity > 0 && !per_tomogram_progress)
{
Expand Down Expand Up @@ -343,7 +345,38 @@ void ReconstructParticleProgram::processTomograms(
part_id, fc, tomogram.centre, tomogram.optics.pixelSize);
std::vector<d4Matrix> projCut(fc), projPart(fc);

const std::vector<bool> isVisible = tomogram.determineVisiblity(traj, s/2.0);
std::vector<bool> isVisible = tomogram.determineVisiblity(traj, s/2.0);

// Intersect geometric visibility with the explicit per-particle
// _rlnTomoVisibleFrames mask that subtomo writes when --max_dose
// (or any frame filter) was used at extraction. Without this,
// reconstruction silently includes frames that were excluded
// from the 2D stacks and from Refine3D alignment, so the
// per-particle CTF + dose-weight math uses a different frame
// set than the data on disk. exp_model.cpp's "Add only the
// visible images for this particle" loop is the authoritative
// pattern that this matches.
if (has_explicit_visible_frames)
{
const std::vector<int> explicitVisible =
particleSet.getVisibleFrames(part_id);

if ((int)explicitVisible.size() != fc)
{
REPORT_ERROR_STR(
"reconstruct_particle: bad "
<< EMDL::label2Str(EMDL_TOMO_VISIBLE_FRAMES)
<< " length for particle "
<< particleSet.getName(part_id)
<< "; expected " << fc
<< " frames, found " << explicitVisible.size());
}

for (int f = 0; f < fc; f++)
{
isVisible[f] = isVisible[f] && (explicitVisible[f] != 0);
}
}

const bool circle_crop = do_circle_crop;

Expand Down