From 832a4060f65efbcb55b7c06abdf9a856d2a9ca8f Mon Sep 17 00:00:00 2001
From: Amin Khosrozadeh <amin.khosrozadeh@unibe.ch>
Date: Wed, 20 May 2026 18:16:14 +0200
Subject: [PATCH] tomo: respect _rlnTomoVisibleFrames in particle
 reconstruction

reconstruct_particle determined per-tilt particle visibility from geometry
only (Tomogram::determineVisiblity on the projection trajectory). This
ignored the explicit visibility mask written by subtomo at extract time
(rlnTomoVisibleFrames in particles.star).

When Extract runs with --max_dose, the 2D-stacks contain only the
dose-filtered frames; ml_optimiser (Refine3D / Class3D) aligns only those
frames (exp_model.cpp 'Add only the visible images for this particle'
loop); but reconstruct_particle was silently bringing high-dose frames
back. The per-particle CTF / dose-weight math then used a different frame
set than the data on disk, producing cloud-of-points-looking merged maps
despite data_*.mrc (the un-Wiener-divided numerator) looking healthy.

Fix: when EMDL_TOMO_VISIBLE_FRAMES is present on particleSet.partTable,
intersect the geometric visibility with the explicit mask before
extractAt3D_Fourier. Backwards-compatible: behavior unchanged for inputs
without the column.

Tested on a 4-tomogram 2D-stack project with --max_dose 50:
- pre-fix: 39.2 mean visible frames per particle at reconstruction time
- post-fix: 16.5 mean visible frames per particle, matching what Extract
  baked into the 2D stacks and what Refine3D used for alignment.
---
 .../programs/reconstruct_particle.cpp         | 35 ++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/jaz/tomography/programs/reconstruct_particle.cpp b/src/jaz/tomography/programs/reconstruct_particle.cpp
index 04b4e85da..126d02551 100644
--- a/src/jaz/tomography/programs/reconstruct_particle.cpp
+++ b/src/jaz/tomography/programs/reconstruct_particle.cpp
@@ -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)
 	{
@@ -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;