fix visiblity determination for subtomo particle reconstruction#1305
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daniel-ji wants to merge 222 commits into
Open
fix visiblity determination for subtomo particle reconstruction#1305daniel-ji wants to merge 222 commits into
daniel-ji wants to merge 222 commits into
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… select and display mics with filaments
…eraging of subtomos
…p-Wiener for reconstruct tomograms in fourier mode
…o change code to debug
…t allow power spectra precalculation, nor float16
…#1346) The special code path for EER movies is unaffected.
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When doing subtomogram reconstruction, visibility of the extracted particles that are to be backprojected is inconsistently / incorrectly determined based on the box size after binning and does not account for the fact that the actual extracted box from the tiltseries is larger than the output box size when a bin factor is set.
The visibility should be based on the extracted dimensions before binning (so
bin factor * box size, i.e.binning * s), to align with the laterTomoExtraction::extractAt3D_Fouriercall that extracts at thes02Ddimension (just a couple lines after).This also then aligns with the logic done in subtomogram extraction as well (using the pre-binned dimensions to determine particle visibility): https://github.com/3dem/relion/blob/master/src/jaz/tomography/programs/subtomo.cpp#L733
Note: I'm still working through a bit of debugging as for why my re-implementation (done to support the reading of ZARR files & files on the cloud in a chunked manner) does not match numerically with RELION's output, so there might be more small bugfixes I suggest in the process of trying to align the two implementations (this code is will soon be open source). So feel free to hold off on a potential merge if you would rather not have me continue to open one-line PR changes, sorry about this. I thought I'd at least open this PR first, to bring attention to this small inconsistency. Thanks so much!