Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Protocol for fast particle alignment #711

Draft
wants to merge 123 commits into
base: devel
Choose a base branch
from
Draft
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
123 commits
Select commit Hold shift + click to select a range
eb7a516
Renamed conda env
oierlauzi Jan 11, 2023
b3654b0
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jan 20, 2023
d283a96
Initial commit
oierlauzi Jan 20, 2023
afe1f23
Continued working
oierlauzi Jan 25, 2023
1d62216
Continued working on the protocol
oierlauzi Jan 26, 2023
23e3a59
Updated output generation
oierlauzi Jan 27, 2023
7cbaa7e
Modified training dataset size
oierlauzi Jan 27, 2023
ba5ae31
Added sampling rate to output
oierlauzi Jan 27, 2023
9054c2f
Renamed protocol to swiftres
oierlauzi Jan 30, 2023
dbf20f7
Added GPU support to fourier reconstruction
oierlauzi Jan 30, 2023
87d3c73
Added iteration structure
oierlauzi Jan 30, 2023
5783f0c
Refined output generation
oierlauzi Jan 30, 2023
85178ae
Added iterations
oierlauzi Jan 31, 2023
e81cb99
Added scratch file
oierlauzi Jan 31, 2023
65ef2a7
Added reprojection comparison
oierlauzi Feb 1, 2023
f7aa385
Added compute weights step
oierlauzi Feb 1, 2023
739de7e
Bugfix
oierlauzi Feb 1, 2023
e902445
Started working on multiclass
oierlauzi Feb 1, 2023
54b1af3
Started working on 3D classification
oierlauzi Feb 2, 2023
654a9ed
Added SetOfClasses to the output
oierlauzi Feb 2, 2023
2a7528d
Renamed gallery.doc to gallery.xmd
oierlauzi Feb 2, 2023
328b16e
Bugfix: Disordered iteration and class
oierlauzi Feb 2, 2023
75ca73c
Added particle filtering
oierlauzi Feb 3, 2023
f7aa755
Added help
oierlauzi Feb 6, 2023
7c309b8
Added maximum DB size parameter
oierlauzi Feb 9, 2023
77b7d9d
Worked with centered particles
oierlauzi Feb 10, 2023
19382ad
Considered moving particle centering to program
oierlauzi Feb 13, 2023
7c704f0
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Feb 13, 2023
5816fd0
Continued removing unused parameters
oierlauzi Feb 13, 2023
ebba207
Worked on automating parameters
oierlauzi Feb 14, 2023
492776b
Fixed mergeAlignmentStep for future use
oierlauzi Feb 14, 2023
d81d58a
Added maxPsi
oierlauzi Feb 14, 2023
27eef64
Re-added mergeGalleriesStep
oierlauzi Feb 16, 2023
deb5f3e
Added merging of metadata
oierlauzi Feb 16, 2023
ccd65df
Updated to use merge function
oierlauzi Feb 17, 2023
727dd62
Updated parameters
oierlauzi Feb 23, 2023
951d7e4
Bugfix
oierlauzi Feb 23, 2023
217d83e
Changed max shift to be in pixels
oierlauzi Feb 23, 2023
59e6157
Created viewer
oierlauzi Feb 24, 2023
81d4c34
Worked in the viewer
oierlauzi Feb 24, 2023
92a68e6
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Feb 27, 2023
fdb8b47
Disabled local refinement temporally
oierlauzi Feb 28, 2023
dbcf3e1
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Feb 28, 2023
3a4e1f2
Added lower limit to resolution cutoff graph
oierlauzi Feb 28, 2023
4741425
Added formatting to frequency axis in the FSC
oierlauzi Feb 28, 2023
8ad8295
Removed print
oierlauzi Feb 28, 2023
0d8bcf9
Updated iteration parameters
oierlauzi Feb 28, 2023
3d66078
Added CTF group calls for each iteration
oierlauzi Mar 1, 2023
0da50e3
Refactored angle comparisons and added viewer
oierlauzi Mar 2, 2023
92d940b
Added table view to angular difference
oierlauzi Mar 2, 2023
3fbad82
Implemented alignment consensus
oierlauzi Mar 3, 2023
a80265f
Updated angular consensus
oierlauzi Mar 7, 2023
7b97809
Tested angular averaging
oierlauzi Mar 9, 2023
d2a5014
Updated angular consensus to use angular_distance
oierlauzi Mar 10, 2023
0439d3f
Added image size getter
oierlauzi Mar 10, 2023
d6c614e
Added threshold to the viewer
oierlauzi Mar 10, 2023
4822252
Continued working on alignment consensus
oierlauzi Mar 10, 2023
1cc4ef3
Updated angular consensus
oierlauzi Mar 10, 2023
2eeaf15
Made CTF optional
oierlauzi Mar 13, 2023
4c7703b
Modified default batch size
oierlauzi Mar 14, 2023
73fac00
Added Noise profile views
oierlauzi Mar 15, 2023
d0b29e8
Added parameters to noise model generation
oierlauzi Mar 15, 2023
cc773ad
Added class size plot
oierlauzi Mar 21, 2023
b1a6940
Added angular distribution plots
oierlauzi Mar 22, 2023
c3cbfa4
Removed extra linebreak
oierlauzi Mar 22, 2023
12d0360
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Mar 22, 2023
e137016
Fixed warning
oierlauzi Mar 23, 2023
1379e93
Added psi visualization
oierlauzi Mar 23, 2023
f11d0d0
Added fp16 support
oierlauzi Mar 28, 2023
0ff049b
Added mask parameter
oierlauzi Apr 3, 2023
c8bba25
Added Chimera viewer
oierlauzi Apr 3, 2023
15f8fe5
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Apr 11, 2023
27c88ba
Added knn support
oierlauzi Apr 12, 2023
4f8e09a
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Apr 13, 2023
537a2f1
Renamed conda env
oierlauzi Apr 13, 2023
ea1505e
Renamed environment and programs to swiftalign
oierlauzi Apr 13, 2023
d090215
Merge branch 'olz_fix_align_volume_and_particles' into olz_faiss_alig…
oierlauzi Apr 17, 2023
bb64118
Merge branch 'olz_fix_align_volume_and_particles' into olz_faiss_alig…
oierlauzi Apr 17, 2023
7a7fb81
Commented unused steps
oierlauzi Apr 21, 2023
fd0e7c8
Made CTF optional
oierlauzi Apr 21, 2023
0c2978b
Added manual step options
oierlauzi Apr 24, 2023
c217a1d
Added CTF grouping
oierlauzi May 8, 2023
afd6539
Merge branch 'devel' into olz_faiss_alignment
oierlauzi May 8, 2023
e5a49b2
Fixed mrc detection
oierlauzi May 8, 2023
bfbe1db
Merge branch 'devel' into olz_faiss_alignment
oierlauzi May 9, 2023
16bd8c8
Added option to copy particles to scratchdir
oierlauzi May 10, 2023
c79faa8
Refactored output generation
oierlauzi May 26, 2023
aa98932
Added local alignment option
oierlauzi May 30, 2023
66329f8
Stupid mistake
oierlauzi May 30, 2023
ee424f3
Adapted to the new alignment program
oierlauzi May 31, 2023
060a36e
Modified default local iteration count
oierlauzi May 31, 2023
1c91453
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jun 8, 2023
de273b2
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jun 14, 2023
7ffc3ec
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jun 22, 2023
09f7439
Removed unused import
oierlauzi Jun 26, 2023
c39c2c0
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jul 5, 2023
7ae5212
Removed method parameter
oierlauzi Jul 13, 2023
346bcbb
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jul 14, 2023
231b5c7
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Jul 28, 2023
0b52234
Integrated the new wiener filter
oierlauzi Jul 28, 2023
be1d659
Added GPU parameter
oierlauzi Jul 28, 2023
64253ac
Bugfix in device formatting
oierlauzi Jul 28, 2023
0e4b38c
Added optional reconstruction
oierlauzi Jul 31, 2023
dd98570
Bugfix
oierlauzi Jul 31, 2023
b940514
Removed unimplemented viewer
oierlauzi Jul 31, 2023
dbb09ee
Bugfix
oierlauzi Aug 1, 2023
b12c7b2
Added pointer dereferencing
oierlauzi Aug 1, 2023
433f7ea
Made wiener filtering optional
oierlauzi Aug 2, 2023
118c216
Integrated precomputed tables option
oierlauzi Aug 3, 2023
c5e79ff
Added projection alignment to the output
oierlauzi Aug 5, 2023
ef58894
Settign alignment type to Class3D
oierlauzi Aug 7, 2023
b22b635
Added particle output for single class refinements
oierlauzi Aug 8, 2023
d929bb7
Added missing information to the output set of particles
oierlauzi Aug 9, 2023
7235a8b
Fixed error
oierlauzi Aug 9, 2023
ef235bf
Merge branch 'devel' into olz_faiss_alignment
oierlauzi Aug 28, 2023
92ae515
Moved extra labels
oierlauzi Aug 28, 2023
63bbb20
Bugfix
oierlauzi Aug 29, 2023
8e41c41
Added gradient descent parameters
oierlauzi Aug 30, 2023
71bdd68
Added rmsprop step
oierlauzi Aug 30, 2023
1cc62a0
Fixed rmsprop call
oierlauzi Aug 31, 2023
0e67555
Merge branch 'devel' into olz_faiss_alignment
oierlauzi May 9, 2024
0aad568
Renaming reconstruct input file
oierlauzi May 16, 2024
1909f3f
Fix
oierlauzi May 16, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions xmipp3/protocols/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -131,4 +131,5 @@
from .protocol_volume_local_adjust import XmippProtLocalVolAdj
from .protocol_classes_2d_mapping import XmippProtCL2DMap
from .protocol_deep_hand import XmippProtDeepHand
from .protocol_reconstruct_swiftres import XmippProtReconstructSwiftres
from .protocol_deep_center import XmippProtDeepCenter
Loading
Loading