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Merged
merged 146 commits into from
Feb 17, 2023
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108d64f
initial commit
chris-langfield Sep 9, 2022
8f8dde3
init file
chris-langfield Sep 9, 2022
305b1c8
add nodes and some functions
chris-langfield Sep 9, 2022
4799c52
computing bessel zeros
chris-langfield Sep 9, 2022
5c57b3e
finished computing and thresholding bessel zeros
chris-langfield Sep 9, 2022
d02f680
organized into subfns
chris-langfield Sep 9, 2022
8630a3e
more of _precomp added
chris-langfield Sep 9, 2022
7c7a6a5
cleanup
chris-langfield Sep 12, 2022
9589880
rename variables to sensible names, add dummy tests
chris-langfield Sep 12, 2022
bc0bb32
add test file
chris-langfield Sep 12, 2022
02d9371
slight change to placeholder evaluate function
chris-langfield Sep 12, 2022
2938bb2
format
chris-langfield Sep 12, 2022
1fbf00b
bandlimit default
chris-langfield Sep 12, 2022
b157e28
frmat
chris-langfield Sep 12, 2022
8575bcb
chebyshev
chris-langfield Sep 13, 2022
1ef7c30
removing comment block description of arrays for now
chris-langfield Sep 21, 2022
27260e9
leftover pdb -- embarrassing
chris-langfield Sep 21, 2022
424cb3a
steps 1 and 2 evaluate_t
chris-langfield Oct 10, 2022
96aa7c9
added some initial constants as well as creating dense matrix B
chris-langfield Oct 10, 2022
bf928a6
some cleanup
chris-langfield Oct 10, 2022
6b2191d
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Oct 18, 2022
c9e39bb
cleaned up evaluate_t steps
chris-langfield Oct 18, 2022
d1c1440
interpolation matrix
chris-langfield Oct 18, 2022
d39c005
step3 and test
chris-langfield Oct 19, 2022
f501d9f
add sparse matrix condn
chris-langfield Oct 19, 2022
1f4b8f5
adjust constants
chris-langfield Oct 19, 2022
7bf2d52
format
chris-langfield Oct 19, 2022
88f3289
bugs in create dense matrix method
chris-langfield Oct 19, 2022
410dfad
bug in evaluate_t and bug in create basis functions
chris-langfield Oct 20, 2022
0416aaa
flake
chris-langfield Oct 20, 2022
1487f57
parameterized test
chris-langfield Oct 20, 2022
3556c2c
formatting
chris-langfield Oct 21, 2022
08fe778
rename evaluate_t steps
chris-langfield Oct 21, 2022
649c18a
step1
chris-langfield Oct 21, 2022
fecb47f
propagate epsilon=1e-8 thru (a)nufft api
chris-langfield Oct 21, 2022
c65b59c
use our nufft with epsilon
chris-langfield Oct 21, 2022
45386e0
all 3 steps)
chris-langfield Oct 21, 2022
6b8a5e4
evaluate
chris-langfield Oct 21, 2022
5b322b0
evaluate test closeness
chris-langfield Oct 21, 2022
e54b623
add docstrings
chris-langfield Oct 21, 2022
c25b526
lowpass()
chris-langfield Oct 21, 2022
b0fed60
test lowpass
chris-langfield Oct 21, 2022
eeca99b
rotate()
chris-langfield Oct 21, 2022
c716dc9
fix rotate
chris-langfield Oct 21, 2022
5b10449
rotate() tests
chris-langfield Oct 21, 2022
81d1625
radial convolution
chris-langfield Oct 21, 2022
69900fe
radial convolution test
chris-langfield Oct 21, 2022
701a07c
get rid of numpy complex warnings
chris-langfield Oct 21, 2022
b069f6e
ctf sample (small)
chris-langfield Oct 21, 2022
e035bc9
create utils file
chris-langfield Oct 24, 2022
786701d
expand
chris-langfield Oct 24, 2022
9195e76
copy()s in evaluate_t and evaluate
chris-langfield Oct 25, 2022
00e3e62
remove large expand() test
chris-langfield Oct 25, 2022
c6ba7c4
cleanup
chris-langfield Oct 25, 2022
b307213
docstrings and cleanup
chris-langfield Oct 25, 2022
0859e79
comments tests
chris-langfield Oct 25, 2022
44ce6f0
docstring
chris-langfield Oct 25, 2022
58ed4dc
remove old comment
chris-langfield Oct 25, 2022
b0dfcc8
private _expand
chris-langfield Oct 26, 2022
4bcc562
black
chris-langfield Oct 26, 2022
3c850f1
FBBasis2D k_max criterion and optional thresholding
chris-langfield Oct 27, 2022
965a604
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Oct 28, 2022
e0bab22
isort
chris-langfield Oct 28, 2022
de5de13
fb comparison test
chris-langfield Oct 28, 2022
06866f5
matching FB option
chris-langfield Oct 31, 2022
7930e61
unused variable
chris-langfield Oct 31, 2022
f0938e2
oscar comments
chris-langfield Nov 1, 2022
e7bbb13
__init__ params
chris-langfield Nov 17, 2022
c082dbb
explicit reshapes
chris-langfield Nov 17, 2022
de4b97a
remove duplicated code
chris-langfield Nov 18, 2022
bacca4b
F ordering and n/ell
chris-langfield Nov 18, 2022
aa22998
fix _expand docstring
chris-langfield Nov 18, 2022
40bb232
remove pointless reshaping
chris-langfield Nov 18, 2022
6796da1
descriptive variable names in util fn
chris-langfield Nov 21, 2022
16a8167
better comments and variable names
chris-langfield Nov 21, 2022
f0b46a3
black
chris-langfield Nov 21, 2022
03b367c
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Nov 22, 2022
9c4a2c9
use grid_2d for cartesian gridpoint. BREAKS TESTS
chris-langfield Nov 22, 2022
83f3dcc
self.h
chris-langfield Nov 22, 2022
833bdf8
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Nov 28, 2022
ba300cd
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Nov 30, 2022
a3d6f18
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Dec 5, 2022
946f1da
catch up with develop
chris-langfield Dec 5, 2022
c0ad06d
relative error
chris-langfield Dec 6, 2022
c99f933
pointless reshape
chris-langfield Dec 6, 2022
7f15b52
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Dec 14, 2022
2e0e97f
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Jan 3, 2023
42026e1
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Jan 23, 2023
c679934
dtype in test
chris-langfield Jan 23, 2023
7dbb0e6
remove numsparse < 0 branch and associated get_weights function per p…
chris-langfield Jan 25, 2023
9efc7e0
better docstring and params for transform_complex_to_real
chris-langfield Jan 25, 2023
b6c052a
comment about complex conjugate
chris-langfield Jan 25, 2023
dbf30ad
barycentric docstring and fixed another docstring
chris-langfield Jan 25, 2023
aec7bb7
barycentric variable names and docstring
chris-langfield Jan 26, 2023
4e28e33
comments in bary interp from paper author
chris-langfield Jan 26, 2023
aabfe10
precomp_txform_complex_to_real comments
chris-langfield Jan 27, 2023
522d832
paper author comments in FLE 2D utils
chris-langfield Jan 27, 2023
352a674
remove unneeded parameter and var from barycentric
chris-langfield Jan 27, 2023
8af79b0
fb compat indices first go
chris-langfield Jan 30, 2023
a1ad2ca
formatting
chris-langfield Jan 30, 2023
82698ce
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Jan 30, 2023
3b99c92
initial remove parameterized from FLE
chris-langfield Jan 30, 2023
16efb67
remove pdb import (embarrassing) and try out pytest skip if GPU backend
chris-langfield Jan 30, 2023
acf45b6
rename test file
chris-langfield Jan 30, 2023
10402bf
match fb indices
chris-langfield Jan 31, 2023
6d6494f
flip sign going into evaluate
chris-langfield Jan 31, 2023
515df7d
matching FB2d forward tests
chris-langfield Jan 31, 2023
0747869
add evaluate_t fb2d matching test
chris-langfield Jan 31, 2023
e53aaff
cleanup gpu and resolution error test skips
chris-langfield Jan 31, 2023
63bc867
last paper author comments
chris-langfield Feb 1, 2023
7d8802d
docstrings
chris-langfield Feb 1, 2023
706201a
stub evaluate_t dense test
chris-langfield Feb 1, 2023
0e94218
implement dense evaluate_t test (worked out matrix reshaping etc)
chris-langfield Feb 1, 2023
ff3217f
Merge remote-tracking branch 'origin/develop' into fle_basis
chris-langfield Feb 1, 2023
b3fea10
cleaner dense evaluate_t
chris-langfield Feb 2, 2023
1722a9e
switch match_fb default, and update docstring with bullet points
chris-langfield Feb 2, 2023
1f043ac
adjust tests for new default
chris-langfield Feb 2, 2023
f626965
compute flip_sign_indices once
chris-langfield Feb 3, 2023
00686f7
naming
chris-langfield Feb 3, 2023
9543aa5
float32 in/out
chris-langfield Feb 10, 2023
e516237
indent
chris-langfield Feb 10, 2023
4eb97e5
rename get_fb_compat_indices
chris-langfield Feb 10, 2023
2753103
numsparse/maxitr logic
chris-langfield Feb 10, 2023
d79066e
grid dtype
chris-langfield Feb 10, 2023
6b644ca
nufft grid dtypes
chris-langfield Feb 10, 2023
1bfc9e7
internal dtype fixes
chris-langfield Feb 10, 2023
23634c6
remove F order
chris-langfield Feb 10, 2023
501d1ec
better comment for nus
chris-langfield Feb 10, 2023
cc6d983
docstring fix
chris-langfield Feb 10, 2023
7da7185
2nd docstring fix
chris-langfield Feb 10, 2023
d718de1
cleaner dtype passthrough
chris-langfield Feb 13, 2023
a7fed82
cleanup fle_ell_sign
chris-langfield Feb 13, 2023
9835429
use Basis.rotate instead of special method
chris-langfield Feb 13, 2023
5f0f92f
test _rotate
chris-langfield Feb 13, 2023
e7af6c5
redundant terms in numsparse/maxitr logic
chris-langfield Feb 13, 2023
78f2089
remove re-signing function
chris-langfield Feb 14, 2023
8181f92
rename ctf vars
chris-langfield Feb 14, 2023
fb5e445
renamed datafile
chris-langfield Feb 14, 2023
73ffd5f
_create_dense_matrix and tests
chris-langfield Feb 16, 2023
958bcd6
remove _expand and _rotate
chris-langfield Feb 16, 2023
4e67056
radial convolve
chris-langfield Feb 16, 2023
3289516
not because they are easy, but because they are hard.
garrettwrong Feb 17, 2023
972da1c
Odd resolution grid patch.
garrettwrong Feb 17, 2023
cf49174
And the another odd resolution grid patch
garrettwrong Feb 17, 2023
1c6fe2b
remove normalization requirement for dense method odd res
chris-langfield Feb 17, 2023
3c22ce8
Merge pull request #858 from ComputationalCryoEM/fle_basis_odd_patch
garrettwrong Feb 17, 2023
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1 change: 1 addition & 0 deletions src/aspire/basis/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from .fb_3d import FBBasis3D
from .ffb_2d import FFBBasis2D
from .ffb_3d import FFBBasis3D
from .fle_2d import FLEBasis2D
from .fpswf_2d import FPSWFBasis2D
from .fpswf_3d import FPSWFBasis3D
from .fspca import FSPCABasis
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