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GitHub / ComputationalCryoEM/ASPIRE-Python issues and pull requests

#939 - Doc updates

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: documentation, cleanup

#938 - Multi-dimensional Rotations

Issue - State: open - Opened by j-c-c over 2 years ago
Labels: enhancement

#937 - Author updates

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: documentation, cleanup

#936 - Fle ordering

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: cleanup

#935 - Volume project

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 1 comment
Labels: enhancement, cleanup

#933 - Fix metadata fill value for int dtypes

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, cleanup

#932 - Merge pull request #905 from ComputationalCryoEM/develop

Pull Request - State: closed - Opened by garrettwrong over 2 years ago

#931 - Workaround patches

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, invalid, cleanup

#930 - add missing assignment in 10073

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: bug, documentation, cleanup

#928 - Downsample bug for integer offsets

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 3 comments
Labels: bug

#927 - Better Logging for CLSymmetryC*

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 1 comment
Labels: cleanup

#926 - `image.downsample` broken for source with integer `offsets

Issue - State: closed - Opened by j-c-c over 2 years ago - 5 comments
Labels: bug

#924 - Check 2D Metadata assignment

Issue - State: open - Opened by garrettwrong over 2 years ago

#923 - `FBBasis3D` NaN values for large resolution

Issue - State: closed - Opened by j-c-c over 2 years ago - 7 comments
Labels: bug

#922 - Remove unneeded threadpool code in `RelionSource`

Issue - State: open - Opened by garrettwrong over 2 years ago - 3 comments

#921 - Potentially simplify _populate_common_metadata

Issue - State: open - Opened by garrettwrong over 2 years ago

#920 - Replace fill values with masked arrays in metadata

Issue - State: open - Opened by garrettwrong over 2 years ago
Labels: enhancement, cleanup

#919 - AsymmetricVolume Patch

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 4 comments
Labels: bug

#918 - Add Contrast Correction to Cov 2D

Issue - State: open - Opened by garrettwrong over 2 years ago - 1 comment

#917 - Volume alignment

Issue - State: open - Opened by janden over 2 years ago - 2 comments
Labels: enhancement

#916 - Basis Reconciliation

Issue - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: enhancement, cleanup

#915 - Expensive Bases Tests

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 2 comments

#912 - Flaky class average unit test

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: CI

#911 - Vb/pdgone

Pull Request - State: closed - Opened by vineetbansal over 2 years ago - 4 comments
Labels: enhancement, cleanup

#910 - test expected to fail - fix

Pull Request - State: closed - Opened by vineetbansal over 2 years ago - 3 comments
Labels: bug, enhancement, cleanup

#909 - test expected to fail

Pull Request - State: closed - Opened by vineetbansal over 2 years ago - 4 comments

#907 - FLEBasis2D rotations incorrect under `match_fb=True`

Issue - State: closed - Opened by garrettwrong over 2 years ago - 4 comments
Labels: bug, cleanup

#906 - correct place to initialize mrc_index_to_particles array

Pull Request - State: closed - Opened by vineetbansal over 2 years ago - 1 comment
Labels: bug, enhancement, cleanup

#905 - `develop` ~~> `master` v0.11.0

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments

#904 - Migrate sources and preprocessing towards lazy evaluation

Issue - State: open - Opened by garrettwrong over 2 years ago
Labels: enhancement, cleanup

#902 - Immutable operations

Pull Request - State: closed - Opened by vineetbansal over 2 years ago - 7 comments
Labels: enhancement, cleanup

#901 - Add FRC and FSC

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement

#900 - Remove redundant Image conversion bug in denoised_src (cov2d)

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, cleanup

#899 - denoised source cache bug

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, cleanup

#898 - ManuallyOrientedSource(rotations) and OrientedSource(estimator)

Pull Request - State: closed - Opened by j-c-c over 2 years ago

#897 - Cov2D src should use image accessor

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, good first issue, cleanup

#896 - Default `n_theta` selection

Issue - State: open - Opened by janden over 2 years ago - 1 comment

#895 - LogFilterByCount

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: enhancement, cleanup, Optimization

#894 - Write Class Selection Indices to STAR file

Issue - State: open - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, good first issue, cleanup

#893 - Bump version: 0.10.1 → 0.11.0

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: documentation

#892 - Smarter `overwrite` flag

Issue - State: open - Opened by garrettwrong over 2 years ago - 3 comments
Labels: enhancement, good first issue

#891 - IndexedSource and ImageSource bug fixes

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug

#890 - OrientedSource

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 4 comments
Labels: enhancement

#889 - Multiple resolution/pixel-size data sets

Issue - State: open - Opened by garrettwrong over 2 years ago - 2 comments
Labels: enhancement

#888 - Asnumpy writable

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: enhancement, good first issue, cleanup

#887 - disable writing to `asnumpy()` references

Issue - State: closed - Opened by garrettwrong over 2 years ago
Labels: enhancement, good first issue, cleanup

#886 - Vectorize `Rotation.angle_dist()`

Issue - State: closed - Opened by j-c-c over 2 years ago - 2 comments
Labels: enhancement, Optimization

#885 - Migrate tutorials/experiments away from imshow subplots

Issue - State: open - Opened by garrettwrong over 2 years ago
Labels: documentation, good first issue, cleanup

#884 - Missed img vol return tutorial updates

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: bug, documentation, cleanup

#883 - Simplify Whiten syntax

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, cleanup

#882 - Feature demo breakup

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 7 comments
Labels: documentation, enhancement, cleanup

#881 - add warning and clamp for extremal snr

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: cleanup

#880 - `CnSymmetricVolume`s center mass accumulation

Issue - State: open - Opened by j-c-c over 2 years ago
Labels: Optimization

#879 - Show patch

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: bug

#878 - Allow `whiten(NoiseEstimator)`

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, cleanup

#877 - Initial addition of RemappedSource

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: enhancement, cleanup

#876 - Source slicing/getter

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, cleanup

#875 - Orientation and Boosting Sources

Issue - State: closed - Opened by garrettwrong over 2 years ago - 9 comments
Labels: enhancement, cleanup, Optimization

#874 - Demo dry run updates

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: documentation, cleanup

#873 - Simulation `eval_coords` bug

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 3 comments
Labels: bug

#872 - DenoiserCov2D always returns doubles

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, cleanup

#871 - RelionSource dtype

Issue - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: enhancement, cleanup

#870 - Minor ctf tweaks

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: bug, documentation, cleanup

#869 - Relative Viewing Direction Estimation for Common-lines (Cn)

Issue - State: open - Opened by j-c-c over 2 years ago
Labels: enhancement, Optimization, theory

#868 - xfail FLE test broken on windows (only on windows).

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug

#866 - Class Source

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 3 comments
Labels: enhancement

#865 - Downgrade windows CI from 2022 to 2019 (fixes single test fail in CI)

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 2 comments
Labels: bug, CI

#864 - Deprecation Warnings

Pull Request - State: closed - Opened by j-c-c over 2 years ago - 1 comment
Labels: CI, cleanup, extern

#863 - Img vol return

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: enhancement, cleanup

#862 - FLE expand unit test failure

Issue - State: closed - Opened by garrettwrong over 2 years ago - 11 comments
Labels: CI, cleanup

#861 - Common Lines: fuzzy mask & Gaussian filter

Issue - State: closed - Opened by j-c-c over 2 years ago - 6 comments
Labels: enhancement

#859 - GRPC fork bug

Issue - State: closed - Opened by garrettwrong over 2 years ago - 1 comment
Labels: bug, extern, dependencies

#858 - Fle basis odd patch

Pull Request - State: closed - Opened by garrettwrong over 2 years ago - 4 comments
Labels: bug, enhancement, cleanup

#852 - Upstream Deprecation Warnings

Issue - State: closed - Opened by garrettwrong over 2 years ago - 4 comments
Labels: CI, cleanup, extern

#849 - FLE Basis GPU tests

Issue - State: open - Opened by chris-langfield almost 3 years ago - 3 comments
Labels: bug, CI, GPU

#843 - `(F)PSWF` bases running in float32

Issue - State: closed - Opened by chris-langfield almost 3 years ago - 2 comments
Labels: bug

#839 - SNR utils

Pull Request - State: closed - Opened by garrettwrong almost 3 years ago - 3 comments
Labels: enhancement, cleanup

#823 - Simulation `eval_coords` bug

Issue - State: closed - Opened by j-c-c almost 3 years ago - 4 comments
Labels: bug

#822 - Image.shift integer shifts

Issue - State: open - Opened by garrettwrong almost 3 years ago - 3 comments
Labels: enhancement, Optimization

#803 - Drop `parameterized_class`

Issue - State: closed - Opened by garrettwrong almost 3 years ago - 4 comments
Labels: CI, cleanup

#786 - APPLE Unit Tests take a long time.

Issue - State: closed - Opened by garrettwrong almost 3 years ago - 1 comment
Labels: CI, cleanup

#762 - Breakup and re-distrbute Lecture Feature Demo

Issue - State: closed - Opened by garrettwrong almost 3 years ago - 2 comments
Labels: documentation, cleanup

#747 - Sign of angle and resulting [Counter]clockwise rotations of `SteerableBasis2D` coefficients

Issue - State: closed - Opened by chris-langfield almost 3 years ago - 13 comments
Labels: theory

#744 - `Source` `copy` method

Issue - State: closed - Opened by garrettwrong almost 3 years ago - 1 comment
Labels: enhancement

#742 - Validating the CTF Estimator

Issue - State: open - Opened by j-c-c almost 3 years ago - 12 comments
Labels: bug, enhancement, help wanted, question, cleanup, theory

#739 - `__getitem__` for `Image` and `Volume` should return same class instead of NumPy

Issue - State: closed - Opened by chris-langfield about 3 years ago - 3 comments
Labels: enhancement, cleanup

#733 - Ab-initio Cn

Pull Request - State: closed - Opened by j-c-c about 3 years ago - 13 comments
Labels: enhancement

#727 - `Volume.project` should not require a `vol_idx` parameter

Issue - State: closed - Opened by janden about 3 years ago - 1 comment
Labels: enhancement, cleanup

#712 - Data Downloader

Issue - State: closed - Opened by garrettwrong about 3 years ago - 8 comments
Labels: documentation, enhancement

#710 - Centerpoint test discrepancies for 3D downsampling

Issue - State: closed - Opened by chris-langfield about 3 years ago - 1 comment
Labels: invalid

#703 - GPU Unit Tests

Issue - State: closed - Opened by garrettwrong about 3 years ago - 6 comments
Labels: bug, wontfix, cleanup, GPU

#699 - User reported FFB2D evaluate_t slowness

Issue - State: closed - Opened by garrettwrong about 3 years ago - 2 comments
Labels: enhancement, Optimization, support

#693 - FLE Basis

Pull Request - State: closed - Opened by chris-langfield about 3 years ago - 9 comments
Labels: enhancement, Optimization

#689 - 3D Downsampling

Pull Request - State: closed - Opened by chris-langfield about 3 years ago - 5 comments
Labels: enhancement, cleanup

#676 - Test common lines method with shifted images

Issue - State: open - Opened by j-c-c over 3 years ago - 3 comments
Labels: CI

#663 - MSE accuracy different for C3 and C4 symmetry

Issue - State: closed - Opened by j-c-c over 3 years ago - 3 comments

#658 - Whiten Extremal Value

Issue - State: closed - Opened by garrettwrong over 3 years ago - 10 comments
Labels: bug, support

#639 - Is there an error while performing the rotation on the mesh?

Issue - State: closed - Opened by ghost over 3 years ago - 4 comments
Labels: duplicate, help wanted, question, support