GitHub / ComputationalCryoEM/ASPIRE-Python issues and pull requests
#1326 - Yeast updates, uniform k=3, keep as singles
Pull Request -
State: open - Opened by garrettwrong about 1 month ago
Labels: documentation, cleanup
#1324 - Migrate `pixel_size` out of filter init
Pull Request -
State: open - Opened by garrettwrong about 2 months ago
Labels: cleanup
#1323 - Legacy Preprocess Example
Pull Request -
State: open - Opened by garrettwrong about 2 months ago
Labels: documentation
#1322 - Commonlines Class Reorg
Pull Request -
State: open - Opened by j-c-c about 2 months ago
Labels: cleanup
#1320 - Default to `DiracBasis3D` for recons
Issue -
State: closed - Opened by garrettwrong 2 months ago
#1319 - fix polar cross corr fft axis
Pull Request -
State: closed - Opened by garrettwrong 3 months ago
- 3 comments
Labels: bug, cleanup
#1318 - Downsample pixel_size bug
Issue -
State: open - Opened by j-c-c 3 months ago
Labels: bug
#1317 - Angstrom offsets
Pull Request -
State: closed - Opened by j-c-c 3 months ago
- 2 comments
Labels: cleanup, extern
#1315 - Matlab CTF
Pull Request -
State: closed - Opened by garrettwrong 3 months ago
- 6 comments
Labels: bug, enhancement, cleanup
#1315 - Matlab CTF
Pull Request -
State: open - Opened by garrettwrong 3 months ago
- 6 comments
Labels: bug, enhancement, cleanup
#1314 - Preprocess updates
Pull Request -
State: open - Opened by garrettwrong 3 months ago
Labels: documentation, enhancement, cleanup
#1313 - FLE2D updates
Issue -
State: open - Opened by garrettwrong 3 months ago
Labels: bug, enhancement, cleanup, extern
#1311 - Alter normalize background legacy defaults
Issue -
State: closed - Opened by garrettwrong 3 months ago
Labels: enhancement, cleanup
#1310 - Add `crop` preprocessing method
Issue -
State: closed - Opened by garrettwrong 3 months ago
Labels: enhancement, cleanup
#1309 - Directly port MATLAB's CTFFilter
Issue -
State: closed - Opened by garrettwrong 3 months ago
- 1 comment
Labels: enhancement, cleanup
#1306 - Validate `ArrayImageSource` stack dimension
Pull Request -
State: open - Opened by garrettwrong 3 months ago
Labels: bug, cleanup
#1305 - `ArrayImageSource` should check shape of input
Issue -
State: open - Opened by janden 3 months ago
#1303 - RelionSource crashes for EMPIAR-10005
Issue -
State: open - Opened by janden 3 months ago
Labels: support
#1302 - Relion >= 3.1 offsets convention: _rlnOriginX(Y)Angst
Pull Request -
State: open - Opened by j-c-c 4 months ago
Labels: cleanup, extern
#1299 - Bump version: 0.13.2 → 0.14.0
Pull Request -
State: closed - Opened by garrettwrong 4 months ago
- 1 comment
Labels: documentation, CI
#1298 - resolve ambiguous dtype in Downsample
Pull Request -
State: open - Opened by garrettwrong 4 months ago
Labels: bug, invalid, extern
#1297 - Update Pipeline Demo
Pull Request -
State: closed - Opened by j-c-c 4 months ago
- 5 comments
Labels: documentation, cleanup
#1295 - CoordinateSource pixel_size handling
Pull Request -
State: closed - Opened by garrettwrong 4 months ago
- 1 comment
Labels: enhancement, cleanup
#1291 - Numpy Casting
Pull Request -
State: closed - Opened by j-c-c 5 months ago
- 2 comments
Labels: bug, cleanup, extern
#1289 - ClassAvgSource pixel_size
Issue -
State: open - Opened by j-c-c 5 months ago
Labels: bug, cleanup
#1287 - MicrographSource need to support rectangular shapes
Issue -
State: open - Opened by garrettwrong 5 months ago
Labels: bug, cleanup
#1285 - Update Windows Runner
Issue -
State: open - Opened by j-c-c 5 months ago
Labels: CI
#1282 - `Image.show()` plot title
Issue -
State: closed - Opened by j-c-c 5 months ago
- 1 comment
#1281 - Use scipy create_group for SymmetryGroups
Pull Request -
State: closed - Opened by j-c-c 5 months ago
- 3 comments
Labels: cleanup
#1280 - Cleanup Duplicate Code
Pull Request -
State: open - Opened by j-c-c 5 months ago
Labels: cleanup
#1279 - Update Downloader Hash
Pull Request -
State: open - Opened by j-c-c 6 months ago
Labels: bug, CI, cleanup, support
#1278 - Cast on Volume.rotate dtype mismatch
Pull Request -
State: open - Opened by garrettwrong 6 months ago
Labels: support
#1277 - Warn and apply vol.rotate(r) with vol.dtype on r.dtype mismatch
Issue -
State: closed - Opened by garrettwrong 6 months ago
- 1 comment
Labels: enhancement, good first issue, support
#1276 - Mismatched (or obsolete) SHA256 hash on aspire.downloader.emdb_14621() call
Issue -
State: open - Opened by mosco 6 months ago
Labels: support
#1275 - SymmetryGroup - use scipy `create_group`
Issue -
State: open - Opened by j-c-c 6 months ago
#1274 - NUFFT Inconsistent dtypes when rotating float32 volume
Issue -
State: closed - Opened by mosco 6 months ago
- 5 comments
Labels: support
#1273 - I symmetry and tests for symmetry_groups
Pull Request -
State: closed - Opened by itamero 6 months ago
- 6 comments
Labels: enhancement
#1272 - Fix `Rotation.find_registration`
Pull Request -
State: open - Opened by janden 6 months ago
#1271 - Problems with `find_registration`
Issue -
State: open - Opened by janden 6 months ago
#1270 - Remove Numpy2 warning
Pull Request -
State: closed - Opened by garrettwrong 6 months ago
- 3 comments
Labels: cleanup
#1269 - Pytest Mark Warnings
Issue -
State: closed - Opened by garrettwrong 6 months ago
- 3 comments
Labels: CI, cleanup
#1267 - `OrientedSource` `save_mode=single`
Pull Request -
State: closed - Opened by garrettwrong 6 months ago
- 2 comments
Labels: bug, cleanup
#1266 - `pixel_size` from STAR file
Pull Request -
State: closed - Opened by j-c-c 6 months ago
- 5 comments
Labels: enhancement
#1265 - OrientedSource single mode `save`
Issue -
State: closed - Opened by garrettwrong 6 months ago
Labels: bug, good first issue, cleanup
#1264 - BOT_align Flaky Test
Pull Request -
State: closed - Opened by j-c-c 6 months ago
- 1 comment
Labels: CI
#1263 - [WIP] IRLS
Pull Request -
State: open - Opened by j-c-c 6 months ago
Labels: enhancement
#1262 - [WIP] Fast (Polar) Rotational Alignment
Pull Request -
State: open - Opened by garrettwrong 6 months ago
Labels: enhancement
#1259 - Resolve Package Build Warnings
Pull Request -
State: open - Opened by j-c-c 7 months ago
Labels: CI, cleanup
#1258 - Validate `normalize_background`
Pull Request -
State: closed - Opened by j-c-c 7 months ago
- 5 comments
Labels: bug, cleanup
#1257 - Validate `Volume.project` against Matlab
Issue -
State: open - Opened by j-c-c 7 months ago
#1256 - Flake8 Release Patch
Pull Request -
State: closed - Opened by j-c-c 7 months ago
- 2 comments
Labels: bug, CI, cleanup
#1255 - Flake8 complaining after release
Issue -
State: closed - Opened by j-c-c 7 months ago
- 1 comment
Labels: bug, CI, cleanup
#1254 - Fix CoordinateSource (allow rectangular micrographs)
Pull Request -
State: closed - Opened by j-c-c 7 months ago
- 1 comment
Labels: bug
#1253 - Fix CoordinateSource for 11028
Issue -
State: closed - Opened by garrettwrong 7 months ago
- 1 comment
Labels: bug, good first issue, cleanup, support
#1252 - Validate Downsample
Pull Request -
State: open - Opened by j-c-c 7 months ago
#1251 - LUD flaky test patch
Pull Request -
State: open - Opened by j-c-c 7 months ago
#1250 - IRLS commonlines
Issue -
State: open - Opened by j-c-c 7 months ago
#1249 - Update Packaging
Issue -
State: open - Opened by garrettwrong 7 months ago
Labels: CI, cleanup
#1247 - Develop v0.13.2~~> main
Pull Request -
State: closed - Opened by garrettwrong 8 months ago
#1246 - Validate invert_contrast against MATLAB
Issue -
State: closed - Opened by garrettwrong 8 months ago
- 3 comments
Labels: cleanup
#1245 - Validate normalize_background against MATLAB
Issue -
State: closed - Opened by garrettwrong 8 months ago
- 1 comment
Labels: cleanup
#1244 - Validate downsampling against MATLAB.
Issue -
State: closed - Opened by garrettwrong 8 months ago
- 5 comments
Labels: cleanup
#1243 - Complete Preprocessing MATLAB Validation/Repro
Issue -
State: open - Opened by garrettwrong 8 months ago
#1242 - Bump version: 0.13.1 → 0.13.2
Pull Request -
State: closed - Opened by garrettwrong 8 months ago
#1241 - Docs Cache Patch
Pull Request -
State: closed - Opened by j-c-c 8 months ago
- 1 comment
Labels: bug, CI
#1239 - Unused imports in Gallery
Issue -
State: open - Opened by j-c-c 8 months ago
#1238 - Fix SymmetryGroup Warnings
Pull Request -
State: closed - Opened by j-c-c 8 months ago
- 3 comments
Labels: bug, cleanup
#1237 - Fix Broken CI Caching
Pull Request -
State: closed - Opened by j-c-c 8 months ago
- 2 comments
Labels: bug, CI, cleanup
#1236 - Validate IndexedSource/Simulation interaction
Issue -
State: open - Opened by garrettwrong 8 months ago
Labels: bug, cleanup
#1235 - Confirm CI Cache
Issue -
State: closed - Opened by garrettwrong 8 months ago
- 2 comments
Labels: bug, CI, cleanup
#1234 - Cleanup `SymmetryGroup` warnings
Issue -
State: closed - Opened by garrettwrong 9 months ago
- 3 comments
Labels: cleanup
#1232 - WIP Pure rotation fix
Pull Request -
State: open - Opened by garrettwrong 9 months ago
Labels: bug, extern
#1231 - Scipy 1.15.2 complaining about our estimated rotations
Issue -
State: closed - Opened by garrettwrong 9 months ago
- 4 comments
Labels: bug, extern, dependencies
#1230 - Fix IndexSource filter mapping
Pull Request -
State: closed - Opened by garrettwrong 9 months ago
- 4 comments
Labels: bug, cleanup
#1226 - OOM for large problem sizes
Pull Request -
State: closed - Opened by garrettwrong 9 months ago
- 2 comments
Labels: bug, enhancement, cleanup, GPU
#1225 - remove cufinufft 3d1 method workaround
Pull Request -
State: open - Opened by garrettwrong 9 months ago
Labels: cleanup, extern, dependencies
#1224 - cufinufft log message
Pull Request -
State: closed - Opened by garrettwrong 9 months ago
- 4 comments
Labels: cleanup, dependencies
#1223 - Legacy Isotropic Whitening
Pull Request -
State: closed - Opened by garrettwrong 9 months ago
- 8 comments
Labels: enhancement, cleanup
#1221 - LUD
Pull Request -
State: closed - Opened by j-c-c 10 months ago
- 8 comments
Labels: enhancement
#1220 - Remove `scipy<1.15.0` workaround
Issue -
State: open - Opened by garrettwrong 10 months ago
Labels: CI, cleanup, extern
#1219 - scipy==1.15.0 `sph_harm` updates
Pull Request -
State: closed - Opened by garrettwrong 10 months ago
- 3 comments
Labels: good first issue, CI, extern
#1218 - Scipy 1.15 release impacting `sph_harm` CI
Issue -
State: closed - Opened by garrettwrong 10 months ago
- 1 comment
Labels: bug, CI, cleanup, extern
#1217 - Correct CTFFilter formula/units
Pull Request -
State: closed - Opened by garrettwrong 10 months ago
- 2 comments
Labels: bug, cleanup
#1216 - Batch class avg
Pull Request -
State: open - Opened by garrettwrong 11 months ago
Labels: enhancement, cleanup, Optimization
#1215 - Add mrcs extension to ext list for Image.load
Pull Request -
State: closed - Opened by garrettwrong 11 months ago
- 2 comments
Labels: bug, good first issue, cleanup
#1214 - Default Class Averager Updates
Pull Request -
State: closed - Opened by garrettwrong 11 months ago
- 3 comments
Labels: documentation, enhancement, cleanup
#1213 - purge m_
Pull Request -
State: closed - Opened by garrettwrong 12 months ago
- 1 comment
Labels: cleanup
#1212 - `grid` and limited `Filter` caching
Pull Request -
State: closed - Opened by garrettwrong 12 months ago
- 1 comment
Labels: enhancement, Optimization
#1211 - Remove sklearn workaround
Pull Request -
State: closed - Opened by j-c-c 12 months ago
- 2 comments
Labels: cleanup
#1210 - Migrate Gallery logger.info --> print
Pull Request -
State: closed - Opened by j-c-c 12 months ago
- 3 comments
Labels: cleanup
#1208 - Another buggy windows MKL package
Pull Request -
State: closed - Opened by garrettwrong 12 months ago
- 1 comment
Labels: CI, extern, dependencies
#1207 - Develop ~~> Main v0.13.1
Pull Request -
State: closed - Opened by garrettwrong 12 months ago
- 1 comment
#1206 - Bump version: 0.13.0 → 0.13.1
Pull Request -
State: closed - Opened by garrettwrong 12 months ago
#1205 - Sphinx Gallery Logs
Issue -
State: closed - Opened by garrettwrong 12 months ago
- 2 comments
Labels: documentation, cleanup
#1204 - try excluding mkl 2024.2.2 from windows
Pull Request -
State: closed - Opened by garrettwrong about 1 year ago
- 2 comments
Labels: bug, CI, extern, dependencies
#1203 - Remove `m_*` functions
Pull Request -
State: closed - Opened by j-c-c about 1 year ago
- 1 comment
Labels: cleanup
#1202 - Caf/Decaf CI patches
Pull Request -
State: closed - Opened by garrettwrong about 1 year ago
- 1 comment
Labels: enhancement, CI, GPU
#1201 - Oriented Source Updates
Pull Request -
State: closed - Opened by garrettwrong about 1 year ago
- 3 comments
#1200 - Propose sim amplitude/offset fix
Pull Request -
State: open - Opened by garrettwrong about 1 year ago
Labels: bug, cleanup
#1199 - Fix gha
Pull Request -
State: open - Opened by garrettwrong about 1 year ago