v2.4.0 release - #19
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- Modified frames.py to add a utility function to print a table containing per file angle estimation information.
- Modified cli.py to add `--print-angles` option for frames command.
- Modified tests/unit/test_frames.py to add a unit test for frames which checks consensus angle doesn't change by printing.
Merge pull request #17 from holsam/print-angles-frames
- Modified frames.py to use a per-series curtaining angle calculation, so series using different pre-tilts don't influence the others destriping angle. - Modified frames.py to use anchor tilts (around median tilt ≈ pre-tilt) to set the destriping angle with subsequent angles compared to this for agreement. - Modified frames.py to update printing angle function to save to csv and only print per-series per-tilt tables.
- Modified cli.py to add `--anchor-tilts` option for `pylisc frames` command.
- Modified frames.py to use nearest accepted tilt angle consensus as fallback value for rejected tilts.
- Modified tests/integration/test_cli.py to increase number of synthetic frames used in pylisc frames test so warning is output. - Modified tests/unit/test_frames.py to update unit tests to reflect recent changes in angle consensus calculation.
Merge pull request #18 from holsam/seeded-consensus
- Modified tests/conftest.py to add existing fixture functions as actual pytest fixtures. - Deleted tests/fixtures.py as now redundant.
- Modified io.py to wrap readMrcFile in a try/except block to catch any invalid MRC files and log a warning for these, returning (None, None) if raised.
- Modified frames.py and stack.py to skip any MRC files which cannot be read when running the curtaining angle pre-pass.
- Modified test files to use pytest fixtures directly instead of importing.
- Modified test_cli.py to add unit tests for `--version` option, deprecation warnings, and frames option validation.
- Modified test_destripe.py to add unit test for dc_protect_frac low-frequency preservation.
- Modified test_frames.py to add unit tests for _process_one, _split_by_tilt_gap, and run_frames edge cases.
- Modified test_io.py to add unit test for nameOutputFile function.
- Modified test_templates.py to refactor tests into class, and add unit tests for invalid field name and unparseable tilt edge cases.
- Added test_blur.py to define unit tests for FFT gaussian blur and highpass bandpass filtering. - Added test_lisc.py to define unit tests for lisc_clear_frame pixel size, filter, and linear dispatch. - Added test_preview.py to define unit tests for generate_strength_preview angular and linear modes. - Added test_stack.py to define unit tests for _process_series and batch error handling.
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Changelog
--print-anglestopylisc frameswhich outputs the consensus angles used per tilt series.--anchor-tiltstopylisc frameswhich sets the number of tilts used as the anchoring seed for angle consensus checks.README.md.