Add preprocessing flags to aspire extract-particles
#551
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@@ Coverage Diff @@
## develop #551 +/- ##
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+ Coverage 87.17% 87.19% +0.02%
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Files 108 108
Lines 7984 7998 +14
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+ Hits 6960 6974 +14
Misses 1024 1024
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Improved the help messages and also standardized the help messages, flags, and lack of periods across |
Great!
Thanks for catching. |
* added --downsample option to aspire extract-particles * added --downsample option to aspire extract-particles * added normalize_bg and invert_contrast flags * add --whiten option * new black version formatting * help messages and standardize preprocess and extract-particles * downsample images not data
As discussed in #502, we can add the option to pre-downsample the data prior to saving.
aspire extract-particlescreates aCoordinateSourcefrom micrograph/coordinate file data and then saves to a STAR file / .mrcs stack.It is probably a good idea to also add other preprocessing options, since it might be best to do certain operations prior to downsampling (e.g. noise estimation).
Overall, the downsampling step is critical because without it, running
extract-particleswill make a copy of the dataset in a different format, but at the same resolution, which would take up unnecessary disk space.