make_lsm_df: Make summary dataframe for lsm files and their key metadata

Description Usage Arguments Details Value See Also

View source: R/lsm_metadata.R

Description

Make summary dataframe for lsm files and their key metadata

Usage

1
make_lsm_df(lsmdir, oldlsmdf = NULL, extrafields = NULL, Verbose = TRUE)

Arguments

lsmdir

Path to directory containing lsm files

oldlsmdf

Dataframe or path to rda file containing one

extrafields

Function to parse extra fields from metadata for each image

Verbose

Logical: Show messages about progress/updating of cached data

Details

Will calculate md5 sums for all input files and then use this to update a dataframe.

If an extrafields function is supplied, it should take one parameter, the list output of parse_key_lsm_metadata, which will include as an attribute the full contents of the metadata file dumped by the loci showinf tool. The function should take care to return values for all fields that it could return each time it is called even if these are NA and to ensure that values have a consistent data type per field.

Value

dataframe

See Also

lsm_metadata, parse_key_lsm_metadata


jefferislab/jimpipeline documentation built on Sept. 14, 2020, 3:41 p.m.